Jade Fauqueux^a ∙ Jean-Pascal Meneboo^b ∙ Roseline Caumes^a,c ∙ Luc Thomès^a ∙ Emilie Ait Yahya^d ∙ Caroline Thuillier^e ∙ Elise Boudry^e ∙ Celine Villenet^b ∙ Martin Figeac^b ∙ Jamal Ghoumid^a,c ∙ Thomas Smol^a,e

Abstract

Structural variants (SVs) significantly contribute to human disease, but their complexity often makes accurate characterization difficult with conventional methods. Advances in long-read sequencing (LRS) offer potential by spanning kilobases and directly resolving SVs. In this study, we examined two individuals with unresolved SVs. LRS on both DNA and cDNA provided single-base resolution of all breakpoint junctions, revealing detailed rearrangement structures and underlying mechanisms. Transcriptomic analyses identified abnormal fusion transcripts and clarified their functional consequences, including haploinsufficiency and potential dominant-negative effects. In one case, a triplication affecting the ZMYM2 gene was precisely mapped, revealing a truncated variant that may escape nonsense-mediated decay. In the second case, a highly complex reciprocal translocation involving RERE and FHAD1 disrupted RERE expression, with Hi-C data showing minimal impact on enhancer-promoter interactions. Due to their complexity, these SVs were not fully resolved by standard methods. By integrating LRS with transcriptomic and chromosomal conformation analyses, we provided a comprehensive understanding of SV formation and its pathogenic impact. Our findings emphasize the need for advanced genomic approaches to resolve complex SVs, enhance diagnostic accuracy, and inform clinical management.

https://doi.org/10.1016/j.csbj.2025.04.031/

Jade Fauqueux  ¹ , Simon Boussion  ^{1   2} , Caroline Thuillier  ³ , Evine Meurisse  ¹ , Didier Lacombe  ^{4   5} , Marjolaine Willems  ^{6   7} , Amélie Piton  ^{8   9} , Emilie Ait-Yahya  ¹⁰ , Jamal Ghoumid  ^{1   2} , Thomas Smol  ^{11   3}

Abstract

Pathogenic variants in the MED13L gene are associated with the autosomal dominant MED13L syndrome, which is characterised by global developmental delay and cardiac malformations. We investigated two heterozygous MED13L variants located at the canonical donor splice site motif of exon 7: c.1009+1G>C and c.1009+5G>C. We report that in silico predictions suggested two possible outcomes: exon 7 skipping, resulting in loss of the phosphodegron motif essential for MED13L regulation, or activation of a cryptic donor site in intron 7, leading to intron retention. RNA analysis confirmed that both variants affected the exon 7 splice donor site, resulting in the retention of 73 bp of intron 7. This retention caused a frameshift and premature translation termination, consistent with haploinsufficiency. Our results highlight the importance of combining predictive and experimental approaches to understand the functional impact of splice site variants. These insights into the molecular consequences of MED13L variants provide a deeper understanding of the genetic basis of MED13L syndrome.

https://doi-org.ressources-electroniques.univ-lille.fr/10.1136/jmg-2024-110154