Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells.

Document Type

Article

Publication Date

5-1-2022

Publication Title

Nature genetics

Keywords

JMG

JAX Source

Nat Genet 2022 May; 54(5):603-612

Volume

54

Issue

5

First Page

603

Last Page

612

ISSN

1546-1718

PMID

35513721

DOI

https://doi.org/10.1038/s41588-022-01056-5

Abstract

Genome-wide association studies (GWASs) have uncovered hundreds of autoimmune disease-associated loci; however, the causal genetic variants within each locus are mostly unknown. Here, we perform high-throughput allele-specific reporter assays to prioritize disease-associated variants for five autoimmune diseases. By examining variants that both promote allele-specific reporter expression and are located in accessible chromatin, we identify 60 putatively causal variants that enrich for statistically fine-mapped variants by up to 57.8-fold. We introduced the risk allele of a prioritized variant (rs72928038) into a human T cell line and deleted the orthologous sequence in mice, both resulting in reduced BACH2 expression. Naive CD8 T cells from mice containing the deletion had reduced expression of genes that suppress activation and maintain stemness and, upon acute viral infection, displayed greater propensity to become effector T cells. Our results represent an example of an effective approach for prioritizing variants and studying their physiologically relevant effects.

Comments

We gratefully acknowledge the contribution of R. Maser and Genetic Engineering Technologies Service, J. Kelmenson and Transgenic Genotyping Service, W. Schott and Flow Cytometry Service and R. Lynch and Genome Technologies Service at The Jackson Laboratory.

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