Immune-response 3′UTR alternative polyadenylation quantitative trait loci contribute to variation in human complex traits and diseases

Lei Li (), Xuelian Ma, Ya Cui, Maxime Rotival, Wenyan Chen, Xudong Zou, Ruofan Ding, Yangmei Qin, Qixuan Wang, Lluis Quintana-Murci and Wei Li ()
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Lei Li: Institute of Systems and Physical Biology, Shenzhen Bay Laboratory
Xuelian Ma: Institute of Systems and Physical Biology, Shenzhen Bay Laboratory
Ya Cui: University of California
Maxime Rotival: Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit
Wenyan Chen: Institute of Systems and Physical Biology, Shenzhen Bay Laboratory
Xudong Zou: Institute of Systems and Physical Biology, Shenzhen Bay Laboratory
Ruofan Ding: Institute of Systems and Physical Biology, Shenzhen Bay Laboratory
Yangmei Qin: Institute of Systems and Physical Biology, Shenzhen Bay Laboratory
Qixuan Wang: Institute of Systems and Physical Biology, Shenzhen Bay Laboratory
Lluis Quintana-Murci: Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit
Wei Li: University of California

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: Abstract Genome-wide association studies (GWASs) have identified thousands of non-coding variants that are associated with human complex traits and diseases. The analysis of such GWAS variants in different contexts and physiological states is essential for deciphering the regulatory mechanisms underlying human disease. Alternative polyadenylation (APA) is a key post-transcriptional modification for most human genes that substantially impacts upon cell behavior. Here, we mapped 9,493 3′-untranslated region APA quantitative trait loci in 18 human immune baseline cell types and 8 stimulation conditions (immune 3′aQTLs). Through the comparison between baseline and stimulation data, we observed the high responsiveness of 3′aQTLs to immune stimulation (response 3′aQTLs). Co-localization and mendelian randomization analyses of immune 3′aQTLs identified 678 genes where 3′aQTL are associated with variation in complex traits, 27.3% of which were derived from response 3′aQTLs. Overall, these analyses reveal the role of immune 3′aQTLs in the determination of complex traits, providing new insights into the regulatory mechanisms underlying disease etiologies.

Date: 2023
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DOI: 10.1038/s41467-023-44191-1

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