Understanding the Landscape of X-linked Variants Causing Intellectual Disability in Females Through Extreme X Chromosome Inactivation Skewing

• Published in: Molecular neurobiology Vol. 57; no. 9; pp. 3671 - 3684
• Main Authors: Vianna, Evelyn Quintanilha, Piergiorge, Rafael Mina, Gonçalves, Andressa Pereira, dos Santos, Jussara Mendonça, Calassara, Veluma, Rosenberg, Carla, Krepischi, Ana Cristina Victorino, Boy da Silva, Raquel Tavares, dos Santos, Suely Rodrigues, Ribeiro, Márcia Gonçalves, Machado, Filipe Brum, Medina-Acosta, Enrique, Pimentel, Márcia Mattos Gonçalves, Santos-Rebouças, Cíntia Barros
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.09.2020; Springer Nature B.V
• Subjects: Biomedical and Life Sciences; Biomedicine; Buccal mucosa; Cell Biology; Central nervous system; DNA methylation; Females; Genetic counseling; Hybridization; Intellectual disabilities; Males; Molecular modelling; Neurobiology; Neurology; Neurosciences; Original Article; Phenotypes; Sex differences; Somatic cells; X chromosomes; X-chromosome inactivation; Array-CGH; X-linked intellectual disability; Whole-exome sequencing; Escape genes; X chromosome inactivation
• ISSN: 0893-7648; 1559-1182
• DOI: 10.1007/s12035-020-01981-8

Intellectual disability (ID) affects 30% more males than females. This sex bias can be attributed to the enrichment of genes on the X chromosome playing essential roles in the central nervous system and their hemizygous state on males. Moreover, as a result of X chromosome inactivation (XCI), most genes on one of the X chromosomes in female somatic cells are epigenetically silenced, so that females carrying X-linked variants are not expected to be so severely affected as males. Consequently, the knowledge about X-linked ID (XLID) in females is still scarce. Herein, we used extreme XCI skewing (≥ 90%) to predict X-linked variants in females with idiopathic ID. XCI profiles from 53 probands were estimated from blood and buccal mucosa through a methylation-sensitive AR / RP2 assay. DNA samples with extreme XCI skewing were then submitted to array-comparative genomic hybridization and whole-exome sequencing. Seven females (13.2%) exhibited extreme XCI skewing, a percentage significantly higher than expected for healthy females in our population. XLID-potentially related variants were identified in five patients with extreme XCI skewing, including one pathogenic rstructural rearrangement [der(X) chromosome from a t(X;2)] and four single nucleotide variants in NLGN4X , HDAC8 , TAF1 , and USP9X genes, two of which affecting XCI escape genes. XCI skewing showed to be an outstanding approach for the characterization of molecular mechanisms underlying XLID in females. Beyond expanding the spectrum of variants/phenotypes associated with ID, our results pointed to compensatory biological pathways underlying XCI and uncover new insights into the involvement of escape genes on XLID, impacting genetic counseling.