Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder

Xenia Latypova, Marie Vincent, Alice Mollé, Oluwadamilare A. Adebambo, Cynthia Fourgeux, Tahir N. Khan, Alfonso Caro, Monica Rosello, Carmen Orellana, Dmitriy Niyazov, Damien Lederer, Marie Deprez, Yline Capri, Peter Kannu, Anne Claude Tabet, Jonathan Levy, Emmelien Aten, Nicolette den Hollander, Miranda Splitt, Jagdeep WaliaLadonna L. Immken, Pawel Stankiewicz, Kirsty McWalter, Sharon Suchy, Raymond J. Louie, Shannon Bell, Roger E. Stevenson, Justine Rousseau, Catherine Willem, Christelle Retiere, Xiang Jiao Yang, Philippe M. Campeau, Francisco Martinez, Jill A. Rosenfeld, Cédric Le Caignec, Sébastien Küry, Sandra Mercier, Kamran Moradkhani, Solène Conrad, Thomas Besnard, Benjamin Cogné, Nicholas Katsanis, Stéphane Bézieau, Jeremie Poschmann, Erica E. Davis, Bertrand Isidor*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Proteins involved in transcriptional regulation harbor a demonstrated enrichment of mutations in neurodevelopmental disorders. The Sin3 (Swi-independent 3)/histone deacetylase (HDAC) complex plays a central role in histone deacetylation and transcriptional repression. Among the two vertebrate paralogs encoding the Sin3 complex, SIN3A variants cause syndromic intellectual disability, but the clinical consequences of SIN3B haploinsufficiency in humans are uncharacterized. Here, we describe a syndrome hallmarked by intellectual disability, developmental delay, and dysmorphic facial features with variably penetrant autism spectrum disorder, congenital malformations, corpus callosum defects, and impaired growth caused by disruptive SIN3B variants. Using chromosomal microarray or exome sequencing, and through international data sharing efforts, we identified nine individuals with heterozygous SIN3B deletion or single-nucleotide variants. Five individuals harbor heterozygous deletions encompassing SIN3B that reside within a ∼230 kb minimal region of overlap on 19p13.11, two individuals have a rare nonsynonymous substitution, and two individuals have a single-nucleotide deletion that results in a frameshift and predicted premature termination codon. To test the relevance of SIN3B impairment to measurable aspects of the human phenotype, we disrupted the orthologous zebrafish locus by genome editing and transient suppression. The mutant and morphant larvae display altered craniofacial patterning, commissural axon defects, and reduced body length supportive of an essential role for Sin3 function in growth and patterning of anterior structures. To investigate further the molecular consequences of SIN3B variants, we quantified genome-wide enhancer and promoter activity states by using H3K27ac ChIP-seq. We show that, similar to SIN3A mutations, SIN3B disruption causes hyperacetylation of a subset of enhancers and promoters in peripheral blood mononuclear cells. Together, these data demonstrate that SIN3B haploinsufficiency leads to a hitherto unknown intellectual disability/autism syndrome, uncover a crucial role of SIN3B in the central nervous system, and define the epigenetic landscape associated with Sin3 complex impairment.

Original languageEnglish (US)
Pages (from-to)929-941
Number of pages13
JournalAmerican journal of human genetics
Volume108
Issue number5
DOIs
StatePublished - May 6 2021
Externally publishedYes

Keywords

  • HDAC
  • SIN3A
  • SINB
  • acetylation
  • autism
  • epigenetics
  • intellectual disability
  • mutation
  • transcription
  • zebrafish

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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