Biology subjects

Martin-Geary, A. C.

Publications and source records attributed to Martin-Geary, A. C..

3 recordsLinked to original sources

bioRxiv2025

Modulating splicing in five prime untranslated regions to treat rare haploinsufficient disease

Rare genetic disorders collectively impact over 300 million people worldwide, yet around 95% have no specific treatments. For the many rare disorders caused by haploinsufficiency, effective therapies need to upregulate protein expression. However, therapeutic upregulation is often not straightforward. Increasing protein translation of the wildtype allele through inhibiting repressive upstream open reading frames (uORFs) has been proposed as a therapeutic approach for a few specific genes. The widespread success of steric-block antisense oligonucleotides (ASOs) for this purpose is, however, debated. Here, we explore an alternative approach, using splice-switching to exclude uORF-containing exons from the mRNA. Through a genome-wide computational screening approach, we identified 79 uORF-containing 5UTR exons in haploinsufficient monogenic disease genes as candidate exon skipping targets. We demonstrate that removing the target exon significantly increased protein translation (between 1.4-5.5 fold) in a luciferase reporter assay for four of six prioritised target 5UTR exons in neurodevelopmental disorder genes (CTCF, GRIN2B, KRIT1, and TSC1). Overall, this work supports the widespread application of 5UTR exon skipping to boost translation of clinically relevant haploinsufficient genes.

genomics↗

bioRxiv2025

Aberrant splicing prediction during human organ development

Developmental disorders constitute a major class of genetic diseases, yet tools to identify splicing-disruptive variants during development are lacking. To address this need we extended the AbSplice framework to incorporate splicing dynamics across developmental stages. Moreover, we introduced several improvements including a refined ground truth from the aberrant splicing caller FRASER2, a continuous representation of splice site usage, and integration of the rich set of predictions from the sequence-based model Pangolin. These advances improve the performance of the original model at predicting aberrant splicing events and enable predictions across embryonic, childhood, and adult tissues. Genome-wide scores for all single-nucleotide variants and a web interface to score indels are available to facilitate the exploration of the predictions. Our genome-wide predictions reveal a class of variants with splicing-disruptive effects confined to early development, particularly abundant in the brain (>18,000 variants). These variants are enriched in loss-of-function intolerant genes and neurodevelopmental disorder genes. Within the rare-disease cohort Solve-RD high-impact brain-specific predictions are significantly enriched in individuals affected by neurodevelopmental disorders (NDD) in NDD-linked genes. Furthermore, the predicted developmental timing of the splicing disruption correlates with the clinical age of onset. Analysis of genomes of individuals with a suspected Mendelian disorder from Genomics England identified 26 unique variants in disease-linked genes, with stronger predicted effects during development than in adulthood, including a candidate new diagnosis in the gene FGFR1. Altogether, these results improve the accuracy of splice-disruptive variant prediction and provide tissue and developmental context to aid interpretation in rare disease diagnostics.

genomics↗

bioRxiv2023

Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes

BackgroundUntranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composition of regulatory elements within them are known to vary substantially across genes, but little is known about the reasons for this variation in humans. Here, we set out to determine whether this variation, specifically in 5UTRs, correlates with gene dosage sensitivity. ResultsWe investigated 5UTR length, the number of alternative transcription start sites, the potential for alternative splicing, the number and type of upstream open reading frames (uORFs) and the propensity of 5UTRs to form secondary structures. We explored how these elements vary by gene tolerance to loss-of-function (LoF; using the LOEUF metric), and in genes where changes in dosage are known to cause disease. We show that LOEUF correlates with 5UTR length and complexity. Genes that are most intolerant to LoF have longer 5UTRs (P<1x10-15), greater TSS diversity (P<1x 10-15), and more upstream regulatory elements than their LoF tolerant counterparts. We show that these differences are evident in disease gene-sets, but not in recessive developmental disorder genes where LoF of a single allele is tolerated. ConclusionsOur results confirm the importance of post-transcriptional regulation through 5UTRs in tight regulation of mRNA and protein levels, particularly for genes where changes in dosage are deleterious and lead to disease. Finally, to support gene-based investigation we release a web-based browser tool, VuTR (https://vutr.rarediseasegenomics.org/), that supports exploration of the composition of individual 5UTRs and the impact of genetic variation within them.

genomics↗