Subramanian, Subbaya

Abstract Many somatic mutations have been detected in pancreatic ductal adenocarcinoma (PDAC), leading to the identification of some key drivers of disease progression, but the involvement of large genomic rearrangements has often been overlooked. In this study, we performed mate pair sequencing (MPseq) on genomic DNA from 24 PDAC tumors, including 15 laser-captured microdissected PDAC and 9 patient-derived xenografts, to identify genome-wide rearrangements. Large genomic rearrangements with intragenic breakpoints altering key regulatory genes involved in PDAC progression were detected in all tumors. SMAD4, ZNF521, and FHIT were among the most frequently hit genes. Conversely, commonly reported genes with copy number gains, including MYC and GATA6, were frequently observed in the absence of direct intragenic breakpoints, suggesting a requirement for sustaining oncogenic function during PDAC progression. Integration of data from MPseq, exome sequencing, and transcriptome analysis of primary PDAC cases identified limited overlap in genes affected by both rearrangements and point mutations. However, significant overlap was observed in major PDAC-associated signaling pathways, with all PDAC exhibiting reduced SMAD4 expression, reduced SMAD-dependent TGFβ signaling, and increased WNT and Hedgehog signaling. The frequent loss of SMAD4 and FHIT due to genomic rearrangements strongly implicates these genes as key drivers of PDAC, thus highlighting the strengths of an integrated genomic and transcriptomic approach for identifying mechanisms underlying disease initiation and progression. Cancer Res; 76(3); 749–61. ©2015 AACR.

Abstract Progression from adenoma to colon cancer is a multi-step process and the role of microRNAs in this transformation is not completely understood. We used both in vitro and in vivo approaches to demonstrate the role of miRNAs in the transformation of adenoma to adenocarcinoma. Reporter assays were used to show the direct interaction of miRNAs to target gene. A Tet-inducible TripZ system and miRzips constructs were used in the in vitro function and xenograft studies. Kaplan-Meier survival curves and Cox regression were used to analyze the survival data in colon cancer patients. Here, we show that the combination of miR-503 and miR-182 contributes to the transformation of colon adenoma to adenocarcinoma by cooperatively regulating the tumor suppressor gene, FBXW7. We found that miR-182 was upregulated in both colon adenoma and adenocarcinoma, whereas miR-503 was upregulated only in adenocarcinoma, indicating a potential hierarchical and stepwise expression of these miRNAs in the regulation of FBXW7. Furthermore, we showed that colon adenoma derived non-tumorigenic AAC1 cells were transformative and tumorigenic in mice when expressing Tet-inducible miR-503. Finally, the combination of miR-503 and miR-182 transcript levels was predictive of poor outcome in colon cancer patients. We conclude that a step-wise expression of miR-182 and miR-503 in benign adenoma synergistically regulates the driver gene FBXW7, thus contributing to the progression of colon adenoma to adenocarcinoma. Citation Format: Lihua Li, Aaron Sarver, Rohini Khatri, Praveensingh Hajeri, Iris Kamenev, Stephen Thibodeau, Clifford J. Steer, Subbaya Subramanian. MicroRNAs miR-503 and -182 regulate FBXW7 contributing to the malignant transformation to colon adenocarcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4368. doi:10.1158/1538-7445.AM2014-4368

AbstractGenetic changes in colon cancer are known to parallel the tissue abnormalities associated with the disease, namely adenoma and adenocarcinoma. The role of microRNA dysregulation in dysplastic progression, however, is not well understood. Here, we show that miR‐182 and miR‐503 undergo sequential up‐regulation and drive the progression of colon adenoma to adenocarcinoma by cooperatively down‐regulating the tumour suppressor FBXW7. We identified that increased expression of miR‐182 is a feature of adenomas. A subsequent increase in miR‐503 expression works cooperatively with miR‐182 to induce transformation of an adenoma to adenocarcinoma. We show that introducing miR‐503 into AAC1 cells, which are derived from a benign adenoma, confers tumourigenic potential. We also demonstrated that blocking both miR‐182 and miR‐503 in HCT116 colon cancer cells resulted in increased FBXW7 expression and significantly reduced tumour size in xenograft models. We confirmed relevance of these results in patients by examining the expression levels of miR‐182 and miR‐503 in over 200 colon cancer patients with 12 year survival outcome data. Decreased patient survival was correlated with elevated expression of both miRNAs, suggesting that elevated levels of both miR‐182 and miR‐503 define a novel prognostic biomarker for colon cancer patients. In conclusion, we show that a sequential expression of miR‐182 and miR‐503 in benign adenoma cooperatively regulates the tumour suppressor FBXW7, contributing to the malignant transformation of colon adenoma to adenocarcinoma and miR‐182 and miR‐503 may prove to be novel therapeutic targets. Array data are available at: http://www.oncomir.umn.edu/ Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd

Abstract Prostate cancer, a complex disease, can be relatively harmless or extremely aggressive. To identify candidate genes involved in causal pathways of aggressive prostate cancer, we implemented a systems biology approach by combining differential expression analysis and coexpression network analysis to evaluate transcriptional profiles using lymphoblastoid cell lines from 62 prostate cancer patients with aggressive phenotype (Gleason grade ≥ 8) and 63 prostate cancer patients with nonaggressive phenotype (Gleason grade ≤ 5). From 13,935 mRNA genes and 273 microRNAs (miRNA) tested, we identified significant differences in 1,100 mRNAs and 7 miRNAs with a false discovery rate (FDR) of <0.01. We also identified a coexpression module demonstrating significant association with the aggressive phenotype of prostate cancer (P = 3.67 × 10−11). The module of interest was characterized by overrepresentation of cell cycle–related genes (FDR = 3.50 × 10−50). From this module, we further defined 20 hub genes that were highly connected to other genes. Interestingly, 5 of the 7 differentially expressed miRNAs have been implicated in cell cycle regulation and 2 (miR-145 and miR-331-3p) are predicted to target 3 of the 20 hub genes. Ectopic expression of these two miRNAs reduced expression of target hub genes and subsequently resulted in cell growth inhibition and apoptosis. These results suggest that cell cycle is likely to be a molecular pathway causing aggressive phenotype of prostate cancer. Further characterization of cell cycle–related genes (particularly, the hub genes) and miRNAs that regulate these hub genes could facilitate identification of candidate genes responsible for the aggressive phenotype and lead to a better understanding of prostate cancer etiology and progression. [Cancer Res 2009;69(24):9490–7]