Abstract 1837: Comprehensive RNA-seq transcriptome interrogation of paired hepatocellular carcinoma and cirrhosis tissues revealed significant molecular features of disease evolution and modulation of tumor immunity
Authors: Liu Bonnie P. , Okrah Kwame , Cheng Jeff , Motlhabi Maipelo , Sun Charlie , Sumiyoshi Teiko , Ikeda Shoji , Koeppen Hartmut , Mounir Zineb , Cummings Craig , Haque Nadia , Hampton Garret , Amler Lukas , Lackner Mark , Huang Shih-Min A. 
Published: July 2016

Abstract
First 2 authors contributed equally
Hepatocellular carcinoma (HCC) is the second most common cause of death from cancer worldwide with extremely poor prognosis. HCC is known to be closely associated with liver injury-induced cirrhosis caused by various etiologies, including HBV infection. The prolonged timeline and heterogeneous nature of HCC adds complexity to dissecting the biology of this disease in humans. While Sorafenib is approved for the first-line treatment of metastatic HCC, most patients rapidly progress on treatment with Sorafenib. Consequently, alternative therapeutic options for HCC are much needed. The identification of molecular subtypes and reliable biomarkers associated with disease evolution is critical in facilitating development of new therapeutic agents in HCC.
To understand the manifestation of early molecular events in HCC disease progression in human, we analyzed genome-wide RNA-seq data derived from 100 paired samples consisting of HCC tumors (most with 60-80% tumor content) and adjacent cirrhotic tissues from early stage patients (TNM system: T1N0M0, T2N0M0, and T3N0M0; similar to BCLC stage A and B). Differential expression analysis revealed a cluster of genes that significantly differentiated HCC from cirrhotic tissues and illustrated a widespread deregulation of cell cycle machinery modulated by probable molecular abnormalities represented by Polo-Like Kinase, Checkpoint kinases, G2/M DNA damage checkpoint regulation, DNA damage-induced 14-3-3σ signaling, ATM signaling, and estrogen-mediated S-phase entry. Prominent down-regulation of FXR/LXR/RXR activation was also observed in HCC tumors. Strikingly, the unsupervised hierarchical clustering of both cirrhotic and HCC tissues revealed 3 groups of genes with mRNA expression closely correlating with disease progression stage-wise from cirrhosis to T1, T2, and T3 stages. Specifically, we made a novel observation illustrating the stage-wise activation of Wnt signaling pathway, but de-activation of MAPK pathway. Upon in-depth analysis, our data also suggests that as HCC progresses, translation machinery and embryonic morphogenesis are stimulated, while angiogenesis, negative regulation of apoptosis, and mesenchymal cell differentiation are possibly impinged. In addition, we found that components of processes crucial for activating immune response appear to be impaired as disease progresses from cirrhosis to stage T3. To confirm the aforementioned finding through focused assessment of immune-microenvironment by gene expression, we utilized Fluidigm platform and corroborated the down-regulation of effector T cell signature.
In conclusion, data presented provides a holistic depiction of evolution of HCC and the associated tumor immunity, thus paving a way for future detailed subtyping and therapeutics discovery.
Citation Format: Bonnie P. Liu, Kwame Okrah, Jeff Cheng, Maipelo Motlhabi, Charlie Sun, Teiko Sumiyoshi, Shoji Ikeda, Hartmut Koeppen, Zineb Mounir, Craig Cummings, Nadia Haque, Garret Hampton, Lukas Amler, Mark Lackner, Shih-Min A. Huang. Comprehensive RNA-seq transcriptome interrogation of paired hepatocellular carcinoma and cirrhosis tissues revealed significant molecular features of disease evolution and modulation of tumor immunity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1837.