Biology subjects

Atla, G.

Publications and source records attributed to Atla, G..

7 recordsLinked to original sources

bioRxiv2026

CAD variants act through ox-LDL-induced enhancer remodelling to alter VSMC gene programmes

BackgroundVascular smooth muscle cells (VSMCs) play a central role in atherosclerotic coronary artery disease (CAD). Oxidised low-density lipoprotein cholesterol (ox-LDL) induces VSMCs dysfunction but the underlying molecular mechanisms are unclear. CAD genome-wide association studies (GWAS) have identified hundreds of disease-associated loci but their biological roles remain poorly defined. We hypothesised that ox-LDL drives pro-atherogenic changes in VSMCs by altering gene regulatory programs involving causal CAD variants. MethodsEx-vivo human coronary VSMCs were exposed to ox-LDL and profiled using RNA-seq, ATAC-seq, and H3K27ac ChIPmentation. Enhancer-gene links were inferred by integrating these data with Hi-C using the Activity-by-Contact (ABC) model. Variant effect predictions were done using AlphaGenome and key target genes functionally tested by CRISPR/Cas9 knockout. ResultsOx-LDL induced widespread transcriptional reprogramming in coronary VSMCs, with 1,487 upregulated and 1,864 downregulated genes (FDR < 0.05). Single-cell RNA-seq meta-analysis demonstrated that ox-LDL-associated programmes enriched in pro-inflammatory and synthetic-inflammatory VSMC clusters in vivo. ATAC-seq identified [~]22k differentially accessible regions following ox-LDL exposure (FDR < 0.05). Integration of ATAC-seq, H3K27ac, and Hi-C using the ABC framework showed that ox-LDL-driven chromatin remodelling was concentrated at distal enhancers, which linked to 2,008 differentially expressed genes via 4,243 peak-gene connections. ABC enhancers were significantly enriched for CAD variants compared with non-vascular disease controls, with stronger enrichment in dynamically accessible enhancers. AlphaGenome predicted larger regulatory effects of prioritised CAD variants in smooth muscle cells than in a non-vascular comparator, and motif analyses indicated allele-dependent transcription factor binding at prioritised enhancer variants. Locus-level prioritisation nominated candidate enhancer-mediated mechanisms at the SPECC1L and MAP1S loci, and CRISPR knockout of the target genes GUCD1 and BACH1 rescued ox-LDL-induced growth arrest/senescence phenotypes in human coronary artery VSMCs. ConclusionsOur unbiased multi-omics framework shows that ox-LDL rewires VSMC regulatory programmes that influence CAD genetic risk. Enhancer-gene mapping refines effector-gene assignment at CAD loci and prioritises regulatory targets in coronary VSMCs.

genomics↗

bioRxiv2022

Control of pancreatic islet function and glucose homeostasis by a novel microexon program misregulated in type 2 diabetes

Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and their abnormal function causes diabetes or hypoglycemia. Here, we uncover a conserved program of alternative microexons included in mRNAs of islet cells, particularly in genes involved in vesicle transport and exocytosis. Islet microexons (IsletMICs) are regulated by the RNA binding protein SRRM3 and represent a subset of the larger neural program that are particularly sensitive to the levels of this regulator. Both SRRM3 and IsletMICs are induced by elevated glucose levels, and depletion of SRRM3 in beta cell lines and mouse islets, or repression of particular IsletMICs using antisense oligonucleotides, leads to inappropriate insulin secretion. Consistently, SRRM3 mutant mice display defects in islet cell identity and function, leading to hyperinsulinemic hypoglycemia. Importantly, human genetic variants that influence SRRM3 expression and IsletMIC inclusion in islets are associated with fasting glucose variation and type 2 diabetes risk.

molecular biology↗

bioRxiv2021

Genetic regulation of RNA splicing in human pancreatic islets

Genetic variants that influence transcriptional regulation in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D). For many susceptibility loci, however, the mechanisms are unknown. We examined splicing QTLs (sQTLs) in islets from 399 donors and observed that genetic variation has a widespread influence on splicing of genes with important functions in islet biology. In parallel, we profiled expression QTLs, and used transcriptome-wide association and co-localization studies to assign islet sQTLs or eQTLs to T2D susceptibility signals that lacked candidate effector genes. We found novel T2D associations, including an sQTL that creates a nonsense isoform in ERO1B, a regulator of ER-stress and proinsulin biosynthesis. The expanded list of T2D risk effectors revealed overrepresented pathways, including regulators of G-protein-mediated cAMP production. This data exposes an underappreciated layer of genetic regulation in pancreatic islets, and nominates molecular mediators of T2D susceptibility.

genetics↗

bioRxiv2021

TIGER: The gene expression regulatory variation landscape of human pancreatic islets

GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.

bioinformatics↗

bioRxiv2021

The transcriptional repressor REST is a major negative regulator of endocrine differentiation during pancreas organogenesis

Understanding genomic regulatory mechanisms of pancreas differentiation is relevant to the pathophysiology of diabetes mellitus, and to the development of replacement therapies. Numerous transcription factors promote {beta} cell differentiation, although less is known about negative regulators. Earlier epigenomic studies suggested that the transcriptional repressor REST could be a suppressor of endocrine gene programs in the embryonic pancreas. However, pancreatic Rest knock-out mice failed to show increased numbers of endocrine cells, suggesting that REST is not a major regulator of endocrine differentiation. Using a different conditional allele that enables profound REST inactivation, we now observe a marked increase in the formation of pancreatic endocrine cells. REST inhibition also promoted endocrinogenesis in zebrafish and mouse early postnatal ducts, and induced {beta}-cell specific genes in human adult duct-derived organoids. Finally, we define REST genomic programs that suppress pancreatic endocrine differentiation. These results establish a crucial role of REST as a negative regulator of pancreatic endocrine differentiation.

developmental biology↗

bioRxiv2019

De novo mutations in fetal brain specific enhancers play a significant role in severe intellectual disability

PurposeThe genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood.\n\nMethodsWe sequenced 70 whole genomes from 24 ID probands and their unaffected parents and analyzed 30 previously sequenced genomes from exome-negative ID probands.\n\nResultsWe found that DNVs were selectively enriched in fetal brain-specific enhancers that show purifying selection in human population. DNV containing enhancers were associated with genes that show preferential expression in the pre-frontal cortex, have been previously implicated in ID or related disorders, and exhibit intolerance to loss of function variants. DNVs from ID probands preferentially disrupted putative binding sites of neuronal transcription factors, as compared to DNVs from healthy individuals and most showed allele-specific enhancer activity. In addition, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1 and POU3F3). Moreover, CRISPR-based perturbation of a DNV-containing enhancer caused CSMD1 overexpression and abnormal expression of neurodevelopmental regulators.\n\nConclusionOur results, therefore, provide new evidence to indicate that DNVs in constrained fetal brain-specific enhancers play a role in the etiology of ID.

genomics↗

bioRxiv2018

Human pancreatic islet 3D chromatin architecture provides insights into the genetics of type 2 diabetes

Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer regions (enhancer clusters, stretch enhancers or super-enhancers). So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in 3D-space. Furthermore, their target genes are generally unknown. We have now created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers with their target genes, often located hundreds of kilobases away. It further revealed sets of islet enhancers, super-enhancers and active promoters that form 3D higher-order hubs, some of which show coordinated glucose-dependent activity. Hub genetic variants impact the heritability of insulin secretion, and help identify individuals in whom genetic variation of islet function is important for T2D. Human islet 3D chromatin architecture thus provides a framework for interpretation of T2D GWAS signals.

genomics↗