{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T07:01:36Z","timestamp":1792047696422,"version":"4.4.0"},"posted":{"date-parts":[[2023,3,20]]},"group-title":"Genetic and Genomic Medicine","reference-count":101,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,3,20]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:sec>\n                  <jats:title>Importance<\/jats:title>\n                  <jats:p>\n                    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\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    , a component of the\n                    <jats:underline>B<\/jats:underline>\n                    RG1-\n                    <jats:underline>a<\/jats:underline>\n                    ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However,\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    variants have not been functionally validated or mechanistically studied\n                    <jats:italic>in vivo<\/jats:italic>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>\n                    The aims of this study are to (i) assess the extent to which rare, damaging\n                    <jats:italic>de novo<\/jats:italic>\n                    mutations (DNMs) in\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    mutations\n                    <jats:italic>in vivo<\/jats:italic>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Design, setting, and participants<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Main outcomes and measures<\/jats:title>\n                  <jats:p>\n                    Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden.\n                    <jats:italic>In silico<\/jats:italic>\n                    biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data.\n                    <jats:italic>Smarcc1<\/jats:italic>\n                    knockdowns and a patient-specific\n                    <jats:italic>Smarcc1<\/jats:italic>\n                    variant were tested in\n                    <jats:italic>Xenopus<\/jats:italic>\n                    and studied using optical coherence tomography imaging,\n                    <jats:italic>in situ<\/jats:italic>\n                    hybridization, and immunofluorescence microscopy.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    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&gt;A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1\n                    <jats:italic>Smarcc1 Xenopus<\/jats:italic>\n                    mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    but not a patient-specific\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    mutant. Hydrocephalic\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    -mutant human fetal brain and\n                    <jats:italic>Smarcc1<\/jats:italic>\n                    -mutant\n                    <jats:italic>Xenopus<\/jats:italic>\n                    brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors\n                    <jats:italic>NEUROD2<\/jats:italic>\n                    and\n                    <jats:italic>MAB21L2<\/jats:italic>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    is a\n                    <jats:italic>bona fide<\/jats:italic>\n                    CH risk gene. DNMs in\n                    <jats:italic>SMARCC1<\/jats:italic>\n                    cause a novel human BAFopathy we term \u201c\n                    <jats:underline>S<\/jats:underline>\n                    MARCC1-\n                    <jats:underline>a<\/jats:underline>\n                    ssociated\n                    <jats:underline>D<\/jats:underline>\n                    evelopmental\n                    <jats:underline>D<\/jats:underline>\n                    ysgenesis\n                    <jats:underline>S<\/jats:underline>\n                    yndrome (SaDDS)\u201d, 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 \u201cneural stem cell\u201d 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.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>KEY POINTS<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Question<\/jats:title>\n                    <jats:p>\n                      What is the role of\n                      <jats:italic>SMARCC1<\/jats:italic>\n                      , a core component of the\n                      <jats:underline>B<\/jats:underline>\n                      RG1-\n                      <jats:underline>a<\/jats:underline>\n                      ssociated factor (BAF) chromatin remodeling complex, in brain morphogenesis and congenital hydrocephalus (CH)?\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>\n                      <jats:italic>SMARCC1<\/jats:italic>\n                      harbored an exome-wide significant burden of rare, protein-damaging\n                      <jats:italic>de novo<\/jats:italic>\n                      mutations (DNMs) (p = 5.83 \u00d7 10\n                      <jats:sup>\u22129<\/jats:sup>\n                      ) in the largest ascertained cohort to date of patients with cerebral ventriculomegaly, including treated CH (2,697 parent-proband trios).\n                      <jats:italic>SMARCC1<\/jats:italic>\n                      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.\n                      <jats:italic>Xenopus Smarcc1<\/jats:italic>\n                      mutants recapitulated core human phenotypes and were rescued by the expression of human wild-type but not patient-mutant\n                      <jats:italic>SMARCC1<\/jats:italic>\n                      . Hydrocephalic\n                      <jats:italic>SMARCC1<\/jats:italic>\n                      -mutant human brain and\n                      <jats:italic>Smarcc1<\/jats:italic>\n                      -mutant\n                      <jats:italic>Xenopus<\/jats:italic>\n                      brain exhibited similar alterationsin the expression of key transcription factors that regulate neural progenitor cell proliferation.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Meaning<\/jats:title>\n                    <jats:p>\n                      <jats:italic>SMARCC1<\/jats:italic>\n                      is essential for human brain morphogenesis and is a\n                      <jats:italic>bona fide<\/jats:italic>\n                      CH risk gene.\n                      <jats:italic>SMARCC1<\/jats:italic>\n                      mutations cause a novel human BAFopathy we term \u201c\n                      <jats:underline>S<\/jats:underline>\n                      MARCC1-\n                      <jats:underline>a<\/jats:underline>\n                      ssociated\n                      <jats:underline>D<\/jats:underline>\n                      evelopmental\n                      <jats:underline>D<\/jats:underline>\n                      ysgenesis\n                      <jats:underline>S<\/jats:underline>\n                      yndrome (SaDDS)\u201d. These data implicate epigenetic dysregulation of fetal neural progenitors in the pathogenesis of hydrocephalus, with diagnostic and prognostic implications for patients and caregivers.\n                    <\/jats:p>\n                  <\/jats:sec>\n                <\/jats:sec>","DOI":"10.1101\/2023.03.19.23287455","type":"posted-content","created":{"date-parts":[[2023,3,20]],"date-time":"2023-03-20T19:20:11Z","timestamp":1679340011000},"source":"Crossref","is-referenced-by-count":1,"title":["A novel\n                  <i>SMARCC1<\/i>\n                  -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus"],"prefix":"10.64898","author":[{"given":"Amrita K.","family":"Singh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Viviano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garrett","family":"Allington","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"McGee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emre","family":"Kiziltug","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2508-387X","authenticated-orcid":false,"given":"Kedous Y.","family":"Mekbib","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P.","family":"Shohfi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phan Q.","family":"Duy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"Tyrone","family":"DeSpenza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charuta G","family":"Furey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin C.","family":"Reeves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaojie","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9 M. 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