Date of Award

2017

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Cell & Molecular Biology

First Advisor

Katalin Susztak

Abstract

The work described in this dissertation aimed to better understand the genetic and epigenetic factors influencing chronic kidney disease (CKD) development. Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic kidney disease. However, these studies have not effectively identified target genes for the CKD variants. Most of the identified variants are localized to non-coding genomic regions, and how they associate with CKD development is not well-understood. As GWAS studies only explain a small fraction of heritability, we hypothesized that epigenetic changes could explain part of this missing heritability.

To identify potential gene targets of the genetic variants, we performed expression quantitative loci (eQTL) analysis, using genotyping arrays and RNA sequencing from human kidney samples. To identify the target genes of CKD-associated SNPs, we integrated the GWAS-identified SNPs with the eQTL results using a Bayesian colocalization method, coloc. This resulted in a short list of target genes, including PGAP3 and CASP9, two genes that have been shown to present with kidney phenotypes in knockout mice. To examine the functional role of a newly identified gene from the integrative analysis, MANBA, we knocked down this gene in zebrafish. This resulted in pericardial edema, a phenotype seen with kidney developmental defect.

While epigenetic dysregulation has been suggested as a mechanism for the development of many diseases, little was known about the epigenome of normal and diseased human kidneys. We performed cytosine methylation analysis in microdissected human kidney tubules in both CKD samples and controls, and found differentially methylated regions (DMRs) in CKD. These DMRs are further validated in the second cohort. The DMRs were mostly localized outside of promoter areas and enriched in intronic enhancer regions, and we found that the DMRs contain consensus-binding motifs for key renal transcription factors (HNF, TCFAP, SIX2). Furthermore, we found these DMRs correlated with the transcript changes. A network analysis of these correlated DMR-transcript pairs revealed an enrichment of a fibrosis network highlighted the TGF-β pathway. In vitro validation experiments established a likely causal relationship between epigenetic changes and CKD development.

In summary, integration of eQTL analysis with GWAS-identified CKD variants has facilitated the identification of likely CKD target genes. We discovered that cytosine methylation changes in human kidney tissue samples in the major fibrotic pathways. Overall, genetic variations as well as cytosine methylation levels have significant impact on gene expression regulation, possibly downstream organ function, and CKD development.

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Additional Files

Appendix2.xlsx (1181 kB)
Appendix3.xlsx (248 kB)
Appendix4.xlsx (3550 kB)
Appendix5.png (119 kB)
Appendix6.xlsx (2210 kB)

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