A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus Article Swipe
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· 2023
· Open Access
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· DOI: https://doi.org/10.1093/brain/awad405
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.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/brain/awad405
- OA Status
- green
- Cited By
- 13
- References
- 112
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4390120745
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4390120745Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/brain/awad405Digital Object Identifier
- Title
-
A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalusWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-12-20Full publication date if available
- Authors
-
Amrita Singh, Garrett Allington, Stephen Viviano, Stephen McGee, Emre Kiziltug, Shaojie Ma, Shujuan Zhao, Kedous Y. Mekbib, John Shohfi, Phan Q. Duy, Tyrone DeSpenza, Charuta G. Furey, Benjamin C. Reeves, Hannah Smith, André M. M. Sousa, Adriana Cherskov, August Allocco, Carol Nelson‐Williams, Shozeb Haider, Syed R A Rizvi, Seth L. Alper, Nenad Šestan, Hermela Shimelis, Lauren K. Walsh, Richard P. Lifton, Andrés Moreno-De-Luca, Sheng Chih Jin, Paul Kruszka, Engin Deniz, Kristopher T. KahleList of authors in order
- Landing page
-
https://doi.org/10.1093/brain/awad405Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.ncbi.nlm.nih.gov/pmc/articles/10994532Direct OA link when available
- Concepts
-
Exome sequencing, Hydrocephalus, Ventriculomegaly, Exome, Biology, Genetics, Pathology, Medicine, Bioinformatics, Phenotype, Gene, Fetus, Psychiatry, PregnancyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
13Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 6, 2024: 7Per-year citation counts (last 5 years)
- References (count)
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112Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| title | A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus |
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| abstract_inverted_index.over | 141 |
| abstract_inverted_index.situ | 210 |
| abstract_inverted_index.stem | 361 |
| abstract_inverted_index.term | 313 |
| abstract_inverted_index.that | 136 |
| abstract_inverted_index.were | 166, 179, 191, 198, 249, 262 |
| abstract_inverted_index.with | 53, 132, 158, 193, 238 |
| abstract_inverted_index.(BAF) | 27 |
| abstract_inverted_index.Here, | 72 |
| abstract_inverted_index.These | 299, 338, 368 |
| abstract_inverted_index.aimed | 74 |
| abstract_inverted_index.brain | 12, 189, 275, 279, 334, 353, 384 |
| abstract_inverted_index.cause | 307 |
| abstract_inverted_index.delay | 328 |
| abstract_inverted_index.fetal | 188, 274 |
| abstract_inverted_index.gene. | 36 |
| abstract_inverted_index.genes | 287 |
| abstract_inverted_index.human | 55, 187, 273, 310, 352 |
| abstract_inverted_index.large | 47 |
| abstract_inverted_index.model | 105 |
| abstract_inverted_index.novel | 102, 309 |
| abstract_inverted_index.rare, | 221 |
| abstract_inverted_index.study | 117 |
| abstract_inverted_index.their | 163 |
| abstract_inverted_index.this, | 111 |
| abstract_inverted_index.total | 127, 137 |
| abstract_inverted_index.using | 118, 204 |
| abstract_inverted_index.vivo. | 71 |
| abstract_inverted_index.years | 143 |
| abstract_inverted_index.Recent | 16 |
| abstract_inverted_index.Simons | 170 |
| abstract_inverted_index.assess | 76, 94 |
| abstract_inverted_index.autism | 159 |
| abstract_inverted_index.cohort | 49, 123, 148 |
| abstract_inverted_index.common | 9 |
| abstract_inverted_index.corpus | 241 |
| abstract_inverted_index.delay, | 245 |
| abstract_inverted_index.exomes | 139, 152 |
| abstract_inverted_index.factor | 26 |
| abstract_inverted_index.highly | 228 |
| abstract_inverted_index.impact | 96, 175 |
| abstract_inverted_index.linked | 52, 288 |
| abstract_inverted_index.trios, | 129 |
| abstract_inverted_index.Effects | 184 |
| abstract_inverted_index.NEUROD2 | 296 |
| abstract_inverted_index.SMARCC1 | 38, 60, 80, 214, 306, 344 |
| abstract_inverted_index.Simplex | 171 |
| abstract_inverted_index.Smarcc1 | 98, 196 |
| abstract_inverted_index.Xenopus | 103, 201, 252, 278 |
| abstract_inverted_index.adjunct | 394 |
| abstract_inverted_index.altered | 283 |
| abstract_inverted_index.cardiac | 247, 259, 336 |
| abstract_inverted_index.cell’ | 362 |
| abstract_inverted_index.cohort, | 86 |
| abstract_inverted_index.common. | 251 |
| abstract_inverted_index.complex | 350 |
| abstract_inverted_index.control | 147 |
| abstract_inverted_index.defects | 248, 260 |
| abstract_inverted_index.factors | 295 |
| abstract_inverted_index.genetic | 115 |
| abstract_inverted_index.optical | 205 |
| abstract_inverted_index.parents | 165 |
| abstract_inverted_index.patient | 48, 85 |
| abstract_inverted_index.protein | 177 |
| abstract_inverted_index.provide | 356 |
| abstract_inverted_index.rescued | 263 |
| abstract_inverted_index.results | 300, 369 |
| abstract_inverted_index.sourced | 167 |
| abstract_inverted_index.studied | 69, 203 |
| abstract_inverted_index.studies | 17 |
| abstract_inverted_index.suggest | 301, 387 |
| abstract_inverted_index.surgery | 13 |
| abstract_inverted_index.utility | 371 |
| abstract_inverted_index.variant | 269 |
| abstract_inverted_index.variety | 331 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.However, | 37 |
| abstract_inverted_index.MAB21L2. | 298 |
| abstract_inverted_index.Patients | 235 |
| abstract_inverted_index.SMARCC1, | 20 |
| abstract_inverted_index.SMARCC1. | 270 |
| abstract_inverted_index.assessed | 180 |
| abstract_inverted_index.callosum | 242 |
| abstract_inverted_index.cerebral | 4, 323 |
| abstract_inverted_index.clinical | 89, 396 |
| abstract_inverted_index.complex, | 30 |
| abstract_inverted_index.defects. | 337 |
| abstract_inverted_index.describe | 87 |
| abstract_inverted_index.disorder | 10, 161 |
| abstract_inverted_index.domains. | 234 |
| abstract_inverted_index.evidence | 357 |
| abstract_inverted_index.examined | 44, 192 |
| abstract_inverted_index.expanded | 84 |
| abstract_inverted_index.imaging, | 208 |
| abstract_inverted_index.paradigm | 363 |
| abstract_inverted_index.patients | 131, 157 |
| abstract_inverted_index.presence | 321 |
| abstract_inverted_index.residues | 230 |
| abstract_inverted_index.siblings | 155 |
| abstract_inverted_index.spectrum | 160 |
| abstract_inverted_index.sporadic | 381 |
| abstract_inverted_index.stenosis | 257 |
| abstract_inverted_index.valuable | 393 |
| abstract_inverted_index.variable | 320 |
| abstract_inverted_index.variants | 39, 61, 81, 225, 304, 379 |
| abstract_inverted_index.yielding | 219 |
| abstract_inverted_index.BAFopathy | 311 |
| abstract_inverted_index.Moreover, | 57 |
| abstract_inverted_index.candidate | 33 |
| abstract_inverted_index.children. | 15 |
| abstract_inverted_index.chromatin | 28, 348 |
| abstract_inverted_index.coherence | 206 |
| abstract_inverted_index.collected | 140 |
| abstract_inverted_index.component | 22 |
| abstract_inverted_index.conserved | 229 |
| abstract_inverted_index.consisted | 149 |
| abstract_inverted_index.depletion | 99 |
| abstract_inverted_index.disorders | 385 |
| abstract_inverted_index.exhibited | 236, 280 |
| abstract_inverted_index.generated | 199 |
| abstract_inverted_index.highlight | 370 |
| abstract_inverted_index.including | 130, 292 |
| abstract_inverted_index.localized | 226 |
| abstract_inverted_index.patients. | 401 |
| abstract_inverted_index.performed | 113 |
| abstract_inverted_index.requiring | 11 |
| abstract_inverted_index.similarly | 282 |
| abstract_inverted_index.stenosis, | 326 |
| abstract_inverted_index.stenosis; | 240 |
| abstract_inverted_index.structure | 178 |
| abstract_inverted_index.surpassed | 215 |
| abstract_inverted_index.syndrome. | 56 |
| abstract_inverted_index.validated | 66 |
| abstract_inverted_index.variants. | 183 |
| abstract_inverted_index.wild-type | 265 |
| abstract_inverted_index.‘neural | 360 |
| abstract_inverted_index.Enrichment | 173 |
| abstract_inverted_index.aqueductal | 239, 256, 325 |
| abstract_inverted_index.associated | 88 |
| abstract_inverted_index.comparison | 146 |
| abstract_inverted_index.congenital | 34, 58, 107, 134, 365, 382, 399 |
| abstract_inverted_index.consisting | 124 |
| abstract_inverted_index.dysgenesis | 316 |
| abstract_inverted_index.expression | 284 |
| abstract_inverted_index.functional | 233 |
| abstract_inverted_index.identified | 182 |
| abstract_inverted_index.implicated | 19 |
| abstract_inverted_index.importance | 342 |
| abstract_inverted_index.knockdowns | 197, 253 |
| abstract_inverted_index.management | 397 |
| abstract_inverted_index.pathogenic | 378 |
| abstract_inverted_index.prevalence | 78 |
| abstract_inverted_index.sequencing | 120, 375, 389 |
| abstract_inverted_index.structural | 333, 383 |
| abstract_inverted_index.tomography | 207 |
| abstract_inverted_index.trio-based | 373 |
| abstract_inverted_index.tropicalis | 104 |
| abstract_inverted_index.unaffected | 154, 164 |
| abstract_inverted_index.underscore | 340 |
| abstract_inverted_index.Collection. | 172 |
| abstract_inverted_index.association | 116 |
| abstract_inverted_index.genome-wide | 216 |
| abstract_inverted_index.identifying | 377 |
| abstract_inverted_index.phenotypes, | 92 |
| abstract_inverted_index.remodelling | 29, 349 |
| abstract_inverted_index.thresholds, | 218 |
| abstract_inverted_index.whole-exome | 119, 374, 388 |
| abstract_inverted_index.(2016–23). | 144 |
| abstract_inverted_index.conclusively | 51 |
| abstract_inverted_index.functionally | 65 |
| abstract_inverted_index.radiographic | 91 |
| abstract_inverted_index.significance | 217 |
| abstract_inverted_index.syndrome’, | 317 |
| abstract_inverted_index.Hydrocephalic | 271 |
| abstract_inverted_index.characterized | 2, 318 |
| abstract_inverted_index.developmental | 244, 315, 327 |
| abstract_inverted_index.hybridization | 211 |
| abstract_inverted_index.hydrocephalus | 35, 237, 366, 400 |
| abstract_inverted_index.morphogenesis | 354 |
| abstract_inverted_index.neurogenesis, | 291 |
| abstract_inverted_index.pathogenesis. | 367 |
| abstract_inverted_index.recapitulated | 254 |
| abstract_inverted_index.transcription | 294 |
| abstract_inverted_index.transcriptome | 190 |
| abstract_inverted_index.Hydrocephalus, | 1 |
| abstract_inverted_index.RNA-sequencing | 194 |
| abstract_inverted_index.abnormalities, | 243 |
| abstract_inverted_index.hydrocephalus, | 135 |
| abstract_inverted_index.hydrocephalus. | 108 |
| abstract_inverted_index.midgestational | 290 |
| abstract_inverted_index.systematically | 43 |
| abstract_inverted_index.BRG1-associated | 25 |
| abstract_inverted_index.SMARCC1-variant | 272 |
| abstract_inverted_index.Smarcc1-variant | 277 |
| abstract_inverted_index.mechanistically | 68 |
| abstract_inverted_index.patient-specific | 268 |
| abstract_inverted_index.protein-altering | 222 |
| abstract_inverted_index.ventriculomegalic | 128 |
| abstract_inverted_index.ventriculomegaly, | 5, 324 |
| abstract_inverted_index.immunofluorescence. | 213 |
| abstract_inverted_index.‘SMARCC1-associated | 314 |
| abstract_inverted_index.neurosurgically-treated | 133 |
| abstract_inverted_index.hydrocephalus-associated | 59 |
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| cited_by_percentile_year.min | 98 |
| corresponding_author_ids | https://openalex.org/A5058936141 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 30 |
| corresponding_institution_ids | https://openalex.org/I107606265, https://openalex.org/I1288882113, https://openalex.org/I136199984, https://openalex.org/I4210087915 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.6600000262260437 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.89326743 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |