Biology subjects

Hiron, T. K.

Publications and source records attributed to Hiron, T. K..

4 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↗

bioRxiv2025

Fatal consequences of feline coronavirus infection are associated with virus persistence and a distinct adaptive immune repertoire

The pathogenesis of feline infectious peritonitis (FIP), arising in a minority of cats infected with feline coronavirus (FCoV), is complex and incompletely understood. Without extended use of direct-acting antivirals FIP is invariably fatal, but there is potential for the emergence of anti-viral resistance. To understand host and viral factors associated with FIP, multiple tissues from cats with and without FIP were subjected to RNA sequencing (RNA-seq), and targeted sequencing of the T cell receptor (TCR) repertoire was conducted for mesenteric lymph nodes in a larger cohort. Samples from cats with FIP demonstrated higher expression of genes involved in type I interferon and proinflammatory cytokine signalling, as well as the adaptive immune response, and expression of these genes was highly correlated with FCoV abundance. Analysis of FCoV genomic variation across tissues revealed dynamic within-host evolution of FCoV, and identified distinct mutations associated with systemic virus spread both within and among cats. Assembly of TCR and B-cell receptor (BCR) sequences identified changes in the immune repertoire associated with FIP, highlighting the polyclonality and ineffectiveness of the immune response to FCoV in cats with FIP, and revealing the presence of potentially protective TCR clonotypes in cats without FIP. Together, these results represent the first analysis of immune repertoire in any feline infectious disease and demonstrate naturally occurring within-host evolution of FCoV. These novel insights into a life-threatening systemic coronaviral disease have the potential to transform therapeutic approaches in FIP.

immunology↗

bioRxiv2025

Hypercholesterolaemia promotes epigenetic memory in hematopoietic stem cells that persists after lipid lowering and causes systemic immunometabolic dysfunction mediated by macrophage metabolic reprogramming

In patients with atherosclerotic cardiovascular disease (ASCVD) lowering LDL cholesterol (LDL-C) reduces the risk of adverse cardiovascular events. However, these patients remain at continued risk of adverse cardiovascular events despite achieving optimal LDL-C lowering. We hypothesised that this residual risk is mediated by epigenetic programming of haematopoietic stem cells (HSC) which persists after cholesterol levels are lowered and results in sustained effects on innate immune cell metabolism, that is not resolved by cholesterol lowering. We found that exposure to high cholesterol (HC) in vivo induced long-term metabolic changes in macrophages differentiated ex vivo from bone marrow, leading to a pro-inflammatory profile; these changes persisted in vivo despite cholesterol lowering. HSC from HC mice had altered chromatin accessibility that persisted after cholesterol lowering and was also present in bone marrow monocytes and tissue resident macrophages. HC provoked RUNX1-dependent downregulation of stearoyl-CoA desaturase (SCD) which reduced mono-unsaturated fatty acid (MUFA) availability for OxPhos in murine and human monocytes and macrophages. Supplementation with MUFA restored OxPhos capacity and promoted a shift towards a less pro-inflammatory macrophage phenotype in HC-trained BMDM. Bone marrow chimera and lineage tracking studies revealed that prior exposure of HSC to HC conferred adverse systemic metabolic effects on normocholesterolemic mice, with increased adipose tissue mass and increased migration of macrophages derived from HC-exposed HSC into adipose tissue, resulting in increased adipose tissue inflammation and systemic glucose intolerance. These findings indicate that HC results in long-lasting immuno-epigenetic memory in HSC which is refractory to lipid lowering, and provide strong evidence that exposure to HC can have prolonged consequences that require new therapeutic approaches, beyond cholesterol lowering.

immunology↗

bioRxiv2023

Partitioning heritability using single-cell multi-omics identifies a novel macrophage subpopulation conveying genetic risks of coronary artery disease.

BackgroundCoronary artery disease (CAD), the leading cause of death worldwide, is influenced by both environmental and genetic factors. While over 250 genetic risk loci have been identified through genome-wide association studies, the specific causal variants and their regulatory mechanisms are still largely unknown, particularly in disease-relevant cell types like macrophages. MethodsWe utilized single-cell RNA-seq (scRNA-seq) and single-cell multi-omics approaches in primary human monocyte-derived macrophages to explore the transcriptional regulatory network involved in a critical pathogenic event of coronary atherosclerosis--the formation of lipid-laden foam cells. Meta-analysis of scRNA-seq datasets from 26 human plaque samples was undertaken to provide a comprehensive atlas of lesional macrophages and to correlate subpopulations in vivo and ex vivo. The genetic risk levels of CAD were assessed by partitioning disease heritability across different macrophage subpopulations. ResultsWe identified a novel macrophage subpopulation, termed lipid-handling macrophages, both ex vivo and in vivo, and identified associated marker genes, transcription regulators, and functional pathways. 18,782 cis-regulatory elements were identified by jointly profiling the gene expression and chromatin accessibility of >5000 macrophages. Integration with CAD GWAS data prioritized 121 CAD-related genetic variants and 56 candidate causal genes. We showed that CAD heritability was not uniformly distributed and was particularly enriched in the gene programs of lipid-handling macrophages. We investigated the cis-regulatory effect of a risk variant rs10488763 on FDX1, implicating the recruitment of AP-1 and C/EBP-beta in the causal mechanisms at this locus. ConclusionsOur results provide genetic evidence of the divergent roles of macrophage subsets in atherogenesis and highlight lipid-handling macrophages as a key sub-population through which genetic variants actively influence disease. These findings provide an unbiased framework for functional fine-mapping of GWAS results using single-cell multi-omics and offer new insights into the genotype-environment interactions underlying atherosclerotic disease.

genetics↗