Transcriptome profiling identifies a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma

Abstract Background Liver hepatocellular carcinoma (LIHC), as the main type of liver cancer, has become a main health issue as the third-most common cause of mortality in cancer patients. However, conventional chemo- or radio- therapies shows little improvement in survival, which calls for novel therapies. Because of the immunotolerance mechanism existing naturally in liver, immunotherapy provides significant effect in treatment of LIHC patients. Up to now, various immunotherapies have been proposed, but due to the complex pathways from which LIHC cancerous cell escape immunosurveillance, combined therapies are often needed, which are still under development. Methods In the current study, with data downloaded from TCGA database, CIBERSORT was performed for identifying the composition of infiltrating immune cells and further statistical analyses using R 3.5.3 were carried out, aiming at connecting specific immune cells with clinical survival. Results With data of immune and stromal scores downloaded from the website of MD Anderson Cancer Centre, both showed significance in survival time. Further analyses based on the result of CIBERSORT demonstrated that the number of macrophages M0 and T cells CD8 infiltration between para-carcinoma and tumour tissues are markedly different. With combination of clinical data, we were able to identify that a higher amount of activated NK cells (p=0.008) and a lower amount of resting NK cells (p=0.047) presented a longer survival time. Conclusion With the help of the TCGA database and multiple techniques, statistical analyses of transcriptome profiling data and clinical data were successfully carried out. The results in this study may pave the way for a new therapeutic strategy which could be combined with current treatments to further improve the clinical outcome of LIHC patients. Further and deeper investigation of other available data, however, were needed in order to verify the results of current study.

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Characterization of a novel mutation in fibrolamellar hepatocellular carcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2015.33.3_suppl.284 ◽

2015 ◽

Vol 33 (3_suppl) ◽

pp. 284-284

Author(s):

Kevin M Riggle ◽

Heidi Kenerson ◽

Machiko Kazami ◽

Renay Bauer ◽

Raymond Sze Yeung ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Normal Liver ◽

Kinase Assay ◽

Mutant Protein ◽

Intrinsic Activity ◽

Chimeric Transcript ◽

Wild Type ◽

Fibrolamellar Hepatocellular Carcinoma ◽

Mutant Transcript ◽

Elevated Expression

284 Background: Fibrolamellar hepatocellular carcinoma (FL-HCC) is a subtype of HCC occurring in children and young adults in the absence of underlying liver disease. Currently, there is no effective therapy for unresectable or metastatic FL-HCC. Recent genomic analysis identified a consistent mutation in FL-HCC involving a deletion on chromosome 19 resulting in a chimeric transcript containing the 5’-region of a heat shock protein (DNAJB1) fused to the catalytic subunit of protein kinase A (PRKACA). We sought to characterize the resultant protein and its effects on PKA activity in human FL-HCC. Methods: We prepared tissue lysates from four snap-frozen FL-HCC samples with paired, non-tumor liver as well as adult HCCs. PKA activity was determined via a radioactive kinase assay in the presence and absence of cAMP, a PKA activator. RNA was extracted using TRIZOL, and used for qRT-PCR. Triple immuno-fluorescent labeling was performed using antibodies to PRKACA, PKA RIIα, and a nuclear marker, DRAQ5. Results: We found that expression of the chimeric transcript was increased 40-fold in FL-HCC compared to normal liver, and was significantly higher than that of wild-type DNAJB1 and PRKACA in FL-HCC. The corresponding mutant protein was highly expressed in the tumors and was unique to FL-HCC. Basal PKA activities from freshly lysed tumors and paired livers were not significantly different, but cAMP-stimulated PKA activity was significantly higher in FL-HCC tumors when compared to normal liver. Using multi-color immuno-fluorescence we detected mutant DNAJB1-PRKACA within the nucleus, while wild-type PRKACA localizes to the cytoplasm. Conclusions: The expression of DNAJB1-PRKACA is unique to FL-HCC and not found in classic forms of HCC. Markedly elevated expression of the mutant transcript is indicative of dysregulated DNAJB1 promoter activity. PKA activity in FL-HCCs remains cAMP-dependent, but is greatly enhanced in the presence of cAMP; this could reflect an altered intrinsic activity of the mutant protein and/or elevated expression. Further, the mutant protein showed aberrant localization to the nucleus. These findings suggest that DNAJB1-PRKACA in FL-HCC leads to over-activation of PKA, which may contribute to tumor development.

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Transcriptome profiling and genome-wide DNA binding define the differential role of fenretinide and all-trans RA in regulating the death and survival of human hepatocellular carcinoma Huh7 cells

Biochemical Pharmacology ◽

10.1016/j.bcp.2013.01.023 ◽

2013 ◽

Vol 85 (7) ◽

pp. 1007-1017 ◽

Cited By ~ 10

Author(s):

Ying Hu ◽

Hui-Xin Liu ◽

Yuqi He ◽

Yaping Fang ◽

Jianwen Fang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Dna Binding ◽

Transcriptome Profiling ◽

Human Hepatocellular Carcinoma ◽

Genome Wide ◽

Huh7 Cells

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Genomic and transcriptome profiling identified both human and HBV genetic variations and their interactions in Chinese hepatocellular carcinoma

Genomics Data ◽

10.1016/j.gdata.2015.07.018 ◽

2015 ◽

Vol 6 ◽

pp. 1-3 ◽

Cited By ~ 8

Author(s):

Hua Dong ◽

Ziliang Qian ◽

Lan Zhang ◽

Yunqin Chen ◽

Zhenggang Ren ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Transcriptome Profiling ◽

Genetic Variations

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Faculty Opinions recommendation of Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718290970.793492546 ◽

2014 ◽

Author(s):

Domenico Alvaro ◽

Vincenzo Cardinale

Keyword(s):

Hepatocellular Carcinoma ◽

Chimeric Transcript ◽

Fibrolamellar Hepatocellular Carcinoma

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Transcriptome Profiling of Hepatocellular Carcinoma Uncovers Multi-Types of Dysregulated ncRNAs

SSRN Electronic Journal ◽

10.2139/ssrn.3258653 ◽

2018 ◽

Author(s):

Li Zhang ◽

Chunmei Wang ◽

Chenkai Lv ◽

Xiaojie Lu ◽

Xiao Xu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Transcriptome Profiling

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Detection of a Recurrent DNAJB1-PRKACA Chimeric Transcript in Fibrolamellar Hepatocellular Carcinoma

Science ◽

10.1126/science.1249484 ◽

2014 ◽

Vol 343 (6174) ◽

pp. 1010-1014 ◽

Cited By ~ 204

Author(s):

J. N. Honeyman ◽

E. P. Simon ◽

N. Robine ◽

R. Chiaroni-Clarke ◽

D. G. Darcy ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Chimeric Transcript ◽

Fibrolamellar Hepatocellular Carcinoma

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Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1424894112 ◽

2015 ◽

Vol 112 (44) ◽

pp. E5916-E5925 ◽

Cited By ~ 56

Author(s):

Elana P. Simon ◽

Catherine A. Freije ◽

Benjamin A. Farber ◽

Gadi Lalazar ◽

David G. Darcy ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Transcriptome Sequencing ◽

Normal Tissue ◽

Kinase Activity ◽

Aurora Kinase ◽

Chimeric Transcript ◽

Fibrolamellar Hepatocellular Carcinoma ◽

False Discovery ◽

Kinase A

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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