Requena, David

Abstract Fibrolamellar carcinoma (FLC) is a rare, usually lethal primary liver tumor that affects children, adolescents and young adults. Sequencing of FLC tumors in hepatocytes reveals that in 99% of the patients there is one recurrent genomic alteration: A deletion of 400 kB. This produces DNAJB1::PRKACA, a fusion of the first exon of DNAJB1 with the 2nd – 10th exons of PRKACA, the catalytic subunit of protein kinase A (PKA). PKA exists as a holoenzyme of two catalytic subunits and two regulatory subunits. The regulatory subunit both inhibits the catalytic and localizes it in the cell. Calibrated mass spectrometry shows that in normal liver there is always an excess of regulatory>catalytic subunits, but in the adjacent FLC tumor tissue there is an excess of catalytic>regulatory subunits. Different biochemistry assays and proximity ligation reveal both free catalytic, unbound to regulatory subunits, and an increase of kinase activity in the tumor cells. Much of the increase of catalytic subunit is in the nucleus. Transducing primary human hepatocytes (PHH) with DNAJB1::PRKACA is sufficient to recapitulate the transcriptome of FLC tumors. Transduction of PHH with just the wt PRKACA is also sufficient to recapitulate the transcriptome of FLC tumors. Thus, just increasing the level of kinase is sufficient, there is nothing special about the fusion domain. From our tissue repository we have four patients who have a tumor that looks like FLC but does not have a fusion to the catalytic subunit. The only alteration in these patients is loss of regulatory subunit. The transcriptome of these patient tumors is indistinguishable from that of classic DNAJB1::PRKACA FLC in hepatocytes. Additionally, we have a few dozen patients who have either DNAJB1::PRKACA or another fusion, ATP1B1::PRKACA in the ductal cells of their liver (producing cholangiocarcinomas) or ductal cells of their pancreas (producing IOPN, Intraductal Oncolytic Pancreatic Neoplasms). The transcriptome of these patients clusters with the transcriptome of the FLC patients with DNAJB1::PRKACA in the hepatocytes. A functional precision medicine drug repurposing screen found that the EC50 of the response of freshly resected tumors from patients to a wide panel of drugs is the same as that of FLC patients with DNAJB1::PRKACA in their hepatocytes. Based on sequencing one could conclude that patients with deletion of regulatory subunit in the hepatocytes, or expression of DNAJB1::PRKACA in the hepatocytes, or expression of DNAJB1::PRKACA or ATP1B1::PRKACA in the cholangiocytes or pancreatic ductal cells are at least three distinct diseases. An analysis of the cell biological changes reveals that they all of an increase of the ratio of catalytic:regulatory subunit, they have an increase of catalytic subunit in the nucleus, and these all result in the same changes of transcriptome and the same drug-response profile. Thus, looking beyond sequencing to the cellular changes leads to a different conclusion, that maybe they should be considered the same disease. Citation Format: Sanford Simon, Mahsa Shirani, David Requena, Denise Ng, Gadi Lalazar, Solomon Levin, Michael S. Torbenson, Aatur D. Singhi, Henrik Molina, Charles M. Rice, Philip Coffino, Barbara A. Lyons. Precision medicine for the fusion protein driven cancer, fibrolamellar carcinoma (FLC): Beyond sequencing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr B022.

Abstract Fibrolamellar hepatocellular carcinoma (FLC) is a rare liver cancer that is driven by the fusion of DNAJB1 and PRKACA, the catalytic subunit of protein kinase A (PKA). PKA activity is controlled through regulatory proteins that both inhibit catalytic activity and control localization, and an excess of regulatory subunits ensures PRKACA activity is inhibited. Here, we found an increase in the ratio of catalytic to regulatory units in FLC patient tumors driven by DNAJB1::PRKACA using mass spectrometry, biochemistry, and immunofluorescence, with increased nuclear localization of the kinase. Overexpression of DNAJB1::PRKACA, ATP1B1::PRKACA, or PRKACA, but not catalytically inactive kinase, caused similar transcriptomic changes in primary human hepatocytes, recapitulating the changes observed in FLC. Consistently, tumors in patients missing a regulatory subunit or harboring an ATP1B1::PRKACA fusion were indistinguishable from FLC based on the histopathological, transcriptomic, and drug–response profiles. Together, these findings indicate that the DNAJB1 domain of DNAJB1::PRKACA is not required for FLC. Instead, changes in PKA activity and localization determine the FLC phenotype. Significance: Alterations leading to unconstrained protein kinase A signaling, regardless of the presence or absence of PRKACA fusions, drive the phenotypes of fibrolamellar hepatocellular carcinoma, reshaping understanding of the pathogenesis of this rare liver cancer.

Fibrolamellar hepatocellular carcinoma (FLC) is a usually lethal primary liver cancer driven by a somatic dysregulation of protein kinase A. We show that the proteome of FLC tumors is distinct from that of adjacent nontransformed tissue. These changes can account for some of the cell biological and pathological alterations in FLC cells, including their drug sensitivity and glycolysis. Hyperammonemic encephalopathy is a recurrent problem in these patients, and established treatments based on the assumption of liver failure are unsuccessful. We show that many of the enzymes that produce ammonia are increased and those that consume ammonia are decreased. We also demonstrate that the metabolites of these enzymes change as expected. Thus, hyperammonemic encephalopathy in FLC may require alternative therapeutics.

Abstract To repurpose therapeutics for fibrolamellar carcinoma (FLC), we developed and validated patient-derived xenografts (PDX) from surgical resections. Most agents used clinically and inhibitors of oncogenes overexpressed in FLC showed little efficacy on PDX. A high-throughput functional drug screen found primary and metastatic FLC were vulnerable to clinically available inhibitors of TOPO1 and HDAC and to napabucasin. Napabucasin's efficacy was mediated through reactive oxygen species and inhibition of translation initiation, and specific inhibition of eIF4A was effective. The sensitivity of each PDX line inversely correlated with expression of the antiapoptotic protein Bcl-xL, and inhibition of Bcl-xL synergized with other drugs. Screening directly on cells dissociated from patient resections validated these results. This demonstrates that a direct functional screen on patient tumors provides therapeutically informative data within a clinically useful time frame. Identifying these novel therapeutic targets and combination therapies is an urgent need, as effective therapeutics for FLC are currently unavailable. Significance: Therapeutics informed by genomics have not yielded effective therapies for FLC. A functional screen identified TOPO1, HDAC inhibitors, and napabucasin as efficacious and synergistic with inhibition of Bcl-xL. Validation on cells dissociated directly from patient tumors demonstrates the ability for functional precision medicine in a solid tumor. This article is highlighted in the In This Issue feature, p. 2355