Genomic analysis of fibrolamellar hepatocellular carcinoma

Abstract

Pediatric tumors are relatively infrequent, but are often associated with significant lethality and lifelong morbidity. A major goal of pediatric cancer research has been to identify key drivers of tumorigenesis to eventually develop targeted therapies to enhance cure rate and minimize acute and long-term toxic effects. Here, we used genomic approaches to identify biomarkers and candidate drivers for fibrolamellar hepatocellular carcinoma (FL-HCC), a very rare subtype of pediatric liver cancer for which limited therapeutic options exist. In-depth genomic analyses of one tumor followed by immunohistochemistry validation on seven other tumors showed expression of neuroendocrine markers in FL-HCC. DNA and RNA sequencing data further showed that common cancer pathways are not visibly altered in FL-HCC but identified two novel structural variants, both resulting in fusion transcripts. The first, a 400 kb deletion, results in a DNAJB1-PRKCA fusion transcript, which leads to increased cAMP-dependent protein kinase (PKA) activity in the index tumor case and other FL-HCC cases compared with normal liver. This PKA fusion protein is oncogenic in HCC cells. The second gene fusion event, a translocation between the CLPTM1L and GLIS3 genes, generates a transcript whose product also promotes cancer phenotypes in HCC cell lines. These experiments further highlight the tumorigenic role of gene fusions in the etiology of pediatric solid tumors and identify both candidate biomarkers and possible therapeutic targets for this lethal pediatric disease.

Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

“…Neuroendocrine tumors. FLHCC carries some hallmarks of neuroendocrine malignancies (16,17). The RNA-seq results presented here are in agreement with recent observations that several genes implicated in neuroendocrine tumors (PCSK1 and CALCA) are significantly up-regulated in FLHCC.…”

“…This generates not only a chimeric RNA transcript, but also a chimeric protein with kinase activity indistinguishable from the native PRKACA (21). Similar findings have been reported in other FLHCC patients (17). Whole-genome analysis showed no other recurrent mutations (22).…”

“…Unlike HCC, FLHCC is not associated with viral hepatitis (2,9,12), increased levels of alpha fetoprotein (AFP) (3,5,13,14), or altered p53 or β-catenin (15). It has been proposed that FLHCC has a neuroendocrine origin based on increased expression of proprotein convertase subtilisin/kexin type 1 (PCSK1), NTS, DNER, and calcitonin-related polypeptide alpha (CALCA) (16,17) or an origin in the biliary tree based on increased levels of EpCAM, mCEA, CA19-9, EMA, and CK7 (14). FLHCC has also been associated with features of the mammary gland.…”

Structural insights into mis-regulation of protein kinase A in human tumors

“…In fibrolamellar hepatocellular carcinoma (FL-HCC), a rare liver tumor affecting young adults, ∼400-kb deletions have been discovered in chromosome 19. These deletions result in fusions of the gene for the molecular chaperone DnaJ (DnaJB1) with PRKACA to produce a predominant chimeric protein derived from exon 1 of DnaJB1 fused to exon 2 of PRKACA (12,13). Both sets of studies similarly postulated that these mutations lead to misregulation of signaling by affecting R-subunit binding.…”

Hepatic adenomas with synchronous or metachronous fibrolamellar carcinomas: both are characterized by LFABP loss

“…In contrast, HNF1-α mutations have not been identified in genomic or transcriptomic study of fibrolamellar carcinomas. 2,19,20 This suggests an alternate mechanism for the downregulation of LFABP in fibrolamellar carcinoma, perhaps through methylation or microRNAs. The mosaic pattern seen in some of the fibrolamellar carcinomas is also unusual, with scattered strongly positive tumor cells in a background of more diffuse loss of staining in tumor cells.…”