How silence shapes the brain: synonymous variants alter codon usage and translation of Sonic Hedgehog in holoprosencephaly

KIM, ARTEM; LE DOUCE, JÉRÔME; DIAB, FARAH; FEROROVA, MONIKA; DUBOURG, CHRISTÈLE; ODENT, SYLVIE; DUPÉ, VALÉRIE; DAVID, VÉRONIQUE; L. DIAMBRA; WATRIN, ERWAN; DE TAYRAC, MARIE

Conferencia; 54th European Society of Human Genetics Conference; 2021

European Society of Human Genetics

Despite their clinical relevance, synonymous Single Nucleotide Variants (sSNVs) are still largely ignored in clinical studies, unless directly associated with splicing defects. In particular, their impact on codon usage and protein translation remains unelucidated. In this work, we explore the clinical significance of sSNVs in the Sonic Hedgehog gene (SHH) identified in patients affected by holoprosencephaly - a developmental defect resulting from incomplete forebrain cleavage. Genetic screening was performed in 931 patients and revealed 8 different SHH sSNVs, selectively enriched in our cohort as compared to healthy individuals, suggesting their role in disease etiology. We systematically assessed their deleterious impact at both transcriptional and translational levels using a series of in silico and in vitro approaches. Although no evidence of impact of these sSNVs on splicing, mRNA structure or miRNA regulation was found, five sSNVs were predicted to impact protein translation by introducing significant changes in codon usage. Cell assays demonstrated that these five sSNVs result in a significantly reduced expression of the SHH protein (up to 23%, p