Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia.

William K Scott ,Erik Sørensen ,Batu K Sharma-Kuinkel ,Henning Bundgaard ,Henrik Ullum ,Flemming Schønning Rosenvinge ,Felicia Ruffin ,Peter Søgaard ,Christian Lerche ,Louise Bruun Østergaard ,Felix Mba Medie ,Shengru Guo ,Mahtab Chehri ,Derek M Dykxhoorn ,Anders Rhod Larsen ,Christian Torp‐Pedersen ,Andreas Petersen ,Henrik Carl Schønheyder ,Anders Dahl ,Paal Skytt Andersen ,Christian Hassager ,Derek D Cyr ,Helle Krogh Johansen ,Niels Eske Bruun ,Trine K Lauridsen ,Lise Tornvig Erikstrup ,Robert Skov ,Magnus Arpi ,Vance G Fowler

doi:10.1371/journal.pgen.1007667

Abstract

The role of host genetic variation in the development of complicated Staphylococcus aureus bacteremia (SAB) is poorly understood. We used whole exome sequencing (WES) to examine the cumulative effect of coding variants in each gene on risk of complicated SAB in a discovery sample of 168 SAB cases (84 complicated and 84 uncomplicated, frequency matched by age, sex, and bacterial clonal complex [CC]), and then evaluated the most significantly associated genes in a replication sample of 240 SAB cases (122 complicated and 118 uncomplicated, frequency matched for age, sex, and CC) using targeted sequence capture. In the discovery sample, gene-based analysis using the SKAT-O program identified 334 genes associated with complicated SAB at p<3.5 x 10−3. These, along with eight biologically relevant candidate genes were examined in the replication sample. Gene-based analysis of the 342 genes in the replication sample using SKAT-O identified one gene, GLS2, significantly associated with complicated SAB (p = 1.2 x 10−4) after Bonferroni correction. In Firth-bias corrected logistic regression analysis of individual variants, the strongest association across all 10,931 variants in the replication sample was with rs2657878 in GLS2 (p = 5 x 10−4). This variant is strongly correlated with a missense variant (rs2657879, p = 4.4 x 10−3) in which the minor allele (associated here with complicated SAB) has been previously associated with lower plasma concentration of glutamine. In a microarray-based gene-expression analysis, individuals with SAB exhibited significantly lower expression levels of GLS2 than healthy controls. Similarly, Gls2 expression is lower in response to S. aureus exposure in mouse RAW 264.7 macrophage cells. Compared to wild-type cells, RAW 264.7 cells with Gls2 silenced by CRISPR-Cas9 genome editing have decreased IL1-β transcription and increased nitric oxide production after S. aureus exposure. GLS2 is an interesting candidate gene for complicated SAB due to its role in regulating glutamine metabolism, a key factor in leukocyte activation.

Highlights

Staphylococcus aureus is a significant human pathogen and leading cause of skin and soft tissue infection (SSTI) and bacteremia (SAB) in community and healthcare settings
We used whole exome sequencing (WES) to examine the cumulative effect of coding variants in each gene on risk of complicated Staphylococcus aureus bacteremia (SAB) in a discovery sample of 168 SAB cases (84 complicated and 84 uncomplicated, frequency matched by age, sex, and bacterial clonal complex [CC]), and evaluated the most significantly associated genes in a replication sample of 240 SAB cases (122 complicated and 118 uncomplicated, frequency matched for age, sex, and CC) using targeted sequence capture
We examined the parts of the human genome that code for proteins to find variations that were more common in people with complicated S. aureus bacteremia (SAB), and identified one gene, called GLS2, in which variation is more common in complicated SAB cases than uncomplicated cases

Summary

Introduction

Staphylococcus aureus is a significant human pathogen and leading cause of skin and soft tissue infection (SSTI) and bacteremia (SAB) in community and healthcare settings. The etiology of SAB is complex, involving host susceptibility, microbial virulence, and healthcare-associated factors [1]. Efforts to identify common host genetic factors underlying SAB initially examined biologically plausible candidate genes involved in the innate immune response in animal models and human samples (reviewed by [2]). Several genes have been implicated in mouse models of infection [3,4,5], but variation in these genes has not yet been associated with SAB in humans. Genome-wide screens of S. aureus infections in individuals of European ancestry [6] and SAB in individuals of African-American ancestry [7] have reproducibly associated S. aureus infections with common genetic variants in the class II region of the major histocompatibility complex (MHC)

Methods

Results

Discussion

Conclusion