Regulatory Noncoding and Predicted Pathogenic Coding Variants of CCR5 Predispose to Severe COVID-19

Genome-wide association studies (GWAS) found locus 3p21.31 associated with severe COVID-19. CCR5 resides at the same locus and, given its known biological role in other infection diseases, we investigated if common noncoding and rare coding variants, affecting CCR5</i&...

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Bibliographic Details
Main Authors:	Sueva Cantalupo, Vito Alessandro Lasorsa, Roberta Russo, Immacolata Andolfo, Giuseppe D’Alterio, Barbara Eleni Rosato, Giulia Frisso, Pasquale Abete, Gian Marco Cassese, Giuseppe Servillo, Ivan Gentile, Carmelo Piscopo, Matteo Della Monica, Giuseppe Fiorentino, Giuseppe Russo, Pellegrino Cerino, Carlo Buonerba, Biancamaria Pierri, Massimo Zollo, Achille Iolascon, Mario Capasso
Format:	Article
Language:	English
Published:	MDPI AG 2021-05-01
Series:	International Journal of Molecular Sciences
Subjects:	<i>CCR5</i> COVID-19 SARS-CoV-2 SNP whole exome sequencing GWAS
Online Access:	https://www.mdpi.com/1422-0067/22/10/5372

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Summary:	Genome-wide association studies (GWAS) found locus 3p21.31 associated with severe COVID-19. <i>CCR5</i> resides at the same locus and, given its known biological role in other infection diseases, we investigated if common noncoding and rare coding variants, affecting <i>CCR5</i>, can predispose to severe COVID-19. We combined single nucleotide polymorphisms (SNPs) that met the suggestive significance level (<i>P</i> ≤ 1 × 10<sup>−5</sup>) at the 3p21.31 locus in public GWAS datasets (6406 COVID-19 hospitalized patients and 902,088 controls) with gene expression data from 208 lung tissues, Hi-C, and Chip-seq data. Through whole exome sequencing (WES), we explored rare coding variants in 147 severe COVID-19 patients. We identified three SNPs (rs9845542, rs12639314, and rs35951367) associated with severe COVID-19 whose risk alleles correlated with low <i>CCR5</i> expression in lung tissues. The rs35951367 resided in a CTFC binding site that interacts with <i>CCR5</i> gene in lung tissues and was confirmed to be associated with severe COVID-19 in two independent datasets. We also identified a rare coding variant (rs34418657) associated with the risk of developing severe COVID-19. Our results suggest a biological role of <i>CCR5</i> in the progression of COVID-19 as common and rare genetic variants can increase the risk of developing severe COVID-19 by affecting the functions of <i>CCR5</i>.
ISSN:	1661-6596 1422-0067

Regulatory Noncoding and Predicted Pathogenic Coding Variants of <i>CCR5</i> Predispose to Severe COVID-19

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