Systems biology analysis of human genomes points to key pathways conferring spina bifida risk.

TitleSystems biology analysis of human genomes points to key pathways conferring spina bifida risk.
Publication TypeJournal Article
Year of Publication2021
AuthorsAguiar-Pulido V, Wolujewicz P, Martinez-Fundichely A, Elhaik E, Thareja G, Aleem AAbdel, Chalhoub N, Cuykendall T, Al-Zamer J, Lei Y, El-Bashir H, Musser JM, Al-Kaabi A, Shaw GM, Khurana E, Suhre K, Mason CE, Elemento O, Finnell RH, M Ross E
JournalProc Natl Acad Sci U S A
Date Published2021 12 21
KeywordsCase-Control Studies, Genetic Predisposition to Disease, Genome, Human, Genome-Wide Association Study, Humans, Spinal Dysraphism, Systems Biology, Transcription Factors

Spina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance, and environmental influences that hamper genome-wide association studies approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases versus controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation, and essential transcriptional regulation consistent with their having impact on the pathogenesis of human SB. Additionally, an interrogation of conserved noncoding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to the interrogation of coding and noncoding sequence variant contributions to rare complex genetic disorders.

Alternate JournalProc Natl Acad Sci U S A
PubMed ID34916285
Grant ListP01 HD067244 / HD / NICHD NIH HHS / United States
R01 NS076465 / NS / NINDS NIH HHS / United States
R01 HD081216 / HD / NICHD NIH HHS / United States
T32 HD060600 / HD / NICHD NIH HHS / United States