MYO5B and the Polygenic Landscape of Very Early-Onset Inflammatory Bowel Disease in an Ethnically Diverse Population

• Published in: Inflammatory bowel diseases Vol. 31; no. 1; pp. 189 - 199
• Main Authors: Watson, Ashleigh, Harris, R Alan, Engevik, Amy C, Oezguen, Numan, Nicholson, Maribeth R, Dooley, Sarah, Stubler, Rachel, Satter, Lisa Forbes, Karam, Lina B, Kellermayer, Richard
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 06.01.2025
• Subjects: Adolescent; Age of Onset; Child; Child, Preschool; Exome Sequencing; Female; Genetic Predisposition to Disease; Hispanic or Latino - genetics; Humans; Infant; Inflammatory bowel disease; Inflammatory Bowel Diseases - genetics; Male; Multifactorial Inheritance; Myosin Type V - genetics; Polymorphism, Single Nucleotide; ulcerative colitis; Crohn’s disease; pediatric
• DOI: 10.1093/ibd/izae169
• ISSN: 1078-0998; 1536-4844

Abstract Background Genetic discovery in very early-onset inflammatory bowel disease (VEO-IBD) can elucidate not only the origins of VEO-IBD, but also later-onset inflammatory bowel disease. We aimed to investigate the polygenic origins of VEO-IBD in a cohort with a high proportion of Hispanic patients. Methods Patients with VEO-IBD who underwent whole exome sequencing at our center were included. Genes were categorized as genes of interest (GOIs) (129 genes previously described to be associated with VEO-IBD) or non-GOIs. VEO-IBD “susceptibility” single nucleotide variants (SNVs) were identified through enrichment compared with gnomAD (Genome Aggregation Database) and ALFA (Allele Frequency Aggregator) and were scored by Combined Annotation Dependent Depletion for deleteriousness. Gene networks carrying susceptibility SNVs were created. Myosin 5b immunofluorescence was also studied. Results Fifty-six patients met inclusion criteria, and 32.1% identified as Hispanic. Monogenic disease was infrequent (8.9%). Significant enrichment of GOI susceptibility SNVs was observed, notably in MYO5B, especially in Hispanics. MEFV, TNFAIP3, SH3TC2, and NCF2 were also central participants in the GOI networks. Myosin 5b immunofluorescence in colonic mucosa was significantly reduced in those with MYO5B susceptibility SNVs compared with control subjects. Seven genes (ESRRA, HLA-DQ1, RETSAT, PABPC1, PARP4, CCDC102A, and SUSD2) were central participants in the non-GOI networks. Conclusions Our results support the polygenic nature of VEO-IBD, in which key participants, like MYO5B, were identified through network analytics. Rare variant load within susceptibility genes may be relevant not only for the genetic origins of inflammatory bowel disease, but also for the age of disease onset. Our findings could guide future work in precision medicine. Lay Summary We used a network tool to determine how multiple genes might play a combined role in the development of inflammatory bowel disease and identified key participants in this network, such as MYO5B. Graphical Abstract Graphical Abstract