Long, M. D. | bioRxiv Science

bioRxiv2018

Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas

Understanding the levels of metabolic dysregulation in different disease settings is vital for the safe and effective incorporation of metabolism-targeted therapeutics in the clinic. Using transcriptomic data from 10,704 tumor and normal samples from The Cancer Genome Atlas, across 26 disease sites, we developed a novel bioinformatics pipeline that distinguishes tumor from normal tissues, based on differential gene expression for 114 metabolic pathways. This pathway dysregulation was confirmed in separate patient populations, further demonstrating the robustness of this approach. A bootstrapping simulation was then applied to assess whether these alterations were biologically meaningful, rather than expected by chance. We provide distinct examples of the types of analysis that can be accomplished with this tool to understand cancer specific metabolic dysregulation, highlighting novel pathways of interest in both common and rare disease sites. Utilizing a pathway mapping approach to understand patterns of metabolic flux, differential drug sensitivity, can accurately be predicted. Further, the identification of Master Metabolic Transcriptional Regulators, whose expression was highly correlated with pathway gene expression, explains why metabolic differences exist in different disease sites. We demonstrate these also have the ability to segregate patient populations and predict responders to different metabolism-targeted therapeutics.

bioinformatics↗

bioRxiv2017

The miR-96/RARγ signaling axis governs androgen signaling and PCa progression

Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RAR{gamma}), are commonly reduced in prostate cancer (PCa). Therefore we sought to establish the cellular and gene regulatory consequences of reduced RAR{gamma} expression, and determine RAR{gamma} regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RAR{gamma} levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. ChIP-Seq defined the RAR{gamma} cistrome which was significantly enriched at active enhancers associated with AR binding sites. Reflecting a significant genomic role for RAR{gamma} to regulate androgen signaling, RAR{gamma} knockdown in HPr1-AR cells significantly regulated the magnitude of the AR transcriptome. RAR{gamma} down-regulation was explained by increased miR-96 in PCa cell and mouse models, and TCGA PCa cohorts. Biochemical approaches confirmed that miR-96 directly regulated RAR{gamma} expression and function Capture of the miR-96 targetome by biotin-miR96 identified that RAR{gamma} and a number of RAR{gamma} interacting co-factors including TACC1 were all targeted by miR-96, and expression of these genes were prominently altered, positively and negatively, in the TCGA-PRAD cohort. Differential gene expression analyses between tumors in the TCGA-PRAD cohort with lower quartile expression levels of RARG and TACC1 and upper quartile miR-96, compared to the reverse, identified a gene network including several RAR{gamma} target genes (e.g. SOX15) that significantly associated with worse disease free survival (hazard ratio 2.23, 95% CI 1.58 to 2.88, p=0.015). In summary, miR-96 targets a RAR{gamma} network to govern AR signaling, PCa progression and disease outcome.\n\nConflict of interestThe authors certify that they have NO affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers bureaus; membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patent-licensing arrangements), or non-financial interest (such as personal or professional relationships, affiliations, knowledge or beliefs) in the subject matter or materials discussed in this manuscript.\n\nFUNDINGLESC acknowledges support, in part, of Roswell Park Comprehensive Cancer Center-University of Pittsburg Cancer Institute Ovarian Cancer Specialized Program of Research Excellence National Institutes of Health [P50CA159981-01A1].\n\nMDL acknowledges support of Molecular Pharmacology and Experimental Therapeutics NRSA T32 program [T32CA009072] held at Roswell Park Comprehensive Cancer Center.\n\nMJC and DJS acknowledges support in part from the Prostate program of the Department of Defense Congressionally Directed Medical Research Programs [W81XWH-14-1-0608, W81XWH-11-2-0033] and the National Cancer Institute (NCI) grant P30CA016056 involving the use of Roswell Park Comprehensive Cancer Centers Genomic Shared Resource.\n\nMJC, GL, AR, HW and PvdB acknowledges support from the European Union-United States Atlantis Program [P116J090011].\n\nMJC and LESC acknowledge support from the National Cancer Institute (NCI) grant P30CA016056 involving the use of OSUCCC The James, CCSG P30CA016058

cancer biology↗