51
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Hammelman J, Gifford DK. Discovering differential genome sequence activity with interpretable and efficient deep learning. PLoS Comput Biol 2021; 17:e1009282. [PMID: 34370721 PMCID: PMC8376110 DOI: 10.1371/journal.pcbi.1009282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/19/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022] Open
Abstract
Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Pattern Effect, two black-box methods that can interpret genome regulatory sequences for cell type-specific or condition specific patterns. We show that these methods identify relevant transcription factor motifs and spacings that are predictive of cell state-specific chromatin accessibility. Finally, we integrate these methods into framework that is readily accessible to non-experts and available for download as a binary or installed via PyPI or bioconda at https://cgs.csail.mit.edu/deepaccess-package/.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, MIT, Cambridge, Massachusetts, United States of America
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts, United States of America
| | - David K. Gifford
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering & Computer Science, MIT, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States of America
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52
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Vasan L, Park E, David LA, Fleming T, Schuurmans C. Direct Neuronal Reprogramming: Bridging the Gap Between Basic Science and Clinical Application. Front Cell Dev Biol 2021; 9:681087. [PMID: 34291049 PMCID: PMC8287587 DOI: 10.3389/fcell.2021.681087] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
Direct neuronal reprogramming is an innovative new technology that involves the conversion of somatic cells to induced neurons (iNs) without passing through a pluripotent state. The capacity to make new neurons in the brain, which previously was not achievable, has created great excitement in the field as it has opened the door for the potential treatment of incurable neurodegenerative diseases and brain injuries such as stroke. These neurological disorders are associated with frank neuronal loss, and as new neurons are not made in most of the adult brain, treatment options are limited. Developmental biologists have paved the way for the field of direct neuronal reprogramming by identifying both intrinsic cues, primarily transcription factors (TFs) and miRNAs, and extrinsic cues, including growth factors and other signaling molecules, that induce neurogenesis and specify neuronal subtype identities in the embryonic brain. The striking observation that postmitotic, terminally differentiated somatic cells can be converted to iNs by mis-expression of TFs or miRNAs involved in neural lineage development, and/or by exposure to growth factors or small molecule cocktails that recapitulate the signaling environment of the developing brain, has opened the door to the rapid expansion of new neuronal reprogramming methodologies. Furthermore, the more recent applications of neuronal lineage conversion strategies that target resident glial cells in situ has expanded the clinical potential of direct neuronal reprogramming techniques. Herein, we present an overview of the history, accomplishments, and therapeutic potential of direct neuronal reprogramming as revealed over the last two decades.
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Affiliation(s)
- Lakshmy Vasan
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Eunjee Park
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Luke Ajay David
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Taylor Fleming
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
| | - Carol Schuurmans
- Sunnybrook Research Institute, Biological Sciences Platform, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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53
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Mitsuzawa S, Suzuki N, Akiyama T, Ishikawa M, Sone T, Kawada J, Funayama R, Shirota M, Mitsuhashi H, Morimoto S, Ikeda K, Shijo T, Ohno A, Nakamura N, Ono H, Ono R, Osana S, Nakagawa T, Nishiyama A, Izumi R, Kaneda S, Ikeuchi Y, Nakayama K, Fujii T, Warita H, Okano H, Aoki M. Reduced PHOX2B stability causes axonal growth impairment in motor neurons with TARDBP mutations. Stem Cell Reports 2021; 16:1527-1541. [PMID: 34048688 PMCID: PMC8190591 DOI: 10.1016/j.stemcr.2021.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult-onset incurable motor neuron (MN) disease. The reasons for selective MN vulnerability in ALS are unknown. Axonal pathology is among the earliest signs of ALS. We searched for novel modulatory genes in human MN axon shortening affected by TARDBP mutations. In transcriptome analysis of RNA present in the axon compartment of human-derived induced pluripotent stem cell (iPSC)-derived MNs, PHOX2B (paired-like homeobox protein 2B) showed lower expression in TARDBP mutant axons, which was consistent with axon qPCR and in situ hybridization. PHOX2B mRNA stability was reduced in TARDBP mutant MNs. Furthermore, PHOX2B knockdown reduced neurite length in human MNs. Finally, phox2b knockdown in zebrafish induced short spinal axons and impaired escape response. PHOX2B is known to be highly express in other types of neurons maintained after ALS progression. Collectively, TARDBP mutations induced loss of axonal resilience, which is an important ALS-related phenotype mediated by PHOX2B downregulation. Human iPSCs were established from a familial ALS with the TARDBP p.G376D mutation PHOX2B mRNA was identified to be decreased in TARDBP mutant MNs by RNA sequencing PHOX2B mRNA bind to TDP-43 and its stability was reduced in TARDBP mutant MNs PHOX2B knockdown reduced neurite length and impaired motor functions in vivo/vitro
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Affiliation(s)
- Shio Mitsuzawa
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Naoki Suzuki
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Tetsuya Akiyama
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Mitsuru Ishikawa
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takefumi Sone
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Jiro Kawada
- Jiksak Bioengineering Inc. 7-7 Shinkawasaki, Saiwai-ku, Kawasaki 212-0032, Japan; Institute of Industrial Science, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Science, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Hiroaki Mitsuhashi
- Department of Applied Biochemistry, School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Satoru Morimoto
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kensuke Ikeda
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Tomomi Shijo
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Akiyuki Ohno
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Naoko Nakamura
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Hiroya Ono
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Risako Ono
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Shion Osana
- Division of Biomedical Engineering for Health and Welfare, Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Tadashi Nakagawa
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan; Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, 1-1-1 Daigaku-Doori, Sanyo-Onoda, Yamaguchi 756-0884, Japan
| | - Ayumi Nishiyama
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Rumiko Izumi
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Shohei Kaneda
- Institute of Industrial Science, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; Department of Mechanical Systems Engineering, Faculty of Engineering, Kogakuin University, 1-24-2 Nishishinjuku, Shinjuku-ku, Tokyo, 163-8677, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan; Institute for AI and Beyond, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Teruo Fujii
- Institute of Industrial Science, the University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Hitoshi Warita
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan.
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54
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Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021; 22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.
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Affiliation(s)
- Anil Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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55
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Nickolls AR, Lee MM, Espinoza DF, Szczot M, Lam RM, Wang Q, Beers J, Zou J, Nguyen MQ, Solinski HJ, AlJanahi AA, Johnson KR, Ward ME, Chesler AT, Bönnemann CG. Transcriptional Programming of Human Mechanosensory Neuron Subtypes from Pluripotent Stem Cells. Cell Rep 2021; 30:932-946.e7. [PMID: 31968264 PMCID: PMC7059559 DOI: 10.1016/j.celrep.2019.12.062] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/17/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022] Open
Abstract
Efficient and homogeneous in vitro generation of peripheral sensory neurons may provide a framework for novel drug screening platforms and disease models of touch and pain. We discover that, by ovesssrexpressing NGN2 and BRN3A, human pluripotent stem cells can be transcriptionally programmed to differentiate into a surprisingly uniform culture of cold- and mechano-sensing neurons. Although such a neuronal subtype is not found in mice, we identify molecular evidence for its existence in human sensory ganglia. Combining NGN2 and BRN3A programming with neural crest patterning, we produce two additional populations of sensory neurons, including a specialized touch receptor neuron subtype. Finally, we apply this system to model a rare inherited sensory disorder of touch and proprioception caused by inactivating mutations in PIEZO2. Together, these findings establish an approach to specify distinct sensory neuron subtypes in vitro, underscoring the utility of stem cell technology to capture human-specific features of physiology and disease. Nickolls et al. develop a method, using human stem cells, to generate specific types of sensory neurons that detect cold temperature and mechanical force. This approach uncovers a class of neuron found in humans, but not mice, and enables the modeling of a rare sensory disorder of touch and proprioception.
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Affiliation(s)
- Alec R Nickolls
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Department of Neuroscience, Brown University, Providence, RI 02912, USA
| | - Michelle M Lee
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - David F Espinoza
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcin Szczot
- National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruby M Lam
- Department of Neuroscience, Brown University, Providence, RI 02912, USA; National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qi Wang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeanette Beers
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jizhong Zou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Minh Q Nguyen
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hans J Solinski
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aisha A AlJanahi
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kory R Johnson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander T Chesler
- National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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56
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Luginbühl J, Kouno T, Nakano R, Chater TE, Sivaraman DM, Kishima M, Roudnicky F, Carninci P, Plessy C, Shin JW. Decoding Neuronal Diversification by Multiplexed Single-cell RNA-Seq. Stem Cell Reports 2021; 16:810-824. [PMID: 33711266 PMCID: PMC8072034 DOI: 10.1016/j.stemcr.2021.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
Cellular reprogramming is driven by a defined set of transcription factors; however, the regulatory logic that underlies cell-type specification and diversification remains elusive. Single-cell RNA-seq provides unprecedented coverage to measure dynamic molecular changes at the single-cell resolution. Here, we multiplex and ectopically express 20 pro-neuronal transcription factors in human dermal fibroblasts and demonstrate a widespread diversification of neurons based on cell morphology and canonical neuronal marker expressions. Single-cell RNA-seq analysis reveals diverse and distinct neuronal subtypes, including reprogramming processes that strongly correlate with the developing brain. Gene mapping of 20 exogenous pro-neuronal transcription factors further unveiled key determinants responsible for neuronal lineage specification and a regulatory logic dictating neuronal diversification, including glutamatergic and cholinergic neurons. The multiplex scRNA-seq approach is a robust and scalable approach to elucidate lineage and cellular specification across various biological systems. Multiplexed scRNA-seq approach reveals combinations of genes to induce neuronal diversification Neuronal diversification is deterministic early in the reprogramming process PAX6 drives induced neurons away from fibroblasts
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Affiliation(s)
- Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Rei Nakano
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Nihon University, College of Bioresource Sciences, Laboratory of Veterinary Radiology, Fujisawa, Kanagawa 252-0880, Japan
| | - Thomas E Chater
- RIKEN Center for Brain Science, Wako-Shi, Saitama 351-0198, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Department of Pathology, Thiruvananthapuram 695-011, Kerala, India
| | - Mami Kishima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Filip Roudnicky
- ETH Zurich, Institute of Pharmaceutical Sciences, 8057 Zurich, Switzerland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan.
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57
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Mollinari C, Merlo D. Direct Reprogramming of Somatic Cells to Neurons: Pros and Cons of Chemical Approach. Neurochem Res 2021; 46:1330-1336. [PMID: 33666839 PMCID: PMC8084785 DOI: 10.1007/s11064-021-03282-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Accepted: 02/20/2021] [Indexed: 12/11/2022]
Abstract
Translating successful preclinical research in neurodegenerative diseases into clinical practice has been difficult. The preclinical disease models used for testing new drugs not always appear predictive of the effects of the agents in the human disease state. Human induced pluripotent stem cells, obtained by reprogramming of adult somatic cells, represent a powerful system to study the molecular mechanisms of the disease onset and pathogenesis. However, these cells require a long time to differentiate into functional neural cells and the resetting of epigenetic information during reprogramming, might miss the information imparted by age. On the contrary, the direct conversion of somatic cells to neuronal cells is much faster and more efficient, it is safer for cell therapy and allows to preserve the signatures of donors’ age. Direct reprogramming can be induced by lineage-specific transcription factors or chemical cocktails and represents a powerful tool for modeling neurological diseases and for regenerative medicine. In this Commentary we present and discuss strength and weakness of several strategies for the direct cellular reprogramming from somatic cells to generate human brain cells which maintain age‐related features. In particular, we describe and discuss chemical strategy for cellular reprogramming as it represents a valuable tool for many applications such as aged brain modeling, drug screening and personalized medicine.
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Affiliation(s)
- Cristiana Mollinari
- Institute of Translational Pharmacology, National Research Council, Via Fosso del Cavaliere 100, 00133, Rome, Italy. .,Department of Neuroscience, Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy.
| | - Daniela Merlo
- Department of Neuroscience, Istituto Superiore di Sanita', Viale Regina Elena 299, 00161, Rome, Italy
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58
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Smith NC, Wilkinson-White LE, Kwan AHY, Trewhella J, Matthews JM. Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification. JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100043. [PMID: 33458649 PMCID: PMC7797366 DOI: 10.1016/j.yjsbx.2020.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/29/2022]
Abstract
The mechanisms by which ISL1 and LHX3 specify neuronal cell identity are unknown. EMSA/SPR data show ISL1 and LHX3 have markedly different DNA-binding behaviours. SAXS shows ISL1/LHX3:DNA complexes are flexible in nature. ISL1 binds DNA poorly but appears to modulate the DNA-binding specificity of LHX3.
The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons.
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Affiliation(s)
- Ngaio C Smith
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | | | - Ann H Y Kwan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, University of Sydney, NSW 2006, Australia
| | - Jill Trewhella
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jacqueline M Matthews
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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59
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Cates K, McCoy MJ, Kwon JS, Liu Y, Abernathy DG, Zhang B, Liu S, Gontarz P, Kim WK, Chen S, Kong W, Ho JN, Burbach KF, Gabel HW, Morris SA, Yoo AS. Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs. Cell Stem Cell 2021; 28:127-140.e9. [PMID: 32961143 PMCID: PMC7796891 DOI: 10.1016/j.stem.2020.08.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/11/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
Cell-fate conversion generally requires reprogramming effectors to both introduce fate programs of the target cell type and erase the identity of starting cell population. Here, we reveal insights into the activity of microRNAs miR-9/9∗ and miR-124 (miR-9/9∗-124) as reprogramming agents that orchestrate direct conversion of human fibroblasts into motor neurons by first eradicating fibroblast identity and promoting uniform transition to a neuronal state in sequence. We identify KLF-family transcription factors as direct target genes for miR-9/9∗-124 and show their repression is critical for erasing fibroblast fate. Subsequent gain of neuronal identity requires upregulation of a small nuclear RNA, RN7SK, which induces accessibilities of chromatin regions and neuronal gene activation to push cells to a neuronal state. Our study defines deterministic components in the microRNA-mediated reprogramming cascade.
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Affiliation(s)
- Kitra Cates
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J McCoy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ji-Sun Kwon
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Computational and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yangjian Liu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel G Abernathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shaopeng Liu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Woo Kyung Kim
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shawei Chen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wenjun Kong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Computational and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua N Ho
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyle F Burbach
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics and Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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60
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Posabella A, Alber AB, Undeutsch HJ, Droeser RA, Hollenberg AN, Ikonomou L, Kotton DN. Derivation of Thyroid Follicular Cells From Pluripotent Stem Cells: Insights From Development and Implications for Regenerative Medicine. Front Endocrinol (Lausanne) 2021; 12:666565. [PMID: 33959101 PMCID: PMC8095374 DOI: 10.3389/fendo.2021.666565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Stem cell-based therapies to reconstitute in vivo organ function hold great promise for future clinical applications to a variety of diseases. Hypothyroidism resulting from congenital lack of functional thyrocytes, surgical tissue removal, or gland ablation, represents a particularly attractive endocrine disease target that may be conceivably cured by transplantation of long-lived functional thyroid progenitors or mature follicular epithelial cells, provided a source of autologous cells can be generated and a variety of technical and biological challenges can be surmounted. Here we review the emerging literature indicating that thyroid follicular epithelial cells can now be engineered in vitro from the pluripotent stem cells (PSCs) of mice, normal humans, or patients with congenital hypothyroidism. We review the in vivo embryonic development of the thyroid gland and explain how emerging discoveries in developmental biology have been utilized as a roadmap for driving PSCs, which resemble cells of the early embryo, into mature functional thyroid follicles in vitro. Finally, we discuss the bioengineering, biological, and clinical hurdles that now need to be addressed if the goals of life-long cure of hypothyroidism through cell- and/or gene-based therapies are to be attained.
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Affiliation(s)
- Alberto Posabella
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, United States
- University Center of Gastrointestinal and Liver Diseases—Clarunis, University of Basel, Basel, Switzerland
| | - Andrea B. Alber
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, United States
| | - Hendrik J. Undeutsch
- Division of Endocrinology, Diabetes and Metabolism, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Raoul A. Droeser
- University Center of Gastrointestinal and Liver Diseases—Clarunis, University of Basel, Basel, Switzerland
| | - Anthony N. Hollenberg
- Division of Endocrinology, Diabetes and Metabolism, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Laertis Ikonomou
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, United States
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York, Buffalo, NY, United States
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, United States
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- *Correspondence: Darrell N. Kotton,
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61
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Ribeiro MM, Okawa S, Del Sol A. TransSynW: A single-cell RNA-sequencing based web application to guide cell conversion experiments. Stem Cells Transl Med 2020; 10:230-238. [PMID: 33125830 PMCID: PMC7848352 DOI: 10.1002/sctm.20-0227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/03/2020] [Accepted: 08/16/2020] [Indexed: 12/16/2022] Open
Abstract
Generation of desired cell types by cell conversion remains a challenge. In particular, derivation of novel cell subtypes identified by single‐cell technologies will open up new strategies for cell therapies. The recent increase in the generation of single‐cell RNA‐sequencing (scRNA‐seq) data and the concomitant increase in the interest expressed by researchers in generating a wide range of functional cells prompted us to develop a computational tool for tackling this challenge. Here we introduce a web application, TransSynW, which uses scRNA‐seq data for predicting cell conversion transcription factors (TFs) for user‐specified cell populations. TransSynW prioritizes pioneer factors among predicted conversion TFs to facilitate chromatin opening often required for cell conversion. In addition, it predicts marker genes for assessing the performance of cell conversion experiments. Furthermore, TransSynW does not require users' knowledge of computer programming and computational resources. We applied TransSynW to different levels of cell conversion specificity, which recapitulated known conversion TFs at each level. We foresee that TransSynW will be a valuable tool for guiding experimentalists to design novel protocols for cell conversion in stem cell research and regenerative medicine.
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Affiliation(s)
- Mariana Messias Ribeiro
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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62
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Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI. Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay. Genome Res 2020; 30:1468-1480. [PMID: 32973041 PMCID: PMC7605270 DOI: 10.1101/gr.263228.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
A key mechanism in cellular regulation is the ability of the transcriptional machinery to physically access DNA. Transcription factors interact with DNA to alter the accessibility of chromatin, which enables changes to gene expression during development or disease or as a response to environmental stimuli. However, the regulation of DNA accessibility via the recruitment of transcription factors is difficult to study in the context of the native genome because every genomic site is distinct in multiple ways. Here we introduce the multiplexed integrated accessibility assay (MIAA), an assay that measures chromatin accessibility of synthetic oligonucleotide sequence libraries integrated into a controlled genomic context with low native accessibility. We apply MIAA to measure the effects of sequence motifs on cell type-specific accessibility between mouse embryonic stem cells and embryonic stem cell-derived definitive endoderm cells, screening 7905 distinct DNA sequences. MIAA recapitulates differential accessibility patterns of 100-nt sequences derived from natively differential genomic regions, identifying E-box motifs common to epithelial-mesenchymal transition driver transcription factors in stem cell-specific accessible regions that become repressed in endoderm. We show that a single binding motif for a key regulatory transcription factor is sufficient to open chromatin, and classify sets of stem cell-specific, endoderm-specific, and shared accessibility-modifying transcription factor motifs. We also show that overexpression of two definitive endoderm transcription factors, T and Foxa2, results in changes to accessibility in DNA sequences containing their respective DNA-binding motifs and identify preferential motif arrangements that influence accessibility.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Budhaditya Banerjee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Hubrecht Institute, 3584 CT Utrecht, Netherlands
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63
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Majidi SP, Reddy NC, Moore MJ, Chen H, Yamada T, Andzelm MM, Cherry TJ, Hu LS, Greenberg ME, Bonni A. Chromatin Environment and Cellular Context Specify Compensatory Activity of Paralogous MEF2 Transcription Factors. Cell Rep 2020; 29:2001-2015.e5. [PMID: 31722213 PMCID: PMC6874310 DOI: 10.1016/j.celrep.2019.10.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/04/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Compensation among paralogous transcription factors (TFs) confers genetic robustness of cellular processes, but how TFs dynamically respond to paralog depletion on a genome-wide scale in vivo remains incompletely understood. Using single and double conditional knockout of myocyte enhancer factor 2 (MEF2) family TFs in granule neurons of the mouse cerebellum, we find that MEF2A and MEF2D play functionally redundant roles in cerebellar-dependent motor learning. Although both TFs are highly expressed in granule neurons, transcriptomic analyses show MEF2D is the predominant genomic regulator of gene expression in vivo. Strikingly, genome-wide occupancy analyses reveal upon depletion of MEF2D, MEF2A occupancy robustly increases at a subset of sites normally bound to MEF2D. Importantly, sites experiencing compensatory MEF2A occupancy are concentrated within open chromatin and undergo functional compensation for genomic activation and gene expression. Finally, motor activity induces a switch from non-compensatory to compensatory MEF2-dependent gene regulation. These studies uncover genome-wide functional interdependency between paralogous TFs in the brain. Majidi et al. study how transcription factors respond to paralog depletion by conditionally depleting MEF2A and MEF2D in mouse cerebellum. Depletion of MEF2D induces functionally compensatory genomic occupancy by MEF2A. Compensation occurs within accessible chromatin in a context-dependent manner. This study explores the interdependency between paralogous transcription factors.
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Affiliation(s)
- Shahriyar P Majidi
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; MD-PhD Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Naveen C Reddy
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hao Chen
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Milena M Andzelm
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy J Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9(th) Ave., Seattle, WA 98101, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda S Hu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA.
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64
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Watanabe Y, Nakagawa T, Akiyama T, Nakagawa M, Suzuki N, Warita H, Aoki M, Nakayama K. An Amyotrophic Lateral Sclerosis-Associated Mutant of C21ORF2 Is Stabilized by NEK1-Mediated Hyperphosphorylation and the Inability to Bind FBXO3. iScience 2020; 23:101491. [PMID: 32891887 PMCID: PMC7481237 DOI: 10.1016/j.isci.2020.101491] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/18/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022] Open
Abstract
C21ORF2 and NEK1 have been identified as amyotrophic lateral sclerosis (ALS)-associated genes. Both genes are also mutated in certain ciliopathies, suggesting that they might contribute to the same signaling pathways. Here we show that FBXO3, the substrate receptor of an SCF ubiquitin ligase complex, binds and ubiquitylates C21ORF2, thereby targeting it for proteasomal degradation. C21ORF2 stabilizes the kinase NEK1, with the result that loss of FBXO3 stabilizes not only C21ORF2 but also NEK1. Conversely, NEK1-mediated phosphorylation stabilizes C21ORF2 by attenuating its interaction with FBXO3. We found that the ALS-associated V58L mutant of C21ORF2 is more susceptible to phosphorylation by NEK1, with the result that it is not ubiquitylated by FBXO3 and therefore accumulates together with NEK1. Expression of C21ORF2(V58L) in motor neurons induced from mouse embryonic stem cells impaired neurite outgrowth. We suggest that inhibition of NEK1 activity is a potential therapeutic approach to ALS associated with C21ORF2 mutation.
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Affiliation(s)
- Yasuaki Watanabe
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan; Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tadashi Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tetsuya Akiyama
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Makiko Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Naoki Suzuki
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Hitoshi Warita
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Masashi Aoki
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan.
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65
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Vitrinel B, Iannitelli DE, Mazzoni EO, Christiaen L, Vogel C. Simple Method to Quantify Protein Abundances from 1000 Cells. ACS OMEGA 2020; 5:15537-15546. [PMID: 32637829 PMCID: PMC7331059 DOI: 10.1021/acsomega.0c01191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/09/2020] [Indexed: 05/29/2023]
Abstract
The rise of single-cell transcriptomics has created an urgent need for similar approaches that use a minimal number of cells to quantify expression levels of proteins. We integrated and optimized multiple recent developments to establish a proteomics workflow to quantify proteins from as few as 1000 mammalian stem cells. The method uses chemical peptide labeling, does not require specific equipment other than cell lysis tools, and quantifies >2500 proteins with high reproducibility. We validated the method by comparing mouse embryonic stem cells and in vitro differentiated motor neurons. We identify differentially expressed proteins with small fold changes and a dynamic range in abundance similar to that of standard methods. Protein abundance measurements obtained with our protocol compared well to corresponding transcript abundance and to measurements using standard inputs. The protocol is also applicable to other systems, such as fluorescence-activated cell sorting (FACS)-purified cells from the tunicate Ciona. Therefore, we offer a straightforward and accurate method to acquire proteomics data from minimal input samples.
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Affiliation(s)
- Burcu Vitrinel
- Center
for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, United States
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
| | - Dylan E. Iannitelli
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
| | - Esteban O. Mazzoni
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
- NYU
Neuroscience Institute, NYU Langone Medical
Center, New York, New York 10016, United
States
| | - Lionel Christiaen
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
| | - Christine Vogel
- Center
for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, United States
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66
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Yeo GHT, Lin L, Qi CY, Cha M, Gifford DK, Sherwood RI. A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation. Cell Stem Cell 2020; 26:938-950.e6. [PMID: 32459995 PMCID: PMC7398619 DOI: 10.1016/j.stem.2020.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/10/2019] [Accepted: 04/27/2020] [Indexed: 01/08/2023]
Abstract
Empirical optimization of stem cell differentiation protocols is time consuming, is laborintensive, and typically does not comprehensively interrogate all relevant signaling pathways. Here we describe barcodelet single-cell RNA sequencing (barRNA-seq), which enables systematic exploration of cellular perturbations by tagging individual cells with RNA "barcodelets" to identify them on the basis of the treatments they receive. We apply barRNA-seq to simultaneously manipulate up to seven developmental pathways and study effects on embryonic stem cell (ESC) germ layer specification and mesodermal specification, uncovering combinatorial effects of signaling pathway activation on gene expression. We further develop a data-driven framework for identifying combinatorial signaling perturbations that drive cells toward specific fates, including several annotated in an existing scRNA-seq gastrulation atlas, and use this approach to guide ESC differentiation into a notochord-like population. We expect that barRNA-seq will have broad utility for investigating and understanding how cooperative signaling pathways drive cell fate acquisition.
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Affiliation(s)
- Grace Hui Ting Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lin Lin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Celine Yueyue Qi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David K Gifford
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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67
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Srivastava D, Mahony S. Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194443. [PMID: 31639474 PMCID: PMC7166147 DOI: 10.1016/j.bbagrm.2019.194443] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/21/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic sequence preferences, cooperative interactions with other regulatory proteins, and cell type-specific chromatin landscapes. Cell type-specific TF binding events are highly correlated with patterns of chromatin accessibility and active histone modifications in the same cell type. However, since concurrent chromatin may itself be a consequence of TF binding, chromatin landscapes measured prior to TF activation provide more useful insights into how cell type-specific TF binding events became established in the first place. Here, we review the various sequence and chromatin determinants of cell type-specific TF binding specificity. We identify the current challenges and opportunities associated with computational approaches to characterizing, imputing, and predicting cell type-specific TF binding patterns. We further focus on studies that characterize TF binding in dynamic regulatory settings, and we discuss how these studies are leading to a more complex and nuanced understanding of dynamic protein-DNA binding activities. We propose that TF binding activities at individual sites can be viewed along a two-dimensional continuum of local sequence and chromatin context. Under this view, cell type-specific TF binding activities may result from either strongly favorable sequence features or strongly favorable chromatin context.
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Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America.
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68
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Flitsch LJ, Laupman KE, Brüstle O. Transcription Factor-Based Fate Specification and Forward Programming for Neural Regeneration. Front Cell Neurosci 2020; 14:121. [PMID: 32508594 PMCID: PMC7251072 DOI: 10.3389/fncel.2020.00121] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
Traditionally, in vitro generation of donor cells for brain repair has been dominated by the application of extrinsic growth factors and morphogens. Recent advances in cell engineering strategies such as reprogramming of somatic cells into induced pluripotent stem cells and direct cell fate conversion have impressively demonstrated the feasibility to manipulate cell identities by the overexpression of cell fate-determining transcription factors. These strategies are now increasingly implemented for transcription factor-guided differentiation of neural precursors and forward programming of pluripotent stem cells toward specific neural subtypes. This review covers major achievements, pros and cons, as well as future prospects of transcription factor-based cell fate specification and the applicability of these approaches for the generation of donor cells for brain repair.
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Affiliation(s)
- Lea J Flitsch
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Karen E Laupman
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Faculty and University Hospital Bonn, Bonn, Germany
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69
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Varderidou-Minasian S, Verheijen BM, Schätzle P, Hoogenraad CC, Pasterkamp RJ, Altelaar M. Deciphering the Proteome Dynamics during Development of Neurons Derived from Induced Pluripotent Stem Cells. J Proteome Res 2020; 19:2391-2403. [PMID: 32357013 PMCID: PMC7281779 DOI: 10.1021/acs.jproteome.0c00070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Neuronal development is a complex
multistep process that shapes
neurons by progressing though several typical stages, including axon
outgrowth, dendrite formation, and synaptogenesis. Knowledge of the
mechanisms of neuronal development is mostly derived from the study
of animal models. Advances in stem cell technology now enable us to
generate neurons from human induced pluripotent stem cells (iPSCs).
Here we provide a mass spectrometry-based quantitative proteomic signature
of human iPSC-derived neurons, i.e., iPSC-derived induced glutamatergic
neurons and iPSC-derived motor neurons, throughout neuronal differentiation.
Tandem mass tag 10-plex labeling was carried out to perform proteomic
profiling of cells at different time points. Our analysis reveals
significant expression changes (FDR < 0.001) of several key proteins
during the differentiation process, e.g., proteins involved in the
Wnt and Notch signaling pathways. Overall, our data provide a rich
resource of information on protein expression during human iPSC neuron
differentiation.
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Affiliation(s)
- Suzy Varderidou-Minasian
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bert M Verheijen
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Philipp Schätzle
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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70
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Sagner A, Briscoe J. Establishing neuronal diversity in the spinal cord: a time and a place. Development 2019; 146:146/22/dev182154. [DOI: 10.1242/dev.182154] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ABSTRACT
The vertebrate spinal cord comprises multiple functionally distinct neuronal cell types arranged in characteristic positions. During development, these different types of neurons differentiate from transcriptionally distinct neural progenitors that are arrayed in discrete domains along the dorsal-ventral and anterior-posterior axes of the embryonic spinal cord. This organization arises in response to morphogen gradients acting upstream of a gene regulatory network, the architecture of which determines the spatial and temporal pattern of gene expression. In recent years, substantial progress has been made in deciphering the regulatory network that underlies the specification of distinct progenitor and neuronal cell identities. In this Review, we outline how distinct neuronal cell identities are established in response to spatial and temporal patterning systems, and outline novel experimental approaches to study the emergence and function of neuronal diversity in the spinal cord.
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71
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Hawrot J, Imhof S, Wainger BJ. Modeling cell-autonomous motor neuron phenotypes in ALS using iPSCs. Neurobiol Dis 2019; 134:104680. [PMID: 31759135 DOI: 10.1016/j.nbd.2019.104680] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 10/29/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an aggressive and uniformly fatal degenerative disease of the motor nervous system. In order to understand underlying disease mechanisms, researchers leverage a host of in vivo and in vitro models, including yeast, worms, flies, zebrafish, mice, and more recently, human induced pluripotent stem cells (iPSCs) derived from ALS patients. While mouse models have been the main workhorse of preclinical ALS research, the development of iPSCs provides a new opportunity to explore molecular phenotypes of ALS within human cells. Importantly, this technology enables modeling of both familial and sporadic ALS in the relevant human genetic backgrounds, as well as a personalized or targeted approach to therapy development. Harnessing these powerful tools requires addressing numerous challenges, including different variance components associated with iPSCs and motor neurons as well as concomitant limits of reductionist approaches. In order to overcome these obstacles, optimization of protocols and assays, confirmation of phenotype robustness at scale, and validation of findings in human tissue and genetics will cement the role for iPSC models as a valuable complement to animal models in ALS and more broadly among neurodegenerative diseases.
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Affiliation(s)
- James Hawrot
- Departments of Neurology and Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sophie Imhof
- Departments of Neurology and Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; University of Amsterdam, Amsterdam, The Netherlands
| | - Brian J Wainger
- Departments of Neurology and Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA.
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72
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Fujiki R, Lee JY, Jurgens JA, Whitman MC, Engle EC. Isolation and Culture of Oculomotor, Trochlear, and Spinal Motor Neurons from Prenatal Islmn:GFP Transgenic Mice. J Vis Exp 2019:10.3791/60440. [PMID: 31789317 PMCID: PMC7036286 DOI: 10.3791/60440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Oculomotor neurons (CN3s) and trochlear neurons (CN4s) exhibit remarkable resistance to degenerative motor neuron diseases such as amyotrophic lateral sclerosis (ALS) when compared to spinal motor neurons (SMNs). The ability to isolate and culture primary mouse CN3s, CN4s, and SMNs would provide an approach to study mechanisms underlying this selective vulnerability. To date, most protocols use heterogeneous cell cultures, which can confound the interpretation of experimental outcomes. To minimize the problems associated with mixed-cell populations, pure cultures are indispensable. Here, the first protocol describes in detail how to efficiently purify and cultivate CN3s/CN4s alongside SMNs counterparts from the same embryos using embryonic day 11.5 (E11.5) IslMN:GFP transgenic mouse embryos. The protocol provides details on the tissue dissection and dissociation, FACS-based cell isolation, and in vitro cultivation of cells from CN3/CN4 and SMN nuclei. This protocol adds a novel in vitro CN3/CN4 culture system to existing protocols and simultaneously provides a pure species- and age-matched SMN culture for comparison. Analyses focusing on the morphological, cellular, molecular, and electrophysiological characteristics of motor neurons are feasible in this culture system. This protocol will enable research into the mechanisms that define motor neuron development, selective vulnerability, and disease.
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Affiliation(s)
- Ryosuke Fujiki
- Department of Neurology, Boston Children's Hospital; FM Kirby Neurobiology Center, Boston Children's Hospital; Department of Neurology, Harvard Medical School; Medical Genetics Training Program, Harvard Medical School; Department of Neurology, Kokura Memorial Hospital
| | - Joun Y Lee
- Department of Neurology, Boston Children's Hospital; FM Kirby Neurobiology Center, Boston Children's Hospital; Department of Genetics, Albert Einstein College of Medicine
| | - Julie A Jurgens
- Department of Neurology, Boston Children's Hospital; FM Kirby Neurobiology Center, Boston Children's Hospital; Department of Neurology, Harvard Medical School; Broad Institute of M.I.T. and Harvard
| | - Mary C Whitman
- FM Kirby Neurobiology Center, Boston Children's Hospital; Department of Ophthalmology, Boston Children's Hospital; Department of Ophthalmology, Harvard Medical School
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital; FM Kirby Neurobiology Center, Boston Children's Hospital; Department of Neurology, Harvard Medical School; Medical Genetics Training Program, Harvard Medical School; Department of Ophthalmology, Boston Children's Hospital; Department of Ophthalmology, Harvard Medical School; Broad Institute of M.I.T. and Harvard; Howard Hughes Medical Institute;
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73
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Huilgol D, Venkataramani P, Nandi S, Bhattacharjee S. Transcription Factors That Govern Development and Disease: An Achilles Heel in Cancer. Genes (Basel) 2019; 10:E794. [PMID: 31614829 PMCID: PMC6826716 DOI: 10.3390/genes10100794] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/22/2022] Open
Abstract
Development requires the careful orchestration of several biological events in order to create any structure and, eventually, to build an entire organism. On the other hand, the fate transformation of terminally differentiated cells is a consequence of erroneous development, and ultimately leads to cancer. In this review, we elaborate how development and cancer share several biological processes, including molecular controls. Transcription factors (TF) are at the helm of both these processes, among many others, and are evolutionarily conserved, ranging from yeast to humans. Here, we discuss four families of TFs that play a pivotal role and have been studied extensively in both embryonic development and cancer-high mobility group box (HMG), GATA, paired box (PAX) and basic helix-loop-helix (bHLH) in the context of their role in development, cancer, and their conservation across several species. Finally, we review TFs as possible therapeutic targets for cancer and reflect on the importance of natural resistance against cancer in certain organisms, yielding knowledge regarding TF function and cancer biology.
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Affiliation(s)
- Dhananjay Huilgol
- Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
| | | | - Saikat Nandi
- Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
| | - Sonali Bhattacharjee
- Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
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74
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Babos KN, Galloway KE, Kisler K, Zitting M, Li Y, Shi Y, Quintino B, Chow RH, Zlokovic BV, Ichida JK. Mitigating Antagonism between Transcription and Proliferation Allows Near-Deterministic Cellular Reprogramming. Cell Stem Cell 2019; 25:486-500.e9. [PMID: 31523028 DOI: 10.1016/j.stem.2019.08.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/24/2019] [Accepted: 08/09/2019] [Indexed: 12/30/2022]
Abstract
Although cellular reprogramming enables the generation of new cell types for disease modeling and regenerative therapies, reprogramming remains a rare cellular event. By examining reprogramming of fibroblasts into motor neurons and multiple other somatic lineages, we find that epigenetic barriers to conversion can be overcome by endowing cells with the ability to mitigate an inherent antagonism between transcription and DNA replication. We show that transcription factor overexpression induces unusually high rates of transcription and that sustaining hypertranscription and transgene expression in hyperproliferative cells early in reprogramming is critical for successful lineage conversion. However, hypertranscription impedes DNA replication and cell proliferation, processes that facilitate reprogramming. We identify a chemical and genetic cocktail that dramatically increases the number of cells capable of simultaneous hypertranscription and hyperproliferation by activating topoisomerases. Further, we show that hypertranscribing, hyperproliferating cells reprogram at 100-fold higher, near-deterministic rates. Therefore, relaxing biophysical constraints overcomes molecular barriers to cellular reprogramming.
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Affiliation(s)
- Kimberley N Babos
- Eli and Edythe Broad CIRM Center, University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Kate E Galloway
- Eli and Edythe Broad CIRM Center, University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Kassandra Kisler
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA; Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Madison Zitting
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA; Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yichen Li
- Eli and Edythe Broad CIRM Center, University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yingxiao Shi
- Eli and Edythe Broad CIRM Center, University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brooke Quintino
- Eli and Edythe Broad CIRM Center, University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Robert H Chow
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA; Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Berislav V Zlokovic
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA; Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin K Ichida
- Eli and Edythe Broad CIRM Center, University of Southern California, 1425 San Pablo Street, Los Angeles, CA 90033, USA; Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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75
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Flitsch LJ, Brüstle O. Evolving principles underlying neural lineage conversion and their relevance for biomedical translation. F1000Res 2019; 8. [PMID: 31559012 PMCID: PMC6743253 DOI: 10.12688/f1000research.18926.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2019] [Indexed: 12/19/2022] Open
Abstract
Scientific and technological advances of the past decade have shed light on the mechanisms underlying cell fate acquisition, including its transcriptional and epigenetic regulation during embryonic development. This knowledge has enabled us to purposefully engineer cell fates
in vitro by manipulating expression levels of lineage-instructing transcription factors. Here, we review the state of the art in the cell programming field with a focus on the derivation of neural cells. We reflect on what we know about the mechanisms underlying fate changes in general and on the degree of epigenetic remodeling conveyed by the distinct reprogramming and direct conversion strategies available. Moreover, we discuss the implications of residual epigenetic memory for biomedical applications such as disease modeling and neuroregeneration. Finally, we cover recent developments approaching cell fate conversion in the living brain and define questions which need to be addressed before cell programming can become an integral part of translational medicine.
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Affiliation(s)
- Lea Jessica Flitsch
- Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, North Rhine Wesphalia, 53127, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, North Rhine Wesphalia, 53127, Germany
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76
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Abstract
Cellular reprogramming experiments from somatic cell types have demonstrated the plasticity of terminally differentiated cell states. Recent efforts in understanding the mechanisms of cellular reprogramming have begun to elucidate the differentiation trajectories along the reprogramming processes. In this review, we focus mainly on direct reprogramming strategies by transcription factors and highlight the variables that contribute to cell fate conversion outcomes. We review key studies that shed light on the cellular and molecular mechanisms by investigating differentiation trajectories and alternative cell states as well as transcription factor regulatory activities during cell fate reprogramming. Finally, we highlight a few concepts that we believe require attention, particularly when measuring the success of cell reprogramming experiments.
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Affiliation(s)
- Begüm Aydin
- Department of Biology, New York University, New York, NY 10003, USA; .,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY 10003, USA; .,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA
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77
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Nam H, Jeon S, An H, Yoo J, Lee HJ, Lee SK, Lee S. Critical roles of ARHGAP36 as a signal transduction mediator of Shh pathway in lateral motor columnar specification. eLife 2019; 8:46683. [PMID: 31305241 PMCID: PMC6658197 DOI: 10.7554/elife.46683] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/14/2019] [Indexed: 01/20/2023] Open
Abstract
During spinal cord development, Sonic hedgehog (Shh), secreted from the floor plate, plays an important role in the production of motor neurons by patterning the ventral neural tube, which establishes MN progenitor identity. It remains unknown, however, if Shh signaling plays a role in generating columnar diversity of MNs that connect distinct target muscles. Here, we report that Shh, expressed in MNs, is essential for the formation of lateral motor column (LMC) neurons in vertebrate spinal cord. This novel activity of Shh is mediated by its downstream effector ARHGAP36, whose expression is directly induced by the MN-specific transcription factor complex Isl1-Lhx3. Furthermore, we found that AKT stimulates the Shh activity to induce LMC MNs through the stabilization of ARHGAP36 proteins. Taken together, our data reveal that Shh, secreted from MNs, plays a crucial role in generating MN diversity via a regulatory axis of Shh-AKT-ARHGAP36 in the developing mouse spinal cord.
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Affiliation(s)
- Heejin Nam
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Shin Jeon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.,Neuroscience Section, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science Uiversity, Portland, United States
| | - Hyejin An
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jaeyoung Yoo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyo-Jong Lee
- College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gyungnam, Republic of Korea
| | - Soo-Kyung Lee
- Neuroscience Section, Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science Uiversity, Portland, United States.,Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Seunghee Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
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78
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Abstract
Single cell biology is currently revolutionizing developmental and evolutionary biology, revealing new cell types and states in an impressive range of biological systems. With the accumulation of data, however, the field is grappling with a central unanswered question: what exactly is a cell type? This question is further complicated by the inherently dynamic nature of developmental processes. In this Hypothesis article, we propose that a 'periodic table of cell types' can be used as a framework for distinguishing cell types from cell states, in which the periods and groups correspond to developmental trajectories and stages along differentiation, respectively. The different states of the same cell type are further analogous to 'isotopes'. We also highlight how the concept of a periodic table of cell types could be useful for predicting new cell types and states, and for recognizing relationships between cell types throughout development and evolution.
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Affiliation(s)
- Bo Xia
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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79
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An D, Fujiki R, Iannitelli DE, Smerdon JW, Maity S, Rose MF, Gelber A, Wanaselja EK, Yagudayeva I, Lee JY, Vogel C, Wichterle H, Engle EC, Mazzoni EO. Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons. eLife 2019; 8:44423. [PMID: 31157617 PMCID: PMC6594754 DOI: 10.7554/elife.44423] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 06/02/2019] [Indexed: 12/14/2022] Open
Abstract
In amyotrophic lateral sclerosis (ALS) spinal motor neurons (SpMN) progressively degenerate while a subset of cranial motor neurons (CrMN) are spared until late stages of the disease. Using a rapid and efficient protocol to differentiate mouse embryonic stem cells (ESC) to SpMNs and CrMNs, we now report that ESC-derived CrMNs accumulate less human (h)SOD1 and insoluble p62 than SpMNs over time. ESC-derived CrMNs have higher proteasome activity to degrade misfolded proteins and are intrinsically more resistant to chemically-induced proteostatic stress than SpMNs. Chemical and genetic activation of the proteasome rescues SpMN sensitivity to proteostatic stress. In agreement, the hSOD1 G93A mouse model reveals that ALS-resistant CrMNs accumulate less insoluble hSOD1 and p62-containing inclusions than SpMNs. Primary-derived ALS-resistant CrMNs are also more resistant than SpMNs to proteostatic stress. Thus, an ESC-based platform has identified a superior capacity to maintain a healthy proteome as a possible mechanism to resist ALS-induced neurodegeneration.
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Affiliation(s)
- Disi An
- Department of Biology, New York University, New York, United States
| | - Ryosuke Fujiki
- Department of Neurology, Boston Children's Hospital, Boston, United States.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States.,Medical Genetics Training Program, Harvard Medical School, Boston, United States
| | | | - John W Smerdon
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
| | - Shuvadeep Maity
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
| | - Matthew F Rose
- Department of Neurology, Boston Children's Hospital, Boston, United States.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States.,Medical Genetics Training Program, Harvard Medical School, Boston, United States.,Department of Pathology, Brigham and Women's Hospital, Boston, United States.,Department of Pathology, Boston Children's Hospital, Boston, United States.,Department of Pathology, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Alon Gelber
- Department of Neurology, Boston Children's Hospital, Boston, United States.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | | | - Ilona Yagudayeva
- Department of Biology, New York University, New York, United States
| | - Joun Y Lee
- Department of Neurology, Boston Children's Hospital, Boston, United States.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States
| | - Christine Vogel
- Department of Biology, New York University, New York, United States.,Center for Genomics and Systems Biology, New York University, New York, United States
| | - Hynek Wichterle
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, United States
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital, Boston, United States.,FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, United States.,Department of Neurology, Harvard Medical School, Boston, United States.,Medical Genetics Training Program, Harvard Medical School, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Department of Ophthalmology, Boston Children's Hospital, Boston, United States.,Department of Ophthalmology, Harvard Medical School, Boston, United States
| | - Esteban Orlando Mazzoni
- Department of Biology, New York University, New York, United States.,NYU Neuroscience Institute, NYU Langone Medical Center, New York, United States
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80
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Ma NX, Yin JC, Chen G. Transcriptome Analysis of Small Molecule-Mediated Astrocyte-to-Neuron Reprogramming. Front Cell Dev Biol 2019; 7:82. [PMID: 31231645 PMCID: PMC6558402 DOI: 10.3389/fcell.2019.00082] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/01/2019] [Indexed: 12/21/2022] Open
Abstract
Chemical reprogramming of astrocytes into neurons represents a promising approach to regenerate new neurons for brain repair, but the underlying mechanisms driving this trans-differentiation process are not well understood. We have recently identified four small molecules – CHIR99021, DAPT, LDN193189, and SB431542 – that can efficiently reprogram cultured human fetal astrocytes into functional neurons. Here we employ the next generation of RNA-sequencing technology to investigate the transcriptome changes during the astrocyte-to-neuron (AtN) conversion process. We found that the four small molecules can rapidly activate the hedgehog signaling pathway while downregulating many glial genes such as FN1 and MYL9 within 24 h of treatment. Chemical reprogramming is mediated by several waves of differential gene expression, including upregulation of hedgehog, Wnt/β-catenin, and Notch signaling pathways, together with downregulation of TGF-β and JAK/STAT signaling pathways. Our gene network analyses reveal many well-connected hub genes such as repulsive guidance molecule A (RGMA), neuronatin (NNAT), neurogenin 2 (NEUROG2), NPTX2, MOXD1, JAG1, and GAP43, which may coordinate the chemical reprogramming process. Together, these findings provide critical insights into the molecular cascades triggered by a combination of small molecules that eventually leads to chemical conversion of astrocytes into neurons.
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Affiliation(s)
- Ning-Xin Ma
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Jiu-Chao Yin
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Gong Chen
- Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States
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81
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Aydin B, Kakumanu A, Rossillo M, Moreno-Estellés M, Garipler G, Ringstad N, Flames N, Mahony S, Mazzoni EO. Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes. Nat Neurosci 2019; 22:897-908. [PMID: 31086315 PMCID: PMC6556771 DOI: 10.1038/s41593-019-0399-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/28/2019] [Indexed: 11/29/2022]
Abstract
Developmental programs that generate the astonishing neuronal diversity of the nervous system are not completely understood and thus present a significant challenge for clinical applications of guided cell differentiation strategies. Using direct neuronal programming of embryonic stem cells, we found that two main vertebrate proneural factors, Ascl1 and Neurog2, induce different neuronal fates by binding to largely different sets of genomic sites. Their divergent binding patterns are not determined by the previous chromatin state but are distinguished by enrichment of specific E-box sequences which reflect the binding preferences of the DNA-binding domains. The divergent Ascl1 and Neurog2 binding patterns result in distinct chromatin accessibility and enhancer activity profiles that differentially shape the binding of downstream transcription factors during neuronal differentiation. This study provides a mechanistic understanding of how transcription factors constrain terminal cell fates, and it delineates the importance of choosing the right proneural factor in neuronal reprogramming strategies.
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Affiliation(s)
- Begüm Aydin
- Department of Biology, New York University, New York, NY, USA.,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY, USA
| | - Akshay Kakumanu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mary Rossillo
- Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, USA
| | - Mireia Moreno-Estellés
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Görkem Garipler
- Department of Biology, New York University, New York, NY, USA.,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY, USA
| | - Niels Ringstad
- Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, USA
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Esteban O Mazzoni
- Department of Biology, New York University, New York, NY, USA. .,Neuroscience Institute, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY, USA.
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82
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Allodi I, Nijssen J, Benitez JA, Schweingruber C, Fuchs A, Bonvicini G, Cao M, Kiehn O, Hedlund E. Modeling Motor Neuron Resilience in ALS Using Stem Cells. Stem Cell Reports 2019; 12:1329-1341. [PMID: 31080111 PMCID: PMC6565614 DOI: 10.1016/j.stemcr.2019.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/17/2022] Open
Abstract
Oculomotor neurons, which regulate eye movement, are resilient to degeneration in the lethal motor neuron disease amyotrophic lateral sclerosis (ALS). It would be highly advantageous if motor neuron resilience could be modeled in vitro. Toward this goal, we generated a high proportion of oculomotor neurons from mouse embryonic stem cells through temporal overexpression of PHOX2A in neuronal progenitors. We demonstrate, using electrophysiology, immunocytochemistry, and RNA sequencing, that in vitro-generated neurons are bona fide oculomotor neurons based on their cellular properties and similarity to their in vivo counterpart in rodent and man. We also show that in vitro-generated oculomotor neurons display a robust activation of survival-promoting Akt signaling and are more resilient to the ALS-like toxicity of kainic acid than spinal motor neurons. Thus, we can generate bona fide oculomotor neurons in vitro that display a resilience similar to that seen in vivo. Bona fide oculomotor neurons can be derived from stem cells by PHOX2A overexpression In vitro- and in vivo-generated oculomotor neurons are transcriptionally similar Stem cell-derived oculomotor neurons display a robust activation of Akt signaling In vitro-generated oculomotor neurons are relatively resilient to ALS-like toxicity
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Affiliation(s)
- Ilary Allodi
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jik Nijssen
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Andrea Fuchs
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Gillian Bonvicini
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ming Cao
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ole Kiehn
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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83
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The Homeodomain Transcription Factor NKX2.1 Is Essential for the Early Specification of Melanocortin Neuron Identity and Activates Pomc Expression in the Developing Hypothalamus. J Neurosci 2019; 39:4023-4035. [PMID: 30886014 DOI: 10.1523/jneurosci.2924-18.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/03/2019] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Food intake is tightly regulated by a group of neurons present in the arcuate nucleus of the hypothalamus, which release Pomc-encoded melanocortins, the absence of which induces marked hyperphagia and early-onset obesity. Although the relevance of hypothalamic POMC neurons in the regulation of body weight and energy balance is well appreciated, little is known about the transcription factors that establish the melanocortin neuron identity during brain development and its phenotypic maintenance in postnatal life. Here, we report that the transcription factor NKX2.1 is present in mouse hypothalamic POMC neurons from early development to adulthood. Electromobility shift assays showed that NKX2.1 binds in vitro to NKX binding motifs present in the neuronal Pomc enhancers nPE1 and nPE2 and chromatin immunoprecipitation assays detected in vivo binding of NKX2.1 to nPE1 and nPE2 in mouse hypothalamic extracts. Transgenic and mutant studies performed in mouse embryos of either sex and adult males showed that the NKX motifs present in nPE1 and nPE2 are essential for their transcriptional enhancer activity. The conditional early inactivation of Nkx2.1 in the ventral hypothalamus prevented the onset of Pomc expression. Selective Nkx2.1 ablation from POMC neurons decreased Pomc expression in adult males and mildly increased their body weight and adiposity. Our results demonstrate that NKX2.1 is necessary to activate Pomc expression by binding to conserved canonical NKX motifs present in nPE1 and nPE2. Therefore, NKX2.1 plays a critical role in the early establishment of hypothalamic melanocortin neuron identity and participates in the maintenance of Pomc expression levels during adulthood.SIGNIFICANCE STATEMENT Food intake and body weight regulation depend on hypothalamic neurons that release satiety-inducing neuropeptides, known as melanocortins. Central melanocortins are encoded byPomc, and Pomc mutations may lead to hyperphagia and severe obesity. Although the importance of central melanocortins is well appreciated, the genetic program that establishes and maintains fully functional POMC neurons remains to be explored. Here, we combined molecular, genetic, developmental, and functional studies that led to the discovery of NKX2.1, a transcription factor that participates in the early morphogenesis of the developing hypothalamus, as a key player in establishing the early identity of melanocortin neurons by activating Pomc expression. Thus, Nkx2.1 adds to the growing list of genes that participate in body weight regulation and adiposity.
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Ichida JK, Staats KA, Davis-Dusenbery BN, Clement K, Galloway KE, Babos KN, Shi Y, Son EY, Kiskinis E, Atwater N, Gu H, Gnirke A, Meissner A, Eggan K. Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons. Development 2018; 145:dev.168617. [PMID: 30337375 DOI: 10.1242/dev.168617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/15/2018] [Indexed: 01/11/2023]
Abstract
Advances in stem cell science allow the production of different cell types in vitro either through the recapitulation of developmental processes, often termed 'directed differentiation', or the forced expression of lineage-specific transcription factors. Although cells produced by both approaches are increasingly used in translational applications, their quantitative similarity to their primary counterparts remains largely unresolved. To investigate the similarity between in vitro-derived and primary cell types, we harvested and purified mouse spinal motor neurons and compared them with motor neurons produced by transcription factor-mediated lineage conversion of fibroblasts or directed differentiation of pluripotent stem cells. To enable unbiased analysis of these motor neuron types and their cells of origin, we then subjected them to whole transcriptome and DNA methylome analysis by RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS). Despite major differences in methodology, lineage conversion and directed differentiation both produce cells that closely approximate the primary motor neuron state. However, we identify differences in Fas signaling, the Hox code and synaptic gene expression between lineage-converted and directed differentiation motor neurons that affect their utility in translational studies.
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Affiliation(s)
- Justin K Ichida
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA .,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA.,Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kim A Staats
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brandi N Davis-Dusenbery
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Kendell Clement
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kate E Galloway
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kimberly N Babos
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yingxiao Shi
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Esther Y Son
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Evangelos Kiskinis
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Nicholas Atwater
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA .,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Kevin Eggan
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA .,Howard Hughes Medical Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
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85
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Ng FSL, Ruau D, Wernisch L, Göttgens B. A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles. Brief Bioinform 2018; 19:162-173. [PMID: 27780826 PMCID: PMC5496675 DOI: 10.1093/bib/bbw102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 11/16/2022] Open
Abstract
Integrated analysis of multiple genome-wide transcription factor (TF)-binding profiles will be vital to advance our understanding of the global impact of TF binding. However, existing methods for measuring similarity in large numbers of chromatin immunoprecipitation assays with sequencing (ChIP-seq), such as correlation, mutual information or enrichment analysis, are limited in their ability to display functionally relevant TF relationships. In this study, we propose the use of graphical models to determine conditional independence between TFs and showed that network visualization provides a promising alternative to distinguish ‘direct’ versus ‘indirect’ TF interactions. We applied four algorithms to measure ‘direct’ dependence to a compendium of 367 mouse haematopoietic TF ChIP-seq samples and obtained a consensus network known as a ‘TF association network’ where edges in the network corresponded to likely causal pairwise relationships between TFs. The ‘TF association network’ illustrates the role of TFs in developmental pathways, is reminiscent of combinatorial TF regulation, corresponds to known protein–protein interactions and indicates substantial TF-binding reorganization in leukemic cell types. With the rapid increase in TF ChIP-Seq data sets, the approach presented here will be a powerful tool to study transcriptional programmes across a wide range of biological systems.
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Affiliation(s)
- Felicia S L Ng
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Hills Road, Cambridge, UK
| | - David Ruau
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Hills Road, Cambridge, UK
| | - Lorenz Wernisch
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Hills Road, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Hills Road, Cambridge, UK
- Corresponding author: Berthold Gottgens, Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 0XY, UK. Tel: 01223-336829; Fax: 01223-762670; E-mail:
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86
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Yen YP, Hsieh WF, Tsai YY, Lu YL, Liau ES, Hsu HC, Chen YC, Liu TC, Chang M, Li J, Lin SP, Hung JH, Chen JA. Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. eLife 2018; 7:38080. [PMID: 30311912 PMCID: PMC6221546 DOI: 10.7554/elife.38080] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/11/2018] [Indexed: 12/28/2022] Open
Abstract
The mammalian imprinted Dlk1-Dio3 locus produces multiple long non-coding RNAs (lncRNAs) from the maternally inherited allele, including Meg3 (i.e., Gtl2) in the mammalian genome. Although this locus has well-characterized functions in stem cell and tumor contexts, its role during neural development is unknown. By profiling cell types at each stage of embryonic stem cell-derived motor neurons (ESC~MNs) that recapitulate spinal cord development, we uncovered that lncRNAs expressed from the Dlk1-Dio3 locus are predominantly and gradually enriched in rostral motor neurons (MNs). Mechanistically, Meg3 and other Dlk1-Dio3 locus-derived lncRNAs facilitate Ezh2/Jarid2 interactions. Loss of these lncRNAs compromises the H3K27me3 landscape, leading to aberrant expression of progenitor and caudal Hox genes in postmitotic MNs. Our data thus illustrate that these lncRNAs in the Dlk1-Dio3 locus, particularly Meg3, play a critical role in maintaining postmitotic MN cell fate by repressing progenitor genes and they shape MN subtype identity by regulating Hox genes. When a gene is active, its DNA sequence is ‘transcribed’ to form a molecule of RNA. Many of these RNAs act as templates for making proteins. But for some genes, the protein molecules are not their final destinations. Their RNA molecules instead help to control gene activity, which can alter the behaviour or the identity of a cell. For example, experiments performed in individual cells suggest that so-called long non-coding RNAs (or lncRNAs for short) guide how stem cells develop into different types of mature cells. However, it is not clear whether lncRNAs play the same critical role in embryos. Yen et al. used embryonic stem cells to model how motor neurons develop in the spinal cord of mouse embryos. This revealed that motor neurons produce large amounts of a specific group of lncRNAs, particularly one called Meg3. Further experiments showed that motor neurons in mouse embryos that lack Meg3 do not correctly silence a set of genes called the Hox genes, which are crucial for laying out the body plans of many different animal embryos. These neurons also incorrectly continue to express genes that are normally active in an early phase of the stem-like cells that make motor neurons. There is wide interest in how lncRNAs help to regulate embryonic development. With this new knowledge of how Meg3 regulates the activity of Hox genes in motor neurons, research could now be directed toward investigating whether lncRNAs help other tissues to develop in a similar way.
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Affiliation(s)
- Ya-Ping Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China.,Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Wen-Fu Hsieh
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Ya-Yin Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ya-Lin Lu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ee Shan Liau
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ho-Chiang Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Yen-Chung Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ting-Chun Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Mien Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Joye Li
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Shau-Ping Lin
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Jui-Hung Hung
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China.,Department of Computer Science, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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87
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Directing neuronal cell fate in vitro : Achievements and challenges. Prog Neurobiol 2018; 168:42-68. [DOI: 10.1016/j.pneurobio.2018.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 12/22/2022]
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88
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Simandi Z, Pajer K, Karolyi K, Sieler T, Jiang LL, Kolostyak Z, Sari Z, Fekecs Z, Pap A, Patsalos A, Contreras GA, Reho B, Papp Z, Guo X, Horvath A, Kiss G, Keresztessy Z, Vámosi G, Hickman J, Xu H, Dormann D, Hortobagyi T, Antal M, Nógrádi A, Nagy L. Arginine Methyltransferase PRMT8 Provides Cellular Stress Tolerance in Aging Motoneurons. J Neurosci 2018; 38:7683-7700. [PMID: 30054395 PMCID: PMC6113905 DOI: 10.1523/jneurosci.3389-17.2018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/22/2018] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
Aging contributes to cellular stress and neurodegeneration. Our understanding is limited regarding the tissue-restricted mechanisms providing protection in postmitotic cells throughout life. Here, we show that spinal cord motoneurons exhibit a high abundance of asymmetric dimethyl arginines (ADMAs) and the presence of this posttranslational modification provides protection against environmental stress. We identify protein arginine methyltransferase 8 (PRMT8) as a tissue-restricted enzyme responsible for proper ADMA level in postmitotic neurons. Male PRMT8 knock-out mice display decreased muscle strength with aging due to premature destabilization of neuromuscular junctions. Mechanistically, inhibition of methyltransferase activity or loss of PRMT8 results in accumulation of unrepaired DNA double-stranded breaks and decrease in the cAMP response-element-binding protein 1 (CREB1) level. As a consequence, the expression of CREB1-mediated prosurvival and regeneration-associated immediate early genes is dysregulated in aging PRMT8 knock-out mice. The uncovered role of PRMT8 represents a novel mechanism of stress tolerance in long-lived postmitotic neurons and identifies PRMT8 as a tissue-specific therapeutic target in the prevention of motoneuron degeneration.SIGNIFICANCE STATEMENT Although most of the cells in our body have a very short lifespan, postmitotic neurons must survive for many decades. Longevity of a cell within the organism depends on its ability to properly regulate signaling pathways that counteract perturbations, such as DNA damage, oxidative stress, or protein misfolding. Here, we provide evidence that tissue-specific regulators of stress tolerance exist in postmitotic neurons. Specifically, we identify protein arginine methyltransferase 8 (PRMT8) as a cell-type-restricted arginine methyltransferase in spinal cord motoneurons (MNs). PRMT8-dependent arginine methylation is required for neuroprotection against age-related increased of cellular stress. Tissue-restricted expression and the enzymatic activity of PRMT8 make it an attractive target for drug development to delay the onset of neurodegenerative disorders.
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Affiliation(s)
- Zoltan Simandi
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Krisztian Pajer
- Department of Anatomy, Histology and Embryology, University of Szeged, Szeged, Hungary, HU 6720
| | - Katalin Karolyi
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827
| | - Tatiana Sieler
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827
| | - Lu-Lin Jiang
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Zsuzsanna Kolostyak
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Zsanett Sari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Zoltan Fekecs
- Department of Anatomy, Histology and Embryology, University of Szeged, Szeged, Hungary, HU 6720
| | - Attila Pap
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Andreas Patsalos
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Gerardo Alvarado Contreras
- Division of Clinical Physiology, Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Balint Reho
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Zoltan Papp
- Division of Clinical Physiology, Institute of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Xiufang Guo
- NanoScience Technology Center, University of Central Florida, Orlando, Florida 32816
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Greta Kiss
- Department of Anatomy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Zsolt Keresztessy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - György Vámosi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
| | - James Hickman
- NanoScience Technology Center, University of Central Florida, Orlando, Florida 32816
| | - Huaxi Xu
- Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Dorothee Dormann
- BioMedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany 80539
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany 80539
| | - Tibor Hortobagyi
- HAS-UD Cerebrovascular and Neurodegenerative Research Group, Department of Neurology and Neuropathology, University of Debrecen, Debrecen, Hungary, HU 4032
| | - Miklos Antal
- Department of Anatomy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
- HAS-UD Neuroscience Research Group, University of Debrecen, Debrecen, Hungary, HU 4032, and
| | - Antal Nógrádi
- Department of Anatomy, Histology and Embryology, University of Szeged, Szeged, Hungary, HU 6720
| | - Laszlo Nagy
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827,
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary, HU 4032
- HAS-UD Momentum Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary, HU 4032
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89
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High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor. PLoS Genet 2018; 14:e1007552. [PMID: 30063705 PMCID: PMC6086484 DOI: 10.1371/journal.pgen.1007552] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/10/2018] [Accepted: 07/10/2018] [Indexed: 12/24/2022] Open
Abstract
In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion. The ongoing ATOH1 gene therapy clinical trial offers promise for hearing restoration in humans. However, in animal models, Atoh1-mediated sensory regeneration is inefficient and incomplete. Here we performed high-resolution gene expression profiling of single cochlear cells at multiple time points in a mouse model whereby we discovered a continuous regeneration process that leads to the formation of immature sensory cells. We identified 51 key reprogramming transcription factors that may increase the efficiency and completion of the regeneration process and confirmed that Isl1 in transgenic mice promotes Atoh1-mediated sensory regeneration as a co-reprogramming factor. Our studies identify molecular mechanisms and novel co-reprogramming factors for sensory restoration in humans with irreversible hearing loss.
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90
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Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift. Nat Commun 2018; 9:2595. [PMID: 29968757 PMCID: PMC6030214 DOI: 10.1038/s41467-018-05016-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 06/06/2018] [Indexed: 11/08/2022] Open
Abstract
Single-cell RNA sequencing allows defining molecularly distinct cell subpopulations. However, the identification of specific sets of transcription factors (TFs) that define the identity of these subpopulations remains a challenge. Here we propose that subpopulation identity emerges from the synergistic activity of multiple TFs. Based on this concept, we develop a computational platform (TransSyn) for identifying synergistic transcriptional cores that determine cell subpopulation identities. TransSyn leverages single-cell RNA-seq data, and performs a dynamic search for an optimal synergistic transcriptional core using an information theoretic measure of synergy. A large-scale TransSyn analysis identifies transcriptional cores for 186 subpopulations, and predicts identity conversion TFs between 3786 pairs of cell subpopulations. Finally, TransSyn predictions enable experimental conversion of human hindbrain neuroepithelial cells into medial floor plate midbrain progenitors, capable of rapidly differentiating into dopaminergic neurons. Thus, TransSyn can facilitate designing strategies for conversion of cell subpopulation identities with potential applications in regenerative medicine.
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91
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Fernandopulle MS, Prestil R, Grunseich C, Wang C, Gan L, Ward ME. Transcription Factor-Mediated Differentiation of Human iPSCs into Neurons. ACTA ACUST UNITED AC 2018; 79:e51. [PMID: 29924488 DOI: 10.1002/cpcb.51] [Citation(s) in RCA: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Accurate modeling of human neuronal cell biology has been a long-standing challenge. However, methods to differentiate human induced pluripotent stem cells (iPSCs) to neurons have recently provided experimentally tractable cell models. Numerous methods that use small molecules to direct iPSCs into neuronal lineages have arisen in recent years. Unfortunately, these methods entail numerous challenges, including poor efficiency, variable cell type heterogeneity, and lengthy, expensive differentiation procedures. We recently developed a new method to generate stable transgenic lines of human iPSCs with doxycycline-inducible transcription factors at safe-harbor loci. Using a simple two-step protocol, these lines can be inducibly differentiated into either cortical (i3 Neurons) or lower motor neurons (i3 LMN) in a rapid, efficient, and scalable manner (Wang et al., 2017). In this manuscript, we describe a set of protocols to assist investigators in the culture and genetic engineering of iPSC lines to enable transcription factor-mediated differentiation of iPSCs into i3 Neurons or i3 LMNs, and we present neuronal culture conditions for various experimental applications. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Michael S Fernandopulle
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Ryan Prestil
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Christopher Grunseich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Chao Wang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, California
| | - Li Gan
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, California
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
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92
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Abernathy DG, Kim WK, McCoy MJ, Lake AM, Ouwenga R, Lee SW, Xing X, Li D, Lee HJ, Heuckeroth RO, Dougherty JD, Wang T, Yoo AS. MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. Cell Stem Cell 2018; 21:332-348.e9. [PMID: 28886366 DOI: 10.1016/j.stem.2017.08.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/26/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
Abstract
Directed reprogramming of human fibroblasts into fully differentiated neurons requires massive changes in epigenetic and transcriptional states. Induction of a chromatin environment permissive for acquiring neuronal subtype identity is therefore a major barrier to fate conversion. Here we show that the brain-enriched miRNAs miR-9/9∗ and miR-124 (miR-9/9∗-124) trigger reconfiguration of chromatin accessibility, DNA methylation, and mRNA expression to induce a default neuronal state. miR-9/9∗-124-induced neurons (miNs) are functionally excitable and uncommitted toward specific subtypes but possess open chromatin at neuronal subtype-specific loci, suggesting that such identity can be imparted by additional lineage-specific transcription factors. Consistently, we show that ISL1 and LHX3 selectively drive conversion to a highly homogeneous population of human spinal cord motor neurons. This study shows that modular synergism between miRNAs and neuronal subtype-specific transcription factors can drive lineage-specific neuronal reprogramming, providing a general platform for high-efficiency generation of distinct subtypes of human neurons.
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Affiliation(s)
- Daniel G Abernathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Woo Kyung Kim
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J McCoy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics & Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allison M Lake
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca Ouwenga
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seong Won Lee
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hyung Joo Lee
- Program in Molecular Genetics & Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert O Heuckeroth
- Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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93
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De Santis R, Garone MG, Pagani F, de Turris V, Di Angelantonio S, Rosa A. Direct conversion of human pluripotent stem cells into cranial motor neurons using a piggyBac vector. Stem Cell Res 2018; 29:189-196. [DOI: 10.1016/j.scr.2018.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/23/2018] [Accepted: 04/24/2018] [Indexed: 12/11/2022] Open
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94
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Watson C, Tvrdik P. Spinal Accessory Motor Neurons in the Mouse: A Special Type of Branchial Motor Neuron? Anat Rec (Hoboken) 2018; 302:505-511. [DOI: 10.1002/ar.23822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 10/10/2017] [Accepted: 10/10/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Charles Watson
- School of Animal Biology; University of Western Australia; Perth Australia
- Neuroscience Research Australia; Sydney Australia
| | - Petr Tvrdik
- Department of Neurosurgery; University of Utah; Salt Lake City Utah
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95
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Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation. Proc Natl Acad Sci U S A 2018; 115:4643-4648. [PMID: 29666277 DOI: 10.1073/pnas.1714646115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered regions are highly represented among mammalian transcription factors, where they often contribute to the formation of multiprotein complexes that regulate gene expression. An example of this occurs with LIM-homeodomain (LIM-HD) proteins in the developing spinal cord. The LIM-HD protein LHX3 and the LIM-HD cofactor LDB1 form a binary complex that gives rise to interneurons, whereas in adjacent cell populations, LHX3 and LDB1 form a rearranged ternary complex with the LIM-HD protein ISL1, resulting in motor neurons. The protein-protein interactions within these complexes are mediated by ordered LIM domains in the LIM-HD proteins and intrinsically disordered LIM interaction domains (LIDs) in LDB1 and ISL1; however, little is known about how the strength or rates of binding contribute to complex assemblies. We have measured the interactions of LIM:LID complexes using FRET-based protein-protein interaction studies and EMSAs and used these data to model population distributions of complexes. The protein-protein interactions within the ternary complexes are much weaker than those in the binary complex, yet surprisingly slow LDB1:ISL1 dissociation kinetics and a substantial increase in DNA binding affinity promote formation of the ternary complex over the binary complex in motor neurons. We have used mutational and protein engineering approaches to show that allostery and modular binding by tandem LIM domains contribute to the LDB1LID binding kinetics. The data indicate that a single intrinsically disordered region can achieve highly disparate binding kinetics, which may provide a mechanism to regulate the timing of transcriptional complex assembly.
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96
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Lloret-Fernández C, Maicas M, Mora-Martínez C, Artacho A, Jimeno-Martín Á, Chirivella L, Weinberg P, Flames N. A transcription factor collective defines the HSN serotonergic neuron regulatory landscape. eLife 2018; 7:32785. [PMID: 29553368 PMCID: PMC5916565 DOI: 10.7554/elife.32785] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/16/2018] [Indexed: 01/02/2023] Open
Abstract
Cell differentiation is controlled by individual transcription factors (TFs) that together activate a selection of enhancers in specific cell types. How these combinations of TFs identify and activate their target sequences remains poorly understood. Here, we identify the cis-regulatory transcriptional code that controls the differentiation of serotonergic HSN neurons in Caenorhabditis elegans. Activation of the HSN transcriptome is directly orchestrated by a collective of six TFs. Binding site clusters for this TF collective form a regulatory signature that is sufficient for de novo identification of HSN neuron functional enhancers. Among C. elegans neurons, the HSN transcriptome most closely resembles that of mouse serotonergic neurons. Mouse orthologs of the HSN TF collective also regulate serotonergic differentiation and can functionally substitute for their worm counterparts which suggests deep homology. Our results identify rules governing the regulatory landscape of a critically important neuronal type in two species separated by over 700 million years.
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Affiliation(s)
- Carla Lloret-Fernández
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Alejandro Artacho
- Departamento de Genómica y Salud, Centro Superior de Investigación en Salud Pública, FISABIO, Valencia, Spain
| | - Ángela Jimeno-Martín
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Laura Chirivella
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Peter Weinberg
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University Medical Center, New York, United States
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
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97
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Quaranta R, Fell J, Rühle F, Rao J, Piccini I, Araúzo-Bravo MJ, Verkerk AO, Stoll M, Greber B. Revised roles of ISL1 in a hES cell-based model of human heart chamber specification. eLife 2018; 7. [PMID: 29337667 PMCID: PMC5770158 DOI: 10.7554/elife.31706] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/02/2018] [Indexed: 12/21/2022] Open
Abstract
The transcription factor ISL1 is thought to be key for conveying the multipotent and proliferative properties of cardiac precursor cells. Here, we investigate its function upon cardiac induction of human embryonic stem cells. We find that ISL1 does not stabilize the transient cardiac precursor cell state but rather serves to accelerate cardiomyocyte differentiation. Conversely, ISL1 depletion delays cardiac differentiation and respecifies nascent cardiomyocytes from a ventricular to an atrial identity. Mechanistic analyses integrate this unrecognized anti-atrial function of ISL1 with known and newly identified atrial inducers. In this revised view, ISL1 is antagonized by retinoic acid signaling via a novel player, MEIS2. Conversely, ISL1 competes with the retinoic acid pathway for prospective cardiomyocyte fate, which converges on the atrial specifier NR2F1. This study reveals a core regulatory network putatively controlling human heart chamber formation and also bears implications for the subtype-specific production of human cardiomyocytes with enhanced functional properties.
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Affiliation(s)
- Roberto Quaranta
- Human Stem Cell Pluripotency Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
| | - Jakob Fell
- Human Stem Cell Pluripotency Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
| | - Frank Rühle
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Münster, Germany
| | - Jyoti Rao
- Human Stem Cell Pluripotency Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
| | - Ilaria Piccini
- Human Stem Cell Pluripotency Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
| | - Marcos J Araúzo-Bravo
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Arie O Verkerk
- Department of Clinical and Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Monika Stoll
- Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Münster, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Boris Greber
- Human Stem Cell Pluripotency Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
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98
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Santiago C, Bashaw GJ. Islet Coordinately Regulates Motor Axon Guidance and Dendrite Targeting through the Frazzled/DCC Receptor. Cell Rep 2017; 18:1646-1659. [PMID: 28199838 DOI: 10.1016/j.celrep.2017.01.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/30/2016] [Accepted: 01/18/2017] [Indexed: 01/27/2023] Open
Abstract
Motor neuron axon targeting in the periphery is correlated with the positions of motor neuron inputs in the CNS, but how these processes are coordinated to form a myotopic map remains poorly understood. We show that the LIM homeodomain factor Islet (Isl) controls targeting of both axons and dendrites in Drosophila motor neurons through regulation of the Frazzled (Fra)/DCC receptor. Isl is required for fra expression in ventrally projecting motor neurons, and isl and fra mutants have similar axon guidance defects. Single-cell labeling indicates that isl and fra are also required for dendrite targeting in a subset of motor neurons. Finally, overexpression of Fra rescues axon and dendrite targeting defects in isl mutants. These results indicate that Fra acts downstream of Isl in both the periphery and the CNS, demonstrating how a single regulatory relationship is used in multiple cellular compartments to coordinate neural circuit wiring.
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Affiliation(s)
- Celine Santiago
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Greg J Bashaw
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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99
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Abstract
Rhee et al. (2016) in this issue of Neuron and Velasco et al. (2016) in Cell Stem Cell find that the activity of transcription factors binding sequentially to a series of transient early and late enhancers directs gene expression that is essential for motor neuron differentiation and function.
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Affiliation(s)
- Clinton Cave
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, PCTB 1004, Baltimore, MD 21205, USA
| | - Shanthini Sockanathan
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, PCTB 1004, Baltimore, MD 21205, USA.
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100
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Kakumanu A, Velasco S, Mazzoni E, Mahony S. Deconvolving sequence features that discriminate between overlapping regulatory annotations. PLoS Comput Biol 2017; 13:e1005795. [PMID: 29049320 PMCID: PMC5663517 DOI: 10.1371/journal.pcbi.1005795] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/31/2017] [Accepted: 09/26/2017] [Indexed: 11/19/2022] Open
Abstract
Genomic loci with regulatory potential can be annotated with various properties. For example, genomic sites bound by a given transcription factor (TF) can be divided according to whether they are proximal or distal to known promoters. Sites can be further labeled according to the cell types and conditions in which they are active. Given such a collection of labeled sites, it is natural to ask what sequence features are associated with each annotation label. However, discovering such label-specific sequence features is often confounded by overlaps between the labels; e.g. if regulatory sites specific to a given cell type are also more likely to be promoter-proximal, it is difficult to assess whether motifs identified in that set of sites are associated with the cell type or associated with promoters. In order to meet this challenge, we developed SeqUnwinder, a principled approach to deconvolving interpretable discriminative sequence features associated with overlapping annotation labels. We demonstrate the novel analysis abilities of SeqUnwinder using three examples. Firstly, SeqUnwinder is able to unravel sequence features associated with the dynamic binding behavior of TFs during motor neuron programming from features associated with chromatin state in the initial embryonic stem cells. Secondly, we characterize distinct sequence properties of multi-condition and cell-specific TF binding sites after controlling for uneven associations with promoter proximity. Finally, we demonstrate the scalability of SeqUnwinder to discover cell-specific sequence features from over one hundred thousand genomic loci that display DNase I hypersensitivity in one or more ENCODE cell lines. Transcription factor proteins control gene expression by recognizing and interacting with short DNA sequence patterns in regulatory regions on the genome. Current genomics experiments allow us to find regulatory regions associated with a particular biochemical activity over the entire genome; for example, all regions where a particular transcription factor interacts with the genome in a given cell type. Given a collection of regulatory regions, we often aim to discover short DNA sequence patterns that are more common in the collection than in other regions. Performing such “DNA motif-finding” analysis can give us hints about the patterns that determine gene regulation in the analyzed cell type. Here we describe a new method for DNA motif-finding called SeqUnwinder. Our approach analyzes collections of regulatory regions where each has been labeled according to various biological properties. For example, the labels could correspond to various cell types in which the regulatory region is active. SeqUnwinder then performs machine-learning analysis to unravel DNA sequence features that are characteristic of each label (e.g. features that distinguish regulatory regions in each cell type from other cell types). SeqUnwinder is the first method to enable analysis of regulatory region collections that contain several overlapping labels.
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Affiliation(s)
- Akshay Kakumanu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Silvia Velasco
- Department of Biology, New York University, 100 Washington Square East, New York, NY, United States of America
| | - Esteban Mazzoni
- Department of Biology, New York University, 100 Washington Square East, New York, NY, United States of America
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
- * E-mail:
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