Biology subjects

Aberra, Y. T.

Publications and source records attributed to Aberra, Y. T..

3 recordsLinked to original sources

bioRxiv2025

Multimodal analysis identifies pericyte-centered signaling programs altered by sex and brain region in Alzheimer's Disease

Pericytes are critical components of the neurovascular unit (NVU), regulating endothelial cell (EC) stability, blood-brain barrier (BBB) integrity, and neuroimmune signaling. However, their role in Alzheimers Disease (AD), particularly in the context of sex differences and brain region specificity, remains poorly defined. Here, we use single-nucleus RNA sequencing (snRNA-seq) to characterize transcriptional and intercellular signaling changes in pericytes across the middle temporal gyrus (MTG) and dorsolateral prefrontal cortex (DLPFC) of the same AD and non-AD donors, stratified by sex. Using LIANA and Tensor-cell2cell, we identify latent communication programs altered in female AD donors, including a pericyte-EC signaling pattern that activates TGF{beta} via extracellular matrix ligands and is upregulated in the MTG but not the DLPFC. A second communication pattern, downregulated in female AD donors, reveals impaired estrogen pathway signaling through ligand-receptor interactions between pericytes and astrocytes. Supporting this, we observe reduced expression of pericyte-derived neuroligins and increased pericyte-astrocyte separation in a spatial transcriptomic subset. Additionally, we identify a microglia-to-pericyte signaling program conserved across brain regions, enriched for inflammatory pathways including hypoxia and p53, and elevated in both male and female AD donors with regional specificity. This result contrasts with the more sex-and region-specific pericyte signaling programs and suggests parallel mechanisms of NVU disruption between brain regions in AD. Our findings reveal brain region-specific and sex-specific pericyte signaling changes in AD and implicate vascular-, immune-, and synapse-associated pathways in NVU dysfunction. Altogether, the data suggest pericyte-driven communication as a mechanistic contributor to female-biased vulnerability in AD and support the need for sex-aware and region-specific approaches in neurodegeneration research.

bioinformatics↗

bioRxiv2022

Predicting mechanisms of action at genetic loci associated with discordant effects on type 2 diabetes and abdominal fat accumulation

Metabolic syndrome (MetSyn) is a cluster of dysregulated metabolic conditions that occur together to increase the risk for cardiometabolic disorders such as type 2 diabetes (T2D). One key condition associated with MetSyn, abdominal obesity, is measured by computing the ratio of waist-to-hip circumference adjusted for the body-mass index (WHRadjBMI). WHRadjBMI and T2D are complex traits with genetic and environmental components, which has enabled genome-wide association studies (GWAS) to identify hundreds of loci associated with both. Statistical genetics analyses of these GWAS have predicted that WHRadjBMI is a strong causal risk factor of T2D and that these traits share genetic architecture at many loci. To date, no variants have been described that are simultaneously associated with protection from T2D but with increased abdominal obesity. Here, we used colocalization analysis to identify genetic variants with a shared association for T2D and abdominal obesity. This analysis revealed the presence of five loci associated with discordant effects on T2D and abdominal obesity. The alleles of the lead genetic variants in these loci that were protective against T2D were also associated with increased abdominal obesity. We further used publicly available expression, epigenomic, and genetic regulatory data to predict the effector genes (eGenes) and functional tissues at the 2p21, 5q21.1, and 19q13.11 loci. We also computed the correlation between the subcutaneous adipose tissue (SAT) expression of predicted effector genes (eGenes) with metabolic phenotypes and adipogenesis. We proposed a model to resolve the discordant effects at the 5q21.1 locus. We find that eGenes gypsy retrotransposon integrase 1 (GIN1), diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2), and peptidylglycine alpha-amidating monooxygenase (PAM) represent the likely causal eGenes at the 5q21.1 locus. Taken together, these results are the first to describe a potential mechanism through which a genetic variant can confer increased abdominal obesity but protection from T2D risk. Understanding precisely how and which genetic variants confer increased risk for MetSyn will develop the basic science needed to design novel therapeutics for metabolic syndrome.

genomics↗

bioRxiv2022

Genetic regulation of human aortic smooth muscle cell gene expression and splicing predict causal coronary artery disease genes

Coronary artery disease (CAD) is the leading cause of death worldwide. Recent meta-analyses of genome-wide association studies (GWAS) have identified over 175 loci associated with CAD. The majority of these loci are in non-coding regions and are predicted to regulate gene expression. Given that vascular smooth muscle cells (SMCs) play critical roles in the development and progression of CAD, we hypothesized that a subset of the CAD GWAS risk loci are associated with the regulation of transcription in distinct SMC phenotypes. Here, we measured gene expression in SMCs isolated from the ascending aortas of 151 ethnically diverse heart transplant donors in quiescent or proliferative conditions and calculated the association of their expression and splicing with [~]6.3 million imputed single nucleotide polymorphism (SNP) markers across the genome. We identified 4,910 expression and 4,412 splice quantitative trait loci (sQTL) that represent regions of the genome associated with transcript abundance and splicing. 3,660 of the eQTLs had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 of the eQTLs were SMC- and sex-specific, respectively. To identify the effector transcript(s) regulated by CAD GWAS loci, we used four distinct colocalization approaches and identified 84 eQTL and 164 sQTLs that colocalized with CAD loci, highlighting the importance of genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. Notably, 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. Two CAD loci colocalized with a SMC sex-specific eQTL (AL160313.1 and TERF2IP) and another locus colocalized with SMC-specific eQTL (ALKBH8). Also, 27% and 37% of the sQTLs were unique to quiescent or proliferative SMCs, respectively. The most significantly associated CAD locus, 9p21, was an sQTL for the long non-coding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. Collectively, these results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in distinct SMC phenotypes.

genetics↗