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SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function.

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Summary

This study identified seven new genetic loci linked to kidney function (eGFRcrea) and novel genes, including SOS2, using exome array data. Zebrafish experiments confirmed the role of ACP1 and SOS2 in kidney development.

Keywords:
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Area of Science:

  • Genetics and Genomics
  • Nephrology
  • Developmental Biology

Background:

  • Genome-wide association studies (GWAS) have identified over 50 common variants associated with kidney function, yet they do not fully explain the variation in estimated glomerular filtration rate (eGFR).
  • Further investigation is needed to uncover additional genetic factors influencing kidney function and development.

Purpose of the Study:

  • To perform a large-scale meta-analysis using exome array data to identify novel genetic loci associated with eGFR.
  • To investigate the role of rare functional variants in kidney function.
  • To explore the developmental impact of identified genes in a model organism.

Main Methods:

  • Two-stage meta-analysis of genotype data from the Illumina exome array and eGFRcrea in participants of European ancestry (N=111,666 for Stage 1, N=48,343 for Stage 2).
  • Single-variant and gene-based association analyses.
  • Experimental follow-up using zebrafish (Danio rerio) embryos to assess the functional impact of candidate genes (acp1 and sos2) on kidney development.

Main Results:

  • Identified single nucleotide polymorphisms at seven novel loci (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, ATXN2L) associated with eGFRcrea (P<3.7×10^-7).
  • Discovered associations of functional rare variants in three genes with eGFRcrea, including a novel association with SOS2 (P=5.4×10^-8).
  • Knockdown of acp1 and sos2 in zebrafish embryos resulted in altered glomerular gene expression, renal tubule morphology, impaired blood clearance, and increased edema.

Conclusions:

  • This study significantly expands the number of known genetic loci associated with kidney function.
  • Identified SOS2 as a novel gene potentially involved in kidney development.
  • Findings highlight the importance of both common and rare variants in kidney function and provide insights into the genetic basis of kidney formation.