Imputation-Powered Whole-Exome Analysis Identifies Rare Coding Variants and Genes Associated With Kidney Function and Disease in the UK Biobank

. Background: Chronic kidney disease (CKD) is a major public health concern affecting ~10% of the global adult population. Genome-wide association studies on imputed common genotypes have identified variants associated with kidney function and CKD, but cannot comprehensively investigate rare coding variation. We aimed to identify rare pathogenic variants and genes impacting human kidney function and disease. Methods: A genotype imputation approach was applied to whole exome sequencing data of European ancestry participants from the UK Biobank to increase our sample size from 166,891 to 408,511. We used exome-wide association studies (ExWAS) and gene-level Burden tests in order to identify rare variants and genes associated with different kidney phenotypes including eGFR, UACR, urea, urate and clinically diagnosed CKD. We performed a phenome-wide association study of the resulting genes. Results: We imputed ~7.5 million exonic variants for 241,620 individuals without WES data. In a validation sample, the overall concordance of sequenced and imputed genotypes was >0.98. We identified 158 rare variants and 106 genes significantly associated with kidney function. Among these genes, there were known monogenic kidney disease genes such as CUBN and PKD2 , for which we highlight novel putatively disease-causing mutations. Furthermore, we implicate genes currently not linked to kidney function and disease in humans, such as FNIP1 and EPB41L5 . Disruption of Fnip1 in mice is sufficient for renal cyst formation, and Epb41l5 -deficient mice are known to develop focal-segmental glomerulosclerosis. Our results not only establish human relevance, but also identify potentially causal variants. Across the phenome, we identified numerous instances where the assumed loss-of-function of implicated genes resulted in increased disease risk, often reflecting known clinical signs and symptoms. For example, carriers of rare damaging variants in COL4A3 showed higher odds of hematuria. Conclusions: Our study underscores the value of imputation-powered analysis and reveals both novel and confirms known variants associated with kidney disease. It generates a comprehensive resource to direct future functional and clinical studies. Results will be shared via an interactive website.

Background: Chronic kidney disease is common, costly and it is associated with cardiovascular disease and increased mortality.Early identification of CKD is imperative to prevent progression and potentially reduce cardiovascular morbidity and mortality.Plasma proneurotensin (ProNT) is a precursor of neurotensin (NT).NT and its related peptides have been linked to risk for disease processes related to kidney disease, including cardiovascular disease, and type 2 diabetes mellitus.It is unknown whether ProNT is directly associated with incident CKD.
Methods: Among 3914 participants who were part of BioMedioR, a nested cohort within the Reasons for Geographic and Racial Differences in Stroke (REGARDS) who completed the second visit, we measured ProNT by Sphingotest (double monoclonal sandwich immunoassay).Primary outcomes were significant eGFR decline (defined as 30% decline), incident albuminuria (defined as albumin/creatinine greater or equal to 30 at second visit) and incident CKD (defined as eGFR less than 60 mL/min/1.73m 2 plus 40% decline in eGFR).Logistic regression with inverse probability sampling weights for analysis.Sequential models adjusted for age sex, and race (Model 1); BMI, SBP, DBP, diabetes, smoking, cholesterol and prevalent CVD (Model 2); and baseline eGFR and albuminuria (Model 3).Using model 3, we tested for interaction ProNT and race and explored analyses by race.We used similar models to evaluate for incident albuminuria, excluding albuminuria in model 3.
Results: Higher ProNT levels were associated with greater eGFR decline among all participants independent of baseline eGFR and albuminuria (OR: 1.12, 95% CI [1.00, 1.26]) and incident albuminuria (OR: 1.31, 95% CI 1.14,1.50).Higher ProNT levels were also associated with greater incidence of CKD; however, this association was attenuated after including baseline eGFR and albuminuria (OR: 1.25, 95% CI 0.98, 1.59).We did not find any interactions between ProNT and race or sex in any of the three outcomes.
Conclusions: Assessment of ProNT provides information about significant eGFR decline and incident albuminuria but not incident CKD among persons at high risk of hypertension and diabetes, known risk factors of incidence and progression of CKD.These associations were independent of race or sex.Further studies should evaluate if ProNT can help tailor treatments to slow progression of CKD in a high-risk population.
Funding: Veterans Affairs Support Background: Mesoamerican nephropathy (MeN) is a leading cause of death amongst working age men in Central America, yet its aetiology remains unclear.Several potential environmental causes have been proposed including heat-stress, pesticides and heavy metals, but intermittent and cumulative exposures are difficult to capture using biomonitoring.Epigenetic studies have identified DNA-methylation (DNAm) at specific loci associated with these exposures.Therefore, we first conducted an epigenome-wide association study (EWAS) focusing on incident cases.Then, using a hypothesis driven approach, explored the association between DNAm at loci previously associated with implicated exposures and MeN.

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Methods: MeN cases from a population-based longitudinal study were empirically derived using a hidden Markov model based on departure from a healthy population eGFR distribution.Our data consisted of 2-3 blood samples collected across a 5-year period from each of 57 incident-cases (pre-and post-evidence of disease onset), 57 matchedcontrols and 16 established cases.DNAm was quantified (Illumina MethylationEPIC BeadChip) in a total of 320 blood-samples.Raw data were processed using established pipelines.Associations between differentially methylated positions (DMPs) and MeN were examined using covariate-adjusted mixed-effect models, allowing for repeat measures.DMPs previously reported to associate with ambient temperature, arsenic, cadmium, chromium and pesticides, were collated from a systematic search, and potential association of MeN with these loci was investigated.
Results: The EWAS demonstrated no DMPs associated with MeN at standard epigenome-wide statistical thresholds.Furthermore, hypothesis driven analyses examining the coefficients of DMPs reported to be associated with ambient temperature, pesticides and metals, demonstrated no associations with MeN.Further calculations suggested adequate power to detect biologically important differences.
Conclusions: DNAm studies in our dataset do not support the hypotheses that pesticides, temperature or the examined metals have a causal role in early-stage MeN.Therefore, other aetiological factors should be considered.
Funding: Private Foundation Support, Government Support -Non-U.S. Background: Untargeted metabolomics is a promising approach for capturing dietary intake with less bias than traditional methods of dietary assessment.An important application of this technique is the identification of biomarkers of specific dietary protein sources, which may explain the diet-chronic kidney disease (CKD) relationship.

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Methods: We analyzed dietary data collected from an interviewer-administered questionnaire and 359 serum metabolites at visit 1 (1987)(1988)(1989) in the Atherosclerosis Risk in Communities (ARIC) study (n=3,724).Multivariable linear regression models were used to estimate cross-sectional associations between specific sources of protein (red and processed meat, nuts, legumes) previously associated with CKD risk in the ARIC study and serum metabolites.For metabolites that were significantly associated with these dietary protein sources, we assessed their prospective associations with incident CKD

Methylation at Loci Associated With Metals, Pesticides, and Temperature Provide No Evidence for a Role of These Exposures in the Aetiology of Mesoamerican Nephropathy
Amin Oomatia, 1 Ali M. Al-Rashed, 1 Marvin A. Gonzalez, 2 Andres Cardenas, 3 Neil Pearce, 4 Simone Ecker, 5 Stephan Beck, 5 Brianna Heggeseth, 6 Olga Chervova, 5 Ben Caplin. 1 The Colt/UK MRC CKDu study group 1 University College London Department of Renal Medicine, London, United Kingdom; 2 Research Centre on Health, Work and Environment at National Autonomous University of Nicaragua, Leon, Nicaragua; 3 School of Public Health, University of Berkeley, Berkley, CA; 4 London School of Hygiene and Tropical Medicine Faculty of Epidemiology and Population Health, London, United Kingdom; 5 University College London Cancer Institute, London, United Kingdom; 6 Macalester College, Saint Paul, MN.