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Characterization of Coding/Noncoding Variants for SHROOM3 in Patients with CKD. J Am Soc Nephrol 2018 05;29(5):1525-1535

Date

02/25/2018

Pubmed ID

29476007

Pubmed Central ID

PMC5967772

DOI

10.1681/ASN.2017080856

Scopus ID

2-s2.0-85046380339   10 Citations

Abstract

Background Interpreting genetic variants is one of the greatest challenges impeding analysis of rapidly increasing volumes of genomic data from patients. For example, SHROOM3 is an associated risk gene for CKD, yet causative mechanism(s) of SHROOM3 allele(s) are unknown.Methods We used our analytic pipeline that integrates genetic, computational, biochemical, CRISPR/Cas9 editing, molecular, and physiologic data to characterize coding and noncoding variants to study the human SHROOM3 risk locus for CKD.Results We identified a novel SHROOM3 transcriptional start site, which results in a shorter isoform lacking the PDZ domain and is regulated by a common noncoding sequence variant associated with CKD (rs17319721, allele frequency: 0.35). This variant disrupted allele binding to the transcription factor TCF7L2 in podocyte cell nuclear extracts and altered transcription levels of SHROOM3 in cultured cells, potentially through the loss of repressive looping between rs17319721 and the novel start site. Although common variant mechanisms are of high utility, sequencing is beginning to identify rare variants involved in disease; therefore, we used our biophysical tools to analyze an average of 112,849 individual human genome sequences for rare SHROOM3 missense variants, revealing 35 high-effect variants. The high-effect alleles include a coding variant (P1244L) previously associated with CKD (P=0.01, odds ratio=7.95; 95% CI, 1.53 to 41.46) that we find to be present in East Asian individuals at an allele frequency of 0.0027. We determined that P1244L attenuates the interaction of SHROOM3 with 14-3-3, suggesting alterations to the Hippo pathway, a known mediator of CKD.Conclusions These data demonstrate multiple new SHROOM3-dependent genetic/molecular mechanisms that likely affect CKD.

Author List

Prokop JW, Yeo NC, Ottmann C, Chhetri SB, Florus KL, Ross EJ, Sosonkina N, Link BA, Freedman BI, Coppola CJ, McDermott-Roe C, Leysen S, Milroy LG, Meijer FA, Geurts AM, Rauscher FJ 3rd, Ramaker R, Flister MJ, Jacob HJ, Mendenhall EM, Lazar J

Authors

Aron Geurts PhD Associate Professor in the Physiology department at Medical College of Wisconsin
Brian A. Link PhD Professor in the Cell Biology, Neurobiology and Anatomy department at Medical College of Wisconsin




MESH terms used to index this publication - Major topics in bold

Alleles
Animals
Cell Nucleus
Gene Frequency
Genetic Loci
HEK293 Cells
Humans
Mice
Microfilament Proteins
Mutation, Missense
Podocytes
Protein Isoforms
Renal Insufficiency, Chronic
Transcription Factor 7-Like 2 Protein
Transcription, Genetic
Zebrafish
jenkins-FCD Prod-486 e3098984f26de787f5ecab75090d0a28e7f4f7c0