Discovery of Candidate Genes for Muscle Traits Based on GWAS Supported by eQTL-analysis
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
Authors: Ponsuksili, Siriluck; Murani, Eduard; Trakooljul, Nares; Schwerin, Manfred; Wimmers, Klaus
Abstract
Biochemical and biophysical processes that take place in muscle under relaxed and stressed conditions depend on the abundance and activity of gene products of metabolic and structural pathways. In livestock at post-mortem, these muscle properties determine aspects of meat quality and are measurable. The conversion of muscle to meat mimics pathological processes associated with muscle ischemia, injury or damage in humans and it is an economic factor in pork production. Linkage, association, and expression analyses independently contributed to the identification of trait-associated molecular pathways and genes. We aim at providing multiple evidences for the role of specific genes in meat quality by integrating a genome-wide association study (GWAS) for meat quality traits and the detection of eQTL based on trait-correlated expressed genes and trait-associated markers. The GWAS revealed 51 and 200 SNPs significantly associated with meat quality in a crossbred Pietrain Chi(German Landrace Chi Large White) (Pi Chi(GL Chi LW)) and a purebred German Landrace (GL) population, respectively. Most significant SNPs in Pi Chi(GL Chi LW) were located on chromosomes (SSC) 4 and 6. The data of 47,836 eQTLs at a significance level of p < 10(-5) were used to scale down the number candidate genes located in these regions. These SNPs on SSC4 showed association with expression levels of ZNF704, IMPA1, and OXSR1; SSC6 SNPs were associated with expression of SIGLEC10 and PIH1D1. Most significant SNPs in GL were located on SSC6 and associated with expression levels of PIH1D1, SIGLEC10, TBCB, LOC100518735, KIF1B, LOC100514845, and two unknown genes. The abundance of transcripts of these genes in muscle, in turn, is significantly correlated with meat quality traits. We identified several genes with evidence for their candidacy for meat quality arising from the integrative approach of a genome-wide association study and eQTL analysis.
Amelioration of sepsis by inhibiting sialidase-mediated disruption of the CD24-SiglecG interaction
NATURE BIOTECHNOLOGY
Authors: Chen, Guo-Yun; Chen, Xi; King, Samantha; Cavassani, Karen A.; Cheng, Jiansong; Zheng, Xincheng; Cao, Hongzhi; Yu, Hai; Qu, Jingyao; Fang, Dexing; Wu, Wei; Bai, Xue-Feng; Liu, Jin-Qing; Woodiga, Shireen A.; Chen, Chong; Sun, Lei; Hogaboam, Cory M.; Kunkel, Steven L.; Zheng, Pan; Liu, Yang
Abstract
Suppression of inflammation is critical for effective therapy of many infectious diseases. However, the high rates of mortality caused by sepsis attest to the need to better understand the basis of the inflammatory sequelae of sepsis and to develop new options for its treatment. In mice, inflammatory responses to host danger-associated molecular patterns (DAMPs), but not to microbial pathogen-associated molecular patterns (PAMPs), are repressed by the t interaction of CD24 and SiglecG (SIGLEC10 in human). Here we use an intestinal perforation model of sepsis to show that microbial sialidases target the sialic acid-based recognition of CD24 by SiglecG/10 to exacerbate inflammation. Sialidase inhibitors protect mice against sepsis by a mechanism involving both CD24 and Siglecg, whereas mutation of either gene exacerbates sepsis. Analysis of sialidase-deficient bacterial mutants confirms the key contribution of disrupting sialic acid-based pattern recognition to microbial virulence and supports the clinical potential of sialidase inhibition for dampening inflammation caused by infection.