Project description:Genomic sequence variation within enhancers and promoters can have a significant impact on the cellular state and phenotype. However, sifting through the millions of candidate variants in a personal genome or cancer genome, to identify only those variants that impact enhancer function, remains a major challenge. Prioritization of non-coding genome variation benefits from explainable AI to predict and interpret the impact of a mutation on gene regulation. Here we apply a specialized deep learning model to 10 phased melanoma genomes and identify functional enhancer mutations with allelic imbalance of chromatin accessibility and gene expression.
Project description:Analysis of the transcriptional changes in the heart resulting from the loss of cardiac enhancers. As there remains a limited understanding of the phenotypic consequences of enhancer mutations, we examined the impact of loss of function mutations by deleting two enhancers near heart disease genes in mice. In both cases, we observed loss of target gene expression, as well as cardiac phenotypes consistent with heart disease in humans, highlighting the functional importance of enhancers for normal heart function, as well as the potential contribution of enhancer mutations to heart disease. Hearts were dissected from wild-type and enhancer-null mice (either embryonic or adult) and processed for deep RNA-seq analysis.
Project description:The Ras-related Rap1A GTPase is implicated in pancreas β-cell insulin secretion, and is stimulated by the cAMP sensor Epac2, a guanine exchange factor and activator of Rap1 GTPase. In this study we examined the differential proteomic profiles by nanoLC-ESI-MS/MS of pancreata from C57BL/6 Rap1A-deficient (Null) and control wild-type (WT) mice, to assess targets of Rap1A potentially involved in insulin regulation. We identified 77 overlapping identifier proteins in both groups, 8 distinct identifier proteins in Null versus 56 distinct identifier proteins in WT mice pancreas. Functional enrichment analysis showed 4 of the 8 Null unique proteins, ERO1-like protein β (Ero1lβ), triosephosphate isomerase (TP1), 14-3-3 protein γ and kallikrein-1, were exclusively involved in insulin biogenesis, with role in insulin metabolism. Specifically, the mRNA expression of Ero1lβ and TP1 was significantly (p<0.05) increased in Null versus WT pancreas. Rap1A-deficiency significantly affected glucose tolerance during the first 15-30 min of glucose challenge, but showed no impact on insulin sensitivity. Ex vivo glucose-stimulated insulin secretion (GSIS) studies on isolated Null islets showed significantly impaired GSIS. Furthermore, in GSIS-impaired islets, the cAMP-Epac2-Rap1A pathway was significantly compromised as compared to WT. Altogether, these studies underscore an essential role of Rap1A GTPase in pancreas physiological function