Preview

PDF, English Download (6MB) | Terms of use

Abstract

Prognosis for primary liver cancer remain poor due to a combination of factors including late presentation of disease, genetic heterogeneity and ineffective therapies. Therefore, there is an urgent need to disentangle genetic heterogeneity by characterizing individual mutations and investigating potential vulnerabilities that these mutations may harbor. BAP1 inactivation is one of the most common genetic alterations in liver cancer with prevalence up to 25% in intrahepatic Cholangiocarcinoma (iCCA) and up to 7% in Hepatocellular Carcinoma (HCC), indicating a potential role in these diseases. BAP1 is an epigenetic modifier that deubiquitinates the mono-ubiquitinated K119 residue on histone 2A. In addition to its deubiquitinase activity, BAP1 also contains a HBM motif that mediates the interaction with host cell factor-1 (HCF-1), O-linked N-acetylglucosamine transferase (OGT), and the polycomb group proteins ASXL1 and ASXL2 and thus is a central point for epigenetic regulation. However, despite its functional properties and mutational prevalence in liver cancer, the role of BAP1 in the liver remains unknown. In order to dissect the functional relevance of BAP1 in the liver, I employed Tet-regulatable shRNA mouse strains and in-vivo CRISPR/Cas9 technology as well as in-vitro models of BAP1 depletion in this study. Surprisingly, liver specific Bap1 depletion (using shRNAs) in dietary models of metabolic distress (CD-HFD and HFD) led to acute fatality and severe hepatic injury characterized by elevated serum transaminases (ALT and AST) and Bilirubin, as well as TUNEL positive hepatocytes. Conversely, endogenous restoration of Bap1 rescued fatality and attenuated liver damage, thereby highlighting the importance of BAP1 in this process. Transcriptional profiling and lipidomics analyses revealed elevated unfolded protein response pathway and dysregulated fatty acid metabolism upon Bap1 depletion under metabolic stress. Moreover, to elucidate the role of BAP1 in liver tumorigenesis and liver plasticity, I combined Bap1 loss with other prevalent oncogenic events in liver cancer in-vivo by hydrodynamic tail vein injection. In contrast to the observations in non-tumorigenic livers, Bap1 loss accelerated liver tumorigenesis in combination with Pten-deficiency and enforced YAP expression (YAPS127A) resulting in HCC like tumors. Furthermore, Bap1 loss also co-operated with YAPS127A alone to drive liver tumorigenesis, thereby reinforcing the notion that BAP1 is a bonafide liver tumor suppressor. Similarly, a cocktail comprising Bap1 loss in combination with Arid1a loss and YAPS127A, delivered to murine hepatocytes resulted in a phenotypic switch and liver cancer lineage reprograming exemplified by tumors bearing hallmarks of iCCA, thereby implicating BAP1 in liver cancer plasticity. Additionally, BAP1 deficiency (in tumorigenic and non-tumorigenic livers) was demonstrated to inversely correlate with strong CHOP (ER stress sensor) expression, thus providing a molecular hallmark and point of convergence for BAP1 deficiency in liver pathologies. Finally, using in-vivo and in-vitro models, I identified BAP1 deficiency as a therapeutic vulnerability in TP53 depletion driven tumors. This highlighted the unexpected utility of a tumor suppressor as a genotype specific therapy in liver cancer. Together, the results from this study implicate BAP1 as a critical determinant of hepatic survival in metabolic distress states, as well as a bonafide liver tumor suppressor. Furthermore, BAP1 deficiency was unraveled as a therapeutic vulnerability in TP53 null tumors. Thus, this study unveils previously undiscovered context dependent functions of BAP1 in the liver.