| This thesis focuses on pharmacogenomics and functional genomics of a novel biomarker FKBP5, the gene encoding for a large immunophilin FK-binding protein 51 (FKBP51). This protein functions as a modulator of the glucocorticoid receptor, and also as a negative regulator of Akt, both pathways that have been shown to play an important role in the pathophysiology of two distinct diseases: cancer and depression, as well as responses to treatment of these diseases, in this case, chemotherapeutics and selective serotonin reuptake inhibitors (SSRIs).;The first Specific Aim of this thesis work focused on the pharmacogenomics of FKBP5 in SSRI Treatment of Major Depressive Disorder (MDD). This particular project began by identifying expression Quantitative Trait Loci (eQTLs) of FKBP5 as well as genetic variations present in FKBP5 by performing in-depth resequencing. This was followed by genotype-phenotype association analysis using MDD patient DNA to determine variants that were associated with response to SSRIs in the treatment of MDD.;We identified 657 common and rare variants of FKBP5 during our in-depth FKBP5 DNA resequencing, with 315 SNPs being novel as compared to the "1000 Genomes Project" data. Sanger sequencing in an additional 96 AA and 96 HCA DNA samples resulted in the identification of another 29 novel SNPs, including 3 nonsynonymous (ns) SNPs (Gly22Arg in HCA, Arg154Gln in AA, and Val437Phe in AA), all with MAFs <5%. Additionally, we identified 431 SNPs associated with FKBP5 expression through FKBP5 trans regulation by performing eQTL analysis for all 287 LCLs from all three ethnic groups. Genotype-phenotype association studies using 529 DNA samples from the Mayo Clinic PGRN-SSRI Pharmacogenomic trial, followed by a replication study in 960 DNA samples from the NIMH-STAR*D study of White non-Hispanic patients identified the rs352428 SNP to be associated with SSRIs response (p-v<0.05; OR<1). Functional genomics studies of this SNP suggested that the region surrounding it is transcriptionally active as a "silencer" and that this SNP could alter binding to transcription factors, which might affect the expression level of FKBP5 and response to SSRIs.;Because of the role of FKBP5 in the regulation of the Akt pathway and the role of the Akt pathway in tumorigenesis and chemoresistance, we utilized a similar approach in Specific Aim 2 - "Pharmacogenomics of FKBP5 in Gemcitabine Treatment in Pancreatic Cancer" to explore the role of genetic variation in FKBP5 in variation of response to gemcitabine in the treatment of pancreatic cancer. Specifically, this study focused on understanding how sequence variation in the FKBP5 gene in pancreatic tumors and germline DNA might impact the clinical response in patients treated with gemcitabine. We sought variations that change the function of FKBP5, which might be important as biomarkers to help predict responses to chemotherapy.;In this project, resequencing of FKBP5 using Next Generation technology was performed in DNA derived from 62 tumor and normal tissue samples, including 19 paired normal and tumor tissues from pancreatic cancer patients. 404 SNPs were identified, including two ns cSNPs (Thr(17)Ala and Glu(383)Leu). Next, genotype-phenotype association studies were performed with the same patient cohort in which resequencing was done, and the phenotypes of overall survival and FKBP5 gene expression in the tumor obtained from the same sample set. Functional genomic studies were performed of resequenced FKBP5 SNPs, including a SNP in the coding region (Thr(17)Ala), and SNPs in the regulatory regions (introns) that showed a trend for association with the clinical response phenotype. These functional characterization studies suggested that rs73748206 might contribute to patients' survival after gemcitabine treatment by increasing FKBP5 expression possibly through increased binding to the glucocorticoid receptor, a known transcription factor regulating FKBP5 expression. (Abstract shortened by UMI.). |
