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Chmykhalo VK, Deev RV, Tokarev AT, Polunina YA, Xue L, Shidlovskii YV. SWI/SNF Complex Connects Signaling and Epigenetic State in Cells of Nervous System. Mol Neurobiol 2024:10.1007/s12035-024-04355-6. [PMID: 39002058 DOI: 10.1007/s12035-024-04355-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
SWI/SNF protein complexes are evolutionarily conserved epigenetic regulators described in all eukaryotes. In metameric animals, the complexes are involved in all processes occurring in the nervous system, from neurogenesis to higher brain functions. On the one hand, the range of roles is wide because the SWI/SNF complexes act universally by mobilizing the nucleosomes in a chromatin template at multiple loci throughout the genome. On the other hand, the complexes mediate the action of multiple signaling pathways that control most aspects of neural tissue development and function. The issues are discussed to provide insight into the molecular basis of the multifaceted role of SWI/SNFs in cell cycle regulation, DNA repair, activation of immediate-early genes, neurogenesis, and brain and connectome formation. An overview is additionally provided for the molecular basis of nervous system pathologies associated with the SWI/SNF complexes and their contribution to neuroinflammation and neurodegeneration. Finally, we discuss the idea that SWI/SNFs act as an integration platform to connect multiple signaling and genetic programs.
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Affiliation(s)
- Victor K Chmykhalo
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia.
| | - Roman V Deev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
| | - Artemiy T Tokarev
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
| | - Yulia A Polunina
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
| | - Lei Xue
- School of Life Science and Technology, The First Rehabilitation Hospital of Shanghai, Tongji University, Shanghai, China
| | - Yulii V Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St, Moscow, 119334, Russia
- Department of Biology and General Genetics, Sechenov University, Moscow, Russia
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Martins-Costa C, Wiegers A, Pham VA, Sidhaye J, Doleschall B, Novatchkova M, Lendl T, Piber M, Peer A, Möseneder P, Stuempflen M, Chow SYA, Seidl R, Prayer D, Höftberger R, Kasprian G, Ikeuchi Y, Corsini NS, Knoblich JA. ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum. Cell Stem Cell 2024; 31:866-885.e14. [PMID: 38718796 DOI: 10.1016/j.stem.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/09/2024]
Abstract
Mutations in ARID1B, a member of the mSWI/SNF complex, cause severe neurodevelopmental phenotypes with elusive mechanisms in humans. The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions. Here, we find that neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids. Molecularly, a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development. Through an in vitro model of the CC tract, we demonstrate that this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity. Our study uncovers new functions of the mSWI/SNF during human corticogenesis, identifying cell-autonomous axonogenesis defects in SATB2+ neurons as a cause of ACC in ARID1B patients.
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Affiliation(s)
- Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Andrea Wiegers
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Vincent A Pham
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Balint Doleschall
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Thomas Lendl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marielle Piber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Angela Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Paul Möseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marlene Stuempflen
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Rainer Seidl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria.
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3
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Katayama R, Kumamoto T, Wada K, Hanashima C, Ohtaka-Maruyama C. Thalamic activity-dependent specification of sensory input neurons in the developing chick entopallium. J Comp Neurol 2024; 532:e25627. [PMID: 38813969 DOI: 10.1002/cne.25627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024]
Abstract
During development, cell-intrinsic and cell-extrinsic factors play important roles in neuronal differentiation; however, the underlying mechanisms in nonmammalian species remain largely unknown. We here investigated the mechanisms responsible for the differentiation of sensory input neurons in the chick entopallium, which receives its primary visual input via the tectofugal pathway from the nucleus rotundus. The results obtained revealed that input neurons in the entopallium expressed Potassium Voltage-Gated Channel Subfamily H Member 5 (KCNH5/EAG2) mRNA from embryonic day (E) 11. On the other hand, the onset of protein expression was E20, which was 1 day before hatching. We confirm that entopallium input neurons in chicks were generated during early neurogenesis in the lateral and ventral ventricular zones. Notably, neurons derived from the lateral (LP) and ventral pallium (VP) exhibited a spatially distinct distribution along the rostro-caudal axis. We further demonstrated that the expression of EAG2 was directly regulated by input activity from thalamic axons. Collectively, the present results reveal that thalamic input activity is essential for specifying input neurons among LP- and VP-derived early-generated neurons in the developing chick entopallium.
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Affiliation(s)
- Ryoka Katayama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Developmental Neuroscience Project, Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takuma Kumamoto
- Developmental Neuroscience Project, Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kyosuke Wada
- Developmental Neuroscience Project, Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- School of Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Carina Hanashima
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Chiaki Ohtaka-Maruyama
- Developmental Neuroscience Project, Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- School of Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Molnár Z, Kwan KY. Development and Evolution of Thalamocortical Connectivity. Cold Spring Harb Perspect Biol 2024; 16:a041503. [PMID: 38167425 PMCID: PMC10759993 DOI: 10.1101/cshperspect.a041503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Conscious perception in mammals depends on precise circuit connectivity between cerebral cortex and thalamus; the evolution and development of these structures are closely linked. During the wiring of reciprocal thalamus-cortex connections, thalamocortical axons (TCAs) first navigate forebrain regions that had undergone substantial evolutionary modifications. In particular, the organization of the pallial-subpallial boundary (PSPB) diverged significantly between mammals, reptiles, and birds. In mammals, transient cell populations in internal capsule and early corticofugal projections from subplate neurons closely interact with TCAs to guide pathfinding through ventral forebrain and PSPB crossing. Prior to thalamocortical axon arrival, cortical areas are initially patterned by intrinsic genetic factors. Thalamocortical axons then innervate cortex in a topographically organized manner to enable sensory input to refine cortical arealization. Here, we review the mechanisms underlying the guidance of thalamocortical axons across forebrain boundaries, the implications of PSPB evolution for thalamocortical axon pathfinding, and the reciprocal influence between thalamus and cortex during development.
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Affiliation(s)
- Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, Sherrington Building, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Kenneth Y Kwan
- Michigan Neuroscience Institute (MNI), Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Simorgh S, Mousavi SA, To SK, Pasque V, Wierda K, Vervliet T, Yeganeh M, Pooyan P, Chai YC, Verfaillie C, Baharvand H. A facile method to generate cerebral organoids from human pluripotent stem cells. EXCLI JOURNAL 2023; 22:1055-1076. [PMID: 37927348 PMCID: PMC10620858 DOI: 10.17179/excli2023-6299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Human cerebral organoids (COs) are self-organizing three-dimensional (3D) neural structures that provide a human-specific platform to study the cellular and molecular processes that underlie different neurological events. The first step of CO generation from human pluripotent stem cells (hPSCs) is neural induction, which is an in vitro simulation of neural ectoderm development. Several signaling pathways cooperate during neural ectoderm development and in vitro differentiation of hPSCs toward neural cell lineages is also affected by them. In this study, we considered some of the known sources of these variable signaling cues arising from cell culture media components and sought to modulate their effects by applying a comprehensive combination of small molecules and growth factors for CO generation. Histological analysis demonstrated that these COs recapitulate the neural progenitor zone and early cortical layer organization, containing different types of neuronal and glial cells which was in accordance with single-nucleus transcriptome profiling results. Moreover, patch clamp and intracellular Ca2+ dynamic studies demonstrated that the COs behave as a functional neural network. Thus, this method serves as a facile protocol for generating hPSC-derived COs that faithfully mimic the features of their in vivo counterparts in the developing human brain. See also Figure 1(Fig. 1).
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Affiliation(s)
- Susan Simorgh
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Seyed Ahmad Mousavi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - San Kit To
- Department of Development and Regeneration, Lab for Epigenetic Reprogramming, Leuven Stem Cell Institute, Leuven Single-Cell Omics Institute and Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven 3000, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Lab for Epigenetic Reprogramming, Leuven Stem Cell Institute, Leuven Single-Cell Omics Institute and Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven 3000, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- Electrophysiology Unit, Leuven 3000, Belgium
| | - Tim Vervliet
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Meghdad Yeganeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Paria Pooyan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Yoke Chin Chai
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Hossein Baharvand
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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6
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Liu PP, Lu SP, Li X, Tang GB, Liu X, Dai SK, Jiao LF, Lin XW, Li XG, Hu B, Jiao J, Teng ZQ, Han CS, Liu CM. Abnormal chromatin remodeling caused by ARID1A deletion leads to malformation of the dentate gyrus. Cell Death Differ 2023; 30:2187-2199. [PMID: 37543710 PMCID: PMC10483045 DOI: 10.1038/s41418-023-01199-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/15/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
ARID1A, an SWI/SNF chromatin-remodeling gene, is commonly mutated in cancer and hypothesized to be a tumor suppressor. Recently, loss-of-function of ARID1A gene has been shown to cause intellectual disability. Here we generate Arid1a conditional knockout mice and investigate Arid1a function in the hippocampus. Disruption of Arid1a in mouse forebrain significantly decreases neural stem/progenitor cells (NSPCs) proliferation and differentiation to neurons within the dentate gyrus (DG), increasing perinatal and postnatal apoptosis, leading to reduced hippocampus size. Moreover, we perform single-cell RNA sequencing (scRNA-seq) to investigate cellular heterogeneity and reveal that Arid1a is necessary for the maintenance of the DG progenitor pool and survival of post-mitotic neurons. Transcriptome and ChIP-seq analysis data demonstrate that ARID1A specifically regulates Prox1 by altering the levels of histone modifications. Overexpression of downstream target Prox1 can rescue proliferation and differentiation defects of NSPCs caused by Arid1a deletion. Overall, our results demonstrate a critical role for Arid1a in the development of the hippocampus and may also provide insight into the genetic basis of intellectual disabilities such as Coffin-Siris syndrome, which is caused by germ-line mutations or microduplication of Arid1a.
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Affiliation(s)
- Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Shi-Ping Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xiao Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gang-Bin Tang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin-Fei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Wen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences, China Medical University, No.91, Hsueh-Shih Road, Taichung, 40402, Taiwan
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chun-Sheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Lear BP, Thompson EAN, Rodriguez K, Arndt ZP, Khullar S, Klosa PC, Lu RJ, Morrow CS, Risgaard R, Peterson ER, Teefy BB, Bhattacharyya A, Sousa AMM, Wang D, Benayoun BA, Moore DL. Age-maintained human neurons demonstrate a developmental loss of intrinsic neurite growth ability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541995. [PMID: 37292613 PMCID: PMC10245848 DOI: 10.1101/2023.05.23.541995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Injury to adult mammalian central nervous system (CNS) axons results in limited regeneration. Rodent studies have revealed a developmental switch in CNS axon regenerative ability, yet whether this is conserved in humans is unknown. Using human fibroblasts from 8 gestational-weeks to 72 years-old, we performed direct reprogramming to transdifferentiate fibroblasts into induced neurons (Fib-iNs), avoiding pluripotency which restores cells to an embryonic state. We found that early gestational Fib-iNs grew longer neurites than all other ages, mirroring the developmental switch in regenerative ability in rodents. RNA-sequencing and screening revealed ARID1A as a developmentally-regulated modifier of neurite growth in human neurons. These data suggest that age-specific epigenetic changes may drive the intrinsic loss of neurite growth ability in human CNS neurons during development. One-Sentence Summary: Directly-reprogrammed human neurons demonstrate a developmental decrease in neurite growth ability.
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8
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Oka Y, Sato M, Chou SJ. Editorial: The earliest-born cortical neurons as multi-tasking pioneers: expanding roles for subplate neurons in cerebral cortex organization and function, volume II. Front Neuroanat 2023; 17:1211678. [PMID: 37265998 PMCID: PMC10230060 DOI: 10.3389/fnana.2023.1211678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Affiliation(s)
- Yuichiro Oka
- Division of Developmental Neuroscience, United Graduate School of Child Development (UGSCD), Osaka University, Suita, Japan
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Makoto Sato
- Division of Developmental Neuroscience, United Graduate School of Child Development (UGSCD), Osaka University, Suita, Japan
- Department of Anatomy and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shen-Ju Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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9
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Njoku IP, Kwan KY. Distinct microtubule networks mediate neuronal migration and polarization. Neuron 2023; 111:1168-1170. [PMID: 37080166 DOI: 10.1016/j.neuron.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/22/2023]
Abstract
During cortical development, microtubules simultaneously mediate neuronal migration up toward cortical plate and axon extension down toward white matter. Using new molecular tools to manipulate microtubule nucleation and dynamics, in this issue of Neuron, Vinopal et al.1 identify the distinct microtubule networks underpinning these processes.
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Affiliation(s)
- Ikenna P Njoku
- Michigan Neuroscience Institute (MNI), University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kenneth Y Kwan
- Michigan Neuroscience Institute (MNI), University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA.
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10
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Jacquemin V, Versbraegen N, Duerinckx S, Massart A, Soblet J, Perazzolo C, Deconinck N, Brischoux-Boucher E, De Leener A, Revencu N, Janssens S, Moorgat S, Blaumeiser B, Avela K, Touraine R, Abou Jaoude I, Keymolen K, Saugier-Veber P, Lenaerts T, Abramowicz M, Pirson I. Congenital hydrocephalus: new Mendelian mutations and evidence for oligogenic inheritance. Hum Genomics 2023; 17:16. [PMID: 36859317 PMCID: PMC9979489 DOI: 10.1186/s40246-023-00464-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Congenital hydrocephalus is characterized by ventriculomegaly, defined as a dilatation of cerebral ventricles, and thought to be due to impaired cerebrospinal fluid (CSF) homeostasis. Primary congenital hydrocephalus is a subset of cases with prenatal onset and absence of another primary cause, e.g., brain hemorrhage. Published series report a Mendelian cause in only a minority of cases. In this study, we analyzed exome data of PCH patients in search of novel causal genes and addressed the possibility of an underlying oligogenic mode of inheritance for PCH. MATERIALS AND METHODS We sequenced the exome in 28 unrelated probands with PCH, 12 of whom from families with at least two affected siblings and 9 of whom consanguineous, thereby increasing the contribution of genetic causes. Patient exome data were first analyzed for rare (MAF < 0.005) transmitted or de novo variants. Population stratification of unrelated PCH patients and controls was determined by principle component analysis, and outliers identified using Mahalanobis distance 5% as cutoff. Patient and control exome data for genes biologically related to cilia (SYScilia database) were analyzed by mutation burden test. RESULTS In 18% of probands, we identify a causal (pathogenic or likely pathogenic) variant of a known hydrocephalus gene, including genes for postnatal, syndromic hydrocephalus, not previously reported in isolated PCH. In a further 11%, we identify mutations in novel candidate genes. Through mutation burden tests, we demonstrate a significant burden of genetic variants in genes coding for proteins of the primary cilium in PCH patients compared to controls. CONCLUSION Our study confirms the low contribution of Mendelian mutations in PCH and reports PCH as a phenotypic presentation of some known genes known for syndromic, postnatal hydrocephalus. Furthermore, this study identifies novel Mendelian candidate genes, and provides evidence for oligogenic inheritance implicating primary cilia in PCH.
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Affiliation(s)
- Valerie Jacquemin
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium.
| | - Nassim Versbraegen
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Duerinckx
- grid.4989.c0000 0001 2348 0746Service de Neuropédiatrie, Hôpital Universitaire de Bruxelles and CUB Hôpital Erasme and Université Libre de Bruxelles, Brussels, Belgium
| | - Annick Massart
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium ,grid.411414.50000 0004 0626 3418Department of Nephrology, University Hospital of Antwerp, Edegem, Belgium
| | - Julie Soblet
- grid.412157.40000 0000 8571 829XHuman Genetics Department, CUB Hôpital Erasme, Brussels, Belgium
| | - Camille Perazzolo
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Deconinck
- grid.412209.c0000 0004 0578 1002Hopital Universitaire des Enfants Reine Fabiola and Hopital Universitaire de Bruxelles and Université Libre de Bruxelles, Brussels, Belgium
| | - Elise Brischoux-Boucher
- grid.493090.70000 0004 4910 6615Centre de génétique humaine - CHU de Besançon, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Anne De Leener
- grid.48769.340000 0004 0461 6320Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc et Université Catholique de Louvain, Brussels, Belgium
| | - Nicole Revencu
- grid.48769.340000 0004 0461 6320Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc et Université Catholique de Louvain, Brussels, Belgium
| | - Sandra Janssens
- grid.410566.00000 0004 0626 3303Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Stèphanie Moorgat
- grid.452439.d0000 0004 0578 0894Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Bettina Blaumeiser
- grid.411414.50000 0004 0626 3418Center of Medical Genetics, Antwerp University and Antwerp University Hospital, Edegem, Belgium
| | - Kristiina Avela
- grid.15485.3d0000 0000 9950 5666Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | - Renaud Touraine
- grid.412954.f0000 0004 1765 1491Génétique Clinique Chromosomique et Moléculaire, CHU de Saint-Etienne, St-Priest-en-Jarez, France
| | - Imad Abou Jaoude
- Department of Gynecology and Obstetrics, Abou Jaoude Hospital, Jal El Dib, Lebanon
| | - Kathelijn Keymolen
- grid.411326.30000 0004 0626 3362Center for Medical Genetics, UZ Brussels, Jette, Belgium
| | - Pascale Saugier-Veber
- grid.10400.350000 0001 2108 3034Department of Genetics and Reference Center for Developmental Disorders, Université Rouen Normandie, Inserm U1245 and CHU Rouen, Rouen, France
| | - Tom Lenaerts
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marc Abramowicz
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium. .,Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
| | - Isabelle Pirson
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
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11
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Abstract
The current understanding of neurological diseases is derived mostly from direct analysis of patients and from animal models of disease. However, most patient studies do not capture the earliest stages of disease development and offer limited opportunities for experimental intervention, so rarely yield complete mechanistic insights. The use of animal models relies on evolutionary conservation of pathways involved in disease and is limited by an inability to recreate human-specific processes. In vitro models that are derived from human pluripotent stem cells cultured in 3D have emerged as a new model system that could bridge the gap between patient studies and animal models. In this Review, we summarize how such organoid models can complement classical approaches to accelerate neurological research. We describe our current understanding of neurodevelopment and how this process differs between humans and other animals, making human-derived models of disease essential. We discuss different methodologies for producing organoids and how organoids can be and have been used to model neurological disorders, including microcephaly, Zika virus infection, Alzheimer disease and other neurodegenerative disorders, and neurodevelopmental diseases, such as Timothy syndrome, Angelman syndrome and tuberous sclerosis. We also discuss the current limitations of organoid models and outline how organoids can be used to revolutionize research into the human brain and neurological diseases. In this Review, Eichmüller and Knoblich discuss how human brain organoids can recapitulate the unique processes that occur in human brain development and how they can complement classical approaches to revolutionize research into neurological diseases. Development of the human brain involves unique processes that are relevant to neurological disease but cannot be studied in animal models, so alternative model systems are required. Organoids are 3D human cell culture models that originate from pluripotent stem cells and recapitulate the hallmarks of human neurodevelopment, enabling studies of human brain development in vitro. Specific mutations can be introduced into organoids to study their effects on neurodevelopment; combined with high-throughput screening methods, this approach can determine the disease relevance of mutations in human tissue. To study specific diseases, brain organoids can be generated from induced pluripotent stem cells from individual patients, thereby preserving the specific genetic background of the individual and generating an insightful model. Through recapitulation of previously inaccessible periods of human brain development, brain organoids have enabled identification of novel mechanisms that underlie neurodevelopmental, neurodegenerative and infectious diseases. Combining organoids, patient research and animal models enables us to take full advantage of each of these systems and will provide unprecedented insights into neurodevelopment and neurological diseases.
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12
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Tai DJC, Razaz P, Erdin S, Gao D, Wang J, Nuttle X, de Esch CE, Collins RL, Currall BB, O'Keefe K, Burt ND, Yadav R, Wang L, Mohajeri K, Aneichyk T, Ragavendran A, Stortchevoi A, Morini E, Ma W, Lucente D, Hastie A, Kelleher RJ, Perlis RH, Talkowski ME, Gusella JF. Tissue- and cell-type-specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models. Am J Hum Genet 2022; 109:1789-1813. [PMID: 36152629 PMCID: PMC9606388 DOI: 10.1016/j.ajhg.2022.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
Chromosome 16p11.2 reciprocal genomic disorder, resulting from recurrent copy-number variants (CNVs), involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia, but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, and white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue-, cell-type-, and dosage-specific, although more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2,163 differentially expressed genes), and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated, loss-of-function constraint, and fragile X messenger ribonucleoprotein target gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, and single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Changes both in neuronal ratios and in gene expression in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption that might contribute to changes in neurodevelopmental and cognitive function in 16p11.2 carriers. Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes and that this disruption has relative impacts that are context specific.
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Affiliation(s)
- Derek J C Tai
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Parisa Razaz
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Serkan Erdin
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dadi Gao
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer Wang
- Center for Quantitative Health, Division of Clinical Research, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Xander Nuttle
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Celine E de Esch
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan L Collins
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn O'Keefe
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicholas D Burt
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rachita Yadav
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lily Wang
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiana Mohajeri
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tatsiana Aneichyk
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elisabetta Morini
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Weiyuan Ma
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Raymond J Kelleher
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Roy H Perlis
- Center for Quantitative Health, Division of Clinical Research, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael E Talkowski
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
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13
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Postmitotic accumulation of histone variant H3.3 in new cortical neurons establishes neuronal chromatin, transcriptome, and identity. Proc Natl Acad Sci U S A 2022; 119:e2116956119. [PMID: 35930666 PMCID: PMC9371731 DOI: 10.1073/pnas.2116956119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone variants, which can be expressed outside of S-phase and deposited DNA synthesis-independently, provide long-term histone replacement in postmitotic cells, including neurons. Beyond replenishment, histone variants also play active roles in gene regulation by modulating chromatin states or enabling nucleosome turnover. Here, we uncover crucial roles for the histone H3 variant H3.3 in neuronal development. We find that newborn cortical excitatory neurons, which have only just completed replication-coupled deposition of canonical H3.1 and H3.2, substantially accumulate H3.3 immediately postmitosis. Codeletion of H3.3-encoding genes H3f3a and H3f3b from newly postmitotic neurons abrogates H3.3 accumulation, markedly alters the histone posttranslational modification landscape, and causes widespread disruptions to the establishment of the neuronal transcriptome. These changes coincide with developmental phenotypes in neuronal identities and axon projections. Thus, preexisting, replication-dependent histones are insufficient for establishing neuronal chromatin and transcriptome; de novo H3.3 is required. Stage-dependent deletion of H3f3a and H3f3b from 1) cycling neural progenitor cells, 2) neurons immediately postmitosis, or 3) several days later, reveals the first postmitotic days to be a critical window for de novo H3.3. After H3.3 accumulation within this developmental window, codeletion of H3f3a and H3f3b does not lead to immediate H3.3 loss, but causes progressive H3.3 depletion over several months without widespread transcriptional disruptions or cellular phenotypes. Our study thus uncovers key developmental roles for de novo H3.3 in establishing neuronal chromatin, transcriptome, identity, and connectivity immediately postmitosis that are distinct from its role in maintaining total histone H3 levels over the neuronal lifespan.
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14
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Neurogenic-angiogenic synchrony via lactate. Nat Neurosci 2022; 25:839-840. [PMID: 35788196 DOI: 10.1038/s41593-022-01111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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PfARID Regulates P. falciparum Malaria Parasite Male Gametogenesis and Female Fertility and Is Critical for Parasite Transmission to the Mosquito Vector. mBio 2022; 13:e0057822. [PMID: 35638735 PMCID: PMC9239086 DOI: 10.1128/mbio.00578-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sexual reproduction of Plasmodium falciparum parasites is critical to the spread of malaria in the human population. The factors that regulate gene expression underlying formation of fertilization-competent gametes, however, remain unknown. Here, we report that P. falciparum expresses a protein with an AT-rich interaction domain (ARID) which, in other organisms, is part of chromatin remodeling complexes. P. falciparum ARID (PfARID) localized to the parasite nucleus and is critical for the formation of male gametes and fertility of female gametes. PfARID gene deletion (Pfarid–) gametocytes showed downregulation of gene expression important for gametogenesis, antigenic variation, and cell signaling and for parasite development in the mosquito. Our study identifies PfARID as a critical nuclear protein involved in regulating the gene expression landscape of mature gametocytes. This establishes fertility and also prepares the parasite for postfertilization events that are essential for infection of the mosquito vector.
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16
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Liu M, Wan L, Wang C, Yuan H, Peng Y, Wan N, Tang Z, Yuan X, Chen D, Long Z, Shi Y, Qiu R, Tang B, Jiang H, Chen Z. Coffin-Siris syndrome in two chinese patients with novel pathogenic variants of ARID1A and SMARCA4. Genes Genomics 2022; 44:1061-1070. [PMID: 35353340 DOI: 10.1007/s13258-022-01231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is a rare congenital syndrome characterized by developmental delay, intellectual disability, microcephaly, coarse face and hypoplastic nail of the fifth digits. Heterozygous variants of different BAF complex-related genes were reported to cause CSS, including ARID1A and SMARCA4. So far, no CSS patients with ARID1A and SMARCA4 variants have been reported in China. OBJECTIVE The aim of the current study was to identify the causes of two Chinese patients with congenital growth deficiency and intellectual disability. METHODS Genomic DNA was extracted from the peripheral venous blood of patients and their family members. Genetic analysis included whole-exome and Sanger sequencing. Pathogenicity assessments of variants were performed according to the guideline of the American College of Medical Genetics and Genomics. The phenotypic characteristics of all CSS subtypes were summarized through literature review. RESULTS We identified two Chinese CSS patients carrying novel variants of ARID1A and SMARCA4 respectively. The cases presented most core symptoms of CSS except for the digits involvement. Additionally, we performed a review of the phenotypic characteristics in CSS, highlighting phenotypic varieties and related potential causes. CONCLUSIONS We reported the first Chinese CSS2 and CSS4 patients with novel variants of ARID1A and SMARCA4. Our study expanded the genetic and phenotypic spectrum of CSS, providing a comprehensive overview of genotype-phenotype correlations of CSS.
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Affiliation(s)
- Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinrong Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Daji Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, Hunan, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
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17
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Sun D, Teng F, Xing P, Li J. ARID1A serves as a receivable biomarker for the resistance to EGFR-TKIs in non-small cell lung cancer. Mol Med 2021; 27:138. [PMID: 34715776 PMCID: PMC8555283 DOI: 10.1186/s10020-021-00400-5] [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: 08/24/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
ARID1A is a key component of the SWI/SNF chromatin remodeling complexes which is important for the maintaining of biological processes of cells. Recent studies had uncovered the potential role of ARID1A alterations or expression loss in the therapeutic sensitivity of cancers, but the studies in this field requires to be further summarized and discussed. Therefore, we proposed a series of mechanisms related to the resistance to EGFR-TKIs induced by ARID1A alterations or expression loss and the potential therapeutic strategies to overcome the resistance based on published studies. It suggested that ARID1A alterations or expression loss might be the regulators in PI3K/Akt, JAK/STAT and NF-κB signaling pathways which are strongly associated with the resistance to EGFR-TKIs in NSCLC patients harboring sensitive EGFR mutations. Besides, ARID1A alterations or expression loss could lead to the resistance to EGFR-TKIs via a variety of processes during the tumorigenesis and development of cancers, including epithelial to mesenchymal transition, angiogenesis and the inhibition of apoptosis. Based on the potential mechanisms related to ARID1A, we summarized that the small molecular inhibitors targeting ARID1A or PI3K/Akt pathway, the anti-angiogenic therapy and immune checkpoint inhibitors could be used for the supplementary treatment for EGFR-TKIs among NSCLC patients harboring the concomitant alterations of sensitive EGFR mutations and ARID1A.
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Affiliation(s)
- Dantong Sun
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fei Teng
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Puyuan Xing
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Junling Li
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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