title: Sequencing of LRP2 reveals multiple rare variants associated with urinary trefoil factor-3.
abstract: Novel biomarkers are being investigated to identify patients with kidney disease. We measured a panel of 13 urinary biomarkers in participants from the Offspring Cohort of the Framingham Heart Study. Using an Affymetrix chip with imputation to 2.5 M single-nucleotide polymorphisms (SNPs), we conducted a GWAS of these biomarkers (n=2640) followed by exonic sequencing and genotyping. Functional studies in zebrafish were used to investigate histologic correlation with renal function. Across all 13 biomarkers, there were 97 significant SNPs at three loci. Lead SNPs at each locus were rs6555820 (P=6.7×10(-49); minor allele frequency [MAF]=0.49) in HAVCR1 (associated with kidney injury molecule-1), rs7565788 (P=2.15×10(-16); MAF=0.22) in LRP2 (associated with trefoil factor 3 [TFF3]), and rs11048230 (P=4.77×10(-8); MAF=0.10) in an intergenic region near RASSF8 (associated with vascular endothelial growth factor). Validation in the CKDGen Consortium (n=67,093) showed that only rs7565788 at LRP2, which encodes megalin, was associated with eGFR (P=0.003). Sequencing of exons 16-72 of LRP2 in 200 unrelated individuals at extremes of urinary TFF3 levels identified 197 variants (152 rare; MAF<0.05), 31 of which (27 rare) were nonsynonymous. In aggregate testing, rare variants were associated with urinary TFF3 levels (P=0.003), and the lead GWAS signal was not explained by these variants. Knockdown of LRP2 in zebrafish did not alter the renal phenotype in static or kidney injury models. In conclusion, this study revealed common variants associated with urinary levels of TFF3, kidney injury molecule-1, and vascular endothelial growth factor and identified a cluster of rare variants independently associated with TFF3.
authors.affiliation: National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; Divisions of Nephrology.
authors.forename: Gearoid M
authors.initials: GM
authors.lastname: McMahon
authors.affiliation: National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts;
authors.forename: Matthias
authors.initials: M
authors.lastname: Olden
authors.affiliation: Genetics, Gastroenterology, and.
authors.forename: Maija
authors.initials: M
authors.lastname: Garnaas
authors.affiliation: Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Yang
authors.affiliation: Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
authors.forename: Xuan
authors.initials: X
authors.lastname: Liu
authors.affiliation: National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts;
authors.forename: Shih-Jen
authors.initials: SJ
authors.lastname: Hwang
authors.affiliation: National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.
authors.forename: Martin G
authors.initials: MG
authors.lastname: Larson
authors.affiliation: Genetics, Gastroenterology, and.
authors.forename: Wolfram
authors.initials: W
authors.lastname: Goessling
authors.affiliation: National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; Endocrinology and Metabolism, Brigham and Women's Hospital, Boston, Massachusetts; and foxca@nhlbi.nih.gov.
authors.forename: Caroline S
authors.initials: CS
authors.lastname: Fox
mesh_terms: D048868:Adaptor Proteins, Signal Transducing; D000368:Aged; D000483:Alleles; D000818:Animals; D015415:Biomarkers / Q000652:urine*; D002352:Carrier Proteins / Q000235:genetics*; D003404:Creatinine / Q000097:blood; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D007674:Kidney Diseases / Q000235:genetics* / Q000378:metabolism / Q000652:urine*; D008137:Longitudinal Studies; D026561:Low Density Lipoprotein Receptor-Related Protein-2; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D010455:Peptides / Q000652:urine*; D010641:Phenotype; D017422:Sequence Analysis, DNA; D016896:Treatment Outcome; D000071165:Trefoil Factor-3; D015027:Zebrafish
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D015415:Biomarkers; D002352:Carrier Proteins; C476844:LRP2BP protein, human; D026561:Low Density Lipoprotein Receptor-Related Protein-2; D010455:Peptides; C082495:TFF3 protein, human; D000071165:Trefoil Factor-3; D003404:Creatinine