Trio Exome Sequencing Implicates Wnt Signaling in the Pathogenesis of Bladder-Exstrophy-Epispadias Complex

Background: Bladder-exstrophy-epispadias complex (BEEC) describes a spectrum of lower abdominal and genitourinary midline malformations, including epispadias, bladder exstrophy, and cloacal exstrophy. Although the cause of BEEC is uncertain, increased concordance rates among monozygotic (62%) vs. dizygotic twins (11%) and previously identified BEEC candidate genes suggest a hereditary component. This study aims to uncover novel genetic causes of BEEC through exome analysis. Methods: We performed exome sequencing for 38 BEEC case-parent trios and 57 singlet probands who received care at a single institution between 09/2022 and 04/2024. For analysis, we employed a candidate gene approach utilizing a list of 130 genes curated from previously published BEEC genomic studies and mouse models. Unbiased exome analysis was also conducted to identify novel BEEC candidate genes. Results: We identified a de novo pathogenic variant in PORCN (c.1186C>T; p.Arg396*) in one proband with bladder exstrophy and focal dermal hypoplasia (FDH). PORCN is required for Wnt protein secretion, and variants have previously been described in patients with both bladder exstrophy and FDH. In addition, we detected 2 potentially deleterious heterozygous variants in Wnt pathway genes among 2 singlet probands: WNT5A (c.1033G>C; p.Asp345His) and WNT8B (c.185G>A; p.Arg62His). Both variants have deleterious in silico prediction scores and show a strong conservation. Interestingly, WNT5A knockout mice display severe defects in urethral tube formation. Through unbiased trio analysis, we also identified 2 novel candidate genes in 2 probands: TAF5L (c.1328C>T, p.Thr443Met) and EVX1 (c.832C>A, p.Pro278Thr). Both variants arose de novo, have deleterious in silico prediction scores, are strongly conserved, and are absent from large population databases. EVX1 is a transcription factor involved in cloacal membrane development and acts downstream of WNT3A. Conclusion: Through exome analysis, we identified a pathogenic PORCN variant in one proband with bladder exstrophy and FDH, along with 3 potentially deleterious variants in Wnt pathway genes among 3 probands with BEEC. This further supports a role of Wnt signaling in disease pathogenesis. Funding: NIDDK Support