Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance

Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy

Finally, we demonstrated that the MAPK signaling pathway is dysregulated in FLC. While the cell line we have derived and used here is, to our knowledge, the only published FLC cell line, it is not without its limitations. As the FLC cells are derived from a PDX model and can be co-cultured with irradiated mouse fibroblasts, we observe a murine component in each derived cell line (see Materials and Methods). However, experiments across multiple cell line derivations with varying degrees of murine component produced similar results (Fig. 7H,I, Fig. S6B ,C). These observations underscore the need for additional models of FLC, including new cell lines. The cell lines described here are all derived from the only published FLC PDX model (Oikawa et al., 2015) , therefore derivations from additional PDX models will be important as they become available. In each cell line derivation, inhibition of the MAPK pathway significantly reduced cell viability, but most effectively in the micromolar range, suggesting these cells exhibit intrinsic drug resistance similar to what has been reported in patients. Combination treatment of MEK inhibitor with the CA12 inhibitor SLC-0111 resulted in enhanced potency compared to MEK inhibitor alone indicating that CA12 inhibition in combination with additional therapeutics might be a viable treatment strategy for FLC. Importantly, inhibitors targeting multiple members of the MAPK cascade are in clinical use for the treatment of other cancers and SLC-0111 is currently in clinical trials for metastatic pancreatic cancer. Repurposing these therapeutics for FLC patients may provide more effective treatments than the limited options currently available. Although we have demonstrated that inhibition of CA12 enhances the potency of MEK inhibitors, inhibition of other FLC enhancer hotspot-associated genes that are potentially involved in drug resistance, such as SLC16A14, TESC, or VCAN, may provide additional therapeutic benefit. Indeed, knockdown of Slc16a14 in AML12 cells expressing Dnajb1-Prkaca both enhances the potency of cobimetinib and demonstrates substantial cytotoxic activity alone.