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Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease.

Yi-An Ko1, Huiguang Yi1, Chengxiang Qiu1

  • 1Renal-Electrolyte and Hypertension Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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Summary

This study identifies new candidate genes for chronic kidney disease (CKD) by integrating genome-wide association studies (GWASs) with kidney gene expression data. The lysosomal enzyme MANBA emerged as a potential CKD target gene, with lower expression linked to disease risk.

Keywords:
CKDGWASeQTLgene networkgene regulationkidney

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Area of Science:

  • Genetics
  • Nephrology
  • Genomics

Background:

  • Chronic kidney disease (CKD) affects nearly 10% of the US population, with genetic factors playing a significant role.
  • Genome-wide association studies (GWASs) have identified genetic variants linked to kidney function, but their functional mechanisms remain unclear.
  • Expression quantitative trait loci (eQTL) analysis links genetic variation to gene expression changes in specific tissues.

Purpose of the Study:

  • To integrate CKD GWAS data with kidney eQTL analysis to identify novel candidate genes for CKD.
  • To investigate the role of genetic variants in non-coding regions associated with CKD pathogenesis.
  • To validate a potential CKD-associated gene, lysosomal beta A mannosidase (MANBA).

Main Methods:

  • Performed eQTL analysis correlating genotype with RNA-seq gene expression in 96 human kidney samples.
  • Applied direct overlap and Bayesian methods to identify candidate genes by integrating GWAS and eQTL data.
  • Utilized zebrafish models to assess the functional impact of MANBA gene suppression on kidney development and function.

Main Results:

  • Detected 1,886 genes with expression significantly altered by sequence variants in kidney tissue.
  • Identified MANBA as a potential CKD target gene, showing significant colocalization between its expression-associated variants and CKD GWAS variants.
  • Observed significantly lower MANBA expression in kidneys with CKD risk alleles and demonstrated that MANBA suppression in zebrafish causes kidney dysfunction phenotypes.

Conclusions:

  • Integrative analysis of GWAS and kidney eQTL data is a powerful approach to uncover novel CKD-associated genes.
  • MANBA is a promising candidate gene for CKD, with genetic variants influencing its expression potentially contributing to disease risk.
  • Gene expression changes driven by genetic variation in the kidney offer insights into CKD development and potential therapeutic targets.