Project description:Diversity in the human genome is one factor that confers resistance and susceptibility to infectious diseases. This is observed most dramatically during pandemics, where individuals exhibit large differences in risk and clinical outcomes against a pathogen infecting large portions of the world’s populations. Here, we developed scHi-HOST (single cell High-throughput Human in vitrO Susceptibility Testing), a method for rapidly identifying genetic variants that confer resistance and susceptibility to pathogens. scHi-HOST leverages scRNA-seq (single-cell RNA-sequencing) to simultaneously assign genetic identity to individual cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral entry and replication, and identify expression quantitative trait loci (eQTLs). Applying scHi-HOST to influenza A virus (IAV), we identified eQTLs at baseline and in genes that are induced by IAV infection. Integration of scHi-HOST with a human IAV challenge study (Prometheus) revealed that a missense variant in ERAP1 (Endoplasmic reticulum aminopeptidase 1; rs27895) was associated with IAV burden in cells and human volunteers. Functional studies using RNA interference, ERAP1 inhibitor, and overexpression of alternative alleles demonstrated that ERAP1 is exploited by IAV to promote infection. Specifically, the nonsynonymous substitution, which results in a glycine to aspartate substitution at ERAP1 residue 348, would disrupt the substrate binding pocket of ERAP1, likely resulting in a significantly altered preference for substrates, poorer catalytic efficiency, or both. Finally, rs27895 exhibits substantial population differentiation, with the higher frequency of the minor T allele in two African populations likely contributing to the greater permissivity of cells from these populations to IAV infection. scHi-HOST is an important resource for understanding susceptibility to influenza and is a broadly applicable method for decoding human genetics of infectious disease.

Project description:Background. A recent study identified a rare variant in the MRC2 gene in individuals with familial reentrant supraventricular tachycardia, a Wolff-Parkinson-White (WPW) ECG pattern, and structurally normal hearts. WPW syndrome is associated with atrial fibrillation (AF), and MRC2 was recently proposed as a protective gene for AF. Objective. We aimed to determine whether the E990G-heterozygous (het) loss-of-function variant in MRC2 increases AF susceptibility and aberrant atrial cardiofibroblast (ACF) function in mice. Methods. Programmed electrical stimulation (PES) was performed to determine AF susceptibility in E990G-het mice and wild-type (WT) controls. ACFs were isolated from these mice and cultured, and their migration, and collagen deposition were quantified. Finally, transcriptomic profiling by RNA sequencing and secretomic/proteomic profiling by mass spectrometry were performed on ACFs and whole atrial tissue. Results. E990G-het mice exhibited increased susceptibility to pacing-induced AF and had decreased atrioventricular effective refractory periods compared to WT controls. ACFs isolated from E990G-het mice deposited greater amounts of acid-soluble collagen in 2D cultures as quantified by Sirius red staining compared with WT controls. Transcriptomic, secretomic, and proteomic profiling of cultured ACFs and whole-atrial tissue suggest that some fibrotic regulators are differentially expressed or secreted, including decreased ACF expression of matrix metalloproteinase 13 (MMP-13), which degrades collagen types I, II, and III; decreased ACF expression, ACF secretion, and atrial tissue levels of matrix metalloproteinase 12 (MMP-12), which degrades collagen types I, III, IV, elastin, and fibronectin; and increased tissue levels of cellular communication network factor 2/connective tissue growth factor (CCN2/CTGF), a profibrotic regulator. Conclusions. MRC2 E990G-het mice exhibit increased AF susceptibility, altered collagen deposition by ACFs, and differentially regulated fibrotic genes and proteins. Together, these findings suggest that excessive collagen deposition and reduced MMP-mediated collagen removal generate a substrate for the development of AF in the presence of a loss-of-function variant in MRC2.

			Action	DRS
	SRR19609900.fastq.gz	Fastqsanger.gz
	SRR19609901.fastq.gz	Fastqsanger.gz
	SRR19609902.fastq.gz	Fastqsanger.gz
	SRR19609903.fastq.gz	Fastqsanger.gz
	SRR19609904_1.fastq.gz	Fastqsanger.gz

Dataset Information

Single-cell genome-wide association reveals a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets