The genomic landscape of fibrolamellar hepatocellular carcinoma: whole genome sequencing of ten patients

Darcy, David G.; Chiaroni-Clarke, Rachel; Murphy, Jennifer; Honeyman, Joshua N.; Bhanot, Umesh; LaQuaglia, Michael P.; Simon, Sanford M.

doi:10.18632/oncotarget.2712

Cited by 63 publications

(61 citation statements)

References 60 publications

(56 reference statements)

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“…Similar findings have been reported in other FLHCC patients (17). Whole-genome analysis showed no other recurrent mutations (22). Here we demonstrate that gene profiles are similar across patients, at the level of both individual genes and gene sets.…”

Section: Discussionsupporting

confidence: 90%

“…This produced a chimeric RNA transcript and a translated chimeric protein that retains the full catalytic activity of wild-type PKA. This chimeric protein was found in 15 of 15 FLHCC patients (21) in the absence of any other recurrent mutations in the DNA (22), which strongly implies a causal link to malignancy. In normal tissue, PKA is involved in many cellular functions (23).…”

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confidence: 82%

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Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

Simon

Freije

Farber

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Fibrolamellar hepatocellular carcinoma (FLHCC) tumors all carry a deletion of ∼400 kb in chromosome 19, resulting in a fusion of the genes for the heat shock protein, DNAJ (Hsp40) homolog, subfamily B, member 1, DNAJB1, and the catalytic subunit of protein kinase A, PRKACA. The resulting chimeric transcript produces a fusion protein that retains kinase activity. No other recurrent genomic alterations have been identified. Here we characterize the molecular pathogenesis of FLHCC with transcriptome sequencing (RNA sequencing). Differential expression (tumor vs. adjacent normal tissue) was detected for more than 3,500 genes (log2 fold change ≥1, false discovery rate ≤0.01), many of which were distinct from those found in hepatocellular carcinoma. Expression of several known oncogenes, such as ErbB2 and Aurora Kinase A, was increased in tumor samples. These and other dysregulated genes may serve as potential targets for therapeutic intervention.

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Section: Discussionsupporting

confidence: 90%

mentioning

confidence: 82%

Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

Simon

Freije

Farber

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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116

174

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“…Human FL-HCC has been concordantly shown to have a relative stable genome with fewer mutations than other liver cancers and, with the exception of the DNAJB1–PRKACA fusion, no known liver cancer genes are recurrently altered 8,11,12,33 . These findings prompted us to analyze the mutational load of our CRISPR/Cas9 generated mouse FL-HCC.…”

Section: Resultsmentioning

confidence: 99%

“…By contrast, this aberration has not been reported in any other cancer 7,9,10 . Mutations in other genes have been detected in FL-HCC tumors along with the DNAJB1–PRKACA alteration 8,11,12 . However, at present, it remains to be established whether any of the genes found mutated in FL-HCC, most notably the DNAJB1–PRKACA fusion, may have a causative role.…”

Section: Introductionmentioning

confidence: 99%

CRISPR/Cas9 Engineering of Adult Mouse Liver Demonstrates That the Dnajb1–Prkaca Gene Fusion Is Sufficient to Induce Tumors Resembling Fibrolamellar Hepatocellular Carcinoma

et al. 2017

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Background & Aims Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects young adults with no underlying liver disease. A somatic, 400 Kb deletion on chromosome 19 that fuses part of the DnaJ heat shock protein family (Hsp40) member B1 gene (DNAJB1) to the protein kinase cAMP-activated catalytic subunit alpha gene (PRKACA) has been repeatedly identified in patients with FL-HCC. However, the DNAJB1–PRKACA gene fusion has not been shown to induce liver tumorigenesis. We used the CRISPR/Cas9 technique to delete in mice the syntenic region on chromosome 8 to create a Dnajb1–Prkaca fusion and monitored the mice for liver tumor development. Methods We delivered CRISPR/Cas9 vectors designed to juxtapose exon 1 of Dnajb1 with exon 2 of Prkaca to create the Dnajb1–Prkaca gene fusion associated with FL-HCC, or control Cas9 vector, via hydrodynamic tail vein injection to livers of 8 week-old female FVB/N mice. These mice did not have any other engineered genetic alterations and were not exposed to liver toxins or carcinogens. Liver tissues were collected 14 months after delivery; genomic DNA was analyzed by PCR to detect the Dnajb1–Prkaca fusion, and tissues were characterized by histology, immunohistochemistry, RNA sequencing, and whole-exome sequencing. Results Livers from 12 of the 15 mice given the vectors to induce the Dnajb1–Prkaca gene fusion, but none of the 11 mice given the control vector, developed neoplasms. The tumors contained the Dnajb1–Prkaca gene fusion and had histologic and cytologic features of human FL-HCCs: large polygonal cells with granular, eosinophilic, and mitochondria-rich cytoplasm, prominent nucleoli, and markers of hepatocytes and cholangiocytes. In comparing expression levels of genes between the mouse tumor and non-tumor liver cells, we identified changes similar to those detected in human FL-HCC, which included genes that affect cell cycle and mitosis regulation. Genomic analysis of mouse neoplasms induced by the Dnajb1–Prkaca fusion revealed a lack of mutations in genes commonly associated with liver cancers, as observed in human FL-HCC. Conclusions Using CRISPR/Cas9 technology, we found generation of the Dnajb1–Prkaca fusion gene in wild-type mice to be sufficient to initiate formation of tumors that have many features of human FL-HCC. Strategies to block DNAJB1–PRKACA might be developed as therapeutics for this form of liver cancer.

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“…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.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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Rare hepatic adenomas are associated with synchronous or metachronous fibrolamellar carcinomas. The morphology of these adenomas has not been well described and they have not been subclassifed using the current molecular classification schema. We examined four hepatic adenomas co-occurring with or preceding a diagnosis of fibrolamellar carcinoma in three patients. On histological examination, three of the adenomas showed the typical morphology of HNF1-α inactivated adenomas, whereas one showed a myxoid adenoma morphology. All of the adenomas were negative for PRKACA rearrangements by Fluorescence in situ Hybridization (FISH) analysis. All four of the adenomas showed complete loss or significant reduction of liver fatty acid binding protein (LFABP) expression by immunohistochemistry. Interestingly, the fibrolamellar carcinomas in each case also showed loss of LFABP by immunohistochemistry. One of the fibrolamellar carcinomas was negative for PRKACA rearrangements by FISH, whereas the others were positive. To investigate if LFBAP loss is typical of fibrolamellar carcinomas in general, an additional cohort of tumors was studied (n = 19). All 19 fibrolamellar carcinomas showed the expected PRKACA rearrangements and immunostains showed loss of LFABP in each case, consistent with HNF1-α inactivation. To validate this observation, mass spectrometry-based proteomics was performed on tumor-normal pairs of six fibrolamellar carcinomas and showed an average 10-fold reduction in LFABP protein levels, compared with matched normal liver tissue. In conclusion, hepatic adenomas co-occurring with fibrolamellar carcinomas show LFABP loss and are negative for PRKACA rearrangements, indicating they are genetically distinct lesions. These data also demonstrate that LFABP loss, which characterizes HNF1-α inactivation, is a consistent feature of fibrolamellar carcinoma, indicating HNF1-α inactivation is an important event in fibrolamellar carcinoma pathogenesis.

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The genomic landscape of fibrolamellar hepatocellular carcinoma: whole genome sequencing of ten patients

Cited by 63 publications

References 60 publications

Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

CRISPR/Cas9 Engineering of Adult Mouse Liver Demonstrates That the Dnajb1–Prkaca Gene Fusion Is Sufficient to Induce Tumors Resembling Fibrolamellar Hepatocellular Carcinoma

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

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