Identification and Functional Characterization of Novel Variants Associated with Sepsis Identified by Whole Exome Sequencing

Abstract

Background Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. It is a leading cause of global mortality. Although sepsis is not considered a classic monogenic trait, there is strong evidence of the role of genetics in its susceptibility. Methods and Results This project uses the previously collected sepsis-affected cohort of 484 whole-exome sequenced (WES) samples to bring insights into genetics of sepsis. The two variants in GNLY gene encoding for antimicrobial peptide granulysin, NM_006433.5:c.255+2T>C and NM_006433.5:c.304C>T, have been prioritised using in silico variant pathogenicity prediction tools for further in vitro evaluation. These variants were present in three patients from sepsis cohort. The criteria for prioritisation were the rarity of the variants in non-affected population, the high impact consequences of the variants on GNLY transcripts and proteins, and the essential role of the GNLY gene as a key component of the immune response. NM_006433.5:c.304C>T variant introduces a premature stop codon and is predicted to lead to truncation of GNLY protein by third: from 148 aa to 102 aa. NM_006433.5:c.255+2T>C variant was predicted to affect splicing of exons 3-4 of GNLY transcript. The presence of the variants in three patients from the cohort in a heterozygous state has been confirmed through Sanger sequencing. In vitro ExonTrap minigene assays have confirmed that NM_006433.5:c.255+2T>C variant leads to aberrant splicing. It has been also investigated whether the two variants are presented in compound heterozygote state using cloning assay. The overall conclusion was that the variants are not likely to be present in the compound heterozygote state in two patients. Conclusion Potential of GNLY being a novel sepsis-susceptibility gene, caveats of variant pathogenicity predictions and the potential genetic mechanisms by which the two variants can contribute to the genetics of susceptibility of sepsis are further discussed.