Michor Lab Publications
All Publications
2024
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2024. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proceedings of the National Academy of Sciences of the United States of America. 121(32):e2406842121. Pubmed: 39093947 DOI:10.1073/pnas.2406842121 Cheng YC, Zhang Y, Tripathi S, Harshavardhan BV, Jolly MK, Schiebinger G, Levine H, McDonald TO, Michor F. 2024. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proceedings of the National Academy of Sciences of the United States of America. 121(32):e2406842121. Pubmed: 39093947 DOI:10.1073/pnas.2406842121 Exploring the complexity of the epithelial-to-mesenchymal transition (EMT) unveils a diversity of potential cell fates; however, the exact timing and mechanisms by which early cell states diverge into distinct EMT trajectories remain unclear. Studying these EMT trajectories through single-cell RNA sequencing is challenging due to the necessity of sacrificing cells for each measurement. In this study, we employed optimal-transport analysis to reconstruct the past trajectories of different cell fates during TGF-beta-induced EMT in the MCF10A cell line. Our analysis revealed three distinct trajectories leading to low EMT, partial EMT, and high EMT states. Cells along the partial EMT trajectory showed substantial variations in the EMT signature and exhibited pronounced stemness. Throughout this EMT trajectory, we observed a consistent downregulation of the and genes. This finding was validated by recent inhibitor screens of EMT regulators and CRISPR screen studies. Moreover, we applied our analysis of early-phase differential gene expression to gene sets associated with stemness and proliferation, pinpointing , , and as genes differentially expressed in the initial stages of the partial versus high EMT trajectories. We also found that , , and showed significant upregulation in the high EMT trajectory. While the first group of genes aligns with findings from previous studies, our work uniquely pinpoints the precise timing of these upregulations. Finally, the identification of the latter group of genes sheds light on potential cell cycle targets for modulating EMT trajectories. -
Kaczanowska S, Murty T, Alimadadi A, Contreras CF, Duault C, Subrahmanyam PB, Reynolds W, Gutierrez NA, Baskar R, Wu CJ, Michor F, Altreuter J, Liu Y, Jhaveri A, Duong V, Anbunathan H, Ong C, Zhang H, Moravec R, Yu J, Biswas R, Van Nostrand S, Lindsay J, Pichavant M, Sotillo E, Bernstein D, Carbonell A, Derdak J, Klicka-Skeels J, Segal JE, Dombi E, Harmon SA, Turkbey B, Sahaf B, Bendall S, Maecker H, Highfill SL, Stroncek D, Glod J, Merchant M, Hedrick CC, Mackall CL, Ramakrishna S, Kaplan RN. 2024. Immune determinants of CAR-T cell expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer cell. 42(1):35-51.e8. Pubmed: 38134936 DOI:S1535-6108(23)00402-6 Kaczanowska S, Murty T, Alimadadi A, Contreras CF, Duault C, Subrahmanyam PB, Reynolds W, Gutierrez NA, Baskar R, Wu CJ, Michor F, Altreuter J, Liu Y, Jhaveri A, Duong V, Anbunathan H, Ong C, Zhang H, Moravec R, Yu J, Biswas R, Van Nostrand S, Lindsay J, Pichavant M, Sotillo E, Bernstein D, Carbonell A, Derdak J, Klicka-Skeels J, Segal JE, Dombi E, Harmon SA, Turkbey B, Sahaf B, Bendall S, Maecker H, Highfill SL, Stroncek D, Glod J, Merchant M, Hedrick CC, Mackall CL, Ramakrishna S, Kaplan RN. 2024. Immune determinants of CAR-T cell expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer cell. 42(1):35-51.e8. Pubmed: 38134936 DOI:S1535-6108(23)00402-6 Chimeric antigen receptor T cells (CAR-Ts) have remarkable efficacy in liquid tumors, but limited responses in solid tumors. We conducted a Phase I trial (NCT02107963) of GD2 CAR-Ts (GD2-CAR.OX40.28.z.iC9), demonstrating feasibility and safety of administration in children and young adults with osteosarcoma and neuroblastoma. Since CAR-T efficacy requires adequate CAR-T expansion, patients were grouped into good or poor expanders across dose levels. Patient samples were evaluated by multi-dimensional proteomic, transcriptomic, and epigenetic analyses. T cell assessments identified naive T cells in pre-treatment apheresis associated with good expansion, and exhausted T cells in CAR-T products with poor expansion. Myeloid cell assessment identified CXCR3 monocytes in pre-treatment apheresis associated with good expansion. Longitudinal analysis of post-treatment samples identified increased CXCR3 classical monocytes in all groups as CAR-T numbers waned. Together, our data uncover mediators of CAR-T biology and correlates of expansion that could be utilized to advance immunotherapies for solid tumor patients.Published by Elsevier Inc. -
Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. 2024. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. Cell genomics. 4(1):100444. Pubmed: 38190106 DOI:10.1016/j.xgen.2023.100444 Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. 2024. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. Cell genomics. 4(1):100444. Pubmed: 38190106 DOI:10.1016/j.xgen.2023.100444 Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.Copyright © 2023. Published by Elsevier Inc. -
Parra ER, Zhang J, Duose DY, Gonzalez-Kozlova E, Redman MW, Chen H, Manyam GC, Kumar G, Zhang J, Song X, Lazcano R, Marques-Piubelli ML, Laberiano-Fernandez C, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Alatrash G, Huang HH, Xie H, Patel M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray JE, Herbst RS, Wistuba II, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee JJ, Zhang J, Haymaker C. 2024. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial. Clinical cancer research : an official journal of the American Association for Cancer Research. 30(8):1655-1668. Pubmed: 38277235 DOI:10.1158/1078-0432.CCR-23-0251 Parra ER, Zhang J, Duose DY, Gonzalez-Kozlova E, Redman MW, Chen H, Manyam GC, Kumar G, Zhang J, Song X, Lazcano R, Marques-Piubelli ML, Laberiano-Fernandez C, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Alatrash G, Huang HH, Xie H, Patel M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray JE, Herbst RS, Wistuba II, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee JJ, Zhang J, Haymaker C. 2024. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial. Clinical cancer research : an official journal of the American Association for Cancer Research. 30(8):1655-1668. Pubmed: 38277235 DOI:10.1158/1078-0432.CCR-23-0251 Array©2024 The Authors; Published by the American Association for Cancer Research. -
Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K. 2024. Author Correction: Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nature cell biology. 26(5):841. Pubmed: 38443568 DOI:10.1038/s41556-024-01385-z Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K. 2024. Author Correction: Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nature cell biology. 26(5):841. Pubmed: 38443568 DOI:10.1038/s41556-024-01385-z -
Dean JA, Reyes J, Tsabar M, Jambhekar A, Lahav G, Michor F. 2024. Functional consequences of a p53-MDM2-p21 incoherent feedforward loop. bioRxiv : the preprint server for biology. Pubmed: 38979342 DOI:10.1101/2024.06.25.600070 Dean JA, Reyes J, Tsabar M, Jambhekar A, Lahav G, Michor F. 2024. Functional consequences of a p53-MDM2-p21 incoherent feedforward loop. bioRxiv : the preprint server for biology. Pubmed: 38979342 DOI:10.1101/2024.06.25.600070 Genetically identical cells can respond heterogeneously to cancer therapy, with a subpopulation of cells often entering a temporarily arrested treatment-tolerant state before repopulating the tumor. To investigate how heterogeneity in the cell cycle arrest protein p21 arises, we imaged the dynamics of p21 transcription and protein expression along with those of p53, its transcriptional regulator, in single cells using live cell fluorescence microscopy. Surprisingly, we found that the rate of p21 transcription depends on the change in p53 rather than its absolute level. Through combined theoretical and experimental modeling, we determined that p21 transcription is governed by an incoherent feedforward loop mediated by MDM2. This network architecture facilitates rapid induction of p21 expression and variability in p21 transcription. Abrogating the feedforward loop overcomes rapid S-phase p21 degradation, with cells transitioning into a quiescent state that transcriptionally resembles a treatment-tolerant persister state. Our findings have important implications for therapeutic strategies based on activating p53. -
Riviere-Cazaux C, Graser CJ, Warrington AE, Hoplin MD, Andersen KM, Malik N, Palmer EA, Carlstrom LP, Dasari S, Munoz-Casabella A, Ikram S, Ghadimi K, Himes BT, Jusue-Torres I, Sarkaria JN, Meyer FB, Van Gompel JJ, Kizilbash SH, Sener U, Michor F, Campian JL, Parney IF, Burns TC. 2024. The dynamic impact of location and resection on the glioma CSF proteome. medRxiv : the preprint server for health sciences. Pubmed: 38798641 DOI:10.1101/2024.05.15.24307463 Riviere-Cazaux C, Graser CJ, Warrington AE, Hoplin MD, Andersen KM, Malik N, Palmer EA, Carlstrom LP, Dasari S, Munoz-Casabella A, Ikram S, Ghadimi K, Himes BT, Jusue-Torres I, Sarkaria JN, Meyer FB, Van Gompel JJ, Kizilbash SH, Sener U, Michor F, Campian JL, Parney IF, Burns TC. 2024. The dynamic impact of location and resection on the glioma CSF proteome. medRxiv : the preprint server for health sciences. Pubmed: 38798641 DOI:10.1101/2024.05.15.24307463 Array 2023
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Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. 2023. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nature protocols. 18(8):2404-2414. Pubmed: 37391666 DOI:10.1038/s41596-023-00841-8 Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. 2023. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nature protocols. 18(8):2404-2414. Pubmed: 37391666 DOI:10.1038/s41596-023-00841-8 RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression data. However, the analysis of large-scale RNA-seq data requires bioinformatics proficiency, large computational resources and cancer genomics and immunology knowledge. In this tutorial, we provide an overview of computational analysis of bulk RNA-seq data for immune characterization of tumors and introduce commonly used computational tools with relevance to cancer immunology and immunotherapy. These tools have diverse functions such as evaluation of expression signatures, estimation of immune infiltration, inference of the immune repertoire, prediction of immunotherapy response, neoantigen detection and microbiome quantification. We describe the RNA-seq IMmune Analysis (RIMA) pipeline integrating many of these tools to streamline RNA-seq analysis. We also developed a comprehensive and user-friendly guide in the form of a GitBook with text and video demos to assist users in analyzing bulk RNA-seq data for immune characterization at both individual sample and cohort levels by using RIMA.© 2023. Springer Nature Limited. -
Dean JA, Tanguturi SK, Cagney D, Shin KY, Youssef G, Aizer A, Rahman R, Hammoudeh L, Reardon D, Lee E, Dietrich J, Tamura K, Aoyagi M, Wickersham L, Wen PY, Catalano P, Haas-Kogan D, Alexander BM, Michor F. 2023. Phase I study of a novel glioblastoma radiation therapy schedule exploiting cell-state plasticity. Neuro-oncology. 25(6):1100-1112. Pubmed: 36402744 DOI:10.1093/neuonc/noac253 Dean JA, Tanguturi SK, Cagney D, Shin KY, Youssef G, Aizer A, Rahman R, Hammoudeh L, Reardon D, Lee E, Dietrich J, Tamura K, Aoyagi M, Wickersham L, Wen PY, Catalano P, Haas-Kogan D, Alexander BM, Michor F. 2023. Phase I study of a novel glioblastoma radiation therapy schedule exploiting cell-state plasticity. Neuro-oncology. 25(6):1100-1112. Pubmed: 36402744 DOI:10.1093/neuonc/noac253 Array© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. -
Sozen B, Flavell RA, Lamming DW, Silver DL, Parrinello S, Abate-Shen C, Michor F, Sankaran VG. 2023. What approaches are needed to understand human development and disease?. Developmental cell. 58(24):2822-2825. Pubmed: 38113848 DOI:S1534-5807(23)00647-0 Sozen B, Flavell RA, Lamming DW, Silver DL, Parrinello S, Abate-Shen C, Michor F, Sankaran VG. 2023. What approaches are needed to understand human development and disease?. Developmental cell. 58(24):2822-2825. Pubmed: 38113848 DOI:S1534-5807(23)00647-0 Researchers are leveraging what we have learned from model organisms to understand if the same principles arise in human physiology, development, and disease. In this collection of Voices, we asked researchers from different fields to discuss what tools and insights they are using to answer fundamental questions in human biology.Copyright © 2023 Elsevier Inc. All rights reserved. -
Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. 2023. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell reports. 42(12):113564. Pubmed: 38100350 DOI:S2211-1247(23)01576-0 Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. 2023. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell reports. 42(12):113564. Pubmed: 38100350 DOI:S2211-1247(23)01576-0 Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity, we defined transcriptional, epigenetic, and metabolic subtypes and subtype-driving super-enhancers and transcription factors by combining functional and molecular profiling with computational analyses. Single-cell RNA sequencing revealed relative homogeneity of the major transcriptional subtypes (luminal, basal, and mesenchymal) within samples. We found that mesenchymal TNBCs share features with mesenchymal neuroblastoma and rhabdoid tumors and that the PRRX1 transcription factor is a key driver of these tumors. PRRX1 is sufficient for inducing mesenchymal features in basal but not in luminal TNBC cells via reprogramming super-enhancer landscapes, but it is not required for mesenchymal state maintenance or for cellular viability. Our comprehensive, large-scale, multiplatform, multiomics study of both experimental and clinical TNBC is an important resource for the scientific and clinical research communities and opens venues for future investigation.Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved. -
Nishida J, Cristea S, Bodapati S, Puleo J, Bai G, Patel A, Hughes M, Snow C, Borges V, Ruddy KJ, Collins LC, Feeney AM, Slowik K, Bossuyt V, Dillon D, Lin NU, Partridge AH, Michor F, Polyak K. 2023. Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression. Proceedings of the National Academy of Sciences of the United States of America. 120(49):e2316763120. Pubmed: 38011567 DOI:10.1073/pnas.2316763120 Nishida J, Cristea S, Bodapati S, Puleo J, Bai G, Patel A, Hughes M, Snow C, Borges V, Ruddy KJ, Collins LC, Feeney AM, Slowik K, Bossuyt V, Dillon D, Lin NU, Partridge AH, Michor F, Polyak K. 2023. Peripheral blood TCR clonotype diversity as an age-associated marker of breast cancer progression. Proceedings of the National Academy of Sciences of the United States of America. 120(49):e2316763120. Pubmed: 38011567 DOI:10.1073/pnas.2316763120 Immune escape is a prerequisite for tumor growth. We previously described a decline in intratumor activated cytotoxic T cells and T cell receptor (TCR) clonotype diversity in invasive breast carcinomas compared to ductal carcinoma in situ (DCIS), implying a central role of decreasing T cell responses in tumor progression. To determine potential associations between peripheral immunity and breast tumor progression, here, we assessed the peripheral blood TCR clonotype of 485 breast cancer patients diagnosed with either DCIS or de novo stage IV disease at younger (<45) or older (≥45) age. TCR clonotype diversity was significantly lower in older compared to younger breast cancer patients regardless of tumor stage at diagnosis. In the younger age group, TCR-α clonotype diversity was lower in patients diagnosed with de novo stage IV breast cancer compared to those diagnosed with DCIS. In the older age group, DCIS patients with higher TCR-α clonotype diversity were more likely to have a recurrence compared to those with lower diversity. Whole blood transcriptome profiles were distinct depending on the TCR-α Chao1 diversity score. There were more CD8 T cells and a more active immune environment in DCIS tumors of young patients with higher peripheral blood TCR-α Chao1 diversity than in those with lower diversity. These results provide insights into the role that host immunity plays in breast cancer development across different age groups. -
Cheng YC, Stein S, Nardone A, Liu W, Ma W, Cohen G, Guarducci C, McDonald TO, Jeselsohn R, Michor F. 2023. Mathematical Modeling Identifies Optimum Palbociclib-fulvestrant Dose Administration Schedules for the Treatment of Patients with Estrogen Receptor-positive Breast Cancer. Cancer research communications. 3(11):2331-2344. Pubmed: 37921419 DOI:10.1158/2767-9764.CRC-23-0257 Cheng YC, Stein S, Nardone A, Liu W, Ma W, Cohen G, Guarducci C, McDonald TO, Jeselsohn R, Michor F. 2023. Mathematical Modeling Identifies Optimum Palbociclib-fulvestrant Dose Administration Schedules for the Treatment of Patients with Estrogen Receptor-positive Breast Cancer. Cancer research communications. 3(11):2331-2344. Pubmed: 37921419 DOI:10.1158/2767-9764.CRC-23-0257 Array© 2023 The Authors; Published by the American Association for Cancer Research. -
Chen Z, Giotti B, Kaluzova M, Vallcorba MP, Rawat K, Price G, Herting CJ, Pinero G, Cristea S, Ross JL, Ackley J, Maximov V, Szulzewsky F, Thomason W, Marquez-Ropero M, Angione A, Nichols N, Tsankova NM, Michor F, Shayakhmetov DM, Gutmann DH, Tsankov AM, Hambardzumyan D. 2023. A paracrine circuit of IL-1β/IL-1R1 between myeloid and tumor cells drives genotype-dependent glioblastoma progression. The Journal of clinical investigation. 133(22). Pubmed: 37733448 DOI:10.1172/JCI163802 Chen Z, Giotti B, Kaluzova M, Vallcorba MP, Rawat K, Price G, Herting CJ, Pinero G, Cristea S, Ross JL, Ackley J, Maximov V, Szulzewsky F, Thomason W, Marquez-Ropero M, Angione A, Nichols N, Tsankova NM, Michor F, Shayakhmetov DM, Gutmann DH, Tsankov AM, Hambardzumyan D. 2023. A paracrine circuit of IL-1β/IL-1R1 between myeloid and tumor cells drives genotype-dependent glioblastoma progression. The Journal of clinical investigation. 133(22). Pubmed: 37733448 DOI:10.1172/JCI163802 Monocytes and monocyte-derived macrophages (MDMs) from blood circulation infiltrate glioblastoma (GBM) and promote growth. Here, we show that PDGFB-driven GBM cells induce the expression of the potent proinflammatory cytokine IL-1β in MDM, which engages IL-1R1 in tumor cells, activates the NF-κB pathway, and subsequently leads to induction of monocyte chemoattractant proteins (MCPs). Thus, a feedforward paracrine circuit of IL-1β/IL-1R1 between tumors and MDM creates an interdependence driving PDGFB-driven GBM progression. Genetic loss or locally antagonizing IL-1β/IL-1R1 leads to reduced MDM infiltration, diminished tumor growth, and reduced exhausted CD8+ T cells and thereby extends the survival of tumor-bearing mice. In contrast to IL-1β, IL-1α exhibits antitumor effects. Genetic deletion of Il1a/b is associated with decreased recruitment of lymphoid cells and loss-of-interferon signaling in various immune populations and subsets of malignant cells and is associated with decreased survival time of PDGFB-driven tumor-bearing mice. In contrast to PDGFB-driven GBM, Nf1-silenced tumors have a constitutively active NF-κB pathway, which drives the expression of MCPs to recruit monocytes into tumors. These results indicate local antagonism of IL-1β could be considered as an effective therapy specifically for proneural GBM. -
Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K. 2023. JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Cancer research. 83(2):264-284. Pubmed: 36409824 DOI:10.1158/0008-5472.CAN-22-0423 Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K. 2023. JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Cancer research. 83(2):264-284. Pubmed: 36409824 DOI:10.1158/0008-5472.CAN-22-0423 Array©2022 The Authors; Published by the American Association for Cancer Research. -
Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K, Hochedlinger K. 2023. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nature cell biology. 25(8):1121-1134. Pubmed: 37460697 DOI:10.1038/s41556-023-01191-z Hoetker MS, Yagi M, Di Stefano B, Langerman J, Cristea S, Wong LP, Huebner AJ, Charlton J, Deng W, Haggerty C, Sadreyev RI, Meissner A, Michor F, Plath K, Hochedlinger K. 2023. H3K36 methylation maintains cell identity by regulating opposing lineage programmes. Nature cell biology. 25(8):1121-1134. Pubmed: 37460697 DOI:10.1038/s41556-023-01191-z The epigenetic mechanisms that maintain differentiated cell states remain incompletely understood. Here we employed histone mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimental induction of pluripotency, we show that H3K36M-mediated depletion of H3K36 methylation endows fibroblasts with a plastic state poised to acquire pluripotency in nearly all cells. At a cellular level, H3K36M facilitates epithelial plasticity by rendering fibroblasts insensitive to TGFβ signals. At a molecular level, H3K36M enables the decommissioning of mesenchymal enhancers and the parallel activation of epithelial/stem cell enhancers. This enhancer rewiring is Tet dependent and redirects Sox2 from promiscuous somatic to pluripotency targets. Our findings reveal a previously unappreciated dual role for H3K36 methylation in the maintenance of cell identity by integrating a crucial developmental pathway into sustained expression of cell-type-specific programmes, and by opposing the expression of alternative lineage programmes through enhancer methylation.© 2023. The Author(s), under exclusive licence to Springer Nature Limited. -
Walentynowicz KA, Engelhardt D, Cristea S, Yadav S, Onubogu U, Salatino R, Maerken M, Vincentelli C, Jhaveri A, Geisberg J, McDonald TO, Michor F, Janiszewska M. 2023. Single-cell heterogeneity of EGFR and CDK4 co-amplification is linked to immune infiltration in glioblastoma. Cell reports. 42(3):112235. Pubmed: 36920905 DOI:S2211-1247(23)00246-2 Walentynowicz KA, Engelhardt D, Cristea S, Yadav S, Onubogu U, Salatino R, Maerken M, Vincentelli C, Jhaveri A, Geisberg J, McDonald TO, Michor F, Janiszewska M. 2023. Single-cell heterogeneity of EGFR and CDK4 co-amplification is linked to immune infiltration in glioblastoma. Cell reports. 42(3):112235. Pubmed: 36920905 DOI:S2211-1247(23)00246-2 Glioblastoma (GBM) is the most aggressive brain tumor, with a median survival of ∼15 months. Targeted approaches have not been successful in this tumor type due to the large extent of intratumor heterogeneity. Mosaic amplification of oncogenes suggests that multiple genetically distinct clones are present in each tumor. To uncover the relationships between genetically diverse subpopulations of GBM cells and their native tumor microenvironment, we employ highly multiplexed spatial protein profiling coupled with single-cell spatial mapping of fluorescence in situ hybridization (FISH) for EGFR, CDK4, and PDGFRA. Single-cell FISH analysis of a total of 35,843 single nuclei reveals that tumors in which amplifications of EGFR and CDK4 more frequently co-occur in the same cell exhibit higher infiltration of CD163 immunosuppressive macrophages. Our results suggest that high-throughput assessment of genomic alterations at the single-cell level could provide a measure for predicting the immune state of GBM.Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved. -
Elkrief A, Makhnin A, Moses KA, Ahn LS, Preeshagul IR, Iqbal AN, Hayes SA, Plodkowski AJ, Paik PK, Ladanyi M, Kris MG, Riely GJ, Michor F, Yu HA. 2023. Brief Report: Combination of Osimertinib and Dacomitinib to Mitigate Primary and Acquired Resistance in EGFR-Mutant Lung Adenocarcinomas. Clinical cancer research : an official journal of the American Association for Cancer Research. 29(8):1423-1428. Pubmed: 36729110 DOI:10.1158/1078-0432.CCR-22-3484 Elkrief A, Makhnin A, Moses KA, Ahn LS, Preeshagul IR, Iqbal AN, Hayes SA, Plodkowski AJ, Paik PK, Ladanyi M, Kris MG, Riely GJ, Michor F, Yu HA. 2023. Brief Report: Combination of Osimertinib and Dacomitinib to Mitigate Primary and Acquired Resistance in EGFR-Mutant Lung Adenocarcinomas. Clinical cancer research : an official journal of the American Association for Cancer Research. 29(8):1423-1428. Pubmed: 36729110 DOI:10.1158/1078-0432.CCR-22-3484 Array©2023 American Association for Cancer Research. -
Penter L, Liu Y, Wolff JO, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Cullen NM, Pfaff KL, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Morgan EA, Chen HX, Song MH, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg DS, Hodi FS, Davids MS, Gnjatic S, Livak KJ, Altreuter J, Michor F, Soiffer RJ, Garcia JS, Wu CJ. 2023. Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease. Blood. 141(15):1817-1830. Pubmed: 36706355 DOI:10.1182/blood.2022018246 Penter L, Liu Y, Wolff JO, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Cullen NM, Pfaff KL, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Morgan EA, Chen HX, Song MH, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg DS, Hodi FS, Davids MS, Gnjatic S, Livak KJ, Altreuter J, Michor F, Soiffer RJ, Garcia JS, Wu CJ. 2023. Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease. Blood. 141(15):1817-1830. Pubmed: 36706355 DOI:10.1182/blood.2022018246 The challenge of eradicating leukemia in patients with acute myelogenous leukemia (AML) after initial cytoreduction has motivated modern efforts to combine synergistic active modalities including immunotherapy. Recently, the ETCTN/CTEP 10026 study tested the combination of the DNA methyltransferase inhibitor decitabine together with the immune checkpoint inhibitor ipilimumab for AML/myelodysplastic syndrome (MDS) either after allogeneic hematopoietic stem cell transplantation (HSCT) or in the HSCT-naïve setting. Integrative transcriptome-based analysis of 304 961 individual marrow-infiltrating cells for 18 of 48 subjects treated on study revealed the strong association of response with a high baseline ratio of T to AML cells. Clinical responses were predominantly driven by decitabine-induced cytoreduction. Evidence of immune activation was only apparent after ipilimumab exposure, which altered CD4+ T-cell gene expression, in line with ongoing T-cell differentiation and increased frequency of marrow-infiltrating regulatory T cells. For post-HSCT samples, relapse could be attributed to insufficient clearing of malignant clones in progenitor cell populations. In contrast to AML/MDS bone marrow, the transcriptomes of leukemia cutis samples from patients with durable remission after ipilimumab monotherapy showed evidence of increased infiltration with antigen-experienced resident memory T cells and higher expression of CTLA-4 and FOXP3. Altogether, activity of combined decitabine and ipilimumab is impacted by cellular expression states within the microenvironmental niche of leukemic cells. The inadequate elimination of leukemic progenitors mandates urgent development of novel approaches for targeting these cell populations to generate long-lasting responses. This trial was registered at www.clinicaltrials.gov as #NCT02890329.© 2023 by The American Society of Hematology. 2022
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Mercier FE, Shi J, Sykes DB, Oki T, Jankovic M, Man CH, Kfoury YS, Miller E, He S, Zhu A, Vasic R, Doench J, Orthwein A, Michor F, Scadden DT. 2022. In vivo genome-wide CRISPR screening in murine acute myeloid leukemia uncovers microenvironmental dependencies. Blood advances. 6(17):5072-5084. Pubmed: 35793392 DOI:10.1182/bloodadvances.2022007250 Mercier FE, Shi J, Sykes DB, Oki T, Jankovic M, Man CH, Kfoury YS, Miller E, He S, Zhu A, Vasic R, Doench J, Orthwein A, Michor F, Scadden DT. 2022. In vivo genome-wide CRISPR screening in murine acute myeloid leukemia uncovers microenvironmental dependencies. Blood advances. 6(17):5072-5084. Pubmed: 35793392 DOI:10.1182/bloodadvances.2022007250 Genome-wide CRISPR screens have been extremely useful in identifying therapeutic targets in diverse cancers by defining genes that are essential for malignant growth. However, most CRISPR screens were performed in vitro and thus cannot identify genes that are essential for interactions with the microenvironment in vivo. Here, we report genome-wide CRISPR screens in 2 in vivo murine models of acute myeloid leukemia (AML) driven by the KMT2A/MLLT3 fusion or by the constitutive coexpression of Hoxa9 and Meis1. Secondary validation using a focused library identified 72 genes specifically essential for leukemic growth in vivo, including components of the major histocompatibility complex class I complex, Cd47, complement receptor Cr1l, and the β-4-galactosylation pathway. Importantly, several of these in vivo-specific hits have a prognostic effect or are inferred to be master regulators of protein activity in human AML cases. For instance, we identified Fermt3, a master regulator of integrin signaling, as having in vivo-specific dependency with high prognostic relevance. Overall, we show an experimental and computational pipeline for genome-wide functional screens in vivo in AML and provide a genome-wide resource of essential drivers of leukemic growth in vivo.© 2022 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved. -
Poels KE, Schoenfeld AJ, Makhnin A, Tobi Y, Wang Y, Frisco-Cabanos H, Chakrabarti S, Shi M, Napoli C, McDonald TO, Tan W, Hata A, Weinrich SL, Yu HA, Michor F. 2022. Author Correction: Identification of optimal dosing schedules of dacomitinib and osimertinib for a phase I/II trial in advanced EGFR-mutant non-small cell lung cancer. Nature communications. 13(1):5579. Pubmed: 36151107 DOI:10.1038/s41467-022-33355-0 Poels KE, Schoenfeld AJ, Makhnin A, Tobi Y, Wang Y, Frisco-Cabanos H, Chakrabarti S, Shi M, Napoli C, McDonald TO, Tan W, Hata A, Weinrich SL, Yu HA, Michor F. 2022. Author Correction: Identification of optimal dosing schedules of dacomitinib and osimertinib for a phase I/II trial in advanced EGFR-mutant non-small cell lung cancer. Nature communications. 13(1):5579. Pubmed: 36151107 DOI:10.1038/s41467-022-33355-0 -
Dean J, Goldberg E, Michor F. 2022. Designing optimal allocations for cancer screening using queuing network models. PLoS computational biology. 18(5):e1010179. Pubmed: 35622852 DOI:10.1371/journal.pcbi.1010179 Dean J, Goldberg E, Michor F. 2022. Designing optimal allocations for cancer screening using queuing network models. PLoS computational biology. 18(5):e1010179. Pubmed: 35622852 DOI:10.1371/journal.pcbi.1010179 Cancer is one of the leading causes of death, but mortality can be reduced by detecting tumors earlier so that treatment is initiated at a less aggressive stage. The tradeoff between costs associated with screening and its benefit makes the decision of whom to screen and when a challenge. To enable comparisons across screening strategies for any cancer type, we demonstrate a mathematical modeling platform based on the theory of queuing networks designed for quantifying the benefits of screening strategies. Our methodology can be used to design optimal screening protocols and to estimate their benefits for specific patient populations. Our method is amenable to exact analysis, thus circumventing the need for simulations, and is capable of exactly quantifying outcomes given variability in the age of diagnosis, rate of progression, and screening sensitivity and intervention outcomes. We demonstrate the power of this methodology by applying it to data from the Surveillance, Epidemiology and End Results (SEER) program. Our approach estimates the benefits that various novel screening programs would confer to different patient populations, thus enabling us to formulate an optimal screening allocation and quantify its potential effects for any cancer type and intervention. -
Van Egeren D, Kamaz B, Liu S, Nguyen M, Reilly CR, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Michor F, Cortes-Ciriano I, Mullally A, Hormoz S. 2022. Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in patients with myeloproliferative neoplasms. Experimental hematology. 107:14-19. Pubmed: 34921959 DOI:S0301-472X(21)00823-7 Van Egeren D, Kamaz B, Liu S, Nguyen M, Reilly CR, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Michor F, Cortes-Ciriano I, Mullally A, Hormoz S. 2022. Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in patients with myeloproliferative neoplasms. Experimental hematology. 107:14-19. Pubmed: 34921959 DOI:S0301-472X(21)00823-7 The JAK2-V617F mutation is the most common cause of myeloproliferative neoplasms. Although experiments have revealed that this gain-of-function mutation is associated with myeloid blood cell expansion and increased production of white cells, red cells, and platelets, the transcriptional consequences of the JAK2-V617F mutation in different cellular compartments of the bone marrow have not yet been fully elucidated. To study the direct effects of JAK2-V617F on bone marrow cells in patients with myeloproliferative neoplasms, we performed joint single-cell RNA sequencing and JAK2 genotyping on CD34-enriched cells from eight patients with newly diagnosed essential thrombocythemia or polycythemia vera. We found that the JAK2-V617F mutation increases the expression of interferon-response genes (e.g., HLAs) and the leptin receptor in hematopoietic progenitor cells. Furthermore, we sequenced a population of CD34 bone marrow monocytes and found that the JAK2 mutation increased expression of intermediate monocyte genes and the fibrocyte-associated surface protein SLAMF7 in these cells.Copyright © 2021 ISEH -- Society for Hematology and Stem Cells. Published by Elsevier Inc. All rights reserved. -
Nguyen Ba AN, Lawrence KR, Rego-Costa A, Gopalakrishnan S, Temko D, Michor F, Desai MM. 2022. Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast. eLife. 11. Pubmed: 35147078 DOI:10.7554/eLife.73983 Nguyen Ba AN, Lawrence KR, Rego-Costa A, Gopalakrishnan S, Temko D, Michor F, Desai MM. 2022. Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast. eLife. 11. Pubmed: 35147078 DOI:10.7554/eLife.73983 Mapping the genetic basis of complex traits is critical to uncovering the biological mechanisms that underlie disease and other phenotypes. Genome-wide association studies (GWAS) in humans and quantitative trait locus (QTL) mapping in model organisms can now explain much of the observed heritability in many traits, allowing us to predict phenotype from genotype. However, constraints on power due to statistical confounders in large GWAS and smaller sample sizes in QTL studies still limit our ability to resolve numerous small-effect variants, map them to causal genes, identify pleiotropic effects across multiple traits, and infer non-additive interactions between loci (epistasis). Here, we introduce barcoded bulk quantitative trait locus (BB-QTL) mapping, which allows us to construct, genotype, and phenotype 100,000 offspring of a budding yeast cross, two orders of magnitude larger than the previous state of the art. We use this panel to map the genetic basis of eighteen complex traits, finding that the genetic architecture of these traits involves hundreds of small-effect loci densely spaced throughout the genome, many with widespread pleiotropic effects across multiple traits. Epistasis plays a central role, with thousands of interactions that provide insight into genetic networks. By dramatically increasing sample size, BB-QTL mapping demonstrates the potential of natural variants in high-powered QTL studies to reveal the highly polygenic, pleiotropic, and epistatic architecture of complex traits.© 2022, Nguyen Ba et al. -
Van Egeren D, Kohli K, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F. 2022. Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Scientific reports. 12(1):19055. Pubmed: 36351964 DOI:10.1038/s41598-022-21448-1 Van Egeren D, Kohli K, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F. 2022. Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Scientific reports. 12(1):19055. Pubmed: 36351964 DOI:10.1038/s41598-022-21448-1 Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.© 2022. The Author(s). -
Alečković M, Cristea S, Gil Del Alcazar CR, Yan P, Ding L, Krop ED, Harper NW, Rojas Jimenez E, Lu D, Gulvady AC, Foidart P, Seehawer M, Diciaccio B, Murphy KC, Pyrdol J, Anand J, Garza K, Wucherpfennig KW, Tamimi RM, Michor F, Polyak K. 2022. Breast cancer prevention by short-term inhibition of TGFβ signaling. Nature communications. 13(1):7558. Pubmed: 36476730 DOI:10.1038/s41467-022-35043-5 Alečković M, Cristea S, Gil Del Alcazar CR, Yan P, Ding L, Krop ED, Harper NW, Rojas Jimenez E, Lu D, Gulvady AC, Foidart P, Seehawer M, Diciaccio B, Murphy KC, Pyrdol J, Anand J, Garza K, Wucherpfennig KW, Tamimi RM, Michor F, Polyak K. 2022. Breast cancer prevention by short-term inhibition of TGFβ signaling. Nature communications. 13(1):7558. Pubmed: 36476730 DOI:10.1038/s41467-022-35043-5 Cancer prevention has a profound impact on cancer-associated mortality and morbidity. We previously identified TGFβ signaling as a candidate regulator of mammary epithelial cells associated with breast cancer risk. Here, we show that short-term TGFBR inhibitor (TGFBRi) treatment of peripubertal ACI inbred and Sprague Dawley outbred rats induces lasting changes and prevents estrogen- and carcinogen-induced mammary tumors, respectively. We identify TGFBRi-responsive cell populations by single cell RNA-sequencing, including a unique epithelial subpopulation designated secretory basal cells (SBCs) with progenitor features. We detect SBCs in normal human breast tissues and find them to be associated with breast cancer risk. Interactome analysis identifies SBCs as the most interactive cell population and the main source of insulin-IGF signaling. Accordingly, inhibition of TGFBR and IGF1R decrease proliferation of organoid cultures. Our results reveal a critical role for TGFβ in regulating mammary epithelial cells relevant to breast cancer and serve as a proof-of-principle cancer prevention strategy.© 2022. The Author(s). -
Wu HJ, Temko D, Maliga Z, Moreira AL, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson CA, Yapp C, Schapiro D, Sorger PK, Seeley EH, Navin N, Downey RJ, Michor F. 2022. Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Cell genomics. 2(8). Pubmed: 36419822 DOI:10.1016/j.xgen.2022.100165 Wu HJ, Temko D, Maliga Z, Moreira AL, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson CA, Yapp C, Schapiro D, Sorger PK, Seeley EH, Navin N, Downey RJ, Michor F. 2022. Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Cell genomics. 2(8). Pubmed: 36419822 DOI:10.1016/j.xgen.2022.100165 Intra-tumor heterogeneity (ITH) of human tumors is important for tumor progression, treatment response, and drug resistance. However, the spatial distribution of ITH remains incompletely understood. Here, we present spatial analysis of ITH in lung adenocarcinomas from 147 patients using multi-region mass spectrometry of >5,000 regions, single-cell copy number sequencing of ~2,000 single cells, and cyclic immunofluorescence of >10 million cells. We identified two distinct spatial patterns among tumors, termed clustered and random geographic diversification (GD). These patterns were observed in the same samples using both proteomic and genomic data. The random proteomic GD pattern, which is characterized by decreased cell adhesion and lower levels of tumor-interacting endothelial cells, was significantly associated with increased risk of recurrence or death in two independent patient cohorts. Our study presents comprehensive spatial mapping of ITH in lung adenocarcinoma and provides insights into the mechanisms and clinical consequences of GD. 2021
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Randles A, Wirsching HG, Dean JA, Cheng YK, Emerson S, Pattwell SS, Holland EC, Michor F. 2021. Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma. Nature biomedical engineering. 5(4):346-359. Pubmed: 33864039 DOI:10.1038/s41551-021-00710-3 Randles A, Wirsching HG, Dean JA, Cheng YK, Emerson S, Pattwell SS, Holland EC, Michor F. 2021. Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma. Nature biomedical engineering. 5(4):346-359. Pubmed: 33864039 DOI:10.1038/s41551-021-00710-3 Glioblastoma stem-like cells dynamically transition between a chemoradiation-resistant state and a chemoradiation-sensitive state. However, physical barriers in the tumour microenvironment restrict the delivery of chemotherapy to tumour compartments that are distant from blood vessels. Here, we show that a massively parallel computational model of the spatiotemporal dynamics of the perivascular niche that incorporates glioblastoma stem-like cells and differentiated tumour cells as well as relevant tissue-level phenomena can be used to optimize the administration schedules of concurrent radiation and temozolomide-the standard-of-care treatment for glioblastoma. In mice with platelet-derived growth factor (PDGF)-driven glioblastoma, the model-optimized treatment schedule increased the survival of the animals. For standard radiation fractionation in patients, the model predicts that chemotherapy may be optimally administered about one hour before radiation treatment. Computational models of the spatiotemporal dynamics of the tumour microenvironment could be used to predict tumour responses to a broader range of treatments and to optimize treatment regimens. -
van Dorp L, Shey MS, Ghedin E, Michor F, Koonin EV, Hampson K. 2021. How Does Large-Scale Genomic Analysis Shape Our Understanding of COVID Variants in Real Time?. Cell systems. 12(2):109-111. Pubmed: 33539725 DOI:S2405-4712(21)00038-7 van Dorp L, Shey MS, Ghedin E, Michor F, Koonin EV, Hampson K. 2021. How Does Large-Scale Genomic Analysis Shape Our Understanding of COVID Variants in Real Time?. Cell systems. 12(2):109-111. Pubmed: 33539725 DOI:S2405-4712(21)00038-7 -
Oki T, Mercier F, Kato H, Jung Y, McDonald TO, Spencer JA, Mazzola MC, van Gastel N, Lin CP, Michor F, Kitamura T, Scadden DT. 2021. Imaging dynamic mTORC1 pathway activity in vivo reveals marked shifts that support time-specific inhibitor therapy in AML. Nature communications. 12(1):245. Pubmed: 33431855 DOI:10.1038/s41467-020-20491-8 Oki T, Mercier F, Kato H, Jung Y, McDonald TO, Spencer JA, Mazzola MC, van Gastel N, Lin CP, Michor F, Kitamura T, Scadden DT. 2021. Imaging dynamic mTORC1 pathway activity in vivo reveals marked shifts that support time-specific inhibitor therapy in AML. Nature communications. 12(1):245. Pubmed: 33431855 DOI:10.1038/s41467-020-20491-8 Acute myeloid leukemia (AML) is a high remission, high relapse fatal blood cancer. Although mTORC1 is a master regulator of cell proliferation and survival, its inhibitors have not performed well as AML treatments. To uncover the dynamics of mTORC1 activity in vivo, fluorescent probes are developed to track single cell proliferation, apoptosis and mTORC1 activity of AML cells in the bone marrow of live animals and to quantify these activities in the context of microanatomical localization and intra-tumoral heterogeneity. When chemotherapy drugs commonly used clinically are given to mice with AML, apoptosis is rapid, diffuse and not preferentially restricted to anatomic sites. Dynamic measurement of mTORC1 activity indicated a decline in mTORC1 activity with AML progression. However, at the time of maximal chemotherapy response, mTORC1 signaling is high and positively correlated with a leukemia stemness transcriptional profile. Cell barcoding reveals the induction of mTORC1 activity rather than selection of mTORC1 high cells and timed inhibition of mTORC1 improved the killing of AML cells. These data define the real-time dynamics of AML and the mTORC1 pathway in association with AML growth, response to and relapse after chemotherapy. They provide guidance for timed intervention with pathway-specific inhibitors. -
Shen YJ, Mishima Y, Shi J, Sklavenitis-Pistofidis R, Redd RA, Moschetta M, Manier S, Roccaro AM, Sacco A, Tai YT, Mercier F, Kawano Y, Su NK, Berrios B, Doench JG, Root DE, Michor F, Scadden DT, Ghobrial IM. 2021. Progression signature underlies clonal evolution and dissemination of multiple myeloma. Blood. 137(17):2360-2372. Pubmed: 33150374 DOI:10.1182/blood.2020005885 Shen YJ, Mishima Y, Shi J, Sklavenitis-Pistofidis R, Redd RA, Moschetta M, Manier S, Roccaro AM, Sacco A, Tai YT, Mercier F, Kawano Y, Su NK, Berrios B, Doench JG, Root DE, Michor F, Scadden DT, Ghobrial IM. 2021. Progression signature underlies clonal evolution and dissemination of multiple myeloma. Blood. 137(17):2360-2372. Pubmed: 33150374 DOI:10.1182/blood.2020005885 Clonal evolution drives tumor progression, dissemination, and relapse in multiple myeloma (MM), with most patients dying of relapsed disease. This multistage process requires tumor cells to enter the circulation, extravasate, and colonize distant bone marrow (BM) sites. Here, we developed a fluorescent or DNA-barcode clone-tracking system on MM PrEDiCT (progression through evolution and dissemination of clonal tumor cells) xenograft mouse model to study clonal behavior within the BM microenvironment. We showed that only the few clones that successfully adapt to the BM microenvironment can enter the circulation and colonize distant BM sites. RNA sequencing of primary and distant-site MM tumor cells revealed a progression signature sequentially activated along human MM progression and significantly associated with overall survival when evaluated against patient data sets. A total of 28 genes were then computationally predicted to be master regulators (MRs) of MM progression. HMGA1 and PA2G4 were validated in vivo using CRISPR-Cas9 in the PrEDiCT model and were shown to be significantly depleted in distant BM sites, indicating their role in MM progression and dissemination. Loss of HMGA1 and PA2G4 also compromised the proliferation, migration, and adhesion abilities of MM cells in vitro. Overall, our model successfully recapitulates key characteristics of human MM disease progression and identified potential new therapeutic targets for MM.© 2021 by The American Society of Hematology. -
Van Egeren D, Escabi J, Nguyen M, Liu S, Reilly CR, Patel S, Kamaz B, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Camargo FD, Michor F, Mullally A, Cortes-Ciriano I, Hormoz S. 2021. Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms. Cell stem cell. 28(3):514-523.e9. Pubmed: 33621486 DOI:S1934-5909(21)00051-5 Van Egeren D, Escabi J, Nguyen M, Liu S, Reilly CR, Patel S, Kamaz B, Kalyva M, DeAngelo DJ, Galinsky I, Wadleigh M, Winer ES, Luskin MR, Stone RM, Garcia JS, Hobbs GS, Camargo FD, Michor F, Mullally A, Cortes-Ciriano I, Hormoz S. 2021. Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms. Cell stem cell. 28(3):514-523.e9. Pubmed: 33621486 DOI:S1934-5909(21)00051-5 Some cancers originate from a single mutation event in a single cell. Blood cancers known as myeloproliferative neoplasms (MPNs) are thought to originate when a driver mutation is acquired by a hematopoietic stem cell (HSC). However, when the mutation first occurs in individuals and how it affects the behavior of HSCs in their native context is not known. Here we quantified the effect of the JAK2-V617F mutation on the self-renewal and differentiation dynamics of HSCs in treatment-naive individuals with MPNs and reconstructed lineage histories of individual HSCs using somatic mutation patterns. We found that JAK2-V617F mutations occurred in a single HSC several decades before MPN diagnosis-at age 9 ± 2 years in a 34-year-old individual and at age 19 ± 3 years in a 63-year-old individual-and found that mutant HSCs have a selective advantage in both individuals. These results highlight the potential of harnessing somatic mutations to reconstruct cancer lineages.Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved. -
Engelhardt D, Michor F. 2021. A Quantitative Paradigm for Decision-Making in Precision Oncology. Trends in cancer. 7(4):293-300. Pubmed: 33637444 DOI:S2405-8033(21)00020-0 Engelhardt D, Michor F. 2021. A Quantitative Paradigm for Decision-Making in Precision Oncology. Trends in cancer. 7(4):293-300. Pubmed: 33637444 DOI:S2405-8033(21)00020-0 The complexity and variability of cancer progression necessitate a quantitative paradigm for therapeutic decision-making that is dynamic, personalized, and capable of identifying optimal treatment strategies for individual patients under substantial uncertainty. Here, we discuss the core components and challenges of such an approach and highlight the need for comprehensive longitudinal clinical and molecular data integration in its development. We describe the complementary and varied roles of mathematical modeling and machine learning in constructing dynamic optimal cancer treatment strategies and highlight the potential of reinforcement learning approaches in this endeavor.Copyright © 2021 Elsevier Inc. All rights reserved. -
Minussi DC, Nicholson MD, Ye H, Davis A, Wang K, Baker T, Tarabichi M, Sei E, Du H, Rabbani M, Peng C, Hu M, Bai S, Lin YW, Schalck A, Multani A, Ma J, McDonald TO, Casasent A, Barrera A, Chen H, Lim B, Arun B, Meric-Bernstam F, Van Loo P, Michor F, Navin NE. 2021. Breast tumours maintain a reservoir of subclonal diversity during expansion. Nature. 592(7853):302-308. Pubmed: 33762732 DOI:10.1038/s41586-021-03357-x Minussi DC, Nicholson MD, Ye H, Davis A, Wang K, Baker T, Tarabichi M, Sei E, Du H, Rabbani M, Peng C, Hu M, Bai S, Lin YW, Schalck A, Multani A, Ma J, McDonald TO, Casasent A, Barrera A, Chen H, Lim B, Arun B, Meric-Bernstam F, Van Loo P, Michor F, Navin NE. 2021. Breast tumours maintain a reservoir of subclonal diversity during expansion. Nature. 592(7853):302-308. Pubmed: 33762732 DOI:10.1038/s41586-021-03357-x Our knowledge of copy number evolution during the expansion of primary breast tumours is limited. Here, to investigate this process, we developed a single-cell, single-molecule DNA-sequencing method and performed copy number analysis of 16,178 single cells from 8 human triple-negative breast cancers and 4 cell lines. The results show that breast tumours and cell lines comprise a large milieu of subclones (7-22) that are organized into a few (3-5) major superclones. Evolutionary analysis suggests that after clonal TP53 mutations, multiple loss-of-heterozygosity events and genome doubling, there was a period of transient genomic instability followed by ongoing copy number evolution during the primary tumour expansion. By subcloning single daughter cells in culture, we show that tumour cells rediversify their genomes and do not retain isogenic properties. These data show that triple-negative breast cancers continue to evolve chromosome aberrations and maintain a reservoir of subclonal diversity during primary tumour growth. -
Janiszewska M, Stein S, Metzger Filho O, Eng J, Kingston NL, Harper NW, Rye IH, Alečković M, Trinh A, Murphy KC, Marangoni E, Cristea S, Oakes B, Winer EP, Krop IE, Russnes HG, Spellman PT, Bucher E, Hu Z, Chin K, Gray JW, Michor F, Polyak K. 2021. The impact of tumor epithelial and microenvironmental heterogeneity on treatment responses in HER2+ breast cancer. JCI insight. 6(11). Pubmed: 33886505 DOI:10.1172/jci.insight.147617 Janiszewska M, Stein S, Metzger Filho O, Eng J, Kingston NL, Harper NW, Rye IH, Alečković M, Trinh A, Murphy KC, Marangoni E, Cristea S, Oakes B, Winer EP, Krop IE, Russnes HG, Spellman PT, Bucher E, Hu Z, Chin K, Gray JW, Michor F, Polyak K. 2021. The impact of tumor epithelial and microenvironmental heterogeneity on treatment responses in HER2+ breast cancer. JCI insight. 6(11). Pubmed: 33886505 DOI:10.1172/jci.insight.147617 Despite the availability of multiple human epidermal growth factor receptor 2-targeted (HER2-targeted) treatments, therapeutic resistance in HER2+ breast cancer remains a clinical challenge. Intratumor heterogeneity for HER2 and resistance-conferring mutations in the PIK3CA gene (encoding PI3K catalytic subunit α) have been investigated in response and resistance to HER2-targeting agents, while the role of divergent cellular phenotypes and tumor epithelial-stromal cell interactions is less well understood. Here, we assessed the effect of intratumor cellular genetic heterogeneity for ERBB2 (encoding HER2) copy number and PIK3CA mutation on different types of neoadjuvant HER2-targeting therapies and clinical outcome in HER2+ breast cancer. We found that the frequency of cells lacking HER2 was a better predictor of response to HER2-targeted treatment than intratumor heterogeneity. We also compared the efficacy of different therapies in the same tumor using patient-derived xenograft models of heterogeneous HER2+ breast cancer and single-cell approaches. Stromal determinants were better predictors of response than tumor epithelial cells, and we identified alveolar epithelial and fibroblastic reticular cells as well as lymphatic vessel endothelial hyaluronan receptor 1-positive (Lyve1+) macrophages as putative drivers of therapeutic resistance. Our results demonstrate that both preexisting and acquired resistance to HER2-targeting agents involve multiple mechanisms including the tumor microenvironment. Furthermore, our data suggest that intratumor heterogeneity for HER2 should be incorporated into treatment design. -
Filho OM, Viale G, Stein S, Trippa L, Yardley DA, Mayer IA, Abramson VG, Arteaga CL, Spring LM, Waks AG, Wrabel E, DeMeo MK, Bardia A, Dell'Orto P, Russo L, King TA, Polyak K, Michor F, Winer EP, Krop IE. 2021. Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab. Cancer discovery. 11(10):2474-2487. Pubmed: 33941592 DOI:10.1158/2159-8290.CD-20-1557 Filho OM, Viale G, Stein S, Trippa L, Yardley DA, Mayer IA, Abramson VG, Arteaga CL, Spring LM, Waks AG, Wrabel E, DeMeo MK, Bardia A, Dell'Orto P, Russo L, King TA, Polyak K, Michor F, Winer EP, Krop IE. 2021. Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab. Cancer discovery. 11(10):2474-2487. Pubmed: 33941592 DOI:10.1158/2159-8290.CD-20-1557 Intratumor heterogeneity is postulated to cause therapeutic resistance. To prospectively assess the impact of HER2 () heterogeneity on response to HER2-targeted therapy, we treated 164 patients with centrally confirmed HER2-positive early-stage breast cancer with neoadjuvant trastuzumab emtansine plus pertuzumab. HER2 heterogeneity was assessed on pretreatment biopsies from two locations of each tumor. HER2 heterogeneity, defined as an area with amplification in >5% but <50% of tumor cells, or a HER2-negative area by FISH, was detected in 10% (16/157) of evaluable cases. The pathologic complete response rate was 55% in the nonheterogeneous subgroup and 0% in the heterogeneous group ( < 0.0001, adjusted for hormone receptor status). Single-cell FISH analysis of cellular heterogeneity identified the fraction of nonamplified cells as a driver of therapeutic resistance. These data suggest HER2 heterogeneity is associated with resistance to HER2-targeted therapy and should be considered in efforts to optimize treatment strategies. SIGNIFICANCE: HER2-targeted therapies improve cure rates in HER2-positive breast cancer, suggesting chemotherapy can be avoided in a subset of patients. We show that HER2 heterogeneity, particularly the fraction of nonamplified cancer cells, is a strong predictor of resistance to HER2 therapies and could potentially be used to optimize treatment selection...©2021 American Association for Cancer Research. -
Nicholson MD, Endler L, Popa A, Genger JW, Bock C, Michor F, Bergthaler A. 2021. Response to comment on "Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2". Science translational medicine. 13(617):eabj3222. Pubmed: 34705522 DOI:10.1126/scitranslmed.abj3222 Nicholson MD, Endler L, Popa A, Genger JW, Bock C, Michor F, Bergthaler A. 2021. Response to comment on "Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2". Science translational medicine. 13(617):eabj3222. Pubmed: 34705522 DOI:10.1126/scitranslmed.abj3222 Further analysis of SARS-CoV-2 genome sequencing data identifies several highly recurrent genetic variants with low allele frequencies, which, if filtered out, provide estimates consistent with tighter transmission bottlenecks. -
Zee BM, Poels KE, Yao CH, Kawabata KC, Wu G, Duy C, Jacobus WD, Senior E, Endress JE, Jambhekar A, Lovitch SB, Ma J, Dhall A, Harris IS, Blanco MA, Sykes DB, Licht JD, Weinstock DM, Melnick A, Haigis MC, Michor F, Shi Y. 2021. Combined epigenetic and metabolic treatments overcome differentiation blockade in acute myeloid leukemia. iScience. 24(6):102651. Pubmed: 34151238 DOI:10.1016/j.isci.2021.102651 Zee BM, Poels KE, Yao CH, Kawabata KC, Wu G, Duy C, Jacobus WD, Senior E, Endress JE, Jambhekar A, Lovitch SB, Ma J, Dhall A, Harris IS, Blanco MA, Sykes DB, Licht JD, Weinstock DM, Melnick A, Haigis MC, Michor F, Shi Y. 2021. Combined epigenetic and metabolic treatments overcome differentiation blockade in acute myeloid leukemia. iScience. 24(6):102651. Pubmed: 34151238 DOI:10.1016/j.isci.2021.102651 A hallmark of acute myeloid leukemia (AML) is the inability of self-renewing malignant cells to mature into a non-dividing terminally differentiated state. This differentiation block has been linked to dysregulation of multiple cellular processes, including transcriptional, chromatin, and metabolic regulation. The transcription factor HOXA9 and the histone demethylase LSD1 are examples of such regulators that promote differentiation blockade in AML. To identify metabolic targets that interact with LSD1 inhibition to promote myeloid maturation, we screened a small molecule library to identify druggable substrates. We found that differentiation caused by LSD1 inhibition is enhanced by combined perturbation of purine nucleotide salvage and lipogenesis pathways, and identified multiple lines of evidence to support the specificity of these pathways and suggest a potential basis of how perturbation of these pathways may interact synergistically to promote myeloid differentiation. In sum, these findings suggest potential drug combination strategies in the treatment of AML.© 2021 The Author(s). -
Wu HJ, Landshammer A, Stamenova EK, Bolondi A, Kretzmer H, Meissner A, Michor F. 2021. Topological isolation of developmental regulators in mammalian genomes. Nature communications. 12(1):4897. Pubmed: 34385432 DOI:10.1038/s41467-021-24951-7 Wu HJ, Landshammer A, Stamenova EK, Bolondi A, Kretzmer H, Meissner A, Michor F. 2021. Topological isolation of developmental regulators in mammalian genomes. Nature communications. 12(1):4897. Pubmed: 34385432 DOI:10.1038/s41467-021-24951-7 Precise control of mammalian gene expression is facilitated through epigenetic mechanisms and nuclear organization. In particular, insulated chromosome structures are important for regulatory control, but the phenotypic consequences of their boundary disruption on developmental processes are complex and remain insufficiently understood. Here, we generated deeply sequenced Hi-C data for human pluripotent stem cells (hPSCs) that allowed us to identify CTCF loop domains that have highly conserved boundary CTCF sites and show a notable enrichment of individual developmental regulators. Importantly, perturbation of such a boundary in hPSCs interfered with proper differentiation through deregulated distal enhancer-promoter activity. Finally, we found that germline variations affecting such boundaries are subject to purifying selection and are underrepresented in the human population. Taken together, our findings highlight the importance of developmental gene isolation through chromosomal folding structures as a mechanism to ensure their proper expression.© 2021. The Author(s). -
Yagi M, Ji F, Charlton J, Cristea S, Messemer K, Horwitz N, Di Stefano B, Tsopoulidis N, Hoetker MS, Huebner AJ, Bar-Nur O, Almada AE, Yamamoto M, Patelunas A, Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI, Hochedlinger K. 2021. Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes & development. 35(17-18):1209-1228. Pubmed: 34413137 DOI:10.1101/gad.348678.121 Yagi M, Ji F, Charlton J, Cristea S, Messemer K, Horwitz N, Di Stefano B, Tsopoulidis N, Hoetker MS, Huebner AJ, Bar-Nur O, Almada AE, Yamamoto M, Patelunas A, Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI, Hochedlinger K. 2021. Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Genes & development. 35(17-18):1209-1228. Pubmed: 34413137 DOI:10.1101/gad.348678.121 The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of transcription factor-induced reprogramming. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced myogenic progenitor cells (iMPCs). Here, we dissected the transcriptional and epigenetic dynamics of mouse fibroblasts undergoing reprogramming to either myotubes or iMPCs using a MyoD-inducible transgenic model. Induction of MyoD in fibroblasts combined with small molecules generated Pax7 iMPCs with high similarity to primary muscle stem cells. Analysis of intermediate stages of iMPC induction revealed that extinction of the fibroblast program preceded induction of the stem cell program. Moreover, key stem cell genes gained chromatin accessibility prior to their transcriptional activation, and these regions exhibited a marked loss of DNA methylation dependent on the Tet enzymes. In contrast, myotube generation was associated with few methylation changes, incomplete and unstable reprogramming, and an insensitivity to Tet depletion. Finally, we showed that MyoD's ability to bind to unique bHLH targets was crucial for generating iMPCs but dispensable for generating myotubes. Collectively, our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity.© 2021 Yagi et al.; Published by Cold Spring Harbor Laboratory Press. -
Koh SB, Dontchos BN, Bossuyt V, Edmonds C, Cristea S, Melkonjan N, Mortensen L, Ma A, Beyerlin K, Denault E, Niehoff E, Hirz T, Sykes DB, Michor F, Specht M, Lehman C, Ellisen LW, Spring LM. 2021. Systematic tissue collection during clinical breast biopsy is feasible, safe and enables high-content translational analyses. NPJ precision oncology. 5(1):85. Pubmed: 34548623 DOI:10.1038/s41698-021-00224-w Koh SB, Dontchos BN, Bossuyt V, Edmonds C, Cristea S, Melkonjan N, Mortensen L, Ma A, Beyerlin K, Denault E, Niehoff E, Hirz T, Sykes DB, Michor F, Specht M, Lehman C, Ellisen LW, Spring LM. 2021. Systematic tissue collection during clinical breast biopsy is feasible, safe and enables high-content translational analyses. NPJ precision oncology. 5(1):85. Pubmed: 34548623 DOI:10.1038/s41698-021-00224-w Systematic collection of fresh tissues for research at the time of diagnostic image-guided breast biopsy has the potential to fuel a wide variety of innovative studies. Here we report the initial experience, including safety, feasibility, and laboratory proof-of-principle, with the collection and analysis of research specimens obtained via breast core needle biopsy immediately following routine clinical biopsy at a single institution over a 14-month period. Patients underwent one or two additional core biopsies following collection of all necessary clinical specimens. In total, 395 patients were approached and 270 consented to the research study, yielding a 68.4% consent rate. Among consenting patients, 238 lesions were biopsied for research, resulting in 446 research specimens collected. No immediate complications were observed. Representative research core specimens showed high diagnostic concordance with clinical core biopsies. Flow cytometry demonstrated consistent recovery of hundreds to thousands of viable cells per research core. Among a group of HER2 + tumor research specimens, HER2 assessment by flow cytometry correlated highly with immunohistochemistry (IHC) staining, and in addition revealed extensive inter- and intra-tumoral variation in HER2 levels of potential clinical relevance. Suitability for single-cell transcriptomic analysis was demonstrated for a triple-negative tumor core biopsy, revealing substantial cellular diversity in the tumor immune microenvironment, including a prognostically relevant T cell subpopulation. Thus, collection of fresh tissues for research purposes at the time of diagnostic breast biopsy is safe, feasible and efficient, and may provide a high-yield mechanism to generate a rich tissue repository for a wide variety of cross-disciplinary research.© 2021. The Author(s). -
Poels KE, Schoenfeld AJ, Makhnin A, Tobi Y, Wang Y, Frisco-Cabanos H, Chakrabarti S, Shi M, Napoli C, McDonald TO, Tan W, Hata A, Weinrich SL, Yu HA, Michor F. 2021. Identification of optimal dosing schedules of dacomitinib and osimertinib for a phase I/II trial in advanced EGFR-mutant non-small cell lung cancer. Nature communications. 12(1):3697. Pubmed: 34140482 DOI:10.1038/s41467-021-23912-4 Poels KE, Schoenfeld AJ, Makhnin A, Tobi Y, Wang Y, Frisco-Cabanos H, Chakrabarti S, Shi M, Napoli C, McDonald TO, Tan W, Hata A, Weinrich SL, Yu HA, Michor F. 2021. Identification of optimal dosing schedules of dacomitinib and osimertinib for a phase I/II trial in advanced EGFR-mutant non-small cell lung cancer. Nature communications. 12(1):3697. Pubmed: 34140482 DOI:10.1038/s41467-021-23912-4 Despite the clinical success of the third-generation EGFR inhibitor osimertinib as a first-line treatment of EGFR-mutant non-small cell lung cancer (NSCLC), resistance arises due to the acquisition of EGFR second-site mutations and other mechanisms, which necessitates alternative therapies. Dacomitinib, a pan-HER inhibitor, is approved for first-line treatment and results in different acquired EGFR mutations than osimertinib that mediate on-target resistance. A combination of osimertinib and dacomitinib could therefore induce more durable responses by preventing the emergence of resistance. Here we present an integrated computational modeling and experimental approach to identify an optimal dosing schedule for osimertinib and dacomitinib combination therapy. We developed a predictive model that encompasses tumor heterogeneity and inter-subject pharmacokinetic variability to predict tumor evolution under different dosing schedules, parameterized using in vitro dose-response data. This model was validated using cell line data and used to identify an optimal combination dosing schedule. Our schedule was subsequently confirmed tolerable in an ongoing dose-escalation phase I clinical trial (NCT03810807), with some dose modifications, demonstrating that our rational modeling approach can be used to identify appropriate dosing for combination therapy in the clinical setting. 2020
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Shank K, Dunbar A, Koppikar P, Kleppe M, Teruya-Feldstein J, Csete I, Bhagwat N, Keller M, Kilpivaara O, Michor F, Levine RL, de Vargas Roditi L. 2020. Mathematical modeling reveals alternative JAK inhibitor treatment in myeloproliferative neoplasms. Haematologica. 105(3):e91-e94. Pubmed: 31413098 DOI:10.3324/haematol.2018.203729 Shank K, Dunbar A, Koppikar P, Kleppe M, Teruya-Feldstein J, Csete I, Bhagwat N, Keller M, Kilpivaara O, Michor F, Levine RL, de Vargas Roditi L. 2020. Mathematical modeling reveals alternative JAK inhibitor treatment in myeloproliferative neoplasms. Haematologica. 105(3):e91-e94. Pubmed: 31413098 DOI:10.3324/haematol.2018.203729 -
Murata K, Jadhav U, Madha S, van Es J, Dean J, Cavazza A, Wucherpfennig K, Michor F, Clevers H, Shivdasani RA. 2020. Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells. Cell stem cell. 26(3):377-390.e6. Pubmed: 32084390 DOI:S1934-5909(19)30569-7 Murata K, Jadhav U, Madha S, van Es J, Dean J, Cavazza A, Wucherpfennig K, Michor F, Clevers H, Shivdasani RA. 2020. Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells. Cell stem cell. 26(3):377-390.e6. Pubmed: 32084390 DOI:S1934-5909(19)30569-7 Ablation of LGR5 intestinal stem cells (ISCs) is associated with rapid restoration of the ISC compartment. Different intestinal crypt populations dedifferentiate to provide new ISCs, but the transcriptional and signaling trajectories that guide this process are unclear, and a large body of work suggests that quiescent "reserve" ISCs contribute to regeneration. By timing the interval between LGR5 lineage tracing and lethal injury, we show that ISC regeneration is explained nearly completely by dedifferentiation, with contributions from absorptive and secretory progenitors. The ISC-restricted transcription factor ASCL2 confers measurable competitive advantage to resting ISCs and is essential to restore the ISC compartment. Regenerating cells re-express Ascl2 days before Lgr5, and single-cell RNA sequencing (scRNA-seq) analyses reveal transcriptional paths underlying dedifferentiation. ASCL2 target genes include the interleukin-11 (IL-11) receptor Il11ra1, and recombinant IL-11 enhances crypt cell regenerative potential. These findings reveal cell dedifferentiation as the principal means for ISC restoration and highlight an ASCL2-regulated signal that enables this adaptive response.Copyright © 2019 Elsevier Inc. All rights reserved. -
Starrett JH, Guernet AA, Cuomo ME, Poels KE, van Alderwerelt van Rosenburgh IK, Nagelberg A, Farnsworth D, Price KS, Khan H, Ashtekar KD, Gaefele M, Ayeni D, Stewart TF, Kuhlmann A, Kaech SM, Unni AM, Homer R, Lockwood WW, Michor F, Goldberg SB, Lemmon MA, Smith PD, Cross DAE, Politi K. 2020. Drug Sensitivity and Allele Specificity of First-Line Osimertinib Resistance Mutations. Cancer research. 80(10):2017-2030. Pubmed: 32193290 DOI:10.1158/0008-5472.CAN-19-3819 Starrett JH, Guernet AA, Cuomo ME, Poels KE, van Alderwerelt van Rosenburgh IK, Nagelberg A, Farnsworth D, Price KS, Khan H, Ashtekar KD, Gaefele M, Ayeni D, Stewart TF, Kuhlmann A, Kaech SM, Unni AM, Homer R, Lockwood WW, Michor F, Goldberg SB, Lemmon MA, Smith PD, Cross DAE, Politi K. 2020. Drug Sensitivity and Allele Specificity of First-Line Osimertinib Resistance Mutations. Cancer research. 80(10):2017-2030. Pubmed: 32193290 DOI:10.1158/0008-5472.CAN-19-3819 Osimertinib, a mutant-specific third-generation EGFR tyrosine kinase inhibitor, is emerging as the preferred first-line therapy for -mutant lung cancer, yet resistance inevitably develops in patients. We modeled acquired resistance to osimertinib in transgenic mouse models of -induced lung adenocarcinoma and found that it is mediated largely through secondary mutations in -either C797S or L718V/Q. Analysis of circulating free DNA data from patients revealed that L718Q/V mutations almost always occur in the context of an L858R driver mutation. Therapeutic testing in mice revealed that both erlotinib and afatinib caused regression of osimertinib-resistant C797S-containing tumors, whereas only afatinib was effective on L718Q mutant tumors. Combination first-line osimertinib plus erlotinib treatment prevented the emergence of secondary mutations in . These findings highlight how knowledge of the specific characteristics of resistance mutations is important for determining potential subsequent treatment approaches and suggest strategies to overcome or prevent osimertinib resistance . SIGNIFICANCE: This study provides insight into the biological and molecular properties of osimertinib resistance mutations and evaluates therapeutic strategies to overcome resistance. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/10/2017/F1.large.jpg.©2020 American Association for Cancer Research. -
Shu S, Wu HJ, Ge JY, Zeid R, Harris IS, Jovanović B, Murphy K, Wang B, Qiu X, Endress JE, Reyes J, Lim K, Font-Tello A, Syamala S, Xiao T, Reddy Chilamakuri CS, Papachristou EK, D'Santos C, Anand J, Hinohara K, Li W, McDonald TO, Luoma A, Modiste RJ, Nguyen QD, Michel B, Cejas P, Kadoch C, Jaffe JD, Wucherpfennig KW, Qi J, Liu XS, Long H, Brown M, Carroll JS, Brugge JS, Bradner J, Michor F, Polyak K. 2020. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. Molecular cell. 78(6):1096-1113.e8. Pubmed: 32416067 DOI:S1097-2765(20)30269-0 Shu S, Wu HJ, Ge JY, Zeid R, Harris IS, Jovanović B, Murphy K, Wang B, Qiu X, Endress JE, Reyes J, Lim K, Font-Tello A, Syamala S, Xiao T, Reddy Chilamakuri CS, Papachristou EK, D'Santos C, Anand J, Hinohara K, Li W, McDonald TO, Luoma A, Modiste RJ, Nguyen QD, Michel B, Cejas P, Kadoch C, Jaffe JD, Wucherpfennig KW, Qi J, Liu XS, Long H, Brown M, Carroll JS, Brugge JS, Bradner J, Michor F, Polyak K. 2020. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. Molecular cell. 78(6):1096-1113.e8. Pubmed: 32416067 DOI:S1097-2765(20)30269-0 BET bromodomain inhibitors (BBDIs) are candidate therapeutic agents for triple-negative breast cancer (TNBC) and other cancer types, but inherent and acquired resistance to BBDIs limits their potential clinical use. Using CRISPR and small-molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance, we identified synthetic lethal interactions with BBDIs and genes that, when deleted, confer resistance. We observed synergy with regulators of cell cycle progression, YAP, AXL, and SRC signaling, and chemotherapeutic agents. We also uncovered functional similarities and differences among BRD2, BRD4, and BRD7. Although deletion of BRD2 enhances sensitivity to BBDIs, BRD7 loss leads to gain of TEAD-YAP chromatin binding and luminal features associated with BBDI resistance. Single-cell RNA-seq, ATAC-seq, and cellular barcoding analysis of BBDI responses in sensitive and resistant cell lines highlight significant heterogeneity among samples and demonstrate that BBDI resistance can be pre-existing or acquired.Copyright © 2020 Elsevier Inc. All rights reserved. -
Ge JY, Shu S, Kwon M, Jovanović B, Murphy K, Gulvady A, Fassl A, Trinh A, Kuang Y, Heavey GA, Luoma A, Paweletz C, Thorner AR, Wucherpfennig KW, Qi J, Brown M, Sicinski P, McDonald TO, Pellman D, Michor F, Polyak K. 2020. Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer. Nature communications. 11(1):2350. Pubmed: 32393766 DOI:10.1038/s41467-020-16170-3 Ge JY, Shu S, Kwon M, Jovanović B, Murphy K, Gulvady A, Fassl A, Trinh A, Kuang Y, Heavey GA, Luoma A, Paweletz C, Thorner AR, Wucherpfennig KW, Qi J, Brown M, Sicinski P, McDonald TO, Pellman D, Michor F, Polyak K. 2020. Acquired resistance to combined BET and CDK4/6 inhibition in triple-negative breast cancer. Nature communications. 11(1):2350. Pubmed: 32393766 DOI:10.1038/s41467-020-16170-3 BET inhibitors are promising therapeutic agents for the treatment of triple-negative breast cancer (TNBC), but the rapid emergence of resistance necessitates investigation of combination therapies and their effects on tumor evolution. Here, we show that palbociclib, a CDK4/6 inhibitor, and paclitaxel, a microtubule inhibitor, synergize with the BET inhibitor JQ1 in TNBC lines. High-complexity DNA barcoding and mathematical modeling indicate a high rate of de novo acquired resistance to these drugs relative to pre-existing resistance. We demonstrate that the combination of JQ1 and palbociclib induces cell division errors, which can increase the chance of developing aneuploidy. Characterizing acquired resistance to combination treatment at a single cell level shows heterogeneous mechanisms including activation of G1-S and senescence pathways. Our results establish a rationale for further investigation of combined BET and CDK4/6 inhibition in TNBC and suggest novel mechanisms of action for these drugs and new vulnerabilities in cells after emergence of resistance. -
Roney JP, Ferlic J, Michor F, McDonald TO. 2020. ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes. Bioinformatics (Oxford, England). 36(15):4372-4373. Pubmed: 32428223 DOI:10.1093/bioinformatics/btaa526 Roney JP, Ferlic J, Michor F, McDonald TO. 2020. ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes. Bioinformatics (Oxford, England). 36(15):4372-4373. Pubmed: 32428223 DOI:10.1093/bioinformatics/btaa526 Array© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. -
Feiger B, Gounley J, Adler D, Leopold JA, Draeger EW, Chaudhury R, Ryan J, Pathangey G, Winarta K, Frakes D, Michor F, Randles A. 2020. Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks. Scientific reports. 10(1):9508. Pubmed: 32528104 DOI:10.1038/s41598-020-66225-0 Feiger B, Gounley J, Adler D, Leopold JA, Draeger EW, Chaudhury R, Ryan J, Pathangey G, Winarta K, Frakes D, Michor F, Randles A. 2020. Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks. Scientific reports. 10(1):9508. Pubmed: 32528104 DOI:10.1038/s41598-020-66225-0 Comorbidities such as anemia or hypertension and physiological factors related to exertion can influence a patient's hemodynamics and increase the severity of many cardiovascular diseases. Observing and quantifying associations between these factors and hemodynamics can be difficult due to the multitude of co-existing conditions and blood flow parameters in real patient data. Machine learning-driven, physics-based simulations provide a means to understand how potentially correlated conditions may affect a particular patient. Here, we use a combination of machine learning and massively parallel computing to predict the effects of physiological factors on hemodynamics in patients with coarctation of the aorta. We first validated blood flow simulations against in vitro measurements in 3D-printed phantoms representing the patient's vasculature. We then investigated the effects of varying the degree of stenosis, blood flow rate, and viscosity on two diagnostic metrics - pressure gradient across the stenosis (ΔP) and wall shear stress (WSS) - by performing the largest simulation study to date of coarctation of the aorta (over 70 million compute hours). Using machine learning models trained on data from the simulations and validated on two independent datasets, we developed a framework to identify the minimal training set required to build a predictive model on a per-patient basis. We then used this model to accurately predict ΔP (mean absolute error within 1.18 mmHg) and WSS (mean absolute error within 0.99 Pa) for patients with this disease. -
Chakrabarti S, Michor F. 2020. Circadian clock effects on cellular proliferation: Insights from theory and experiments. Current opinion in cell biology. 67:17-26. Pubmed: 32771864 DOI:S0955-0674(20)30095-8 Chakrabarti S, Michor F. 2020. Circadian clock effects on cellular proliferation: Insights from theory and experiments. Current opinion in cell biology. 67:17-26. Pubmed: 32771864 DOI:S0955-0674(20)30095-8 Oscillations of the cellular circadian clock have emerged as an important regulator of many physiological processes, both in health and in disease. One such process, cellular proliferation, is being increasingly recognized to be affected by the circadian clock. Here, we review how a combination of experimental and theoretical work has furthered our understanding of the way circadian clocks couple to the cell cycle and play a role in tissue homeostasis and cancer. Finally, we discuss recently introduced methods for modeling coupling of clocks based on techniques from survival analysis and machine learning and highlight their potential importance for future studies.Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved. -
Popa A, Genger JW, Nicholson MD, Penz T, Schmid D, Aberle SW, Agerer B, Lercher A, Endler L, Colaço H, Smyth M, Schuster M, Grau ML, Martínez-Jiménez F, Pich O, Borena W, Pawelka E, Keszei Z, Senekowitsch M, Laine J, Aberle JH, Redlberger-Fritz M, Karolyi M, Zoufaly A, Maritschnik S, Borkovec M, Hufnagl P, Nairz M, Weiss G, Wolfinger MT, von Laer D, Superti-Furga G, Lopez-Bigas N, Puchhammer-Stöckl E, Allerberger F, Michor F, Bock C, Bergthaler A. 2020. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Science translational medicine. 12(573). Pubmed: 33229462 DOI:10.1126/scitranslmed.abe2555 Popa A, Genger JW, Nicholson MD, Penz T, Schmid D, Aberle SW, Agerer B, Lercher A, Endler L, Colaço H, Smyth M, Schuster M, Grau ML, Martínez-Jiménez F, Pich O, Borena W, Pawelka E, Keszei Z, Senekowitsch M, Laine J, Aberle JH, Redlberger-Fritz M, Karolyi M, Zoufaly A, Maritschnik S, Borkovec M, Hufnagl P, Nairz M, Weiss G, Wolfinger MT, von Laer D, Superti-Furga G, Lopez-Bigas N, Puchhammer-Stöckl E, Allerberger F, Michor F, Bock C, Bergthaler A. 2020. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Science translational medicine. 12(573). Pubmed: 33229462 DOI:10.1126/scitranslmed.abe2555 Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections in Austria, a country that played a major role in initial virus transmissions in Europe. Capitalizing on Austria's well-developed epidemiological surveillance system, we identified major SARS-CoV-2 clusters during the first wave of infections and performed deep whole-genome sequencing of more than 500 virus samples. Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020. Moreover, we exploited epidemiologically well-defined clusters to quantify SARS-CoV-2 mutational dynamics, including the observation of low-frequency mutations that progressed to fixation within the infection chain. Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 10 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2 and to gain fundamental insights into mutational dynamics and transmission properties.Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). -
Irurzun-Arana I, McDonald TO, Trocóniz IF, Michor F. 2020. Pharmacokinetic Profiles Determine Optimal Combination Treatment Schedules in Computational Models of Drug Resistance. Cancer research. 80(16):3372-3382. Pubmed: 32561532 DOI:10.1158/0008-5472.CAN-20-0056 Irurzun-Arana I, McDonald TO, Trocóniz IF, Michor F. 2020. Pharmacokinetic Profiles Determine Optimal Combination Treatment Schedules in Computational Models of Drug Resistance. Cancer research. 80(16):3372-3382. Pubmed: 32561532 DOI:10.1158/0008-5472.CAN-20-0056 Identification of optimal schedules for combination drug administration relies on accurately estimating the correct pharmacokinetics, pharmacodynamics, and drug interaction effects. Misspecification of pharmacokinetics can lead to wrongly predicted timing or order of treatments, leading to schedules recommended on the basis of incorrect assumptions about absorption and elimination of a drug and its effect on tumor growth. Here, we developed a computational modeling platform and software package for combination treatment strategies with flexible pharmacokinetic profiles and multidrug interaction curves that are estimated from data. The software can be used to compare prespecified schedules on the basis of the number of resistant cells where drug interactions and pharmacokinetic curves can be estimated from user-provided data or models. We applied our approach to publicly available data of treatment with different tyrosine kinase inhibitors of BT-20 triple-negative breast cancer cells and of treatment with erlotinib of PC-9 non-small cell lung cancer cells. Our approach is publicly available in the form of an R package called ACESO (https://github.com/Michorlab/aceso) and can be used to investigate optimum dosing for any combination treatment. SIGNIFICANCE: These findings introduce a computational modeling platform and software package for combination treatment strategies with flexible pharmacokinetic profiles and multidrug interaction curves that are estimated from data.©2020 American Association for Cancer Research. 2019
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Ferlic J, Shi J, McDonald TO, Michor F. 2019. DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding. Bioinformatics (Oxford, England). 35(19):3849-3851. Pubmed: 30816920 DOI:10.1093/bioinformatics/btz074 Ferlic J, Shi J, McDonald TO, Michor F. 2019. DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding. Bioinformatics (Oxford, England). 35(19):3849-3851. Pubmed: 30816920 DOI:10.1093/bioinformatics/btz074 Array© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. -
Hinohara K, Wu HJ, Sébastien Vigneau, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. 2019. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer cell. 35(2):330-332. Pubmed: 30753830 DOI:S1535-6108(19)30046-7 Hinohara K, Wu HJ, Sébastien Vigneau, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. 2019. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer cell. 35(2):330-332. Pubmed: 30753830 DOI:S1535-6108(19)30046-7 -
Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K. 2019. Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nature cell biology. 21(7):879-888. Pubmed: 31263265 DOI:10.1038/s41556-019-0346-x Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K. 2019. Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nature cell biology. 21(7):879-888. Pubmed: 31263265 DOI:10.1038/s41556-019-0346-x Most human tumours are heterogeneous, composed of cellular clones with different properties present at variable frequencies. Highly heterogeneous tumours have poor clinical outcomes, yet the underlying mechanism remains poorly understood. Here, we show that minor subclones of breast cancer cells expressing IL11 and FIGF (VEGFD) cooperate to promote metastatic progression and generate polyclonal metastases composed of driver and neutral subclones. Expression profiling of the epithelial and stromal compartments of monoclonal and polyclonal primary and metastatic lesions revealed that this cooperation is indirect, mediated through the local and systemic microenvironments. We identified neutrophils as a leukocyte population stimulated by the IL11-expressing minor subclone and showed that the depletion of neutrophils prevents metastatic outgrowth. Single-cell RNA-seq of CD45 cell populations from primary tumours, blood and lungs demonstrated that IL11 acts on bone-marrow-derived mesenchymal stromal cells, which induce pro-tumorigenic and pro-metastatic neutrophils. Our results indicate key roles for non-cell-autonomous drivers and minor subclones in metastasis. -
Yamamoto KN, Nakamura A, Liu LL, Stein S, Tramontano AC, Kartoun U, Shimizu T, Inoue Y, Asakuma M, Haeno H, Kong CY, Uchiyama K, Gonen M, Hur C, Michor F. 2019. Computational modeling of pancreatic cancer patients receiving FOLFIRINOX and gemcitabine-based therapies identifies optimum intervention strategies. PloS one. 14(4):e0215409. Pubmed: 31026288 DOI:10.1371/journal.pone.0215409 Yamamoto KN, Nakamura A, Liu LL, Stein S, Tramontano AC, Kartoun U, Shimizu T, Inoue Y, Asakuma M, Haeno H, Kong CY, Uchiyama K, Gonen M, Hur C, Michor F. 2019. Computational modeling of pancreatic cancer patients receiving FOLFIRINOX and gemcitabine-based therapies identifies optimum intervention strategies. PloS one. 14(4):e0215409. Pubmed: 31026288 DOI:10.1371/journal.pone.0215409 Pancreatic ductal adenocarcinoma (PDAC) exhibits a variety of phenotypes with regard to disease progression and treatment response. This variability complicates clinical decision-making despite the improvement of survival due to the recent introduction of FOLFIRINOX (FFX) and nab-paclitaxel. Questions remain as to the timing and sequence of therapies and the role of radiotherapy for unresectable PDAC. Here we developed a computational analysis platform to investigate the dynamics of growth, metastasis and treatment response to FFX, gemcitabine (GEM), and GEM+nab-paclitaxel. Our approach was informed using data of 1,089 patients treated at the Massachusetts General Hospital and validated using an independent cohort from Osaka Medical College. Our framework establishes a logistic growth pattern of PDAC and defines the Local Advancement Index (LAI), which determines the eventual primary tumor size and predicts the number of metastases. We found that a smaller LAI leads to a larger metastatic burden. Furthermore, our analyses ascertain that i) radiotherapy after induction chemotherapy improves survival in cases receiving induction FFX or with larger LAI, ii) neoadjuvant chemotherapy improves survival in cases with resectable PDAC, and iii) temporary cessations of chemotherapies do not impact overall survival, which supports the feasibility of treatment holidays for patients with FFX-associated adverse effects. Our findings inform clinical decision-making for PDAC patients and allow for the rational design of clinical strategies using FFX, GEM, GEM+nab-paclitaxel, neoadjuvant chemotherapy, and radiation. -
Yamamoto KN, Liu LL, Nakamura A, Haeno H, Michor F. 2019. Stochastic Evolution of Pancreatic Cancer Metastases During Logistic Clonal Expansion. JCO clinical cancer informatics. 3:1-11. Pubmed: 30901235 DOI:10.1200/CCI.18.00079 Yamamoto KN, Liu LL, Nakamura A, Haeno H, Michor F. 2019. Stochastic Evolution of Pancreatic Cancer Metastases During Logistic Clonal Expansion. JCO clinical cancer informatics. 3:1-11. Pubmed: 30901235 DOI:10.1200/CCI.18.00079 Despite recent progress in diagnostic and multimodal treatment approaches, most cancer deaths are still caused by metastatic spread and the subsequent growth of tumor cells in sites distant from the primary organ. So far, few quantitative studies are available that allow for the estimation of metastatic parameters and the evaluation of alternative treatment strategies. Most computational studies have focused on situations in which the tumor cell population expands exponentially over time; however, tumors may eventually be subject to resource and space limitations so that their growth patterns deviate from exponential growth to adhere to density-dependent growth models. In this study, we developed a stochastic evolutionary model of cancer progression that considers alterations in metastasis-related genes and intercellular growth competition leading to density effects described by logistic growth. Using this stochastic model, we derived analytical approximations for the time between the initiation of tumorigenesis and diagnosis, the expected number of metastatic sites, the total number of metastatic cells, the size of the primary tumor, and survival. Furthermore, we investigated the effects of drug administration and surgical resection on these quantities and predicted outcomes for different treatment regimens. Parameter values used in the analysis were estimated from data obtained from a pancreatic cancer rapid autopsy program. Our theoretical approach allows for flexible modeling of metastatic progression dynamics. 2018
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McDonald TO, Chakrabarti S, Michor F. 2018. Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution. Nature genetics. 50(12):1620-1623. Pubmed: 30374067 DOI:10.1038/s41588-018-0217-6 McDonald TO, Chakrabarti S, Michor F. 2018. Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution. Nature genetics. 50(12):1620-1623. Pubmed: 30374067 DOI:10.1038/s41588-018-0217-6 -
Jun HJ, Appleman VA, Wu HJ, Rose CM, Pineda JJ, Yeo AT, Delcuze B, Lee C, Gyuris A, Zhu H, Woolfenden S, Bronisz A, Nakano I, Chiocca EA, Bronson RT, Ligon KL, Sarkaria JN, Gygi SP, Michor F, Mitchison TJ, Charest A. 2018. A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine. Nature communications. 9(1):3116. Pubmed: 30082792 DOI:10.1038/s41467-018-05036-4 Jun HJ, Appleman VA, Wu HJ, Rose CM, Pineda JJ, Yeo AT, Delcuze B, Lee C, Gyuris A, Zhu H, Woolfenden S, Bronisz A, Nakano I, Chiocca EA, Bronson RT, Ligon KL, Sarkaria JN, Gygi SP, Michor F, Mitchison TJ, Charest A. 2018. A PDGFRα-driven mouse model of glioblastoma reveals a stathmin1-mediated mechanism of sensitivity to vinblastine. Nature communications. 9(1):3116. Pubmed: 30082792 DOI:10.1038/s41467-018-05036-4 Glioblastoma multiforme (GBM) is an aggressive primary brain cancer that includes focal amplification of PDGFRα and for which there are no effective therapies. Herein, we report the development of a genetically engineered mouse model of GBM based on autocrine, chronic stimulation of overexpressed PDGFRα, and the analysis of GBM signaling pathways using proteomics. We discover the tubulin-binding protein Stathmin1 (STMN1) as a PDGFRα phospho-regulated target, and that this mis-regulation confers sensitivity to vinblastine (VB) cytotoxicity. Treatment of PDGFRα-positive mouse and a patient-derived xenograft (PDX) GBMs with VB in mice prolongs survival and is dependent on STMN1. Our work reveals a previously unconsidered link between PDGFRα activity and STMN1, and highlight an STMN1-dependent cytotoxic effect of VB in GBM. -
Stein S, Zhao R, Haeno H, Vivanco I, Michor F. 2018. Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients. PLoS computational biology. 14(1):e1005924. Pubmed: 29293494 DOI:10.1371/journal.pcbi.1005924 Stein S, Zhao R, Haeno H, Vivanco I, Michor F. 2018. Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients. PLoS computational biology. 14(1):e1005924. Pubmed: 29293494 DOI:10.1371/journal.pcbi.1005924 Human primary glioblastomas (GBM) often harbor mutations within the epidermal growth factor receptor (EGFR). Treatment of EGFR-mutant GBM cell lines with the EGFR/HER2 tyrosine kinase inhibitor lapatinib can effectively induce cell death in these models. However, EGFR inhibitors have shown little efficacy in the clinic, partly because of inappropriate dosing. Here, we developed a computational approach to model the in vitro cellular dynamics of the EGFR-mutant cell line SF268 in response to different lapatinib concentrations and dosing schedules. We then used this approach to identify an effective treatment strategy within the clinical toxicity limits of lapatinib, and developed a partial differential equation modeling approach to study the in vivo GBM treatment response by taking into account the heterogeneous and diffusive nature of the disease. Despite the inability of lapatinib to induce tumor regressions with a continuous daily schedule, our modeling approach consistently predicts that continuous dosing remains the best clinically feasible strategy for slowing down tumor growth and lowering overall tumor burden, compared to pulsatile schedules currently known to be tolerated, even when considering drug resistance, reduced lapatinib tumor concentrations due to the blood brain barrier, and the phenotypic switch from proliferative to migratory cell phenotypes that occurs in hypoxic microenvironments. Our mathematical modeling and statistical analysis platform provides a rational method for comparing treatment schedules in search for optimal dosing strategies for glioblastoma and other cancer types. -
Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW. 2018. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nature communications. 9(1):3588. Pubmed: 30181541 DOI:10.1038/s41467-018-06052-0 Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW. 2018. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nature communications. 9(1):3588. Pubmed: 30181541 DOI:10.1038/s41467-018-06052-0 Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conducted single-cell RNA-sequencing (scRNA-seq) of >1500 cells from six primary TNBC. Here, we show that intercellular heterogeneity of gene expression programs within each tumor is variable and largely correlates with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations. Clustering of gene expression profiles identified distinct subgroups of malignant cells shared by multiple tumors, including a single subpopulation associated with multiple signatures of treatment resistance and metastasis, and characterized functionally by activation of glycosphingolipid metabolism and associated innate immunity pathways. A novel signature defining this subpopulation predicts long-term outcomes for TNBC patients in a large cohort. Collectively, this analysis reveals the functional heterogeneity and its association with genomic evolution in TNBC, and uncovers unanticipated biological principles dictating poor outcomes in this disease. -
Van Egeren D, Madsen T, Michor F. 2018. Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys. Communications biology. 1:151. Pubmed: 30272027 DOI:10.1038/s42003-018-0160-1 Van Egeren D, Madsen T, Michor F. 2018. Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys. Communications biology. 1:151. Pubmed: 30272027 DOI:10.1038/s42003-018-0160-1 Individuals in a population often have different fitnesses even when they have identical genotypes, but the effect of this variation on the evolution of a population through complicated fitness landscapes is unknown. Here, we investigate how populations with non-genetic fitness variation cross fitness valleys, common barriers to adaptation in rugged fitness landscapes in which a population must pass through a deleterious intermediate to arrive at a final advantageous stage. We develop a stochastic computational model describing the dynamics of an asexually reproducing population crossing a fitness valley, in which individuals of the same evolutionary stage can have variable fitnesses. We find that fitness variation that persists over multiple generations increases the rate of valley crossing through a novel evolutionary mechanism different from previously characterized mechanisms such as stochastic tunneling. By reducing the strength of selection against deleterious intermediates, persistent fitness variation allows for faster adaptation through rugged fitness landscapes. -
Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. 2018. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer cell. 34(6):939-953.e9. Pubmed: 30472020 DOI:S1535-6108(18)30480-X Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. 2018. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer cell. 34(6):939-953.e9. Pubmed: 30472020 DOI:S1535-6108(18)30480-X Members of the KDM5 histone H3 lysine 4 demethylase family are associated with therapeutic resistance, including endocrine resistance in breast cancer, but the underlying mechanism is poorly defined. Here we show that genetic deletion of KDM5A/B or inhibition of KDM5 activity increases sensitivity to anti-estrogens by modulating estrogen receptor (ER) signaling and by decreasing cellular transcriptomic heterogeneity. Higher KDM5B expression levels are associated with higher transcriptomic heterogeneity and poor prognosis in ER breast tumors. Single-cell RNA sequencing, cellular barcoding, and mathematical modeling demonstrate that endocrine resistance is due to selection for pre-existing genetically distinct cells, while KDM5 inhibitor resistance is acquired. Our findings highlight the importance of cellular phenotypic heterogeneity in therapeutic resistance and identify KDM5A/B as key regulators of this process.Copyright © 2018 Elsevier Inc. All rights reserved. -
Altrock PM, Ferlic J, Galla T, Tomasson MH, Michor F. 2018. Computational Model of Progression to Multiple Myeloma Identifies Optimum Screening Strategies. JCO clinical cancer informatics. 2:1-12. Pubmed: 30652561 DOI:10.1200/CCI.17.00131 Altrock PM, Ferlic J, Galla T, Tomasson MH, Michor F. 2018. Computational Model of Progression to Multiple Myeloma Identifies Optimum Screening Strategies. JCO clinical cancer informatics. 2:1-12. Pubmed: 30652561 DOI:10.1200/CCI.17.00131 Array -
Stover DG, Gil Del Alcazar CR, Brock J, Guo H, Overmoyer B, Balko J, Xu Q, Bardia A, Tolaney SM, Gelman R, Lloyd M, Wang Y, Xu Y, Michor F, Wang V, Winer EP, Polyak K, Lin NU. 2018. Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer. NPJ breast cancer. 4:10. Pubmed: 29761158 DOI:10.1038/s41523-018-0060-z Stover DG, Gil Del Alcazar CR, Brock J, Guo H, Overmoyer B, Balko J, Xu Q, Bardia A, Tolaney SM, Gelman R, Lloyd M, Wang Y, Xu Y, Michor F, Wang V, Winer EP, Polyak K, Lin NU. 2018. Phase II study of ruxolitinib, a selective JAK1/2 inhibitor, in patients with metastatic triple-negative breast cancer. NPJ breast cancer. 4:10. Pubmed: 29761158 DOI:10.1038/s41523-018-0060-z Preclinical data support a role for the IL-6/JAK2/STAT3 signaling pathway in breast cancer. Ruxolitinib is an orally bioavailable receptor tyrosine inhibitor targeting JAK1 and JAK2. We evaluated the safety and efficacy of ruxolitinib in patients with metastatic breast cancer. This was a non-randomized phase II study enrolling patients with refractory, metastatic triple-negative breast cancer. The primary endpoint was objective response by RECIST 1.1. The study was designed to enroll patients whose archival tumor tissue was pSTAT3-positive (-score >5) by central immunohistochemistry. pSTAT3 staining was available from 171 of 217 consented patients and pSTAT3 -score was positive in 67/171 (39.2%) tumors, suggesting that JAK-STAT activation is frequent. Twenty-three patients including one patient with inflammatory breast cancer were enrolled. Ruxolitinib was well-tolerated with infrequent grade 3 or higher toxicities with fatigue as the most common toxicity. Among 21 patients who received at least one dose of protocol therapy, no objective responses were observed and the study was closed to further accrual. Pharmacodynamic analyses of baseline vs. cycle 2 biopsies suggest on-target activity, including a significant decrease in the proportion of pSTAT3 cells in three patients with paired biopsies and downregulation of JAK-STAT target genes and signatures via transcriptional analyses of 11 total baseline and four metastatic biopsies. Immuno-FISH analyses demonstrate intratumoral heterogeneity of pSTAT3 and amplification. Ruxolitinib, as a single agent, did not meet the primary efficacy endpoint in this refractory patient population despite evidence of on-target activity. -
Riester M, Xu Q, Moreira A, Zheng J, Michor F, Downey RJ. 2018. The Warburg effect: persistence of stem-cell metabolism in cancers as a failure of differentiation. Annals of oncology : official journal of the European Society for Medical Oncology. 29(1):264-270. Pubmed: 29045536 DOI:10.1093/annonc/mdx645 Riester M, Xu Q, Moreira A, Zheng J, Michor F, Downey RJ. 2018. The Warburg effect: persistence of stem-cell metabolism in cancers as a failure of differentiation. Annals of oncology : official journal of the European Society for Medical Oncology. 29(1):264-270. Pubmed: 29045536 DOI:10.1093/annonc/mdx645 Array© The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For Permissions, please email: journals.permissions@oup.com. -
Chakrabarti S, Paek AL, Reyes J, Lasick KA, Lahav G, Michor F. 2018. Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages. Nature communications. 9(1):5372. Pubmed: 30560953 DOI:10.1038/s41467-018-07788-5 Chakrabarti S, Paek AL, Reyes J, Lasick KA, Lahav G, Michor F. 2018. Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages. Nature communications. 9(1):5372. Pubmed: 30560953 DOI:10.1038/s41467-018-07788-5 The origin of lineage correlations among single cells and the extent of heterogeneity in their intermitotic times (IMT) and apoptosis times (AT) remain incompletely understood. Here we developed single cell lineage-tracking experiments and computational algorithms to uncover correlations and heterogeneity in the IMT and AT of a colon cancer cell line before and during cisplatin treatment. These correlations could not be explained using simple protein production/degradation models. Sister cell fates were similar regardless of whether they divided before or after cisplatin administration and did not arise from proximity-related factors, suggesting fate determination early in a cell's lifetime. Based on these findings, we developed a theoretical model explaining how the observed correlation structure can arise from oscillatory mechanisms underlying cell fate control. Our model recapitulated the data only with very specific oscillation periods that fit measured circadian rhythms, thereby suggesting an important role of the circadian clock in controlling cellular fates. -
Cimino PJ, Kim Y, Wu HJ, Alexander J, Wirsching HG, Szulzewsky F, Pitter K, Ozawa T, Wang J, Vazquez J, Arora S, Rabadan R, Levine R, Michor F, Holland EC. 2018. Increased expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma. Genes & development. 32(7-8):512-523. Pubmed: 29632085 DOI:10.1101/gad.312157.118 Cimino PJ, Kim Y, Wu HJ, Alexander J, Wirsching HG, Szulzewsky F, Pitter K, Ozawa T, Wang J, Vazquez J, Arora S, Rabadan R, Levine R, Michor F, Holland EC. 2018. Increased expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma. Genes & development. 32(7-8):512-523. Pubmed: 29632085 DOI:10.1101/gad.312157.118 Glioblastoma is the most frequently occurring and invariably fatal primary brain tumor in adults. The vast majority of glioblastomas is characterized by chromosomal copy number alterations, including gain of whole chromosome 7 and loss of whole chromosome 10. Gain of whole chromosome 7 is an early event in gliomagenesis that occurs in proneural-like precursor cells, which give rise to all isocitrate dehydrogenase (IDH) wild-type glioblastoma transcriptional subtypes. () is one gene on chromosome 7 known to drive gliomagenesis, but, given its location near the end of 7p, there are likely several other genes located along chromosome 7 that select for its increased whole-chromosome copy number within glioblastoma cells. To identify other potential genes that could select for gain of whole chromosome 7, we developed an unbiased bioinformatics approach that identified () as a gene whose expression correlated with gain of chromosome 7 and a more aggressive phenotype of the resulting glioma. High expression of in glioblastoma was associated with a proneural gene expression pattern and decreased overall survival in both human proneural and PDGF-driven mouse glioblastoma. Furthermore, overexpression promoted cellular proliferation and potentiated radioresistance. We also found enrichment of expression in recurrent human and mouse glioblastoma at first recurrence after radiotherapy. Overall, this study implicates as a chromosome 7-associated gene-level locus that promotes selection for gain of whole chromosome 7 and an aggressive phenotype in glioblastoma.© 2018 Cimino et al.; Published by Cold Spring Harbor Laboratory Press. 2017
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Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A. 2017. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature. 549(7673):543-547. Pubmed: 28959968 DOI:10.1038/nature23891 Smith ZD, Shi J, Gu H, Donaghey J, Clement K, Cacchiarelli D, Gnirke A, Michor F, Meissner A. 2017. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature. 549(7673):543-547. Pubmed: 28959968 DOI:10.1038/nature23891 In mammals, the canonical somatic DNA methylation landscape is established upon specification of the embryo proper and subsequently disrupted within many cancer types. However, the underlying mechanisms that direct this genome-scale transformation remain elusive, with no clear model for its systematic acquisition or potential developmental utility. Here, we analysed global remethylation from the mouse preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions with substantial disruption of bimodal, CpG density-dependent methylation in the placental progenitor. The extraembryonic epigenome includes specific de novo methylation at hundreds of embryonically protected CpG island promoters, particularly those that are associated with key developmental regulators and are orthologously methylated across most human cancer types. Our data suggest that the evolutionary innovation of extraembryonic tissues may have required co-option of DNA methylation-based suppression as an alternative to regulation by Polycomb-group proteins, which coordinate embryonic germ-layer formation in response to extraembryonic cues. Moreover, we establish that this decision is made deterministically, downstream of promiscuously used-and frequently oncogenic-signalling pathways, via a novel combination of epigenetic cofactors. Methylation of developmental gene promoters during tumorigenesis may therefore reflect the misappropriation of an innate trajectory and the spontaneous reacquisition of a latent, developmentally encoded epigenetic landscape. -
Malone CF, Emerson C, Ingraham R, Barbosa W, Guerra S, Yoon H, Liu LL, Michor F, Haigis M, Macleod KF, Maertens O, Cichowski K. 2017. mTOR and HDAC Inhibitors Converge on the TXNIP/Thioredoxin Pathway to Cause Catastrophic Oxidative Stress and Regression of RAS-Driven Tumors. Cancer discovery. 7(12):1450-1463. Pubmed: 28963352 DOI:10.1158/2159-8290.CD-17-0177 Malone CF, Emerson C, Ingraham R, Barbosa W, Guerra S, Yoon H, Liu LL, Michor F, Haigis M, Macleod KF, Maertens O, Cichowski K. 2017. mTOR and HDAC Inhibitors Converge on the TXNIP/Thioredoxin Pathway to Cause Catastrophic Oxidative Stress and Regression of RAS-Driven Tumors. Cancer discovery. 7(12):1450-1463. Pubmed: 28963352 DOI:10.1158/2159-8290.CD-17-0177 Although agents that inhibit specific oncogenic kinases have been successful in a subset of cancers, there are currently few treatment options for malignancies that lack a targetable oncogenic driver. Nevertheless, during tumor evolution cancers engage a variety of protective pathways, which may provide alternative actionable dependencies. Here, we identify a promising combination therapy that kills -mutant tumors by triggering catastrophic oxidative stress. Specifically, we show that mTOR and HDAC inhibitors kill aggressive nervous system malignancies and shrink tumors by converging on the TXNIP/thioredoxin antioxidant pathway, through cooperative effects on chromatin and transcription. Accordingly, TXNIP triggers cell death by inhibiting thioredoxin and activating apoptosis signal-regulating kinase 1 (ASK1). Moreover, this drug combination also kills -mutant and -mutant non-small cell lung cancers. Together, these studies identify a promising therapeutic combination for several currently untreatable malignancies and reveal a protective nodal point of convergence between these important epigenetic and oncogenic enzymes. There are no effective therapies for - or -mutant cancers. We show that combined mTOR/HDAC inhibitors kill these RAS-driven tumors by causing catastrophic oxidative stress. This study identifies a promising therapeutic combination and demonstrates that selective enhancement of oxidative stress may be more broadly exploited for developing cancer therapies. .©2017 American Association for Cancer Research. -
Gil Del Alcazar CR, Huh SJ, Ekram MB, Trinh A, Liu LL, Beca F, Zi X, Kwak M, Bergholtz H, Su Y, Ding L, Russnes HG, Richardson AL, Babski K, Min Hui Kim E, McDonnell CH, Wagner J, Rowberry R, Freeman GJ, Dillon D, Sorlie T, Coussens LM, Garber JE, Fan R, Bobolis K, Allred DC, Jeong J, Park SY, Michor F, Polyak K. 2017. Immune Escape in Breast Cancer During to Invasive Carcinoma Transition. Cancer discovery. 7(10):1098-1115. Pubmed: 28652380 DOI:10.1158/2159-8290.CD-17-0222 Gil Del Alcazar CR, Huh SJ, Ekram MB, Trinh A, Liu LL, Beca F, Zi X, Kwak M, Bergholtz H, Su Y, Ding L, Russnes HG, Richardson AL, Babski K, Min Hui Kim E, McDonnell CH, Wagner J, Rowberry R, Freeman GJ, Dillon D, Sorlie T, Coussens LM, Garber JE, Fan R, Bobolis K, Allred DC, Jeong J, Park SY, Michor F, Polyak K. 2017. Immune Escape in Breast Cancer During to Invasive Carcinoma Transition. Cancer discovery. 7(10):1098-1115. Pubmed: 28652380 DOI:10.1158/2159-8290.CD-17-0222 To investigate immune escape during breast tumor progression, we analyzed the composition of leukocytes in normal breast tissues, ductal carcinoma (DCIS), and invasive ductal carcinomas (IDC). We found significant tissue and tumor subtype-specific differences in multiple cell types including T cells and neutrophils. Gene expression profiling of CD45CD3 T cells demonstrated a decrease in CD8 signatures in IDCs. Immunofluorescence analysis showed fewer activated GZMBCD8 T cells in IDC than in DCIS, including in matched DCIS and recurrent IDC. T-cell receptor clonotype diversity was significantly higher in DCIS than in IDCs. Immune checkpoint protein TIGIT-expressing T cells were more frequent in DCIS, whereas high PD-L1 expression and amplification of (encoding PD-L1) was only detected in triple-negative IDCs. Coamplification of a 17q12 chemokine cluster with subdivided HER2 breast tumors into immunologically and clinically distinct subtypes. Our results show coevolution of cancer cells and the immune microenvironment during tumor progression. The design of effective cancer immunotherapies requires the understanding of mechanisms underlying immune escape during tumor progression. Here we demonstrate a switch to a less active tumor immune environment during the to invasive breast carcinoma transition, and identify immune regulators and genomic alterations that shape tumor evolution. .©2017 American Association for Cancer Research. -
Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X. 2017. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic acids research. 45(10):e77. Pubmed: 28126923 DOI:10.1093/nar/gkx026 Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X. 2017. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic acids research. 45(10):e77. Pubmed: 28126923 DOI:10.1093/nar/gkx026 Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population.© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. -
Chakrabarti S, Michor F. 2017. Pharmacokinetics and Drug Interactions Determine Optimum Combination Strategies in Computational Models of Cancer Evolution. Cancer research. 77(14):3908-3921. Pubmed: 28566331 DOI:10.1158/0008-5472.CAN-16-2871 Chakrabarti S, Michor F. 2017. Pharmacokinetics and Drug Interactions Determine Optimum Combination Strategies in Computational Models of Cancer Evolution. Cancer research. 77(14):3908-3921. Pubmed: 28566331 DOI:10.1158/0008-5472.CAN-16-2871 The identification of optimal drug administration schedules to battle the emergence of resistance is a major challenge in cancer research. The existence of a multitude of resistance mechanisms necessitates administering drugs in combination, significantly complicating the endeavor of predicting the evolutionary dynamics of cancers and optimal intervention strategies. A thorough understanding of the important determinants of cancer evolution under combination therapies is therefore crucial for correctly predicting treatment outcomes. Here we developed the first computational strategy to explore pharmacokinetic and drug interaction effects in evolutionary models of cancer progression, a crucial step towards making clinically relevant predictions. We found that incorporating these phenomena into our multiscale stochastic modeling framework significantly changes the optimum drug administration schedules identified, often predicting nonintuitive strategies for combination therapies. We applied our approach to an ongoing phase Ib clinical trial (TATTON) administering AZD9291 and selumetinib to EGFR-mutant lung cancer patients. Our results suggest that the schedules used in the three trial arms have almost identical efficacies, but slight modifications in the dosing frequencies of the two drugs can significantly increase tumor cell eradication. Interestingly, we also predict that drug concentrations lower than the MTD are as efficacious, suggesting that lowering the total amount of drug administered could lower toxicities while not compromising on the effectiveness of the drugs. Our approach highlights the fact that quantitative knowledge of pharmacokinetic, drug interaction, and evolutionary processes is essential for identifying best intervention strategies. Our method is applicable to diverse cancer and treatment types and allows for a rational design of clinical trials. .©2017 American Association for Cancer Research. -
Mishima Y, Paiva B, Shi J, Park J, Manier S, Takagi S, Massoud M, Perilla-Glen A, Aljawai Y, Huynh D, Roccaro AM, Sacco A, Capelletti M, Detappe A, Alignani D, Anderson KC, Munshi NC, Prosper F, Lohr JG, Ha G, Freeman SS, Van Allen EM, Adalsteinsson VA, Michor F, San Miguel JF, Ghobrial IM. 2017. The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell reports. 19(1):218-224. Pubmed: 28380360 DOI:S2211-1247(17)30357-1 Mishima Y, Paiva B, Shi J, Park J, Manier S, Takagi S, Massoud M, Perilla-Glen A, Aljawai Y, Huynh D, Roccaro AM, Sacco A, Capelletti M, Detappe A, Alignani D, Anderson KC, Munshi NC, Prosper F, Lohr JG, Ha G, Freeman SS, Van Allen EM, Adalsteinsson VA, Michor F, San Miguel JF, Ghobrial IM. 2017. The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell reports. 19(1):218-224. Pubmed: 28380360 DOI:S2211-1247(17)30357-1 The development of sensitive and non-invasive "liquid biopsies" presents new opportunities for longitudinal monitoring of tumor dissemination and clonal evolution. The number of circulating tumor cells (CTCs) is prognostic in multiple myeloma (MM), but there is little information on their genetic features. Here, we have analyzed the genomic landscape of CTCs from 29 MM patients, including eight cases with matched/paired bone marrow (BM) tumor cells. Our results show that 100% of clonal mutations in patient BM were detected in CTCs and that 99% of clonal mutations in CTCs were present in BM MM. These include typical driver mutations in MM such as in KRAS, NRAS, or BRAF. These data suggest that BM and CTC samples have similar clonal structures, as discordances between the two were restricted to subclonal mutations. Accordingly, our results pave the way for potentially less invasive mutation screening of MM patients through characterization of CTCs.Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved. -
Smith KS, Liu LL, Ganesan S, Michor F, De S. 2017. Nuclear topology modulates the mutational landscapes of cancer genomes. Nature structural & molecular biology. 24(11):1000-1006. Pubmed: 28967881 DOI:10.1038/nsmb.3474 Smith KS, Liu LL, Ganesan S, Michor F, De S. 2017. Nuclear topology modulates the mutational landscapes of cancer genomes. Nature structural & molecular biology. 24(11):1000-1006. Pubmed: 28967881 DOI:10.1038/nsmb.3474 Nuclear organization of genomic DNA affects processes of DNA damage and repair, yet its effects on mutational landscapes in cancer genomes remain unclear. Here we analyzed genome-wide somatic mutations from 366 samples of six cancer types. We found that lamina-associated regions, which are typically localized at the nuclear periphery, displayed higher somatic mutation frequencies than did the interlamina regions at the nuclear core. This effect was observed even after adjustment for features such as GC percentage, chromatin, and replication timing. Furthermore, mutational signatures differed between the nuclear core and periphery, thus indicating differences in the patterns of DNA-damage or DNA-repair processes. For instance, smoking and UV-related signatures, as well as substitutions at certain motifs, were more enriched in the nuclear periphery. Thus, the nuclear architecture may influence mutational landscapes in cancer genomes beyond the previously described effects of chromatin structure and replication timing. -
Gibson CJ, Lindsley RC, Tchekmedyian V, Mar BG, Shi J, Jaiswal S, Bosworth A, Francisco L, He J, Bansal A, Morgan EA, Lacasce AS, Freedman AS, Fisher DC, Jacobsen E, Armand P, Alyea EP, Koreth J, Ho V, Soiffer RJ, Antin JH, Ritz J, Nikiforow S, Forman SJ, Michor F, Neuberg D, Bhatia R, Bhatia S, Ebert BL. 2017. Clonal Hematopoiesis Associated With Adverse Outcomes After Autologous Stem-Cell Transplantation for Lymphoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 35(14):1598-1605. Pubmed: 28068180 DOI:10.1200/JCO.2016.71.6712 Gibson CJ, Lindsley RC, Tchekmedyian V, Mar BG, Shi J, Jaiswal S, Bosworth A, Francisco L, He J, Bansal A, Morgan EA, Lacasce AS, Freedman AS, Fisher DC, Jacobsen E, Armand P, Alyea EP, Koreth J, Ho V, Soiffer RJ, Antin JH, Ritz J, Nikiforow S, Forman SJ, Michor F, Neuberg D, Bhatia R, Bhatia S, Ebert BL. 2017. Clonal Hematopoiesis Associated With Adverse Outcomes After Autologous Stem-Cell Transplantation for Lymphoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 35(14):1598-1605. Pubmed: 28068180 DOI:10.1200/JCO.2016.71.6712 Purpose Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related condition characterized by somatic mutations in the blood of otherwise healthy adults. We hypothesized that in patients undergoing autologous stem-cell transplantation (ASCT) for lymphoma, CHIP at the time of ASCT would be associated with an increased risk of myelodysplastic syndrome and acute myeloid leukemia, collectively termed therapy-related myeloid neoplasm (TMN), and other adverse outcomes. Methods We performed whole-exome sequencing on pre- and post-ASCT samples from 12 patients who developed TMN after autologous transplantation for Hodgkin lymphoma or non-Hodgkin lymphoma and targeted sequencing on cryopreserved aliquots of autologous stem-cell products from 401 patients who underwent ASCT for non-Hodgkin lymphoma between 2003 and 2010. We assessed the effect of CHIP at the time of ASCT on subsequent outcomes, including TMN, cause-specific mortality, and overall survival. Results For six of 12 patients in the exome sequencing cohort, mutations found in the TMN specimen were also detectable in the pre-ASCT specimen. In the targeted sequencing cohort, 120 patients (29.9%) had CHIP at the time of ASCT, which was associated with an increased rate of TMN (10-year cumulative incidence, 14.1% v 4.3% for those with and without CHIP, respectively; P = .002). Patients with CHIP had significantly inferior overall survival compared with those without CHIP (10-year overall survival, 30.4% v 60.9%, respectively; P < .001), including increased risk of death from TMN and cardiovascular disease. Conclusion In patients undergoing ASCT for lymphoma, CHIP at the time of transplantation is associated with inferior survival and increased risk of TMN. -
Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S. 2017. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer causes & control : CCC. 28(2):167-176. Pubmed: 28097472 DOI:10.1007/s10552-016-0845-z Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S. 2017. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer causes & control : CCC. 28(2):167-176. Pubmed: 28097472 DOI:10.1007/s10552-016-0845-z Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases. Recent successes in MPE studies include: (1) the development of new statistical methods to address etiologic heterogeneity; (2) the enhancement of causal inference; (3) the identification of previously unknown exposure-subtype disease associations; and (4) better understanding of the role of lifestyle/behavioral factors on modifying prognosis according to disease subtype. Central challenges to MPE include the relative lack of transdisciplinary experts, educational programs, and forums to discuss issues related to the advancement of the field. To address these challenges, highlight recent successes in the field, and identify new opportunities, a series of MPE meetings have been held at the Dana-Farber Cancer Institute in Boston, MA. Herein, we share the proceedings of the Third International MPE Meeting, held in May 2016 and attended by 150 scientists from 17 countries. Special topics included integration of MPE with immunology and health disparity research. This meeting series will continue to provide an impetus to foster further transdisciplinary integration of divergent scientific fields. -
Yu HA, Sima C, Feldman D, Liu LL, Vaitheesvaran B, Cross J, Rudin CM, Kris MG, Pao W, Michor F, Riely GJ. 2017. Phase 1 study of twice weekly pulse dose and daily low-dose erlotinib as initial treatment for patients with EGFR-mutant lung cancers. Annals of oncology : official journal of the European Society for Medical Oncology. 28(2):278-284. Pubmed: 28073786 DOI:10.1093/annonc/mdw556 Yu HA, Sima C, Feldman D, Liu LL, Vaitheesvaran B, Cross J, Rudin CM, Kris MG, Pao W, Michor F, Riely GJ. 2017. Phase 1 study of twice weekly pulse dose and daily low-dose erlotinib as initial treatment for patients with EGFR-mutant lung cancers. Annals of oncology : official journal of the European Society for Medical Oncology. 28(2):278-284. Pubmed: 28073786 DOI:10.1093/annonc/mdw556 Array© The Author 2016. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For Permissions, please email: journals.permissions@oup.com. -
Riester M, Wu HJ, Zehir A, Gönen M, Moreira AL, Downey RJ, Michor F. 2017. Distance in cancer gene expression from stem cells predicts patient survival. PloS one. 12(3):e0173589. Pubmed: 28333954 DOI:10.1371/journal.pone.0173589 Riester M, Wu HJ, Zehir A, Gönen M, Moreira AL, Downey RJ, Michor F. 2017. Distance in cancer gene expression from stem cells predicts patient survival. PloS one. 12(3):e0173589. Pubmed: 28333954 DOI:10.1371/journal.pone.0173589 The degree of histologic cellular differentiation of a cancer has been associated with prognosis but is subjectively assessed. We hypothesized that information about tumor differentiation of individual cancers could be derived objectively from cancer gene expression data, and would allow creation of a cancer phylogenetic framework that would correlate with clinical, histologic and molecular characteristics of the cancers, as well as predict prognosis. Here we utilized mRNA expression data from 4,413 patient samples with 7 diverse cancer histologies to explore the utility of ordering samples by their distance in gene expression from that of stem cells. A differentiation baseline was obtained by including expression data of human embryonic stem cells (hESC) and human mesenchymal stem cells (hMSC) for solid tumors, and of hESC and CD34+ cells for liquid tumors. We found that the correlation distance (the degree of similarity) between the gene expression profile of a tumor sample and that of stem cells orients cancers in a clinically coherent fashion. For all histologies analyzed (including carcinomas, sarcomas, and hematologic malignancies), patients with cancers with gene expression patterns most similar to that of stem cells had poorer overall survival. We also found that the genes in all undifferentiated cancers of diverse histologies that were most differentially expressed were associated with up-regulation of specific oncogenes and down-regulation of specific tumor suppressor genes. Thus, a stem cell-oriented phylogeny of cancers allows for the derivation of a novel cancer gene expression signature found in all undifferentiated forms of diverse cancer histologies, that is competitive in predicting overall survival in cancer patients compared to previously published prediction models, and is coherent in that gene expression was associated with up-regulation of specific oncogenes and down-regulation of specific tumor suppressor genes associated with regulation of the multicellular state. -
Zhao R, Catalano P, DeGruttola VG, Michor F. 2017. Estimating mono- and bi-phasic regression parameters using a mixture piecewise linear Bayesian hierarchical model. PloS one. 12(7):e0180756. Pubmed: 28723910 DOI:10.1371/journal.pone.0180756 Zhao R, Catalano P, DeGruttola VG, Michor F. 2017. Estimating mono- and bi-phasic regression parameters using a mixture piecewise linear Bayesian hierarchical model. PloS one. 12(7):e0180756. Pubmed: 28723910 DOI:10.1371/journal.pone.0180756 The dynamics of tumor burden, secreted proteins or other biomarkers over time, is often used to evaluate the effectiveness of therapy and to predict outcomes for patients. Many methods have been proposed to investigate longitudinal trends to better characterize patients and to understand disease progression. However, most approaches assume a homogeneous patient population and a uniform response trajectory over time and across patients. Here, we present a mixture piecewise linear Bayesian hierarchical model, which takes into account both population heterogeneity and nonlinear relationships between biomarkers and time. Simulation results show that our method was able to classify subjects according to their patterns of treatment response with greater than 80% accuracy in the three scenarios tested. We then applied our model to a large randomized controlled phase III clinical trial of multiple myeloma patients. Analysis results suggest that the longitudinal tumor burden trajectories in multiple myeloma patients are heterogeneous and nonlinear, even among patients assigned to the same treatment cohort. In addition, between cohorts, there are distinct differences in terms of the regression parameters and the distributions among categories in the mixture. Those results imply that longitudinal data from clinical trials may harbor unobserved subgroups and nonlinear relationships; accounting for both may be important for analyzing longitudinal data. -
McDonald TO, Michor F. 2017. SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. Bioinformatics (Oxford, England). 33(14):2221-2223. Pubmed: 28334409 DOI:10.1093/bioinformatics/btx146 McDonald TO, Michor F. 2017. SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. Bioinformatics (Oxford, England). 33(14):2221-2223. Pubmed: 28334409 DOI:10.1093/bioinformatics/btx146 Array© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com -
Maruvka YE, Mouw KW, Karlic R, Parasuraman P, Kamburov A, Polak P, Haradhvala NJ, Hess JM, Rheinbay E, Brody Y, Koren A, Braunstein LZ, D'Andrea A, Lawrence MS, Bass A, Bernards A, Michor F, Getz G. 2017. Analysis of somatic microsatellite indels identifies driver events in human tumors. Nature biotechnology. 35(10):951-959. Pubmed: 28892075 DOI:10.1038/nbt.3966 Maruvka YE, Mouw KW, Karlic R, Parasuraman P, Kamburov A, Polak P, Haradhvala NJ, Hess JM, Rheinbay E, Brody Y, Koren A, Braunstein LZ, D'Andrea A, Lawrence MS, Bass A, Bernards A, Michor F, Getz G. 2017. Analysis of somatic microsatellite indels identifies driver events in human tumors. Nature biotechnology. 35(10):951-959. Pubmed: 28892075 DOI:10.1038/nbt.3966 Microsatellites (MSs) are tracts of variable-length repeats of short DNA motifs that exhibit high rates of mutation in the form of insertions or deletions (indels) of the repeated motif. Despite their prevalence, the contribution of somatic MS indels to cancer has been largely unexplored, owing to difficulties in detecting them in short-read sequencing data. Here we present two tools: MSMuTect, for accurate detection of somatic MS indels, and MSMutSig, for identification of genes containing MS indels at a higher frequency than expected by chance. Applying MSMuTect to whole-exome data from 6,747 human tumors representing 20 tumor types, we identified >1,000 previously undescribed MS indels in cancer genes. Additionally, we demonstrate that the number and pattern of MS indels can accurately distinguish microsatellite-stable tumors from tumors with microsatellite instability, thus potentially improving classification of clinically relevant subgroups. Finally, we identified seven MS indel driver hotspots: four in known cancer genes (ACVR2A, RNF43, JAK1, and MSH3) and three in genes not previously implicated as cancer drivers (ESRP1, PRDM2, and DOCK3). -
Temko D, Cheng YK, Polyak K, Michor F. 2017. Mathematical Modeling Links Pregnancy-Associated Changes and Breast Cancer Risk. Cancer research. 77(11):2800-2809. Pubmed: 28360138 DOI:10.1158/0008-5472.CAN-16-2504 Temko D, Cheng YK, Polyak K, Michor F. 2017. Mathematical Modeling Links Pregnancy-Associated Changes and Breast Cancer Risk. Cancer research. 77(11):2800-2809. Pubmed: 28360138 DOI:10.1158/0008-5472.CAN-16-2504 Recent debate has concentrated on the contribution of bad luck to cancer development. The tight correlation between the number of tissue-specific stem cell divisions and cancer risk of the same tissue suggests that bad luck has an important role to play in tumor development, but the full extent of this contribution remains an open question. Improved understanding of the interplay between extrinsic and intrinsic factors at the molecular level is one promising route to identifying the limits on extrinsic control of tumor initiation, which is highly relevant to cancer prevention. Here, we use a simple mathematical model to show that recent data on the variation in numbers of breast epithelial cells with progenitor features due to pregnancy are sufficient to explain the known protective effect of full-term pregnancy in early adulthood for estrogen receptor-positive (ER) breast cancer later in life. Our work provides a mechanism for this previously ill-understood effect and illuminates the complex influence of extrinsic factors at the molecular level in breast cancer. These findings represent an important contribution to the ongoing research into the role of bad luck in human tumorigenesis. .©2017 American Association for Cancer Research. 2016
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Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. 2016. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell reports. 17(12):3395-3406. Pubmed: 28009305 DOI:S2211-1247(16)31654-0 Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. 2016. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell reports. 17(12):3395-3406. Pubmed: 28009305 DOI:S2211-1247(16)31654-0 Reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) is typically an inefficient and asynchronous process. A variety of technological efforts have been made to accelerate and/or synchronize this process. To define a unified framework to study and compare the dynamics of reprogramming under different conditions, we developed an in silico analysis platform based on mathematical modeling. Our approach takes into account the variability in experimental results stemming from probabilistic growth and death of cells and potentially heterogeneous reprogramming rates. We suggest that reprogramming driven by the Yamanaka factors alone is a more heterogeneous process, possibly due to cell-specific reprogramming rates, which could be homogenized by the addition of additional factors. We validated our approach using publicly available reprogramming datasets, including data on early reprogramming dynamics as well as cell count data, and thus we demonstrated the general utility and predictive power of our methodology for investigating reprogramming and other cell fate change systems.Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved. -
Wu HJ, Michor F. 2016. A computational strategy to adjust for copy number in tumor Hi-C data. Bioinformatics (Oxford, England). 32(24):3695-3701. Pubmed: 27531101 Wu HJ, Michor F. 2016. A computational strategy to adjust for copy number in tumor Hi-C data. Bioinformatics (Oxford, England). 32(24):3695-3701. Pubmed: 27531101 Array© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. -
Tang M, Zhao R, van de Velde H, Tross JG, Mitsiades C, Viselli S, Neuwirth R, Esseltine DL, Anderson K, Ghobrial IM, San Miguel JF, Richardson PG, Tomasson MH, Michor F. 2016. Myeloma Cell Dynamics in Response to Treatment Supports a Model of Hierarchical Differentiation and Clonal Evolution. Clinical cancer research : an official journal of the American Association for Cancer Research. 22(16):4206-4214. Pubmed: 27006493 DOI:10.1158/1078-0432.CCR-15-2793 Tang M, Zhao R, van de Velde H, Tross JG, Mitsiades C, Viselli S, Neuwirth R, Esseltine DL, Anderson K, Ghobrial IM, San Miguel JF, Richardson PG, Tomasson MH, Michor F. 2016. Myeloma Cell Dynamics in Response to Treatment Supports a Model of Hierarchical Differentiation and Clonal Evolution. Clinical cancer research : an official journal of the American Association for Cancer Research. 22(16):4206-4214. Pubmed: 27006493 DOI:10.1158/1078-0432.CCR-15-2793 Array©2016 American Association for Cancer Research. -
Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE. 2016. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nature genetics. 48(10):1119-30. Pubmed: 27526321 DOI:10.1038/ng.3641 Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE. 2016. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nature genetics. 48(10):1119-30. Pubmed: 27526321 DOI:10.1038/ng.3641 Aneuploidy is a hallmark of breast cancer; however, knowledge of how these complex genomic rearrangements evolve during tumorigenesis is limited. In this study, we developed a highly multiplexed single-nucleus sequencing method to investigate copy number evolution in patients with triple-negative breast cancer. We sequenced 1,000 single cells from tumors in 12 patients and identified 1-3 major clonal subpopulations in each tumor that shared a common evolutionary lineage. For each tumor, we also identified a minor subpopulation of non-clonal cells that were classified as metastable, pseudodiploid or chromazemic. Phylogenetic analysis and mathematical modeling suggest that these data are unlikely to be explained by the gradual accumulation of copy number events over time. In contrast, our data challenge the paradigm of gradual evolution, showing that the majority of copy number aberrations are acquired at the earliest stages of tumor evolution, in short punctuated bursts, followed by stable clonal expansions that form the tumor mass. -
Wee B, Pietras A, Ozawa T, Bazzoli E, Podlaha O, Antczak C, Westermark B, Nelander S, Uhrbom L, Forsberg-Nilsson K, Djaballah H, Michor F, Holland EC. 2016. ABCG2 regulates self-renewal and stem cell marker expression but not tumorigenicity or radiation resistance of glioma cells. Scientific reports. 6:25956. Pubmed: 27456282 DOI:10.1038/srep25956 Wee B, Pietras A, Ozawa T, Bazzoli E, Podlaha O, Antczak C, Westermark B, Nelander S, Uhrbom L, Forsberg-Nilsson K, Djaballah H, Michor F, Holland EC. 2016. ABCG2 regulates self-renewal and stem cell marker expression but not tumorigenicity or radiation resistance of glioma cells. Scientific reports. 6:25956. Pubmed: 27456282 DOI:10.1038/srep25956 Glioma cells with stem cell traits are thought to be responsible for tumor maintenance and therapeutic failure. Such cells can be enriched based on their inherent drug efflux capability mediated by the ABC transporter ABCG2 using the side population assay, and their characteristics include increased self-renewal, high stem cell marker expression and high tumorigenic capacity in vivo. Here, we show that ABCG2 can actively drive expression of stem cell markers and self-renewal in glioma cells. Stem cell markers and self-renewal was enriched in cells with high ABCG2 activity, and could be specifically inhibited by pharmacological and genetic ABCG2 inhibition. Importantly, despite regulating these key characteristics of stem-like tumor cells, ABCG2 activity did not affect radiation resistance or tumorigenicity in vivo. ABCG2 effects were Notch-independent and mediated by diverse mechanisms including the transcription factor Mef. Our data demonstrate that characteristics of tumor stem cells are separable, and highlight ABCG2 as a potential driver of glioma stemness. -
Badri H, Pitter K, Holland EC, Michor F, Leder K. 2016. Optimization of radiation dosing schedules for proneural glioblastoma. Journal of mathematical biology. 72(5):1301-36. Pubmed: 26094055 DOI:10.1007/s00285-015-0908-x Badri H, Pitter K, Holland EC, Michor F, Leder K. 2016. Optimization of radiation dosing schedules for proneural glioblastoma. Journal of mathematical biology. 72(5):1301-36. Pubmed: 26094055 DOI:10.1007/s00285-015-0908-x Glioblastomas are the most aggressive primary brain tumor. Despite treatment with surgery, radiation and chemotherapy, these tumors remain uncurable and few significant increases in survival have been observed over the last half-century. We recently employed a combined theoretical and experimental approach to predict the effectiveness of radiation administration schedules, identifying two schedules that led to superior survival in a mouse model of the disease (Leder et al., Cell 156(3):603-616, 2014). Here we extended this approach to consider fractionated schedules to best minimize toxicity arising in early- and late-responding tissues. To this end, we decomposed the problem into two separate solvable optimization tasks: (i) optimization of the amount of radiation per dose, and (ii) optimization of the amount of time that passes between radiation doses. To ensure clinical applicability, we then considered the impact of clinical operating hours by incorporating time constraints consistent with operational schedules of the radiology clinic. We found that there was no significant loss incurred by restricting dosage to an 8:00 a.m. to 5:00 p.m. window. Our flexible approach is also applicable to other tumor types treated with radiotherapy. -
Altrock PM, Brendel C, Renella R, Orkin SH, Williams DA, Michor F. 2016. Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease. American journal of hematology. 91(9):931-7. Pubmed: 27299299 DOI:10.1002/ajh.24449 Altrock PM, Brendel C, Renella R, Orkin SH, Williams DA, Michor F. 2016. Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease. American journal of hematology. 91(9):931-7. Pubmed: 27299299 DOI:10.1002/ajh.24449 Recent advances in gene therapy and genome-engineering technologies offer the opportunity to correct sickle cell disease (SCD), a heritable disorder caused by a point mutation in the β-globin gene. The developmental switch from fetal γ-globin to adult β-globin is governed in part by the transcription factor (TF) BCL11A. This TF has been proposed as a therapeutic target for reactivation of γ-globin and concomitant reduction of β-sickle globin. In this and other approaches, genetic alteration of a portion of the hematopoietic stem cell (HSC) compartment leads to a mixture of sickling and corrected red blood cells (RBCs) in periphery. To reverse the sickling phenotype, a certain proportion of corrected RBCs is necessary; the degree of HSC alteration required to achieve a desired fraction of corrected RBCs remains unknown. To address this issue, we developed a mathematical model describing aging and survival of sickle-susceptible and normal RBCs; the former can have a selective survival advantage leading to their overrepresentation. We identified the level of bone marrow chimerism required for successful stem cell-based gene therapies in SCD. Our findings were further informed using an experimental mouse model, where we transplanted mixtures of Berkeley SCD and normal murine bone marrow cells to establish chimeric grafts in murine hosts. Our integrative theoretical and experimental approach identifies the target frequency of HSC alterations required for effective treatment of sickling syndromes in humans. Our work replaces episodic observations of such target frequencies with a mathematical modeling framework that covers a large and continuous spectrum of chimerism conditions. Am. J. Hematol. 91:931-937, 2016. © 2016 Wiley Periodicals, Inc.© 2016 Wiley Periodicals, Inc. 2015
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Altrock PM, Liu LL, Michor F. 2015. The mathematics of cancer: integrating quantitative models. Nature reviews. Cancer. 15(12):730-45. Pubmed: 26597528 DOI:10.1038/nrc4029 Altrock PM, Liu LL, Michor F. 2015. The mathematics of cancer: integrating quantitative models. Nature reviews. Cancer. 15(12):730-45. Pubmed: 26597528 DOI:10.1038/nrc4029 Mathematical modelling approaches have become increasingly abundant in cancer research. The complexity of cancer is well suited to quantitative approaches as it provides challenges and opportunities for new developments. In turn, mathematical modelling contributes to cancer research by helping to elucidate mechanisms and by providing quantitative predictions that can be validated. The recent expansion of quantitative models addresses many questions regarding tumour initiation, progression and metastases as well as intra-tumour heterogeneity, treatment responses and resistance. Mathematical models can complement experimental and clinical studies, but also challenge current paradigms, redefine our understanding of mechanisms driving tumorigenesis and shape future research in cancer biology. -
Michor F, Beal K. 2015. Improving Cancer Treatment via Mathematical Modeling: Surmounting the Challenges Is Worth the Effort. Cell. 163(5):1059-1063. Pubmed: 26590416 DOI:S0092-8674(15)01482-8 Michor F, Beal K. 2015. Improving Cancer Treatment via Mathematical Modeling: Surmounting the Challenges Is Worth the Effort. Cell. 163(5):1059-1063. Pubmed: 26590416 DOI:S0092-8674(15)01482-8 Drug delivery schedules are key factors in the efficacy of cancer therapies, and mathematical modeling of population dynamics and treatment responses can be applied to identify better drug administration regimes as well as provide mechanistic insights. To capitalize on the promise of this approach, the cancer field must meet the challenges of moving this type of work into clinics.Copyright © 2015 Elsevier Inc. All rights reserved. -
Foo J, Liu LL, Leder K, Riester M, Iwasa Y, Lengauer C, Michor F. 2015. An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer. PLoS computational biology. 11(9):e1004350. Pubmed: 26379039 DOI:10.1371/journal.pcbi.1004350 Foo J, Liu LL, Leder K, Riester M, Iwasa Y, Lengauer C, Michor F. 2015. An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer. PLoS computational biology. 11(9):e1004350. Pubmed: 26379039 DOI:10.1371/journal.pcbi.1004350 The traditional view of cancer as a genetic disease that can successfully be treated with drugs targeting mutant onco-proteins has motivated whole-genome sequencing efforts in many human cancer types. However, only a subset of mutations found within the genomic landscape of cancer is likely to provide a fitness advantage to the cell. Distinguishing such "driver" mutations from innocuous "passenger" events is critical for prioritizing the validation of candidate mutations in disease-relevant models. We design a novel statistical index, called the Hitchhiking Index, which reflects the probability that any observed candidate gene is a passenger alteration, given the frequency of alterations in a cross-sectional cancer sample set, and apply it to a mutational data set in colorectal cancer. Our methodology is based upon a population dynamics model of mutation accumulation and selection in colorectal tissue prior to cancer initiation as well as during tumorigenesis. This methodology can be used to aid in the prioritization of candidate mutations for functional validation and contributes to the process of drug discovery. -
Roccaro AM, Mishima Y, Sacco A, Moschetta M, Tai YT, Shi J, Zhang Y, Reagan MR, Huynh D, Kawano Y, Sahin I, Chiarini M, Manier S, Cea M, Aljawai Y, Glavey S, Morgan E, Pan C, Michor F, Cardarelli P, Kuhne M, Ghobrial IM. 2015. CXCR4 Regulates Extra-Medullary Myeloma through Epithelial-Mesenchymal-Transition-like Transcriptional Activation. Cell reports. 12(4):622-35. Pubmed: 26190113 DOI:S2211-1247(15)00685-3 Roccaro AM, Mishima Y, Sacco A, Moschetta M, Tai YT, Shi J, Zhang Y, Reagan MR, Huynh D, Kawano Y, Sahin I, Chiarini M, Manier S, Cea M, Aljawai Y, Glavey S, Morgan E, Pan C, Michor F, Cardarelli P, Kuhne M, Ghobrial IM. 2015. CXCR4 Regulates Extra-Medullary Myeloma through Epithelial-Mesenchymal-Transition-like Transcriptional Activation. Cell reports. 12(4):622-35. Pubmed: 26190113 DOI:S2211-1247(15)00685-3 Extra-medullary disease (EMD) in multiple myeloma (MM) is associated with poor prognosis and resistance to chemotherapy. However, molecular alterations that lead to EMD have not been well defined. We developed bone marrow (BM)- and EMD-prone MM syngeneic cell lines; identified that epithelial-to-mesenchymal transition (EMT) transcriptional patterns were significantly enriched in both clones compared to parental cells, together with higher levels of CXCR4 protein; and demonstrated that CXCR4 enhanced the acquisition of an EMT-like phenotype in MM cells with a phenotypic conversion for invasion, leading to higher bone metastasis and EMD dissemination in vivo. In contrast, CXCR4 silencing led to inhibited tumor growth and reduced survival. Ulocuplumab, a monoclonal anti-CXCR4 antibody, inhibited MM cell dissemination, supported by suppression of the CXCR4-driven EMT-like phenotype. These results suggest that targeting CXCR4 may act as a regulator of EMD through EMT-like transcriptional modulation, thus representing a potential therapeutic strategy to prevent MM disease progression.Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved. -
Janiszewska M, Liu L, Almendro V, Kuang Y, Paweletz C, Sakr RA, Weigelt B, Hanker AB, Chandarlapaty S, King TA, Reis-Filho JS, Arteaga CL, Park SY, Michor F, Polyak K. 2015. In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nature genetics. 47(10):1212-9. Pubmed: 26301495 DOI:10.1038/ng.3391 Janiszewska M, Liu L, Almendro V, Kuang Y, Paweletz C, Sakr RA, Weigelt B, Hanker AB, Chandarlapaty S, King TA, Reis-Filho JS, Arteaga CL, Park SY, Michor F, Polyak K. 2015. In situ single-cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2-positive breast cancer. Nature genetics. 47(10):1212-9. Pubmed: 26301495 DOI:10.1038/ng.3391 Detection of minor, genetically distinct subpopulations within tumors is a key challenge in cancer genomics. Here we report STAR-FISH (specific-to-allele PCR-FISH), a novel method for the combined detection of single-nucleotide and copy number alterations in single cells in intact archived tissues. Using this method, we assessed the clinical impact of changes in the frequency and topology of PIK3CA mutation and HER2 (ERBB2) amplification within HER2-positive breast cancer during neoadjuvant therapy. We found that these two genetic events are not always present in the same cells. Chemotherapy selects for PIK3CA-mutant cells, a minor subpopulation in nearly all treatment-naive samples, and modulates genetic diversity within tumors. Treatment-associated changes in the spatial distribution of cellular genetic diversity correlated with poor long-term outcome following adjuvant therapy with trastuzumab. Our findings support the use of in situ single cell-based methods in cancer genomics and imply that chemotherapy before HER2-targeted therapy may promote treatment resistance. -
Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P. 2015. The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells. Cancer informatics. 14(Suppl 4):19-31. Pubmed: 26244007 DOI:10.4137/CIN.S19338 Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P. 2015. The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells. Cancer informatics. 14(Suppl 4):19-31. Pubmed: 26244007 DOI:10.4137/CIN.S19338 Therapeutic resistance arises as a result of evolutionary processes driven by dynamic feedback between a heterogeneous cell population and environmental selective pressures. Previous studies have suggested that mutations conferring resistance to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) in non-small-cell lung cancer (NSCLC) cells lower the fitness of resistant cells relative to drug-sensitive cells in a drug-free environment. Here, we hypothesize that the local tumor microenvironment could influence the magnitude and directionality of the selective effect, both in the presence and absence of a drug. Using a combined experimental and computational approach, we developed a mathematical model of preexisting drug resistance describing multiple cellular compartments, each representing a specific tumor environmental niche. This model was parameterized using a novel experimental dataset derived from the HCC827 erlotinib-sensitive and -resistant NSCLC cell lines. We found that, in contrast to in the drug-free environment, resistant cells may hold a fitness advantage compared to parental cells in microenvironments deficient in oxygen and nutrients. We then utilized the model to predict the impact of drug and nutrient gradients on tumor composition and recurrence times, demonstrating that these endpoints are strongly dependent on the microenvironment. Our interdisciplinary approach provides a model system to quantitatively investigate the impact of microenvironmental effects on the evolutionary dynamics of tumor cells. -
Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, McKenney AS, Papalexi E, Abdel-Wahab O, Rampal R, Marubayashi S, Chen JJ, Romanet V, Fridman JS, Bromberg J, Teruya-Feldstein J, Murakami M, Radimerski T, Michor F, Fan R, Levine RL. 2015. JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response. Cancer discovery. 5(3):316-31. Pubmed: 25572172 DOI:10.1158/2159-8290.CD-14-0736 Kleppe M, Kwak M, Koppikar P, Riester M, Keller M, Bastian L, Hricik T, Bhagwat N, McKenney AS, Papalexi E, Abdel-Wahab O, Rampal R, Marubayashi S, Chen JJ, Romanet V, Fridman JS, Bromberg J, Teruya-Feldstein J, Murakami M, Radimerski T, Michor F, Fan R, Levine RL. 2015. JAK-STAT pathway activation in malignant and nonmalignant cells contributes to MPN pathogenesis and therapeutic response. Cancer discovery. 5(3):316-31. Pubmed: 25572172 DOI:10.1158/2159-8290.CD-14-0736 Array©2015 American Association for Cancer Research. -
Bhang HE, Ruddy DA, Krishnamurthy Radhakrishna V, Caushi JX, Zhao R, Hims MM, Singh AP, Kao I, Rakiec D, Shaw P, Balak M, Raza A, Ackley E, Keen N, Schlabach MR, Palmer M, Leary RJ, Chiang DY, Sellers WR, Michor F, Cooke VG, Korn JM, Stegmeier F. 2015. Studying clonal dynamics in response to cancer therapy using high-complexity barcoding. Nature medicine. 21(5):440-8. Pubmed: 25849130 DOI:10.1038/nm.3841 Bhang HE, Ruddy DA, Krishnamurthy Radhakrishna V, Caushi JX, Zhao R, Hims MM, Singh AP, Kao I, Rakiec D, Shaw P, Balak M, Raza A, Ackley E, Keen N, Schlabach MR, Palmer M, Leary RJ, Chiang DY, Sellers WR, Michor F, Cooke VG, Korn JM, Stegmeier F. 2015. Studying clonal dynamics in response to cancer therapy using high-complexity barcoding. Nature medicine. 21(5):440-8. Pubmed: 25849130 DOI:10.1038/nm.3841 Resistance to cancer therapies presents a significant clinical challenge. Recent studies have revealed intratumoral heterogeneity as a source of therapeutic resistance. However, it is unclear whether resistance is driven predominantly by pre-existing or de novo alterations, in part because of the resolution limits of next-generation sequencing. To address this, we developed a high-complexity barcode library, ClonTracer, which enables the high-resolution tracking of more than 1 million cancer cells under drug treatment. In two clinically relevant models, ClonTracer studies showed that the majority of resistant clones were part of small, pre-existing subpopulations that selectively escaped under therapeutic challenge. Moreover, the ClonTracer approach enabled quantitative assessment of the ability of combination treatments to suppress resistant clones. These findings suggest that resistant clones are present before treatment, which would make up-front therapeutic combinations that target non-overlapping resistance a preferred approach. Thus, ClonTracer barcoding may be a valuable tool for optimizing therapeutic regimens with the goal of curative combination therapies for cancer. -
Bambury RM, Bhatt AS, Riester M, Pedamallu CS, Duke F, Bellmunt J, Stack EC, Werner L, Park R, Iyer G, Loda M, Kantoff PW, Michor F, Meyerson M, Rosenberg JE. 2015. DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors. BMC cancer. 15:242. Pubmed: 25886454 DOI:10.1186/s12885-015-1192-2 Bambury RM, Bhatt AS, Riester M, Pedamallu CS, Duke F, Bellmunt J, Stack EC, Werner L, Park R, Iyer G, Loda M, Kantoff PW, Michor F, Meyerson M, Rosenberg JE. 2015. DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors. BMC cancer. 15:242. Pubmed: 25886454 DOI:10.1186/s12885-015-1192-2 Array -
Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D. 2015. Polyploidy can drive rapid adaptation in yeast. Nature. 519(7543):349-52. Pubmed: 25731168 DOI:10.1038/nature14187 Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D. 2015. Polyploidy can drive rapid adaptation in yeast. Nature. 519(7543):349-52. Pubmed: 25731168 DOI:10.1038/nature14187 Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood. Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through complex effects on the frequency or fitness of beneficial mutations. For example, in diverse cell types and organisms, immediately after a whole-genome duplication, newly formed polyploids missegregate chromosomes and undergo genetic instability. The instability following whole-genome duplications is thought to provide adaptive mutations in microorganisms and can promote tumorigenesis in mammalian cells. Polyploidy may also affect adaptation independently of beneficial mutations through ploidy-specific changes in cell physiology. Here we perform in vitro evolution experiments to test directly whether polyploidy can accelerate evolutionary adaptation. Compared with haploids and diploids, tetraploids undergo significantly faster adaptation. Mathematical modelling suggests that rapid adaptation of tetraploids is driven by higher rates of beneficial mutations with stronger fitness effects, which is supported by whole-genome sequencing and phenotypic analyses of evolved clones. Chromosome aneuploidy, concerted chromosome loss, and point mutations all provide large fitness gains. We identify several mutations whose beneficial effects are manifest specifically in the tetraploid strains. Together, these results provide direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation. -
Ashcroft P, Michor F, Galla T. 2015. Stochastic tunneling and metastable states during the somatic evolution of cancer. Genetics. 199(4):1213-28. Pubmed: 25624316 DOI:10.1534/genetics.114.171553 Ashcroft P, Michor F, Galla T. 2015. Stochastic tunneling and metastable states during the somatic evolution of cancer. Genetics. 199(4):1213-28. Pubmed: 25624316 DOI:10.1534/genetics.114.171553 Tumors initiate when a population of proliferating cells accumulates a certain number and type of genetic and/or epigenetic alterations. The population dynamics of such sequential acquisition of (epi)genetic alterations has been the topic of much investigation. The phenomenon of stochastic tunneling, where an intermediate mutant in a sequence does not reach fixation in a population before generating a double mutant, has been studied using a variety of computational and mathematical methods. However, the field still lacks a comprehensive analytical description since theoretical predictions of fixation times are available only for cases in which the second mutant is advantageous. Here, we study stochastic tunneling in a Moran model. Analyzing the deterministic dynamics of large populations we systematically identify the parameter regimes captured by existing approaches. Our analysis also reveals fitness landscapes and mutation rates for which finite populations are found in long-lived metastable states. These are landscapes in which the final mutant is not the most advantageous in the sequence, and resulting metastable states are a consequence of a mutation-selection balance. The escape from these states is driven by intrinsic noise, and their location affects the probability of tunneling. Existing methods no longer apply. In these regimes it is the escape from the metastable states that is the key bottleneck; fixation is no longer limited by the emergence of a successful mutant lineage. We used the so-called Wentzel-Kramers-Brillouin method to compute fixation times in these parameter regimes, successfully validated by stochastic simulations. Our work fills a gap left by previous approaches and provides a more comprehensive description of the acquisition of multiple mutations in populations of somatic cells.Copyright © 2015 by the Genetics Society of America. -
Liu LL, Li F, Pao W, Michor F. 2015. Dose-Dependent Mutation Rates Determine Optimum Erlotinib Dosing Strategies for EGFR Mutant Non-Small Cell Lung Cancer Patients. PloS one. 10(11):e0141665. Pubmed: 26536620 DOI:10.1371/journal.pone.0141665 Liu LL, Li F, Pao W, Michor F. 2015. Dose-Dependent Mutation Rates Determine Optimum Erlotinib Dosing Strategies for EGFR Mutant Non-Small Cell Lung Cancer Patients. PloS one. 10(11):e0141665. Pubmed: 26536620 DOI:10.1371/journal.pone.0141665 Array 2014
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Guancial EA, Werner L, Bellmunt J, Bamias A, Choueiri TK, Ross R, Schutz FA, Park RS, O'Brien RJ, Hirsch MS, Barletta JA, Berman DM, Lis R, Loda M, Stack EC, Garraway LA, Riester M, Michor F, Kantoff PW, Rosenberg JE. 2014. FGFR3 expression in primary and metastatic urothelial carcinoma of the bladder. Cancer medicine. 3(4):835-44. Pubmed: 24846059 DOI:10.1002/cam4.262 Guancial EA, Werner L, Bellmunt J, Bamias A, Choueiri TK, Ross R, Schutz FA, Park RS, O'Brien RJ, Hirsch MS, Barletta JA, Berman DM, Lis R, Loda M, Stack EC, Garraway LA, Riester M, Michor F, Kantoff PW, Rosenberg JE. 2014. FGFR3 expression in primary and metastatic urothelial carcinoma of the bladder. Cancer medicine. 3(4):835-44. Pubmed: 24846059 DOI:10.1002/cam4.262 While fibroblast growth factor receptor 3 (FGFR3) is frequently mutated or overexpressed in nonmuscle-invasive urothelial carcinoma (UC), the prevalence of FGFR3 protein expression and mutation remains unknown in muscle-invasive disease. FGFR3 protein and mRNA expression, mutational status, and copy number variation were retrospectively analyzed in 231 patients with formalin-fixed paraffin-embedded primary UCs, 33 metastases, and 14 paired primary and metastatic tumors using the following methods: immunohistochemistry, NanoString nCounterTM, OncoMap or Affymetrix OncoScanTM array, and Gain and Loss of Analysis of DNA and Genomic Identification of Significant Targets in Cancer software. FGFR3 immunohistochemistry staining was present in 29% of primary UCs and 49% of metastases and did not impact overall survival (P = 0.89, primary tumors; P = 0.78, metastases). FGFR3 mutations were observed in 2% of primary tumors and 9% of metastases. Mutant tumors expressed higher levels of FGFR3 mRNA than wild-type tumors (P < 0.001). FGFR3 copy number gain and loss were rare events in primary and metastatic tumors (0.8% each; 3.0% and 12.3%, respectively). FGFR3 immunohistochemistry staining is present in one third of primary muscle-invasive UCs and half of metastases, while FGFR3 mutations and copy number changes are relatively uncommon.© 2014 The Authors. Cancer Medicine published by John Wiley & Sons Ltd. -
Podlaha O, De S, Gonen M, Michor F. 2014. Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS computational biology. 10(6):e1003611. Pubmed: 24901363 DOI:10.1371/journal.pcbi.1003611 Podlaha O, De S, Gonen M, Michor F. 2014. Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS computational biology. 10(6):e1003611. Pubmed: 24901363 DOI:10.1371/journal.pcbi.1003611 Mechanisms that generate transcript diversity are of fundamental importance in eukaryotes. Although a large fraction of human protein-coding genes and lincRNAs produce more than one mRNA isoform each, the regulation of this phenomenon is still incompletely understood. Much progress has been made in deciphering the role of sequence-specific features as well as DNA-and RNA-binding proteins in alternative splicing. Recently, however, several experimental studies of individual genes have revealed a direct involvement of epigenetic factors in alternative splicing and transcription initiation. While histone modifications are generally correlated with overall gene expression levels, it remains unclear how histone modification enrichment affects relative isoform abundance. Therefore, we sought to investigate the associations between histone modifications and transcript diversity levels measured by the rates of transcription start-site switching and alternative splicing on a genome-wide scale across protein-coding genes and lincRNAs. We found that the relationship between enrichment levels of epigenetic marks and transcription start-site switching is similar for protein-coding genes and lincRNAs. Furthermore, we found associations between splicing rates and enrichment levels of H2az, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3K79me2, and H4K20me, marks traditionally associated with enhancers, transcription initiation, transcriptional repression, and others. These patterns were observed in both normal and cancer cell lines. Additionally, we developed a novel computational method that identified 840 epigenetically regulated candidate genes and predicted transcription start-site switching and alternative exon splicing with up to 92% accuracy based on epigenetic patterning alone. Our results suggest that the epigenetic regulation of transcript isoform diversity may be a relatively common genome-wide phenomenon representing an avenue of deregulation in tumor development. -
Maruvka YE, Tang M, Michor F. 2014. On the validity of using increases in 5-year survival rates to measure success in the fight against cancer. PloS one. 9(7):e83100. Pubmed: 25054541 DOI:10.1371/journal.pone.0083100 Maruvka YE, Tang M, Michor F. 2014. On the validity of using increases in 5-year survival rates to measure success in the fight against cancer. PloS one. 9(7):e83100. Pubmed: 25054541 DOI:10.1371/journal.pone.0083100 Array -
Marusyk A, Tabassum DP, Altrock PM, Almendro V, Michor F, Polyak K. 2014. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity. Nature. 514(7520):54-8. Pubmed: 25079331 DOI:10.1038/nature13556 Marusyk A, Tabassum DP, Altrock PM, Almendro V, Michor F, Polyak K. 2014. Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity. Nature. 514(7520):54-8. Pubmed: 25079331 DOI:10.1038/nature13556 Cancers arise through a process of somatic evolution that can result in substantial sub-clonal heterogeneity within tumours. The mechanisms responsible for the coexistence of distinct sub-clones and the biological consequences of this coexistence remain poorly understood. Here we used a mouse xenograft model to investigate the impact of sub-clonal heterogeneity on tumour phenotypes and the competitive expansion of individual clones. We found that tumour growth can be driven by a minor cell subpopulation, which enhances the proliferation of all cells within a tumour by overcoming environmental constraints and yet can be outcompeted by faster proliferating competitors, resulting in tumour collapse. We developed a mathematical modelling framework to identify the rules underlying the generation of intra-tumour clonal heterogeneity. We found that non-cell-autonomous driving of tumour growth, together with clonal interference, stabilizes sub-clonal heterogeneity, thereby enabling inter-clonal interactions that can lead to new phenotypic traits. -
Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. 2014. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 512(7513):155-60. Pubmed: 25079324 DOI:10.1038/nature13600 Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. 2014. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 512(7513):155-60. Pubmed: 25079324 DOI:10.1038/nature13600 Sequencing studies of breast tumour cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumours. Here we developed a whole-genome and exome single cell sequencing approach called nuc-seq that uses G2/M nuclei to achieve 91% mean coverage breadth. We applied this method to sequence single normal and tumour nuclei from an oestrogen-receptor-positive (ER(+)) breast cancer and a triple-negative ductal carcinoma. In parallel, we performed single nuclei copy number profiling. Our data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Using targeted single-molecule sequencing, many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumour mass. Using mathematical modelling we found that the triple-negative tumour cells had an increased mutation rate (13.3×), whereas the ER(+) tumour cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer. -
Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. 2014. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. Journal of the National Cancer Institute. 106(5). Pubmed: 24700803 DOI:10.1093/jnci/dju048 Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. 2014. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. Journal of the National Cancer Institute. 106(5). Pubmed: 24700803 DOI:10.1093/jnci/dju048 Array© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. -
Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson NA, Morin RD, Scott DW, Godley LA, Gascoyne RD, Melnick A, Campagne F, Shaknovich R. 2014. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 123(11):1699-708. Pubmed: 24385541 DOI:10.1182/blood-2013-07-509885 Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson NA, Morin RD, Scott DW, Godley LA, Gascoyne RD, Melnick A, Campagne F, Shaknovich R. 2014. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 123(11):1699-708. Pubmed: 24385541 DOI:10.1182/blood-2013-07-509885 Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive form of non-Hodgkin lymphoma with variable biology and clinical behavior. The current classification does not fully explain the biological and clinical heterogeneity of DLBCLs. In this study, we carried out genomewide DNA methylation profiling of 140 DLBCL samples and 10 normal germinal center B cells using the HpaII tiny fragment enrichment by ligation-mediated polymerase chain reaction assay and hybridization to a custom Roche NimbleGen promoter array. We defined methylation disruption as a main epigenetic event in DLBCLs and designed a method for measuring the methylation variability of individual cases. We then used a novel approach for unsupervised hierarchical clustering based on the extent of DNA methylation variability. This approach identified 6 clusters (A-F). The extent of methylation variability was associated with survival outcomes, with significant differences in overall and progression-free survival. The novel clusters are characterized by disruption of specific biological pathways such as cytokine-mediated signaling, ephrin signaling, and pathways associated with apoptosis and cell-cycle regulation. In a subset of patients, we profiled gene expression and genomic variation to investigate their interplay with methylation changes. This study is the first to identify novel epigenetic clusters of DLBCLs and their aberrantly methylated genes, molecular associations, and survival. -
Ozawa T, Riester M, Cheng YK, Huse JT, Squatrito M, Helmy K, Charles N, Michor F, Holland EC. 2014. Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma. Cancer cell. 26(2):288-300. Pubmed: 25117714 DOI:S1535-6108(14)00265-7 Ozawa T, Riester M, Cheng YK, Huse JT, Squatrito M, Helmy K, Charles N, Michor F, Holland EC. 2014. Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma. Cancer cell. 26(2):288-300. Pubmed: 25117714 DOI:S1535-6108(14)00265-7 To understand the relationships between the non-GCIMP glioblastoma (GBM) subgroups, we performed mathematical modeling to predict the temporal sequence of driver events during tumorigenesis. The most common order of evolutionary events is 1) chromosome (chr) 7 gain and chr10 loss, followed by 2) CDKN2A loss and/or TP53 mutation, and 3) alterations canonical for specific subtypes. We then developed a computational methodology to identify drivers of broad copy number changes, identifying PDGFA (chr7) and PTEN (chr10) as driving initial nondisjunction events. These predictions were validated using mouse modeling, showing that PDGFA is sufficient to induce proneural-like gliomas and that additional NF1 loss converts proneural to the mesenchymal subtype. Our findings suggest that most non-GCIMP mesenchymal GBMs arise as, and evolve from, a proneural-like precursor.Copyright © 2014 Elsevier Inc. All rights reserved. -
Almendro V, Kim HJ, Cheng YK, Gönen M, Itzkovitz S, Argani P, van Oudenaarden A, Sukumar S, Michor F, Polyak K. 2014. Genetic and phenotypic diversity in breast tumor metastases. Cancer research. 74(5):1338-48. Pubmed: 24448237 DOI:10.1158/0008-5472.CAN-13-2357-T Almendro V, Kim HJ, Cheng YK, Gönen M, Itzkovitz S, Argani P, van Oudenaarden A, Sukumar S, Michor F, Polyak K. 2014. Genetic and phenotypic diversity in breast tumor metastases. Cancer research. 74(5):1338-48. Pubmed: 24448237 DOI:10.1158/0008-5472.CAN-13-2357-T Metastatic disease is the main cause of cancer-related mortality due to almost universal therapeutic resistance. Despite its high clinical relevance, our knowledge of how cancer cell populations change during metastatic progression is limited. Here, we investigated intratumor genetic and phenotypic heterogeneity during metastatic progression of breast cancer. We analyzed cellular genotypes and phenotypes at the single cell level by performing immunoFISH in intact tissue sections of distant metastatic tumors from rapid autopsy cases and from primary tumors and matched lymph node metastases collected before systemic therapy. We calculated the Shannon index of intratumor diversity in all cancer cells and within phenotypically distinct cell populations. We found that the extent of intratumor genetic diversity was similar regardless of the chromosomal region analyzed, implying that it may reflect an inherent property of the tumors. We observed that genetic diversity was highest in distant metastases and was generally concordant across lesions within the same patient, whereas treatment-naïve primary tumors and matched lymph node metastases were frequently genetically more divergent. In contrast, cellular phenotypes were more discordant between distant metastases than primary tumors and matched lymph node metastases. Diversity for 8q24 was consistently higher in HER2(+) tumors compared with other subtypes and in metastases of triple-negative tumors relative to primary sites. We conclude that our integrative method that couples ecologic models with experimental data in human tissue samples could be used for the improved prognostication of patients with cancer and for the design of more effective therapies for progressive disease.©2014 AACR -
Almendro V, Cheng YK, Randles A, Itzkovitz S, Marusyk A, Ametller E, Gonzalez-Farre X, Muñoz M, Russnes HG, Helland A, Rye IH, Borresen-Dale AL, Maruyama R, van Oudenaarden A, Dowsett M, Jones RL, Reis-Filho J, Gascon P, Gönen M, Michor F, Polyak K. 2014. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell reports. 6(3):514-27. Pubmed: 24462293 DOI:S2211-1247(13)00799-7 Almendro V, Cheng YK, Randles A, Itzkovitz S, Marusyk A, Ametller E, Gonzalez-Farre X, Muñoz M, Russnes HG, Helland A, Rye IH, Borresen-Dale AL, Maruyama R, van Oudenaarden A, Dowsett M, Jones RL, Reis-Filho J, Gascon P, Gönen M, Michor F, Polyak K. 2014. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell reports. 6(3):514-27. Pubmed: 24462293 DOI:S2211-1247(13)00799-7 Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and posttreatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution.Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved. -
Leder K, Pitter K, LaPlant Q, Hambardzumyan D, Ross BD, Chan TA, Holland EC, Michor F. 2014. Mathematical modeling of PDGF-driven glioblastoma reveals optimized radiation dosing schedules. Cell. 156(3):603-616. Pubmed: 24485463 DOI:10.1016/j.cell.2013.12.029 Leder K, Pitter K, LaPlant Q, Hambardzumyan D, Ross BD, Chan TA, Holland EC, Michor F. 2014. Mathematical modeling of PDGF-driven glioblastoma reveals optimized radiation dosing schedules. Cell. 156(3):603-616. Pubmed: 24485463 DOI:10.1016/j.cell.2013.12.029 Glioblastomas (GBMs) are the most common and malignant primary brain tumors and are aggressively treated with surgery, chemotherapy, and radiotherapy. Despite this treatment, recurrence is inevitable and survival has improved minimally over the last 50 years. Recent studies have suggested that GBMs exhibit both heterogeneity and instability of differentiation states and varying sensitivities of these states to radiation. Here, we employed an iterative combined theoretical and experimental strategy that takes into account tumor cellular heterogeneity and dynamically acquired radioresistance to predict the effectiveness of different radiation schedules. Using this model, we identified two delivery schedules predicted to significantly improve efficacy by taking advantage of the dynamic instability of radioresistance. These schedules led to superior survival in mice. Our interdisciplinary approach may also be applicable to other human cancer types treated with radiotherapy and, hence, may lay the foundation for significantly increasing the effectiveness of a mainstay of oncologic therapy. PAPERCLIP:Copyright © 2014 Elsevier Inc. All rights reserved. -
Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial EA, Weir BA, Stack EC, Park RS, O'Brien R, Schutz FA, Choueiri TK, Signoretti S, Lloreta J, Marchionni L, Gallardo E, Rojo F, Garcia DI, Chekaluk Y, Kwiatkowski DJ, Bochner BH, Hahn WC, Ligon AH, Barletta JA, Loda M, Berman DM, Kantoff PW, Michor F, Rosenberg JE. 2014. Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma. Clinical cancer research : an official journal of the American Association for Cancer Research. 20(7):1873-83. Pubmed: 24486590 DOI:10.1158/1078-0432.CCR-13-0759 Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial EA, Weir BA, Stack EC, Park RS, O'Brien R, Schutz FA, Choueiri TK, Signoretti S, Lloreta J, Marchionni L, Gallardo E, Rojo F, Garcia DI, Chekaluk Y, Kwiatkowski DJ, Bochner BH, Hahn WC, Ligon AH, Barletta JA, Loda M, Berman DM, Kantoff PW, Michor F, Rosenberg JE. 2014. Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma. Clinical cancer research : an official journal of the American Association for Cancer Research. 20(7):1873-83. Pubmed: 24486590 DOI:10.1158/1078-0432.CCR-13-0759 Array©2014 AACR. -
Foo J, Michor F. 2014. Evolution of acquired resistance to anti-cancer therapy. Journal of theoretical biology. 355:10-20. Pubmed: 24681298 DOI:S0022-5193(14)00100-3 Foo J, Michor F. 2014. Evolution of acquired resistance to anti-cancer therapy. Journal of theoretical biology. 355:10-20. Pubmed: 24681298 DOI:S0022-5193(14)00100-3 Acquired drug resistance is a major limitation for the successful treatment of cancer. Resistance can emerge due to a variety of reasons including host environmental factors as well as genetic or epigenetic alterations in the cancer cells. Evolutionary theory has contributed to the understanding of the dynamics of resistance mutations in a cancer cell population, the risk of resistance pre-existing before the initiation of therapy, the composition of drug cocktails necessary to prevent the emergence of resistance, and optimum drug administration schedules for patient populations at risk of evolving acquired resistance. Here we review recent advances towards elucidating the evolutionary dynamics of acquired drug resistance and outline how evolutionary thinking can contribute to outstanding questions in the field.Published by Elsevier Ltd. -
Michor F, Weaver VM. 2014. Understanding tissue context influences on intratumour heterogeneity. Nature cell biology. 16(4):301-2. Pubmed: 24691256 DOI:10.1038/ncb2942 Michor F, Weaver VM. 2014. Understanding tissue context influences on intratumour heterogeneity. Nature cell biology. 16(4):301-2. Pubmed: 24691256 DOI:10.1038/ncb2942 Although human cancers exhibit intratumour heterogeneity, the influence of the tumour environment on this property is unclear. Single basal-like mammary epithelial cells are now shown to engage a dynamic TGFBR3-JUND signalling circuit in an extracellular-matrix-dependent manner. Cell transition between the distinct gene expression states underlying this circuit alters their properties and may modulate their propensity to malignancy. -
Shaknovich R, De S, Michor F. 2014. Epigenetic diversity in hematopoietic neoplasms. Biochimica et biophysica acta. 1846(2):477-84. Pubmed: 25240947 DOI:S0304-419X(14)00085-7 Shaknovich R, De S, Michor F. 2014. Epigenetic diversity in hematopoietic neoplasms. Biochimica et biophysica acta. 1846(2):477-84. Pubmed: 25240947 DOI:S0304-419X(14)00085-7 Tumor cell populations display a remarkable extent of variability in non-genetic characteristics such as DNA methylation, histone modification patterns, and differentiation levels of individual cells. It remains to be elucidated whether non-genetic heterogeneity is simply a byproduct of tumor evolution or instead a manifestation of a higher-order tissue organization that is maintained within the neoplasm to establish a differentiation hierarchy, a favorable microenvironment, or a buffer against changing selection pressures during tumorigenesis. Here, we review recent findings on epigenetic diversity, particularly heterogeneity in DNA methylation patterns in hematologic malignancies. We also address the implications of epigenetic heterogeneity for the clonal evolution of tumors and discuss its effects on gene expression and other genome functions in cancer.Copyright © 2014. Published by Elsevier B.V. -
Olshen A, Tang M, Cortes J, Gonen M, Hughes T, Branford S, Quintás-Cardama A, Michor F. 2014. Dynamics of chronic myeloid leukemia response to dasatinib, nilotinib, and high-dose imatinib. Haematologica. 99(11):1701-9. Pubmed: 25216683 DOI:10.3324/haematol.2013.085977 Olshen A, Tang M, Cortes J, Gonen M, Hughes T, Branford S, Quintás-Cardama A, Michor F. 2014. Dynamics of chronic myeloid leukemia response to dasatinib, nilotinib, and high-dose imatinib. Haematologica. 99(11):1701-9. Pubmed: 25216683 DOI:10.3324/haematol.2013.085977 Treatment with the tyrosine kinase inhibitor imatinib is the standard of care for newly diagnosed patients with chronic myeloid leukemia. In recent years, several second-generation inhibitors - such as dasatinib and nilotinib - have become available: these promise to overcome some of the mutations associated with acquired resistance to imatinib. Despite eliciting similar clinical responses, the molecular effects of these agents on different subpopulations of leukemic cells remain incompletely understood. Furthermore, the consequences of using high-dose imatinib therapy have not been investigated in detail. Here we utilized clinical data from patients treated with dasatinib, nilotinib, or high-dose imatinib, together with a statistical data analysis and mathematical modeling approach, to investigate the molecular treatment response of leukemic cells to these agents. We found that these drugs elicit very similar responses if administered front-line. However, patients display significantly different kinetics when treated second-line, both in terms of differences between front-line and second-line treatment for the same drug, and among agents when used as second-line. We then utilized a mathematical framework describing the behavior of four differentiation levels of leukemic cells during therapy to predict the treatment response kinetics for the different cohorts of patients. The dynamics of BCR-ABL1 clearance observed in our study suggest that the use of standard or high-dose imatinib or a second-generation tyrosine kinase inhibitor such as nilotinib or dasatinib elicits similar responses when administered as front-line therapy for patients with chronic myeloid leukemia in chronic phase.Copyright© Ferrata Storti Foundation. 2013
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Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O'Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH. 2013. A physical sciences network characterization of non-tumorigenic and metastatic cells. Scientific reports. 3:1449. Pubmed: 23618955 DOI:10.1038/srep01449 Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O'Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH. 2013. A physical sciences network characterization of non-tumorigenic and metastatic cells. Scientific reports. 3:1449. Pubmed: 23618955 DOI:10.1038/srep01449 To investigate the transition from non-cancerous to metastatic from a physical sciences perspective, the Physical Sciences-Oncology Centers (PS-OC) Network performed molecular and biophysical comparative studies of the non-tumorigenic MCF-10A and metastatic MDA-MB-231 breast epithelial cell lines, commonly used as models of cancer metastasis. Experiments were performed in 20 laboratories from 12 PS-OCs. Each laboratory was supplied with identical aliquots and common reagents and culture protocols. Analyses of these measurements revealed dramatic differences in their mechanics, migration, adhesion, oxygen response, and proteomic profiles. Model-based multi-omics approaches identified key differences between these cells' regulatory networks involved in morphology and survival. These results provide a multifaceted description of cellular parameters of two widely used cell lines and demonstrate the value of the PS-OC Network approach for integration of diverse experimental observations to elucidate the phenotypes associated with cancer metastasis. -
Gallipoli P, Stobo J, Heaney N, Nicolini FE, Clark R, Wilson G, Tighe J, McLintock L, Hughes T, Michor F, Paul J, Drummond M, Holyoake TL. 2013. Safety and efficacy of pulsed imatinib with or without G-CSF versus continuous imatinib in chronic phase chronic myeloid leukaemia patients at 5 years follow-up. British journal of haematology. 163(5):674-6. Pubmed: 24032404 DOI:10.1111/bjh.12532 Gallipoli P, Stobo J, Heaney N, Nicolini FE, Clark R, Wilson G, Tighe J, McLintock L, Hughes T, Michor F, Paul J, Drummond M, Holyoake TL. 2013. Safety and efficacy of pulsed imatinib with or without G-CSF versus continuous imatinib in chronic phase chronic myeloid leukaemia patients at 5 years follow-up. British journal of haematology. 163(5):674-6. Pubmed: 24032404 DOI:10.1111/bjh.12532 -
Liu L, De S, Michor F. 2013. DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nature communications. 4:1502. Pubmed: 23422670 DOI:10.1038/ncomms2502 Liu L, De S, Michor F. 2013. DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nature communications. 4:1502. Pubmed: 23422670 DOI:10.1038/ncomms2502 Single-nucleotide substitutions are a defining characteristic of cancer genomes. Many single-nucleotide substitutions in cancer genomes arise because of errors in DNA replication, which is spatio-temporally stratified. Here we propose that DNA replication patterns help shape the mutational landscapes of normal and cancer genomes. Using data on five fully sequenced cancer types and two personal genomes, we determined that the frequency of intergenic single-nucleotide substitution is significantly higher in late DNA replication timing regions, even after controlling for a number of genomic features. Furthermore, some substitution signatures are more frequent in certain DNA replication timing zones. Finally, integrating data on higher-order nuclear organization, we found that genomic regions in close spatial proximity to late-replicating domains display similar mutation spectra as the late-replicating regions themselves. These data suggest that DNA replication timing together with higher-order genomic organization contribute to the patterns of single-nucleotide substitution in normal and cancer genomes. -
De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A, Michor F. 2013. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS genetics. 9(1):e1003137. Pubmed: 23326238 DOI:10.1371/journal.pgen.1003137 De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A, Michor F. 2013. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS genetics. 9(1):e1003137. Pubmed: 23326238 DOI:10.1371/journal.pgen.1003137 Despite mounting evidence that epigenetic abnormalities play a key role in cancer biology, their contributions to the malignant phenotype remain poorly understood. Here we studied genome-wide DNA methylation in normal B-cell populations and subtypes of B-cell non-Hodgkin lymphoma: follicular lymphoma and diffuse large B-cell lymphomas. These lymphomas display striking and progressive intra-tumor heterogeneity and also inter-patient heterogeneity in their cytosine methylation patterns. Epigenetic heterogeneity is initiated in normal germinal center B-cells, increases markedly with disease aggressiveness, and is associated with unfavorable clinical outcome. Moreover, patterns of abnormal methylation vary depending upon chromosomal regions, gene density and the status of neighboring genes. DNA methylation abnormalities arise via two distinct processes: i) lymphomagenic transcriptional regulators perturb promoter DNA methylation in a target gene-specific manner, and ii) aberrant epigenetic states tend to spread to neighboring promoters in the absence of CTCF insulator binding sites. -
Ohashi K, Maruvka YE, Michor F, Pao W. 2013. Epidermal growth factor receptor tyrosine kinase inhibitor-resistant disease. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 31(8):1070-80. Pubmed: 23401451 DOI:10.1200/JCO.2012.43.3912 Ohashi K, Maruvka YE, Michor F, Pao W. 2013. Epidermal growth factor receptor tyrosine kinase inhibitor-resistant disease. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 31(8):1070-80. Pubmed: 23401451 DOI:10.1200/JCO.2012.43.3912 Array -
Jia P, Jin H, Meador CB, Xia J, Ohashi K, Liu L, Pirazzoli V, Dahlman KB, Politi K, Michor F, Zhao Z, Pao W. 2013. Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome research. 23(9):1434-45. Pubmed: 23733853 DOI:10.1101/gr.152322.112 Jia P, Jin H, Meador CB, Xia J, Ohashi K, Liu L, Pirazzoli V, Dahlman KB, Politi K, Michor F, Zhao Z, Pao W. 2013. Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome research. 23(9):1434-45. Pubmed: 23733853 DOI:10.1101/gr.152322.112 Somatic mutations in kinase genes are associated with sensitivity of solid tumors to kinase inhibitors, but patients with metastatic cancer eventually develop disease progression. In EGFR mutant lung cancer, modeling of acquired resistance (AR) with drug-sensitive cell lines has identified clinically relevant EGFR tyrosine kinase inhibitor (TKI) resistance mechanisms such as the second-site mutation, EGFR T790M, amplification of the gene encoding an alternative kinase, MET, and epithelial-mesenchymal transition (EMT). The full spectrum of DNA changes associated with AR remains unknown. We used next-generation sequencing to characterize mutational changes associated with four populations of EGFR mutant drug-sensitive and five matched drug-resistant cell lines. Comparing resistant cells with parental counterparts, 18-91 coding SNVs/indels were predicted to be acquired and 1-27 were lost; few SNVs/indels were shared across resistant lines. Comparison of two related parental lines revealed no unique coding SNVs/indels, suggesting that changes in the resistant lines were due to drug selection. Surprisingly, we observed more CNV changes across all resistant lines, and the line with EMT displayed significantly higher levels of CNV changes than the other lines with AR. These results demonstrate a framework for studying the evolution of AR and provide the first genome-wide spectrum of mutations associated with the development of cellular drug resistance in an oncogene-addicted cancer. Collectively, the data suggest that CNV changes may play a larger role than previously appreciated in the acquisition of drug resistance and highlight that resistance may be heterogeneous in the context of different tumor cell backgrounds. -
Choudhury S, Almendro V, Merino VF, Wu Z, Maruyama R, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macintyre G, Cheng YK, Lopez-Bujanda Z, Kaspi A, Hu R, Robens J, Nikolskaya T, Haakensen VD, Schnitt SJ, Argani P, Ethington G, Panos L, Grant M, Clark J, Herlihy W, Lin SJ, Chew G, Thompson EW, Greene-Colozzi A, Richardson AL, Rosson GD, Pike M, Garber JE, Nikolsky Y, Blum JL, Au A, Hwang ES, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K. 2013. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell stem cell. 13(1):117-30. Pubmed: 23770079 DOI:S1934-5909(13)00197-5 Choudhury S, Almendro V, Merino VF, Wu Z, Maruyama R, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macintyre G, Cheng YK, Lopez-Bujanda Z, Kaspi A, Hu R, Robens J, Nikolskaya T, Haakensen VD, Schnitt SJ, Argani P, Ethington G, Panos L, Grant M, Clark J, Herlihy W, Lin SJ, Chew G, Thompson EW, Greene-Colozzi A, Richardson AL, Rosson GD, Pike M, Garber JE, Nikolsky Y, Blum JL, Au A, Hwang ES, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K. 2013. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell stem cell. 13(1):117-30. Pubmed: 23770079 DOI:S1934-5909(13)00197-5 Early full-term pregnancy is one of the most effective natural protections against breast cancer. To investigate this effect, we have characterized the global gene expression and epigenetic profiles of multiple cell types from normal breast tissue of nulliparous and parous women and carriers of BRCA1 or BRCA2 mutations. We found significant differences in CD44(+) progenitor cells, where the levels of many stem cell-related genes and pathways, including the cell-cycle regulator p27, are lower in parous women without BRCA1/BRCA2 mutations. We also noted a significant reduction in the frequency of CD44(+)p27(+) cells in parous women and showed, using explant cultures, that parity-related signaling pathways play a role in regulating the number of p27(+) cells and their proliferation. Our results suggest that pathways controlling p27(+) mammary epithelial cells and the numbers of these cells relate to breast cancer risk and can be explored for cancer risk assessment and prevention.Copyright © 2013 Elsevier Inc. All rights reserved. -
Haeno H, Maruvka YE, Iwasa Y, Michor F. 2013. Stochastic Tunneling of Two Mutations in a Population of Cancer Cells. PloS one. 8(6):e65724. Pubmed: 23840359 DOI:10.1371/journal.pone.0065724 Haeno H, Maruvka YE, Iwasa Y, Michor F. 2013. Stochastic Tunneling of Two Mutations in a Population of Cancer Cells. PloS one. 8(6):e65724. Pubmed: 23840359 DOI:10.1371/journal.pone.0065724 Cancer initiation, progression, and the emergence of drug resistance are driven by specific genetic and/or epigenetic alterations such as point mutations, structural alterations, DNA methylation and histone modification changes. These alterations may confer advantageous, deleterious or neutral effects to mutated cells. Previous studies showed that cells harboring two particular alterations may arise in a fixed-size population even in the absence of an intermediate state in which cells harboring only the first alteration take over the population; this phenomenon is called stochastic tunneling. Here, we investigated a stochastic Moran model in which two alterations emerge in a cell population of fixed size. We developed a novel approach to comprehensively describe the evolutionary dynamics of stochastic tunneling of two mutations. We considered the scenarios of large mutation rates and various fitness values and validated the accuracy of the mathematical predictions with exact stochastic computer simulations. Our theory is applicable to situations in which two alterations are accumulated in a fixed-size population of binary dividing cells. -
Zhao R, Michor F. 2013. Patterns of proliferative activity in the colonic crypt determine crypt stability and rates of somatic evolution. PLoS computational biology. 9(6):e1003082. Pubmed: 23785264 DOI:10.1371/journal.pcbi.1003082 Zhao R, Michor F. 2013. Patterns of proliferative activity in the colonic crypt determine crypt stability and rates of somatic evolution. PLoS computational biology. 9(6):e1003082. Pubmed: 23785264 DOI:10.1371/journal.pcbi.1003082 Epithelial cells in the colon are arranged in cylindrical structures called crypts in which cellular proliferation and migration are tightly regulated. We hypothesized that the proliferation patterns of cells may determine the stability of crypts as well as the rates of somatic evolution towards colorectal tumorigenesis. Here, we propose a linear process model of colonic epithelial cells that explicitly takes into account the proliferation kinetics of cells as a function of cell position within the crypt. Our results indicate that proliferation kinetics has significant influence on the speed of cell movement, kinetics of mutation propagation, and sensitivity of the system to selective effects of mutated cells. We found that, of all proliferation curves tested, those with mitotic activities concentrated near the stem cell, including the actual proliferation kinetics determined in in vivo labeling experiments, have a greater ability of delaying the rate of mutation accumulation in colonic stem cells compared to hypothetical proliferation curves with mitotic activities focused near the top of the crypt column. Our model can be used to investigate the dynamics of proliferation and mutation accumulation in spatially arranged tissues. 2012
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Foo J, Chmielecki J, Pao W, Michor F. 2012. Effects of pharmacokinetic processes and varied dosing schedules on the dynamics of acquired resistance to erlotinib in EGFR-mutant lung cancer. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer. 7(10):1583-93. Pubmed: 22982659 DOI:10.1097/JTO.0b013e31826146ee Foo J, Chmielecki J, Pao W, Michor F. 2012. Effects of pharmacokinetic processes and varied dosing schedules on the dynamics of acquired resistance to erlotinib in EGFR-mutant lung cancer. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer. 7(10):1583-93. Pubmed: 22982659 DOI:10.1097/JTO.0b013e31826146ee Array -
Martins FC, De S, Almendro V, Gönen M, Park SY, Blum JL, Herlihy W, Ethington G, Schnitt SJ, Tung N, Garber JE, Fetten K, Michor F, Polyak K. 2012. Evolutionary pathways in BRCA1-associated breast tumors. Cancer discovery. 2(6):503-11. Pubmed: 22628410 DOI:10.1158/2159-8290.CD-11-0325 Martins FC, De S, Almendro V, Gönen M, Park SY, Blum JL, Herlihy W, Ethington G, Schnitt SJ, Tung N, Garber JE, Fetten K, Michor F, Polyak K. 2012. Evolutionary pathways in BRCA1-associated breast tumors. Cancer discovery. 2(6):503-11. Pubmed: 22628410 DOI:10.1158/2159-8290.CD-11-0325 BRCA1-associated breast tumors display loss of BRCA1 and frequent somatic mutations of PTEN and TP53. Here we describe the analysis of BRCA1, PTEN, and p53 at the single cell level in 55 BRCA1-associated breast tumors and computational methods to predict the relative temporal order of somatic events, on the basis of the frequency of cells with single or combined alterations. Although there is no obligatory order of events, we found that loss of PTEN is the most common first event and is associated with basal-like subtype, whereas in the majority of luminal tumors, mutation of TP53 occurs first and mutant PIK3CA is rarely detected. We also observed intratumor heterogeneity for the loss of wild-type BRCA1 and increased cell proliferation and centrosome amplification in the normal breast epithelium of BRCA1 mutation carriers. Our results have important implications for the design of chemopreventive and therapeutic interventions in this high-risk patient population. -
Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F. 2012. A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS computational biology. 8(1):e1002337. Pubmed: 22241976 DOI:10.1371/journal.pcbi.1002337 Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F. 2012. A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS computational biology. 8(1):e1002337. Pubmed: 22241976 DOI:10.1371/journal.pcbi.1002337 Human cancer is caused by the accumulation of genetic alterations in cells. Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and thus represent promising targets for therapeutic intervention. We have previously described a computational approach, called Retracing the Evolutionary Steps in Cancer (RESIC), to determine the temporal sequence of genetic alterations during tumorigenesis from cross-sectional genomic data of tumors at their fully transformed stage. Since alterations within a set of genes belonging to a particular signaling pathway may have similar or equivalent effects, we applied a pathway-based systems biology approach to the RESIC methodology. This method was used to determine whether alterations of specific pathways develop early or late during malignant transformation. When applied to primary glioblastoma (GBM) copy number data from The Cancer Genome Atlas (TCGA) project, RESIC identified a temporal order of pathway alterations consistent with the order of events in secondary GBMs. We then further subdivided the samples into the four main GBM subtypes and determined the relative contributions of each subtype to the overall results: we found that the overall ordering applied for the proneural subtype but differed for mesenchymal samples. The temporal sequence of events could not be identified for neural and classical subtypes, possibly due to a limited number of samples. Moreover, for samples of the proneural subtype, we detected two distinct temporal sequences of events: (i) RAS pathway activation was followed by TP53 inactivation and finally PI3K2 activation, and (ii) RAS activation preceded only AKT activation. This extension of the RESIC methodology provides an evolutionary mathematical approach to identify the temporal sequence of pathway changes driving tumorigenesis and may be useful in guiding the understanding of signaling rearrangements in cancer development.© 2012 Cheng et al. -
Iwami S, Haeno H, Michor F. 2012. A race between tumor immunoescape and genome maintenance selects for optimum levels of (epi)genetic instability. PLoS computational biology. 8(2):e1002370. Pubmed: 22359489 DOI:10.1371/journal.pcbi.1002370 Iwami S, Haeno H, Michor F. 2012. A race between tumor immunoescape and genome maintenance selects for optimum levels of (epi)genetic instability. PLoS computational biology. 8(2):e1002370. Pubmed: 22359489 DOI:10.1371/journal.pcbi.1002370 The human immune system functions to provide continuous body-wide surveillance to detect and eliminate foreign agents such as bacteria and viruses as well as the body's own cells that undergo malignant transformation. To counteract this surveillance, tumor cells evolve mechanisms to evade elimination by the immune system; this tumor immunoescape leads to continuous tumor expansion, albeit potentially with a different composition of the tumor cell population ("immunoediting"). Tumor immunoescape and immunoediting are products of an evolutionary process and are hence driven by mutation and selection. Higher mutation rates allow cells to more rapidly acquire new phenotypes that help evade the immune system, but also harbor the risk of an inability to maintain essential genome structure and functions, thereby leading to an error catastrophe. In this paper, we designed a novel mathematical framework, based upon the quasispecies model, to study the effects of tumor immunoediting and the evolution of (epi)genetic instability on the abundance of tumor and immune system cells. We found that there exists an optimum number of tumor variants and an optimum magnitude of mutation rates that maximize tumor progression despite an active immune response. Our findings provide insights into the dynamics of tumorigenesis during immune system attacks and help guide the choice of treatment strategies that best inhibit diverse tumor cell populations. -
Riester M, Taylor JM, Feifer A, Koppie T, Rosenberg JE, Downey RJ, Bochner BH, Michor F. 2012. Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clinical cancer research : an official journal of the American Association for Cancer Research. 18(5):1323-33. Pubmed: 22228636 DOI:10.1158/1078-0432.CCR-11-2271 Riester M, Taylor JM, Feifer A, Koppie T, Rosenberg JE, Downey RJ, Bochner BH, Michor F. 2012. Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clinical cancer research : an official journal of the American Association for Cancer Research. 18(5):1323-33. Pubmed: 22228636 DOI:10.1158/1078-0432.CCR-11-2271 Array -
Haeno H, Gonen M, Davis MB, Herman JM, Iacobuzio-Donahue CA, Michor F. 2012. Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies. Cell. 148(1-2):362-75. Pubmed: 22265421 DOI:10.1016/j.cell.2011.11.060 Haeno H, Gonen M, Davis MB, Herman JM, Iacobuzio-Donahue CA, Michor F. 2012. Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies. Cell. 148(1-2):362-75. Pubmed: 22265421 DOI:10.1016/j.cell.2011.11.060 Pancreatic cancer is a leading cause of cancer-related death, largely due to metastatic dissemination. We investigated pancreatic cancer progression by utilizing a mathematical framework of metastasis formation together with comprehensive data of 228 patients, 101 of whom had autopsies. We found that pancreatic cancer growth is initially exponential. After estimating the rates of pancreatic cancer growth and dissemination, we determined that patients likely harbor metastases at diagnosis and predicted the number and size distribution of metastases as well as patient survival. These findings were validated in an independent database. Finally, we analyzed the effects of different treatment modalities, finding that therapies that efficiently reduce the growth rate of cells earlier in the course of treatment appear to be superior to upfront tumor resection. These predictions can be validated in the clinic. Our interdisciplinary approach provides insights into the dynamics of pancreatic cancer metastasis and identifies optimum therapeutic interventions.Copyright © 2012 Elsevier Inc. All rights reserved. -
Podlaha O, Riester M, De S, Michor F. 2012. Evolution of the cancer genome. Trends in genetics : TIG. 28(4):155-63. Pubmed: 22342180 DOI:10.1016/j.tig.2012.01.003 Podlaha O, Riester M, De S, Michor F. 2012. Evolution of the cancer genome. Trends in genetics : TIG. 28(4):155-63. Pubmed: 22342180 DOI:10.1016/j.tig.2012.01.003 Human tumors result from an evolutionary process operating on somatic cells within tissues, whereby natural selection operates on the phenotypic variability generated by the accumulation of genetic, genomic and epigenetic alterations. This somatic evolution leads to adaptations such as increased proliferative, angiogenic, and invasive phenotypes. In this review we outline how cancer genomes are beginning to be investigated from an evolutionary perspective. We describe recent progress in the cataloging of somatic genetic and genomic alterations, and investigate the contributions of germline as well as epigenetic factors to cancer genome evolution. Finally, we outline the challenges facing researchers who investigate the processes driving the evolution of the cancer genome.Copyright © 2012. Published by Elsevier Ltd. -
Tang M, Foo J, Gönen M, Guilhot J, Mahon FX, Michor F. 2012. Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials. Haematologica. 97(10):1553-61. Pubmed: 22419579 DOI:10.3324/haematol.2012.062844 Tang M, Foo J, Gönen M, Guilhot J, Mahon FX, Michor F. 2012. Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials. Haematologica. 97(10):1553-61. Pubmed: 22419579 DOI:10.3324/haematol.2012.062844 Array 2011
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De Vargas Roditi L, Michor F. 2011. Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis. Journal of theoretical biology. 273(1):207-15. Pubmed: 21194536 DOI:10.1016/j.jtbi.2010.12.033 De Vargas Roditi L, Michor F. 2011. Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis. Journal of theoretical biology. 273(1):207-15. Pubmed: 21194536 DOI:10.1016/j.jtbi.2010.12.033 Cancer results from the accumulation of alterations in oncogenes and tumor suppressor genes. Tumor suppressors are classically defined as genes which contribute to tumorigenesis if their function is lost. Genetic or epigenetic alterations inactivating such genes may arise during somatic cell divisions or alternatively may be inherited from a parent. One notable exception to this rule is the BRCA1 tumor suppressor that predisposes to hereditary breast cancer when lost. Genetic alterations of this gene are hardly ever observed in sporadic breast cancer, while individuals harboring a germline mutation readily accumulate a second alteration inactivating the remaining allele--a finding which represents a conundrum in cancer genetics. In this paper, we present a novel mathematical framework of sporadic and hereditary breast tumorigenesis. We study the dynamics of genetic alterations driving breast tumorigenesis and explore those scenarios which can explain the absence of somatic BRCA1 alterations while replicating all other disease statistics. Our results support the existence of a heterozygous phenotype of BRCA1 and suggest that the loss of one BRCA1 allele may suppress the fitness advantage caused by the inactivation of other tumor suppressor genes. This paper contributes to the mathematical investigation of breast tumorigenesis.Copyright © 2011 Elsevier Ltd. All rights reserved. -
Hambardzumyan D, Cheng YK, Haeno H, Holland EC, Michor F. 2011. The probable cell of origin of NF1- and PDGF-driven glioblastomas. PloS one. 6(9):e24454. Pubmed: 21931722 DOI:10.1371/journal.pone.0024454 Hambardzumyan D, Cheng YK, Haeno H, Holland EC, Michor F. 2011. The probable cell of origin of NF1- and PDGF-driven glioblastomas. PloS one. 6(9):e24454. Pubmed: 21931722 DOI:10.1371/journal.pone.0024454 Primary glioblastomas are subdivided into several molecular subtypes. There is an ongoing debate over the cell of origin for these tumor types where some suggest a progenitor while others argue for a stem cell origin. Even within the same molecular subgroup, and using lineage tracing in mouse models, different groups have reached different conclusions. We addressed this problem from a combined mathematical modeling and experimental standpoint. We designed a novel mathematical framework to identify the most likely cells of origin of two glioma subtypes. Our mathematical model of the unperturbed in vivo system predicts that if a genetic event contributing to tumor initiation imparts symmetric self-renewing cell division (such as PDGF overexpression), then the cell of origin is a transit amplifier. Otherwise, the initiating mutations arise in stem cells. The mathematical framework was validated with the RCAS/tv-a system of somatic gene transfer in mice. We demonstrated that PDGF-induced gliomas can be derived from GFAP-expressing cells of the subventricular zone or the cortex (reactive astrocytes), thus validating the predictions of our mathematical model. This interdisciplinary approach allowed us to determine the likelihood that individual cell types serve as the cells of origin of gliomas in an unperturbed system. -
Foo J, Leder K, Michor F. 2011. Stochastic dynamics of cancer initiation. Physical biology. 8(1):015002. Pubmed: 21301064 DOI:10.1088/1478-3975/8/1/015002 Foo J, Leder K, Michor F. 2011. Stochastic dynamics of cancer initiation. Physical biology. 8(1):015002. Pubmed: 21301064 DOI:10.1088/1478-3975/8/1/015002 Most human cancer types result from the accumulation of multiple genetic and epigenetic alterations in a single cell. Once the first change (or changes) have arisen, tumorigenesis is initiated and the subsequent emergence of additional alterations drives progression to more aggressive and ultimately invasive phenotypes. Elucidation of the dynamics of cancer initiation is of importance for an understanding of tumor evolution and cancer incidence data. In this paper, we develop a novel mathematical framework to study the processes of cancer initiation. Cells at risk of accumulating oncogenic mutations are organized into small compartments of cells and proliferate according to a stochastic process. During each cell division, an (epi)genetic alteration may arise which leads to a random fitness change, drawn from a probability distribution. Cancer is initiated when a cell gains a fitness sufficiently high to escape from the homeostatic mechanisms of the cell compartment. To investigate cancer initiation during a human lifetime, a 'race' between this fitness process and the aging process of the patient is considered; the latter is modeled as a second stochastic Markov process in an aging dimension. This model allows us to investigate the dynamics of cancer initiation and its dependence on the mutational fitness distribution. Our framework also provides a methodology to assess the effects of different life expectancy distributions on lifetime cancer incidence. We apply this methodology to colorectal tumorigenesis while considering life expectancy data of the US population to inform the dynamics of the aging process. We study how the probability of cancer initiation prior to death, the time until cancer initiation, and the mutational profile of the cancer-initiating cell depends on the shape of the mutational fitness distribution and life expectancy of the population. -
Michor F, Liphardt J, Ferrari M, Widom J. 2011. What does physics have to do with cancer?. Nature reviews. Cancer. 11(9):657-70. Pubmed: 21850037 DOI:10.1038/nrc3092 Michor F, Liphardt J, Ferrari M, Widom J. 2011. What does physics have to do with cancer?. Nature reviews. Cancer. 11(9):657-70. Pubmed: 21850037 DOI:10.1038/nrc3092 Large-scale cancer genomics, proteomics and RNA-sequencing efforts are currently mapping in fine detail the genetic and biochemical alterations that occur in cancer. However, it is becoming clear that it is difficult to integrate and interpret these data and to translate them into treatments. This difficulty is compounded by the recognition that cancer cells evolve, and that initiation, progression and metastasis are influenced by a wide variety of factors. To help tackle this challenge, the US National Cancer Institute Physical Sciences-Oncology Centers initiative is bringing together physicists, cancer biologists, chemists, mathematicians and engineers. How are we beginning to address cancer from the perspective of the physical sciences? -
Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. 2011. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood. 118(13):3559-69. Pubmed: 21828137 DOI:10.1182/blood-2011-06-357996 Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. 2011. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood. 118(13):3559-69. Pubmed: 21828137 DOI:10.1182/blood-2011-06-357996 The phenotype of germinal center (GC) B cells includes the unique ability to tolerate rapid proliferation and the mutagenic actions of activation induced cytosine deaminase (AICDA). Given the importance of epigenetic patterning in determining cellular phenotypes, we examined DNA methylation and the role of DNA methyltransferases in the formation of GCs. DNA methylation profiling revealed a marked shift in DNA methylation patterning in GC B cells versus resting/naive B cells. This shift included significant differential methylation of 235 genes, with concordant inverse changes in gene expression affecting most notably genes of the NFkB and MAP kinase signaling pathways. GC B cells were predominantly hypomethylated compared with naive B cells and AICDA binding sites were highly overrepresented among hypomethylated loci. GC B cells also exhibited greater DNA methylation heterogeneity than naive B cells. Among DNA methyltransferases (DNMTs), only DNMT1 was significantly up-regulated in GC B cells. Dnmt1 hypomorphic mice displayed deficient GC formation and treatment of mice with the DNA methyltransferase inhibitor decitabine resulted in failure to form GCs after immune stimulation. Notably, the GC B cells of Dnmt1 hypomorphic animals showed evidence of increased DNA damage, suggesting dual roles for DNMT1 in DNA methylation and double strand DNA break repair. -
Durrett R, Foo J, Leder K, Mayberry J, Michor F. 2011. Intratumor heterogeneity in evolutionary models of tumor progression. Genetics. 188(2):461-77. Pubmed: 21406679 DOI:10.1534/genetics.110.125724 Durrett R, Foo J, Leder K, Mayberry J, Michor F. 2011. Intratumor heterogeneity in evolutionary models of tumor progression. Genetics. 188(2):461-77. Pubmed: 21406679 DOI:10.1534/genetics.110.125724 With rare exceptions, human tumors arise from single cells that have accumulated the necessary number and types of heritable alterations. Each such cell leads to dysregulated growth and eventually the formation of a tumor. Despite their monoclonal origin, at the time of diagnosis most tumors show a striking amount of intratumor heterogeneity in all measurable phenotypes; such heterogeneity has implications for diagnosis, treatment efficacy, and the identification of drug targets. An understanding of the extent and evolution of intratumor heterogeneity is therefore of direct clinical importance. In this article, we investigate the evolutionary dynamics of heterogeneity arising during exponential expansion of a tumor cell population, in which heritable alterations confer random fitness changes to cells. We obtain analytical estimates for the extent of heterogeneity and quantify the effects of system parameters on this tumor trait. Our work contributes to a mathematical understanding of intratumor heterogeneity and is also applicable to organisms like bacteria, agricultural pests, and other microbes. -
De S, Michor F. 2011. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nature structural & molecular biology. 18(8):950-5. Pubmed: 21725294 DOI:10.1038/nsmb.2089 De S, Michor F. 2011. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nature structural & molecular biology. 18(8):950-5. Pubmed: 21725294 DOI:10.1038/nsmb.2089 An unstable genome is a hallmark of many cancers. It is unclear, however, whether some mutagenic features driving somatic alterations in cancer are encoded in the genome sequence and whether they can operate in a tissue-specific manner. We performed a genome-wide analysis of 663,446 DNA breakpoints associated with somatic copy-number alterations (SCNAs) from 2,792 cancer samples classified into 26 cancer types. Many SCNA breakpoints are spatially clustered in cancer genomes. We observed a significant enrichment for G-quadruplex sequences (G4s) in the vicinity of SCNA breakpoints and established that SCNAs show a strand bias consistent with G4-mediated structural alterations. Notably, abnormal hypomethylation near G4s-rich regions is a common signature for many SCNA breakpoint hotspots. We propose a mechanistic hypothesis that abnormal hypomethylation in genomic regions enriched for G4s acts as a mutagenic factor driving tissue-specific mutational landscapes in cancer. -
Tang M, Gonen M, Quintas-Cardama A, Cortes J, Kantarjian H, Field C, Hughes TP, Branford S, Michor F. 2011. Dynamics of chronic myeloid leukemia response to long-term targeted therapy reveal treatment effects on leukemic stem cells. Blood. 118(6):1622-31. Pubmed: 21653938 DOI:10.1182/blood-2011-02-339267 Tang M, Gonen M, Quintas-Cardama A, Cortes J, Kantarjian H, Field C, Hughes TP, Branford S, Michor F. 2011. Dynamics of chronic myeloid leukemia response to long-term targeted therapy reveal treatment effects on leukemic stem cells. Blood. 118(6):1622-31. Pubmed: 21653938 DOI:10.1182/blood-2011-02-339267 Treatment of chronic myeloid leukemia (CML) with the tyrosine kinase inhibitors (TKIs) imatinib mesylate and nilotinib represents a successful application of molecularly targeted anticancer therapy. However, the effect of TKIs on leukemic stem cells remains incompletely understood. On the basis of a statistical modeling approach that used the 10-year imatinib mesylate treatment response of patients with CML and a patient cohort receiving first-line nilotinib therapy, we found that successful long-term therapy results in a triphasic exponential decline of BCR-ABL1 transcripts in many patients. Within our framework, the first slope of -0.052 ± 0.018 (imatinib mesylate) and -0.042 ± 0.015 (nilotinib) per day represents the turnover rate of leukemic differentiated cells, whereas the second slope of -0.0057 ± 0.0038 (imatinib mesylate) and -0.0019 ± 0.0013 (nilotinib) per day represents the turnover rate of leukemic progenitor cells. The third slope allows an inference of the behavior of immature leukemic cells, potentially stem cells. This third slope is negative in most patients, positive in others, and not observable in some patients. This variability in response may be because of insufficient follow-up, missing data, disease heterogeneity, inconsistent compliance to drug, or acquired resistance. Our approach suggests that long-term TKI therapy may reduce the abundance of leukemic stem cells in some patients. -
Chmielecki J, Foo J, Oxnard GR, Hutchinson K, Ohashi K, Somwar R, Wang L, Amato KR, Arcila M, Sos ML, Socci ND, Viale A, de Stanchina E, Ginsberg MS, Thomas RK, Kris MG, Inoue A, Ladanyi M, Miller VA, Michor F, Pao W. 2011. Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling. Science translational medicine. 3(90):90ra59. Pubmed: 21734175 DOI:10.1126/scitranslmed.3002356 Chmielecki J, Foo J, Oxnard GR, Hutchinson K, Ohashi K, Somwar R, Wang L, Amato KR, Arcila M, Sos ML, Socci ND, Viale A, de Stanchina E, Ginsberg MS, Thomas RK, Kris MG, Inoue A, Ladanyi M, Miller VA, Michor F, Pao W. 2011. Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling. Science translational medicine. 3(90):90ra59. Pubmed: 21734175 DOI:10.1126/scitranslmed.3002356 Non-small cell lung cancers (NSCLCs) that harbor mutations within the epidermal growth factor receptor (EGFR) gene are sensitive to the tyrosine kinase inhibitors (TKIs) gefitinib and erlotinib. Unfortunately, all patients treated with these drugs will acquire resistance, most commonly as a result of a secondary mutation within EGFR (T790M). Because both drugs were developed to target wild-type EGFR, we hypothesized that current dosing schedules were not optimized for mutant EGFR or to prevent resistance. To investigate this further, we developed isogenic TKI-sensitive and TKI-resistant pairs of cell lines that mimic the behavior of human tumors. We determined that the drug-sensitive and drug-resistant EGFR-mutant cells exhibited differential growth kinetics, with the drug-resistant cells showing slower growth. We incorporated these data into evolutionary mathematical cancer models with constraints derived from clinical data sets. This modeling predicted alternative therapeutic strategies that could prolong the clinical benefit of TKIs against EGFR-mutant NSCLCs by delaying the development of resistance. -
Iwasa Y, Michor F. 2011. Evolutionary dynamics of intratumor heterogeneity. PloS one. 6(3):e17866. Pubmed: 21479218 DOI:10.1371/journal.pone.0017866 Iwasa Y, Michor F. 2011. Evolutionary dynamics of intratumor heterogeneity. PloS one. 6(3):e17866. Pubmed: 21479218 DOI:10.1371/journal.pone.0017866 Intraneoplastic diversity in human tumors is a widespread phenomenon of critical importance for tumor progression and the response to therapeutic intervention. Insights into the evolutionary events that control tumor heterogeneity would be a major breakthrough in our comprehension of cancer development and could lead to more effective prevention methods and therapies. In this paper, we design an evolutionary mathematical framework to study the dynamics of heterogeneity over time. We consider specific situations arising during tumorigenesis, such as the emergence of positively selected mutations ("drivers") and the accumulation of neutral variation ("passengers"). We perform exact computer simulations of the emergence of diverse tumor cell clones over time, and derive analytical estimates for the extent of heterogeneity within a population of cancer cells. Our methods contribute to a quantitative understanding of tumor heterogeneity and the impact of heritable alterations on this tumor trait. -
Leder K, Foo J, Skaggs B, Gorre M, Sawyers CL, Michor F. 2011. Fitness conferred by BCR-ABL kinase domain mutations determines the risk of pre-existing resistance in chronic myeloid leukemia. PloS one. 6(11):e27682. Pubmed: 22140458 DOI:10.1371/journal.pone.0027682 Leder K, Foo J, Skaggs B, Gorre M, Sawyers CL, Michor F. 2011. Fitness conferred by BCR-ABL kinase domain mutations determines the risk of pre-existing resistance in chronic myeloid leukemia. PloS one. 6(11):e27682. Pubmed: 22140458 DOI:10.1371/journal.pone.0027682 Chronic myeloid leukemia (CML) is the first human malignancy to be successfully treated with a small molecule inhibitor, imatinib, targeting a mutant oncoprotein (BCR-ABL). Despite its successes, acquired resistance to imatinib leads to reduced drug efficacy and frequent progression of disease. Understanding the characteristics of pre-existing resistant cells is important for evaluating the benefits of first-line combination therapy with second generation inhibitors. However, due to limitations of assay sensitivity, determining the existence and characteristics of resistant cell clones at the start of therapy is difficult. Here we combined a mathematical modeling approach using branching processes with experimental data on the fitness changes (i.e., changes in net reproductive rate) conferred by BCR-ABL kinase domain mutations to investigate the likelihood, composition, and diversity of pre-existing resistance. Furthermore, we studied the impact of these factors on the response to tyrosine kinase inhibitors. Our approach predicts that in most patients, there is at most one resistant clone present at the time of diagnosis of their disease. Interestingly, patients are no more likely to harbor the most aggressive, pan-resistant T315I mutation than any other resistance mutation; however, T315I cells on average establish larger-sized clones at the time of diagnosis. We established that for patients diagnosed late, the relative benefit of combination therapy over monotherapy with imatinib is significant, while this benefit is modest for patients with a typically early diagnosis time. These findings, after pre-clinical validation, will have implications for the clinical management of CML: we recommend that patients with advanced-phase disease be treated with combination therapy with at least two tyrosine kinase inhibitors. -
De S, Michor F. 2011. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nature biotechnology. 29(12):1103-8. Pubmed: 22101487 DOI:10.1038/nbt.2030 De S, Michor F. 2011. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nature biotechnology. 29(12):1103-8. Pubmed: 22101487 DOI:10.1038/nbt.2030 Somatic copy-number alterations (SCNA) are a hallmark of many cancer types, but the mechanistic basis underlying their genome-wide patterns remains incompletely understood. Here we integrate data on DNA replication timing, long-range interactions between genomic material, and 331,724 SCNAs from 2,792 cancer samples classified into 26 cancer types. We report that genomic regions of similar replication timing are clustered spatially in the nucleus, that the two boundaries of SCNAs tend to be found in such regions, and that regions replicated early and late display distinct patterns of frequencies of SCNA boundaries, SCNA size and a preference for deletions over insertions. We show that long-range interaction and replication timing data alone can identify a significant proportion of SCNAs in an independent test data set. We propose a model for the generation of SCNAs in cancer, suggesting that data on spatial proximity of regions replicating at the same time can be used to predict the mutational landscapes of cancer genomes. -
Mumenthaler SM, Foo J, Leder K, Choi NC, Agus DB, Pao W, Mallick P, Michor F. 2011. Evolutionary modeling of combination treatment strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer. Molecular pharmaceutics. 8(6):2069-79. Pubmed: 21995722 DOI:10.1021/mp200270v Mumenthaler SM, Foo J, Leder K, Choi NC, Agus DB, Pao W, Mallick P, Michor F. 2011. Evolutionary modeling of combination treatment strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer. Molecular pharmaceutics. 8(6):2069-79. Pubmed: 21995722 DOI:10.1021/mp200270v Many initially successful anticancer therapies lose effectiveness over time, and eventually, cancer cells acquire resistance to the therapy. Acquired resistance remains a major obstacle to improving remission rates and achieving prolonged disease-free survival. Consequently, novel approaches to overcome or prevent resistance are of significant clinical importance. There has been considerable interest in treating non-small cell lung cancer (NSCLC) with combinations of EGFR-targeted therapeutics (e.g., erlotinib) and cytotoxic therapeutics (e.g., paclitaxel); however, acquired resistance to erlotinib, driven by a variety of mechanisms, remains an obstacle to treatment success. In about 50% of cases, resistance is due to a T790M point mutation in EGFR, and T790M-containing cells ultimately dominate the tumor composition and lead to tumor regrowth. We employed a combined experimental and mathematical modeling-based approach to identify treatment strategies that impede the outgrowth of primary T790M-mediated resistance in NSCLC populations. Our mathematical model predicts the population dynamics of mixtures of sensitive and resistant cells, thereby describing how the tumor composition, initial fraction of resistant cells, and degree of selective pressure influence the time until progression of disease. Model development relied upon quantitative experimental measurements of cell proliferation and death using a novel microscopy approach. Using this approach, we systematically explored the space of combination treatment strategies and demonstrated that optimally timed sequential strategies yielded large improvements in survival outcome relative to monotherapies at the same concentrations. Our investigations revealed regions of the treatment space in which low-dose sequential combination strategies, after preclinical validation, may lead to a tumor reduction and improved survival outcome for patients with T790M-mediated resistance. -
Klinakis A, Lobry C, Abdel-Wahab O, Oh P, Haeno H, Buonamici S, van De Walle I, Cathelin S, Trimarchi T, Araldi E, Liu C, Ibrahim S, Beran M, Zavadil J, Efstratiadis A, Taghon T, Michor F, Levine RL, Aifantis I. 2011. A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia. Nature. 473(7346):230-3. Pubmed: 21562564 DOI:10.1038/nature09999 Klinakis A, Lobry C, Abdel-Wahab O, Oh P, Haeno H, Buonamici S, van De Walle I, Cathelin S, Trimarchi T, Araldi E, Liu C, Ibrahim S, Beran M, Zavadil J, Efstratiadis A, Taghon T, Michor F, Levine RL, Aifantis I. 2011. A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia. Nature. 473(7346):230-3. Pubmed: 21562564 DOI:10.1038/nature09999 Notch signalling is a central regulator of differentiation in a variety of organisms and tissue types. Its activity is controlled by the multi-subunit γ-secretase (γSE) complex. Although Notch signalling can play both oncogenic and tumour-suppressor roles in solid tumours, in the haematopoietic system it is exclusively oncogenic, notably in T-cell acute lymphoblastic leukaemia, a disease characterized by Notch1-activating mutations. Here we identify novel somatic-inactivating Notch pathway mutations in a fraction of patients with chronic myelomonocytic leukaemia (CMML). Inactivation of Notch signalling in mouse haematopoietic stem cells (HSCs) results in an aberrant accumulation of granulocyte/monocyte progenitors (GMPs), extramedullary haematopoieisis and the induction of CMML-like disease. Transcriptome analysis revealed that Notch signalling regulates an extensive myelomonocytic-specific gene signature, through the direct suppression of gene transcription by the Notch target Hes1. Our studies identify a novel role for Notch signalling during early haematopoietic stem cell differentiation and suggest that the Notch pathway can play both tumour-promoting and -suppressive roles within the same tissue. 2010
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Leder K, Holland EC, Michor F. 2010. The therapeutic implications of plasticity of the cancer stem cell phenotype. PloS one. 5(12):e14366. Pubmed: 21179426 DOI:10.1371/journal.pone.0014366 Leder K, Holland EC, Michor F. 2010. The therapeutic implications of plasticity of the cancer stem cell phenotype. PloS one. 5(12):e14366. Pubmed: 21179426 DOI:10.1371/journal.pone.0014366 The cancer stem cell hypothesis suggests that tumors contain a small population of cancer cells that have the ability to undergo symmetric self-renewing cell division. In tumors that follow this model, cancer stem cells produce various kinds of specified precursors that divide a limited number of times before terminally differentiating or undergoing apoptosis. As cells within the tumor mature, they become progressively more restricted in the cell types to which they can give rise. However, in some tumor types, the presence of certain extra- or intracellular signals can induce committed cancer progenitors to revert to a multipotential cancer stem cell state. In this paper, we design a novel mathematical model to investigate the dynamics of tumor progression in such situations, and study the implications of a reversible cancer stem cell phenotype for therapeutic interventions. We find that higher levels of dedifferentiation substantially reduce the effectiveness of therapy directed at cancer stem cells by leading to higher rates of resistance. We conclude that plasticity of the cancer stem cell phenotype is an important determinant of the prognosis of tumors. This model represents the first mathematical investigation of this tumor trait and contributes to a quantitative understanding of cancer. -
Michor F, Polyak K. 2010. The origins and implications of intratumor heterogeneity. Cancer prevention research (Philadelphia, Pa.). 3(11):1361-4. Pubmed: 20959519 DOI:10.1158/1940-6207.CAPR-10-0234 Michor F, Polyak K. 2010. The origins and implications of intratumor heterogeneity. Cancer prevention research (Philadelphia, Pa.). 3(11):1361-4. Pubmed: 20959519 DOI:10.1158/1940-6207.CAPR-10-0234 Human tumors often display startling intratumor heterogeneity in various features including histology, gene expression, genotype, and metastatic and proliferative potential. This phenotypic and genetic heterogeneity plays an important role in neoplasia, cancer progression, and therapeutic resistance. In this issue of the journal (beginning on page 1388), Merlo et al. report their use of molecular data from 239 patients with Barrett's esophagus to evaluate the propensity of major diversity indices for predicting progression to esophageal adenocarcinoma. This work helps elucidate the implications of molecular heterogeneity for the evolution of neoplasia.©2010 AACR. -
Attolini CS, Cheng YK, Beroukhim R, Getz G, Abdel-Wahab O, Levine RL, Mellinghoff IK, Michor F. 2010. A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proceedings of the National Academy of Sciences of the United States of America. 107(41):17604-9. Pubmed: 20864632 DOI:10.1073/pnas.1009117107 Attolini CS, Cheng YK, Beroukhim R, Getz G, Abdel-Wahab O, Levine RL, Mellinghoff IK, Michor F. 2010. A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proceedings of the National Academy of Sciences of the United States of America. 107(41):17604-9. Pubmed: 20864632 DOI:10.1073/pnas.1009117107 Human cancer is caused by the accumulation of genetic alterations in cells. Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and represent promising targets for therapeutic intervention. Here we describe a computational approach, called Retracing the Evolutionary Steps in Cancer (RESIC), to deduce the temporal sequence of genetic events during tumorigenesis from cross-sectional genomic data of tumors at their fully transformed stage. When applied to a dataset of 70 advanced colorectal cancers, our algorithm accurately predicts the sequence of APC, KRAS, and TP53 mutations previously defined by analyzing tumors at different stages of colon cancer formation. We further validate the method with glioblastoma and leukemia sample data and then apply it to complex integrated genomics databases, finding that high-level EGFR amplification appears to be a late event in primary glioblastomas. RESIC represents the first evolutionary mathematical approach to identify the temporal sequence of mutations driving tumorigenesis and may be useful to guide the validation of candidate genes emerging from cancer genome surveys. -
Park SY, Gönen M, Kim HJ, Michor F, Polyak K. 2010. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. The Journal of clinical investigation. 120(2):636-44. Pubmed: 20101094 DOI:40724 Park SY, Gönen M, Kim HJ, Michor F, Polyak K. 2010. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. The Journal of clinical investigation. 120(2):636-44. Pubmed: 20101094 DOI:40724 Intratumor genetic heterogeneity is a key mechanism underlying tumor progression and therapeutic resistance. The prevailing model for explaining intratumor diversity, the clonal evolution model, has recently been challenged by proponents of the cancer stem cell hypothesis. To investigate this issue, we performed combined analyses of markers associated with cellular differentiation states and genotypic alterations in human breast carcinomas and evaluated diversity with ecological and evolutionary methods. Our analyses showed a high degree of genetic heterogeneity both within and between distinct tumor cell populations that were defined based on markers of cellular phenotypes including stem cell-like characteristics. In several tumors, stem cell-like and more-differentiated cancer cell populations were genetically distinct, leading us to question the validity of a simple differentiation hierarchy-based cancer stem cell model. The degree of diversity correlated with clinically relevant breast tumor subtypes and in some tumors was markedly different between the in situ and invasive cell populations. We also found that diversity measures were associated with clinical variables. Our findings highlight the importance of genetic diversity in intratumor heterogeneity and the value of analyzing tumors as distinct populations of cancer cells to more effectively plan treatments. -
Foo J, Michor F. 2010. Evolution of resistance to anti-cancer therapy during general dosing schedules. Journal of theoretical biology. 263(2):179-88. Pubmed: 20004211 DOI:10.1016/j.jtbi.2009.11.022 Foo J, Michor F. 2010. Evolution of resistance to anti-cancer therapy during general dosing schedules. Journal of theoretical biology. 263(2):179-88. Pubmed: 20004211 DOI:10.1016/j.jtbi.2009.11.022 Anti-cancer drugs targeted to specific oncogenic pathways have shown promising therapeutic results in the past few years; however, drug resistance remains an important obstacle for these therapies. Resistance to these drugs can emerge due to a variety of reasons including genetic or epigenetic changes which alter the binding site of the drug target, cellular metabolism or export mechanisms. Obtaining a better understanding of the evolution of resistant populations during therapy may enable the design of more effective therapeutic regimens which prevent or delay progression of disease due to resistance. In this paper, we use stochastic mathematical models to study the evolutionary dynamics of resistance under time-varying dosing schedules and pharmacokinetic effects. The populations of sensitive and resistant cells are modeled as multi-type non-homogeneous birth-death processes in which the drug concentration affects the birth and death rates of both the sensitive and resistant cell populations in continuous time. This flexible model allows us to consider the effects of generalized treatment strategies as well as detailed pharmacokinetic phenomena such as drug elimination and accumulation over multiple doses. We develop estimates for the probability of developing resistance and moments of the size of the resistant cell population. With these estimates, we optimize treatment schedules over a subspace of tolerated schedules to minimize the risk of disease progression due to resistance as well as locate ideal schedules for controlling the population size of resistant clones in situations where resistance is inevitable. Our methodology can be used to describe dynamics of resistance arising due to a single (epi)genetic alteration in any tumor type.Copyright 2009 Elsevier Ltd. All rights reserved. -
Danielson LS, Menendez S, Attolini CS, Guijarro MV, Bisogna M, Wei J, Socci ND, Levine DA, Michor F, Hernando E. 2010. A differentiation-based microRNA signature identifies leiomyosarcoma as a mesenchymal stem cell-related malignancy. The American journal of pathology. 177(2):908-17. Pubmed: 20558575 DOI:10.2353/ajpath.2010.091150 Danielson LS, Menendez S, Attolini CS, Guijarro MV, Bisogna M, Wei J, Socci ND, Levine DA, Michor F, Hernando E. 2010. A differentiation-based microRNA signature identifies leiomyosarcoma as a mesenchymal stem cell-related malignancy. The American journal of pathology. 177(2):908-17. Pubmed: 20558575 DOI:10.2353/ajpath.2010.091150 Smooth muscle (SM) is a spontaneously contractile tissue that provides physical support and function to organs such as the uterus. Uterine smooth muscle-related neoplasia comprise common well-differentiated benign lesions called leiomyomas (ULM), and rare, highly aggressive and pleomorphic tumors named leiomyosarcomas (ULMS). MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in normal cellular development and tissue homeostasis that can be used to accurately subclassify different tumor types. Here, we demonstrate that miRNAs are required for full smooth muscle cell (SMC) differentiation of bone marrow-derived human mesenchymal stem cells (hMSCs). We also report a miRNA signature associated with this process. Moreover, we show that this signature, along with miRNA profiles for ULMS and ULM, are able to subclassify tumors of smooth muscle origin along SM differentiation. Using multiple computational analyses, we determined that ULMS are more similar to hMSCs as opposed to ULM, which are linked with more mature SMCs and myometrium. Furthermore, a comparison of the SM differentiation and ULMS miRNA signatures identified miRNAs strictly associated with SM maturation or transformation, as well as those modulated in both processes indicating a possible dual role. These results support separate origins and/or divergent transformation pathways for ULM and ULMS, resulting in drastically different states of differentiation. In summary, this work expands on our knowledge of the regulation of SM differentiation and sarcoma pathogenesis. -
Durrett R, Foo J, Leder K, Mayberry J, Michor F. 2010. Evolutionary dynamics of tumor progression with random fitness values. Theoretical population biology. 78(1):54-66. Pubmed: 20488197 DOI:10.1016/j.tpb.2010.05.001 Durrett R, Foo J, Leder K, Mayberry J, Michor F. 2010. Evolutionary dynamics of tumor progression with random fitness values. Theoretical population biology. 78(1):54-66. Pubmed: 20488197 DOI:10.1016/j.tpb.2010.05.001 Most human tumors result from the accumulation of multiple genetic and epigenetic alterations in a single cell. Mutations that confer a fitness advantage to the cell are known as driver mutations and are causally related to tumorigenesis. Other mutations, however, do not change the phenotype of the cell or even decrease cellular fitness. While much experimental effort is being devoted to the identification of the functional effects of individual mutations, mathematical modeling of tumor progression generally considers constant fitness increments as mutations are accumulated. In this paper we study a mathematical model of tumor progression with random fitness increments. We analyze a multi-type branching process in which cells accumulate mutations whose fitness effects are chosen from a distribution. We determine the effect of the fitness distribution on the growth kinetics of the tumor. This work contributes to a quantitative understanding of the accumulation of mutations leading to cancer.Copyright 2010 Elsevier Inc. All rights reserved. -
Haeno H, Michor F. 2010. The evolution of tumor metastases during clonal expansion. Journal of theoretical biology. 263(1):30-44. Pubmed: 19917298 DOI:10.1016/j.jtbi.2009.11.005 Haeno H, Michor F. 2010. The evolution of tumor metastases during clonal expansion. Journal of theoretical biology. 263(1):30-44. Pubmed: 19917298 DOI:10.1016/j.jtbi.2009.11.005 Cancer is a leading cause of morbidity and mortality in many countries. Solid tumors generally initiate at one particular site called the primary tumor, but eventually disseminate and form new colonies in other organs. The development of such metastases greatly diminishes the potential for a cure of patients and is thought to represent the final stage of the multi-stage progression of human cancer. The concept of early metastatic dissemination, however, postulates that cancer cell spread might arise early during the development of a tumor. It is important to know whether metastases are present at diagnosis since this determines treatment strategies and outcome. In this paper, we design a stochastic mathematical model of the evolution of tumor metastases in an expanding cancer cell population. We calculate the probability of metastasis at a given time during tumor evolution, the expected number of metastatic sites, and the total number of cancer cells as well as metastasized cells. Furthermore, we investigate the effect of drug administration and tumor resection on these quantities and predict the survival time of cancer patients. The model presented in this paper allows us to determine the probability and number of metastases at diagnosis and to identify the optimum treatment strategy to maximally prolong survival of cancer patients.2009 Elsevier Ltd. All rights reserved. -
Riester M, Stephan-Otto Attolini C, Downey RJ, Singer S, Michor F. 2010. A differentiation-based phylogeny of cancer subtypes. PLoS computational biology. 6(5):e1000777. Pubmed: 20463876 DOI:10.1371/journal.pcbi.1000777 Riester M, Stephan-Otto Attolini C, Downey RJ, Singer S, Michor F. 2010. A differentiation-based phylogeny of cancer subtypes. PLoS computational biology. 6(5):e1000777. Pubmed: 20463876 DOI:10.1371/journal.pcbi.1000777 Histopathological classification of human tumors relies in part on the degree of differentiation of the tumor sample. To date, there is no objective systematic method to categorize tumor subtypes by maturation. In this paper, we introduce a novel computational algorithm to rank tumor subtypes according to the dissimilarity of their gene expression from that of stem cells and fully differentiated tissue, and thereby construct a phylogenetic tree of cancer. We validate our methodology with expression data of leukemia, breast cancer and liposarcoma subtypes and then apply it to a broader group of sarcomas. This ranking of tumor subtypes resulting from the application of our methodology allows the identification of genes correlated with differentiation and may help to identify novel therapeutic targets. Our algorithm represents the first phylogeny-based tool to analyze the differentiation status of human tumors. 2009
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Attolini CS, Michor F. 2009. Evolutionary theory of cancer. Annals of the New York Academy of Sciences. 1168:23-51. Pubmed: 19566702 DOI:10.1111/j.1749-6632.2009.04880.x Attolini CS, Michor F. 2009. Evolutionary theory of cancer. Annals of the New York Academy of Sciences. 1168:23-51. Pubmed: 19566702 DOI:10.1111/j.1749-6632.2009.04880.x As Theodosius Dobzhansky famously noted in 1973, "Nothing in biology makes sense except in the light of evolution," and cancer is no exception to this rule. Our understanding of cancer initiation, progression, treatment, and resistance has advanced considerably by regarding cancer as the product of evolutionary processes. Here we review the literature of mathematical models of cancer evolution and provide a synthesis and discussion of the field. -
Foo J, Drummond MW, Clarkson B, Holyoake T, Michor F. 2009. Eradication of chronic myeloid leukemia stem cells: a novel mathematical model predicts no therapeutic benefit of adding G-CSF to imatinib. PLoS computational biology. 5(9):e1000503. Pubmed: 19749982 DOI:10.1371/journal.pcbi.1000503 Foo J, Drummond MW, Clarkson B, Holyoake T, Michor F. 2009. Eradication of chronic myeloid leukemia stem cells: a novel mathematical model predicts no therapeutic benefit of adding G-CSF to imatinib. PLoS computational biology. 5(9):e1000503. Pubmed: 19749982 DOI:10.1371/journal.pcbi.1000503 Imatinib mesylate induces complete cytogenetic responses in patients with chronic myeloid leukemia (CML), yet many patients have detectable BCR-ABL transcripts in peripheral blood even after prolonged therapy. Bone marrow studies have shown that this residual disease resides within the stem cell compartment. Quiescence of leukemic stem cells has been suggested as a mechanism conferring insensitivity to imatinib, and exposure to the Granulocyte-Colony Stimulating Factor (G-CSF), together with imatinib, has led to a significant reduction in leukemic stem cells in vitro. In this paper, we design a novel mathematical model of stem cell quiescence to investigate the treatment response to imatinib and G-CSF. We find that the addition of G-CSF to an imatinib treatment protocol leads to observable effects only if the majority of leukemic stem cells are quiescent; otherwise it does not modulate the leukemic cell burden. The latter scenario is in agreement with clinical findings in a pilot study administering imatinib continuously or intermittently, with or without G-CSF (GIMI trial). Furthermore, our model predicts that the addition of G-CSF leads to a higher risk of resistance since it increases the production of cycling leukemic stem cells. Although the pilot study did not include enough patients to draw any conclusion with statistical significance, there were more cases of progression in the experimental arms as compared to continuous imatinib. Our results suggest that the additional use of G-CSF may be detrimental to patients in the clinic. -
Foo J, Michor F. 2009. Evolution of resistance to targeted anti-cancer therapies during continuous and pulsed administration strategies. PLoS computational biology. 5(11):e1000557. Pubmed: 19893626 DOI:10.1371/journal.pcbi.1000557 Foo J, Michor F. 2009. Evolution of resistance to targeted anti-cancer therapies during continuous and pulsed administration strategies. PLoS computational biology. 5(11):e1000557. Pubmed: 19893626 DOI:10.1371/journal.pcbi.1000557 The discovery of small molecules targeted to specific oncogenic pathways has revolutionized anti-cancer therapy. However, such therapy often fails due to the evolution of acquired resistance. One long-standing question in clinical cancer research is the identification of optimum therapeutic administration strategies so that the risk of resistance is minimized. In this paper, we investigate optimal drug dosing schedules to prevent, or at least delay, the emergence of resistance. We design and analyze a stochastic mathematical model describing the evolutionary dynamics of a tumor cell population during therapy. We consider drug resistance emerging due to a single (epi)genetic alteration and calculate the probability of resistance arising during specific dosing strategies. We then optimize treatment protocols such that the risk of resistance is minimal while considering drug toxicity and side effects as constraints. Our methodology can be used to identify optimum drug administration schedules to avoid resistance conferred by one (epi)genetic alteration for any cancer and treatment type. -
Haeno H, Levine RL, Gilliland DG, Michor F. 2009. A progenitor cell origin of myeloid malignancies. Proceedings of the National Academy of Sciences of the United States of America. 106(39):16616-21. Pubmed: 19805346 DOI:10.1073/pnas.0908107106 Haeno H, Levine RL, Gilliland DG, Michor F. 2009. A progenitor cell origin of myeloid malignancies. Proceedings of the National Academy of Sciences of the United States of America. 106(39):16616-21. Pubmed: 19805346 DOI:10.1073/pnas.0908107106 All cancers rely on cells that have properties of long-term self-renewal or "stemness" to maintain and propagate the tumor, but the cell of origin of most cancers is still unknown. Here, we design a stochastic mathematical model of hematopoietic stem and progenitor cells to study the evolutionary dynamics of cancer initiation. We consider different evolutionary pathways leading to cancer-initiating cells in JAK2V617F-positive myeloproliferative neoplasms (MPN): (i) the JAK2V617F mutation may arise in a stem cell; (ii) a progenitor cell may first acquire a mutation conferring self-renewal, followed by acquisition of the JAK2V617F mutation; (iii) the JAK2V617F mutation may first emerge in a progenitor cell, followed by a mutation conferring self-renewal; and (iv) a mutation conferring self-renewal to progenitors may arise in the stem cell population without causing a change in the stem cell's phenotype, followed by the JAK2V617F mutation emerging in a progenitor cell. We find mathematical evidence that a progenitor is the most likely cell of origin of JAK2V617F-mutant MPN. These results may also have relevance to other tumor types arising in tissues that are organized as a differentiation hierarchy. 2008
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Liso A, Castiglione F, Cappuccio A, Stracci F, Schlenk RF, Amadori S, Thiede C, Schnittger S, Valk PJ, Döhner K, Martelli MF, Schaich M, Krauter J, Ganser A, Martelli MP, Bolli N, Löwenberg B, Haferlach T, Ehninger G, Mandelli F, Döhner H, Michor F, Falini B. 2008. A one-mutation mathematical model can explain the age incidence of acute myeloid leukemia with mutated nucleophosmin (NPM1). Haematologica. 93(8):1219-26. Pubmed: 18603563 DOI:10.3324/haematol.13209 Liso A, Castiglione F, Cappuccio A, Stracci F, Schlenk RF, Amadori S, Thiede C, Schnittger S, Valk PJ, Döhner K, Martelli MF, Schaich M, Krauter J, Ganser A, Martelli MP, Bolli N, Löwenberg B, Haferlach T, Ehninger G, Mandelli F, Döhner H, Michor F, Falini B. 2008. A one-mutation mathematical model can explain the age incidence of acute myeloid leukemia with mutated nucleophosmin (NPM1). Haematologica. 93(8):1219-26. Pubmed: 18603563 DOI:10.3324/haematol.13209 Acute myeloid leukemia with mutated NPM1 gene and aberrant cytoplasmic expression of nucleophosmin (NPMc(+) acute myeloid leukemia) shows distinctive biological and clinical features. Experimental evidence of the oncogenic potential of the nucleophosmin mutant is, however, still lacking, and it is unclear whether other genetic lesion(s), e.g. FLT3 internal tandem duplication, cooperate with NPM1 mutations in acute myeloid leukemia development. An analysis of age-specific incidence, together with mathematical modeling of acute myeloid leukemia epidemiology, can help to uncover the number of genetic events needed to cause leukemia. We collected data on age at diagnosis of acute myeloid leukemia patients from five European Centers in Germany, The Netherlands and Italy, and determined the age-specific incidence of AML with mutated NPM1 (a total of 1,444 cases) for each country. Linear regression of the curves representing age-specific rates of diagnosis per year showed similar slopes of about 4 on a double logarithmic scale. We then adapted a previously designed mathematical model of hematopoietic tumorigenesis to analyze the age incidence of acute myeloid leukemia with mutated NPM1 and found that a one-mutation model can explain the incidence curve of this leukemia entity. This model fits with the hypothesis that NPMc(+) acute myeloid leukemia arises from an NPM1 mutation with haploinsufficiency of the wild-type NPM1 allele. -
Michor F. 2008. Mathematical models of cancer stem cells. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 26(17):2854-61. Pubmed: 18539964 DOI:10.1200/JCO.2007.15.2421 Michor F. 2008. Mathematical models of cancer stem cells. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 26(17):2854-61. Pubmed: 18539964 DOI:10.1200/JCO.2007.15.2421 Human cancers are thought to be sustained in their growth by a pathologic counterpart of normal adult stem cells: cancer stem cells. This concept was first developed in human myeloid leukemias and is today being extended to solid tumors such as breast and brain cancers. A quantitative understanding of cancer stem cells requires a mathematical framework to describe the dynamics of cancer initiation and progression, the response to treatment, and the evolution of resistance. In this review, I use chronic myeloid leukemia as an example to discuss how mathematical and computational techniques have been used to gain insights into the biology of cancer stem cells. 2007
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Dingli D, Traulsen A, Michor F. 2007. (A)symmetric stem cell replication and cancer. PLoS computational biology. 3(3):e53. Pubmed: 17367205 DOI:e53 Dingli D, Traulsen A, Michor F. 2007. (A)symmetric stem cell replication and cancer. PLoS computational biology. 3(3):e53. Pubmed: 17367205 DOI:e53 Most tissues in metazoans undergo continuous turnover due to cell death or epithelial shedding. Since cellular replication is associated with an inherent risk of mutagenesis, tissues are maintained by a small group of stem cells (SCs) that replicate slowly to maintain their own population and that give rise to differentiated cells. There is increasing evidence that many tumors are also maintained by a small population of cancer stem cells that may arise by mutations from normal SCs. SC replication can be either symmetric or asymmetric. The former can lead to expansion of the SC pool. We describe a simple model to evaluate the impact of (a)symmetric SC replication on the expansion of mutant SCs and to show that mutations that increase the probability of asymmetric replication can lead to rapid mutant SC expansion in the absence of a selective fitness advantage. Mutations in several genes can lead to this process and may be at the root of the carcinogenic process. -
Dingli D, Michor F, Antal T, Pacheco JM. 2007. The emergence of tumor metastases. Cancer biology & therapy. 6(3):383-90. Pubmed: 17312385 Dingli D, Michor F, Antal T, Pacheco JM. 2007. The emergence of tumor metastases. Cancer biology & therapy. 6(3):383-90. Pubmed: 17312385 The appearance of metastases is an ominous sign in the natural history of any malignant tumor. Their presence implies a high tumor burden and greatly decreases the probability of a cure. Metastasis development requires the evolution of tumor cells that can survive in an environment that is normally not supportive to their growth and such cells must leave the tumor to establish tumor niches elsewhere. The interactions between the appearance of cells with metastatic ability in the primary tumor and their exit from the tumor lead to complex dynamics that can be either beneficial or detrimental to the tumor. We develop a simple mathematical model to illustrate how the interplay between mutation rate and export probability affects the intratumoral dynamics of metastasis-enabled cells and the rate of metastases formation. -
Haeno H, Iwasa Y, Michor F. 2007. The evolution of two mutations during clonal expansion. Genetics. 177(4):2209-21. Pubmed: 18073428 Haeno H, Iwasa Y, Michor F. 2007. The evolution of two mutations during clonal expansion. Genetics. 177(4):2209-21. Pubmed: 18073428 Knudson's two-hit hypothesis proposes that two genetic changes in the RB1 gene are the rate-limiting steps of retinoblastoma. In the inherited form of this childhood eye cancer, only one mutation emerges during somatic cell divisions while in sporadic cases, both alleles of RB1 are inactivated in the growing retina. Sporadic retinoblastoma serves as an example of a situation in which two mutations are accumulated during clonal expansion of a cell population. Other examples include evolution of resistance against anticancer combination therapy and inactivation of both alleles of a metastasis-suppressor gene during tumor growth. In this article, we consider an exponentially growing population of cells that must evolve two mutations to (i) evade treatment, (ii) make a step toward (invasive) cancer, or (iii) display a disease phenotype. We calculate the probability that the population has evolved both mutations before it reaches a certain size. This probability depends on the rates at which the two mutations arise; the growth and death rates of cells carrying none, one, or both mutations; and the size the cell population reaches. Further, we develop a formula for the expected number of cells carrying both mutations when the final population size is reached. Our theory establishes an understanding of the dynamics of two mutations during clonal expansion. -
Michor F. 2007. Chronic myeloid leukemia blast crisis arises from progenitors. Stem cells (Dayton, Ohio). 25(5):1114-8. Pubmed: 17218393 Michor F. 2007. Chronic myeloid leukemia blast crisis arises from progenitors. Stem cells (Dayton, Ohio). 25(5):1114-8. Pubmed: 17218393 Chronic myeloid leukemia (CML) progresses through three distinct clinical stages: chronic phase, accelerated phase, and blast crisis. The progression to accelerated phase and blast crisis is driven by activation of oncogenes, inactivation of tumor suppressor genes, and/or amplification of the BCR-ABL fusion gene, which causes the chronic phase of the disease. The cell of origin of blast crisis is a subject of speculation. Here, I develop a simple mathematical model of CML blast crisis to investigate whether blasts arise from leukemic stem cells or more differentiated leukemic cells. I use data of patients treated with imatinib and previous agents to estimate the effects of therapy on the rate of progression. Imatinib reduces the progression rate 10-fold as compared with previous (ineffective) therapies. If blasts were produced by leukemic stem cells, there would be no difference in the rate of progression between patients treated with imatinib and previous therapies, because imatinib seems to be incapable of depleting leukemic stem cells. Imatinib does, however, deplete leukemic progenitors. Therefore, CML blasts are likely to arise from leukemic progenitors. Disclosure of potential conflicts of interest is found at the end of this article. -
Michor F. 2007. Quantitative approaches to analyzing imatinib-treated chronic myeloid leukemia. Trends in pharmacological sciences. 28(5):197-9. Pubmed: 17412430 Michor F. 2007. Quantitative approaches to analyzing imatinib-treated chronic myeloid leukemia. Trends in pharmacological sciences. 28(5):197-9. Pubmed: 17412430 Progress in understanding the genetic changes that drive tumorigenesis has enabled the development of molecularly targeted anticancer therapy. The first small molecule targeted to a specific protein was imatinib mesylate (Gleevec, STI571), which is used to treat chronic myeloid leukemia (CML). A recent article presents a computational model with which to study the treatment response in CML patients and investigates the effect that imatinib exerts on leukemic stem cells. Here, I discuss insights derived from this study and their implications for imatinib therapy against CML. 2006
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Michor F, Iwasa Y. 2006. Dynamics of metastasis suppressor gene inactivation. Journal of theoretical biology. 241(3):676-89. Pubmed: 16497335 Michor F, Iwasa Y. 2006. Dynamics of metastasis suppressor gene inactivation. Journal of theoretical biology. 241(3):676-89. Pubmed: 16497335 For most cancer cell types, the acquisition of metastatic ability leads to clinically incurable disease. Twelve metastasis suppressor genes (MSGs) have been identified that reduce the metastatic propensity of cancer cells. If these genes are inactivated in both alleles, metastatic ability is promoted. Here, we develop a mathematical model of the dynamics of MSG inactivation and calculate the expected number of metastases formed by a tumor. We analyse the effects of increased mutation rates and different fitness values of cells with one or two inactivated alleles on the ability of a tumor to form metastases. We find that mutations that are negatively selected in the main tumor are unlikely to be responsible for the majority of metastases produced by a tumor. Most metastases-causing mutations will be present in all (or most) cells in the main tumor. -
Iwasa Y, Nowak MA, Michor F. 2006. Evolution of resistance during clonal expansion. Genetics. 172(4):2557-66. Pubmed: 16636113 Iwasa Y, Nowak MA, Michor F. 2006. Evolution of resistance during clonal expansion. Genetics. 172(4):2557-66. Pubmed: 16636113 Acquired drug resistance is a major limitation for cancer therapy. Often, one genetic alteration suffices to confer resistance to an otherwise successful therapy. However, little is known about the dynamics of the emergence of resistant tumor cells. In this article, we consider an exponentially growing population starting from one cancer cell that is sensitive to therapy. Sensitive cancer cells can mutate into resistant ones, which have relative fitness alpha prior to therapy. In the special case of no cell death, our model converges to the one investigated by Luria and Delbrück. We calculate the probability of resistance and the mean number of resistant cells once the cancer has reached detection size M. The probability of resistance is an increasing function of the detection size M times the mutation rate u. If Mu << 1, then the expected number of resistant cells in cancers with resistance is independent of the mutation rate u and increases with M in proportion to M(1-1/alpha) for advantageous mutants with relative fitness alpha>1, to l nM for neutral mutants (alpha = 1), but converges to an upper limit for deleterious mutants (alpha<1). Further, the probability of resistance and the average number of resistant cells increase with the number of cell divisions in the history of the tumor. Hence a tumor subject to high rates of apoptosis will show a higher incidence of resistance than expected on its detection size only. -
Dingli D, Michor F. 2006. Successful therapy must eradicate cancer stem cells. Stem cells (Dayton, Ohio). 24(12):2603-10. Pubmed: 16931775 Dingli D, Michor F. 2006. Successful therapy must eradicate cancer stem cells. Stem cells (Dayton, Ohio). 24(12):2603-10. Pubmed: 16931775 Despite significant improvements in cancer therapy, tumor recurrence is frequent and can be due to a variety of mechanisms, including the evolution of resistance and tumor progression. Cancer stem cells have been postulated to maintain tumor growth similar to normal stem cells maintaining tissue homeostasis. Recently, the existence of these malignant stem cells has been proven for hematological as well as some solid tumors. Tumor stem cells are not targeted by standard therapy and might be responsible for treatment failure and tumor recurrence in many patients. We designed a simple mathematical model to demonstrate the importance of eliminating tumor stem cells. We explored different therapeutic scenarios to illustrate the properties required from novel therapeutic agents for successful tumor treatment. We show that successful therapy must eradicate tumor stem cells. -
Michor F, Iwasa Y, Nowak MA. 2006. The age incidence of chronic myeloid leukemia can be explained by a one-mutation model. Proceedings of the National Academy of Sciences of the United States of America. 103(40):14931-4. Pubmed: 17001000 Michor F, Iwasa Y, Nowak MA. 2006. The age incidence of chronic myeloid leukemia can be explained by a one-mutation model. Proceedings of the National Academy of Sciences of the United States of America. 103(40):14931-4. Pubmed: 17001000 Chronic myeloid leukemia (CML) is associated with the Philadelphia chromosome, which arises by a reciprocal translocation between chromosomes 9 and 22 and harbors the BCR-ABL fusion oncogene. It is unknown whether any other mutations are needed for the chronic phase of the disease. The CML incidence increases as a function of age with an exponent of approximately 3. A slope of 3 could indicate that there are two mutations, in addition to the Philadelphia translocation, that have not yet been discovered. In this work, we explore an alternative hypothesis: We study a model of cancer initiation requiring only a single mutation. A mutated cell has a net reproductive advantage over normal cells and, therefore, might give rise to clonal expansion. The cancer is detected with a probability that is proportional to the size of the mutated cell clone. This model has three waiting times: (i) the time until a mutated cell is produced, (ii) the time of clonal expansion, and (iii) the time until the clone is detected. Surprisingly, this simple process can give rise to cancer incidence curves with exponents up to 3. Therefore, the CML incidence data are consistent with the hypothesis that the Philadelphia translocation alone is sufficient to cause chronic phase CML. -
Abbott LH, Michor F. 2006. Mathematical models of targeted cancer therapy. British journal of cancer. 95(9):1136-41. Pubmed: 17031409 Abbott LH, Michor F. 2006. Mathematical models of targeted cancer therapy. British journal of cancer. 95(9):1136-41. Pubmed: 17031409 Improved understanding of the molecular underpinnings of cancer initiation and progression has led to the development of targeted cancer therapies. The importance of these new methods of cancer treatment necessitates further research into the dynamic interactions between cancer cells and therapeutic agents, as well as a means of analysing their relationship quantitatively. The present review outlines the application of mathematical modelling to the dynamics of targeted cancer therapy, focusing particular attention on chronic myeloid leukaemia and its treatment with imatinib (Glivec). -
Hauert C, Michor F, Nowak MA, Doebeli M. 2006. Synergy and discounting of cooperation in social dilemmas. Journal of theoretical biology. 239(2):195-202. Pubmed: 16242728 Hauert C, Michor F, Nowak MA, Doebeli M. 2006. Synergy and discounting of cooperation in social dilemmas. Journal of theoretical biology. 239(2):195-202. Pubmed: 16242728 The emergence and maintenance of cooperation by natural selection is an enduring conundrum in evolutionary biology, which has been studied using a variety of game theoretical models inspired by different biological situations. The most widely studied games are the Prisoner's Dilemma, the Snowdrift game and by-product mutualism for pairwise interactions, as well as Public Goods games in larger groups of interacting individuals. Here, we present a general framework for cooperation in social dilemmas in which all the traditional scenarios can be recovered as special cases. In social dilemmas, cooperators provide a benefit to the group at some cost, while defectors exploit the group by reaping the benefits without bearing the costs of cooperation. Using the concepts of discounting and synergy for describing how benefits accumulate when more than one cooperator is present in a group of interacting individuals, we recover the four basic scenarios of evolutionary dynamics given by (i) dominating defection, (ii) coexistence of defectors and cooperators, (iii) dominating cooperation and (iv) bi-stability, in which cooperators and defectors cannot invade each other. Generically, for groups of three or more interacting individuals further, more complex, dynamics can occur. Our framework provides the first unifying approach to model cooperation in different kinds of social dilemmas. -
Michor F, Nowak MA, Iwasa Y. 2006. Stochastic dynamics of metastasis formation. Journal of theoretical biology. 240(4):521-30. Pubmed: 16343545 Michor F, Nowak MA, Iwasa Y. 2006. Stochastic dynamics of metastasis formation. Journal of theoretical biology. 240(4):521-30. Pubmed: 16343545 Tumor metastasis accounts for the majority of deaths in cancer patients. The metastatic behavior of cancer cells is promoted by mutations in many genes, including activation of oncogenes such as RAS and MYC. Here, we develop a mathematical framework to analyse the dynamics of mutations enabling cells to metastasize. We consider situations in which one mutation is necessary to confer metastatic ability to the cell. We study different population sizes of the main tumor and different somatic fitness values of metastatic cells. We compare mutations that are positively selected in the main tumor with those that are neutral or negatively selected, but faster at forming metastases. We study whether metastatic potential is the property of all (or the majority of) cells in the main tumor or only the property of a small subset. Our theory shows how to calculate the expected number of metastases that are formed by a tumor. -
Michor F, Nowak MA, Iwasa Y. 2006. Evolution of resistance to cancer therapy. Current pharmaceutical design. 12(3):261-71. Pubmed: 16454743 Michor F, Nowak MA, Iwasa Y. 2006. Evolution of resistance to cancer therapy. Current pharmaceutical design. 12(3):261-71. Pubmed: 16454743 Acquired drug resistance is a major limitation for successful treatment of cancer. Resistance emerges due to drug exclusion, drug metabolism and alteration of the drug target by mutation or overexpression. Depending on therapy, the type of cancer and its stage, one or several genetic or epigenetic alterations are necessary to confer resistance to treatment. The fundamental question is the following: if a genetically diverse population of replicating cancer cells is subjected to chemotherapy that has the potential to eradicate it, what is the probability of emergence of resistance? Here, we review a general mathematical framework based on multi-type branching processes designed to study the dynamics of escape of replicating organisms from selection pressures. We apply the general model to evolution of resistance of cancer cells and discuss examples for diverse mechanisms of resistance. Our theory shows how to estimate the probability of success for any treatment regimen. -
Brumer Y, Michor F, Shakhnovich EI. 2006. Genetic instability and the quasispecies model. Journal of theoretical biology. 241(2):216-22. Pubmed: 16386760 Brumer Y, Michor F, Shakhnovich EI. 2006. Genetic instability and the quasispecies model. Journal of theoretical biology. 241(2):216-22. Pubmed: 16386760 Genetic instability is a defining characteristic of cancers. Microsatellite instability (MIN) leads to by elevated point mutation rates, whereas chromosomal instability (CIN) refers to increased rates of losing or gaining whole chromosomes or parts of chromosomes during cell division. CIN and MIN are, in general, mutually exclusive. The quasispecies model is a very successful theoretical framework for the study of evolution at high mutation rates. It predicts the existence of an experimentally verified error catastrophe. This catastrophe occurs when the mutation rates exceed a threshold value, the error threshold, above which replicative infidelity is incompatible with cell survival. We analyse the semiconservative quasispecies model of both MIN and CIN tumors. We consider the role of post-methylation DNA repair in tumor cells and demonstrate that DNA repair is fundamental to the nature of the error catastrophe in both types of tumors. We find that CIN introduces a plateau in the maximum viable mutation rate for a repair-free model, which does not exist in the case of MIN. This provides a plausible explanation for the mutual exclusivity of CIN and MIN. -
Nowak MA, Michor F, Iwasa Y. 2006. Genetic instability and clonal expansion. Journal of theoretical biology. 241(1):26-32. Pubmed: 16405914 Nowak MA, Michor F, Iwasa Y. 2006. Genetic instability and clonal expansion. Journal of theoretical biology. 241(1):26-32. Pubmed: 16405914 Inactivation of tumor suppressor genes can lead to clonal expansion. We study the evolutionary dynamics of this process and calculate the probability that inactivation of a tumor suppressor gene is preceded by mutations in genes that confer genetic instability. Unstable cells might have a slower rate of clonal expansion than stable cells because of an increased probability of generating lethal mutations or inducing apoptosis. We show that the different growth rates of genetically stable and unstable cells during clonal expansion represent, in general, only a small disadvantage for genetic instability. The intuitive reason for this conclusion is that robust clonal expansion, where cellular birth rates are significantly greater than death rates, occurs on a much faster time scale than waiting for those mutations that allow clonal expansion. Moreover, in special cases where clonal expansion is very slow, genetically unstable cells have a higher probability to accumulate additional mutations during clonal expansion that confer a selective advantage. Clonal expansion represents a major disadvantage for genetic instability only when inactivation of the tumor suppressor gene leads to a very small increase of the cellular reproductive rate that is cancelled by the increased mortality of unstable cells. 2005
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Michor F, Iwasa Y, Lengauer C, Nowak MA. 2005. Dynamics of colorectal cancer. Seminars in cancer biology. 15(6):484-93. Pubmed: 16055342 Michor F, Iwasa Y, Lengauer C, Nowak MA. 2005. Dynamics of colorectal cancer. Seminars in cancer biology. 15(6):484-93. Pubmed: 16055342 Colorectal cancer results from an accumulation of mutations in tumor suppressor genes and oncogenes. An additional defining characteristic of colorectal cancer is its genetic instability. Two main types of genetic instability have been identified. Microsatellite instability leads to an increased point mutation rate, whereas chromosomal instability refers to an enhanced rate of accumulating gross chromosomal aberrations. All colon cancer cell lines are genetically unstable. An interesting question is whether genetic instability arises early in tumorigenesis. An early emergence of genetic instability could drive most of the somatic evolution of cancer. Here, we review mathematical models of colorectal tumorigenesis and discuss the role of genetic instability. -
Iwasa Y, Michor F, Nowak MA. 2005. Virus evolution within patients increases pathogenicity. Journal of theoretical biology. 232(1):17-26. Pubmed: 15498589 Iwasa Y, Michor F, Nowak MA. 2005. Virus evolution within patients increases pathogenicity. Journal of theoretical biology. 232(1):17-26. Pubmed: 15498589 Viruses like the human immunodeficiency virus (HIV), the hepatitis B virus (HBV), the hepatitis C virus (HCV) and many others undergo numerous rounds of inaccurate reproduction within an infected host. The resulting viral quasispecies is heterogeneous and sensitive to any selection pressure. Here we extend earlier work by showing that for a wide class of models describing the interaction between the virus population and the immune system, virus evolution has a well-defined direction toward increased pathogenicity. In particular, we study virus-induced impairment of the immune response and certain cross-reactive stimulation of specific immune responses. For eight different mathematical models, we show that virus evolution reduces the equilibrium abundance of uninfected cells and increases the rate at which uninfected cells are infected. Thus, in general, virus evolution makes things worse. An idea for combating HIV infection, however, is constructing a virus mutant that could outcompete the existing infection without being pathogenic itself. -
Michor F, Iwasa Y, Vogelstein B, Lengauer C, Nowak MA. 2005. Can chromosomal instability initiate tumorigenesis?. Seminars in cancer biology. 15(1):43-9. Pubmed: 15613287 Michor F, Iwasa Y, Vogelstein B, Lengauer C, Nowak MA. 2005. Can chromosomal instability initiate tumorigenesis?. Seminars in cancer biology. 15(1):43-9. Pubmed: 15613287 Cancers result from the accumulation of inherited and somatic mutations in oncogenes and tumor suppressor genes. These genes encode proteins that function in growth regulatory and differentiation pathways. Mutations in those genes increase the net reproductive rate of cells. Chromosomal instability (CIN) is a feature of most human cancers. Mutations in CIN genes increase the rate at which whole chromosomes or large parts of chromosomes are lost or gained during cell division. CIN causes an imbalance in chromosome number (aneuploidy) and an enhanced rate of loss of heterozygosity, which is an important mechanism of inactivating tumor suppressor genes. A crucial question of cancer biology is whether CIN is an early event and thus a driving force of tumorigenesis. Here we discuss mathematical models of situations where inactivation of one or two tumor suppressor genes is required for tumorigenesis. If two tumor suppressor genes have to be inactivated in rate-limiting steps, then CIN is likely to emerge before the inactivation of the first tumor suppressor gene. -
Michor F. 2005. Chromosomal instability and human cancer. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 360(1455):631-5. Pubmed: 15897185 Michor F. 2005. Chromosomal instability and human cancer. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 360(1455):631-5. Pubmed: 15897185 Genetic instability is a defining feature of human cancer. The main type of genetic instability, chromosomal instability (CIN), enhances the rate of gross chromosomal changes during cell division. CIN is brought about by mutations of CIN genes, i.e. genes that are involved in maintaining the genomic integrity of the cell. A major question in cancer genetics is whether genetic instability is a cause and hence a driving force of tumorigenesis. A mathematical framework for studying the somatic evolution of cancer sheds light onto the causal relations between CIN and human cancer. -
Michor F, Hughes TP, Iwasa Y, Branford S, Shah NP, Sawyers CL, Nowak MA. 2005. Dynamics of chronic myeloid leukaemia. Nature. 435(7046):1267-70. Pubmed: 15988530 Michor F, Hughes TP, Iwasa Y, Branford S, Shah NP, Sawyers CL, Nowak MA. 2005. Dynamics of chronic myeloid leukaemia. Nature. 435(7046):1267-70. Pubmed: 15988530 The clinical success of the ABL tyrosine kinase inhibitor imatinib in chronic myeloid leukaemia (CML) serves as a model for molecularly targeted therapy of cancer, but at least two critical questions remain. Can imatinib eradicate leukaemic stem cells? What are the dynamics of relapse due to imatinib resistance, which is caused by mutations in the ABL kinase domain? The precise understanding of how imatinib exerts its therapeutic effect in CML and the ability to measure disease burden by quantitative polymerase chain reaction provide an opportunity to develop a mathematical approach. We find that a four-compartment model, based on the known biology of haematopoietic differentiation, can explain the kinetics of the molecular response to imatinib in a 169-patient data set. Successful therapy leads to a biphasic exponential decline of leukaemic cells. The first slope of 0.05 per day represents the turnover rate of differentiated leukaemic cells, while the second slope of 0.008 per day represents the turnover rate of leukaemic progenitors. The model suggests that imatinib is a potent inhibitor of the production of differentiated leukaemic cells, but does not deplete leukaemic stem cells. We calculate the probability of developing imatinib resistance mutations and estimate the time until detection of resistance. Our model provides the first quantitative insights into the in vivo kinetics of a human cancer. -
Iwasa Y, Michor F, Komarova NL, Nowak MA. 2005. Population genetics of tumor suppressor genes. Journal of theoretical biology. 233(1):15-23. Pubmed: 15615616 Iwasa Y, Michor F, Komarova NL, Nowak MA. 2005. Population genetics of tumor suppressor genes. Journal of theoretical biology. 233(1):15-23. Pubmed: 15615616 Cancer emerges when a single cell receives multiple mutations. For example, the inactivation of both alleles of a tumor suppressor gene (TSG) can imply a net reproductive advantage of the cell and might lead to clonal expansion. In this paper, we calculate the probability as a function of time that a population of cells has generated at least one cell with two inactivated alleles of a TSG. Different kinetic laws hold for small and large populations. The inactivation of the first allele can either be neutral or lead to a selective advantage or disadvantage. The inactivation of the first and of the second allele can occur at equal or different rates. Our calculations provide insights into basic aspects of population genetics determining cancer initiation and progression. 2004
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Nowak MA, Michor F, Komarova NL, Iwasa Y. 2004. Evolutionary dynamics of tumor suppressor gene inactivation. Proceedings of the National Academy of Sciences of the United States of America. 101(29):10635-8. Pubmed: 15252197 Nowak MA, Michor F, Komarova NL, Iwasa Y. 2004. Evolutionary dynamics of tumor suppressor gene inactivation. Proceedings of the National Academy of Sciences of the United States of America. 101(29):10635-8. Pubmed: 15252197 Tumor suppressor genes (TSGs) are important gatekeepers that protect against somatic evolution of cancer. Losing both alleles of a TSG in a single cell represents a step toward cancer. We study how the kinetics of TSG inactivation depends on the population size of cells and the mutation rates for the first and second hit. We calculate the probability as function of time that at least one cell has been generated with two inactivated alleles of a TSG. We find three different kinetic laws: in small, intermediate, and large populations, it takes, respectively, two, one, and zero rate-limiting steps to inactivate a TSG. We also study the effect of chromosomal and other genetic instabilities. Small lesions without genetic instability can take a very long time to inactivate the next TSG, whereas the same lesions with genetic instability pose a much greater risk for cancer progression. -
Iwasa Y, Michor F, Nowak M. 2004. Some basic properties of immune selection. Journal of theoretical biology. 229(2):179-88. Pubmed: 15207473 Iwasa Y, Michor F, Nowak M. 2004. Some basic properties of immune selection. Journal of theoretical biology. 229(2):179-88. Pubmed: 15207473 We analyze models for the evolutionary dynamics of viral or other infectious agents within a host. We study how the invasion of a new strain affects the composition and diversity of the viral population. We show that--under strain-specific immunity--the equilibrium abundance of uninfected cells declines during viral evolution. In addition, for cytotoxic immunity the absolute force of infection, and for non-cytotoxic immunity the absolute cellular virulence increases during viral evolution. We prove global stability by means of Lyapunov functions. These unidirectional trends of virus evolution under immune selection do not hold for general cross-reactive immune responses, which introduce frequency-dependent selection among viral strains. Therefore, appropriate cross-reactive immunity can lead to a viral evolution within a host which limits the extent of the disease. -
Jones NA, Wei X, Flower DR, Wong M, Michor F, Saag MS, Hahn BH, Nowak MA, Shaw GM, Borrow P. 2004. Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. The Journal of experimental medicine. 200(10):1243-56. Pubmed: 15545352 Jones NA, Wei X, Flower DR, Wong M, Michor F, Saag MS, Hahn BH, Nowak MA, Shaw GM, Borrow P. 2004. Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. The Journal of experimental medicine. 200(10):1243-56. Pubmed: 15545352 CD8+ cytotoxic T lymphocytes (CTLs) play an important role in containment of virus replication in primary human immunodeficiency virus (HIV) infection. HIV's ability to mutate to escape from CTL pressure is increasingly recognized; but comprehensive studies of escape from the CD8 T cell response in primary HIV infection are currently lacking. Here, we have fully characterized the primary CTL response to autologous virus Env, Gag, and Tat proteins in three patients, and investigated the extent, kinetics, and mechanisms of viral escape from epitope-specific components of the response. In all three individuals, we observed variation beginning within weeks of infection at epitope-containing sites in the viral quasispecies, which conferred escape by mechanisms including altered peptide presentation/recognition and altered antigen processing. The number of epitope-containing regions exhibiting evidence of early CTL escape ranged from 1 out of 21 in a subject who controlled viral replication effectively to 5 out of 7 in a subject who did not. Evaluation of the extent and kinetics of HIV-1 escape from >40 different epitope-specific CD8 T cell responses enabled analysis of factors determining escape and suggested that escape is restricted by costs to intrinsic viral fitness and by broad, codominant distribution of CTL-mediated pressure on viral replication. -
Michor F, Iwasa Y, Rajagopalan H, Lengauer C, Nowak MA. 2004. Linear model of colon cancer initiation. Cell cycle (Georgetown, Tex.). 3(3):358-62. Pubmed: 14726709 Michor F, Iwasa Y, Rajagopalan H, Lengauer C, Nowak MA. 2004. Linear model of colon cancer initiation. Cell cycle (Georgetown, Tex.). 3(3):358-62. Pubmed: 14726709 Cancer results if regulatory mechanisms of cell birth and death are disrupted. Colorectal tumorigenesis is initiated by somatic or inherited mutations in the APC tumor suppressor gene pathway. Several additional genetic hits in other tumor suppressor genes and oncogenes drive the progression from polyps to malignant, invasive cancer. The majority of colorectal cancers present chromosomal instability, CIN, which is caused by mutations in genes that are required to maintain chromosomal stability. A major question in cancer genetics is whether CIN is an early event and thus a driving force of tumor progression. We present a new mathematical model of colon cancer initiation assuming a linear flow from stem cells to differentiated cells to apoptosis. We study the consequences of mutations in different cell types and calculate the conditions for CIN to precede APC inactivation. We find that early emergence of CIN is very likely in colorectal tumorigenesis. -
Iwasa Y, Michor F, Nowak MA. 2004. Stochastic tunnels in evolutionary dynamics. Genetics. 166(3):1571-9. Pubmed: 15082570 Iwasa Y, Michor F, Nowak MA. 2004. Stochastic tunnels in evolutionary dynamics. Genetics. 166(3):1571-9. Pubmed: 15082570 We study a situation that arises in the somatic evolution of cancer. Consider a finite population of replicating cells and a sequence of mutations: type 0 can mutate to type 1, which can mutate to type 2. There is no back mutation. We start with a homogeneous population of type 0. Mutants of type 1 emerge and either become extinct or reach fixation. In both cases, they can generate type 2, which also can become extinct or reach fixation. If mutation rates are small compared to the inverse of the population size, then the stochastic dynamics can be described by transitions between homogeneous populations. A "stochastic tunnel" arises, when the population moves from all 0 to all 2 without ever being all 1. We calculate the exact rate of stochastic tunneling for the case when type 1 is as fit as type 0 or less fit. Type 2 has the highest fitness. We discuss implications for the elimination of tumor suppressor genes and the activation of genetic instability. Although our theory is developed for cancer genetics, stochastic tunnels are general phenomena that could arise in many circumstances. -
Michor F, Iwasa Y, Nowak MA. 2004. Dynamics of cancer progression. Nature reviews. Cancer. 4(3):197-205. Pubmed: 14993901 Michor F, Iwasa Y, Nowak MA. 2004. Dynamics of cancer progression. Nature reviews. Cancer. 4(3):197-205. Pubmed: 14993901 -
Iwasa Y, Michor F, Nowak MA. 2004. Evolutionary dynamics of invasion and escape. Journal of theoretical biology. 226(2):205-14. Pubmed: 14643190 Iwasa Y, Michor F, Nowak MA. 2004. Evolutionary dynamics of invasion and escape. Journal of theoretical biology. 226(2):205-14. Pubmed: 14643190 Whenever life wants to invade a new habitat or escape from a lethal selection pressure, some mutations may be necessary to yield sustainable replication. We imagine situations like (i) a parasite infecting a new host, (ii) a species trying to invade a new ecological niche, (iii) cancer cells escaping from chemotherapy, (iv) viruses or microbes evading anti-microbial therapy, and also (v) the repeated attempts of combinatorial chemistry in the very beginning of life to produce self-replicating molecules. All such seemingly unrelated situations have a common structure in terms of Darwinian dynamics: a replicator with a basic reproductive ratio less than one attempts to find some mutations that allow indefinite survival. We develop a general theory, based on multitype branching processes, to describe the evolutionary dynamics of invasion and escape. 2003
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Nowak MA, Michor F, Iwasa Y. 2003. The linear process of somatic evolution. Proceedings of the National Academy of Sciences of the United States of America. 100(25):14966-9. Pubmed: 14657359 Nowak MA, Michor F, Iwasa Y. 2003. The linear process of somatic evolution. Proceedings of the National Academy of Sciences of the United States of America. 100(25):14966-9. Pubmed: 14657359 Cancer is the consequence of an unwanted evolutionary process. Cells receive mutations that alter their phenotype. Especially dangerous are those mutations that increase the net reproductive rate of cells, thereby leading to neoplasia and later to cancer. The standard models of evolutionary dynamics consider well mixed populations of individuals in symmetric positions. Here we introduce a spatially explicit, asymmetric stochastic process that captures the essential architecture of evolutionary dynamics operating within tissues of multicellular organisms. The "linear process" has the property of cancelling out selective differences among cells yet retaining the protective function of apoptosis. This design can slow down the rate of somatic evolution dramatically and therefore delay the onset of cancer. -
Michor F, Frank SA, May RM, Iwasa Y, Nowak MA. 2003. Somatic selection for and against cancer. Journal of theoretical biology. 225(3):377-82. Pubmed: 14604590 Michor F, Frank SA, May RM, Iwasa Y, Nowak MA. 2003. Somatic selection for and against cancer. Journal of theoretical biology. 225(3):377-82. Pubmed: 14604590 In multicellular organisms, cells cooperate within a well-defined developmental program. Cancer is a breakdown of such cooperation: cells mutate to phenotypes of uncoordinated proliferation. We study basic principles of the architecture of solid tissues that influence the rate of cancer initiation. In particular, we explore how somatic selection acts to prevent or to promote cancer. Cells with mutations in oncogenes or tumor suppressor genes often have increased proliferation rates. Somatic selection increases their abundance and thus enhances the risk of cancer. Many potentially harmful mutations, however, increase the probability of triggering apoptosis and, hence, initially lead to cells with reduced net proliferation rates. Such cells are eliminated by somatic selection, which therefore also works to reduce the risk of cancer. We show that a tissue organization into small compartments avoids the rapid spread of mutations in oncogenes and tumor suppressor genes, but promotes genetic instability. In small compartments, genetic instability, which confers a selective disadvantage for the cell, can spread by random drift. If both deleterious and advantageous mutations participate in tumor initiation, then we find an intermediate optimum for the compartment size. -
Iwasa Y, Michor F, Nowak MA. 2003. Evolutionary dynamics of escape from biomedical intervention. Proceedings. Biological sciences. 270(1533):2573-8. Pubmed: 14728779 Iwasa Y, Michor F, Nowak MA. 2003. Evolutionary dynamics of escape from biomedical intervention. Proceedings. Biological sciences. 270(1533):2573-8. Pubmed: 14728779 Viruses, bacteria, eukaryotic parasites, cancer cells, agricultural pests and other inconvenient animates have an unfortunate tendency to escape from selection pressures that are meant to control them. Chemotherapy, anti-viral drugs or antibiotics fail because their targets do not hold still, but evolve resistance. A major problem in developing vaccines is that microbes evolve and escape from immune responses. The fundamental question is the following: if a genetically diverse population of replicating organisms is challenged with a selection pressure that has the potential to eradicate it, what is the probability that this population will produce escape mutants? Here, we use multi-type branching processes to describe the accumulation of mutants in independent lineages. We calculate escape dynamics for arbitrary mutation networks and fitness landscapes. Our theory shows how to estimate the probability of success or failure of biomedical intervention, such as drug treatment and vaccination, against rapidly evolving organisms. -
Michor F, Nowak MA, Frank SA, Iwasa Y. 2003. Stochastic elimination of cancer cells. Proceedings. Biological sciences. 270(1528):2017-24. Pubmed: 14561289 Michor F, Nowak MA, Frank SA, Iwasa Y. 2003. Stochastic elimination of cancer cells. Proceedings. Biological sciences. 270(1528):2017-24. Pubmed: 14561289 Tissues of multicellular organisms consist of stem cells and differentiated cells. Stem cells divide to produce new stem cells or differentiated cells. Differentiated cells divide to produce new differentiated cells. We show that such a tissue design can reduce the rate of fixation of mutations that increase the net proliferation rate of cells. It has, however, no consequence for the rate of fixation of neutral mutations. We calculate the optimum relative abundance of stem cells that minimizes the rate of generating cancer cells. There is a critical fraction of stem cell divisions that is required for a stochastic elimination ('wash out') of cancer cells. -
Michor F, Iwasa Y, Komarova NL, Nowak MA. 2003. Local regulation of homeostasis favors chromosomal instability. Current biology : CB. 13(7):581-4. Pubmed: 12676089 Michor F, Iwasa Y, Komarova NL, Nowak MA. 2003. Local regulation of homeostasis favors chromosomal instability. Current biology : CB. 13(7):581-4. Pubmed: 12676089 Tissues of long-lived multicellular organisms have to maintain a constant number of functioning cells for many years. This process is called homeostasis. Homeostasis breaks down when cells emerge with mutations in tumor suppressor genes or oncogenes. Such mutated cells can have increased net rates of proliferation, which is increased somatic fitness. We show that the best protection against such mutations is achieved when homeostasis is regulated locally via small compartments. Small compartments, on the other hand, allow the accumulation of cells with reduced somatic fitness. Cells with mutations conferring genetic instability normally have a reduced somatic fitness because they have an increased probability of producing deleterious mutations or triggering apoptosis. Thus, small compartments protect against mutations in tumor suppressor genes or oncogenes but promote the emergence of genetic instability. 2002
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Michor F, Nowak MA. 2002. Evolution: the good, the bad and the lonely. Nature. 419(6908):677, 679. Pubmed: 12384681 Michor F, Nowak MA. 2002. Evolution: the good, the bad and the lonely. Nature. 419(6908):677, 679. Pubmed: 12384681