Project description:Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in coronary artery disease (CAD). However, non-European populations are underrepresented in GWAS and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotype information to identify quantitative trait loci (QTL) for gene expression and splicing in coronary arteries obtained from 138 ancestrally diverse Americans.

2023-11-14 | GSE225650 | GEO

Multimodal single cell analyses reveal mechanisms of perianal fistula in diverse Crohn’s disease [scRNA-seq]

Project description:Crohn’s disease (CD) is a chronic inflammatory condition that can affect any part of the gastrointestinal tract. African ancestry (AA) populations have been substantially under-represented in genome-wide association studies (GWAS) of CD and inflammatory bowel disease (IBD), reflecting in part the lower prevalence of CD in AA compared to European ancestry (EA) populations. Importantly, CD complicated by perianal fistulae has been found to be more prevalent and severe in African-ancestry patients. Perianal fistulae arise from the distal rectal mucosa and can course to a cutaneous surface, resulting in highly morbid complications. Monoclonal antibodies against anti-TNF are the mainstay of treatment, but recurrence and secondary loss-of-response is common. In severe, uncontrolled cases, complete proctectomy is required. The intestine is unique among adult tissues in that under homeostasis, residential macrophages are continually replenished from recruited blood monocytes. In EA cohorts, we established that chronic monocyte cultures stimulated with NOD2 agonists result in aberrant myeloid-stromal differentiation stratified by risk allele carrier status. NOD2 risk alleles are not associated with perianal fistulae; African-American patients with CD do not carry them (except via recent European ancestry admixture). There is no direct association between known CD GWAS risk loci and the risk of developing perianal fistula. Here, we present direct ex-vivo, single cell multiomic analyses of colorectal tissues and perianal fistulous tracts in AA and EA cases to define mechanisms of perianal fistula development. We implicate myeloid-stromal crosstalk and define cell subtypes using single cell RNA (scRNASeq), ATAC sequencing, and chronic, unstimulated monocyte cultures. Transcription factor motifs and ATAC signals co-localized with fine-mapped GWAS loci provide insight to cell-specific and transcriptional network regulation.

2024-05-16 | GSE260842 | GEO

Multimodal single cell analyses reveal mechanisms of perianal fistula in diverse Crohn’s disease [Multiome]

2024-05-16 | GSE260833 | GEO

Crystal structure of Homo sapiens kynureninase.

Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.

| S-EPMC2531291 | biostudies-literature

Homo sapiens whole blood.

Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.

2019-07-31 | GSE114179 | GEO