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Publications in Review
- Jokhi V, Domínguez-Iturza N, Kim K, Shetty AS, Yuan W, Di Bella DJ, Abbate C, Oyler-Castrillo P, Jin X, Simmons S, Levin JZ, Brown JR, Arlotta P. Neuronal-class specific molecular cues drive differential myelination in the neocortex. 2024. bioRxiv. DOI:10.1101/2024.02.20.581268
Featured Publications
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2024. Brain Chimeroids reveal individual susceptibility to neurotoxic triggers. Nature. 631(8019):142-149. Pubmed: 38926573 DOI:10.1038/s41586-024-07578-8 Antón-Bolaños N, Faravelli I, Faits T, Andreadis S, Kastli R, Trattaro S, Adiconis X, Wei A, Sampath Kumar A, Di Bella DJ, Tegtmeyer M, Nehme R, Levin JZ, Regev A, Arlotta P. 2024. Brain Chimeroids reveal individual susceptibility to neurotoxic triggers. Nature. 631(8019):142-149. Pubmed: 38926573 DOI:10.1038/s41586-024-07578-8 Interindividual genetic variation affects the susceptibility to and progression of many diseases. However, efforts to study how individual human brains differ in normal development and disease phenotypes are limited by the paucity of faithful cellular human models, and the difficulty of scaling current systems to represent multiple people. Here we present human brain Chimeroids, a highly reproducible, multidonor human brain cortical organoid model generated by the co-development of cells from a panel of individual donors in a single organoid. By reaggregating cells from multiple single-donor organoids at the neural stem cell or neural progenitor cell stage, we generate Chimeroids in which each donor produces all cell lineages of the cerebral cortex, even when using pluripotent stem cell lines with notable growth biases. We used Chimeroids to investigate interindividual variation in the susceptibility to neurotoxic triggers that exhibit high clinical phenotypic variability: ethanol and the antiepileptic drug valproic acid. Individual donors varied in both the penetrance of the effect on target cell types, and the molecular phenotype within each affected cell type. Our results suggest that human genetic background may be an important mediator of neurotoxin susceptibility and introduce Chimeroids as a scalable system for high-throughput investigation of interindividual variation in processes of brain development and disease.© 2024. The Author(s), under exclusive licence to Springer Nature Limited. -
Ostrem BEL, Domínguez-Iturza N, Stogsdill JA, Faits T, Kim K, Levin JZ, Arlotta P. 2024. Fetal brain response to maternal inflammation requires microglia. Development (Cambridge, England). 151(10). Pubmed: 38775708 DOI:10.1242/dev.202252 Ostrem BEL, Domínguez-Iturza N, Stogsdill JA, Faits T, Kim K, Levin JZ, Arlotta P. 2024. Fetal brain response to maternal inflammation requires microglia. Development (Cambridge, England). 151(10). Pubmed: 38775708 DOI:10.1242/dev.202252 In utero infection and maternal inflammation can adversely impact fetal brain development. Maternal systemic illness, even in the absence of direct fetal brain infection, is associated with an increased risk of neuropsychiatric disorders in affected offspring. The cell types mediating the fetal brain response to maternal inflammation are largely unknown, hindering the development of novel treatment strategies. Here, we show that microglia, the resident phagocytes of the brain, highly express receptors for relevant pathogens and cytokines throughout embryonic development. Using a rodent maternal immune activation (MIA) model in which polyinosinic:polycytidylic acid is injected into pregnant mice, we demonstrate long-lasting transcriptional changes in fetal microglia that persist into postnatal life. We find that MIA induces widespread gene expression changes in neuronal and non-neuronal cells; importantly, these responses are abolished by selective genetic deletion of microglia, indicating that microglia are required for the transcriptional response of other cortical cell types to MIA. These findings demonstrate that microglia play a crucial durable role in the fetal response to maternal inflammation, and should be explored as potential therapeutic cell targets.© 2024. Published by The Company of Biologists Ltd. -
Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. 2024. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron. 112(13):2091-2111. Pubmed: 38754415 DOI:S0896-6273(24)00282-4 Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. 2024. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron. 112(13):2091-2111. Pubmed: 38754415 DOI:S0896-6273(24)00282-4 Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.Copyright © 2024 Elsevier Inc. All rights reserved. -
Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. Pubmed: 36179669 DOI:S0092-8674(22)01168-0 Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. Pubmed: 36179669 DOI:S0092-8674(22)01168-0 Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell types during organoid development, identify genes with predicted human-specific roles in lineage establishment, and uncover early transcriptional diversity of human callosal neurons. The findings validate this comprehensive atlas of human corticogenesis in vitro as a resource to prime investigation into the mechanisms of human cortical development.Copyright © 2022 Elsevier Inc. All rights reserved. -
Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P. 2022. Autism genes converge on asynchronous development of shared neuron classes. Nature. 602(7896):268-273. Pubmed: 35110736 DOI:10.1038/s41586-021-04358-6 Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P. 2022. Autism genes converge on asynchronous development of shared neuron classes. Nature. 602(7896):268-273. Pubmed: 35110736 DOI:10.1038/s41586-021-04358-6 Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes-SUV420H1 (also known as KMT5B), ARID1B and CHD8-in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages-γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons-but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology.© 2022. The Author(s), under exclusive licence to Springer Nature Limited.
All Publications
2025
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Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH, Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids and transplantation studies. Nature. 639(8054):315-320. Pubmed: 39653126 DOI:10.1038/s41586-024-08487-6 Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH, Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids and transplantation studies. Nature. 639(8054):315-320. Pubmed: 39653126 DOI:10.1038/s41586-024-08487-6 As the field of neural organoids and assembloids expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. In this Perspective, we present a framework for the experimental process that encompasses ensuring the quality and integrity of human pluripotent stem cells, characterizing and manipulating neural cells in vitro, transplantation techniques and considerations for modelling human development, evolution and disease. As with all scientific endeavours, we advocate for rigorous experimental designs tailored to explicit scientific questions as well as transparent methodologies and data sharing to provide useful knowledge for current research practices and for developing regulatory standards.© 2024. Springer Nature Limited. -
Mangena V, Chanoch-Myers R, Sartore R, Paulsen B, Gritsch S, Weisman H, Hara T, Breakefield XO, Breyne K, Regev A, Chung K, Arlotta P, Tirosh I, Suvà ML. 2025. Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer. Cancer discovery. 15(2):299-315. Pubmed: 39373549 DOI:10.1158/2159-8290.CD-23-1336 Mangena V, Chanoch-Myers R, Sartore R, Paulsen B, Gritsch S, Weisman H, Hara T, Breakefield XO, Breyne K, Regev A, Chung K, Arlotta P, Tirosh I, Suvà ML. 2025. Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer. Cancer discovery. 15(2):299-315. Pubmed: 39373549 DOI:10.1158/2159-8290.CD-23-1336 Glioblastoma (GBM) is characterized by heterogeneous malignant cells that are functionally integrated within the neuroglial microenvironment. In this study, we model this ecosystem by growing GBM into long-term cultured human cortical organoids that contain the major neuroglial cell types found in the cerebral cortex. Single-cell RNA sequencing analysis suggests that, compared with matched gliomasphere models, GBM cortical organoids more faithfully recapitulate the diversity and expression programs of malignant cell states found in patient tumors. Additionally, we observe widespread transfer of GBM transcripts and GFP to nonmalignant cells in the organoids. Mechanistically, this transfer involves extracellular vesicles and is biased toward defined GBM cell states and astroglia cell types. These results extend previous GBM organoid modeling efforts and suggest widespread intercellular transfer in the GBM neuroglial microenvironment. Significance: Models that recapitulate intercellular communications in GBM are limited. In this study, we leverage GBM cortical organoids to characterize widespread mRNA and GFP transfer from malignant to nonmalignant cells in the GBM neuroglial microenvironment. This transfer involves extracellular vesicles, may contribute to reprogramming the microenvironment, and may extend to other cancer types. See related commentary by Shakya et al., p. 261.©2024 The Authors; Published by the American Association for Cancer Research. 2024
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Waichman TV, Vercesi ML, Berardino AA, Beckel MS, Giacomini D, Rasetto NB, Herrero M, Di Bella DJ, Arlotta P, Schinder AF, Chernomoretz A. 2024. scX: A user-friendly tool for scRNA-seq exploration. ArXiv. Pubmed: 37961742 DOI:arXiv:2311.00012v2 Waichman TV, Vercesi ML, Berardino AA, Beckel MS, Giacomini D, Rasetto NB, Herrero M, Di Bella DJ, Arlotta P, Schinder AF, Chernomoretz A. 2024. scX: A user-friendly tool for scRNA-seq exploration. ArXiv. Pubmed: 37961742 DOI:arXiv:2311.00012v2 Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on the Shiny framework that streamlines the analysis, exploration, and visualization of single-cell experiments. With an interactive graphic interface, implemented as a web application, scX provides easy access to key scRNAseq analyses, including marker identification, gene expression profiling, and differential gene expression analysis. Additionally, scX seamlessly integrates with commonly used single-cell Seurat and Single-CellExperiment R objects, resulting in efficient processing and visualization of varied datasets. Overall, scX serves as a valuable and user-friendly tool for effortless exploration and sharing of single-cell data, simplifying some of the complexities inherent in scRNAseq analysis. -
Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. 2024. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. bioRxiv : the preprint server for biology. Pubmed: 38260428 DOI:10.1101/2023.11.03.565477 Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. 2024. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. bioRxiv : the preprint server for biology. Pubmed: 38260428 DOI:10.1101/2023.11.03.565477 The adult hippocampus generates new granule cells (aGCs) that exhibit distinct functional capabilities along development, conveying a unique form of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like neural stem cells (RGL) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to follow newborn aGCs along differentiation using single-nuclei RNA sequencing (snRNA-seq). Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple sequential immature stages bearing increasing levels of effector genes supporting growth, excitability and synaptogenesis. Remarkably, four discrete cellular states were defined by the expression of distinct sets of transcription factors (TFs): quiescent neural stem cells, proliferative progenitors, postmitotic immature aGCs, and mature aGCs. The transition from immature to mature aCGs involved a transcriptional switch that shutdown molecular cascades promoting cell growth, such as the SoxC family of TFs, to activate programs controlling neuronal homeostasis. Indeed, aGCs overexpressing or remained stalled at the immature state. Our results unveil precise molecular mechanisms driving adult neural stem cells through the pathway of neuronal differentiation. -
Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. 2024. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron. 112(13):2091-2111. Pubmed: 38754415 DOI:S0896-6273(24)00282-4 Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. 2024. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron. 112(13):2091-2111. Pubmed: 38754415 DOI:S0896-6273(24)00282-4 Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.Copyright © 2024 Elsevier Inc. All rights reserved. -
Ostrem BEL, Domínguez-Iturza N, Stogsdill JA, Faits T, Kim K, Levin JZ, Arlotta P. 2024. Fetal brain response to maternal inflammation requires microglia. Development (Cambridge, England). 151(10). Pubmed: 38775708 DOI:10.1242/dev.202252 Ostrem BEL, Domínguez-Iturza N, Stogsdill JA, Faits T, Kim K, Levin JZ, Arlotta P. 2024. Fetal brain response to maternal inflammation requires microglia. Development (Cambridge, England). 151(10). Pubmed: 38775708 DOI:10.1242/dev.202252 In utero infection and maternal inflammation can adversely impact fetal brain development. Maternal systemic illness, even in the absence of direct fetal brain infection, is associated with an increased risk of neuropsychiatric disorders in affected offspring. The cell types mediating the fetal brain response to maternal inflammation are largely unknown, hindering the development of novel treatment strategies. Here, we show that microglia, the resident phagocytes of the brain, highly express receptors for relevant pathogens and cytokines throughout embryonic development. Using a rodent maternal immune activation (MIA) model in which polyinosinic:polycytidylic acid is injected into pregnant mice, we demonstrate long-lasting transcriptional changes in fetal microglia that persist into postnatal life. We find that MIA induces widespread gene expression changes in neuronal and non-neuronal cells; importantly, these responses are abolished by selective genetic deletion of microglia, indicating that microglia are required for the transcriptional response of other cortical cell types to MIA. These findings demonstrate that microglia play a crucial durable role in the fetal response to maternal inflammation, and should be explored as potential therapeutic cell targets.© 2024. Published by The Company of Biologists Ltd. -
Waichman TV, Vercesi ML, Berardino AA, Beckel MS, Giacomini D, Rasetto NB, Herrero M, Di Bella DJ, Arlotta P, Schinder AF, Chernomoretz A. 2024. scX: a user-friendly tool for scRNAseq exploration. Bioinformatics advances. 4(1):vbae062. Pubmed: 38779177 DOI:10.1093/bioadv/vbae062 Waichman TV, Vercesi ML, Berardino AA, Beckel MS, Giacomini D, Rasetto NB, Herrero M, Di Bella DJ, Arlotta P, Schinder AF, Chernomoretz A. 2024. scX: a user-friendly tool for scRNAseq exploration. Bioinformatics advances. 4(1):vbae062. Pubmed: 38779177 DOI:10.1093/bioadv/vbae062 Array© The Author(s) 2024. Published by Oxford University Press. -
Antón-Bolaños N, Faravelli I, Faits T, Andreadis S, Kastli R, Trattaro S, Adiconis X, Wei A, Sampath Kumar A, Di Bella DJ, Tegtmeyer M, Nehme R, Levin JZ, Regev A, Arlotta P. 2024. Brain Chimeroids reveal individual susceptibility to neurotoxic triggers. Nature. 631(8019):142-149. Pubmed: 38926573 DOI:10.1038/s41586-024-07578-8 Antón-Bolaños N, Faravelli I, Faits T, Andreadis S, Kastli R, Trattaro S, Adiconis X, Wei A, Sampath Kumar A, Di Bella DJ, Tegtmeyer M, Nehme R, Levin JZ, Regev A, Arlotta P. 2024. Brain Chimeroids reveal individual susceptibility to neurotoxic triggers. Nature. 631(8019):142-149. Pubmed: 38926573 DOI:10.1038/s41586-024-07578-8 Interindividual genetic variation affects the susceptibility to and progression of many diseases. However, efforts to study how individual human brains differ in normal development and disease phenotypes are limited by the paucity of faithful cellular human models, and the difficulty of scaling current systems to represent multiple people. Here we present human brain Chimeroids, a highly reproducible, multidonor human brain cortical organoid model generated by the co-development of cells from a panel of individual donors in a single organoid. By reaggregating cells from multiple single-donor organoids at the neural stem cell or neural progenitor cell stage, we generate Chimeroids in which each donor produces all cell lineages of the cerebral cortex, even when using pluripotent stem cell lines with notable growth biases. We used Chimeroids to investigate interindividual variation in the susceptibility to neurotoxic triggers that exhibit high clinical phenotypic variability: ethanol and the antiepileptic drug valproic acid. Individual donors varied in both the penetrance of the effect on target cell types, and the molecular phenotype within each affected cell type. Our results suggest that human genetic background may be an important mediator of neurotoxin susceptibility and introduce Chimeroids as a scalable system for high-throughput investigation of interindividual variation in processes of brain development and disease.© 2024. The Author(s), under exclusive licence to Springer Nature Limited. -
Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. 2024. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. Science advances. 10(29):eadp6039. Pubmed: 39028813 DOI:10.1126/sciadv.adp6039 Rasetto NB, Giacomini D, Berardino AA, Waichman TV, Beckel MS, Di Bella DJ, Brown J, Davies-Sala MG, Gerhardinger C, Lie DC, Arlotta P, Chernomoretz A, Schinder AF. 2024. Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus. Science advances. 10(29):eadp6039. Pubmed: 39028813 DOI:10.1126/sciadv.adp6039 The adult hippocampus generates new granule cells (aGCs) with functional capabilities that convey unique forms of plasticity to the preexisting circuits. While early differentiation of adult radial glia-like cells (RGLs) has been studied extensively, the molecular mechanisms guiding the maturation of postmitotic neurons remain unknown. Here, we used a precise birthdating strategy to study aGC differentiation using single-nuclei RNA sequencing. Transcriptional profiling revealed a continuous trajectory from RGLs to mature aGCs, with multiple immature stages bearing increasing levels of effector genes supporting growth, excitability, and synaptogenesis. Analysis of differential gene expression, pseudo-time trajectory, and transcription factors (TFs) revealed critical transitions defining four cellular states: quiescent RGLs, proliferative progenitors, immature aGCs, and mature aGCs. Becoming mature aGCs involved a transcriptional switch that shuts down pathways promoting cell growth, such SoxC TFs, to activate programs that likely control neuronal homeostasis. aGCs overexpressing or remained immature. Our results unveil precise molecular mechanisms driving adult RGLs through the pathway of neuronal differentiation. 2023
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Weninger A, Arlotta P. 2023. A family portrait of human brain cells. Science (New York, N.Y.). 382(6667):168-169. Pubmed: 37824657 DOI:10.1126/science.adk4857 Weninger A, Arlotta P. 2023. A family portrait of human brain cells. Science (New York, N.Y.). 382(6667):168-169. Pubmed: 37824657 DOI:10.1126/science.adk4857 A cell census provides information on the source of human brain specialization. -
Arlotta P, Gage FH. 2023. Neural Organoids and the Quest to Understand and Treat Psychiatric Disease. Biological psychiatry. 93(7):588-589. Pubmed: 36889858 DOI:S0006-3223(23)00049-5 Arlotta P, Gage FH. 2023. Neural Organoids and the Quest to Understand and Treat Psychiatric Disease. Biological psychiatry. 93(7):588-589. Pubmed: 36889858 DOI:S0006-3223(23)00049-5 -
Pigoni M, Uzquiano A, Paulsen B, Kedaigle AJ, Yang SM, Symvoulidis P, Adiconis X, Velasco S, Sartore R, Kim K, Tucewicz A, Tropp SY, Tsafou K, Jin X, Barrett L, Chen F, Boyden ES, Regev A, Levin JZ, Arlotta P. 2023. Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity. Human molecular genetics. 32(18):2773-2786. Pubmed: 37384417 DOI:10.1093/hmg/ddad107 Pigoni M, Uzquiano A, Paulsen B, Kedaigle AJ, Yang SM, Symvoulidis P, Adiconis X, Velasco S, Sartore R, Kim K, Tucewicz A, Tropp SY, Tsafou K, Jin X, Barrett L, Chen F, Boyden ES, Regev A, Levin JZ, Arlotta P. 2023. Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity. Human molecular genetics. 32(18):2773-2786. Pubmed: 37384417 DOI:10.1093/hmg/ddad107 De novo heterozygous loss-of-function mutations in phosphatase and tensin homolog (PTEN) are strongly associated with autism spectrum disorders; however, it is unclear how heterozygous mutations in this gene affect different cell types during human brain development and how these effects vary across individuals. Here, we used human cortical organoids from different donors to identify cell-type specific developmental events that are affected by heterozygous mutations in PTEN. We profiled individual organoids by single-cell RNA-seq, proteomics and spatial transcriptomics and revealed abnormalities in developmental timing in human outer radial glia progenitors and deep-layer cortical projection neurons, which varied with the donor genetic background. Calcium imaging in intact organoids showed that both accelerated and delayed neuronal development phenotypes resulted in similar abnormal activity of local circuits, irrespective of genetic background. The work reveals donor-dependent, cell-type specific developmental phenotypes of PTEN heterozygosity that later converge on disrupted neuronal activity.© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. 2022
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Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Muotri AR, Park IH, Reiner O, Song H, Studer L, Temple S, Testa G, Treutlein B, Vaccarino FM. 2022. A nomenclature consensus for nervous system organoids and assembloids. Nature. 609(7929):907-910. Pubmed: 36171373 DOI:10.1038/s41586-022-05219-6 Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Muotri AR, Park IH, Reiner O, Song H, Studer L, Temple S, Testa G, Treutlein B, Vaccarino FM. 2022. A nomenclature consensus for nervous system organoids and assembloids. Nature. 609(7929):907-910. Pubmed: 36171373 DOI:10.1038/s41586-022-05219-6 Self-organizing three-dimensional cellular models derived from human pluripotent stem cells or primary tissue have great potential to provide insights into how the human nervous system develops, what makes it unique and how disorders of the nervous system arise, progress and could be treated. Here, to facilitate progress and improve communication with the scientific community and the public, we clarify and provide a basic framework for the nomenclature of human multicellular models of nervous system development and disease, including organoids, assembloids and transplants.© 2022. Springer Nature Limited. -
Uzquiano A, Arlotta P. 2022. Brain organoids: the quest to decipher human-specific features of brain development. Current opinion in genetics & development. 75:101955. Pubmed: 35816938 DOI:S0959-437X(22)00064-8 Uzquiano A, Arlotta P. 2022. Brain organoids: the quest to decipher human-specific features of brain development. Current opinion in genetics & development. 75:101955. Pubmed: 35816938 DOI:S0959-437X(22)00064-8 The development of the human brain occurs largely in utero over long periods of time and is thus experimentally inaccessible; therefore, tractable experimental models are needed. Human brain organoid have emerged as powerful model systems to investigate human-specific features of brain development. Focusing on the cerebral cortex, here, we discuss how brain, and more specifically cortical, organoid models have newly enabled discovery of aspects of progenitor biology and cortical-cell diversification that are unique to humans. We foresee that as advancements in organoid generation increase the complexity of these models, more complete replicas of the brain will empower future studies investigating higher-order aspects of brain biology, toward an understanding of the unique processing capabilities of the human brain.Copyright © 2022 Elsevier Ltd. All rights reserved. -
Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, Bruna Paulsen, Xian Adiconis, Kwanho Kim, Tyler Faits, Surya Nagaraja, Noelia Antón-Bolaños, Chiara Gerhardinger, Ashley Tucewicz, Evan Murray, Xin Jin, Jason Buenrostro, Fei Chen, Silvia Velasco, Aviv Regev, Joshua Z Levin, Paola Arlotta. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. DOI:10.1016/j.cell.2022.09.010 Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, Bruna Paulsen, Xian Adiconis, Kwanho Kim, Tyler Faits, Surya Nagaraja, Noelia Antón-Bolaños, Chiara Gerhardinger, Ashley Tucewicz, Evan Murray, Xin Jin, Jason Buenrostro, Fei Chen, Silvia Velasco, Aviv Regev, Joshua Z Levin, Paola Arlotta. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. DOI:10.1016/j.cell.2022.09.010 -
Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. Pubmed: 36179669 DOI:S0092-8674(22)01168-0 Uzquiano A, Kedaigle AJ, Pigoni M, Paulsen B, Adiconis X, Kim K, Faits T, Nagaraja S, Antón-Bolaños N, Gerhardinger C, Tucewicz A, Murray E, Jin X, Buenrostro J, Chen F, Velasco S, Regev A, Levin JZ, Arlotta P. 2022. Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex. Cell. 185(20):3770-3788.e27. Pubmed: 36179669 DOI:S0092-8674(22)01168-0 Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell types during organoid development, identify genes with predicted human-specific roles in lineage establishment, and uncover early transcriptional diversity of human callosal neurons. The findings validate this comprehensive atlas of human corticogenesis in vitro as a resource to prime investigation into the mechanisms of human cortical development.Copyright © 2022 Elsevier Inc. All rights reserved. -
Yuan W, Ma S, Brown JR, Kim K, Murek V, Trastulla L, Meissner A, Lodato S, Shetty AS, Levin JZ, Buenrostro JD, Ziller MJ, Arlotta P. 2022. Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nature neuroscience. 25(8):1049-1058. Pubmed: 35915179 DOI:10.1038/s41593-022-01123-4 Yuan W, Ma S, Brown JR, Kim K, Murek V, Trastulla L, Meissner A, Lodato S, Shetty AS, Levin JZ, Buenrostro JD, Ziller MJ, Arlotta P. 2022. Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nature neuroscience. 25(8):1049-1058. Pubmed: 35915179 DOI:10.1038/s41593-022-01123-4 Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.© 2022. The Author(s). -
Cable J, Arlotta P, Parker KK, Hughes AJ, Goodwin K, Mummery CL, Kamm RD, Engle SJ, Tagle DA, Boj SF, Stanton AE, Morishita Y, Kemp ML, Norfleet DA, May EE, Lu A, Bashir R, Feinberg AW, Hull SM, Gonzalez AL, Blatchley MR, Montserrat Pulido N, Morizane R, McDevitt TC, Mishra D, Mulero-Russe A. 2022. Engineering multicellular living systems-a Keystone Symposia report. Annals of the New York Academy of Sciences. 1518(1):183-195. Pubmed: 36177947 DOI:10.1111/nyas.14896 Cable J, Arlotta P, Parker KK, Hughes AJ, Goodwin K, Mummery CL, Kamm RD, Engle SJ, Tagle DA, Boj SF, Stanton AE, Morishita Y, Kemp ML, Norfleet DA, May EE, Lu A, Bashir R, Feinberg AW, Hull SM, Gonzalez AL, Blatchley MR, Montserrat Pulido N, Morizane R, McDevitt TC, Mishra D, Mulero-Russe A. 2022. Engineering multicellular living systems-a Keystone Symposia report. Annals of the New York Academy of Sciences. 1518(1):183-195. Pubmed: 36177947 DOI:10.1111/nyas.14896 The ability to engineer complex multicellular systems has enormous potential to inform our understanding of biological processes and disease and alter the drug development process. Engineering living systems to emulate natural processes or to incorporate new functions relies on a detailed understanding of the biochemical, mechanical, and other cues between cells and between cells and their environment that result in the coordinated action of multicellular systems. On April 3-6, 2022, experts in the field met at the Keystone symposium "Engineering Multicellular Living Systems" to discuss recent advances in understanding how cells cooperate within a multicellular system, as well as recent efforts to engineer systems like organ-on-a-chip models, biological robots, and organoids. Given the similarities and common themes, this meeting was held in conjunction with the symposium "Organoids as Tools for Fundamental Discovery and Translation".© 2022 New York Academy of Sciences. -
Hyun I, Scharf-Deering JC, Sullivan S, Aach JD, Arlotta P, Baum ML, Church GM, Goldenberg A, Greely HT, Khoshakhlagh P, Kohman RE, Lopes M, Lowenthal C, Lu A, Ng AHM, Pasca SP, Paulsen B, Pigoni M, Scott CT, Silbersweig DA, Skylar-Scott MA, Truog RD, Lunshof JE. 2022. How collaboration between bioethicists and neuroscientists can advance research. Nature neuroscience. 25(11):1399-1401. Pubmed: 36258039 DOI:10.1038/s41593-022-01187-2 Hyun I, Scharf-Deering JC, Sullivan S, Aach JD, Arlotta P, Baum ML, Church GM, Goldenberg A, Greely HT, Khoshakhlagh P, Kohman RE, Lopes M, Lowenthal C, Lu A, Ng AHM, Pasca SP, Paulsen B, Pigoni M, Scott CT, Silbersweig DA, Skylar-Scott MA, Truog RD, Lunshof JE. 2022. How collaboration between bioethicists and neuroscientists can advance research. Nature neuroscience. 25(11):1399-1401. Pubmed: 36258039 DOI:10.1038/s41593-022-01187-2 -
Stogsdill JA, Kim K, Binan L, Farhi SL, Levin JZ, Arlotta P. 2022. Pyramidal neuron subtype diversity governs microglia states in the neocortex. Nature. 608(7924):750-756. Pubmed: 35948630 DOI:10.1038/s41586-022-05056-7 Stogsdill JA, Kim K, Binan L, Farhi SL, Levin JZ, Arlotta P. 2022. Pyramidal neuron subtype diversity governs microglia states in the neocortex. Nature. 608(7924):750-756. Pubmed: 35948630 DOI:10.1038/s41586-022-05056-7 Microglia are specialized macrophages in the brain parenchyma that exist in multiple transcriptional states and reside within a wide range of neuronal environments. However, how and where these states are generated remains poorly understood. Here, using the mouse somatosensory cortex, we demonstrate that microglia density and molecular state acquisition are determined by the local composition of pyramidal neuron classes. Using single-cell and spatial transcriptomic profiling, we unveil the molecular signatures and spatial distributions of diverse microglia populations and show that certain states are enriched in specific cortical layers, whereas others are broadly distributed throughout the cortex. Notably, conversion of deep-layer pyramidal neurons to an alternate class identity reconfigures the distribution of local, layer-enriched homeostatic microglia to match the new neuronal niche. Leveraging the transcriptional diversity of pyramidal neurons in the neocortex, we construct a ligand-receptor atlas describing interactions between individual pyramidal neuron subtypes and microglia states, revealing rules of neuron-microglia communication. Our findings uncover a fundamental role for neuronal diversity in instructing the acquisition of microglia states as a potential mechanism for fine-tuning neuroimmune interactions within the cortical local circuitry.© 2022. The Author(s), under exclusive licence to Springer Nature Limited. -
Fossati V, Greco V, Arlotta P, Aiyar RS. 2022. Susan L. Solomon (1951-2022): Advocate, Innovator, Catalyst. Stem cell reports. 17(12):2579-2581. Pubmed: 36516737 DOI:S2213-6711(22)00546-X Fossati V, Greco V, Arlotta P, Aiyar RS. 2022. Susan L. Solomon (1951-2022): Advocate, Innovator, Catalyst. Stem cell reports. 17(12):2579-2581. Pubmed: 36516737 DOI:S2213-6711(22)00546-X -
Arlotta P, Chen F, Lodato S, Margrie TW, Nowakowski TJ, Pederson T, Rico B. 2022. Dissecting cellular diversity of cortical GABAergic cells across multiple modalities: A turning point in neuronal taxonomy. Faculty reviews. 11:13. Pubmed: 35719130 DOI:10.12703/r-01-000009 Arlotta P, Chen F, Lodato S, Margrie TW, Nowakowski TJ, Pederson T, Rico B. 2022. Dissecting cellular diversity of cortical GABAergic cells across multiple modalities: A turning point in neuronal taxonomy. Faculty reviews. 11:13. Pubmed: 35719130 DOI:10.12703/r-01-000009 Decoding the complexity of the brain requires an understanding of the architecture, function, and development of its neuronal circuits. Neuronal classifications that group neurons based on specific features/behaviors have become essential to further analyze the different subtypes in a systematic and reproducible way. A comprehensive taxonomic framework, accounting for multiple defining and quantitative features, will provide the reference to infer generalized rules for cells ascribed to the same neuronal type, and eventually predict cellular behaviors, even in the absence of experimental measures. Technologies that enable cell-type classification in the nervous system are rapidly evolving in scalability and resolution. While these approaches depict astonishing diversity in neuronal morphology, electrophysiology, and gene expression, a robust metric of the coherence between different profiling modalities leading to a unified classification is still largely missing. Focusing on GABAergic neurons of the cerebral cortex, Gouwens . pioneered the first integrated cell-type classification based on the simultaneous analysis of the transcriptional networks, the recording of intrinsic electrophysiological properties, and the reconstruction of 3D morphologies of the same cell. Their comprehensive and high-quality data provide a new framework to shed light on what may be considered a "neuronal cell type."Copyright: © 2022 Faculty Opinions Ltd. -
Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P. 2022. Autism genes converge on asynchronous development of shared neuron classes. Nature. 602(7896):268-273. Pubmed: 35110736 DOI:10.1038/s41586-021-04358-6 Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P. 2022. Autism genes converge on asynchronous development of shared neuron classes. Nature. 602(7896):268-273. Pubmed: 35110736 DOI:10.1038/s41586-021-04358-6 Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes-SUV420H1 (also known as KMT5B), ARID1B and CHD8-in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages-γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons-but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology.© 2022. The Author(s), under exclusive licence to Springer Nature Limited. 2021
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Di Bella DJ, Habibi E, Stickels RR, Scalia G, Brown J, Yadollahpour P, Yang SM, Abbate C, Biancalani T, Macosko EZ, Chen F, Regev A, Arlotta P. 2021. Molecular logic of cellular diversification in the mouse cerebral cortex. Nature. 595(7868):554-559. Pubmed: 34163074 DOI:10.1038/s41586-021-03670-5 Di Bella DJ, Habibi E, Stickels RR, Scalia G, Brown J, Yadollahpour P, Yang SM, Abbate C, Biancalani T, Macosko EZ, Chen F, Regev A, Arlotta P. 2021. Molecular logic of cellular diversification in the mouse cerebral cortex. Nature. 595(7868):554-559. Pubmed: 34163074 DOI:10.1038/s41586-021-03670-5 The mammalian cerebral cortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function. However, the molecular logic that governs the establishment and organization of cortical cell types remains unknown, largely due to the large number of cell classes that undergo dynamic cell-state transitions over extended developmental timelines. Here we generate a comprehensive atlas of the developing mouse neocortex, using single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin using sequencing. We sampled the neocortex every day throughout embryonic corticogenesis and at early postnatal ages, and complemented the sequencing data with a spatial transcriptomics time course. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer their spatial organization and the gene regulatory programs that accompany their lineage bifurcation decisions and differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities that are linked to aberrant corticogenesis in mutant mice. The data provide a global picture of the regulatory mechanisms that govern cellular diversification in the neocortex.© 2021. The Author(s), under exclusive licence to Springer Nature Limited. -
Matho KS, Huilgol D, Galbavy W, He M, Kim G, An X, Lu J, Wu P, Di Bella DJ, Shetty AS, Palaniswamy R, Hatfield J, Raudales R, Narasimhan A, Gamache E, Levine JM, Tucciarone J, Szelenyi E, Harris JA, Mitra PP, Osten P, Arlotta P, Huang ZJ. 2021. Genetic dissection of the glutamatergic neuron system in cerebral cortex. Nature. 598(7879):182-187. Pubmed: 34616069 DOI:10.1038/s41586-021-03955-9 Matho KS, Huilgol D, Galbavy W, He M, Kim G, An X, Lu J, Wu P, Di Bella DJ, Shetty AS, Palaniswamy R, Hatfield J, Raudales R, Narasimhan A, Gamache E, Levine JM, Tucciarone J, Szelenyi E, Harris JA, Mitra PP, Osten P, Arlotta P, Huang ZJ. 2021. Genetic dissection of the glutamatergic neuron system in cerebral cortex. Nature. 598(7879):182-187. Pubmed: 34616069 DOI:10.1038/s41586-021-03955-9 Diverse types of glutamatergic pyramidal neurons mediate the myriad processing streams and output channels of the cerebral cortex, yet all derive from neural progenitors of the embryonic dorsal telencephalon. Here we establish genetic strategies and tools for dissecting and fate-mapping subpopulations of pyramidal neurons on the basis of their developmental and molecular programs. We leverage key transcription factors and effector genes to systematically target temporal patterning programs in progenitors and differentiation programs in postmitotic neurons. We generated over a dozen temporally inducible mouse Cre and Flp knock-in driver lines to enable the combinatorial targeting of major progenitor types and projection classes. Combinatorial strategies confer viral access to subsets of pyramidal neurons defined by developmental origin, marker expression, anatomical location and projection targets. These strategies establish an experimental framework for understanding the hierarchical organization and developmental trajectory of subpopulations of pyramidal neurons that assemble cortical processing networks and output channels.© 2021. The Author(s). -
Stickels RR, Murray E, Kumar P, Li J, Marshall JL, Di Bella DJ, Arlotta P, Macosko EZ, Chen F. 2021. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nature biotechnology. 39(3):313-319. Pubmed: 33288904 DOI:10.1038/s41587-020-0739-1 Stickels RR, Murray E, Kumar P, Li J, Marshall JL, Di Bella DJ, Arlotta P, Macosko EZ, Chen F. 2021. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nature biotechnology. 39(3):313-319. Pubmed: 33288904 DOI:10.1038/s41587-020-0739-1 Measurement of the location of molecules in tissues is essential for understanding tissue formation and function. Previously, we developed Slide-seq, a technology that enables transcriptome-wide detection of RNAs with a spatial resolution of 10 μm. Here we report Slide-seqV2, which combines improvements in library generation, bead synthesis and array indexing to reach an RNA capture efficiency ~50% that of single-cell RNA-seq data (~10-fold greater than Slide-seq), approaching the detection efficiency of droplet-based single-cell RNA-seq techniques. First, we leverage the detection efficiency of Slide-seqV2 to identify dendritically localized mRNAs in neurons of the mouse hippocampus. Second, we integrate the spatial information of Slide-seqV2 data with single-cell trajectory analysis tools to characterize the spatiotemporal development of the mouse neocortex, identifying underlying genetic programs that were poorly sampled with Slide-seq. The combination of near-cellular resolution and high transcript detection efficiency makes Slide-seqV2 useful across many experimental contexts. -
Harris JM, Yu-Der Wang A, Arlotta P. 2021. Optogenetic axon guidance in embryonic zebrafish. STAR protocols. 2(4):100947. Pubmed: 34841275 DOI:10.1016/j.xpro.2021.100947 Harris JM, Yu-Der Wang A, Arlotta P. 2021. Optogenetic axon guidance in embryonic zebrafish. STAR protocols. 2(4):100947. Pubmed: 34841275 DOI:10.1016/j.xpro.2021.100947 Axons form the long-range connections of biological neuronal networks, which are built through the developmental process of axon guidance. Here, we describe a protocol to precisely and non-invasively control axonal growth trajectories in live zebrafish embryos using focal light activation of a photoactivatable Rac1. We outline techniques for photostimulation, time-lapse imaging, and immunohistochemistry. These approaches enable engineering of long-range axonal circuitry or repair of defective circuits in living zebrafish, despite a milieu of competing endogenous signals and repulsive barriers. For complete details on the use and execution of this protocol, please refer to Harris et al. (2020).© 2021. -
Di Bella DJ, Habibi E, Stickels RR, Scalia G, Brown J, Yadollahpour P, Yang SM, Abbate C, Biancalani T, Macosko EZ, Chen F, Regev A, Arlotta P. 2021. Author Correction: Molecular logic of cellular diversification in the mouse cerebral cortex. Nature. 596(7873):E11. Pubmed: 34341543 DOI:10.1038/s41586-021-03797-5 Di Bella DJ, Habibi E, Stickels RR, Scalia G, Brown J, Yadollahpour P, Yang SM, Abbate C, Biancalani T, Macosko EZ, Chen F, Regev A, Arlotta P. 2021. Author Correction: Molecular logic of cellular diversification in the mouse cerebral cortex. Nature. 596(7873):E11. Pubmed: 34341543 DOI:10.1038/s41586-021-03797-5 2020
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Albanese A, Swaney JM, Yun DH, Evans NB, Antonucci JM, Velasco S, Sohn CH, Arlotta P, Gehrke L, Chung K. 2020. Multiscale 3D phenotyping of human cerebral organoids. Scientific reports. 10(1):21487. Pubmed: 33293587 DOI:10.1038/s41598-020-78130-7 Albanese A, Swaney JM, Yun DH, Evans NB, Antonucci JM, Velasco S, Sohn CH, Arlotta P, Gehrke L, Chung K. 2020. Multiscale 3D phenotyping of human cerebral organoids. Scientific reports. 10(1):21487. Pubmed: 33293587 DOI:10.1038/s41598-020-78130-7 Brain organoids grown from human pluripotent stem cells self-organize into cytoarchitectures resembling the developing human brain. These three-dimensional models offer an unprecedented opportunity to study human brain development and dysfunction. Characterization currently sacrifices spatial information for single-cell or histological analysis leaving whole-tissue analysis mostly unexplored. Here, we present the SCOUT pipeline for automated multiscale comparative analysis of intact cerebral organoids. Our integrated technology platform can rapidly clear, label, and image intact organoids. Algorithmic- and convolutional neural network-based image analysis extract hundreds of features characterizing molecular, cellular, spatial, cytoarchitectural, and organoid-wide properties from fluorescence microscopy datasets. Comprehensive analysis of 46 intact organoids and ~ 100 million cells reveals quantitative multiscale "phenotypes" for organoid development, culture protocols and Zika virus infection. SCOUT provides a much-needed framework for comparative analysis of emerging 3D in vitro models using fluorescence microscopy. -
Jin X, Simmons SK, Guo A, Shetty AS, Ko M, Nguyen L, Jokhi V, Robinson E, Oyler P, Curry N, Deangeli G, Lodato S, Levin JZ, Regev A, Zhang F, Arlotta P. 2020. In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science (New York, N.Y.). 370(6520). Pubmed: 33243861 DOI:10.1126/science.aaz6063 Jin X, Simmons SK, Guo A, Shetty AS, Ko M, Nguyen L, Jokhi V, Robinson E, Oyler P, Curry N, Deangeli G, Lodato S, Levin JZ, Regev A, Zhang F, Arlotta P. 2020. In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science (New York, N.Y.). 370(6520). Pubmed: 33243861 DOI:10.1126/science.aaz6063 The number of disease risk genes and loci identified through human genetic studies far outstrips the capacity to systematically study their functions. We applied a scalable genetic screening approach, in vivo Perturb-Seq, to functionally evaluate 35 autism spectrum disorder/neurodevelopmental delay (ASD/ND) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing mouse brain in utero, followed by single-cell RNA-sequencing of perturbed cells in the postnatal brain. We identified cell type-specific and evolutionarily conserved gene modules from both neuronal and glial cell classes. Recurrent gene modules and cell types are affected across this cohort of perturbations, representing key cellular effects across sets of ASD/ND risk genes. In vivo Perturb-Seq allows us to investigate how diverse mutations affect cell types and states in the developing organism.Copyright © 2020, American Association for the Advancement of Science. -
Velasco S, Paulsen B, Arlotta P. 2020. 3D Brain Organoids: Studying Brain Development and Disease Outside the Embryo. Annual review of neuroscience. 43:375-389. Pubmed: 32640930 DOI:10.1146/annurev-neuro-070918-050154 Velasco S, Paulsen B, Arlotta P. 2020. 3D Brain Organoids: Studying Brain Development and Disease Outside the Embryo. Annual review of neuroscience. 43:375-389. Pubmed: 32640930 DOI:10.1146/annurev-neuro-070918-050154 Scientists have been fascinated by the human brain for centuries, yet knowledge of the cellular and molecular events that build the human brain during embryogenesis and of how abnormalities in this process lead to neurological disease remains very superficial. In particular, the lack of experimental models for a process that largely occurs during human in utero development, and is therefore poorly accessible for study, has hindered progress in mechanistic understanding. Advances in stem cell-derived models of human organogenesis, in the form of three-dimensional organoid cultures, and transformative new analytic technologies have opened new experimental pathways for investigation of aspects of development, evolution, and pathology of the human brain. Here, we consider the biology of brain organoids, compared and contrasted with the endogenous human brain, and highlight experimental strategies to use organoids to pioneer new understanding of human brain pathology. -
Harris JM, Wang AY, Boulanger-Weill J, Santoriello C, Foianini S, Lichtman JW, Zon LI, Arlotta P. 2020. Long-Range Optogenetic Control of Axon Guidance Overcomes Developmental Boundaries and Defects. Developmental cell. 53(5):577-588.e7. Pubmed: 32516597 DOI:S1534-5807(20)30398-1 Harris JM, Wang AY, Boulanger-Weill J, Santoriello C, Foianini S, Lichtman JW, Zon LI, Arlotta P. 2020. Long-Range Optogenetic Control of Axon Guidance Overcomes Developmental Boundaries and Defects. Developmental cell. 53(5):577-588.e7. Pubmed: 32516597 DOI:S1534-5807(20)30398-1 Axons connect neurons together, establishing the wiring architecture of neuronal networks. Axonal connectivity is largely built during embryonic development through highly constrained processes of axon guidance, which have been extensively studied. However, the inability to control axon guidance, and thus neuronal network architecture, has limited investigation of how axonal connections influence subsequent development and function of neuronal networks. Here, we use zebrafish motor neurons expressing a photoactivatable Rac1 to co-opt endogenous growth cone guidance machinery to precisely and non-invasively direct axon growth using light. Axons can be guided over large distances, within complex environments of living organisms, overriding competing endogenous signals and redirecting axons across potent repulsive barriers to construct novel circuitry. Notably, genetic axon guidance defects can be rescued, restoring functional connectivity. These data demonstrate that intrinsic growth cone guidance machinery can be co-opted to non-invasively build new connectivity, allowing investigation of neural network dynamics in intact living organisms.Copyright © 2020 Elsevier Inc. All rights reserved. -
Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P. 2020. FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system. Nucleic acids research. 48(1):e4. Pubmed: 31728515 DOI:10.1093/nar/gkz968 Amamoto R, Zuccaro E, Curry NC, Khurana S, Chen HH, Cepko CL, Arlotta P. 2020. FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system. Nucleic acids research. 48(1):e4. Pubmed: 31728515 DOI:10.1093/nar/gkz968 Thousands of frozen, archived tissue samples from the human central nervous system (CNS) are currently available in brain banks. As recent developments in RNA sequencing technologies are beginning to elucidate the cellular diversity present within the human CNS, it is becoming clear that an understanding of this diversity would greatly benefit from deeper transcriptional analyses. Single cell and single nucleus RNA profiling provide one avenue to decipher this heterogeneity. An alternative, complementary approach is to profile isolated, pre-defined cell types and use methods that can be applied to many archived human tissue samples that have been stored long-term. Here, we developed FIN-Seq (Frozen Immunolabeled Nuclei Sequencing), a method that accomplishes these goals. FIN-Seq uses immunohistochemical isolation of nuclei of specific cell types from frozen human tissue, followed by bulk RNA-Sequencing. We applied this method to frozen postmortem samples of human cerebral cortex and retina and were able to identify transcripts, including low abundance transcripts, in specific cell types.© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. -
Yang SM, Michel K, Jokhi V, Nedivi E, Arlotta P. 2020. Neuron class-specific responses govern adaptive myelin remodeling in the neocortex. Science (New York, N.Y.). 370(6523). Pubmed: 33335032 DOI:10.1126/science.abd2109 Yang SM, Michel K, Jokhi V, Nedivi E, Arlotta P. 2020. Neuron class-specific responses govern adaptive myelin remodeling in the neocortex. Science (New York, N.Y.). 370(6523). Pubmed: 33335032 DOI:10.1126/science.abd2109 Myelin plasticity is critical for neurological function, including learning and memory. However, it is unknown whether this plasticity reflects uniform changes across all neuronal subtypes, or whether myelin dynamics vary between neuronal classes to enable fine-tuning of adaptive circuit responses. We performed in vivo two-photon imaging of myelin sheaths along single axons of excitatory callosal neurons and inhibitory parvalbumin-expressing interneurons in adult mouse visual cortex. We found that both neuron types show homeostatic myelin remodeling under normal vision. However, monocular deprivation results in adaptive myelin remodeling only in parvalbumin-expressing interneurons. An initial increase in elongation of myelin segments is followed by contraction of a separate cohort of segments. This data indicates that distinct classes of neurons individualize remodeling of their myelination profiles to diversify circuit tuning in response to sensory experience.Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. 2019
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Arlotta P, Paşca SP. 2019. Cell diversity in the human cerebral cortex: from the embryo to brain organoids. Current opinion in neurobiology. 56:194-198. Pubmed: 31051421 DOI:S0959-4388(19)30025-X Arlotta P, Paşca SP. 2019. Cell diversity in the human cerebral cortex: from the embryo to brain organoids. Current opinion in neurobiology. 56:194-198. Pubmed: 31051421 DOI:S0959-4388(19)30025-X The development and wiring of the central nervous system is a remarkable biological process that starts with the generation of and interaction between a large diversity of cell types. Our understanding of the developmental logic that drives cellular diversification in the mammalian brain comes, to a large extent, from studies in rodents. However, identifying the unique cellular processes underlying primate corticogenesis has been slow, due to the challenges associated with directly observing and manipulating brain tissue from these species. Recent technological advances in two areas hold promise to accelerate discovery of the mechanisms that govern human brain development, evolution, and pathophysiology of disease. Molecular profiling of large numbers of single cells can now capture cell identity and cell states within a complex tissue. Furthermore, modeling aspects of human organogenesis in vitro, even for tissues as complex as the brain, has been advanced by the use of three-dimensional organoid systems. Here, we describe how these approaches have been applied to date and how they promise to uncover the principles of cell diversification in the developing human brain.Copyright © 2019. Published by Elsevier Ltd. -
Velasco S, Kedaigle AJ, Simmons SK, Nash A, Rocha M, Quadrato G, Paulsen B, Nguyen L, Adiconis X, Regev A, Levin JZ, Arlotta P. 2019. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature. 570(7762):523-527. Pubmed: 31168097 DOI:10.1038/s41586-019-1289-x Velasco S, Kedaigle AJ, Simmons SK, Nash A, Rocha M, Quadrato G, Paulsen B, Nguyen L, Adiconis X, Regev A, Levin JZ, Arlotta P. 2019. Individual brain organoids reproducibly form cell diversity of the human cerebral cortex. Nature. 570(7762):523-527. Pubmed: 31168097 DOI:10.1038/s41586-019-1289-x Experimental models of the human brain are needed for basic understanding of its development and disease. Human brain organoids hold unprecedented promise for this purpose; however, they are plagued by high organoid-to-organoid variability. This has raised doubts as to whether developmental processes of the human brain can occur outside the context of embryogenesis with a degree of reproducibility that is comparable to the endogenous tissue. Here we show that an organoid model of the dorsal forebrain can reliably generate a rich diversity of cell types appropriate for the human cerebral cortex. We performed single-cell RNA-sequencing analysis of 166,242 cells isolated from 21 individual organoids, finding that 95% of the organoids generate a virtually indistinguishable compendium of cell types, following similar developmental trajectories and with a degree of organoid-to-organoid variability comparable to that of individual endogenous brains. Furthermore, organoids derived from different stem cell lines show consistent reproducibility in the cell types produced. The data demonstrate that reproducible development of the complex cellular diversity of the central nervous system does not require the context of the embryo, and that establishment of terminal cell identity is a highly constrained process that can emerge from diverse stem cell origins and growth environments. -
Zonouzi M, Berger D, Jokhi V, Kedaigle A, Lichtman J, Arlotta P. 2019. Individual Oligodendrocytes Show Bias for Inhibitory Axons in the Neocortex. Cell reports. 27(10):2799-2808.e3. Pubmed: 31167127 DOI:S2211-1247(19)30629-1 Zonouzi M, Berger D, Jokhi V, Kedaigle A, Lichtman J, Arlotta P. 2019. Individual Oligodendrocytes Show Bias for Inhibitory Axons in the Neocortex. Cell reports. 27(10):2799-2808.e3. Pubmed: 31167127 DOI:S2211-1247(19)30629-1 Reciprocal communication between neurons and oligodendrocytes is essential for the generation and localization of myelin, a critical feature of the CNS. In the neocortex, individual oligodendrocytes can myelinate multiple axons; however, the neuronal origin of the myelinated axons has remained undefined and, while largely assumed to be from excitatory pyramidal neurons, it also includes inhibitory interneurons. This raises the question of whether individual oligodendrocytes display bias for the class of neurons that they myelinate. Here, we find that different classes of cortical interneurons show distinct patterns of myelin distribution starting from the onset of myelination, suggesting that oligodendrocytes can recognize the class identity of individual types of interneurons that they target. Notably, we show that some oligodendrocytes disproportionately myelinate the axons of inhibitory interneurons, whereas others primarily target excitatory axons or show no bias. These results point toward very specific interactions between oligodendrocytes and neurons and raise the interesting question of why myelination is differentially directed toward different neuron types.Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved. -
Adam Y, Kim JJ, Lou S, Zhao Y, Xie ME, Brinks D, Wu H, Mostajo-Radji MA, Kheifets S, Parot V, Chettih S, Williams KJ, Gmeiner B, Farhi SL, Madisen L, Buchanan EK, Kinsella I, Zhou D, Paninski L, Harvey CD, Zeng H, Arlotta P, Campbell RE, Cohen AE. 2019. Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics. Nature. 569(7756):413-417. Pubmed: 31043747 DOI:10.1038/s41586-019-1166-7 Adam Y, Kim JJ, Lou S, Zhao Y, Xie ME, Brinks D, Wu H, Mostajo-Radji MA, Kheifets S, Parot V, Chettih S, Williams KJ, Gmeiner B, Farhi SL, Madisen L, Buchanan EK, Kinsella I, Zhou D, Paninski L, Harvey CD, Zeng H, Arlotta P, Campbell RE, Cohen AE. 2019. Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics. Nature. 569(7756):413-417. Pubmed: 31043747 DOI:10.1038/s41586-019-1166-7 A technology that simultaneously records membrane potential from multiple neurons in behaving animals will have a transformative effect on neuroscience research. Genetically encoded voltage indicators are a promising tool for these purposes; however, these have so far been limited to single-cell recordings with a marginal signal-to-noise ratio in vivo. Here we developed improved near-infrared voltage indicators, high-speed microscopes and targeted gene expression schemes that enabled simultaneous in vivo recordings of supra- and subthreshold voltage dynamics in multiple neurons in the hippocampus of behaving mice. The reporters revealed subcellular details of back-propagating action potentials and correlations in subthreshold voltage between multiple cells. In combination with stimulation using optogenetics, the reporters revealed changes in neuronal excitability that were dependent on the behavioural state, reflecting the interplay of excitatory and inhibitory synaptic inputs. These tools open the possibility for detailed explorations of network dynamics in the context of behaviour. Fig. 1 PHOTOACTIVATED QUASAR3 (PAQUASAR3) REPORTS NEURONAL ACTIVITY IN VIVO.: a, Schematic of the paQuasAr3 construct. b, Photoactivation by blue light enhanced voltage signals excited by red light in cultured neurons that expressed paQuasAr3 (representative example of n = 4 cells). c, Model of the photocycle of paQuasAr3. d, Confocal images of sparsely expressed paQuasAr3 in brain slices. Scale bars, 50 μm. Representative images, experiments were repeated in n = 3 mice. e, Simultaneous fluorescence and patch-clamp recordings from a neuron expressing paQuasAr3 in acute brain slice. Top, magnification of boxed regions. Schematic shows brain slice, patch pipette and microscope objective. f, Simultaneous fluorescence and patch-clamp recordings of inhibitory post synaptic potentials in an L2-3 neuron induced by electrical stimulation of L5-6 in acute slice. g, Normalized change in fluorescence (ΔF/F) and SNR of optically recorded post-synaptic potentials (PSPs) as a function of the amplitude of the post-synaptic potentials. The voltage sensitivity was ΔF/F = 40 ± 1.7% per 100 mV. The SNR was 0.93 ± 0.07 per 1 mV in a 1-kHz bandwidth (n = 42 post-synaptic potentials from 5 cells, data are mean ± s.d.). Schematic shows brain slice, patch pipette, field stimulation electrodes and microscope objective. h, Optical measurements of paQuasAr3 fluorescence in the CA1 region of the hippocampus (top) and glomerular layer of the olfactory bulb (bottom) of anaesthetized mice (representative traces from n = 7 CA1 cells and n = 13 olfactory bulb cells, n = 3 mice). Schematics show microscope objective and the imaged brain region. i, STA fluorescence from 88 spikes in a CA1 oriens neuron. j, Frames from the STA video showing the delay in the back-propagating action potential in the dendrites relative to the soma. k, Sub-Nyquist fitting of the action potential delay and width shows electrical compartmentalization in the dendrites. Experiments in k-m were repeated in n = 2 cells from n = 2 mice. 2018
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Arlotta P. 2018. Organoids required! A new path to understanding human brain development and disease. Nature methods. 15(1):27-29. Pubmed: 29298289 DOI:10.1038/nmeth.4557 Arlotta P. 2018. Organoids required! A new path to understanding human brain development and disease. Nature methods. 15(1):27-29. Pubmed: 29298289 DOI:10.1038/nmeth.4557 Our ability to study the developing human brain has recently been dramatically advanced by the development of human 'brain organoids', three-dimensional culture systems that recapitulate selected aspects of human brain development in reductionist, yet complex, tissues in vitro. Here I discuss the promises and challenges this new model system presents. -
Farahany NA, Greely HT, Hyman S, Koch C, Grady C, Pașca SP, Sestan N, Arlotta P, Bernat JL, Ting J, Lunshof JE, Iyer EPR, Hyun I, Capestany BH, Church GM, Huang H, Song H. 2018. The ethics of experimenting with human brain tissue. Nature. 556(7702):429-432. Pubmed: 29691509 DOI:10.1038/d41586-018-04813-x Farahany NA, Greely HT, Hyman S, Koch C, Grady C, Pașca SP, Sestan N, Arlotta P, Bernat JL, Ting J, Lunshof JE, Iyer EPR, Hyun I, Capestany BH, Church GM, Huang H, Song H. 2018. The ethics of experimenting with human brain tissue. Nature. 556(7702):429-432. Pubmed: 29691509 DOI:10.1038/d41586-018-04813-x -
Brown J, Quadrato G, Arlotta P. 2018. Studying the Brain in a Dish: 3D Cell Culture Models of Human Brain Development and Disease. Current topics in developmental biology. 129:99-122. Pubmed: 29801532 DOI:S0070-2153(18)30045-0 Brown J, Quadrato G, Arlotta P. 2018. Studying the Brain in a Dish: 3D Cell Culture Models of Human Brain Development and Disease. Current topics in developmental biology. 129:99-122. Pubmed: 29801532 DOI:S0070-2153(18)30045-0 The study of the cellular and molecular processes of the developing human brain has been hindered by access to suitable models of living human brain tissue. Recently developed 3D cell culture models offer the promise of studying fundamental brain processes in the context of human genetic background and species-specific developmental mechanisms. Here, we review the current state of 3D human brain organoid models and consider their potential to enable investigation of complex aspects of human brain development and the underpinning of human neurological disease.© 2018 Elsevier Inc. All rights reserved. -
Nehme R, Zuccaro E, Ghosh SD, Li C, Sherwood JL, Pietilainen O, Barrett LE, Limone F, Worringer KA, Kommineni S, Zang Y, Cacchiarelli D, Meissner A, Adolfsson R, Haggarty S, Madison J, Muller M, Arlotta P, Fu Z, Feng G, Eggan K. 2018. Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission. Cell reports. 23(8):2509-2523. Pubmed: 29791859 DOI:S2211-1247(18)30625-9 Nehme R, Zuccaro E, Ghosh SD, Li C, Sherwood JL, Pietilainen O, Barrett LE, Limone F, Worringer KA, Kommineni S, Zang Y, Cacchiarelli D, Meissner A, Adolfsson R, Haggarty S, Madison J, Muller M, Arlotta P, Fu Z, Feng G, Eggan K. 2018. Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission. Cell reports. 23(8):2509-2523. Pubmed: 29791859 DOI:S2211-1247(18)30625-9 Transcription factor programming of pluripotent stem cells (PSCs) has emerged as an approach to generate human neurons for disease modeling. However, programming schemes produce a variety of cell types, and those neurons that are made often retain an immature phenotype, which limits their utility in modeling neuronal processes, including synaptic transmission. We report that combining NGN2 programming with SMAD and WNT inhibition generates human patterned induced neurons (hpiNs). Single-cell analyses showed that hpiN cultures contained cells along a developmental continuum, ranging from poorly differentiated neuronal progenitors to well-differentiated, excitatory glutamatergic neurons. The most differentiated neurons could be identified using a CAMK2A::GFP reporter gene and exhibited greater functionality, including NMDAR-mediated synaptic transmission. We conclude that utilizing single-cell and reporter gene approaches for selecting successfully programmed cells for study will greatly enhance the utility of hpiNs and other programmed neuronal populations in the modeling of nervous system disorders.Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved. 2017
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Quadrato G, Arlotta P. 2017. Present and future of modeling human brain development in 3D organoids. Current opinion in cell biology. 49:47-52. Pubmed: 29227864 DOI:S0955-0674(17)30109-6 Quadrato G, Arlotta P. 2017. Present and future of modeling human brain development in 3D organoids. Current opinion in cell biology. 49:47-52. Pubmed: 29227864 DOI:S0955-0674(17)30109-6 Three-dimensional (3D) brain organoids derived from human pluripotent stem cells hold great potential to investigate complex human genetic states and to model aspects of human brain development and pathology. However, the field of brain organoids is still in its infancy, and their use has been limited by their variability and their inability to differentiate into 3D structures with reproducible anatomical organization. Here, starting from a review of basic principles of in vitro 'brain organogenesis', we discuss which aspects of human brain development and disease can be faithfully modeled with current brain organoid protocols, and discuss improvements that would allow them to become reliable tools to investigate complex features of human brain development and disease.Copyright © 2017 Elsevier Ltd. All rights reserved. -
Kim J, Hughes EG, Shetty AS, Arlotta P, Goff LA, Bergles DE, Brown SP. 2017. Changes in the Excitability of Neocortical Neurons in a Mouse Model of Amyotrophic Lateral Sclerosis Are Not Specific to Corticospinal Neurons and Are Modulated by Advancing Disease. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37(37):9037-9053. Pubmed: 28821643 DOI:10.1523/JNEUROSCI.0811-17.2017 Kim J, Hughes EG, Shetty AS, Arlotta P, Goff LA, Bergles DE, Brown SP. 2017. Changes in the Excitability of Neocortical Neurons in a Mouse Model of Amyotrophic Lateral Sclerosis Are Not Specific to Corticospinal Neurons and Are Modulated by Advancing Disease. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37(37):9037-9053. Pubmed: 28821643 DOI:10.1523/JNEUROSCI.0811-17.2017 Cell type-specific changes in neuronal excitability have been proposed to contribute to the selective degeneration of corticospinal neurons in amyotrophic lateral sclerosis (ALS) and to neocortical hyperexcitability, a prominent feature of both inherited and sporadic variants of the disease, but the mechanisms underlying selective loss of specific cell types in ALS are not known. We analyzed the physiological properties of distinct classes of cortical neurons in the motor cortex of mice of both sexes and found that they all exhibit increases in intrinsic excitability that depend on disease stage. Targeted recordings and calcium imaging further revealed that neurons adapt their functional properties to normalize cortical excitability as the disease progresses. Although different neuron classes all exhibited increases in intrinsic excitability, transcriptional profiling indicated that the molecular mechanisms underlying these changes are cell type specific. The increases in excitability in both excitatory and inhibitory cortical neurons show that selective dysfunction of neuronal cell types cannot account for the specific vulnerability of corticospinal motor neurons in ALS. Furthermore, the stage-dependent alterations in neuronal function highlight the ability of cortical circuits to adapt as disease progresses. These findings show that both disease stage and cell type must be considered when developing therapeutic strategies for treating ALS. It is not known why certain classes of neurons preferentially die in different neurodegenerative diseases. It has been proposed that the enhanced excitability of affected neurons is a major contributor to their selective loss. We show using a mouse model of amyotrophic lateral sclerosis (ALS), a disease in which corticospinal neurons exhibit selective vulnerability, that changes in excitability are not restricted to this neuronal class and that excitability does not increase monotonically with disease progression. Moreover, although all neuronal cell types tested exhibited abnormal functional properties, analysis of their gene expression demonstrated cell type-specific responses to the ALS-causing mutation. These findings suggest that therapies for ALS may need to be tailored for different cell types and stages of disease.Copyright © 2017 the authors 0270-6474/17/379038-17$15.00/0. -
Arlotta P, Vanderhaeghen P. 2017. Editorial overview: Developmental neuroscience 2017. Current opinion in neurobiology. 42:A1-A4. Pubmed: 28117212 DOI:S0959-4388(17)30009-0 Arlotta P, Vanderhaeghen P. 2017. Editorial overview: Developmental neuroscience 2017. Current opinion in neurobiology. 42:A1-A4. Pubmed: 28117212 DOI:S0959-4388(17)30009-0 -
Quadrato G, Nguyen T, Macosko EZ, Sherwood JL, Min Yang S, Berger DR, Maria N, Scholvin J, Goldman M, Kinney JP, Boyden ES, Lichtman JW, Williams ZM, McCarroll SA, Arlotta P. 2017. Cell diversity and network dynamics in photosensitive human brain organoids. Nature. 545(7652):48-53. Pubmed: 28445462 DOI:10.1038/nature22047 Quadrato G, Nguyen T, Macosko EZ, Sherwood JL, Min Yang S, Berger DR, Maria N, Scholvin J, Goldman M, Kinney JP, Boyden ES, Lichtman JW, Williams ZM, McCarroll SA, Arlotta P. 2017. Cell diversity and network dynamics in photosensitive human brain organoids. Nature. 545(7652):48-53. Pubmed: 28445462 DOI:10.1038/nature22047 In vitro models of the developing brain such as three-dimensional brain organoids offer an unprecedented opportunity to study aspects of human brain development and disease. However, the cells generated within organoids and the extent to which they recapitulate the regional complexity, cellular diversity and circuit functionality of the brain remain undefined. Here we analyse gene expression in over 80,000 individual cells isolated from 31 human brain organoids. We find that organoids can generate a broad diversity of cells, which are related to endogenous classes, including cells from the cerebral cortex and the retina. Organoids could be developed over extended periods (more than 9 months), allowing for the establishment of relatively mature features, including the formation of dendritic spines and spontaneously active neuronal networks. Finally, neuronal activity within organoids could be controlled using light stimulation of photosensitive cells, which may offer a way to probe the functionality of human neuronal circuits using physiological sensory stimuli. 2016
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Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G, Hochedlinger K. 2016. A serial shRNA screen for roadblocks to reprogramming identifies the protein modifier SUMO2. Stem Cell Reports. 6(5) 704-716. DOI:10.1016/j.stemcr.2016.02.004 Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G, Hochedlinger K. 2016. A serial shRNA screen for roadblocks to reprogramming identifies the protein modifier SUMO2. Stem Cell Reports. 6(5) 704-716. DOI:10.1016/j.stemcr.2016.02.004 -
Chen HH, Arlotta P. 2016. Seq-ing the cortex one neuron at a time. Nature neuroscience. 19(2):179-81. Pubmed: 26814585 DOI:10.1038/nn.4230 Chen HH, Arlotta P. 2016. Seq-ing the cortex one neuron at a time. Nature neuroscience. 19(2):179-81. Pubmed: 26814585 DOI:10.1038/nn.4230 -
Quadrato G, Zhang AC, Arlotta P. 2016. Stressed out? Healing Tips for Newly Reprogrammed Neurons. Cell stem cell. 18(3):297-9. Pubmed: 26942845 DOI:S1934-5909(16)00070-9 Quadrato G, Zhang AC, Arlotta P. 2016. Stressed out? Healing Tips for Newly Reprogrammed Neurons. Cell stem cell. 18(3):297-9. Pubmed: 26942845 DOI:S1934-5909(16)00070-9 How do astrocyte-derived neurons deal with the sudden loss of their glial identity? Exciting new findings from Gascón et al. (2016) single out metabolic conversion as a critical checkpoint for direct neuronal reprogramming.Copyright © 2016 Elsevier Inc. All rights reserved. -
Amamoto R, Huerta VG, Takahashi E, Dai G, Grant AK, Fu Z, Arlotta P. 2016. Adult axolotls can regenerate original neuronal diversity in response to brain injury. eLife. 5. Pubmed: 27156560 DOI:10.7554/eLife.13998 Amamoto R, Huerta VG, Takahashi E, Dai G, Grant AK, Fu Z, Arlotta P. 2016. Adult axolotls can regenerate original neuronal diversity in response to brain injury. eLife. 5. Pubmed: 27156560 DOI:10.7554/eLife.13998 The axolotl can regenerate multiple organs, including the brain. It remains, however, unclear whether neuronal diversity, intricate tissue architecture, and axonal connectivity can be regenerated; yet, this is critical for recovery of function and a central aim of cell replacement strategies in the mammalian central nervous system. Here, we demonstrate that, upon mechanical injury to the adult pallium, axolotls can regenerate several of the populations of neurons present before injury. Notably, regenerated neurons acquire functional electrophysiological traits and respond appropriately to afferent inputs. Despite the ability to regenerate specific, molecularly-defined neuronal subtypes, we also uncovered previously unappreciated limitations by showing that newborn neurons organize within altered tissue architecture and fail to re-establish the long-distance axonal tracts and circuit physiology present before injury. The data provide a direct demonstration that diverse, electrophysiologically functional neurons can be regenerated in axolotls, but challenge prior assumptions of functional brain repair in regenerative species. -
Tomassy GS, Dershowitz LB, Arlotta P. 2016. Diversity Matters: A Revised Guide to Myelination. Trends in cell biology. 26(2):135-147. Pubmed: 26442841 DOI:S0962-8924(15)00164-6 Tomassy GS, Dershowitz LB, Arlotta P. 2016. Diversity Matters: A Revised Guide to Myelination. Trends in cell biology. 26(2):135-147. Pubmed: 26442841 DOI:S0962-8924(15)00164-6 The evolutionary success of the vertebrate nervous system is largely due to a unique structural feature--the myelin sheath, a fatty envelope that surrounds the axons of neurons. By increasing the speed by which electrical signals travel along axons, myelin facilitates neuronal communication between distant regions of the nervous system. We review the cellular and molecular mechanisms that regulate the development of myelin as well as its homeostasis in adulthood. We discuss how finely tuned neuron-oligodendrocyte interactions are central to myelin formation during development and in the adult, and how these interactions can have profound implications for the plasticity of the adult brain. We also speculate how the functional diversity of both neurons and oligodendrocytes may impact on the myelination process in both health and disease.Copyright © 2015 Elsevier Ltd. All rights reserved. -
Quadrato G, Brown J, Arlotta P. 2016. The promises and challenges of human brain organoids as models of neuropsychiatric disease. Nature medicine. 22(11):1220-1228. Pubmed: 27783065 DOI:10.1038/nm.4214 Quadrato G, Brown J, Arlotta P. 2016. The promises and challenges of human brain organoids as models of neuropsychiatric disease. Nature medicine. 22(11):1220-1228. Pubmed: 27783065 DOI:10.1038/nm.4214 Neuropsychiatric disorders such as autism spectrum disorder (ASD), schizophrenia (SCZ) and bipolar disorder (BPD) are of great societal and medical importance, but the complexity of these diseases and the challenges of modeling the development and function of the human brain have made these disorders difficult to study experimentally. The recent development of 3D brain organoids derived from human pluripotent stem cells offers a promising approach for investigating the phenotypic underpinnings of these highly polygenic disorders and for understanding the contribution of individual risk variants and complex genetic background to human pathology. Here we discuss the advantages, limitations and future applications of human brain organoids as in vitro models of neuropsychiatric disease. 2015
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Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K. 2015. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 33(11) 1173-1181. DOI:10.1038/nbt.3388 Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K. 2015. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nat Biotechnol. 33(11) 1173-1181. DOI:10.1038/nbt.3388 -
Goff LA, Groff AF, Sauvageau M, Trayes-Gibson Z, Sanchez-Gomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalez-Celeiro M, Plana O, Li E, Gerhardinger C, Tomassy GS, Arlotta P, Rinn JL. 2015. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. 112(22):6855-62. Pubmed: 26034286 Goff LA, Groff AF, Sauvageau M, Trayes-Gibson Z, Sanchez-Gomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalez-Celeiro M, Plana O, Li E, Gerhardinger C, Tomassy GS, Arlotta P, Rinn JL. 2015. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America. 112(22):6855-62. Pubmed: 26034286 Long noncoding RNAs (lncRNAs) have been implicated in numerous cellular processes including brain development. However, the in vivo expression dynamics and molecular pathways regulated by these loci are not well understood. Here, we leveraged a cohort of 13 lncRNAnull mutant mouse models to investigate the spatiotemporal expression of lncRNAs in the developing and adult brain and the transcriptome alterations resulting from the loss of these lncRNA loci. We show that several lncRNAs are differentially expressed both in time and space, with some presenting highly restricted expression in only selected brain regions. We further demonstrate altered regulation of genes for a large variety of cellular pathways and processes upon deletion of the lncRNA loci. Finally, we found that 4 of the 13 lncRNAs significantly affect the expression of several neighboring proteincoding genes in a cis-like manner. By providing insight into the endogenous expression patterns and the transcriptional perturbations caused by deletion of the lncRNA locus in the developing and postnatal mammalian brain, these data provide a resource to facilitate future examination of the specific functional relevance of these genes in neural development, brain function, and disease. -
Lodato S, Arlotta P. 2015. Generating neuronal diversity in the mammalian cerebral cortex. Annual review of cell and developmental biology. 31:699-720. Pubmed: 26359774 DOI:10.1146/annurev-cellbio-100814-125353 Lodato S, Arlotta P. 2015. Generating neuronal diversity in the mammalian cerebral cortex. Annual review of cell and developmental biology. 31:699-720. Pubmed: 26359774 DOI:10.1146/annurev-cellbio-100814-125353 The neocortex is the part of the brain responsible for execution of higher-order brain functions, including cognition, sensory perception, and sophisticated motor control. During evolution, the neocortex has developed an unparalleled neuronal diversity, which still remains partly unclassified and unmapped at the functional level. Here, we broadly review the structural blueprint of the neocortex and discuss the current classification of its neuronal diversity. We then cover the principles and mechanisms that build neuronal diversity during cortical development and consider the impact of neuronal class-specific identity in shaping cortical connectivity and function. -
Ye Z, Mostajo-Radji MA, Brown JR, Rouaux C, Tomassy GS, Hensch TK, Arlotta P. 2015. Instructing Perisomatic Inhibition by Direct Lineage Reprogramming of Neocortical Projection Neurons. Neuron. 88(3):475-83. Pubmed: 26539889 DOI:S0896-6273(15)00872-7 Ye Z, Mostajo-Radji MA, Brown JR, Rouaux C, Tomassy GS, Hensch TK, Arlotta P. 2015. Instructing Perisomatic Inhibition by Direct Lineage Reprogramming of Neocortical Projection Neurons. Neuron. 88(3):475-83. Pubmed: 26539889 DOI:S0896-6273(15)00872-7 During development of the cerebral cortex, local GABAergic interneurons recognize and pair with excitatory projection neurons to ensure the fine excitatory-inhibitory balance essential for proper circuit function. Whether the class-specific identity of projection neurons has a role in the establishment of afferent inhibitory synapses is debated. Here, we report that direct in vivo lineage reprogramming of layer 2/3 (L2/3) callosal projection neurons (CPNs) into induced corticofugal projection neurons (iCFuPNs) increases inhibitory input onto the converted neurons to levels similar to that of endogenous CFuPNs normally found in layer 5 (L5). iCFuPNs recruit increased numbers of inhibitory perisomatic synapses from parvalbumin (PV)-positive interneurons, with single-cell precision and despite their ectopic location in L2/3. The data show that individual reprogrammed excitatory projection neurons extrinsically modulate afferent input by local PV(+) interneurons, suggesting that projection neuron class-specific identity can actively control the wiring of the cortical microcircuit.Copyright © 2015 Elsevier Inc. All rights reserved. -
Arlotta P, Hobert O. 2015. Homeotic Transformations of Neuronal Cell Identities. Trends in neurosciences. 38(12):751-762. Pubmed: 26596501 DOI:S0166-2236(15)00229-5 Arlotta P, Hobert O. 2015. Homeotic Transformations of Neuronal Cell Identities. Trends in neurosciences. 38(12):751-762. Pubmed: 26596501 DOI:S0166-2236(15)00229-5 Homeosis is classically defined as the transformation of one body part into something that resembles another body part. We propose here to broaden the concept of homeosis to the many neuronal cell identity transformations that have been uncovered over the past few years upon removal of specific regulatory factors in organisms from Caenorhabditis elegans to Drosophila, zebrafish, and mice. The concept of homeosis provides a framework for the evolution of cell type diversity in the brain.Copyright © 2015. Published by Elsevier Ltd. -
Lodato S, Shetty AS, Arlotta P. 2015. Cerebral cortex assembly: generating and reprogramming projection neuron diversity. Trends in neurosciences. 38(2):117-25. Pubmed: 25529141 DOI:S0166-2236(14)00211-2 Lodato S, Shetty AS, Arlotta P. 2015. Cerebral cortex assembly: generating and reprogramming projection neuron diversity. Trends in neurosciences. 38(2):117-25. Pubmed: 25529141 DOI:S0166-2236(14)00211-2 The mammalian cerebral cortex is responsible for the highest levels of associative, cognitive and motor functions. In the central nervous system (CNS) the cortex stands as a prime example of extreme neuronal diversity, broadly classified into excitatory projection neurons (PNs) and inhibitory interneurons (INs). We review here recent progress made in understanding the strategies and mechanisms that shape PN diversity during embryogenesis, and discuss how PN classes may be maintained, postnatally, for the life of the organism. In addition, we consider the intriguing possibility that PNs may be amenable to directed reprogramming of their class-specific features to allow enhanced cortical plasticity in the adult.Copyright © 2014 Elsevier Ltd. All rights reserved. -
Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P. 2015. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron. 85(2):275-288. Pubmed: 25556833 DOI:10.1016/j.neuron.2014.12.024 Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P. 2015. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron. 85(2):275-288. Pubmed: 25556833 DOI:10.1016/j.neuron.2014.12.024 Neuronal development requires a complex choreography of transcriptional decisions to obtain specific cellular identities. Realizing the ultimate goal of identifying genome-wide signatures that define and drive specific neuronal fates has been hampered by enormous complexity in both time and space during development. Here, we have paired high-throughput purification of pyramidal neuron subclasses with deep profiling of spatiotemporal transcriptional dynamics during corticogenesis to resolve lineage choice decisions. We identified numerous features ranging from spatial and temporal usage of alternative mRNA isoforms and promoters to a host of mRNA genes modulated during fate specification. Notably, we uncovered numerous long noncoding RNAs with restricted temporal and cell-type-specific expression. To facilitate future exploration, we provide an interactive online database to enable multidimensional data mining and dissemination. This multifaceted study generates a powerful resource and informs understanding of the transcriptional regulation underlying pyramidal neuron diversity in the neocortex.Copyright © 2015 Elsevier Inc. All rights reserved. -
Smith KA, Arlotta P, Watt FM, Solomon SL. 2015. Seven actionable strategies for advancing women in science, engineering, and medicine. Cell stem cell. 16(3):221-4. Pubmed: 25748929 DOI:S1934-5909(15)00068-5 Smith KA, Arlotta P, Watt FM, Solomon SL. 2015. Seven actionable strategies for advancing women in science, engineering, and medicine. Cell stem cell. 16(3):221-4. Pubmed: 25748929 DOI:S1934-5909(15)00068-5 Achieving gender equality in science will require devising and implementing strategies to overcome the political, administrative, financial, and cultural challenges that exist in the current environment. In this forum, we propose an initial shortlist of recommendations to promote gender equality in science and stimulate future efforts to level the field.Copyright © 2015 Elsevier Inc. All rights reserved. -
Harris J, Tomassy GS, Arlotta P. 2015. Building blocks of the cerebral cortex: from development to the dish. Wiley interdisciplinary reviews. Developmental biology. 4(5):529-44. Pubmed: 25926310 DOI:10.1002/wdev.192 Harris J, Tomassy GS, Arlotta P. 2015. Building blocks of the cerebral cortex: from development to the dish. Wiley interdisciplinary reviews. Developmental biology. 4(5):529-44. Pubmed: 25926310 DOI:10.1002/wdev.192 Since Ramon y Cajal's examination of the cellular makeup of the cerebral cortex, it has been appreciated that this tissue exhibits some of the greatest degrees of cellular heterogeneity in the entire nervous system. This intricate structure emerges during a well-choreographed developmental process. Here, we review current classifications of the cellular constituents of the cerebral cortex and examine how these building blocks are forged during development. We also look at how basic developmental features underlying cortex formation in vivo have been applied to protocols aimed at generating cortical tissue in vitro.© 2015 Wiley Periodicals, Inc. 2014
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Arlotta P, Berninger B. 2014. Brains in metamorphosis: reprogramming cell identity within the central nervous system. Current opinion in neurobiology. 27:208-14. Pubmed: 24800935 DOI:S0959-4388(14)00086-5 Arlotta P, Berninger B. 2014. Brains in metamorphosis: reprogramming cell identity within the central nervous system. Current opinion in neurobiology. 27:208-14. Pubmed: 24800935 DOI:S0959-4388(14)00086-5 During embryonic development, uncommitted pluripotent cells undergo progressive epigenetic changes that lock them into a final differentiated state. Can mammalian cells change identity within the living organism? Direct lineage reprogramming of cells has attracted attention as a means to achieve organ regeneration. However, it is unclear whether cells in the CNS are endowed with the plasticity to reprogram. Neurons in particular are considered among the most immutable cell types, able to retain their class-specific traits for the lifespan of the organism. Here we focus on two experimental paradigms, glia-to-neuron and neuron-to-neuron conversion, to consider how lineage reprogramming has challenged the notion of CNS immutability, paving the way for the application of reprogramming strategies to reshape neurons and circuits in vivo.Copyright © 2014 Elsevier Ltd. All rights reserved. -
Tomassy GS, Berger DR, Chen HH, Kasthuri N, Hayworth KJ, Vercelli A, Seung HS, Lichtman JW, Arlotta P. 2014. Distinct profiles of myelin distribution along single axons of pyramidal neurons in the neocortex. Science (New York, N.Y.). 344(6181):319-24. Pubmed: 24744380 DOI:10.1126/science.1249766 Tomassy GS, Berger DR, Chen HH, Kasthuri N, Hayworth KJ, Vercelli A, Seung HS, Lichtman JW, Arlotta P. 2014. Distinct profiles of myelin distribution along single axons of pyramidal neurons in the neocortex. Science (New York, N.Y.). 344(6181):319-24. Pubmed: 24744380 DOI:10.1126/science.1249766 Myelin is a defining feature of the vertebrate nervous system. Variability in the thickness of the myelin envelope is a structural feature affecting the conduction of neuronal signals. Conversely, the distribution of myelinated tracts along the length of axons has been assumed to be uniform. Here, we traced high-throughput electron microscopy reconstructions of single axons of pyramidal neurons in the mouse neocortex and built high-resolution maps of myelination. We find that individual neurons have distinct longitudinal distribution of myelin. Neurons in the superficial layers displayed the most diversified profiles, including a new pattern where myelinated segments are interspersed with long, unmyelinated tracts. Our data indicate that the profile of longitudinal distribution of myelin is an integral feature of neuronal identity and may have evolved as a strategy to modulate long-distance communication in the neocortex. -
Amamoto R, Arlotta P. 2014. Development-inspired reprogramming of the mammalian central nervous system. Science (New York, N.Y.). 343(6170):1239882. Pubmed: 24482482 DOI:10.1126/science.1239882 Amamoto R, Arlotta P. 2014. Development-inspired reprogramming of the mammalian central nervous system. Science (New York, N.Y.). 343(6170):1239882. Pubmed: 24482482 DOI:10.1126/science.1239882 In 2012, John Gurdon and Shinya Yamanaka shared the Nobel Prize for the demonstration that the identity of differentiated cells is not irreversibly determined but can be changed back to a pluripotent state under appropriate instructive signals. The principle that differentiated cells can revert to an embryonic state and even be converted directly from one cell type into another not only turns fundamental principles of development on their heads but also has profound implications for regenerative medicine. Replacement of diseased tissue with newly reprogrammed cells and modeling of human disease are concrete opportunities. Here, we focus on the central nervous system to consider whether and how reprogramming of cell identity may affect regeneration and modeling of a system historically considered immutable and hardwired. -
Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P. 2014. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nature neuroscience. 17(8):1046-54. Pubmed: 24997765 DOI:10.1038/nn.3757 Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P. 2014. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nature neuroscience. 17(8):1046-54. Pubmed: 24997765 DOI:10.1038/nn.3757 The neocortex contains an unparalleled diversity of neuronal subtypes, each defined by distinct traits that are developmentally acquired under the control of subtype-specific and pan-neuronal genes. The regulatory logic that orchestrates the expression of these unique combinations of genes is unknown for any class of cortical neuron. Here, we report that Fezf2 is a selector gene able to regulate the expression of gene sets that collectively define mouse corticospinal motor neurons (CSMN). We find that Fezf2 directly induces the glutamatergic identity of CSMN via activation of Vglut1 (Slc17a7) and inhibits a GABAergic fate by repressing transcription of Gad1. In addition, we identify the axon guidance receptor EphB1 as a target of Fezf2 necessary to execute the ipsilateral extension of the corticospinal tract. Our data indicate that co-regulated expression of neuron subtype-specific and pan-neuronal gene batteries by a single transcription factor is one component of the regulatory logic responsible for the establishment of CSMN identity. 2013
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Amamoto R, Arlotta P. 2013. Reshaping the brain: direct lineage conversion in the nervous system. F1000prime reports. 5:33. Pubmed: 24049637 DOI:10.12703/P5-33 Amamoto R, Arlotta P. 2013. Reshaping the brain: direct lineage conversion in the nervous system. F1000prime reports. 5:33. Pubmed: 24049637 DOI:10.12703/P5-33 During embryonic development, cells in an uncommitted pluripotent state undergo progressive epigenetic changes that lock them into a final restrictive differentiated state. However, recent advances have shown that not only is it possible for a fully differentiated cell to revert back to a pluripotent state, a process called nuclear reprogramming, but also that differentiated cells can be directly converted from one class into another without generating progenitor intermediates, a process known as direct lineage conversion. In this review, we discuss recent progress made in direct lineage reprogramming of differentiated cells into neurons and discuss some of the therapeutic implications of the findings. -
Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL. 2013. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. eLife. 2:e01749. Pubmed: 24381249 DOI:10.7554/eLife.01749 Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL. 2013. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. eLife. 2:e01749. Pubmed: 24381249 DOI:10.7554/eLife.01749 Many studies are uncovering functional roles for long noncoding RNAs (lncRNAs), yet few have been tested for in vivo relevance through genetic ablation in animal models. To investigate the functional relevance of lncRNAs in various physiological conditions, we have developed a collection of 18 lncRNA knockout strains in which the locus is maintained transcriptionally active. Initial characterization revealed peri- and postnatal lethal phenotypes in three mutant strains (Fendrr, Peril, and Mdgt), the latter two exhibiting incomplete penetrance and growth defects in survivors. We also report growth defects for two additional mutant strains (linc-Brn1b and linc-Pint). Further analysis revealed defects in lung, gastrointestinal tract, and heart in Fendrr(-/-) neonates, whereas linc-Brn1b(-/-) mutants displayed distinct abnormalities in the generation of upper layer II-IV neurons in the neocortex. This study demonstrates that lncRNAs play critical roles in vivo and provides a framework and impetus for future larger-scale functional investigation into the roles of lncRNA molecules. DOI: http://dx.doi.org/10.7554/eLife.01749.001. -
Rouaux C, Arlotta P. 2013. Direct lineage reprogramming of post-mitotic callosal neurons into corticofugal neurons in vivo. Nature cell biology. 15(2):214-21. Pubmed: 23334497 DOI:10.1038/ncb2660 Rouaux C, Arlotta P. 2013. Direct lineage reprogramming of post-mitotic callosal neurons into corticofugal neurons in vivo. Nature cell biology. 15(2):214-21. Pubmed: 23334497 DOI:10.1038/ncb2660 Once programmed to acquire a specific identity and function, cells rarely change in vivo. Neurons of the mammalian central nervous system (CNS) in particular are a classic example of a stable, terminally differentiated cell type. With the exception of the adult neurogenic niches, where a limited set of neuronal subtypes continue to be generated throughout life, CNS neurons are born only during embryonic and early postnatal development. Once generated, neurons become permanently post-mitotic and do not change their identity for the lifespan of the organism. Here, we have investigated whether excitatory neurons of the neocortex can be instructed to directly reprogram their identity post-mitotically from one subtype into another, in vivo. We show that embryonic and early postnatal callosal projection neurons of layer II/III can be post-mitotically lineage reprogrammed into layer-V/VI corticofugal projection neurons following expression of the transcription factor encoded by Fezf2. Reprogrammed callosal neurons acquire molecular properties of corticofugal projection neurons and change their axonal connectivity from interhemispheric, intracortical projections to corticofugal projections directed below the cortex. The data indicate that during a window of post-mitotic development neurons can change their identity, acquiring critical features of alternative neuronal lineages. -
Tomassy GS, Lodato S, Arlotta P. 2013. A sip of GABA for the cerebral cortex. Neuron. 77(1):1-3. Pubmed: 23312509 DOI:S0896-6273(12)01165-8 Tomassy GS, Lodato S, Arlotta P. 2013. A sip of GABA for the cerebral cortex. Neuron. 77(1):1-3. Pubmed: 23312509 DOI:S0896-6273(12)01165-8 Cortical and striatal interneurons are both generated within the ventral telencephalon, but their migratory journey takes them to very different destinations. Two articles in this issue (van den Berge et al., 2013; McKinsey et al., 2013) add an important molecular component to our understanding of how, during development, interneurons reach the cerebral cortex.Copyright © 2013 Elsevier Inc. All rights reserved. -
Zuccaro E, Arlotta P. 2013. The quest for myelin in the adult brain. Nature cell biology. 15(6):572-5. Pubmed: 23644465 DOI:10.1038/ncb2750 Zuccaro E, Arlotta P. 2013. The quest for myelin in the adult brain. Nature cell biology. 15(6):572-5. Pubmed: 23644465 DOI:10.1038/ncb2750 Although myelination largely occurs during early postnatal life, myelinating oligodendrocytes are still generated in the adult brain. Myelin turnover in the adult is necessary for proper neuronal function and is gravely compromised in myelin disorders. The lineage relationship between adult neural stem cells and adult-born oligodendrocytes has been clarified, highlighting molecular pathways that could potentially be targeted to favour de novo myelination in pathological situations. 2012
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Sohur US, Arlotta P, Macklis JD. 2012. Developmental Controls are Re-Expressed during Induction of Neurogenesis in the Neocortex of Young Adult Mice. Frontiers in neuroscience. 6:12. Pubmed: 22347158 DOI:10.3389/fnins.2012.00012 Sohur US, Arlotta P, Macklis JD. 2012. Developmental Controls are Re-Expressed during Induction of Neurogenesis in the Neocortex of Young Adult Mice. Frontiers in neuroscience. 6:12. Pubmed: 22347158 DOI:10.3389/fnins.2012.00012 Whether induction of low-level neurogenesis in normally non-neurogenic regions of the adult brain mimics aspects of developmental neurogenesis is currently unknown. Previously, we and others identified that biophysically induced, neuron subtype-specific apoptosis in mouse neocortex results in induction of neurogenesis of limited numbers of subtype-appropriate projection neurons with axonal projections to either thalamus or spinal cord, depending on the neuron subtype activated to undergo targeted apoptosis. Here, we test the hypothesis that developmental genes from embryonic corticogenesis are re-activated, and that some of these genes might underlie induction of low-level adult neocortical neurogenesis. We directly investigated this hypothesis via microarray analysis of microdissected regions of young adult mouse neocortex undergoing biophysically activated targeted apoptosis of neocortical callosal projection neurons. We compared the microarray results identifying differentially expressed genes with public databases of embryonic developmental genes. We find that, following activation of subtype-specific neuronal apoptosis, three distinct sets of normal developmental genes are selectively re-expressed in neocortical regions of induced neurogenesis in young adult mice: (1) genes expressed by subsets of progenitors and immature neurons in the developing ventricular and/or subventricular zones; (2) genes normally expressed by developmental radial glial progenitors; and (3) genes involved in synaptogenesis. Together with previous results, the data indicate that at least some developmental molecular controls over embryonic neurogenesis can be re-activated in the setting of induction of neurogenesis in the young adult neocortex, and suggest that some of these activate and initiate adult neuronal differentiation from endogenous progenitor populations. Understanding molecular mechanisms contributing to induced adult neurogenesis might enable directed CNS repair. -
Cappello S, Böhringer CR, Bergami M, Conzelmann KK, Ghanem A, Tomassy GS, Arlotta P, Mainardi M, Allegra M, Caleo M, van Hengel J, Brakebusch C, Götz M. 2012. A radial glia-specific role of RhoA in double cortex formation. Neuron. 73(5):911-24. Pubmed: 22405202 DOI:10.1016/j.neuron.2011.12.030 Cappello S, Böhringer CR, Bergami M, Conzelmann KK, Ghanem A, Tomassy GS, Arlotta P, Mainardi M, Allegra M, Caleo M, van Hengel J, Brakebusch C, Götz M. 2012. A radial glia-specific role of RhoA in double cortex formation. Neuron. 73(5):911-24. Pubmed: 22405202 DOI:10.1016/j.neuron.2011.12.030 The positioning of neurons in the cerebral cortex is of crucial importance for its function as highlighted by the severe consequences of migrational disorders in patients. Here we show that genetic deletion of the small GTPase RhoA in the developing cerebral cortex results in two migrational disorders: subcortical band heterotopia (SBH), a heterotopic cortex underlying the normotopic cortex, and cobblestone lissencephaly, in which neurons protrude beyond layer I at the pial surface of the brain. Surprisingly, RhoA(-/-) neurons migrated normally when transplanted into wild-type cerebral cortex, whereas the converse was not the case. Alterations in the radial glia scaffold are demonstrated to cause these migrational defects through destabilization of both the actin and the microtubules cytoskeleton. These data not only demonstrate that RhoA is largely dispensable for migration in neurons but also showed that defects in radial glial cells, rather than neurons, can be sufficient to produce SBH.Copyright © 2012 Elsevier Inc. All rights reserved. -
López-Bendito G, Arlotta P. 2012. Cell replacement therapies for nervous system regeneration. Developmental neurobiology. 72(2):145-52. Pubmed: 21557508 DOI:10.1002/dneu.20897 López-Bendito G, Arlotta P. 2012. Cell replacement therapies for nervous system regeneration. Developmental neurobiology. 72(2):145-52. Pubmed: 21557508 DOI:10.1002/dneu.20897 The adult brain was thought to be a slowly decaying organ, a sophisticated but flawed machine condemned to inevitable decline. Today we know that the brain is more plastic than previously assumed, as most prominently demonstrated by the constitutive birth of new neurons that occurs in selected regions of the adult brain, even in humans. However, the overall modest capacity for endogenous repair of the central nervous system (CNS) has sparked interest in understanding the barriers to neuronal regeneration and in developing novel approaches to enable neuronal and circuit repair for therapeutic benefit in neurodegenerative disorders and traumatic injuries. Scientists recently assembled in Baeza, a picturesque town in the south of Spain, to discuss aspects of CNS regeneration. The picture that emerged shows how an integrated view of developmental and adult neurogenesis may inform the manipulation of neural progenitors, differentiated cells, and pluripotent stem cells for therapeutic benefit and foster new understanding of the inner limits of brain plasticity.Copyright © 2011 Wiley Periodicals, Inc. -
Rouaux C, Bhai S, Arlotta P. 2012. Programming and reprogramming neuronal subtypes in the central nervous system. Developmental neurobiology. 72(7):1085-98. Pubmed: 22378700 DOI:10.1002/dneu.22018 Rouaux C, Bhai S, Arlotta P. 2012. Programming and reprogramming neuronal subtypes in the central nervous system. Developmental neurobiology. 72(7):1085-98. Pubmed: 22378700 DOI:10.1002/dneu.22018 Recent discoveries in nuclear reprogramming have challenged the dogma that the identity of terminally differentiated cells cannot be changed. The identification of molecular mechanisms that reprogram differentiated cells to a new identity carries profound implications for regenerative medicine across organ systems. The central nervous system (CNS) has historically been considered to be largely immutable. However, recent studies indicate that even the adult CNS is imparted with the potential to change under the appropriate stimuli. Here, we review current knowledge regarding the capability of distinct cells within the CNS to reprogram their identity and consider the role of developmental signals in directing these cell fate decisions. Finally, we discuss the progress and current challenges of using developmental signals to precisely direct the generation of individual neuronal subtypes in the postnatal CNS and in the dish.Copyright © 2012 Wiley Periodicals, Inc. 2011
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Lodato S, Rouaux C, Quast KB, Jantrachotechatchawan C, Studer M, Hensch TK, Arlotta P. 2011. Excitatory projection neuron subtypes control the distribution of local inhibitory interneurons in the cerebral cortex. Neuron. 69(4):763-79. Pubmed: 21338885 DOI:10.1016/j.neuron.2011.01.015 Lodato S, Rouaux C, Quast KB, Jantrachotechatchawan C, Studer M, Hensch TK, Arlotta P. 2011. Excitatory projection neuron subtypes control the distribution of local inhibitory interneurons in the cerebral cortex. Neuron. 69(4):763-79. Pubmed: 21338885 DOI:10.1016/j.neuron.2011.01.015 In the mammalian cerebral cortex, the developmental events governing the integration of excitatory projection neurons and inhibitory interneurons into balanced local circuitry are poorly understood. We report that different subtypes of projection neurons uniquely and differentially determine the laminar distribution of cortical interneurons. We find that in Fezf2⁻/⁻ cortex, the exclusive absence of subcerebral projection neurons and their replacement by callosal projection neurons cause distinctly abnormal lamination of interneurons and altered GABAergic inhibition. In addition, experimental generation of either corticofugal neurons or callosal neurons below the cortex is sufficient to recruit cortical interneurons to these ectopic locations. Strikingly, the identity of the projection neurons generated, rather than strictly their birthdate, determines the specific types of interneurons recruited. These data demonstrate that in the neocortex individual populations of projection neurons cell-extrinsically control the laminar fate of interneurons and the assembly of local inhibitory circuitry.Copyright © 2011 Elsevier Inc. All rights reserved. -
Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P. 2011. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nature biotechnology. 29(2):149-53. Pubmed: 21248753 DOI:10.1038/nbt.1775 Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P. 2011. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nature biotechnology. 29(2):149-53. Pubmed: 21248753 DOI:10.1038/nbt.1775 The ability to direct functional proteins to specific DNA sequences is a long-sought goal in the study and engineering of biological processes. Transcription activator-like effectors (TALEs) from Xanthomonas sp. are site-specific DNA-binding proteins that can be readily designed to target new sequences. Because TALEs contain a large number of repeat domains, it can be difficult to synthesize new variants. Here we describe a method that overcomes this problem. We leverage codon degeneracy and type IIs restriction enzymes to generate orthogonal ligation linkers between individual repeat monomers, thus allowing full-length, customized, repeat domains to be constructed by hierarchical ligation. We synthesized 17 TALEs that are customized to recognize specific DNA-binding sites, and demonstrate that they can specifically modulate transcription of endogenous genes (SOX2 and KLF4) in human cells. -
Lodato S, Tomassy GS, De Leonibus E, Uzcategui YG, Andolfi G, Armentano M, Touzot A, Gaztelu JM, Arlotta P, Menendez de la Prida L, Studer M. 2011. Loss of COUP-TFI alters the balance between caudal ganglionic eminence- and medial ganglionic eminence-derived cortical interneurons and results in resistance to epilepsy. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31(12):4650-62. Pubmed: 21430164 DOI:10.1523/JNEUROSCI.6580-10.2011 Lodato S, Tomassy GS, De Leonibus E, Uzcategui YG, Andolfi G, Armentano M, Touzot A, Gaztelu JM, Arlotta P, Menendez de la Prida L, Studer M. 2011. Loss of COUP-TFI alters the balance between caudal ganglionic eminence- and medial ganglionic eminence-derived cortical interneurons and results in resistance to epilepsy. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31(12):4650-62. Pubmed: 21430164 DOI:10.1523/JNEUROSCI.6580-10.2011 In rodents, cortical interneurons originate from the medial ganglionic eminence (MGE) and caudal ganglionic eminence (CGE) according to precise temporal schedules. The mechanisms controlling the specification of CGE-derived interneurons and their role in cortical circuitry are still unknown. Here, we show that COUP-TFI expression becomes restricted to the dorsal MGE and CGE at embryonic day 13.5 in the basal telencephalon. Conditional loss of function of COUP-TFI in subventricular precursors and postmitotic cells leads to a decrease of late-born, CGE-derived, VIP (vasoactive intestinal peptide)- and CR (calretinin)-expressing bipolar cortical neurons, compensated by the concurrent increase of early-born MGE-derived, PV (parvalbumin)-expressing interneurons. Strikingly, COUP-TFI mutants are more resistant to pharmacologically induced seizures, a phenotype that is dependent on GABAergic signaling. Together, our data indicate that COUP-TFI controls the delicate balance between MGE- and CGE-derived cortical interneurons by regulating intermediate progenitor divisions and ultimately affecting the activity of the cortical inhibitory circuitry. 2010
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Rouaux C, Arlotta P. 2010. Fezf2 directs the differentiation of corticofugal neurons from striatal progenitors in vivo. Nature neuroscience. 13(11):1345-7. Pubmed: 20953195 DOI:10.1038/nn.2658 Rouaux C, Arlotta P. 2010. Fezf2 directs the differentiation of corticofugal neurons from striatal progenitors in vivo. Nature neuroscience. 13(11):1345-7. Pubmed: 20953195 DOI:10.1038/nn.2658 In the developing cerebral cortex, cell-extrinsic and cell-intrinsic signals govern the establishment of neuron subtype-specific identity. Here we show that, within the niche of the striatum, the expression of a single transcription factor, Fezf2, is sufficient to generate corticofugal neurons from progenitors fated to become medium spiny neurons. This demonstrates that a specific population of cortical projection neurons can be directed to differentiate outside of the cortex by cell-autonomous signaling. -
Shoemaker LD, Arlotta P. 2010. Untangling the cortex: Advances in understanding specification and differentiation of corticospinal motor neurons. BioEssays : news and reviews in molecular, cellular and developmental biology. 32(3):197-206. Pubmed: 20108227 DOI:10.1002/bies.200900114 Shoemaker LD, Arlotta P. 2010. Untangling the cortex: Advances in understanding specification and differentiation of corticospinal motor neurons. BioEssays : news and reviews in molecular, cellular and developmental biology. 32(3):197-206. Pubmed: 20108227 DOI:10.1002/bies.200900114 The mature cerebral cortex contains a staggering variety of projection neuron subtypes, and a number of complementary studies have recently begun to define their identity and embryonic origin. Among the different types of cortical projection neurons, subcerebral projection neurons, including corticospinal motor neurons (CSMN), have been extensively studied and some of the molecular controls over their differentiation have been elucidated. Here, we first provide an overview of the approaches used to purify and molecularly profile neuronal populations of the neocortex and, more broadly, of the central nervous system (CNS). Next, we specifically review recent progress in understanding the genes that define and control development of the CSMN population. Finally, we briefly discuss the relevance of this work to current questions regarding the mechanisms of the establishment of projection neuron subtype identity in the neocortex and its implications to direct the differentiation of CSMN for therapeutic benefit. -
Tomassy GS, Lodato S, Trayes-Gibson Z, Arlotta P. 2010. Development and regeneration of projection neuron subtypes of the cerebral cortex. Science progress. 93(Pt 2):151-69. Pubmed: 20681320 Tomassy GS, Lodato S, Trayes-Gibson Z, Arlotta P. 2010. Development and regeneration of projection neuron subtypes of the cerebral cortex. Science progress. 93(Pt 2):151-69. Pubmed: 20681320 The idea of repairing damaged neuronal circuitry in the mammalian central nervous system (CNS) has challenged neuroscientists for centuries. This is mainly due to the notorious inability of neurons to regenerate and the unparalleled cellular diversity of the nervous system. In the mammalian cerebral cortex, one of the most complex areas of the CNS, multipotent neural stem and progenitor cells undergo progressive specification during development to generate the staggering variety of projection neuron subtypes that are found in the adult. How is this process orchestrated in the embryo? And, can developmental signals be used to regenerate projection neuron subtypes in the adult or in the dish? Here, we first provide an overview of the diversity and fate potential of neural progenitors of the cerebral cortex during development. Further, we discuss the plasticity of neural progenitors and the roles of intrinsic and extrinsic signals over progenitor fate. Finally, we discuss the relevance of developmental signals for efforts to direct the differentiation of pluripotent stem cells into specific types of cortical projection neurons for therapeutic benefit. 2009
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Molyneaux BJ, Arlotta P, Fame RM, MacDonald JL, MacQuarrie KL, Macklis JD. 2009. Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 29(39):12343-54. Pubmed: 19793993 DOI:10.1523/JNEUROSCI.6108-08.2009 Molyneaux BJ, Arlotta P, Fame RM, MacDonald JL, MacQuarrie KL, Macklis JD. 2009. Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 29(39):12343-54. Pubmed: 19793993 DOI:10.1523/JNEUROSCI.6108-08.2009 Little is known about the molecular development and heterogeneity of callosal projection neurons (CPN), cortical commissural neurons that connect homotopic regions of the two cerebral hemispheres via the corpus callosum and that are critical for bilateral integration of cortical information. Here we report on the identification of a series of genes that individually and in combination define CPN and novel CPN subpopulations during embryonic and postnatal development. We used in situ hybridization analysis, immunocytochemistry, and retrograde labeling to define the layer-specific and neuron-type-specific distribution of these newly identified CPN genes across different stages of maturation. We demonstrate that a subset of these genes (e.g., Hspb3 and Lpl) appear specific to all CPN (in layers II/III and V-VI), whereas others (e.g., Nectin-3, Plexin-D1, and Dkk3) discriminate between CPN of the deep layers and those of the upper layers. Furthermore, the data show that several genes finely subdivide CPN within individual layers and appear to label CPN subpopulations that have not been described previously using anatomical or morphological criteria. The genes identified here likely reflect the existence of distinct programs of gene expression governing the development, maturation, and function of the newly identified subpopulations of CPN. Together, these data define the first set of genes that identify and molecularly subcategorize distinct populations of callosal projection neurons, often located in distinct subdivisions of the canonical cortical laminae. 2008
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Lai T, Jabaudon D, Molyneaux BJ, Azim E, Arlotta P, Menezes JR, Macklis JD. 2008. SOX5 controls the sequential generation of distinct corticofugal neuron subtypes. Neuron. 57(2):232-47. Pubmed: 18215621 DOI:10.1016/j.neuron.2007.12.023 Lai T, Jabaudon D, Molyneaux BJ, Azim E, Arlotta P, Menezes JR, Macklis JD. 2008. SOX5 controls the sequential generation of distinct corticofugal neuron subtypes. Neuron. 57(2):232-47. Pubmed: 18215621 DOI:10.1016/j.neuron.2007.12.023 The molecular mechanisms controlling the development of distinct subtypes of neocortical projection neurons, and CNS neuronal diversity more broadly, are only now emerging. We report that the transcription factor SOX5 controls the sequential generation of distinct corticofugal neuron subtypes by preventing premature emergence of normally later-born corticofugal neurons. SOX5 loss-of-function causes striking overlap of the identities of the three principal sequentially born corticofugal neuron subtypes: subplate neurons, corticothalamic neurons, and subcerebral projection neurons. In Sox5(-/-) cortex, subplate neurons aberrantly develop molecular hallmarks and connectivity of subcerebral projection neurons; corticothalamic neurons are imprecisely differentiated, while differentiation of subcerebral projection neurons is accelerated. Gain-of-function analysis reinforces the critical role of SOX5 in controlling the sequential generation of corticofugal neurons--SOX5 overexpression at late stages of corticogenesis causes re-emergence of neurons with corticofugal features. These data indicate that SOX5 controls the timing of critical fate decisions during corticofugal neuron production and thus subtype-specific differentiation and neocortical neuron diversity. -
Arlotta P, Molyneaux BJ, Jabaudon D, Yoshida Y, Macklis JD. 2008. Ctip2 controls the differentiation of medium spiny neurons and the establishment of the cellular architecture of the striatum. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28(3):622-32. Pubmed: 18199763 DOI:10.1523/JNEUROSCI.2986-07.2008 Arlotta P, Molyneaux BJ, Jabaudon D, Yoshida Y, Macklis JD. 2008. Ctip2 controls the differentiation of medium spiny neurons and the establishment of the cellular architecture of the striatum. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28(3):622-32. Pubmed: 18199763 DOI:10.1523/JNEUROSCI.2986-07.2008 Striatal medium spiny neurons (MSN) are critically involved in motor control, and their degeneration is a principal component of Huntington's disease. We find that the transcription factor Ctip2 (also known as Bcl11b) is central to MSN differentiation and striatal development. Within the striatum, it is expressed by all MSN, although it is excluded from essentially all striatal interneurons. In the absence of Ctip2, MSN do not fully differentiate, as demonstrated by dramatically reduced expression of a large number of MSN markers, including DARPP-32, FOXP1, Chrm4, Reelin, MOR1 (mu-opioid receptor 1), glutamate receptor 1, and Plexin-D1. Furthermore, MSN fail to aggregate into patches, resulting in severely disrupted patch-matrix organization within the striatum. Finally, heterotopic cellular aggregates invade the Ctip2-/- striatum, suggesting a failure by MSN to repel these cells in the absence of Ctip2. This is associated with abnormal dopaminergic innervation of the mutant striatum and dramatic changes in gene expression, including dysregulation of molecules involved in cellular repulsion. Together, these data indicate that Ctip2 is a critical regulator of MSN differentiation, striatal patch development, and the establishment of the cellular architecture of the striatum. 2007
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Molyneaux BJ, Arlotta P, Menezes JR, Macklis JD. 2007. Neuronal subtype specification in the cerebral cortex. Nature reviews. Neuroscience. 8(6):427-37. Pubmed: 17514196 Molyneaux BJ, Arlotta P, Menezes JR, Macklis JD. 2007. Neuronal subtype specification in the cerebral cortex. Nature reviews. Neuroscience. 8(6):427-37. Pubmed: 17514196 In recent years, tremendous progress has been made in understanding the mechanisms underlying the specification of projection neurons within the mammalian neocortex. New experimental approaches have made it possible to identify progenitors and study the lineage relationships of different neocortical projection neurons. An expanding set of genes with layer and neuronal subtype specificity have been identified within the neocortex, and their function during projection neuron development is starting to be elucidated. Here, we assess recent data regarding the nature of neocortical progenitors, review the roles of individual genes in projection neuron specification and discuss the implications for progenitor plasticity. -
Molyneaux BJ, Arlotta P, Macklis JD. 2007. Molecular development of corticospinal motor neuron circuitry. Novartis Foundation symposium. 288:3-15; discussion 15-20, 96-8. Pubmed: 18494249 Molyneaux BJ, Arlotta P, Macklis JD. 2007. Molecular development of corticospinal motor neuron circuitry. Novartis Foundation symposium. 288:3-15; discussion 15-20, 96-8. Pubmed: 18494249 The organization, function and evolution of the brain depends centrally on the precise development of a wide diversity of distinct neuronal subtypes. Furthermore, given the heterogeneity of neuronal subtypes within the CNS and the complexity of their connections, attempts to functionally repair circuitry will require a detailed understanding of the molecular controls over differentiation, connectivity and survival of specific lineages. Toward these goals, we recently identified developmentally regulated transcriptional programmes for specific lineages of long-distance neocortical projection neurons as they develop in vivo (in particular, for corticospinal motor neurons; CSMN). We purified CSMN, a clinically important population of neocortical projection neurons, at distinct stages of development in vivo, and compared their gene expression to that of two other pure populations of neocortical projection neurons. We identified novel and largely uncharacterized genes that are instructive for CSMN development and implicated in key developmental processes. These include Fezf2 (also known as Fezl), a regulator of subcerebral projection neuron identity, and Ctip2 (also known as Bcl1b), a regulator of the fasciculation, outgrowth and pathfinding of CSMN axonal projections to the spinal cord. Loss-of-function and gain-of-function analysis for multiple identified genes reveal programmes of combinatorial molecular controls over the precise development of key neocortical and other forebrain projection neuron populations that elucidate organization and function of the forebrain, and that might be manipulated toward functional cellular repair of complex brain circuitry. -
Gao X, Arlotta P, Macklis JD, Chen J. 2007. Conditional knock-out of beta-catenin in postnatal-born dentate gyrus granule neurons results in dendritic malformation. The Journal of neuroscience : the official journal of the Society for Neuroscience. 27(52):14317-25. Pubmed: 18160639 Gao X, Arlotta P, Macklis JD, Chen J. 2007. Conditional knock-out of beta-catenin in postnatal-born dentate gyrus granule neurons results in dendritic malformation. The Journal of neuroscience : the official journal of the Society for Neuroscience. 27(52):14317-25. Pubmed: 18160639 Neurons are continuously added to the brain throughout life, and these neurons must develop dendritic arbors and functional connections with existing neurons to be integrated into neuronal circuitry. The molecular mechanisms that regulate dendritic development of newborn neurons in the hippocampal dentate gyrus are still unclear. Here, we show that beta-catenin is expressed in newborn granule neurons and in neural progenitor cells in the hippocampal dentate gyrus. Specific knock-out of beta-catenin in newborn neurons, without affecting beta-catenin expression in neural progenitor cells, led to defects in dendritic morphology of these newborn neurons in vivo. Majority of newborn neurons that cannot extend dendrites survive <1 month after they were born. Our results indicate that beta-catenin plays an important role in dendritic development of postnatal-born neurons in vivo, and is therefore essential for the neurogenesis in the postnatal brain. 2005
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Molyneaux BJ, Arlotta P, Hirata T, Hibi M, Macklis JD. 2005. Fezl is required for the birth and specification of corticospinal motor neurons. Neuron. 47(6):817-31. Pubmed: 16157277 Molyneaux BJ, Arlotta P, Hirata T, Hibi M, Macklis JD. 2005. Fezl is required for the birth and specification of corticospinal motor neurons. Neuron. 47(6):817-31. Pubmed: 16157277 The molecular mechanisms controlling the differentiation of neural progenitors into distinct subtypes of neurons during neocortical development are unknown. Here, we report that Fezl is required for the specification of corticospinal motor neurons and other subcerebral projection neurons, which are absent from Fezl null mutant neocortex. There is neither an increase in cell death in Fezl(-/-) cortex nor abnormalities in migration, indicating that the absence of subcerebral projection neurons is due to a failure in fate specification. In striking contrast, other neuronal populations in the same and other cortical layers are born normally. Overexpression of Fezl results in excess production of subcerebral projection neurons and arrested migration of these neurons in the germinal zone. These data indicate that Fezl plays a central role in the specification of corticospinal motor neurons and other subcerebral projection neurons, controlling early decisions regarding lineage-specific differentiation from neural progenitors. -
Arlotta P, Macklis JD. 2005. Archeo-cell biology: carbon dating is not just for pots and dinosaurs. Cell. 122(1):4-6. Pubmed: 16009125 Arlotta P, Macklis JD. 2005. Archeo-cell biology: carbon dating is not just for pots and dinosaurs. Cell. 122(1):4-6. Pubmed: 16009125 Defining the life span of specific human cell populations is limited by our inability to mark the exact time when cells are born in a way that can be detected over many years. In this issue of Cell, Spalding et al. (2005) describe a clever strategy for retrospectively birth dating human cells in vivo, based on their incorporation of 14C during a peak in atmospheric levels of this isotope resulting from above-ground nuclear arms testing in the 1950s. -
Arlotta P, Molyneaux BJ, Chen J, Inoue J, Kominami R, Macklis JD. 2005. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron. 45(2):207-21. Pubmed: 15664173 Arlotta P, Molyneaux BJ, Chen J, Inoue J, Kominami R, Macklis JD. 2005. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron. 45(2):207-21. Pubmed: 15664173 Within the vertebrate nervous system, the presence of many different lineages of neurons and glia complicates the molecular characterization of single neuronal populations. In order to elucidate molecular mechanisms underlying the specification and development of corticospinal motor neurons (CSMN), we purified CSMN at distinct stages of development in vivo and compared their gene expression to two other pure populations of cortical projection neurons: callosal projection neurons and corticotectal projection neurons. We found genes that are potentially instructive for CSMN development, as well as genes that are excluded from CSMN and are restricted to other populations of neurons, even within the same cortical layer. Loss-of-function experiments in null mutant mice for Ctip2 (also known as Bcl11b), one of the newly characterized genes, demonstrate that it plays a critical role in the development of CSMN axonal projections to the spinal cord in vivo, confirming that we identified central genetic determinants of the CSMN population. 2004
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Catapano LA, Arlotta P, Cage TA, Macklis JD. 2004. Stage-specific and opposing roles of BDNF, NT-3 and bFGF in differentiation of purified callosal projection neurons toward cellular repair of complex circuitry. The European journal of neuroscience. 19(9):2421-34. Pubmed: 15128396 Catapano LA, Arlotta P, Cage TA, Macklis JD. 2004. Stage-specific and opposing roles of BDNF, NT-3 and bFGF in differentiation of purified callosal projection neurons toward cellular repair of complex circuitry. The European journal of neuroscience. 19(9):2421-34. Pubmed: 15128396 Cellular repair of neuronal circuitry affected by neurodegenerative disease or injury may be approached in the adult neocortex via transplantation of neural precursors ("neural stem cells") or via molecular manipulation and recruitment of new neurons from endogenous precursors in situ. A major challenge for potential future approaches to neuronal replacement will be to specifically direct and control progressive differentiation, axonal projection and connectivity of neural precursors along a specific neuronal lineage. This goal will require a progressively more detailed understanding of the molecular controls over morphologic differentiation of specific neuronal lineages, including neurite outgrowth and elongation, in order to accurately permit and direct proper neuronal integration and connectivity. Here, we investigate controls over the morphologic differentiation of a specific prototypical lineage of cortical neurons: callosal projection neurons (CPN). We highly enriched CPN to an essentially pure population, and cultured them at three distinct stages of development from embryonic and postnatal mouse cortex by retrograde fluorescence labelling, followed by fluorescence-activated cell sorting. We find that specific peptide growth factors exert direct stage-specific positive and negative effects over the morphologic differentiation and process outgrowth of CPN. These effects are distinct from the effects of these growth factors on CPN survival [Catapano et al. (2001)J. Neurosci., 21, 8863-8872]. These data may be critical for the future goal of directing lineage-specific neuronal differentiation of transplanted or endogenous precursors/"stem cells" toward cellular repair of complex cortical circuitry. -
Emsley JG, Mitchell BD, Magavi SS, Arlotta P, Macklis JD. 2004. The repair of complex neuronal circuitry by transplanted and endogenous precursors. NeuroRx : the journal of the American Society for Experimental NeuroTherapeutics. 1(4):452-71. Pubmed: 15717047 Emsley JG, Mitchell BD, Magavi SS, Arlotta P, Macklis JD. 2004. The repair of complex neuronal circuitry by transplanted and endogenous precursors. NeuroRx : the journal of the American Society for Experimental NeuroTherapeutics. 1(4):452-71. Pubmed: 15717047 During the past three decades, research exploring potential neuronal replacement therapies has focused on replacing lost neurons by transplanting cells or grafting tissue into diseased regions of the brain. However, in the last decade, the development of novel approaches has resulted in an explosion of new research showing that neurogenesis, the birth of new neurons, normally occurs in two limited and specific regions of the adult mammalian brain, and that there are significant numbers of multipotent neural precursors in many parts of the adult mammalian brain. Recent advances in our understanding of related events of neural development and plasticity, including the role of radial glia in developmental neurogenesis, and the ability of endogenous precursors present in the adult brain to be induced to produce neurons and partially repopulate brain regions affected by neurodegenerative processes, have led to fundamental changes in the views about how the brain develops, as well as to approaches by which transplanted or endogenous precursors might be used to repair the adult brain. For example, recruitment of new neurons can be induced in a region-specific, layer-specific, and neuronal type-specific manner, and, in some cases, newly recruited neurons can form long-distance connections to appropriate targets. Elucidation of the relevant molecular controls may both allow control over transplanted precursor cells and potentially allow for the development of neuronal replacement therapies for neurodegenerative disease and other CNS injuries that might not require transplantation of exogenous cells. -
Mitchell BD, Emsley JG, Magavi SS, Arlotta P, Macklis JD. 2004. Constitutive and induced neurogenesis in the adult mammalian brain: manipulation of endogenous precursors toward CNS repair. Developmental neuroscience. 26(2-4):101-17. Pubmed: 15711054 Mitchell BD, Emsley JG, Magavi SS, Arlotta P, Macklis JD. 2004. Constitutive and induced neurogenesis in the adult mammalian brain: manipulation of endogenous precursors toward CNS repair. Developmental neuroscience. 26(2-4):101-17. Pubmed: 15711054 Over most of the past century of modern neuroscience, it was thought that the adult brain was completely incapable of generating new neurons. During the past 3 decades, research exploring potential neuronal replacement therapies has focused on replacing lost neurons by transplanting cells or grafting tissue into diseased regions of the brain. However, in the last decade, the development of new techniques has resulted in an explosion of new research showing that neurogenesis, the birth of new neurons, normally occurs in two limited and specific regions of the adult mammalian brain and that there are significant numbers of multipotent neural precursors in many parts of the adult mammalian brain. Recent advances in our understanding of related events of neural development and plasticity, including the role of radial glia in developmental neurogenesis and the ability of endogenous precursors present in the adult brain to be induced to produce neurons and partially repopulate brain regions affected by neurodegenerative processes, have led to fundamental changes in the views about how the brain develops as well as to approaches by which endogenous precursors might be recruited to repair the adult brain. Recruitment of new neurons can be induced in a region-specific, layer-specific and neuronal-type-specific manner, and, in some cases, newly recruited neurons can form long-distance connections to appropriate targets. Elucidation of the relevant molecular controls may both allow control over transplanted precursor cells and potentially allow the development of neuronal replacement therapies for neurodegenerative disease and other CNS injuries that do not require transplantation of exogenous cells.Copyright 2004 S. Karger AG, Basel. -
Emsley JG, Arlotta P, Macklis JD. 2004. Star-cross'd neurons: astroglial effects on neural repair in the adult mammalian CNS. Trends in neurosciences. 27(5):238-40. Pubmed: 15111002 Emsley JG, Arlotta P, Macklis JD. 2004. Star-cross'd neurons: astroglial effects on neural repair in the adult mammalian CNS. Trends in neurosciences. 27(5):238-40. Pubmed: 15111002 Astroglia have long been thought to play merely a supporting role in the life of the neuron. However, these star-shaped cells have recently been the focus of intense study that has begun to emphasize remarkable and novel roles for these amazing cells. While astroglia play positive roles in the life of the neuron, they can simultaneously exert negative influences. Kinouchi et al. convincingly demonstrate and characterize an inhibitory role played by astroglia after neuronal transplantation. These findings remind us that astroglia exert positive and negative influences on neuronal survival, migration, neurite outgrowth and functional integration. Here, we review the complementary and often contradictory roles of astroglia during neuronal integration. 2003
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Arlotta P, Magavi SS, Macklis JD. 2003. Molecular manipulation of neural precursors in situ: induction of adult cortical neurogenesis. Experimental gerontology. 38(1-2):173-82. Pubmed: 12543275 Arlotta P, Magavi SS, Macklis JD. 2003. Molecular manipulation of neural precursors in situ: induction of adult cortical neurogenesis. Experimental gerontology. 38(1-2):173-82. Pubmed: 12543275 Over the past three decades, research exploring potential neuronal replacement therapies have focused on replacing lost neurons by transplanting cells or grafting tissue into diseased regions of the brain. Over most of the past century of modern neuroscience, it was thought that the adult brain was completely incapable of generating new neurons. However, in the last decade, the development of new techniques has resulted in an explosion of new research showing that neurogenesis, the birth of new neurons, normally occurs in two limited and specific regions of the adult mammalian brain, and that there are significant numbers of multipotent neural precursors in many parts of the adult mammalian brain. Recent findings from our lab demonstrate that it is possible to induce neurogenesis de novo in the adult mammalian brain, particularly in the neocortex where it does not normally occur, and that it may become possible to manipulate endogenous multipotent precursors in situ to replace lost or damaged neurons. Recruitment of new neurons can be induced in a region-specific, layer-specific, and neuronal type-specific manner, and newly recruited neurons can form long-distance connections to appropriate targets. Elucidation of the relevant molecular controls may both allow control over transplanted precursor cells and potentially allow the development of neuronal replacement therapies for neurodegenerative disease and other CNS injuries that do not require transplantation of exogenous cells. -
Arlotta P, Magavi SS, Macklis JD. 2003. Induction of adult neurogenesis: molecular manipulation of neural precursors in situ. Annals of the New York Academy of Sciences. 991:229-36. Pubmed: 12846990 Arlotta P, Magavi SS, Macklis JD. 2003. Induction of adult neurogenesis: molecular manipulation of neural precursors in situ. Annals of the New York Academy of Sciences. 991:229-36. Pubmed: 12846990 Over most of the past century, it was thought that the adult brain was completely incapable of generating new neurons. However, in the last decade, the development of new techniques has resulted in an explosion of new research showing that (i) neurogenesis, the birth of new neurons, is not restricted to embryonic development, but normally also occurs in two limited regions of the adult mammalian brain (the olfactory bulb and the dentate gyrus of the hippocampus); (ii) that there are significant numbers of multipotent neural precursors in many parts of the adult mammalian brain; and (iii) that it is possible to induce neurogenesis even in regions of the adult mammalian brain, like the neocortex, where it does not normally occur, via manipulation of endogenous multipotent precursors in situ. In the neocortex, recruitment of small numbers of new neurons can be induced in a region-specific, layer-specific, and neuronal type-specific manner, and newly recruited neurons can form long-distance connections to appropriate targets. This suggests that elucidation of the relevant molecular controls over adult neurogenesis from endogenous neural precursors/stem cells may allow the development of neuronal replacement therapies for neurodegenerative disease and other central nervous system injuries that may not require transplantation of exogenous cells. 2002
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Arlotta P, Miyazaki D, Copeland NG, Gilbert DJ, Jenkins NA, Ono SJ. 2002. Murine NFX.1: isolation and characterization of its messenger RNA, mapping of its chromosomal location and assessment of its developmental expression. Immunology. 106(2):173-81. Pubmed: 12047746 Arlotta P, Miyazaki D, Copeland NG, Gilbert DJ, Jenkins NA, Ono SJ. 2002. Murine NFX.1: isolation and characterization of its messenger RNA, mapping of its chromosomal location and assessment of its developmental expression. Immunology. 106(2):173-81. Pubmed: 12047746 We have previously isolated (by expression cloning) a human cDNA, termed NFX.1, encoding a nucleic acid-binding protein that interacts with the conserved X1 box cis-element first discovered in class II major histocompatibility complex (MHC) genes. Functional studies involving expression of NFX.1 and assessment of expression from class II reporter constructs and endogenous class II MHC genes indicated that the factor could repress transcription of class II MHC genes. Subsequent studies have extended the biological significance of the factor, indicating that it plays an important role in neuronal development. Indeed, the reiterated RING finger motifs in the central domain of the polypeptide strongly suggest that NF-XI is a probable E3 ubiquitin protein ligase, indicating that the protein may have multiple activities. Here we report the cloning of the mouse homologue of the human NfX.1 cDNA: m-Nfx.1. Comparison of the deduced primary sequence of mouse and human NFX.1 proteins shows very high homology and confirms that m-NFX.1 contains the conserved cysteine-rich DNA-binding motif first described in human NFX.1 (95% homology). Expression of MHC class II genes is substantially reduced following expression of m-NFX.1, which confirms that we have isolated the functional murine homologue of human NfX.1 cDNA. Further evidence comes from the mapping of m-Nfx.1 gene to the proximal region of mouse chromosome 4, a region syntenic to the location of human Nfx.1 (short arm of chromosome 9). Expression profiling shows that m-NFX.1 is expressed ubiquitously in both adult tissues and during development, supporting the hypothesis that it may have yet-undescribed roles in distinct biological processes. 2001
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Liu F, Chau KY, Arlotta P, Ono SJ. 2001. The HMG I proteins: dynamic roles in gene activation, development, and tumorigenesis. Immunologic research. 24(1):13-29. Pubmed: 11485207 Liu F, Chau KY, Arlotta P, Ono SJ. 2001. The HMG I proteins: dynamic roles in gene activation, development, and tumorigenesis. Immunologic research. 24(1):13-29. Pubmed: 11485207 The high mobility group I, Y, and I-C proteins are low-molecular-weight, nonhistone chromosomal proteins that play a general role modulating gene expression during development and the immune response. Consistent with their role in early development, all three proteins are expressed at high levels during embryogenesis, and their expression is markedly diminished in differentiated cells. Exceptions to the general repression of these genes in adult tissues involve (1) A burst of synthesis of the HMG I protein during the immune response (during lymphocyte activation and preceding cytokine/adhesion molecule gene expression), (2) A constitutive expression of the HMG I and Y proteins in photoreceptor cells, and (3) Derepression of HMG I, Y, and often I-C expression in neoplastic cells. Work from several laboratories has now uncovered how these proteins participate in gene activation: (1) By altering the chromatin structure around an inducible gene-and thus influencing accessibility of the locus to regulatory proteins-(2) By facilitating the loading of transcription factors onto the promoters, and (3) By bridging adjacent transcription factors on a promoter via protein/protein interactions. Despite the similar structures and biochemical properties of the three proteins, the work has also provided clues to a division of labor between these proteins. HMG I and Y have demonstrable roles in enhanceosome formation, whereas HMG I-C has a specific role in adipogenesis. C-terminal truncations of HMG I-C and wild-type HMG Y appear to function in a manner analogous to oncogenes, as assessed by cellular transforation assays and transgenic mice. Future work should clearly define the similarities and differences in the biological roles of the three proteins, and should evolve to include attempts at pharmaceutical intervention in disease, based upon structural information concerning HMG I interactions with DNA and with regulatory proteins. 2000
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Fedoseyeva EV, Boisgérault F, Anosova NG, Wollish WS, Arlotta P, Jensen PE, Ono SJ, Benichou G. 2000. CD4+ T cell responses to self- and mutated p53 determinants during tumorigenesis in mice. Journal of immunology (Baltimore, Md. : 1950). 164(11):5641-51. Pubmed: 10820239 Fedoseyeva EV, Boisgérault F, Anosova NG, Wollish WS, Arlotta P, Jensen PE, Ono SJ, Benichou G. 2000. CD4+ T cell responses to self- and mutated p53 determinants during tumorigenesis in mice. Journal of immunology (Baltimore, Md. : 1950). 164(11):5641-51. Pubmed: 10820239 We analyzed CD4+ T helper responses to wild-type (wt) and mutated (mut) p53 protein in normal and tumor-bearing mice. In normal mice, we observed that although some self-p53 determinants induced negative selection of p53-reactive CD4+ T cells, other p53 determinants (cryptic) were immunogenic. Next, BALB/c mice were inoculated with J774 syngeneic tumor cell line expressing mut p53. BALB/c tumor-bearing mice mounted potent CD4+ T cell responses to two formerly cryptic peptides on self-p53. This response was characterized by massive production of IL-5, a Th2-type lymphokine. Interestingly, we found that T cell response was induced by different p53 peptides depending upon the stage of cancer. Mut p53 gene was shown to contain a single mutation resulting in the substitution of a tyrosine by a histidine at position 231 of the protein. Two peptides corresponding to wt and mutated sequences of this region were synthesized. Both peptides bound to the MHC class II-presenting molecule (Ed) with similar affinities. However, only mut p53.225-239 induced T cell responses in normal BALB/c mice, a result strongly suggesting that high-affinity wt p53.225-239 autoreactive T cells had been eliminated in these mice. Surprisingly, CD4+ T cell responses to both mut and wt p53.225-239 peptides were recorded in J774 tumor-bearing mice, a phenomenon attributed to the recruitment of low-avidity p53.225-239 self-reactive T cells. -
Arlotta P, Tai AK, Manfioletti G, Clifford C, Jay G, Ono SJ. 2000. Transgenic mice expressing a truncated form of the high mobility group I-C protein develop adiposity and an abnormally high prevalence of lipomas. The Journal of biological chemistry. 275(19):14394-400. Pubmed: 10747931 Arlotta P, Tai AK, Manfioletti G, Clifford C, Jay G, Ono SJ. 2000. Transgenic mice expressing a truncated form of the high mobility group I-C protein develop adiposity and an abnormally high prevalence of lipomas. The Journal of biological chemistry. 275(19):14394-400. Pubmed: 10747931 Chromosomal translocations in human lipomas frequently create fusion transcripts encoding high mobility group (HMG) I-C DNA-binding domains and C-terminal sequences from different presumed transcription factors, suggesting a potential role for HMG I-C in the development of lipomas. To evaluate the role of the HMG I-C component, the three DNA-binding domains of HMG I-C have now been expressed in transgenic mice. Despite the ubiquitous expression of the truncated HMG I-C protein, the transgenic mice develop a selective abundance of fat tissue early in life, show marked adipose tissue inflammation, and have an abnormally high incidence of lipomas. These findings demonstrate that the DNA-binding domains of HMG I-C, in the absence of a C-terminal fusion partner, are sufficient to perturb adipogenesis and predispose to lipomas. We provide data supporting the central utility of this animal model as a tool to understand the molecular mechanisms underlying the development of one of the most common kind of human benign tumors. 1999
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Chau K, Arlotta P, Patel UA, Crane-Robinson C, Manfioletti G, Ono SJ. 1999. A novel downstream positive regulatory element mediating transcription of the human high mobility group (HMG) I-C gene. FEBS letters. 457(3):429-36. Pubmed: 10471823 Chau K, Arlotta P, Patel UA, Crane-Robinson C, Manfioletti G, Ono SJ. 1999. A novel downstream positive regulatory element mediating transcription of the human high mobility group (HMG) I-C gene. FEBS letters. 457(3):429-36. Pubmed: 10471823 The high mobility group (HMG) I proteins are small, non-histone chromosomal proteins that promote gene activation during development and within rapidly dividing cells. They do so by facilitating enhanceosome formation on inducible genes, via both protein/DNA and protein/protein interactions. The HMG I-C gene is tightly regulated, normally being expressed exclusively during embryonic development. However, HMG I-C expression is also observed frequently in a number of tumor types, and this expression has been shown to contribute to the malignant transformation process. With the aim of dissecting pathways that lead to aberrant expression of HMG I-C in tumor cells, we have analyzed HMG I-C gene regulation in the human hepatoma cell line PLC/PRF/5. One of the two HMG I-C transcripts detected in this cell line originates from a novel downstream initiation site at nucleotide -161 relative to the first methionine. Transcription from the downstream initiation site is mediated by a PRE located between nt -222 and -217. We show here that the Sp1 and Sp3 transcription factors interact with the PRE and transactivate the HMG I-C promoter in a cooperative fashion. This study provides the first characterization of this downstream HMG I-C promoter. 1997
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Arlotta P, Rustighi A, Mantovani F, Manfioletti G, Giancotti V, Tell G, Damante G. 1997. High mobility group I proteins interfere with the homeodomains binding to DNA. The Journal of biological chemistry. 272(47):29904-10. Pubmed: 9368066 Arlotta P, Rustighi A, Mantovani F, Manfioletti G, Giancotti V, Tell G, Damante G. 1997. High mobility group I proteins interfere with the homeodomains binding to DNA. The Journal of biological chemistry. 272(47):29904-10. Pubmed: 9368066 Homeodomains (HDs) constitute the DNA binding domain of several transcription factors that control cell differentiation and development in a wide variety of organisms. Most HDs recognize sequences that contain a 5'-TAAT-3' core motif. However, the DNA binding specificity of HD-containing proteins does not solely determine their biological effects, and other molecular mechanisms should be responsible for their ultimate functional activity. Interference by other factors in the HD/DNA interaction could be one of the processes by which HD-containing proteins achieve the functional complexity required for their effects on the expression of target genes. Using gel-retardation assay, we demonstrate that two members of the high mobility group I (HMGI) family of nuclear proteins (HMGI-C and HMGY) can bind to a subset of HD target sequences and inhibit HDs from binding to the same sequences. The inhibition of the HD/DNA interaction occurs while incubating HMGI-C with DNA either before or after the addition of the HD. The reduced half-life of the HD.DNA complex in the presence of HMGI-C, and the shift observed in the CD spectra recorded upon HMGI-C binding to DNA, strongly suggest that structural modifications of the DNA are responsible for the inhibition of the HD.DNA complex formation. Moreover, by co-transfection experiments we provide evidence that this inhibition can occur also in vivo. The data reported here would suggest that HMGI proteins may be potential regulators of the function of HD-containing proteins and that they are able to interfere with the access of the HD to their target genes. 1980
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Arlotta P, Curci G, Perazzoli CA, Santori L. 1980. Reconstruction of severe loss of mandibular bone substance using metal prostheses. Minerva stomatologica. 29(6):515-26. Pubmed: 6939966 Arlotta P, Curci G, Perazzoli CA, Santori L. 1980. Reconstruction of severe loss of mandibular bone substance using metal prostheses. Minerva stomatologica. 29(6):515-26. Pubmed: 6939966 1976
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Arlotta P, Santori L, de Vecchi A. 1976. A case of mixed tumor of the palate. Acta biologica et medica Germanica. 2(3):34. Pubmed: 209648 Arlotta P, Santori L, de Vecchi A. 1976. A case of mixed tumor of the palate. Acta biologica et medica Germanica. 2(3):34. Pubmed: 209648 1975
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Arlotta P, Tassarotti B, Santori L. 1975. Surgical therapy of submandibular sialolithiasis. Odontostomatologia E Implantoprotesi. Pubmed: 802397 Arlotta P, Tassarotti B, Santori L. 1975. Surgical therapy of submandibular sialolithiasis. Odontostomatologia E Implantoprotesi. Pubmed: 802397 1972
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Arlotta P, Silla M. 1972. Solitary plasmacytoma of the mandible. Rassegna internazionale di stomatologia pratica. 23(5):153-61. Pubmed: 4515384 Arlotta P, Silla M. 1972. Solitary plasmacytoma of the mandible. Rassegna internazionale di stomatologia pratica. 23(5):153-61. Pubmed: 4515384 -
Arlotta P, Curci G, Morelli-Coghi A, Pizzoni D. 1972. Treatment of fracture of the zygomatic arch by means of metallic osteosynthesis. Rassegna internazionale di stomatologia pratica. 23(6):189-203. Pubmed: 4515386 Arlotta P, Curci G, Morelli-Coghi A, Pizzoni D. 1972. Treatment of fracture of the zygomatic arch by means of metallic osteosynthesis. Rassegna internazionale di stomatologia pratica. 23(6):189-203. Pubmed: 4515386 1970
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Grampa G, Bestetti-Bosisio M, Bergamini F, Arlotta P. 1970. A case of Burkitt's tumor in Italy. Pathologia Europaea. 5(4):470-84. Pubmed: 5515049 Grampa G, Bestetti-Bosisio M, Bergamini F, Arlotta P. 1970. A case of Burkitt's tumor in Italy. Pathologia Europaea. 5(4):470-84. Pubmed: 5515049 1967
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Arlotta P, Pizzoni D. 1967. Fractures of the zygomatic complex. The British journal of oral surgery. 4(3):192-3. Pubmed: 5228979 Arlotta P, Pizzoni D. 1967. Fractures of the zygomatic complex. The British journal of oral surgery. 4(3):192-3. Pubmed: 5228979 1954
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ARLOTTA P, TALAMAZZI F. 1954. Clinico-statistical study of tumors of the upper jaw. Rivista italiana di stomatologia. 9(5):539-50. Pubmed: 13195472 ARLOTTA P, TALAMAZZI F. 1954. Clinico-statistical study of tumors of the upper jaw. Rivista italiana di stomatologia. 9(5):539-50. Pubmed: 13195472 1953
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ARLOTTA P. 1953. Transalveolar route in novocaine analgesia with gelatin sponge in periodontitis. Minerva stomatologica. 2(3):141-3. Pubmed: 13086831 ARLOTTA P. 1953. Transalveolar route in novocaine analgesia with gelatin sponge in periodontitis. Minerva stomatologica. 2(3):141-3. Pubmed: 13086831 1951
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ARLOTTA P. 1951. Xylocaine in use at the Milan Dental Clinic. Rivista italiana di stomatologia. 6(11):1187-91. Pubmed: 14912893 ARLOTTA P. 1951. Xylocaine in use at the Milan Dental Clinic. Rivista italiana di stomatologia. 6(11):1187-91. Pubmed: 14912893 -
ARLOTTA P. 1951. Trichloroethylene in dentin hyperesthesia. Rivista italiana di stomatologia. 6(9):916-20. Pubmed: 14900859 ARLOTTA P. 1951. Trichloroethylene in dentin hyperesthesia. Rivista italiana di stomatologia. 6(9):916-20. Pubmed: 14900859 -
ARLOTTA P. 1951. Gingival hyperplasia due to sodium diphenylhydantoinate. Rivista italiana di stomatologia. 6(2):180-7. Pubmed: 14845570 ARLOTTA P. 1951. Gingival hyperplasia due to sodium diphenylhydantoinate. Rivista italiana di stomatologia. 6(2):180-7. Pubmed: 14845570