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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
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. -
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. -
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. -
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 2016
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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. -
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. -
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. -
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 2015
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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. -
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. -
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. -
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. -
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. -
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 -
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. -
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. -
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. 2014
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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. -
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. -
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. -
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. 2013
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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. -
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. -
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. -
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. -
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. 2012
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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. -
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. -
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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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, 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. -
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. -
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. -
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. 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, 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. -
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. -
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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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. -
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. -
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. 2004
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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. 2003
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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.