Association between GATM gene polymorphism and progression of chronic kidney disease: a mitochondrial related genome-wide Mendelian randomization study

• Published in: Scientific reports 2024-09, Vol.14 (1), p.20346-10
• Main Authors: Liu, Bin, Gao, Xin, Teng, Haolin, Zhou, Honglan, Gao, Baoshan, Li, Faping
• Format: Article
• Language: English
• Subjects: 631/114; 692/4022; CKD; Colocalization; Datasets; Disease Progression; DNA methylation; Epidermal growth factor receptors; Gene polymorphism; Genes; Genetic analysis; Genetic diversity; Genetic Predisposition to Disease; Genome-Wide Association Study; GFR; Global health; Glomerular filtration rate; Glomerular Filtration Rate - genetics; Glycine amidinotransferase; Humanities and Social Sciences; Humans; Kidney diseases; Kidneys; Localization; Mendelian randomization; Mendelian Randomization Analysis; Methylation; Mitochondria; Mitochondria - genetics; Mitochondrial dysfunction; multidisciplinary; Polymorphism, Single Nucleotide; Public health; Quantitative Trait Loci; Renal function; Renal Insufficiency, Chronic - genetics; Science; Science (multidisciplinary); Therapeutic applications; Therapeutic targets
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-68448-x

Chronic Kidney Disease (CKD) stands as a substantial challenge within the global health landscape. The elevated metabolic demands essential for sustaining normal kidney function have propelled an increasing interest in unraveling the intricate relationship between mitochondrial dysfunction and CKD. However, the authentic causal relationship between these two factors remains to be conclusively elucidated. This study endeavors to address this knowledge gap through the Mendelian Randomization (MR) method. We utilized large-scale QTL datasets (including 31,684 eQTLs samples, 1980 mQTLs samples, and 35,559 pQTLs samples) to precisely identify key genes related to mitochondrial function as exposure factors. Subsequently, we employed GWAS datasets (comprising 480,698 CKD samples and 1,004,040 eGFRcrea samples) as outcome factors. Through a comprehensive multi-level analysis (encompassing expression, methylation, and protein quantification loci), we evaluated the causal impact of these genes on CKD and estimated glomerular filtration rate (eGFR). The integration and validation of diverse genetic data, complemented by the application of co-localization analysis, bi-directional MR analysis, and various MR methods, notably including inverse variance weighted, have collectively strengthened our confidence in the robustness of these findings. Lastly, we validate the outcomes through examination in human RNA sequencing datasets encompassing various subtypes of CKD. This study unveils significant associations between the glycine amidinotransferase (GATM) and CKD, as well as eGFR. Notably, an augmentation in GATM gene and protein expression corresponds to a diminished risk of CKD, whereas distinct methylation patterns imply an increased risk. Furthermore, a discernible reduction in GATM expression is observed across diverse pathological subtypes of CKD, exhibiting a noteworthy positive correlation with GFR. These findings establish a causal relationship between GATM and CKD, thereby highlighting its potential as a therapeutic target. This insight lays the foundation for the development of potential therapeutic interventions for CKD, presenting substantial clinical promise.