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Altered Gene Expression Along the Glycolysis– Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer Joanna M

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Altered Gene Expression Along the Glycolysis– Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer Joanna M Published OnlineFirst September 3, 2019; DOI: 10.1158/1078-0432.CCR-19-1543 CLINICAL CANCER RESEARCH | PRECISION MEDICINE AND IMAGING Altered Gene Expression along the Glycolysis– Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer Joanna M. Karasinska1, James T. Topham1, Steve E. Kalloger1,2, Gun Ho Jang3, Robert E. Denroche3, Luka Culibrk4, Laura M. Williamson4, Hui-Li Wong5, Michael K.C. Lee5, Grainne M. O’Kane6, Richard A. Moore4, Andrew J. Mungall4, Malcolm J. Moore5, Cassia Warren1, Andrew Metcalfe1, Faiyaz Notta3, Jennifer J. Knox6, Steven Gallinger3,6, Janessa Laskin4,5, Marco A. Marra4,7, Steven J.M. Jones4,7, Daniel J. Renouf1,5,8, and David F. Schaeffer1,2,9 ABSTRACT ◥ Purpose: Identification of clinically actionable molecular Results: On the basis of the median normalized expression of subtypes of pancreatic ductal adenocarcinoma (PDAC) is key glycolytic and cholesterogenic genes, four subgroups were iden- to improving patient outcome. Intertumoral metabolic het- tified: quiescent, glycolytic, cholesterogenic, and mixed. Glyco- erogeneity contributes to cancer survival and the balance lytic tumors were associated with the shortest median survival in between distinct metabolic pathways may influence PDAC resectable (log-rank test P ¼ 0.018) and metastatic settings (log- outcome. We hypothesized that PDAC can be stratified into rank test P ¼ 0.027). Patients with cholesterogenic tumors had the prognostic metabolic subgroups based on alterations in the longest median survival. KRAS and MYC-amplified tumors had expression of genes involved in glycolysis and cholesterol higher expression of glycolytic genes than tumors with normal or synthesis. lost copies of the oncogenes (Wilcoxon rank sum test P ¼ 0.015). Experimental Design: We performed bioinformatics analysis Glycolytic tumors had the lowest expression of mitochondrial of genomic, transcriptomic, and clinical data in an integrated pyruvate carriers MPC1 and MPC2. Glycolytic and cholestero- cohort of 325 resectable and nonresectable PDAC. The resectable genic gene expression correlated with the expression of prognos- datasets included retrospective The Cancer Genome Atlas tic PDAC subtype classifier genes. (TCGA) and the International Cancer Genome Consortium Conclusions: Metabolic classification specific to glycolytic and (ICGC) cohorts. The nonresectable PDAC cohort studies included cholesterogenic pathways provides novel biological insight into prospective COMPASS, PanGen, and BC Cancer Personalized previously established PDAC subtypes and may help develop OncoGenomics program (POG). personalized therapies targeting unique tumor metabolic profiles. specific cellular tumor progression pathways contribute to PDAC Introduction prognostic stratification is needed to enable customized treatment The 5-year survival rate in pancreatic ductal adenocarcinoma design and novel therapeutics development. (PDAC) is less than 10% and remains one of the lowest in all Oncogene-driven metabolic adaptations allow cancer cells to sur- cancers. Effective therapy is limited by the treatment-refractory vive and thrive in the tumor microenvironment (9). A pan-cancer nature of PDAC and a short supply of clinically validated biomar- analysis of global metabolic pathways showed that tumor metabolic kers capable of predicting treatment response (1). Emerging molec- heterogeneity is associated with survival, somatic driver mutations, ular subtypes of PDAC have defined intertumoral heterogeneity and tumor subtypes (10), but whether heterogeneity in distinct met- at the genome and transcriptome levels (2–6), driving efforts to abolic pathways can be used to stratify PDAC into clinically relevant identify clinically relevant biomarker signatures and actionable subgroups has not been well established. A vast majority of PDACs genomic alterations (7, 8). However, a better understanding of how harbor oncogenic KRAS and loss-of-function TP53 mutations (6), in 1Pancreas Centre BC, Vancouver, British Columbia, Canada. 2Department of Clinical trial information: Personalized OncoGenomics (POG) Program of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia: Utilization of Genomic Analysis to Better Understand Tumour British Columbia, Canada. 3Ontario Institute for Cancer Research, Toronto, Heterogeneity and Evolution (NCT02155621); Prospectively Defining Metastatic Ontario, Canada. 4Canada's Michael Smith Genome Sciences Centre, Vancouver, Pancreatic Ductal Adenocarcinoma Subtypes by Comprehensive Genomic British Columbia, Canada. 5Division of Medical Oncology, BC Cancer, Vancouver, Analysis (PanGen; NCT02869802); Comprehensive Molecular Characterization British Columbia, Canada. 6University Health Network, University of Toronto, of Advanced Pancreatic Ductal Adenocarcinoma for Better Treatment Selection Toronto, Ontario, Canada. 7Department of Medical Genetics, University of British (COMPASS; NCT02750657). Columbia, Vancouver, British Columbia, Canada. 8Department of Medicine, Corresponding Author: David F. Schaeffer, University of British Columbia, University of British Columbia, Vancouver, British Columbia, Canada. 9Division Vancouver General Hospital, 910 West 10th Avenue, Vancouver V5Z 1M9, of Anatomic Pathology, Vancouver General Hospital, Vancouver, British Colum- Canada. Phone: 604-875-4480; Fax: 604-875-5707; E-mail: bia, Canada. [email protected] Note: Supplementary data for this article are available at Clinical Cancer Clin Cancer Res 2019;XX:XX–XX Research Online (http://clincancerres.aacrjournals.org/). doi: 10.1158/1078-0432.CCR-19-1543 J.M. Karasinska, J.T. Topham, S.E. Kalloger, D.J. Renouf, and D.F. Schaeffer contributed equally to this article. Ó2019 American Association for Cancer Research. AACRJournals.org | OF1 Downloaded from clincancerres.aacrjournals.org on September 27, 2021. © 2019 American Association for Cancer Research. Published OnlineFirst September 3, 2019; DOI: 10.1158/1078-0432.CCR-19-1543 Karasinska et al. NCT02750657) studies at the BC Cancer Agency (PanGen, POG) Translational Relevance and Ontario Institute for Cancer Research (COMPASS) as Pancreatic ductal adenocarcinoma (PDAC) has one of the described previously (7, 29). The PanGen and POG studies were lowest survival rates of all cancers due in part to a limited approved by the University of British Columbia Research Ethics knowledge of clinically relevant tumor subtypes that would facil- Committee (REB# H12-00137, H14-00681, H16-00291) and itate better treatment stratification and the development of new the COMPASS study was approved by the University Health therapies targeting unique molecular signatures. Tumor metabolic Network Research Ethics Board (REB# 15-9596). The studies were heterogeneity contributes to clinical outcome in cancer and repre- conducted in accordance with international ethical guidelines. sents a potential avenue for the development of personalized Written informed consent was obtained from each patient prior treatment strategies. How alterations in distinct metabolic path- to genomic profiling. ways influence PDAC outcome is not well known. We profiled the expression of glycolytic and cholesterogenic genes in 325 resectable Whole genome and transcriptome sequencing and non-resectable PDAC patients and identified distinct sub- POG and PanGen samples were subjected to whole genome and fl groups associated with differences in survival and known prog- transcriptome sequencing as described previously (30). Brie y, nostic pancreatic tumor subtypes. Our findings demonstrate that fresh tumor biopsies were sequenced to a depth of approximately  distinct metabolic gene expression pathways may provide a func- 80 , with approximately 200 million reads generated for transcrip- tional correlate to transcriptome-based pancreatic cancer subtypes, tomes. RNA sequencing (RNA-seq) libraries were prepared using fi which may enable the development of subtype-specific treatment inactive magnetic bead-based mRNA puri cation. RNA-seq was strategies targeting unique metabolic vulnerabilities. performed on COMPASS samples as described previously (7). TCGA (PAAD-US) and ICGC (PACA-CA) data Normalized RNA-seq data (sequence-based gene expression; GRCh37) for all available PAAD-US (n ¼ 142) and PACA-CA addition to prevalent hypoxia (11), which are known inducers of the (n ¼ 234) samples were downloaded from the ICGC data portal – glycolytic pathway in cancer (12 15), and glycolysis contributes to (dcc.icgc.org/) on November 8, 2018 (ICGC data release 27). PACA- tumor progression and chemoresistance in PDAC (13, 16, 17). The CA samples were filtered to exclude any samples labeled as cell lines, effects of glycolysis on tumor progression can be diminished by xenografts, metastatic, normal, or non-laser microdissected enriched. diverting the metabolite pyruvate from conversion to lactate in part PAAD-US samples were filtered to exclude non-PDAC samples as through transport into the mitochondria via the activity of the outlined in a previous study (6). mitochondrial pyruvate complex (MPC), comprised of pyruvate car- Somatic mutation data [those with both copy number variants – rier 1 and 2 (MPC1 and MPC2; refs. 18 20). Reduced MPC activity is (CNV) and single nucleotide variants/indels (SNV/indels) available; associated with poor prognosis in some cancer types (20). Pyruvate is a GRCh37] for all filtered samples with RNA-seq data available (PAAD- metabolic intermediate for the tricarboxylic cycle, providing the US n ¼ 60, PACA-CA n ¼ 86) were downloaded from the ICGC
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