Biology subjects

Usa, K.

Publications and source records attributed to Usa, K..

3 recordsLinked to original sources

bioRxiv2024

A single-cell map of hypertension

Hypertension is a leading risk factor for disease burden and death worldwide. Several organ systems are involved in the development of hypertension, which contributes to stroke, heart disease, and kidney disease. Despite the broad health relevance, our understanding of the molecular landscape in hypertension is limited and lags other major diseases. Here we report an extensive analysis of the molecular landscape in hypertension and its end-organ damage and uncover novel mechanisms linking human genetic variants to the development of these diseases. We obtained single-nucleus RNA-seq (612,984 nuclei), single-nucleus ATAC-seq (179,637 nuclei), or spatial transcriptome data from five organs (hypothalamus, kidney, heart, 3rd order mesenteric artery, middle cerebral artery) in three mouse and rat models under twelve experimental conditions. More than one third of all hypertension research in animal models involves these three models. We identified both model-specific and convergent responses in cell types, genes, and pathways. By integrating our data with human genomic data, we partitioned the blood pressure and end-organ damage traits into cell type-specific transcriptional contributions and cell types common across multiple traits. Using genomic editing in animal models and human induced pluripotent stem cells, we extended key findings and identified new mechanisms linking human genetic variants to the development of hypertension and related renal injury. We anticipate that our rich data sets and findings will broadly drive forward the research of hypertension and hypertensive end-organ damage. Our approach of integrating multi-model and multi-tissue single-cell analysis with human genetic data and in vivo and in vitro genome editing can be applied to investigate other complex traits.

physiology↗

bioRxiv2024

Chromatin interaction maps of human arterioles reveal new mechanisms for the genetic regulation of blood pressure

Arterioles are small blood vessels located just upstream of capillaries in nearly all tissues. The constriction and dilation of arterioles regulate tissue perfusion and are primary determinants of systemic blood pressure (BP). Abnormalities in arterioles are central to the development of major diseases such as hypertension, stroke, and microvascular complications of diabetes. Despite the broad and essential role of arterioles in physiology and disease, current knowledge of the functional genomics of arterioles is largely absent, partly because it is challenging to obtain and analyze human arteriole samples. Here, we report extensive maps of chromatin interactions, single-cell expression, and other molecular features in human arterioles and uncover new mechanisms linking human genetic variants to gene expression in vascular cells and the development of hypertension. Compared to large arteries, arterioles exhibited a higher proportion of pericytes which were strongly associated with BP traits. BP-associated single nucleotide polymorphisms (SNPs) were enriched in chromatin interaction regions in arterioles, particularly through enhancer SNP-promoter interactions, which were further linked to gene expression specificity across tissue components and cell types. Using genomic editing in animal models and human induced pluripotent stem cells, we discovered novel mechanisms linking BP-associated noncoding SNP rs1882961 to gene expression through long-range chromatin contacts and revealed remarkable effects of a 4-bp noncoding genomic segment on hypertension in vivo. We anticipate that our rich data and findings will advance the study of the numerous diseases involving arterioles. Moreover, our approach of integrating chromatin interaction mapping in trait-relevant tissues with SNP analysis and in vivo and in vitro genome editing can be applied broadly to bridge the critical gap between genetic discoveries and physiological understanding.

genomics↗

bioRxiv2024

Physiological role and mechanisms of action for a long noncoding haplotype region

Most common sequence variants associated with human traits are in noncoding regions of the genome, form haplotypes with other noncoding variants, and exhibit small effect sizes in the general population. Determining the physiological roles and mechanisms of action for these noncoding variants, particularly large haplotypes containing multiple variants, is both critical and challenging. To address this challenge, we developed an approach that integrates physiological studies in genetically engineered and phenotypically permissive animal models, precise editing of large haplotypes in human induced pluripotent stem cells (hiPSCs), and targeted chromatin conformation analysis. We applied this approach to examine the blood pressure associated rs1173771 locus, which includes a haplotype containing 11 single nucleotide polymorphisms (SNPs) spanning 17.4 kbp. Deleting the orthologous noncoding region in the genome of the Dahl salt-sensitive rat attenuated the salt-induced increase in systolic blood pressure by nearly 10 mmHg. This attenuation of hypertension appeared to be mediated by upregulation of the adjacent gene Npr3 (natriuretic peptide receptor 3) in arteries, enhancing vasodilation. The blood pressure-elevating and -lowering haplotypes were precisely reconstituted in hiPSCs using an efficient, two-step genome editing technique. The blood pressure-elevating haplotype decreased NPR3 expression in endothelial cells and vascular smooth muscle cells derived from the edited, isogenic hiPSCs. The influence of the haplotype was partially recapitulated by the sentinel SNP rs1173771. Additionally, the blood pressure-elevating haplotype showed significantly greater chromatin interactions with the NPR3 promoter region. This study illustrates the feasibility of ascertaining the physiological roles and mechanisms of action for large noncoding haplotypes. Our efficient, integrated, and targeted approach can be applied to investigate other noncoding variants.

genetics↗