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Characterization of Coding and Noncoding Variants for Human CKD Using Novel Strategies
Author(s) -
Prokop Jeremy W.,
Yeo Nan C.,
Ottmann Christian,
Link Brian A.,
Mendenhall Eric M.,
Freedman Barry I.,
Lazar Jozef,
Jacob Howard J.
Publication year - 2018
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2018.32.1_supplement.754.2
Subject(s) - biology , genome wide association study , genetics , human genome , linkage disequilibrium , computational biology , genetic association , gene , exome , population , 1000 genomes project , genome , exome sequencing , allele , phenotype , haplotype , single nucleotide polymorphism , genotype , medicine , environmental health
Interpreting the mechanism of genetic variants is one of the greatest challenges impeding the analysis of the rapidly increasing volume of patients' genomic data, particularly for rare variants that do not reach GWAS significance due to low population frequencies. There are 153 GWAS hits for altered kidney function due to commonly inherited genetic variants, yet minimal knowledge of the mechanism of these variations is known at the current time. Utilizing a computational strategy to filter 3,921 genetic variants that are found within linkage disequilibrium of the GWAS hits we have nominated 4 damaging protein coding variants and more importantly 30 noncoding variants predicted to alter transcription factor based gene regulation. One of these noncoding variants, rs17319721 associated with risk of chronic kidney disease (CKD), is found near the SHROOM3 gene and is thought to play a functional role in podocytes of the kidney. In this study we show this variant falls upstream of a novel transcriptional start site that results in a shorter SHROOM3 isoform lacking the PDZ domain. This variant disrupts binding of TCF7L2 in podocytes and the single variant (rs17319721) alters transcription levels of SHROOM3 as determined by variant mutation into the genome using CRISPR/Cas9 technology. To begin deciphering the role of rare variants within human genomes we performed a full assessment of the ExAC database for >60,000 sequenced human exomes, revealing several coding variants in SHROOM3 that are likely to alter function, including a coding variant (P1244L) we show to have association to CKD in humans. We determined that P1244L attenuates the interaction of SHROOM3 with 14‐3‐3 binding and alters signaling through the Hippo pathway, a known mediator of CKD. Animal studies show a loss of function in zebrafish kidney due to the variant, resulting in increased glomerular permeability. These data demonstrate multiple new SHROOM3 ‐dependent genetic and molecular mechanisms that regulate CKD and demonstrate a novel analytical pipeline with broad application to systematically characterizing risk mechanisms of CKD and other complex diseases. Support or Funding Information Support for this study was from NIH‐K01ES025435 (to JWP), NIH‐R01HL069321 (to HJJ), NIH‐R01EY014167 (to BL), the Collaborative Research Centre 1093 through the Deutsche Forschungsgemeinschaft (DFG, to CO), and HudsonAlpha Institute for Biotechnology. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .