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Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
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Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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2
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Apicella M, Battisti A, Pisaneschi E, Menghini D, Digilio MC, Vicari S. First report of Coffin-Siris Syndrome with SMARCB1 variant, normal intelligence and mild selective neuropsychological deficits: A case report and literature review. Clin Neuropsychol 2024:1-23. [PMID: 38963150 DOI: 10.1080/13854046.2024.2372879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/23/2024] [Indexed: 07/05/2024]
Abstract
Background: The SMARCB1 gene encodes a subunit of the BRG1-Associated Factor (BAF) complex, and mutations in this gene have been linked to Coffin-Siris Syndrome (CSS) type 3. CSS is characterized by a range of developmental disabilities, facial dysmorphic features, and feeding difficulties. There's been noted genotype-phenotype correlation in CSS, with cases involving SMARCB1 mutations often exhibiting more severe language impairment and intellectual disability. Method: We conducted a review of reported CSS type 3 cases and presented the first instance of CSS associated with a SMARCB1 variant wherein the patient exhibited normal intelligence and only mild selective neuropsychological deficits. The patient underwent evaluation for feeding challenges, growth delay, and dysmorphic features during their second year of life. Subsequently, CSS diagnosis was confirmed due to a de novo heterozygous c.568C > T (p.Arg190Trp) variant in the SMARCB1 gene. Due to learning difficulties, the patient underwent a comprehensive neuropsychological assessment, which was related to the retrospective reconstruction of her medical and developmental history. Results: The patient demonstrated normal intelligence and adaptive functioning, with specific deficits in arithmetic and selective difficulties in verbal learning and long-term memory. Feeding difficulties and language delay observed in early childhood showed significant improvement over time. Discussion: We discuss this case in relation to previously reported CSS type 3 cases, emphasizing neuropsychological aspects. It's evident that neuropsychological features of CSS can vary among affected individuals, highlighting the importance of personalized support and interventions tailored to specific cognitive and emotional needs by healthcare professionals. Our case suggests avenues for future research to identify specific modifiers of phenotypic expression to explain variability in intellect among patients and pinpoint potential targets for gene therapy.
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Affiliation(s)
- Massimo Apicella
- Child & Adolescent Neuropsychiatry Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Neuroscience, Catholic University of the Sacred Heart, Rome, Italy
| | - Andrea Battisti
- Child & Adolescent Neuropsychiatry Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Human Science, LUMSA University, Rome, Italy
| | - Elisa Pisaneschi
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Deny Menghini
- Child & Adolescent Neuropsychiatry Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Stefano Vicari
- Child & Adolescent Neuropsychiatry Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Life Science and Public Health, Catholic University of the Sacred Heart, Rome, Italy
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3
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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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4
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Marshall AH, Hanson MA, Boyle DJ, Nagarajan D, Bibi N, Fitzgerald J, Gaitten E, Kokiko-Cochran ON, Gu B, Wester JC. Arid1b haploinsufficiency in pyramidal neurons causes cellular and circuit changes in neocortex but is not sufficient to produce behavioral or seizure phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597344. [PMID: 38895205 PMCID: PMC11185765 DOI: 10.1101/2024.06.04.597344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Arid1b is a high confidence risk gene for autism spectrum disorder that encodes a subunit of a chromatin remodeling complex expressed in neuronal progenitors. Haploinsufficiency causes a broad range of social, behavioral, and intellectual disability phenotypes, including Coffin-Siris syndrome. Recent work using transgenic mouse models suggests pathology is due to deficits in proliferation, survival, and synaptic development of cortical neurons. However, there is conflicting evidence regarding the relative roles of excitatory projection neurons and inhibitory interneurons in generating abnormal cognitive and behavioral phenotypes. Here, we conditionally knocked out either one or both copies of Arid1b from excitatory projection neuron progenitors and systematically investigated the effects on intrinsic membrane properties, synaptic physiology, social behavior, and seizure susceptibility. We found that disrupting Arid1b expression in excitatory neurons alters their membrane properties, including hyperpolarizing action potential threshold; however, these changes depend on neuronal subtype. Using paired whole-cell recordings, we found increased synaptic connectivity rate between projection neurons. Furthermore, we found reduced strength of excitatory synapses to parvalbumin (PV)-expression inhibitory interneurons. These data suggest an increase in the ratio of excitation to inhibition. However, the strength of inhibitory synapses from PV interneurons to excitatory neurons was enhanced, which may rebalance this ratio. Indeed, Arid1b haploinsufficiency in projection neurons was insufficient to cause social deficits and seizure phenotypes observed in a preclinical germline haploinsufficient mouse model. Our data suggest that while excitatory projection neurons likely contribute to autistic phenotypes, pathology in these cells is not the primary cause.
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5
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Liao J, Ho J, Burns M, Dykhuizen EC, Hargreaves DC. Collaboration between distinct SWI/SNF chromatin remodeling complexes directs enhancer selection and activation of macrophage inflammatory genes. Immunity 2024:S1074-7613(24)00262-0. [PMID: 38843835 DOI: 10.1016/j.immuni.2024.05.008] [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: 09/12/2023] [Revised: 02/08/2024] [Accepted: 05/08/2024] [Indexed: 06/22/2024]
Abstract
Macrophages elicit immune responses to pathogens through induction of inflammatory genes. Here, we examined the role of three variants of the SWI/SNF nucleosome remodeling complex-cBAF, ncBAF, and PBAF-in the macrophage response to bacterial endotoxin (lipid A). All three SWI/SNF variants were prebound in macrophages and retargeted to genomic sites undergoing changes in chromatin accessibility following stimulation. Cooperative binding of all three variants associated with de novo chromatin opening and latent enhancer activation. Isolated binding of ncBAF and PBAF, in contrast, associated with activation and repression of active enhancers, respectively. Chemical and genetic perturbations of variant-specific subunits revealed pathway-specific regulation in the activation of lipid A response genes, corresponding to requirement for cBAF and ncBAF in inflammatory and interferon-stimulated gene (ISG) activation, respectively, consistent with differential engagement of SWI/SNF variants by signal-responsive transcription factors. Thus, functional diversity among SWI/SNF variants enables increased regulatory control of innate immune transcriptional programs, with potential for specific therapeutic targeting.
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Affiliation(s)
- Jingwen Liao
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92039, USA; Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Josephine Ho
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Mannix Burns
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Diana C Hargreaves
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
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6
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Nazim M, Lin CH, Feng AC, Xiao W, Yeom KH, Li M, Daly AE, Tan X, Vu H, Ernst J, Carey MF, Smale ST, Black DL. Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation. Cell Stem Cell 2024; 31:754-771.e6. [PMID: 38701759 PMCID: PMC11126784 DOI: 10.1016/j.stem.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/24/2024] [Accepted: 04/01/2024] [Indexed: 05/05/2024]
Abstract
Development of embryonic stem cells (ESCs) into neurons requires intricate regulation of transcription, splicing, and translation, but how these processes interconnect is not understood. We found that polypyrimidine tract binding protein 1 (PTBP1) controls splicing of DPF2, a subunit of BRG1/BRM-associated factor (BAF) chromatin remodeling complexes. Dpf2 exon 7 splicing is inhibited by PTBP1 to produce the DPF2-S isoform early in development. During neuronal differentiation, loss of PTBP1 allows exon 7 inclusion and DPF2-L expression. Different cellular phenotypes and gene expression programs were induced by these alternative DPF2 isoforms. We identified chromatin binding sites enriched for each DPF2 isoform, as well as sites bound by both. In ESC, DPF2-S preferential sites were bound by pluripotency factors. In neuronal progenitors, DPF2-S sites were bound by nuclear factor I (NFI), while DPF2-L sites were bound by CCCTC-binding factor (CTCF). DPF2-S sites exhibited enhancer modifications, while DPF2-L sites showed promoter modifications. Thus, alternative splicing redirects BAF complex targeting to impact chromatin organization during neuronal development.
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Affiliation(s)
- Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - An-Chieh Feng
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Mulin Li
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Allison E Daly
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xianglong Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Ha Vu
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Jason Ernst
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
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7
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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8
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Singh AK, Allington G, Viviano S, McGee S, Kiziltug E, Ma S, Zhao S, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus. Brain 2024; 147:1553-1570. [PMID: 38128548 PMCID: PMC10994532 DOI: 10.1093/brain/awad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/01/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023] Open
Abstract
Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery in children. Recent studies have implicated SMARCC1, a component of the BRG1-associated factor (BAF) chromatin remodelling complex, as a candidate congenital hydrocephalus gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, congenital hydrocephalus-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo. Here, we aimed to assess the prevalence of SMARCC1 variants in an expanded patient cohort, describe associated clinical and radiographic phenotypes, and assess the impact of Smarcc1 depletion in a novel Xenopus tropicalis model of congenital hydrocephalus. To do this, we performed a genetic association study using whole-exome sequencing from a cohort consisting of 2697 total ventriculomegalic trios, including patients with neurosurgically-treated congenital hydrocephalus, that total 8091 exomes collected over 7 years (2016-23). A comparison control cohort consisted of 1798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents were sourced from the Simons Simplex Collection. Enrichment and impact on protein structure were assessed in identified variants. Effects on the human fetal brain transcriptome were examined with RNA-sequencing and Smarcc1 knockdowns were generated in Xenopus and studied using optical coherence tomography imaging, in situ hybridization and immunofluorescence. SMARCC1 surpassed genome-wide significance thresholds, yielding six rare, protein-altering de novo variants localized to highly conserved residues in key functional domains. Patients exhibited hydrocephalus with aqueductal stenosis; corpus callosum abnormalities, developmental delay, and cardiac defects were also common. Xenopus knockdowns recapitulated both aqueductal stenosis and cardiac defects and were rescued by wild-type but not patient-specific variant SMARCC1. Hydrocephalic SMARCC1-variant human fetal brain and Smarcc1-variant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2. These results suggest de novo variants in SMARCC1 cause a novel human BAFopathy we term 'SMARCC1-associated developmental dysgenesis syndrome', characterized by variable presence of cerebral ventriculomegaly, aqueductal stenosis, developmental delay and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodelling complex for human brain morphogenesis and provide evidence for a 'neural stem cell' paradigm of congenital hydrocephalus pathogenesis. These results highlight utility of trio-based whole-exome sequencing for identifying pathogenic variants in sporadic congenital structural brain disorders and suggest whole-exome sequencing may be a valuable adjunct in clinical management of congenital hydrocephalus patients.
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Affiliation(s)
- Amrita K Singh
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Garrett Allington
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Genetics, Yale University, New Haven, CT 06510, USA
| | - Stephen Viviano
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaojie Ma
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Shujuan Zhao
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John P Shohfi
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | | | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, UK
| | - Syed R A Rizvi
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
| | - Seth L Alper
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nenad Sestan
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Hermela Shimelis
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Lauren K Walsh
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
- Department of Radiology, Diagnostic Medicine Institute, Geisinger, Danville, PA, 17822, USA
| | - Sheng Chih Jin
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | | | - Engin Deniz
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
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9
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Keskinen S, Paakkola T, Mattila M, Hietala M, Koillinen H, Laine J, Haanpää MK. Prenatal Coffin-Siris Syndrome: Expanding the Phenotypic and Genotypic Spectrum of the Disease. Pediatr Dev Pathol 2024; 27:181-186. [PMID: 37981638 PMCID: PMC11015708 DOI: 10.1177/10935266231210155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Coffin-Siris syndrome is an autosomal dominant disorder with neurological, cardiovascular, and gastrointestinal symptoms. Patients with Coffin-Siris syndrome typically have variable degree of developmental delay or intellectual disability, muscular hypotonia, dysmorphic facial features, sparse scalp hair, but otherwise hirsutism and fifth digit nail or distal phalanx hypoplasia or aplasia. Coffin-Siris syndrome is caused by pathogenic variants in 12 different genes including SMARCB1 and ARID1A. Pathogenic SMARCB1 gene variants cause Coffin-Siris syndrome 3 whereas pathogenic ARID1A gene variants cause Coffin-Siris syndrome 2. Here, we present two prenatal Coffin-Siris syndrome cases with autosomal dominant pathogenic variants: SMARCB1 gene c.1066_1067del, p.(Leu356AspfsTer4) variant, and a novel ARID1A gene c.1920+3_1920+6del variant. The prenatal phenotype in Coffin-Siris syndrome has been rarely described. This article widens the phenotypic spectrum of prenatal Coffin-Siris syndrome with severely hypoplastic right ventricle with VSD and truncus arteriosus type III, persisting left superior and inferior caval vein, bilateral olfactory nerve aplasia, and hypoplastic thymus. A detailed clinical description of the patients with ultrasound, MRI, and post mortem pictures of the affected fetuses showing the wide phenotypic spectrum of the disease is presented.
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Affiliation(s)
- Sini Keskinen
- Tyks Laboratories, Genomics, Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Teija Paakkola
- Tyks Laboratories, Genomics, Clinical Genetics, Turku University Hospital, Turku, Finland
- Northern Finland Laboratory Centre NordLab and Oulu University Hospital, Oulu, Finland
| | - Mirjami Mattila
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Marja Hietala
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Hannele Koillinen
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jukka Laine
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Maria K. Haanpää
- Tyks Laboratories, Genomics, Clinical Genetics, Turku University Hospital, Turku, Finland
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
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10
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Liu C, Xie Y, Chen X, Liu L, Liu C, Yin Z. BAF45D-binding to HOX genes was differentially targeted in H9-derived spinal cord neural stem cells. Sci Rep 2024; 14:29. [PMID: 38168763 PMCID: PMC10761701 DOI: 10.1038/s41598-023-50939-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Chromatin accessibility has been used to define how cells adopt region-specific neural fates. BAF45D is one of the subunits of a specialised chromatin remodelling BAF complex. It has been reported that BAF45D is expressed in spinal cord neural stem cells (NSCs) and regulates their fate specification. Within the developing vertebrate spinal cord, HOX genes exhibit spatially restricted expression patterns. However, the chromatin accessibility of BAF45D binding HOX genes in spinal cord NSCs is unclear. In the present study, we found that in H9-derived spinal cord NSCs, BAF45D targets TBX6, a gene that regulates spinal cord neural mesodermal progenitors. Furthermore, BAF45D binding to the NES gene is much more enriched in H9-derived spinal cord NSCs chromatin compared to ESCs chromatin. In addition, BAF45D binding to anterior and trunk/central HOX genes, but not to lumbosacral HOX genes, was much more enriched in NSCs chromatin compared to ESCs chromatin. These results may shed new light on the role of BAF45D in regulating region-specific spinal cord NSCs by targeting HOX genes.
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Affiliation(s)
- Chang Liu
- Department of Orthopedics, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yuxin Xie
- Department of Histology and Embryology, Institute of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xueying Chen
- Department of Histology and Embryology, Institute of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Lihua Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Chao Liu
- Department of Histology and Embryology, Institute of Stem Cell and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Zongsheng Yin
- Department of Orthopedics, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China.
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11
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Liu NQ, Paassen I, Custers L, Zeller P, Teunissen H, Ayyildiz D, He J, Buhl JL, Hoving EW, van Oudenaarden A, de Wit E, Drost J. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors. Nat Commun 2023; 14:7762. [PMID: 38040699 PMCID: PMC10692191 DOI: 10.1038/s41467-023-43498-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.
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Affiliation(s)
- Ning Qing Liu
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Zeller
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Jiayou He
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Juliane Laura Buhl
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute-KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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12
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Wiggans M, Zhu SJ, Molinaro AM, Pearson BJ. The BAF chromatin remodeling complex licenses planarian stem cells access to ectodermal and mesodermal cell fates. BMC Biol 2023; 21:227. [PMID: 37864247 PMCID: PMC10589948 DOI: 10.1186/s12915-023-01730-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND The flatworm planarian, Schmidtea mediterranea, has a large population of adult stem cells (ASCs) that replace any cell type during tissue turnover or regeneration. How planarian ASCs (called neoblasts) manage self-renewal with the ability to produce daughter cells of different cell lineages (multipotency) is not well understood. Chromatin remodeling complexes ultimately control access to DNA regions of chromosomes and together with specific transcription factors determine whether a gene is transcribed in a given cell type. Previous work in planarians determined that RNAi of core components of the BAF chromatin remodeling complex, brg1 and smarcc2, caused increased ASCs and failed regeneration, but how these cellular defects arise at the level of gene regulation in neoblasts is unknown. RESULTS Here, we perform ATAC and RNA sequencing on purified neoblasts, deficient for the BAF complex subunits brg-1 and smarcc2. The data demonstrate that the BAF complex promotes chromatin accessibility and facilitates transcription at target loci, as in other systems. Interestingly, we find that the BAF complex enables access to genes known to be required for the generation of mesoderm- and ectoderm-derived lineages, including muscle, parenchymal cathepsin, neural, and epithelial lineages. BAF complex knockdowns result in disrupted differentiation into these cell lineages and functional consequences on planarian regeneration and tissue turnover. Notably, we did not detect a role for the BAF complex in neoblasts making endodermal lineages. CONCLUSIONS Our study provides functional insights into how the BAF complex contributes to cell fate decisions in planarian ASCs in vivo.
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Affiliation(s)
- Mallory Wiggans
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Shu Jun Zhu
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Alyssa M Molinaro
- Present address: Oregon Health & Science University, Portland, OR, 97239, USA
| | - Bret J Pearson
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, M5G0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada.
- Present address: Oregon Health & Science University, Portland, OR, 97239, USA.
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13
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Gourisankar S, Wenderski W, Paulo JA, Kim SH, Roepke K, Ellis C, Gygi SP, Crabtree GR. Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562244. [PMID: 37873481 PMCID: PMC10592824 DOI: 10.1101/2023.10.13.562244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genes encoding subunits of the SWI/SNF or BAF ATP-dependent chromatin remodeling complex are among the most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not fully known 1,2 . Synaptic activity in neurons is critical for learning and memory and proper neural development 3 . Neural activity prompts calcium influx and transcription within minutes, facilitated in the nucleus by various transcription factors (TFs) and chromatin modifiers 4 . While BAF is required for activity-dependent developmental processes such as dendritic outgrowth 5-7 , the immediate molecular consequences of neural activity on BAF complexes and their functions are unknown. Here we mapped minute-scale biochemical consequences of neural activity, modeled by membrane depolarization of embryonic mouse primary cortical neurons, on BAF complexes. We used acute chemical perturbations of BAF ATPase activity and kinase signaling to define the activity-dependent effects on BAF complexes and activity-dependent BAF functions. Our studies found that BAF complexes change in subunit composition and are selectively phosphorylated within 10 minutes of depolarization. Increased levels of the core PBAF subunit Baf200/ Arid2 , uniquely containing an RFX-like DNA-binding domain, are concurrent with ATPase-dependent opening of chromatin at RFX/X-box motifs. Changes in BAF composition and phosphorylation lead to the regulation of chromatin accessibility for critical neurogenesis TFs. These biochemical effects are a convergent phenomenon downstream of multiple growth factor signaling pathways in mouse neurons and fibroblasts suggesting that BAF integrates signaling information from the membrane. In support of such a membrane-to-nucleus signaling cascade, we also identified a BAF-interacting kinase, Dclk2, whose inhibition attenuates BAF phosphorylation selectively. Our findings support a direct role of BAF complexes in responding to synaptic activity to regulate TF binding and transcription.
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14
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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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15
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Ke NY, Zhao TY, Wang WR, Qian YT, Liu C. Role of brahma-related gene 1/brahma-associated factor subunits in neural stem/progenitor cells and related neural developmental disorders. World J Stem Cells 2023; 15:235-247. [PMID: 37181007 PMCID: PMC10173807 DOI: 10.4252/wjsc.v15.i4.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/12/2023] [Accepted: 03/20/2023] [Indexed: 04/26/2023] Open
Abstract
Different fates of neural stem/progenitor cells (NSPCs) and their progeny are determined by the gene regulatory network, where a chromatin-remodeling complex affects synergy with other regulators. Here, we review recent research progress indicating that the BRG1/BRM-associated factor (BAF) complex plays an important role in NSPCs during neural development and neural developmental disorders. Several studies based on animal models have shown that mutations in the BAF complex may cause abnormal neural differentiation, which can also lead to various diseases in humans. We discussed BAF complex subunits and their main characteristics in NSPCs. With advances in studies of human pluripotent stem cells and the feasibility of driving their differentiation into NSPCs, we can now investigate the role of the BAF complex in regulating the balance between self-renewal and differentiation of NSPCs. Considering recent progress in these research areas, we suggest that three approaches should be used in investigations in the near future. Sequencing of whole human exome and genome-wide association studies suggest that mutations in the subunits of the BAF complex are related to neurodevelopmental disorders. More insight into the mechanism of BAF complex regulation in NSPCs during neural cell fate decisions and neurodevelopment may help in exploiting new methods for clinical applications.
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Affiliation(s)
- Nai-Yu Ke
- The First Clinical Medical College, Anhui Medical University, Hefei 230032, Anhui Province, China
- Institute of Stem cells and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Tian-Yi Zhao
- Institute of Stem cells and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Wan-Rong Wang
- The First Clinical Medical College, Anhui Medical University, Hefei 230032, Anhui Province, China
- Institute of Stem cells and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Yu-Tong Qian
- The First Clinical Medical College, Anhui Medical University, Hefei 230032, Anhui Province, China
- Institute of Stem cells and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Chao Liu
- Institute of Stem cells and Tissue Engineering, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, Anhui Province, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, Anhui Province, China
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16
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D'Incal CP, Van Rossem KE, De Man K, Konings A, Van Dijck A, Rizzuti L, Vitriolo A, Testa G, Gozes I, Vanden Berghe W, Kooy RF. Chromatin remodeler Activity-Dependent Neuroprotective Protein (ADNP) contributes to syndromic autism. Clin Epigenetics 2023; 15:45. [PMID: 36945042 PMCID: PMC10031977 DOI: 10.1186/s13148-023-01450-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individuals affected with autism often suffer additional co-morbidities such as intellectual disability. The genes contributing to autism cluster on a relatively limited number of cellular pathways, including chromatin remodeling. However, limited information is available on how mutations in single genes can result in such pleiotropic clinical features in affected individuals. In this review, we summarize available information on one of the most frequently mutated genes in syndromic autism the Activity-Dependent Neuroprotective Protein (ADNP). RESULTS Heterozygous and predicted loss-of-function ADNP mutations in individuals inevitably result in the clinical presentation with the Helsmoortel-Van der Aa syndrome, a frequent form of syndromic autism. ADNP, a zinc finger DNA-binding protein has a role in chromatin remodeling: The protein is associated with the pericentromeric protein HP1, the SWI/SNF core complex protein BRG1, and other members of this chromatin remodeling complex and, in murine stem cells, with the chromodomain helicase CHD4 in a ChAHP complex. ADNP has recently been shown to possess R-loop processing activity. In addition, many additional functions, for instance, in association with cytoskeletal proteins have been linked to ADNP. CONCLUSIONS We here present an integrated evaluation of all current aspects of gene function and evaluate how abnormalities in chromatin remodeling might relate to the pleiotropic clinical presentation in individual"s" with Helsmoortel-Van der Aa syndrome.
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Affiliation(s)
- Claudio Peter D'Incal
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Kirsten Esther Van Rossem
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Kevin De Man
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anthony Konings
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Ludovico Rizzuti
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Alessandro Vitriolo
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Giuseppe Testa
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Sackler School of Medicine, 727, 69978, Tel Aviv, Israel
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium.
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17
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Singh AK, Viviano S, Allington G, McGee S, Kiziltug E, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Ma S, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.19.23287455. [PMID: 36993720 PMCID: PMC10055611 DOI: 10.1101/2023.03.19.23287455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Importance Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery. A few familial forms of congenital hydrocephalus (CH) have been identified, but the cause of most sporadic cases of CH remains elusive. Recent studies have implicated SMARCC1 , a component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo . Objectives The aims of this study are to (i) assess the extent to which rare, damaging de novo mutations (DNMs) in SMARCC1 are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of SMARCC1 -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated SMARCC1 mutations in vivo . Design setting and participants A genetic association study was conducted using whole-exome sequencing from a cohort consisting of 2,697 ventriculomegalic trios, including patients with neurosurgically-treated CH, totaling 8,091 exomes collected over 5 years (2016-2021). Data were analyzed in 2023. A comparison control cohort consisted of 1,798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents sourced from the Simons simplex consortium. Main outcomes and measures Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden. In silico biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated SMARCC1 mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data. Smarcc1 knockdowns and a patient-specific Smarcc1 variant were tested in Xenopus and studied using optical coherence tomography imaging, in situ hybridization, and immunofluorescence microscopy. Results SMARCC1 surpassed genome-wide significance thresholds in DNM enrichment tests. Six rare protein-altering DNMs, including four loss-of-function mutations and one recurrent canonical splice site mutation (c.1571+1G>A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of SMARCC1 . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1 Smarcc1 Xenopus mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type SMARCC1 but not a patient-specific SMARCC1 mutant. Hydrocephalic SMARCC1 -mutant human fetal brain and Smarcc1 -mutant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2 . Conclusions SMARCC1 is a bona fide CH risk gene. DNMs in SMARCC1 cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)", characterized by cerebral ventriculomegaly, aqueductal stenosis, DD, and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodeling complex for human brain morphogenesis and provide evidence for a "neural stem cell" paradigm of human CH pathogenesis. These results highlight the utility of trio-based WES for identifying risk genes for congenital structural brain disorders and suggest WES may be a valuable adjunct in the clinical management of CH patients. KEY POINTS Question: What is the role of SMARCC1 , a core component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, in brain morphogenesis and congenital hydrocephalus (CH)? Findings: SMARCC1 harbored an exome-wide significant burden of rare, protein-damaging de novo mutations (DNMs) (p = 5.83 × 10 -9 ) in the largest ascertained cohort to date of patients with cerebral ventriculomegaly, including treated CH (2,697 parent-proband trios). SMARCC1 contained four loss-of-function DNMs and two identical canonical splice site DNMs in a total of six unrelated patients. Patients exhibited developmental delay, aqueductal stenosis, and other structural brain and cardiac defects. Xenopus Smarcc1 mutants recapitulated core human phenotypes and were rescued by the expression of human wild-type but not patient-mutant SMARCC1 . Hydrocephalic SMARCC1 -mutant human brain and Smarcc1 -mutant Xenopus brain exhibited similar alterationsin the expression of key transcription factors that regulate neural progenitor cell proliferation. Meaning: SMARCC1 is essential for human brain morphogenesis and is a bona fide CH risk gene. SMARCC1 mutations cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)". These data implicate epigenetic dysregulation of fetal neural progenitors in the pathogenesis of hydrocephalus, with diagnostic and prognostic implications for patients and caregivers.
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Păun O, Tan YX, Patel H, Strohbuecker S, Ghanate A, Cobolli-Gigli C, Llorian Sopena M, Gerontogianni L, Goldstone R, Ang SL, Guillemot F, Dias C. Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation. Genes Dev 2023; 37:218-242. [PMID: 36931659 PMCID: PMC10111863 DOI: 10.1101/gad.350269.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
Pioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression, though mechanisms through which pioneer transcription factors remodel chromatin remain unclear. Here, using single-cell transcriptomics, we show that endogenous expression of neurogenic transcription factor ASCL1, considered a classical pioneer factor, defines a transient population of progenitors in human neural differentiation. Testing ASCL1's pioneer function using a knockout model to define the unbound state, we found that endogenous expression of ASCL1 drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a nonpioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. ASCL1 interacts with BAF SWI/SNF chromatin remodeling complexes, primarily at targets where it acts as a nonpioneer factor, and we provide evidence for codependent DNA binding and remodeling at a subset of ASCL1 and SWI/SNF cotargets. Our findings provide new insights into ASCL1 function regulating activation of long-range regulatory elements in human neurogenesis and uncover a novel mechanism of its chromatin remodeling function codependent on partner ATPase activity.
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Affiliation(s)
- Oana Păun
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Yu Xuan Tan
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Harshil Patel
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephanie Strohbuecker
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Avinash Ghanate
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Clementina Cobolli-Gigli
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Miriam Llorian Sopena
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Lina Gerontogianni
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Siew-Lan Ang
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - François Guillemot
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
| | - Cristina Dias
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
- Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
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19
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Molecular Mechanisms Involved in the Regulation of Neurodevelopment by miR-124. Mol Neurobiol 2023; 60:3569-3583. [PMID: 36840845 DOI: 10.1007/s12035-023-03271-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/04/2023] [Indexed: 02/26/2023]
Abstract
miR-124 is a miRNA predominantly expressed in the nervous system and accounts for more than a quarter of the total miRNAs in the brain. It regulates neurogenesis, neuronal differentiation, neuronal maturation, and synapse formation and is the most important miRNA in the brain. Furthermore, emerging evidence has suggested miR-124 may be associated with the pathogenesis of various neurodevelopmental and neuropsychiatric disorders. Here, we provide an overview of the role of miR-124 in neurodevelopment and the underling mechanisms, and finally, we prospect the significance of miR-124 research to the field of neuroscience.
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20
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Liu P, Dai S, Mi T, Tang G, Wang Z, Wang H, Du H, Tang Y, Teng Z, Liu C. Acetate supplementation restores cognitive deficits caused by ARID1A haploinsufficiency in excitatory neurons. EMBO Mol Med 2022; 14:e15795. [PMID: 36385502 PMCID: PMC9728054 DOI: 10.15252/emmm.202215795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations in AT-rich interactive domain-containing protein 1A (ARID1A) cause Coffin-Siris syndrome (CSS), a rare genetic disorder that results in mild to severe intellectual disabilities. However, the biological role of ARID1A in the brain remains unclear. In this study, we report that the haploinsufficiency of ARID1A in excitatory neurons causes cognitive impairment and defects in hippocampal synaptic transmission and dendritic morphology in mice. Similarly, human embryonic stem cell-derived excitatory neurons with deleted ARID1A exhibit fewer dendritic branches and spines, and abnormal electrophysiological activity. Importantly, supplementation of acetate, an epigenetic metabolite, can ameliorate the morphological and electrophysiological deficits observed in mice with Arid1a haploinsufficiency, as well as in ARID1A-null human excitatory neurons. Mechanistically, transcriptomic and ChIP-seq analyses demonstrate that acetate supplementation can increase the levels of H3K27 acetylation at the promoters of key regulatory genes associated with neural development and synaptic transmission. Collectively, these findings support the essential roles of ARID1A in the excitatory neurons and cognition and suggest that acetate supplementation could be a potential therapeutic intervention for CSS.
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Affiliation(s)
- Pei‐Pei Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Shang‐Kun Dai
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,School of Life Sciences and MedicineShandong University of TechnologyZiboChina
| | - Ting‐Wei Mi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Gang‐Bin Tang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Zhuo Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Hui Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Hong‐Zhen Du
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Yi Tang
- Department of Neurology, Innovation Center for Neurological Disorders, Xuanwu HospitalCapital Medical UniversityBeijingChina
| | - Zhao‐Qian Teng
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Chang‐Mei Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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21
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Wischhof L, Lee H, Tutas J, Overkott C, Tedt E, Stork M, Peitz M, Brüstle O, Ulas T, Händler K, Schultze JL, Ehninger D, Nicotera P, Salomoni P, Bano D. BCL7A-containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation. EMBO J 2022; 41:e110595. [PMID: 36305367 PMCID: PMC9713712 DOI: 10.15252/embj.2022110595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 01/15/2023] Open
Abstract
Mammalian SWI/SNF/BAF chromatin remodeling complexes influence cell lineage determination. While the contribution of these complexes to neural progenitor cell (NPC) proliferation and differentiation has been reported, little is known about the transcriptional profiles that determine neurogenesis or gliogenesis. Here, we report that BCL7A is a modulator of the SWI/SNF/BAF complex that stimulates the genome-wide occupancy of the ATPase subunit BRG1. We demonstrate that BCL7A is dispensable for SWI/SNF/BAF complex integrity, whereas it is essential to regulate Notch/Wnt pathway signaling and mitochondrial bioenergetics in differentiating NPCs. Pharmacological stimulation of Wnt signaling restores mitochondrial respiration and attenuates the defective neurogenic patterns observed in NPCs lacking BCL7A. Consistently, treatment with an enhancer of mitochondrial biogenesis, pioglitazone, partially restores mitochondrial respiration and stimulates neuronal differentiation of BCL7A-deficient NPCs. Using conditional BCL7A knockout mice, we reveal that BCL7A expression in NPCs and postmitotic neurons is required for neuronal plasticity and supports behavioral and cognitive performance. Together, our findings define the specific contribution of BCL7A-containing SWI/SNF/BAF complexes to mitochondria-driven NPC commitment, thereby providing a better understanding of the cell-intrinsic transcriptional processes that connect metabolism, neuronal morphogenesis, and cognitive flexibility.
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Affiliation(s)
- Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Hang‐Mao Lee
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Janine Tutas
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | | | - Eileen Tedt
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Miriam Stork
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Michael Peitz
- Institute of Reconstructive NeurobiologyUniversity of Bonn Medical Faculty and University Hospital BonnBonnGermany,Cell Programming Core FacilityUniversity of Bonn Medical FacultyBonnGermany
| | - Oliver Brüstle
- Institute of Reconstructive NeurobiologyUniversity of Bonn Medical Faculty and University Hospital BonnBonnGermany
| | - Thomas Ulas
- PRECISE Platform for Single Cell Genomics and EpigenomicsGerman Center for Neurodegenerative Diseases (DZNE) and the University of BonnBonnGermany
| | - Kristian Händler
- PRECISE Platform for Single Cell Genomics and EpigenomicsGerman Center for Neurodegenerative Diseases (DZNE) and the University of BonnBonnGermany
| | - Joachim L Schultze
- PRECISE Platform for Single Cell Genomics and EpigenomicsGerman Center for Neurodegenerative Diseases (DZNE) and the University of BonnBonnGermany,Department for Genomics and Immunoregulation, LIMES InstituteUniversity of BonnBonnGermany
| | - Dan Ehninger
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | | | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
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22
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FBXW7 Reduces the Cancer Stem Cell-Like Properties of Hepatocellular Carcinoma by Regulating the Ubiquitination and Degradation of ACTL6A. Stem Cells Int 2022; 2022:3242482. [PMID: 36159747 PMCID: PMC9492413 DOI: 10.1155/2022/3242482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/05/2022] [Indexed: 02/05/2023] Open
Abstract
Cancer stem cells (CSCs) comprise a subset of tumor cells that can initiate tumorigenesis and promote tumor advance. A previous study showed that the expression of FBXW7 in hepatocellular carcinoma (HCC) clinical samples was lower than that in the adjacent nontumor tissues and was negatively correlated with the invasion and migration of HCC cells. However, the biological characteristics and the underlying molecular mechanisms of FBXW7 in HCC stemness are yet to be elucidated. In present study, we found that FBXW7 participates in the self-renewal, tumorigenicity, sorafenib therapy, and stem cell-like properties of HCC cells in vivo and in vitro. The upregulation of FBXW7 inhibited the stemness and reduced the tumorigenicity and drug resistance of HCC cells. Mechanistically, proteins binding to FBXW7 were identified by coimmunoprecipitation and protein colocalization assays. We confirmed ACTL6A as a novel downstream target for FBXW7. The in vivo ubiquitination assay showed that FBXW7 repressed HCC malignancy by regulating the oncogenic activity of ACTL6A in a ubiquitin-dependent manner. Furthermore, we found that ACTL6A overexpression inversed the self-renewal abilities and tumorigenic abilities depressed by overexpressing FBXW7. The current findings suggested that FBXW7 reduces the stemness of HCC cells by targeting and degrading ACTL6A and provides a novel target for the diagnosis and treatment of HCC.
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23
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Du H, Wang Z, Guo R, Yang L, Liu G, Zhang Z, Xu Z, Tian Y, Yang Z, Li X, Chen B. Transcription factors Bcl11a and Bcl11b are required for the production and differentiation of cortical projection neurons. Cereb Cortex 2022; 32:3611-3632. [PMID: 34963132 PMCID: PMC9433425 DOI: 10.1093/cercor/bhab437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/02/2021] [Indexed: 12/31/2022] Open
Abstract
The generation and differentiation of cortical projection neurons are extensively regulated by interactive programs of transcriptional factors. Here, we report the cooperative functions of transcription factors Bcl11a and Bcl11b in regulating the development of cortical projection neurons. Among the cells derived from the cortical neural stem cells, Bcl11a is expressed in the progenitors and the projection neurons, while Bcl11b expression is restricted to the projection neurons. Using conditional knockout mice, we show that deficiency of Bcl11a leads to reduced proliferation and precocious differentiation of cortical progenitor cells, which is exacerbated when Bcl11b is simultaneously deleted. Besides defective neuronal production, the differentiation of cortical projection neurons is blocked in the absence of both Bcl11a and Bcl11b: Expression of both pan-cortical and subtype-specific genes is reduced or absent; axonal projections to the thalamus, hindbrain, spinal cord, and contralateral cortical hemisphere are reduced or absent. Furthermore, neurogenesis-to-gliogenesis switch is accelerated in the Bcl11a-CKO and Bcl11a/b-DCKO mice. Bcl11a likely regulates neurogenesis through repressing the Nr2f1 expression. These results demonstrate that Bcl11a and Bcl11b jointly play critical roles in the generation and differentiation of cortical projection neurons and in controlling the timing of neurogenesis-to-gliogenesis switch.
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Affiliation(s)
- Heng Du
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Ziwu Wang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Rongliang Guo
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Lin Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Guoping Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhuangzhi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhejun Xu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Yu Tian
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Xiaosu Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Bin Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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24
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Zhang X, Chen H, Song Y, Chen Z, Liu X, Rong P, Ma R. Ten-year follow-up of Nicolaides-Baraitser syndrome with a de novo mutation and analysis of 58 gene loci of SMARCA2-associated NCBRS. Mol Genet Genomic Med 2022; 10:e2009. [PMID: 35811451 PMCID: PMC9482403 DOI: 10.1002/mgg3.2009] [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] [Received: 12/22/2021] [Revised: 05/10/2022] [Accepted: 06/08/2022] [Indexed: 01/11/2023] Open
Abstract
As a clinical subtype of SWI/SNF‐related intellectual disability syndromes, Nicolaides–Baraitser syndrome (NCBRS, OMIM601358) has a unique genotype–phenotype. Due to the scarcity of the number of cases reported and the limitations of diagnosis methods, so far only more than 80 cases have been reported worldwide. In this article, a new patient with a de novo mutation was followed up for 10 years; it includes the epilepsy treatment process, the characteristics of NBCRS with seizures, typical faces, sparse hair, prominent interphalangeal joints, and intellectual disability, and we also summarized the genotype–phenotype of the 80 reported cases for comparison. Due to insufficient studies and lack of attention paid to the syndrome, it is believed that the actual number of cases should be far more than the reported number. The syndrome is phased and progressive. The genotype–phenotype correlation of the disease is related to the location of the gene locus, especially closely related to the SNF2 ATPase domain.
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Affiliation(s)
- Xilian Zhang
- Department of Pediatrics, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Hanjiang Chen
- Department of Pediatrics, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Ying Song
- Graduate College of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhaoyuan Chen
- Graduate College of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuan Liu
- Department of Pediatrics, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Ping Rong
- Department of Pediatrics, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Rong Ma
- Department of Pediatrics, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.,National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
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25
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Rhoades R, Solomon S, Johnson C, Teng S. Impact of SARS-CoV-2 on Host Factors Involved in Mental Disorders. Front Microbiol 2022; 13:845559. [PMID: 35444632 PMCID: PMC9014212 DOI: 10.3389/fmicb.2022.845559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/14/2022] [Indexed: 11/23/2022] Open
Abstract
COVID-19, caused by SARS-CoV-2, is a systemic illness due to its multiorgan effects in patients. The disease has a detrimental impact on respiratory and cardiovascular systems. One early symptom of infection is anosmia or lack of smell; this implicates the involvement of the olfactory bulb in COVID-19 disease and provides a route into the central nervous system. However, little is known about how SARS-CoV-2 affects neurological or psychological symptoms. SARS-CoV-2 exploits host receptors that converge on pathways that impact psychological symptoms. This systemic review discusses the ways involved by coronavirus infection and their impact on mental health disorders. We begin by briefly introducing the history of coronaviruses, followed by an overview of the essential proteins to viral entry. Then, we discuss the downstream effects of viral entry on host proteins. Finally, we review the literature on host factors that are known to play critical roles in neuropsychiatric symptoms and mental diseases and discuss how COVID-19 could impact mental health globally. Our review details the host factors and pathways involved in the cellular mechanisms, such as systemic inflammation, that play a significant role in the development of neuropsychological symptoms stemming from COVID-19 infection.
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Affiliation(s)
- Raina Rhoades
- Department of Biology, Howard University, Washington, DC, United States
| | - Sarah Solomon
- Department of Biology, Howard University, Washington, DC, United States
| | - Christina Johnson
- Department of Biology, Howard University, Washington, DC, United States
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26
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Di Fraia D, Anitei M, Mackmull MT, Parca L, Behrendt L, Andres-Pons A, Gilmour D, Helmer Citterich M, Kaether C, Beck M, Ori A. Conserved exchange of paralog proteins during neuronal differentiation. Life Sci Alliance 2022; 5:5/6/e202201397. [PMID: 35273078 PMCID: PMC8917807 DOI: 10.26508/lsa.202201397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
Paralog proteins promote fine tuning of protein complexes. The author identified a specific paralog signature conserved across vertebrate neuronal differentiation. Altering the ratio of SEC23 paralogs in the COPII complex influences neuronal differentiation in a opposite way. Gene duplication enables the emergence of new functions by lowering the evolutionary pressure that is posed on the ancestral genes. Previous studies have highlighted the role of specific paralog genes during cell differentiation, for example, in chromatin remodeling complexes. It remains unexplored whether similar mechanisms extend to other biological functions and whether the regulation of paralog genes is conserved across species. Here, we analyze the expression of paralogs across human tissues, during development and neuronal differentiation in fish, rodents and humans. Whereas ∼80% of paralog genes are co-regulated, a subset of paralogs shows divergent expression profiles, contributing to variability of protein complexes. We identify 78 substitutions of paralog pairs that occur during neuronal differentiation and are conserved across species. Among these, we highlight a substitution between the paralogs SEC23A and SEC23B members of the COPII complex. Altering the ratio between these two genes via RNAi-mediated knockdown is sufficient to influence neuron differentiation. We propose that remodeling of the vesicular transport system via paralog substitutions is an evolutionary conserved mechanism enabling neuronal differentiation.
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Affiliation(s)
| | - Mihaela Anitei
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Marie-Therese Mackmull
- Eidgenössische Technische Hochschule (ETH) Zürich Inst. f. Molekulare Systembiologie, Zürich, Switzerland
| | - Luca Parca
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Laura Behrendt
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | | | - Darren Gilmour
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | | | | | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
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27
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Rowland ME, Jajarmi JM, Osborne TSM, Ciernia AV. Insights Into the Emerging Role of Baf53b in Autism Spectrum Disorder. Front Mol Neurosci 2022; 15:805158. [PMID: 35185468 PMCID: PMC8852769 DOI: 10.3389/fnmol.2022.805158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Accurate and precise regulation of gene expression is necessary to ensure proper brain development and plasticity across the lifespan. As an ATP-dependent chromatin-remodeling complex, the BAF (Brg1 Associated Factor) complex can alter histone-DNA interactions, facilitating dynamic changes in gene expression by controlling DNA accessibility to the transcriptional machinery. Mutations in 12 of the potential 29 subunit genes that compose the BAF nucleosome remodeling complex have been identified in several developmental disorders including Autism spectrum disorders (ASD) and intellectual disability. A novel, neuronal version of BAF (nBAF) has emerged as promising candidate in the development of ASD as its expression is tied to neuron differentiation and it’s hypothesized to coordinate expression of synaptic genes across brain development. Recently, mutations in BAF53B, one of the neuron specific subunits of the nBAF complex, have been identified in patients with ASD and Developmental and epileptic encephalopathy-76 (DEE76), indicating BAF53B is essential for proper brain development. Recent work in cultured neurons derived from patients with BAF53B mutations suggests links between loss of nBAF function and neuronal dendritic spine formation. Deletion of one or both copies of mouse Baf53b disrupts dendritic spine development, alters actin dynamics and results in fewer synapses in vitro. In the mouse, heterozygous loss of Baf53b severely impacts synaptic plasticity and long-term memory that is reversible with reintroduction of Baf53b or manipulations of the synaptic plasticity machinery. Furthermore, surviving Baf53b-null mice display ASD-related behaviors, including social impairments and repetitive behaviors. This review summarizes the emerging evidence linking deleterious variants of BAF53B identified in human neurodevelopmental disorders to abnormal transcriptional regulation that produces aberrant synapse development and behavior.
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28
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Shinko Y, Okazaki S, Otsuka I, Horai T, Kim S, Tanifuji T, Hishimoto A. Accelerated epigenetic age and shortened telomere length based on DNA methylation in Nicolaides-Baraitser syndrome. Mol Genet Genomic Med 2022; 10:e1876. [PMID: 35092358 PMCID: PMC8922957 DOI: 10.1002/mgg3.1876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/06/2021] [Accepted: 01/06/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS) is a rare disorder characterized by neurodevelopmental delays, seizures, and diverse physical characteristics. The DNA methylation (DNAm) profile in NCBRS is significantly different. DNAm is linked to the biological aging of cells and the health risks associated with biological aging. In this study, we examined changes in biological ages in NCBRS to provide insights into the prognosis and health risks of NCBRS. METHODS We used a publicly available dataset to examine biological aging in NCBRS using DNAm-based epigenetic ages, such as PhenoAge and GrimAge, as well as DNAm-based estimator of telomere length (DNAmTL). We investigated 12 cases, clinically diagnosed as NCBRS, and 27 controls. RESULTS Compared to controls, NCBRS cases exhibited significantly accelerated PhenoAge and GrimAge as well as significantly shortened DNAmTL. CONCLUSION These results suggest an acceleration of biological aging in NCBRS and provide insights into the prognosis and health risks of NCBRS.
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Affiliation(s)
- Yutaka Shinko
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Saehyeon Kim
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takaki Tanifuji
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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29
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Neurobiology of ARID1B haploinsufficiency related to neurodevelopmental and psychiatric disorders. Mol Psychiatry 2022; 27:476-489. [PMID: 33686214 PMCID: PMC8423853 DOI: 10.1038/s41380-021-01060-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/04/2021] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
ARID1B haploinsufficiency is a frequent cause of intellectual disability (ID) and autism spectrum disorder (ASD), and also leads to emotional disturbances. In this review, we examine past and present clinical and preclinical research into the neurobiological function of ARID1B. The presentation of ARID1B-related disorders (ARID1B-RD) is highly heterogeneous, including varying degrees of ID, ASD, and physical features. Recent research includes the development of suitable clinical readiness assessments for the treatment of ARID1B-RD, as well as similar neurodevelopmental disorders. Recently developed mouse models of Arid1b haploinsufficiency successfully mirror many of the behavioral phenotypes of ASD and ID. These animal models have helped to solidify the molecular mechanisms by which ARID1B regulates brain development and function, including epigenetic regulation of the Pvalb gene and promotion of Wnt/β-catenin signaling in neural progenitors in the ventral telencephalon. Finally, preclinical studies have identified the use of a positive allosteric modulator of the GABAA receptor as an effective treatment for some Arid1b haploinsufficiency-related behavioral phenotypes, and there is potential for the refinement of this therapy in order to translate it into clinical use.
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30
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Smith JJ, Xiao Y, Parsan N, Medwig-Kinney TN, Martinez MAQ, Moore FEQ, Palmisano NJ, Kohrman AQ, Chandhok Delos Reyes M, Adikes RC, Liu S, Bracht SA, Zhang W, Wen K, Kratsios P, Matus DQ. The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo. PLoS Genet 2022; 18:e1009981. [PMID: 34982771 PMCID: PMC8759636 DOI: 10.1371/journal.pgen.1009981] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/14/2022] [Accepted: 12/07/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors are associated with a variety of disease mechanisms including cancer metastasis, in which cancer co-opts cellular invasion programs functioning in healthy cells during development. Here we utilize Caenorhabditis elegans anchor cell (AC) invasion as an in vivo model to identify the suite of chromatin agents and chromatin regulating factors that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0 cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and enhanced RNA interference (RNAi) vectors, we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Our data specifically implicate the SWI/SNF BAF assembly in the regulation of the G0 cell cycle arrest in the AC, whereas the SWI/SNF PBAF assembly promotes AC invasion via cell cycle-independent mechanisms, including attachment to the basement membrane (BM) and activation of the pro-invasive fos-1/FOS gene. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis. Cellular invasion is required for animal development and homeostasis. Inappropriate activation of invasion however can result in cancer metastasis. Invasion programs are orchestrated by complex gene regulatory networks (GRN) that function in a coordinated fashion to turn on and off pro-invasive genes. While the core of GRNs are DNA binding transcription factors, they require aid from chromatin remodelers to access the genome. To identify the suite of pro-invasive chromatin remodelers, we paired high resolution imaging with RNA interference to individually knockdown 269 chromatin factors, identifying the evolutionarily conserved SWItching defective/Sucrose Non-Fermenting (SWI/SNF) ATP-dependent chromatin remodeling complex as a new regulator of Caenorhabditis elegans anchor cell (AC) invasion. Using a combination of CRISPR/Cas9 genome engineering and targeted protein degradation we demonstrate that the core SWI/SNF complex functions in a dose-dependent manner to control invasion. Further, we determine that the accessory SWI/SNF complexes, BAF and PBAF, contribute to invasion via distinctive mechanisms: BAF is required to prevent inappropriate proliferation while PBAF promotes AC attachment and remodeling of the basement membrane. Together, our data provide insights into how the SWI/SNF complex, which is mutated in many human cancers, can function in a dose-dependent fashion to regulate switching from invasive to proliferative fates.
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Affiliation(s)
- Jayson J. Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Yutong Xiao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nithin Parsan
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Taylor N. Medwig-Kinney
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Michael A. Q. Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Frances E. Q. Moore
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Nicholas J. Palmisano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Abraham Q. Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Mana Chandhok Delos Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Rebecca C. Adikes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Biology Department, Siena College, Loudonville, New York, United States of America
| | - Simeiyun Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sydney A. Bracht
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- Department of Cell Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wan Zhang
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Kailong Wen
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - Paschalis Kratsios
- The Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior, University of Chicago, Chicago, Illinois, United States of America
- Department of Neurobiology, University of Chicago, Chicago, Illinois, United States of America
| | - David Q. Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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31
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BAF45b Is Required for Efficient Zika Virus Infection of HAP1 Cells. Viruses 2021; 13:v13102007. [PMID: 34696437 PMCID: PMC8540262 DOI: 10.3390/v13102007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 01/10/2023] Open
Abstract
The 2016 Zika virus (ZIKV) epidemic illustrates the impact of flaviviruses as emerging human pathogens. For unknown reasons, ZIKV replicates more efficiently in neural progenitor cells (NPCs) than in postmitotic neurons. Here, we identified host factors used by ZIKV using the NCI-60 library of cell lines and COMPARE analysis, and cross-analyzed this library with two other libraries of host factors with importance for ZIKV infection. We identified BAF45b, a subunit of the BAF (Brg1/Brm-associated factors) protein complexes that regulate differentiation of NPCs to post-mitotic neurons. ZIKV (and other flaviviruses) infected HAP1 cells deficient in expression of BAF45b and other BAF subunits less efficiently than wildtype (WT) HAP1 cells. We concluded that subunits of the BAF complex are important for infection of ZIKV and other flavivirus. Given their function in cell and tissue differentiation, such regulators may be important determinants of tropism and pathogenesis of arthropod-borne flaviviruses.
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32
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Oates S, Absoud M, Goyal S, Bayley S, Baulcomb J, Sims A, Riddett A, Allis K, Brasch-Andersen C, Balasubramanian M, Bai R, Callewaert B, Hüffmeier U, Le Duc D, Radtke M, Korff C, Kennedy J, Low K, Møller RS, Nielsen JEK, Popp B, Quteineh L, Rønde G, Schönewolf-Greulich B, Shillington A, Taylor MR, Todd E, Torring PM, Tümer Z, Vasileiou G, Yates TM, Zweier C, Rosch R, Basson MA, Pal DK. ZMYND11 variants are a novel cause of centrotemporal and generalised epilepsies with neurodevelopmental disorder. Clin Genet 2021; 100:412-429. [PMID: 34216016 DOI: 10.1111/cge.14023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
ZMYND11 is the critical gene in chromosome 10p15.3 microdeletion syndrome, a syndromic cause of intellectual disability. The phenotype of ZMYND11 variants has recently been extended to autism and seizures. We expand on the epilepsy phenotype of 20 individuals with pathogenic variants in ZMYND11. We obtained clinical descriptions of 16 new and nine published individuals, plus detailed case history of two children. New individuals were identified through GeneMatcher, ClinVar and the European Network for Therapies in Rare Epilepsy (NETRE). Genetic evaluation was performed using gene panels or exome sequencing; variants were classified using American College of Medical Genetics (ACMG) criteria. Individuals with ZMYND11 associated epilepsy fell into three groups: (i) atypical benign partial epilepsy or idiopathic focal epilepsy (n = 8); (ii) generalised epilepsies/infantile epileptic encephalopathy (n = 4); (iii) unclassified (n = 8). Seizure prognosis ranged from spontaneous remission to drug resistant. Neurodevelopmental deficits were invariable. Dysmorphic features were variable. Variants were distributed across the gene and mostly de novo with no precise genotype-phenotype correlation. ZMYND11 is one of a small group of chromatin reader genes associated in the pathogenesis of epilepsy, and specifically ABPE. More detailed epilepsy descriptions of larger cohorts and functional studies might reveal genotype-phenotype correlation. The epileptogenic mechanism may be linked to interaction with histone H3.3.
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Affiliation(s)
- Stephanie Oates
- Department of Paediatric Neuroscience, King's College Hospital, London, UK
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, UK
| | - Michael Absoud
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
- Department of Women and Children's Health, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Sushma Goyal
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Sophie Bayley
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, UK
| | - Jennifer Baulcomb
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Annemarie Sims
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Amy Riddett
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
| | - Katrina Allis
- Genetic Counselor, Mitochondrial and Metabolic Genetics, GeneDx, Gaithersburg, Maryland, USA
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Renkui Bai
- Genetic Counselor, Mitochondrial and Metabolic Genetics, GeneDx, Gaithersburg, Maryland, USA
| | - Bert Callewaert
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander Universitat of Erlangen-Nurnberg, Erlangen, Germany
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Medical Centre, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Centre, Leipzig, Germany
| | - Christian Korff
- Pediatric Neurology Unit, University Hospitals, Geneva, Switzerland
| | - Joanna Kennedy
- Department of Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Karen Low
- Department of Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Jens Erik Klint Nielsen
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Bernt Popp
- Institute of Human Genetics, Friedrich-Alexander Universitat of Erlangen-Nurnberg, Erlangen, Germany
| | - Lina Quteineh
- Pediatric Neurology Unit, University Hospitals, Geneva, Switzerland
- Service of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Gitte Rønde
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | | | | | - Matthew Rg Taylor
- University of Colorado Anschutz Medical Campus, Adult Medical Genetics Program, Aurora, Colorado, USA
| | - Emily Todd
- University of Colorado Anschutz Medical Campus, Adult Medical Genetics Program, Aurora, Colorado, USA
| | - Pernille M Torring
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Zeynep Tümer
- Department of Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander Universitat of Erlangen-Nurnberg, Erlangen, Germany
| | - T Michael Yates
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK
| | - Christiane Zweier
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Richard Rosch
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - M Albert Basson
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Centre for Craniofacial and Regenerative Biology, King's College London, London, UK
| | - Deb K Pal
- Department of Paediatric Neuroscience, King's College Hospital, London, UK
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, Kings College London, London, UK
- Newcomen Children's Neurosciences Centre, Evelina London Children's Hospital, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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Liu X, Dai SK, Liu PP, Liu CM. Arid1a regulates neural stem/progenitor cell proliferation and differentiation during cortical development. Cell Prolif 2021; 54:e13124. [PMID: 34562292 PMCID: PMC8560606 DOI: 10.1111/cpr.13124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/03/2021] [Accepted: 09/03/2021] [Indexed: 12/26/2022] Open
Abstract
Objective Neurodevelopmental diseases are common disorders caused by the disruption of essential neurodevelopmental processes. Recent human exome sequencing and genome‐wide association studies have shown that mutations in the subunits of the SWI/SNF (BAF) complex are risk factors for neurodevelopmental diseases. Clinical studies have found that ARID1A (BAF250a) is the most frequently mutated SWI/SNF gene and its mutations lead to mental retardation and microcephaly. However, the function of ARID1A in brain development and its underlying mechanisms still remain elusive. Methods The present study used Cre/loxP system to generate an Arid1a conditional knockout mouse line. Cell proliferation, cell apoptosis and cell differentiation of NSPCs were studied by immunofluorescence staining. In addition, RNA‐seq and RT‐PCR were performed to dissect the molecular mechanisms of Arid1a underlying cortical neurogenesis. Finally, rescue experiments were conducted to evaluate the effects of Neurod1 or Fezf2 overexpression on the differentiation of NSPCs in vitro. Results Conditional knockout of Arid1a reduces cortical thickness in the developing cortex. Arid1a loss of function inhibits the proliferation of radial glial cells, and increases cell death during late cortical development, and leads to dysregulated expression of genes associated with proliferation and differentiation. Overexpression of Neurod1 or Fezf2 in Arid1a cKO NSPCs rescues their neural differentiation defect in vitro. Conclusions This study demonstrates for the first time that Arid1a plays an important role in regulating the proliferation and differentiation of NSPCs during cortical development, and proposes several gene candidates that are worth to understand the pathological mechanisms and to develop novel interventions of neurodevelopment disorders caused by Arid1a mutations.
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Affiliation(s)
- Xiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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34
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Hornbachner R, Lackner A, Papuchova H, Haider S, Knöfler M, Mechtler K, Latos PA. MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells. Proc Natl Acad Sci U S A 2021; 118:e2105130118. [PMID: 34507999 PMCID: PMC8449346 DOI: 10.1073/pnas.2105130118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
Multiple placental pathologies are associated with failures in trophoblast differentiation, yet the underlying transcriptional regulation is poorly understood. Here, we discovered msh homeobox 2 (MSX2) as a key transcriptional regulator of trophoblast identity using the human trophoblast stem cell model. Depletion of MSX2 resulted in activation of the syncytiotrophoblast transcriptional program, while forced expression of MSX2 blocked it. We demonstrated that a large proportion of the affected genes were directly bound and regulated by MSX2 and identified components of the SWItch/Sucrose nonfermentable (SWI/SNF) complex as strong MSX2 interactors and target gene cobinders. MSX2 cooperated specifically with the SWI/SNF canonical BAF (cBAF) subcomplex and cooccupied, together with H3K27ac, a number of differentiation genes. Increased H3K27ac and cBAF occupancy upon MSX2 depletion imply that MSX2 prevents premature syncytiotrophoblast differentiation. Our findings established MSX2 as a repressor of the syncytiotrophoblast lineage and demonstrated its pivotal role in cell fate decisions that govern human placental development and disease.
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Affiliation(s)
- Ruth Hornbachner
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Andreas Lackner
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Henrieta Papuchova
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Sandra Haider
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, A-1090 Vienna, Austria
| | - Martin Knöfler
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, A-1090 Vienna, Austria
| | - Karl Mechtler
- Protein Chemistry Facility, Institute of Molecular Pathology, A-1030 Vienna, Austria
| | - Paulina A Latos
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria;
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35
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Qi Z, Li J, Li M, Du X, Zhang L, Wang S, Xu B, Liu W, Xu Z, Deng Y. The Essential Role of Epigenetic Modifications in Neurodegenerative Diseases with Dyskinesia. Cell Mol Neurobiol 2021; 42:2459-2472. [PMID: 34383231 DOI: 10.1007/s10571-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022]
Abstract
Epigenetics play an essential role in the occurrence and improvement of many diseases. Evidence shows that epigenetic modifications are crucial to the regulation of gene expression. DNA methylation is closely linked to embryonic development in mammalian. In recent years, epigenetic drugs have shown unexpected therapeutic effects on neurological diseases, leading to the study of the epigenetic mechanism in neurodegenerative diseases. Unlike genetics, epigenetics modify the genome without changing the DNA sequence. Research shows that epigenetics is involved in all aspects of neurodegenerative diseases. The study of epigenetic will provide valuable insights into the molecular mechanism of neurodegenerative diseases, which may lead to new treatments and diagnoses. This article reviews the role of epigenetic modifications neurodegenerative diseases with dyskinesia, and discusses the therapeutic potential of epigenetic drugs in neurodegenerative diseases.
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Affiliation(s)
- Zhipeng Qi
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Jiashuo Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Minghui Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Xianchao Du
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Lei Zhang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Shuang Wang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Zhaofa Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China.
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36
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Wang Q, Cao Z, Wei Y, Zhang J, Cheng Z. Potential Role of SWI/SNF Complex Subunit Actin-Like Protein 6A in Cervical Cancer. Front Oncol 2021; 11:724832. [PMID: 34395295 PMCID: PMC8358818 DOI: 10.3389/fonc.2021.724832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
SWI/SNF complex subunit Actin-like protein 6A (ACTL6A) has been regarded as an oncogene, regulating the proliferation, migration and invasion of cancer cells. However, the expression pattern and biological role of ACTL6A in cervical cancer have not been reported. In this study, the mRNA expression and protein level of ACTL6A in cervical cancer samples were determined by public database and immunohistochemical (IHC) analysis. The effects of ACTL6A on cervical cancer cells were investigated via MTT, colony-formation assay, tumor xenografts and flow cytometry. Gene set enrichment analysis (GSEA) was used to explore the potential mechanism of ACTL6A in regulating tumorigenesis of cervical cancer. The results revealed that ACTL6A was markedly upregulated in cervical cancer tissues. Silencing ACTL6A expression resulted in decreased cervical cancer cell proliferation, colony formation and tumorigenesis in vitro and in vivo. Furthermore, we demonstrated that knockdown of ACTL6A induced cell cycle arrest at G1 phase, ACTL6A-mediated proliferation and cell cycle progression were c-Myc dependent. Our study provides the role of ACTL6A in cervical oncogenesis and reveals a potential target for therapeutic intervention in this cancer type.
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Affiliation(s)
- Qingying Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zuozeng Cao
- Department of Obstetrics and Gynecology, Xinhua Hospital Chongming Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingze Wei
- Department of Pathology, Nantong Tumor Hospital, Nantong, China
| | - Jiawen Zhang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China.,Reproductive Medicine Center, Department of Obstetrics and Gynecology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhongping Cheng
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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37
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Kim B, Luo Y, Zhan X, Zhang Z, Shi X, Yi J, Xuan Z, Wu J. Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation. Cell Rep 2021; 36:109357. [PMID: 34260936 PMCID: PMC8315893 DOI: 10.1016/j.celrep.2021.109357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Neuronal activity-induced enhancers drive gene activation. We demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. We identify a serine phosphorylation site in BRG1 that is induced by neuronal stimulations and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, including the NuRD repressor complex and cohesin, possibly modulating BRG1-mediated transcription outcomes. Using mice with knockin mutations, we show that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases enhancer activity and inducibility. These mutant mice display anxiety-like phenotypes and altered responses to stress. Therefore, we reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.
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Affiliation(s)
- BongWoo Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Luo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zilai Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuanming Shi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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38
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Jayabal P, Zhou F, Lei X, Ma X, Blackman B, Weintraub ST, Houghton PJ, Shiio Y. NELL2-cdc42 signaling regulates BAF complexes and Ewing sarcoma cell growth. Cell Rep 2021; 36:109254. [PMID: 34233189 PMCID: PMC8312579 DOI: 10.1016/j.celrep.2021.109254] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
BAF chromatin remodeling complexes play important roles in chromatin regulation and cancer. Here, we report that Ewing sarcoma cells are dependent on the autocrine signaling mediated by NELL2, a secreted glycoprotein that has been characterized as an axon guidance molecule. NELL2 uses Robo3 as the receptor to transmit critical growth signaling. NELL2 signaling inhibits cdc42 and upregulates BAF complexes and EWS-FLI1 transcriptional output. We demonstrate that cdc42 is a negative regulator of BAF complexes, inducing actin polymerization and complex disassembly. Furthermore, we identify NELL2highCD133highEWS-FLI1high and NELL2lowCD133lowEWS-FLI1low populations in Ewing sarcoma, which display phenotypes consistent with high and low NELL2 signaling, respectively. We show that NELL2, CD133, and EWS-FLI1 positively regulate each other and upregulate BAF complexes and cell proliferation in Ewing sarcoma. These results reveal a signaling pathway regulating critical chromatin remodeling complexes and cancer cell proliferation.
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Affiliation(s)
- Panneerselvam Jayabal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Fuchun Zhou
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiufen Lei
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Xiuye Ma
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Barron Blackman
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Molecular Medicine, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229, USA; Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX 78229, USA.
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39
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D'Souza L, Channakkar AS, Muralidharan B. Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders. Neurochem Int 2021; 147:105055. [PMID: 33964373 PMCID: PMC7611358 DOI: 10.1016/j.neuint.2021.105055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/11/2021] [Accepted: 04/24/2021] [Indexed: 12/19/2022]
Abstract
The diverse number of neurons in the cerebral cortex are generated during development by neural stem cells lining the ventricle, and they continue maturing postnatally. Dynamic chromatin regulation in these neural stem cells is a fundamental determinant of the emerging property of the functional neural network, and the chromatin remodellers are critical determinants of this process. Chromatin remodellers participate in several steps of this process from proliferation, differentiation, migration leading to complex network formation which forms the basis of higher-order functions of cognition and behaviour. Here we review the role of these ATP-dependent chromatin remodellers in cortical development in health and disease and highlight several key mouse mutants of the subunits of the complexes which have revealed how the remodelling mechanisms control the cortical stem cell chromatin landscape for expression of stage-specific transcripts. Consistent with their role in cortical development, several putative risk variants in the subunits of the remodelling complexes have been identified as the underlying causes of several neurodevelopmental disorders. A basic understanding of the detailed molecular mechanism of their action is key to understating how mutations in the same networks lead to disease pathologies and perhaps pave the way for therapeutic development for these complex multifactorial disorders.
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Affiliation(s)
- Leora D'Souza
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Asha S Channakkar
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Bhavana Muralidharan
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India.
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40
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Sokpor G, Kerimoglu C, Nguyen H, Pham L, Rosenbusch J, Wagener R, Nguyen HP, Fischer A, Staiger JF, Tuoc T. Loss of BAF Complex in Developing Cortex Perturbs Radial Neuronal Migration in a WNT Signaling-Dependent Manner. Front Mol Neurosci 2021; 14:687581. [PMID: 34220450 PMCID: PMC8243374 DOI: 10.3389/fnmol.2021.687581] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022] Open
Abstract
Radial neuronal migration is a key neurodevelopmental event indispensable for proper cortical laminar organization. Cortical neurons mainly use glial fiber guides, cell adhesion dynamics, and cytoskeletal remodeling, among other discrete processes, to radially trek from their birthplace to final layer positions. Dysregulated radial migration can engender cortical mis-lamination, leading to neurodevelopmental disorders. Epigenetic factors, including chromatin remodelers have emerged as formidable regulators of corticogenesis. Notably, the chromatin remodeler BAF complex has been shown to regulate several aspects of cortical histogenesis. Nonetheless, our understanding of how BAF complex regulates neuronal migration is limited. Here, we report that BAF complex is required for neuron migration during cortical development. Ablation of BAF complex in the developing mouse cortex caused alteration in the cortical gene expression program, leading to loss of radial migration-related factors critical for proper cortical layer formation. Of note, BAF complex inactivation in cortex caused defective neuronal polarization resulting in diminished multipolar-to-bipolar transition and eventual disruption of radial migration of cortical neurons. The abnormal radial migration and cortical mis-lamination can be partly rescued by downregulating WNT signaling hyperactivity in the BAF complex mutant cortex. By implication, the BAF complex modulates WNT signaling to establish the gene expression program required for glial fiber-dependent neuronal migration, and cortical lamination. Overall, BAF complex has been identified to be crucial for cortical morphogenesis through instructing multiple aspects of radial neuronal migration in a WNT signaling-dependent manner.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center Goettingen, Göttingen, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Cemil Kerimoglu
- German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Huong Nguyen
- Institute for Neuroanatomy, University Medical Center Goettingen, Göttingen, Germany.,Faculty of Biotechnology, Thai Nguyen University of Sciences, Thai Nguyen, Vietnam
| | - Linh Pham
- Institute for Neuroanatomy, University Medical Center Goettingen, Göttingen, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center Goettingen, Göttingen, Germany
| | - Robin Wagener
- Institute for Neuroanatomy, University Medical Center Goettingen, Göttingen, Germany.,Department of Neurology, University Medical Center Heidelberg, Heidelberg, Germany.,Neurooncology Clinical Cooperation Unit, German Cancer Research Center, Heidelberg, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Andre Fischer
- German Center for Neurodegenerative Diseases, Göttingen, Germany.,Department for Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center Goettingen, Göttingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center Goettingen, Göttingen, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
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41
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Holdhof D, Schoof M, Al-Kershi S, Spohn M, Kresbach C, Göbel C, Hellwig M, Indenbirken D, Moreno N, Kerl K, Schüller U. Brahma-related gene 1 has time-specific roles during brain and eye development. Development 2021; 148:268382. [PMID: 34042968 DOI: 10.1242/dev.196147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 05/04/2021] [Indexed: 11/20/2022]
Abstract
During development, gene expression is tightly controlled to facilitate the generation of the diverse cell types that form the central nervous system. Brahma-related gene 1 (Brg1, also known as Smarca4) is the catalytic subunit of the SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex that regulates transcription. We investigated the role of Brg1 between embryonic day 6.5 (E6.5) and E14.5 in Sox2-positive neural stem cells (NSCs). Being without major consequences at E6.5 and E14.5, loss of Brg1 between E7.5 and E12.5 resulted in the formation of rosette-like structures in the subventricular zone, as well as morphological alterations and enlargement of neural retina (NR). Additionally, Brg1-deficient cells showed decreased survival in vitro and in vivo. Furthermore, we uncovered distinct changes in gene expression upon Brg1 loss, pointing towards impaired neuron functions, especially those involving synaptic communication and altered composition of the extracellular matrix. Comparison with mice deficient for integrase interactor 1 (Ini1, also known as Smarcb1) revealed that the enlarged NR was Brg1 specific and was not caused by a general dysfunction of the SWI/SNF complex. These results suggest a crucial role for Brg1 in NSCs during brain and eye development.
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Affiliation(s)
- Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Sina Al-Kershi
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany.,Bioinformatics Facility, University Medical Center, Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Malte Hellwig
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Natalia Moreno
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, 48149 Münster, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, 20251 Hamburg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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42
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Chromatin remodeler Arid1a regulates subplate neuron identity and wiring of cortical connectivity. Proc Natl Acad Sci U S A 2021; 118:2100686118. [PMID: 34011608 PMCID: PMC8166177 DOI: 10.1073/pnas.2100686118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Loss-of-function mutations in chromatin remodeler gene ARID1A are a cause of Coffin-Siris syndrome, a developmental disorder characterized by dysgenesis of corpus callosum. Here, we characterize Arid1a function during cortical development and find unexpectedly selective roles for Arid1a in subplate neurons (SPNs). SPNs, strategically positioned at the interface of cortical gray and white matter, orchestrate multiple developmental processes indispensable for neural circuit wiring. We find that pancortical deletion of Arid1a leads to extensive mistargeting of intracortical axons and agenesis of corpus callosum. Sparse Arid1a deletion, however, does not autonomously misroute callosal axons, implicating noncell-autonomous Arid1a functions in axon guidance. Supporting this possibility, the ascending axons of thalamocortical neurons, which are not autonomously affected by cortical Arid1a deletion, are also disrupted in their pathfinding into cortex and innervation of whisker barrels. Coincident with these miswiring phenotypes, which are reminiscent of subplate ablation, we unbiasedly find a selective loss of SPN gene expression following Arid1a deletion. In addition, multiple characteristics of SPNs crucial to their wiring functions, including subplate organization, subplate axon-thalamocortical axon cofasciculation ("handshake"), and extracellular matrix, are severely disrupted. To empirically test Arid1a sufficiency in subplate, we generate a cortical plate deletion of Arid1a that spares SPNs. In this model, subplate Arid1a expression is sufficient for subplate organization, subplate axon-thalamocortical axon cofasciculation, and subplate extracellular matrix. Consistent with these wiring functions, subplate Arid1a sufficiently enables normal callosum formation, thalamocortical axon targeting, and whisker barrel development. Thus, Arid1a is a multifunctional regulator of subplate-dependent guidance mechanisms essential to cortical circuit wiring.
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43
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Yang QQ, Zhai YQ, Wang HF, Cai YC, Ma XY, Yin YQ, Li YD, Zhou GM, Zhang X, Hu G, Zhou JW. Nuclear isoform of FGF13 regulates post-natal neurogenesis in the hippocampus through an epigenomic mechanism. Cell Rep 2021; 35:109127. [PMID: 34010636 DOI: 10.1016/j.celrep.2021.109127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 02/13/2021] [Accepted: 04/22/2021] [Indexed: 10/21/2022] Open
Abstract
The hippocampus is one of two niches in the mammalian brain with persistent neurogenesis into adulthood. The neurogenic capacity of hippocampal neural stem cells (NSCs) declines with age, but the molecular mechanisms of this process remain unknown. In this study, we find that fibroblast growth factor 13 (FGF13) is essential for the post-natal neurogenesis in mouse hippocampus, and FGF13 deficiency impairs learning and memory. In particular, we find that FGF13A, the nuclear isoform of FGF13, is involved in the maintenance of NSCs and the suppression of neuronal differentiation during post-natal hippocampal development. Furthermore, we find that FGF13A interacts with ARID1B, a unit of Brahma-associated factor chromatin remodeling complex, and suppresses the expression of neuron differentiation-associated genes through chromatin modification. Our results suggest that FGF13A is an important regulator for maintaining the self-renewal and neurogenic capacity of NSCs in post-natal hippocampus, revealing an epigenomic regulatory function of FGFs in neurogenesis.
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Affiliation(s)
- Qiao-Qiao Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ying-Qi Zhai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hai-Fang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Chen Cai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin-Yue Ma
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yan-Qing Yin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan-Dong Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Min Zhou
- Department of Anatomy, Histology and Embryology, Shanghai Medical School of Fudan University, Shanghai 200032, China
| | - Xu Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Gang Hu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 210029, China; Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Jia-Wei Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China; Co-innovation Center of Neuroregeneration, School of Medicine, Nantong University, Nantong, Jiangsu 226001, China.
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44
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Moffat JJ, Jung EM, Ka M, Jeon BT, Lee H, Kim WY. Differential roles of ARID1B in excitatory and inhibitory neural progenitors in the developing cortex. Sci Rep 2021; 11:3856. [PMID: 33594090 PMCID: PMC7886865 DOI: 10.1038/s41598-021-82974-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/21/2021] [Indexed: 11/08/2022] Open
Abstract
Genetic evidence indicates that haploinsufficiency of ARID1B causes intellectual disability (ID) and autism spectrum disorder (ASD), but the neural function of ARID1B is largely unknown. Using both conditional and global Arid1b knockout mouse strains, we examined the role of ARID1B in neural progenitors. We detected an overall decrease in the proliferation of cortical and ventral neural progenitors following homozygous deletion of Arid1b, as well as altered cell cycle regulation and increased cell death. Each of these phenotypes was more pronounced in ventral neural progenitors. Furthermore, we observed decreased nuclear localization of β-catenin in Arid1b-deficient neurons. Conditional homozygous deletion of Arid1b in ventral neural progenitors led to pronounced ID- and ASD-like behaviors in mice, whereas the deletion in cortical neural progenitors resulted in minor cognitive deficits. This study suggests an essential role for ARID1B in forebrain neurogenesis and clarifies its more pronounced role in inhibitory neural progenitors. Our findings also provide insights into the pathogenesis of ID and ASD.
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Affiliation(s)
- Jeffrey J Moffat
- Developmental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94153, USA
| | - Eui-Man Jung
- Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Minhan Ka
- Research Center for Substance Abuse Pharmacology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Byeong Tak Jeon
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA
| | - Hyunkyoung Lee
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA.
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45
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BAF Complex in Embryonic Stem Cells and Early Embryonic Development. Stem Cells Int 2021; 2021:6668866. [PMID: 33510794 PMCID: PMC7826211 DOI: 10.1155/2021/6668866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Embryonic stem cells (ESCs) can self-renew indefinitely and maintain their pluripotency status. The pluripotency gene regulatory network is critical in controlling these properties and particularly chromatin remodeling complexes. In this review, we summarize the research progresses of the functional and mechanistic studies of BAF complex in mouse ESCs and early embryonic development. A discussion of the mechanistic bases underlying the distinct phenotypes upon the deletion of different BAF subunits in ESCs and embryos will be highlighted.
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Chen X, Xiang Z, Li D, Zhu X, Peng X. ACTL6A knockdown inhibits cell migration by suppressing the AKT signaling pathway and enhances the sensitivity of glioma cells to temozolomide. Exp Ther Med 2020; 21:175. [PMID: 33456542 PMCID: PMC7792480 DOI: 10.3892/etm.2020.9606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Molecular-targeted therapy has had a significant impact on glioma. Notably, actin-like 6A (ACTL6A) has been indicated to be essential for embryonic development and tumor progression. However, the role of ACTL6A in glioma remains unclear. The present study aimed to investigate the effects of ACTL6A on glioma cell migration and sensitivity to temozolomide (TMZ). The expression levels of ACTL6A were analyzed in patients with glioma, and survival curves were created using data from The Cancer Genome Atlas. U251 and T98G cells were transfected with short hairpin (sh)RNA for use in loss-of-function experiments to investigate the biological function and molecular mechanisms of ACTL6A. Furthermore, an MTT assay was used to assess the effect of ACTL6A on the sensitivity of glioma cells to TMZ. The results demonstrated that ACTL6A was expressed at higher levels in glioma tissues compared with normal brain tissues. Furthermore, high expression of ACTL6A was associated with a poor prognosis. The knockdown of ACTL6A significantly inhibited the migration phenotype in glioma cells and significantly decreased the levels of phosphorylated AKT in glioma cells. The AKT signaling activator SC79 partly attenuated the inhibitory effects of ACTL6A shRNA on glioma cell migration. Additionally, the knockdown of ACTL6A enhanced the sensitivity of glioma cells to TMZ. In conclusion, these results suggest that ACTL6A knockdown inhibited the migration of human glioma cells, at least in part through inactivation of the AKT signaling pathway, and increased the sensitivity of glioma cells to TMZ. Therefore, ACTL6A may be a potential therapeutic target for glioma.
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Affiliation(s)
- Xueru Chen
- Department of Pharmacy, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Zijin Xiang
- Department of Pharmacy, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Dangchi Li
- Jiangxi University of Technology High School, Nanchang, Jiangxi 330029, P.R. China
| | - Xiuting Zhu
- Department of Pharmacy, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Xiangdong Peng
- Department of Pharmacy, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
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Yi M, Tan Y, Wang L, Cai J, Li X, Zeng Z, Xiong W, Li G, Li X, Tan P, Xiang B. TP63 links chromatin remodeling and enhancer reprogramming to epidermal differentiation and squamous cell carcinoma development. Cell Mol Life Sci 2020; 77:4325-4346. [PMID: 32447427 PMCID: PMC7588389 DOI: 10.1007/s00018-020-03539-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/21/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022]
Abstract
Squamous cell carcinoma (SCC) is an aggressive malignancy that can originate from various organs. TP63 is a master regulator that plays an essential role in epidermal differentiation. It is also a lineage-dependent oncogene in SCC. ΔNp63α is the prominent isoform of TP63 expressed in epidermal cells and SCC, and overexpression promotes SCC development through a variety of mechanisms. Recently, ΔNp63α was highlighted to act as an epidermal-specific pioneer factor that binds closed chromatin and enhances chromatin accessibility at epidermal enhancers. ΔNp63α coordinates chromatin-remodeling enzymes to orchestrate the tissue-specific enhancer landscape and three-dimensional high-order architecture of chromatin. Moreover, ΔNp63α establishes squamous-like enhancer landscapes to drive oncogenic target expression during SCC development. Importantly, ΔNp63α acts as an upstream regulator of super enhancers to activate a number of oncogenic transcripts linked to poor prognosis in SCC. Mechanistically, ΔNp63α activates genes transcription through physically interacting with a number of epigenetic modulators to establish enhancers and enhance chromatin accessibility. In contrast, ΔNp63α also represses gene transcription via interacting with repressive epigenetic regulators. ΔNp63α expression is regulated at multiple levels, including transcriptional, post-transcriptional, and post-translational levels. In this review, we summarize recent advances of p63 in epigenomic and transcriptional control, as well as the mechanistic regulation of p63.
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Affiliation(s)
- Mei Yi
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yixin Tan
- Department of Dermatology, The Second Xiangya Hospital, The Central South University, Changsha, 410011, Hunan, China
| | - Li Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Cai
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
| | - Pingqing Tan
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Department of Head and Neck Surgery, Hunan Provincial Cancer Hospital and Cancer Hospital Affiliated to Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Provincial Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medical Sciences, Central South University, Changsha, 410078, Hunan, China.
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Pijuan J, Rodríguez-Sanz M, Natera-de Benito D, Ortez C, Altimir A, Osuna-López M, Roura M, Ugalde M, Van de Vondel L, Reina-Castillón J, Fons C, Benítez R, Nascimento A, Hoenicka J, Palau F. Translational Diagnostics: An In-House Pipeline to Validate Genetic Variants in Children with Undiagnosed and Rare Diseases. J Mol Diagn 2020; 23:71-90. [PMID: 33223419 DOI: 10.1016/j.jmoldx.2020.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/10/2020] [Accepted: 10/13/2020] [Indexed: 12/26/2022] Open
Abstract
Diagnosis is essential for the management and treatment of patients with rare diseases. In a group of patients, the genetic study identifies variants of uncertain significance or inconsistent with the phenotype; therefore, it is urgent to develop novel strategies to reach the definitive diagnosis. Herein, we develop the in-house Translational Diagnostics Program (TDP) to validate genetic variants as part of the diagnostic process with the close collaboration of physicians, clinical scientists, and research scientists. The first 7 of 33 consecutive patients for whom exome-based tests were not diagnostic were investigated. The TDP pipeline includes four steps: (i) phenotype assessment, (ii) literature review and prediction of in silico pathogenicity, (iii) experimental functional studies, and (iv) diagnostic decision-making. Re-evaluation of the phenotype and re-analysis of the exome allowed the diagnosis in one patient. In the remaining patients, the studies included either cDNA cloning or PCR-amplified genomic DNA, or the use of patients' fibroblasts. A comparative computational analysis of confocal microscopy images and studies related to the protein function was performed. In five of these six patients, evidence of pathogenicity of the genetic variant was found, which was validated by physicians. The current research demonstrates the feasibility of the TDP to support and resolve intramural medical problems when the clinical significance of the patient variant is unknown or inconsistent with the phenotype.
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Affiliation(s)
- Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - María Rodríguez-Sanz
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - Arola Altimir
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Mireia Osuna-López
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Montserrat Roura
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Maddi Ugalde
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Liedewei Van de Vondel
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Judith Reina-Castillón
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Carme Fons
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain; Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Raúl Benítez
- Automatic Control Department and Biomedical Engineering Research Center, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Andrés Nascimento
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - Janet Hoenicka
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain.
| | - Francesc Palau
- Laboratory of Neurogenetics and Molecular Medicine-Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain; Department of Genetic Medicine-IPER, Hospital Sant Joan de Déu, Barcelona, Spain; Clinic Institute of Medicine and Dermatology, Hospital Clínic, Barcelona, Spain; Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.
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Actin-like 6A enhances the proliferative and invasive capacities of laryngeal squamous cell carcinoma by potentiating the activation of YAP signaling. J Bioenerg Biomembr 2020; 52:453-463. [DOI: 10.1007/s10863-020-09855-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/11/2020] [Indexed: 02/07/2023]
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Abstract
The Trithorax group (TrxG) of proteins is a large family of epigenetic regulators that form multiprotein complexes to counteract repressive developmental gene expression programmes established by the Polycomb group of proteins and to promote and maintain an active state of gene expression. Recent studies are providing new insights into how two crucial families of the TrxG - the COMPASS family of histone H3 lysine 4 methyltransferases and the SWI/SNF family of chromatin remodelling complexes - regulate gene expression and developmental programmes, and how misregulation of their activities through genetic abnormalities leads to pathologies such as developmental disorders and malignancies.
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