1
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Shirani M, Levin S, Shebl B, Requena D, Finkelstein TM, Johnson DS, Ng D, Lalazar G, Heissel S, Hojrup P, Molina H, de Jong YP, Rice CM, Singhi AD, Torbenson MS, Coffino P, Lyons B, Simon SM. Increased Protein Kinase A Activity Induces Fibrolamellar Hepatocellular Carcinoma Features Independent of DNAJB1. Cancer Res 2024; 84:2626-2644. [PMID: 38888469 PMCID: PMC11325150 DOI: 10.1158/0008-5472.can-23-4110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/15/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024]
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.
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Affiliation(s)
- Mahsa Shirani
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - Solomon Levin
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - Tova M. Finkelstein
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - Daniel S. Johnson
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
- Department of Physics and Astronomy, Hofstra University, Hempstead, New York.
| | - Denise Ng
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - Gadi Lalazar
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, New York.
| | - Peter Hojrup
- Department of Biochemistry and Molecular Biology. University of Southern Denmark, Odense, Denmark.
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York.
| | - Ype P. de Jong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York.
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York.
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York.
| | - Aatur D. Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
| | | | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
| | - Barbara Lyons
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico.
| | - Sanford M. Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
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2
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Melehy A, Agopian V. Treating rare tumors with liver transplantation. Curr Opin Organ Transplant 2024; 29:30-36. [PMID: 37851086 DOI: 10.1097/mot.0000000000001118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
PURPOSE OF REVIEW The success of liver transplantation (LT) in treating unresectable hepatocellular carcinoma (HCC) has resulted in interest in LT for other oncologic conditions. Here, we discuss the role of LT for rare oncologic indications including metastatic gastroenteropancreatic neuroendocrine tumors (GEP-NETs), hepatic epitheliod hemangioendothelioma (HEHE), fibrolamellar hepatocellular carcinoma (FLC), and hepatic angiosarcoma (HAS). RECENT FINDINGS Conditions reviewed have been documented indications for LT in the available literature. We summarize the experience of LT for these indications and proposed management guidelines. SUMMARY GEP-NETs with isolated metastases to the liver can be treated with LT with excellent long-term outcomes (10-year survival 88%) if strict selection criteria are used (low-intermediate grade, Ki-67% < 20%, complete resection of primary tumor, stable disease for 6 months, <50% hepatic involvement). HEHE is a rare hepatic tumor for which LT can be performed with reported 10-year survival around 70%. FLC is a distinct clinical entity to HCC and is optimally treated with surgical resection though experience with LT is described in observational series (5-year survival 50%, recurrence in 10%). HAS is a rapidly progressive tumor with a dismal prognosis with or without treatment, including LT.
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Affiliation(s)
- Andrew Melehy
- Dumont-UCLA Transplant and Liver Cancer Centers, Department of Surgery, David Geffen School of Medicine at University of California, Los Angeles, California, USA
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3
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Singh AK, Chaube B, Citrin KM, Fowler JW, Lee S, Catarino J, Knight J, Lowery S, Shree S, Boutagy N, Ruz-Maldonado I, Harry K, Shanabrough M, Ross TT, Malaker S, Suárez Y, Fernández-Hernando C, Grabinska K, Sessa WC. Loss of cis-PTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566870. [PMID: 38014178 PMCID: PMC10680637 DOI: 10.1101/2023.11.13.566870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Obesity-linked fatty liver is a significant risk factor for hepatocellular carcinoma (HCC)1,2; however, the molecular mechanisms underlying the transition from non-alcoholic fatty liver disease (NAFLD) to HCC remains unclear. The present study explores the role of the endoplasmic reticulum (ER)-associated protein NgBR, an essential component of the cis-prenyltransferases (cis-PTase) enzyme3, in chronic liver disease. Here we show that genetic depletion of NgBR in hepatocytes of mice (N-LKO) intensifies triacylglycerol (TAG) accumulation, inflammatory responses, ER/oxidative stress, and liver fibrosis, ultimately resulting in HCC development with 100% penetrance after four months on a high-fat diet. Comprehensive genomic and single cell transcriptomic atlas from affected livers provides a detailed molecular analysis of the transition from liver pathophysiology to HCC development. Importantly, pharmacological inhibition of diacylglycerol acyltransferase-2 (DGAT2), a key enzyme in hepatic TAG synthesis, abrogates diet-induced liver damage and HCC burden in N-LKO mice. Overall, our findings establish NgBR/cis-PTase as a critical suppressor of NAFLD-HCC conversion and suggests that DGAT2 inhibition may serve as a promising therapeutic approach to delay HCC formation in patients with advanced non-alcoholic steatohepatitis (NASH).
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Affiliation(s)
- Abhishek K. Singh
- Department of Pharmacology, and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Balkrishna Chaube
- Department of Comparative Medicine, Yale Center for Molecular and Systems Metabolism and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Kathryn M Citrin
- Department of Comparative Medicine, Yale Center for Molecular and Systems Metabolism and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph Wayne Fowler
- Department of Pharmacology, and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Sungwoon Lee
- Department of Pharmacology, and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Jonatas Catarino
- Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - James Knight
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Sarah Lowery
- Chemistry Research Building, Yale University, New Haven, CT, USA
| | - Sonal Shree
- Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Nabil Boutagy
- Department of Pharmacology, and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Inmaculada Ruz-Maldonado
- Department of Comparative Medicine, Yale Center for Molecular and Systems Metabolism and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Kathy Harry
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Marya Shanabrough
- Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Stacy Malaker
- Chemistry Research Building, Yale University, New Haven, CT, USA
| | - Yajaira Suárez
- Department of Comparative Medicine, Yale Center for Molecular and Systems Metabolism and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Carlos Fernández-Hernando
- Department of Comparative Medicine, Yale Center for Molecular and Systems Metabolism and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Kariona Grabinska
- Department of Pharmacology, and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - William C. Sessa
- Department of Pharmacology, and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
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4
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Alshareefy Y, Shen CY, Prekash RJ. Exploring the molecular pathogenesis, diagnosis and treatment of fibrolamellar hepatocellular carcinoma: A state of art review of the current literature. Pathol Res Pract 2023; 248:154655. [PMID: 37429175 DOI: 10.1016/j.prp.2023.154655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/25/2023] [Indexed: 07/12/2023]
Abstract
This paper aims to present a detailed overview of fibrolamellar carcinoma (FLC), a variant of hepatocellular carcinoma (HCC) that accounts for approximately 1-9% of all cases a. according to the SEER database. Despite ongoing research, the aetiology of FLC tumours remains unclear. Nevertheless, FLC is believed to have a better overall prognosis than other primary liver tumours, such as hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma. This study aims to present a comprehensive overview of fibrolamellar carcinoma (FLC), with a focus on its epidemiology, pathogenesis, diagnosis, treatment, and prognosis. FLC frequently incorporate features of stomach pain, weight loss, and malaise in their clinical signs and symptoms, which are generally nonspecific Ultimately, the most common physical finding is an abdominal mass or hepatomegaly. With this said, several unusual presentations have been documented such as Budd Chiari syndrome, severe anaemia, non-bacterial thrombotic endocarditis and many more. In regards to this tumour's genetic analysis, it is characterised by a 400 kb deletion on chromosome 19 leading to a functional DNAJB1-PRKACA chimeric transcript in addition to tetraploidy in 50% of cases. FLC is chromosomally stable as compared to typical HCC. mTOR pathway activation has also been found to play a critical role in 47% of these tumours and EFGR over-expression is also evident. Fibrolamellar carcinomas (FLCs) exhibit a distinctive gross appearance, characterized by a yellow to pale tan colour, with a consistency that can vary from soft to firm and hard. In addition, a central scar is observed in 60-70% of FLC cases. The central scar is typically white or grey in colour and has a fibrous appearance, which is often surrounded by nodular, tumour-like tissue. Its histologic appearance is characterized by large polygonal cells with abundant eosinophilic cytoplasm, large vesiculated nuclei, large nucleoli, and arranged in lamellar bands of collagen fibres. Lamellar bands of fibrosis, consisting of collagen type I, III and IV, have also been identified as a distinctive histologic feature that is observed under low power magnification. Ultrasound, CT and MRI along with image guided biopsy are the primary modalities in diagnosis. Current management options include systemic therapy which has thus far been unremarkable with platinum-based therapies as well combination therapy with interferon alpha-2b being the most successful options. Surgical resection remains the primary treatment modality and there have been no advances in targeted therapies. Although the prognosis for FLC is favourable as compared to other hepatic cancer subtypes such as intrahepatic cholangiocarcinoma, there is a high rate of recurrence ranging from 33% to 100% with a median recurrence-free survival of 20-48 months. As a result of this there is a low overall cure rate associated with this tumour type and much more research is required to gain an in-depth understanding of the molecular mechanisms occurring in order to provide more adequate treatment to patients who suffer from this condition.
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Affiliation(s)
- Yasir Alshareefy
- School of Medicine, Trinity College Dublin, University of Dublin, Ireland.
| | - Chai Yu Shen
- Department of Medicine, Manipal University College, Malaysia
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5
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Levin SN, Tomasini MD, Knox J, Shirani M, Shebl B, Requena D, Clark J, Heissel S, Alwaseem H, Surjan R, Lahasky R, Molina H, Torbenson MS, Lyons B, Migler RD, Coffino P, Simon SM. Disruption of proteome by an oncogenic fusion kinase alters metabolism in fibrolamellar hepatocellular carcinoma. SCIENCE ADVANCES 2023; 9:eadg7038. [PMID: 37343102 PMCID: PMC10284549 DOI: 10.1126/sciadv.adg7038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
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.
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Affiliation(s)
- Solomon N. Levin
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michael D. Tomasini
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - James Knox
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Mahsa Shirani
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jackson Clark
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Rodrigo Surjan
- General Surgery Division, Surgery Department, Hospital Nove de Julho, São Paulo, Brazil
| | - Ron Lahasky
- Lahasky Medical Clinic, Abbeville, LA 70510, USA
- The Fibrolamellar Registry, New York, NY 10028, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | | | - Barbara Lyons
- The Fibrolamellar Registry, New York, NY 10028, USA
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
| | | | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sanford M. Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- The Fibrolamellar Registry, New York, NY 10028, USA
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6
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Gummadi J, Wang X, Xie C. Current Advances in the Treatment of Fibrolamellar Carcinoma of Liver. J Hepatocell Carcinoma 2023; 10:745-752. [PMID: 37215364 PMCID: PMC10198173 DOI: 10.2147/jhc.s406902] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
Fibrolamellar carcinoma (FLC) of the liver is a rare type of liver cancer that is prevalent in children and young adults, often less than 40 years old. The etiology is unclear. It presents without underlying liver disease with distinctive histological features such as fibrous collagen bands surrounding the tumor cells. Fusion protein DNAJB1-PRKACA is found in most of the cases. The prognosis of FLC is poor. Even though curative treatment option is surgery for a certain patient population, other treatment modalities including radiation, chemotherapy are currently being used without significant improvement of overall survival. Recently, targeted therapy and immunotherapy have been studied which may provide survival advantage in the future. This review sought to compile data from clinical trials and case reports/series to outline the current state of FLC treatment.
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Affiliation(s)
- Jyotsna Gummadi
- Department of Medicine, MedStar Franklin Square Medical Center, Baltimore, MD, 21237, USA
| | - Xin Wang
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Changqing Xie
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20814, USA
- NCI CCR Liver Cancer Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20814, USA
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7
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Rüland L, Andreatta F, Massalini S, Chuva de Sousa Lopes S, Clevers H, Hendriks D, Artegiani B. Organoid models of fibrolamellar carcinoma mutations reveal hepatocyte transdifferentiation through cooperative BAP1 and PRKAR2A loss. Nat Commun 2023; 14:2377. [PMID: 37137901 PMCID: PMC10156813 DOI: 10.1038/s41467-023-37951-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 04/06/2023] [Indexed: 05/05/2023] Open
Abstract
Fibrolamellar carcinoma (FLC) is a lethal primary liver cancer, affecting young patients in absence of chronic liver disease. Molecular understanding of FLC tumorigenesis is limited, partly due to the scarcity of experimental models. Here, we CRISPR-engineer human hepatocyte organoids to recreate different FLC backgrounds, including the predominant genetic alteration, the DNAJB1-PRKACA fusion, as well as a recently reported background of FLC-like tumors, encompassing inactivating mutations of BAP1 and PRKAR2A. Phenotypic characterizations and comparisons with primary FLC tumor samples revealed mutant organoid-tumor similarities. All FLC mutations caused hepatocyte dedifferentiation, yet only combined loss of BAP1 and PRKAR2A resulted in hepatocyte transdifferentiation into liver ductal/progenitor-like cells that could exclusively grow in a ductal cell environment. BAP1-mutant hepatocytes represent primed cells attempting to proliferate in this cAMP-stimulating environment, but require concomitant PRKAR2A loss to overcome cell cycle arrest. In all analyses, DNAJB1-PRKACAfus organoids presented with milder phenotypes, suggesting differences between FLC genetic backgrounds, or for example the need for additional mutations, interactions with niche cells, or a different cell-of-origin. These engineered human organoid models facilitate the study of FLC.
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Affiliation(s)
- Laura Rüland
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Simone Massalini
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Hans Clevers
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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8
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Simon SM. Fighting rare cancers: lessons from fibrolamellar hepatocellular carcinoma. Nat Rev Cancer 2023; 23:335-346. [PMID: 36932129 PMCID: PMC10022574 DOI: 10.1038/s41568-023-00554-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/12/2023] [Indexed: 03/19/2023]
Abstract
The fight against rare cancers faces myriad challenges, including missed or wrong diagnoses, lack of information and diagnostic tools, too few samples and too little funding. Yet many advances in cancer biology, such as the realization that there are tumour suppressor genes, have come from studying well-defined, albeit rare, cancers. Fibrolamellar hepatocellular carcinoma (FLC), a typically lethal liver cancer, mainly affects adolescents and young adults. FLC is both rare, 1 in 5 million, and problematic to diagnose. From the paucity of data, it was not known whether FLC was one cancer or a collection with similar phenotypes, or whether it was genetically inherited or the result of a somatic mutation. A personal journey through a decade of work reveals answers to these questions and a road map of steps and missteps in our fight against a rare cancer.
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9
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Wang WC, Lai YC. DUSP5 and PHLDA1 mutations in mature cystic teratomas of the ovary identified on whole-exome sequencing may explain teratoma characteristics. Hum Genomics 2022; 16:50. [PMID: 36289533 PMCID: PMC9609193 DOI: 10.1186/s40246-022-00424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/19/2022] [Indexed: 11/21/2022] Open
Abstract
Background Mature cystic teratomas of the ovary are the most common type of germ cell tumor, comprising 33% of ovarian tumors. Studying these tumors may result in a better understanding of their stepwise developmental processes and molecular bases and provide useful information for the development of tissue-engineering technologies. Methods In the present study, 9 mature cystic teratomas of the ovary were analyzed by whole-exome sequencing and the results were compared with the Catalogue of Somatic Mutations in Cancer and dbSNP databases. Results Mutations were validated in 15 genes with alterations in all 9 (100%) samples and changes in protein coding. The top 10 mutated genes were FLG, MUC17, MUC5B, RP1L1, NBPF1, GOLGA6L2, SLC29A3, SGK223, PTGFRN, and FAM186A. Moreover, 7 variants in exons with changes in protein coding are likely of importance in the development of mature cystic teratomas of the ovary, namely PTGFRN, DUSP5, MPP2, PHLDA1, PRR21, GOLGA6L2, and KRTAP4-2. Conclusions These genetic alterations may play an important etiological role in teratoma formation. Moreover, novel mutations in DUSP5 and PHLDA1 genes found on whole-exome sequencing may help to explain the characteristics of teratomas. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00424-w.
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Affiliation(s)
- Wen-Chung Wang
- grid.414969.70000 0004 0642 8534Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung, 412 Taiwan
| | - Yen-Chein Lai
- grid.411641.70000 0004 0532 2041Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, No. 110, Sec. 1, Chien Kuo N. Road, Taichung, 402 Taiwan ,grid.411645.30000 0004 0638 9256Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
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10
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Shebl B, Ng D, Lalazar G, Rosemore C, Finkelstein TM, Migler RD, Zheng G, Zhang P, Jiang CS, Qureshi A, Vaughan R, Yarchoan M, de Jong YP, Rice CM, Coffino P, Ortiz MV, Zhou D, Simon SM. Targeting BCL-XL in fibrolamellar hepatocellular carcinoma. JCI Insight 2022; 7:e161820. [PMID: 36073545 PMCID: PMC9536265 DOI: 10.1172/jci.insight.161820] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Fibrolamellar hepatocellular carcinoma (FLC) is a rare and often lethal liver cancer with no proven effective systemic therapy. Inhibition of the antiapoptotic protein BCL-XL was found to synergize with a variety of systemic therapies in vitro using cells dissociated from patient-derived xenografts (PDX) of FLC or cells dissociated directly from surgical patient resections. As BCL-XL is physiologically expressed in platelets, prior efforts to leverage this vulnerability in other cancers have been hampered by severe thrombocytopenia. To overcome this toxicity, we treated FLC models with DT2216, a proteolysis targeting chimera (PROTAC) that directs BCL-XL for degradation via the von Hippel-Lindau (VHL) E3 ligase, which is minimally expressed in platelets. The combination of irinotecan and DT2216 in vitro on cells directly acquired from patients or in vivo using several xenografts derived from patients with FLC demonstrated remarkable synergy and at clinically achievable doses not associated with significant thrombocytopenia.
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Affiliation(s)
- Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
| | - Denise Ng
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
| | - Gadi Lalazar
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
| | - Carly Rosemore
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tova M. Finkelstein
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
| | | | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Peiyi Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Caroline S. Jiang
- Hospital Biostatistics, The Rockefeller University, New York, New York, USA
| | - Adam Qureshi
- Hospital Biostatistics, The Rockefeller University, New York, New York, USA
| | - Roger Vaughan
- Hospital Biostatistics, The Rockefeller University, New York, New York, USA
| | - Mark Yarchoan
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ype P. de Jong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
| | - Michael V. Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Sanford M. Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
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11
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Narayan NJC, Requena D, Lalazar G, Ramos-Espiritu L, Ng D, Levin S, Shebl B, Wang R, Hammond WJ, Saltsman JA, Gehart H, Torbenson MS, Clevers H, LaQuaglia MP, Simon SM. Human liver organoids for disease modeling of fibrolamellar carcinoma. Stem Cell Reports 2022; 17:1874-1888. [PMID: 35803261 PMCID: PMC9391427 DOI: 10.1016/j.stemcr.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
Fibrolamellar carcinoma (FLC) is a rare, often lethal, liver cancer affecting adolescents and young adults, for which there are no approved therapeutics. The development of therapeutics is hampered by a lack of in vitro models. Organoids have shown utility as a model system for studying many diseases. In this study, tumor tissue and the adjacent non-tumor liver were obtained at the time of surgery. The tissue was dissociated and grown as organoids. We developed 21 patient-derived organoid lines: 12 from metastases, three from the liver tumor and six from adjacent non-tumor liver. These patient-derived FLC organoids recapitulate the histologic morphology, immunohistochemistry, and transcriptome of the patient tumor. Patient-derived FLC organoids were used in a preliminary high-throughput drug screen to show proof of concept for the identification of therapeutics. This model system has the potential to improve our understanding of this rare cancer and holds significant promise for drug testing and development.
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Affiliation(s)
- Nicole J C Narayan
- Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Gadi Lalazar
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Lavoisier Ramos-Espiritu
- High Throughput and Spectroscopy Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Denise Ng
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Solomon Levin
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ruisi Wang
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - William J Hammond
- Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - James A Saltsman
- Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Helmuth Gehart
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands
| | - Michael S Torbenson
- Department of Laboratory Medicine and Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hans Clevers
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands
| | - Michael P LaQuaglia
- Pediatric Surgical Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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12
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Abdelhamed W, El-Kassas M. Fibrolamellar hepatocellular carcinoma: A rare but unpleasant event. World J Gastrointest Oncol 2022; 14:1103-1114. [PMID: 35949219 PMCID: PMC9244987 DOI: 10.4251/wjgo.v14.i6.1103] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/19/2022] [Accepted: 05/08/2022] [Indexed: 02/06/2023] Open
Abstract
Fibrolamellar carcinoma (FLC) is a rare variant of hepatocellular carcinoma (HCC), comprising 1%–9% of all HCCs. FLC is a poorly understood malignancy, which seems to be more prevalent in young patients with no underlying liver diseases. The term “fibrolamellar” is derived from thick fibrous collagen bands surrounding the tumor cells. Unlike HCC, cirrhosis and viral hepatitis infection are not predisposing to FLC, and it is not associated with elevations in serum alpha-fetoprotein. FLC patients often present with vague abdominal pain, nausea, malaise, and weight loss. Most cases present are at an advanced stage at the time of initial diagnosis. However, curative treatment options can still be offered to up to 70% of patients. Surgery (resection/liver transplantation) is the mainstay of treatment and the only potentially curative option. FLCs have been less chemo-responsive than the conventional HCC, however, in advanced cases, multimodality treatments can be effective. Recent advances in molecular studies of FLC have found a unique DNAJB1–PRKACA fusion transcript in most of the cases studied. The review aims to describe clinical characteristics, diagnostic methods, and therapeutic modalities for this rare tumor to raise awareness among clinicians and surgeons.
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Affiliation(s)
- Walaa Abdelhamed
- Department of Endemic Medicine, Sohag University, Sohag 14322, Egypt
| | - Mohamed El-Kassas
- Department of Endemic Medicine, Faculty of Medicine, Helwan University, Cairo 11795, Egypt
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13
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Dinh TA, Utria AF, Barry KC, Ma R, Abou-Alfa GK, Gordan JD, Jaffee EM, Scott JD, Zucman-Rossi J, O’Neill AF, Furth ME, Sethupathy P. A framework for fibrolamellar carcinoma research and clinical trials. Nat Rev Gastroenterol Hepatol 2022; 19:328-342. [PMID: 35190728 PMCID: PMC9516439 DOI: 10.1038/s41575-022-00580-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 12/17/2022]
Abstract
Fibrolamellar carcinoma (FLC), a rare, lethal hepatic cancer, occurs primarily in adolescents and young adults. Unlike hepatocellular carcinoma, FLC has no known association with viral, metabolic or chemical agents that cause cirrhosis. Currently, surgical resection is the only treatment demonstrated to achieve cure, and no standard of care exists for systemic therapy. Progress in FLC research illuminates a transition from an obscure cancer to one for which an interactive community seems poised to uncover fundamental mechanisms and initiate translation towards novel therapies. In this Roadmap, we review advances since the seminal discovery in 2014 that nearly all FLC tumours express a signature oncogene (DNAJB1-PRKACA) encoding a fusion protein (DNAJ-PKAc) in which the J-domain of a heat shock protein 40 (HSP40) co-chaperone replaces an amino-terminal segment of the catalytic subunit of the cyclic AMP-dependent protein kinase (PKA). Important gains include increased understanding of oncogenic pathways driven by DNAJ-PKAc; identification of potential therapeutic targets; development of research models; elucidation of immune mechanisms with potential for the development of immunotherapies; and completion of the first multicentre clinical trials of targeted therapy for FLC. In each of these key areas we propose a Roadmap for future progress.
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Affiliation(s)
- Timothy A. Dinh
- Medical Scientist Training Program, University of North Carolina, Chapel Hill, NC, USA.,Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA.,These authors contributed equally: Timothy A. Dinh, Alan F. Utria, Kevin C. Barry
| | - Alan F. Utria
- Department of Surgery, University of Washington, Seattle, WA, USA.,These authors contributed equally: Timothy A. Dinh, Alan F. Utria, Kevin C. Barry
| | - Kevin C. Barry
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,These authors contributed equally: Timothy A. Dinh, Alan F. Utria, Kevin C. Barry
| | - Rosanna Ma
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Ghassan K. Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Medical College at Cornell University, New York, NY, USA
| | - John D. Gordan
- Gastrointestinal oncology, University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Elizabeth M. Jaffee
- Department of oncology, Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - John D. Scott
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne université, Inserm, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Allison F. O’Neill
- Department of Paediatric Hematology/oncology, Dana-Farber Cancer Institute, Harvard University, Boston, MA, USA
| | - Mark E. Furth
- Fibrolamellar Cancer Foundation, Greenwich, CT, USA.,;
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA.,;
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14
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Refractory Hyperammonemic encephalopathy in Fibrolamellar hepatocellular carcinoma, a case report and literature review. Curr Probl Cancer 2022; 46:100847. [PMID: 35276469 DOI: 10.1016/j.currproblcancer.2022.100847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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Polychronidis G, Feng J, Murtha-Lemekhova A, Heger U, Mehrabi A, Hoffmann K. Factors Influencing Overall Survival for Patients with Fibrolamellar Hepatocellular Carcinoma: Analysis of the Surveillance, Epidemiology, and End Results Database. Int J Gen Med 2022; 15:393-406. [PMID: 35035232 PMCID: PMC8754463 DOI: 10.2147/ijgm.s338066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/03/2021] [Indexed: 12/19/2022] Open
Abstract
Background The study aimed to develop a nomogram to predict overall survival (OS) for patients with FLC using a national database. Methods The Surveillance, Epidemiology, and End Results database of the National Cancer Institute was reviewed to identify FLC cases with histological confirmation between 2004 and 2014. Cox proportional hazards models were used to identify factors associated with OS. The validation of the nomogram was performed using concordance index (C-index) and calibration curves. Results Out of 170 cases with complete follow-up, 87 received surgery/ablation and 12 received transplantation with significantly higher OS than chemotherapy alone while transplantation combined with chemotherapy showed better survival than solely transplantation. The combination of surgery and chemotherapy showed worse OS than surgery alone. Survival was negatively influenced by T4 stadium (HR = 5.91), while young age and surgery were positive predictive factors. There was no influence of gender, ethnicity or nodal status on survival. The rate of AFP positivity was comparable with and without the presence of distal metastases. Conclusion FLC survival is greatly dependent upon appropriate surgical management irrespective of tumor stadium.
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Affiliation(s)
- Georgios Polychronidis
- Department of General, Visceral and Transplant Surgery, Heidelberg University Clinic, Heidelberg, Germany
| | - Jincheng Feng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Anastasia Murtha-Lemekhova
- Department of General, Visceral and Transplant Surgery, Heidelberg University Clinic, Heidelberg, Germany
| | - Ulrike Heger
- Department of General, Visceral and Transplant Surgery, Heidelberg University Clinic, Heidelberg, Germany
| | - Arianeb Mehrabi
- Department of General, Visceral and Transplant Surgery, Heidelberg University Clinic, Heidelberg, Germany
| | - Katrin Hoffmann
- Department of General, Visceral and Transplant Surgery, Heidelberg University Clinic, Heidelberg, Germany
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16
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Karamafrooz A, Brennan J, Thomas DD, Parker LL. Integrated Phosphoproteomics for Identifying Substrates of Human Protein Kinase A ( PRKACA) and Its Oncogenic Mutant DNAJB1 -PRKACA. J Proteome Res 2021; 20:4815-4830. [PMID: 34436901 PMCID: PMC10153428 DOI: 10.1021/acs.jproteome.1c00500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The DNAJB1-PRKACA fusion is the signature genetic event of fibrolamellar hepatocellular carcinoma (FL-HCC), a rare but lethal liver cancer that primarily affects adolescents and young adults. A deletion fuses the first exon of the HSP40 gene (DNAJB1), with exons 2-10 of protein kinase A (PRKACA), producing the chimeric kinase DNAJB1-PKAca (J-PKAca). The HSP40 portion's scaffolding/chaperone function has been implicated in redirecting substrate recognition to upregulate oncogenic pathways, but the direct substrates of this fusion are not fully known. We integrated cell-based and in vitro phosphoproteomics to identify substrates targeted directly by PKA and J-PKAca, comparing phosphoproteome profiles from cells with in vitro rephosphorylation of peptides and proteins from lysates using recombinant enzymes. We identified a subset of phosphorylation sites in both cell-based and in vitro experiments, as well as altered pathways and proteins consistent with observations from related studies. We also treated cells with PKA inhibitors that function by two different mechanisms (rpcAMPs and PKI) and examined phosphoproteome profiles, finding some substrates that persisted in the presence of inhibitors and revealing differences between WT and chimera. Overall, these results provide potential insights into J-PKAca's oncogenic activity in a complex cellular system and may provide candidate targets for therapeutic follow-up.
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Affiliation(s)
- Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Current affiliation: Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Jack Brennan
- Independent Technology Consultant, LIC, Boston, Massachusetts 02129, United States
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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17
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Lalazar G, Requena D, Ramos-Espiritu L, Ng D, Bhola PD, de Jong YP, Wang R, Narayan NJC, Shebl B, Levin S, Michailidis E, Kabbani M, Vercauteren KOA, Hurley AM, Farber BA, Hammond WJ, Saltsman JA, Weinberg EM, Glickman JF, Lyons BA, Ellison J, Schadde E, Hertl M, Leiting JL, Truty MJ, Smoot RL, Tierney F, Kato T, Wendel HG, LaQuaglia MP, Rice CM, Letai A, Coffino P, Torbenson MS, Ortiz MV, Simon SM. Identification of Novel Therapeutic Targets for Fibrolamellar Carcinoma Using Patient-Derived Xenografts and Direct-from-Patient Screening. Cancer Discov 2021; 11:2544-2563. [PMID: 34127480 PMCID: PMC8734228 DOI: 10.1158/2159-8290.cd-20-0872] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/12/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022]
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.
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Affiliation(s)
- Gadi Lalazar
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York
| | - David Requena
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
| | - Lavoisier Ramos-Espiritu
- High Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, New York
| | - Denise Ng
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
| | - Patrick D Bhola
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ype P de Jong
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, New York
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York
| | - Ruisi Wang
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
| | - Nicole J C Narayan
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
- Pediatric Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bassem Shebl
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
| | - Solomon Levin
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York
| | - Mohammad Kabbani
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York
| | - Koen O A Vercauteren
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York
- Laboratory of Liver Infectious Diseases, Ghent University, Ghent, Belgium
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Arlene M Hurley
- Hospital Program Direction, The Rockefeller University, New York, New York
| | - Benjamin A Farber
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
- Department of Surgery, Division of Pediatric Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - William J Hammond
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
- Pediatric Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - James A Saltsman
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
- Pediatric Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, Mount Sinai Hospital, New York, New York
| | - Ethan M Weinberg
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - J Fraser Glickman
- High Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, New York
| | - Barbara A Lyons
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico
| | - Jessica Ellison
- Division of Transplantation, Rush University Medical Center, Chicago, Illinois
| | - Erik Schadde
- Department of Surgery, Division of Transplantation and Division of Surgical Oncology, Rush University Medical Center, Chicago, Illinois
| | - Martin Hertl
- Division of Transplantation, Rush University Medical Center, Chicago, Illinois
| | - Jennifer L Leiting
- Division of Subspecialty General Surgery, Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Mark J Truty
- Division of Subspecialty General Surgery, Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Rory L Smoot
- Division of Subspecialty General Surgery, Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Faith Tierney
- Division of Abdominal Organ Transplantation, New York-Presbyterian/Columbia University, New York, New York
| | - Tomoaki Kato
- Division of Abdominal Organ Transplantation, New York-Presbyterian/Columbia University, New York, New York
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael P LaQuaglia
- Pediatric Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Philip Coffino
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
| | | | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
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18
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Abstract
Fibrolamellar carcinoma (FLC) is a rare malignant entity arising from the liver and primarily affecting patients in late adolescence and young adulthood. FLC tumors are characterized by their unique histologic features and an only recently discovered genomic alteration: a chimeric fusion protein found in nearly all tumors. The rarity of these tumors coupled with the only recent acknowledgement of this genomic abnormality has likely led to disease under-recognition and de-prioritization of collaborative efforts aimed at establishing an evidence-guided standard of care. Surgical resection undoubtedly remains a mainstay of therapy and a necessity for cure but given the incidence of metastatic disease at diagnosis and high rates of distant relapse, systemic therapies remain a key component of disease control. There are few systemic therapies that have demonstrated proven benefit. Recent efforts have galvanized around single-institute or small consortia-based studies specifically focused on the enrollment of patients with FLC or use of agents with biologic rationale. This review will outline the current state of FLC epidemiology, histology, biology and trialed therapies derived from available published literature.
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19
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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20
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El Dika I, Bowman AS, Berger MF, Capanu M, Chou JF, Benayed R, Zehir A, Shia J, O'Reilly EM, Klimstra DS, Solit DB, Abou-Alfa GK. Molecular profiling and analysis of genetic aberrations aimed at identifying potential therapeutic targets in fibrolamellar carcinoma of the liver. Cancer 2020; 126:4126-4135. [PMID: 32663328 DOI: 10.1002/cncr.32960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/23/2020] [Accepted: 04/13/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Fibrolamellar carcinoma (FLC) is a rare primary liver cancer of young adults. A functional chimeric transcript resulting from the in-frame fusion of the DNAJ homolog, subfamily B, member 1 (DNAJB1), and the catalytic subunit of protein kinase A (PRKACA) genes on chromosome 19 is believed to be unique in FLC, with a possible role in pathogenesis, yet with no established therapeutic value. The objective of the current study was to understand the molecular landscape of FLC and to identify potential novel therapeutic targets. METHODS Archival fresh, formalin-fixed, paraffin-embedded samples from patients with FLC who prospectively consented to an institutional review board-approved protocol were analyzed using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a next-generation sequencing assay encompassing up to 468 key cancer genes. Custom targeted RNA-Seq was performed in selected patients. Demographics, treatment, and outcome data were collected prospectively. Survival outcomes were estimated and correlated with mutation and/or copy number alterations. RESULTS A total of 33 tumor samples from 31 patients with FLC were analyzed. The median age of the patients at the time of diagnosis was 18 years and approximately 53% were women. The DNAJB1-PRKACA fusion transcript was detected in 100% of patients. In 10 of 31 patients in which MSK-IMPACT did not detect the fusion, its presence was confirmed by targeted RNA-Seq. TERT promoter mutation was the second most common, and was detected in 7 patients. The median follow up was 30 months (range, 6-153 months). The 3-year overall survival rate was 84% (95% CI, 61%-93%). CONCLUSIONS The DNAJB1-PRKACA fusion transcript is nonspecific and nonsensitive to FLC. Its potential therapeutic value currently is under evaluation. Opportunities currently are under development for therapy that may be driven or related to the DNAJB1-PRKACA fusion transcript or any therapeutic target identified from next-generation sequencing in patients with FLC.
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Affiliation(s)
- Imane El Dika
- Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell College of Medicine, New York, New York, USA
| | - Anita S Bowman
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell College of Medicine, New York, New York, USA
| | - Marinela Capanu
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Joanne F Chou
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell College of Medicine, New York, New York, USA
| | - Eileen M O'Reilly
- Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell College of Medicine, New York, New York, USA
| | - David S Klimstra
- Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell College of Medicine, New York, New York, USA
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell College of Medicine, New York, New York, USA
| | - Ghassan K Abou-Alfa
- Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell College of Medicine, New York, New York, USA
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21
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Cebrián A, Elosua A, González-de la Higuera B, Irisarri R, Ruiz-Clavijo D. Clavicle tumor as an initial manifestation of fibrolamellar hepatocellular carcinoma. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO (ENGLISH EDITION) 2020. [DOI: 10.1016/j.rgmxen.2019.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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22
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Cebrián A, Elosua A, González-de la Higuera B, Irisarri R, Ruiz-Clavijo D. Clavicle tumor as an initial manifestation of fibrolamellar hepatocellular carcinoma. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO 2019; 85:104-106. [PMID: 31677896 DOI: 10.1016/j.rgmx.2019.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/07/2019] [Indexed: 11/19/2022]
Affiliation(s)
- A Cebrián
- Aparato Digestivo, Hospital García Orcoyen, Estella, España.
| | - A Elosua
- Aparato Digestivo, Complejo Hospitalario de Navarra, Pamplona, España
| | | | - R Irisarri
- Aparato Digestivo, Hospital García Orcoyen, Estella, España
| | - D Ruiz-Clavijo
- Aparato Digestivo, Hospital García Orcoyen, Estella, España
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Lafaro KJ, Eng OS, Raoof M, Ituarte P, Warner SG, Singh G, Fong Y, Melstrom LG. A prognostic nomogram for patients with resected fibrolamellar hepatocellular carcinoma. Hepatobiliary Surg Nutr 2019; 8:338-344. [PMID: 31489303 DOI: 10.21037/hbsn.2019.05.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Fibrolamellar hepatocellular carcinoma (FLHC) is a unique entity compared to conventional hepatocellular carcinoma. The aim of this study was to examine post-resection outcomes and prognostic indicators for survival in this group of FLHC patients. Methods A retrospective analysis of the National Cancer Database (NCDB) for patients with FLHC who underwent resection from 2004 to 2014 was performed. Univariate and multivariate Cox proportional hazard models were used to identify factors associated with overall survival, and a prognostic nomogram was generated. Results There were 197 patients identified, 171 (86.8%) of whom had long-term follow-up data. Univariate and multivariate analyses were performed using patient and tumor demographics with the outcome variable of overall survival. On multivariate analysis, age [hazard ratio (HR) 1.03, P=0.003], vascular invasion (HR 1.75, P=0.05), tumor size >7 cm (HR 2.18, P=0.044), multifocal disease (HR 3.34, P=0.002), and node positive (pN+) disease (HR 2.75, P=0.003) were all negative predictors of overall survival. A prognostic nomogram was generated using these factors with a c-statistic superior to that of American Joint Committee on Cancer (AJCC) staging (0.710 vs. 0.654). Conclusions Independent predictors of decreased overall survival in patients with FLHC include age, vascular invasion, tumor size >7 cm, multifocal disease, and pN+ disease. This is the first study to develop a nomogram exclusively for FLHC that may predict survival in future studies.
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Affiliation(s)
- Kelly J Lafaro
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Oliver S Eng
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Mustafa Raoof
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Philip Ituarte
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Susanne G Warner
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Gagandeep Singh
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Yuman Fong
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Laleh G Melstrom
- Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
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24
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Riehle KJ, Kenerson HL, Riggle KM, Turnham R, Sullivan K, Bauer R, Scott JD, Yeung RS. Neurotensin as a source of cyclic AMP and co-mitogen in fibrolamellar hepatocellular carcinoma. Oncotarget 2019; 10:5092-5102. [PMID: 31489118 PMCID: PMC6707953 DOI: 10.18632/oncotarget.27149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/28/2019] [Indexed: 12/20/2022] Open
Abstract
Fibrolamellar hepatocellular carcinomas (FL-HCCs) possess a unique mutation that encodes a chimeric form of protein kinase A (DNAJ-PKAc), which includes a chaperonin binding domain. DNAJ-PKAc retains most of the biochemical properties of the native enzyme, however, and activity remains dependent on cAMP. We thus speculated that a persistent source of cAMP is necessary to promote FL-HCC carcinogenesis, and that neurotensin (NTS) may drive cAMP production in this setting, given that NS serum and tumor levels are elevated in many patients with FL-HCC. We examined expression of NTS pathway components in human FL-HCCs and paired normal livers, and determined the role of NTS in driving proliferation in tumor slice cultures. Cultured hepatocytes were used to determine interactions between NTS and other proliferative pathways, and to determine the effects of NTS on cAMP production and PKA activity. We found that the NTS pathway is up-regulated in human FL-HCCs, and that NTS activates cAMP and PKA in hepatocytes. NTS increases proliferation in the presence of epidermal growth factor (EGF), and NTS-induced proliferation is dependent on NTSR1 and the EGFR/MEK pathway. We conclude that NTS serves as a co-mitogen in FL-HCC, and provides a source of cAMP to facilitate ongoing activation of DNAJ-PKAc.
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Affiliation(s)
| | | | - Kevin M. Riggle
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Rigney Turnham
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Kevin Sullivan
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Renay Bauer
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - John D. Scott
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Raymond S. Yeung
- Department of Surgery, University of Washington, Seattle, WA, USA
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25
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Cai Y, Lin Y, Xiong X, Lu J, Zhou R, Jin Y, You Z, Ye H, Li F, Cheng N. Knockdown expression of MECR, a novel gene of mitochondrial FAS II inhibits growth and colony-formation, promotes apoptosis of hepatocelluar carcinoma cells. Biosci Trends 2019; 13:234-244. [PMID: 31178528 DOI: 10.5582/bst.2019.01109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mitochondrial trans-2-enoyl-CoA reductase (MECR) is a protein-coding gene, and the protein encoded by this gene is an oxidoreductase that catalyzes the last step in mitochondrial fatty acid synthesis (mtFASII). Numerous studies have shown disorder of lipid metabolism is closely related with malignance, especially in liver cancer. Through pre-experiment, we found that the expression of MECR gene was highly expressed in hepatocelluar carcinoma (HCC) cell lines in vitro. This suggests that the MECR gene may play a role of oncogene in HCC. Therefore, we conducted a preliminary experimental study on the role of MECR gene in HCC cells in vitro. Objective to explore whether the MECR gene can affect the malignant biological behavior of HCC. We selected HCC cell line BEL-7404 as experimental cell, which involves the highest expression of MECR in the pre-experiment. We constructed MECR knockdwon lentivirus vector, and then infected HCC cell lines to down-regulate MECR expression, and establish negative control group (NC). Through various experiments of cytology, our study showed that knockdown of MECR inhibited cell proliferation and colony formation, promoted apoptosis, and inhibited metastasis in HCC cell lines BEL-7404. MECR might serve as a novel gene therapeutic target for the treatment of HCC. Further study is needed to elucidate the signaling pathway through which MECR functions in HCC.
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Affiliation(s)
- Yulong Cai
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Yixin Lin
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Xianze Xiong
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Jiong Lu
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Rongxing Zhou
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Yanwen Jin
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Zhen You
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Hui Ye
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Fuyu Li
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Nansheng Cheng
- Department of Biliary Surgery, West China Hospital, Sichuan University
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26
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Middleton LW, Shen Z, Varma S, Pollack AS, Gong X, Zhu S, Zhu C, Foley JW, Vennam S, Sweeney RT, Tu K, Biscocho J, Eminaga O, Nolley R, Tibshirani R, Brooks JD, West RB, Pollack JR. Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis. JCI Insight 2019; 5:129749. [PMID: 31094703 DOI: 10.1172/jci.insight.129749] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Benign prostatic hyperplasia (BPH) is the most common cause of lower urinary tract symptoms in men. Current treatments target prostate physiology rather than BPH pathophysiology and are only partially effective. Here, we applied next-generation sequencing to gain new insight into BPH. By RNAseq, we uncovered transcriptional heterogeneity among BPH cases, where a 65-gene BPH stromal signature correlated with symptom severity. Stromal signaling molecules BMP5 and CXCL13 were enriched in BPH while estrogen regulated pathways were depleted. Notably, BMP5 addition to cultured prostatic myofibroblasts altered their expression profile towards a BPH profile that included the BPH stromal signature. RNAseq also suggested an altered cellular milieu in BPH, which we verified by immunohistochemistry and single-cell RNAseq. In particular, BPH tissues exhibited enrichment of myofibroblast subsets, whilst depletion of neuroendocrine cells and an estrogen receptor (ESR1)-positive fibroblast cell type residing near epithelium. By whole-exome sequencing, we uncovered somatic single-nucleotide variants (SNVs) in BPH, of uncertain pathogenic significance but indicative of clonal cell expansions. Thus, genomic characterization of BPH has identified a clinically-relevant stromal signature and new candidate disease pathways (including a likely role for BMP5 signaling), and reveals BPH to be not merely a hyperplasia, but rather a fundamental re-landscaping of cell types.
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Affiliation(s)
| | | | | | | | - Xue Gong
- Department of Pathology.,Department of Urology
| | | | | | | | | | | | | | | | | | | | - Robert Tibshirani
- Department of Biomedical Data Science, and.,Department of Statistics, Stanford University School of Medicine, Stanford, California, USA
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27
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Cao B, Lu TW, Martinez Fiesco JA, Tomasini M, Fan L, Simon SM, Taylor SS, Zhang P. Structures of the PKA RIα Holoenzyme with the FLHCC Driver J-PKAcα or Wild-Type PKAcα. Structure 2019; 27:816-828.e4. [PMID: 30905674 PMCID: PMC6506387 DOI: 10.1016/j.str.2019.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/11/2019] [Accepted: 02/28/2019] [Indexed: 01/07/2023]
Abstract
Fibrolamellar hepatocellular carcinoma (FLHCC) is driven by J-PKAcα, a kinase fusion chimera of the J domain of DnaJB1 with PKAcα, the catalytic subunit of protein kinase A (PKA). Here we report the crystal structures of the chimeric fusion RIα2:J-PKAcα2 holoenzyme formed by J-PKAcα and the PKA regulatory (R) subunit RIα, and the wild-type (WT) RIα2:PKAcα2 holoenzyme. The chimeric and WT RIα holoenzymes have quaternary structures different from the previously solved WT RIβ and RIIβ holoenzymes. The WT RIα holoenzyme showed the same configuration as the chimeric RIα2:J-PKAcα2 holoenzyme and a distinct second conformation. The J domains are positioned away from the symmetrical interface between the two RIα:J-PKAcα heterodimers in the chimeric fusion holoenzyme and are highly dynamic. The structural and dynamic features of these holoenzymes enhance our understanding of the fusion chimera protein J-PKAcα that drives FLHCC as well as the isoform specificity of PKA.
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Affiliation(s)
- Baohua Cao
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Juliana A Martinez Fiesco
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Michael Tomasini
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - Lixin Fan
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Ping Zhang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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28
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Hashem EM, Mabrouk MS, Eldeib AM. Analyzing cytogenetic chromosomal aberrations on fibrolamellar hepatocellular carcinoma detected by single-nucleotide polymorphs array. Neural Comput Appl 2019. [DOI: 10.1007/s00521-017-3034-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Sullivan KM, Kenerson HL, Pillarisetty VG, Riehle KJ, Yeung RS. Precision oncology in liver cancer. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:285. [PMID: 30105235 DOI: 10.21037/atm.2018.06.14] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
With the widespread adoption of molecular profiling in clinical oncology practice, many physicians are faced with making therapeutic decisions based upon isolated genomic alterations. For example, epidermal growth factor receptor tyrosine kinase inhibitors (TKIs) are effective in EGFR-mutant non-small cell lung cancers (NSCLC) while anti-EGFR monoclonal antibodies are ineffective in Ras-mutant colorectal cancers. The matching of mutations with drugs aimed at their respective gene products represents the current state of "precision" oncology. Despite the great expectations of this approach, only a fraction of cancers responds to 'targeted' interventions, and many early responders will ultimately develop resistance to these agents. The underwhelming success of mutation-driven therapies across all cancer types is not due to an inability to detect genetic changes in tumors; rather a deficit in functional insight into the genomic alterations that give rise to each cancer. The Achilles heel of precision oncology thus remains the lack of a robust functional understanding of an individual cancer genome that then allows prediction of the best therapy and resultant outcome for that patient. Current practice focuses on one 'actionable' mutation at a time, while solid cancers typically possess many mutations that involve different cellular sub-populations within a tumor. No method or platform currently exists to guide the interpretation of these complex data, nor to accurately predict response to treatment. This problem is particularly germane to primary liver cancers (PLC), for which only a handful of targeted therapies have been introduced. Here, we will review strategies aimed at overcoming some of these challenges in precision oncology, using liver cancer as an example.
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Affiliation(s)
- Kevin M Sullivan
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Heidi L Kenerson
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Venu G Pillarisetty
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Kimberly J Riehle
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Raymond S Yeung
- Northwest Liver Research Program, Department of Surgery, University of Washington, Seattle, Washington, USA
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30
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Rajendran BK, Deng CX. Characterization of potential driver mutations involved in human breast cancer by computational approaches. Oncotarget 2018; 8:50252-50272. [PMID: 28477017 PMCID: PMC5564847 DOI: 10.18632/oncotarget.17225] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.
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Affiliation(s)
- Barani Kumar Rajendran
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Cancer Research Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
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31
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Kersten CA, Sloey EN, Zhou E, Peng Y, Torbenson MS, Guo Y. WITHDRAWN: Fibrolamellar hepatocellular carcinoma: Exploring molecular mechanisms and differentiation pathways to better understand disease outcomes and prognosis. LIVER RESEARCH 2018. [DOI: 10.1016/j.livres.2017.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Abstract
Fibrolamellar hepatocellular carcinoma (FLC) is a rare form of primary liver cancer that affects adolescents and young adults without underlying liver disease. Surgery remains the mainstay of therapy; however, most patients are either not surgical candidates or suffer from recurrence. There is no approved systemic therapy and the overall survival remains poor. Historically classified as a subtype of hepatocellular carcinoma (HCC), FLC has a unique clinical, histological, and molecular presentation. At the genomic level, FLC contains a single 400kB deletion in chromosome 19, leading to a functional DNAJB1-PRKACA fusion protein. In this review, we detail the recent advances in our understanding of the molecular underpinnings of FLC and outline the current knowledge gaps.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/antagonists & inhibitors
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/therapy
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Chromosomes, Human, Pair 19
- Cyclic AMP-Dependent Protein Kinase Catalytic Subunits/antagonists & inhibitors
- Cyclic AMP-Dependent Protein Kinase Catalytic Subunits/genetics
- Cyclic AMP-Dependent Protein Kinase Catalytic Subunits/metabolism
- Gene Fusion
- Genetic Predisposition to Disease
- HSP40 Heat-Shock Proteins/genetics
- Humans
- Molecular Targeted Therapy
- Neoplasm Recurrence, Local
- Phenotype
- Protein Kinase Inhibitors/therapeutic use
- Treatment Outcome
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Affiliation(s)
- Gadi Lalazar
- The Laboratory for Cellular Biophysics, The Rockefeller University, New York, New York
| | - Sanford M Simon
- The Laboratory for Cellular Biophysics, The Rockefeller University, New York, New York
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Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM. Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Sci Rep 2018; 8:720. [PMID: 29335433 PMCID: PMC5768683 DOI: 10.1038/s41598-017-18956-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/19/2017] [Indexed: 01/14/2023] Open
Abstract
In fibrolamellar hepatocellular carcinoma a single genetic deletion results in the fusion of the first exon of the heat shock protein 40, DNAJB1, which encodes the J domain, with exons 2-10 of the catalytic subunit of protein kinase A, PRKACA. This produces an enzymatically active chimeric protein J-PKAcα. We used molecular dynamics simulations and NMR to analyze the conformational landscape of native and chimeric kinase, and found an ensemble of conformations. These ranged from having the J-domain tucked under the large lobe of the kinase, similar to what was reported in the crystal structure, to others where the J-domain was dislodged from the core of the kinase and swinging free in solution. These simulated dislodged states were experimentally captured by NMR. Modeling of the different conformations revealed no obvious steric interactions of the J-domain with the rest of the RIIβ holoenzyme.
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Affiliation(s)
- Michael D Tomasini
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Yingjie Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Biochemistry, Molecular Biology, and Biophysics. University of Minnesota, Minneapolis, MN, 55455, USA
| | - Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics. University of Minnesota, Minneapolis, MN, 55455, USA
| | - Geoffrey Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thijs Beuming
- Schrödinger Inc., 120 West 45th Street, New York, NY, 10036, USA
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province, 130028, People's Republic of China
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, CA, 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, CA, 92093, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Biochemistry, Molecular Biology, and Biophysics. University of Minnesota, Minneapolis, MN, 55455, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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Abstract
Fibrolamellar hepatocellular carcinoma (FLC) is a rare primary liver cancer found in adolescents and young adults without underlying liver disease. A deletion of ~400 kD has been found in one copy of chromosome 19 in the tumor tissue of all patients tested. This produces a fusion of the genes DNAJB1 and PRKACA which, in turn, produces a chimeric transcript and protein. Transcriptomic analysis of the tumor has shown upregulation of various oncologically relevant pathways, including EGF/ErbB, Aurora Kinase A, pak21 and wnt. To explore other factors that may contribute to oncogenesis, we examined the microRNA (miRNA) and long non-coding RNA (lncRNA) expression in FLC. The non-coding RNA expression profile in tumor tissue samples is distinctly different from the adjacent normal liver and from other liver tumors. Furthermore, miRZip knock down or over expression of certain miRNAs led to changes in the levels of coding genes that recapitulated changes observed in FLC, suggesting mechanistically that the changes in the cellular levels of miRNA are not merely correlative. Thus, in addition to serving as diagnostic tools for FLC, non-coding RNAs may serve as therapeutic targets.
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35
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Engelholm LH, Riaz A, Serra D, Dagnæs-Hansen F, Johansen JV, Santoni-Rugiu E, Hansen SH, Niola F, Frödin M. CRISPR/Cas9 Engineering of Adult Mouse Liver Demonstrates That the Dnajb1-Prkaca Gene Fusion Is Sufficient to Induce Tumors Resembling Fibrolamellar Hepatocellular Carcinoma. Gastroenterology 2017; 153:1662-1673.e10. [PMID: 28923495 PMCID: PMC5801691 DOI: 10.1053/j.gastro.2017.09.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/09/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects children and 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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Affiliation(s)
- Lars H Engelholm
- Finsen Laboratory, Rigshospitalet, Copenhagen Biocenter, Copenhagen, Denmark,Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anjum Riaz
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Denise Serra
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Jens V Johansen
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Steen H Hansen
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark,GI Cell Biology Research Laboratory, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Francesco Niola
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Morten Frödin
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Kersten CA, Sloey EN, Zhou E, Peng Y, Torbenson MS, Guo Y. Fibrolamellar hepatocellular carcinoma: Exploring molecular mechanisms and differentiation pathways to better understand disease outcomes and prognosis. LIVER RESEARCH 2017. [DOI: 10.1016/j.livres.2017.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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DNAJB1-PRKACA fusion kinase interacts with β-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma. Proc Natl Acad Sci U S A 2017; 114:13076-13084. [PMID: 29162699 DOI: 10.1073/pnas.1716483114] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A segmental deletion resulting in DNAJB1-PRKACA gene fusion is now recognized as the signature genetic event of fibrolamellar hepatocellular carcinoma (FL-HCC), a rare but lethal liver cancer that primarily affects adolescents and young adults. Here we implement CRISPR-Cas9 genome editing and transposon-mediated somatic gene transfer to demonstrate that expression of either the endogenous fusion protein or a chimeric cDNA leads to the formation of indolent liver tumors in mice that closely resemble human FL-HCC. Notably, overexpression of the wild-type PRKACA was unable to fully recapitulate the oncogenic activity of DNAJB1-PRKACA, implying that FL-HCC does not simply result from enhanced PRKACA expression. Tumorigenesis was significantly enhanced by genetic activation of β-catenin, an observation supported by evidence of recurrent Wnt pathway mutations in human FL-HCC, as well as treatment with the hepatotoxin 3,5-diethoxycarbonyl-1,4-dihydrocollidine, which causes tissue injury, inflammation, and fibrosis. Our study validates the DNAJB1-PRKACA fusion kinase as an oncogenic driver and candidate drug target for FL-HCC, and establishes a practical model for preclinical studies to identify strategies to treat this disease.
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38
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Castelli G, Pelosi E, Testa U. Liver Cancer: Molecular Characterization, Clonal Evolution and Cancer Stem Cells. Cancers (Basel) 2017; 9:cancers9090127. [PMID: 28930164 PMCID: PMC5615342 DOI: 10.3390/cancers9090127] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Liver cancer is the second most common cause of cancer-related death. The major forms of primary liver cancer are hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). Both these tumors develop against a background of cirrhotic liver, non-alcoholic fatty liver disease, chronic liver damage and fibrosis. HCC is a heterogeneous disease which usually develops within liver cirrhosis related to various etiologies: hepatitis B virus (HBV) infection (frequent in Asia and Africa), hepatitis C virus (HCV), chronic alcohol abuse, or metabolic syndrome (frequent in Western countries). In cirrhosis, hepatocarcinogenesis is a multi-step process where pre-cancerous dysplastic macronodules transform progressively into HCC. The patterns of genomic alterations observed in these tumors were recently identified and were instrumental for the identification of potential targeted therapies that could improve patient care. Liver cancer stem cells are a small subset of undifferentiated liver tumor cells, responsible for cancer initiation, metastasis, relapse and chemoresistance, enriched and isolated according to immunophenotypic and functional properties: cell surface proteins (CD133, CD90, CD44, EpCAM, OV-6, CD13, CD24, DLK1, α2δ1, ICAM-1 and CD47); the functional markers corresponding to side population, high aldehyde dehydrogenase (ALDH) activity and autofluorescence. The identification and definition of liver cancer stem cells requires both immunophenotypic and functional properties.
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Affiliation(s)
- Germana Castelli
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00141, Italy.
| | - Elvira Pelosi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00141, Italy.
| | - Ugo Testa
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00141, Italy.
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Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non-coding RNA signature of fibrolamellar carcinoma. Sci Rep 2017; 7:44653. [PMID: 28304380 PMCID: PMC5356346 DOI: 10.1038/srep44653] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/13/2017] [Indexed: 12/13/2022] Open
Abstract
Fibrolamellar carcinoma (FLC) is a unique liver cancer primarily affecting young adults and characterized by a fusion event between DNAJB1 and PRKACA. By analyzing RNA-sequencing data from The Cancer Genome Atlas (TCGA) for >9,100 tumors across ~30 cancer types, we show that the DNAJB1-PRKACA fusion is specific to FLCs. We demonstrate that FLC tumors (n = 6) exhibit distinct messenger RNA (mRNA) and long intergenic non-coding RNA (lincRNA) profiles compared to hepatocellular carcinoma (n = 263) and cholangiocarcinoma (n = 36), the two most common liver cancers. We also identify a set of mRNAs (n = 16) and lincRNAs (n = 4), including LINC00473, that distinguish FLC from ~25 other liver and non-liver cancer types. We confirm this unique FLC signature by analysis of two independent FLC cohorts (n = 20 and 34). Lastly, we validate the overexpression of one specific gene in the FLC signature, carbonic anhydrase XII (CA12), at the protein level by western blot and immunohistochemistry. Both the mRNA and lincRNA signatures support a major role for protein kinase A (PKA) signaling in shaping the FLC gene expression landscape, and present novel candidate FLC oncogenes that merit further investigation.
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40
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Surjan RC, Dos Santos ES, Basseres T, Makdissi FF, Machado MA. A Proposed Physiopathological Pathway to Hyperammonemic Encephalopathy in a Non-Cirrhotic Patient with Fibrolamellar Hepatocellular Carcinoma without Ornithine Transcarbamylase (OTC) Mutation. AMERICAN JOURNAL OF CASE REPORTS 2017; 18:234-241. [PMID: 28270654 PMCID: PMC5358858 DOI: 10.12659/ajcr.901682] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Patient: Male, 31 Final Diagnosis: Fibrolamellar hepatocellular carcinoma Symptoms: Encephalopathy Medication:— Clinical Procedure: — Specialty: Gastroenterology and Hepatology
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Affiliation(s)
- Rodrigo C Surjan
- Department of Surgery, University of São Paulo, São Paulo, SP, Brazil
| | | | - Tiago Basseres
- Department of Surgery, University of São Paulo, São Paulo, SP, Brazil
| | - Fabio F Makdissi
- Department of Gastroenterology, University of São Paulo, São Paulo, SP, Brazil
| | - Marcel A Machado
- Department of Surgery, University of São Paulo, São Paulo, SP, Brazil
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41
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Kyrochristos ID, Glantzounis GK, Ziogas DE, Gizas I, Schizas D, Lykoudis EG, Felekouras E, Machairas A, Katsios C, Liakakos T, Cho WC, Roukos DH. From Clinical Standards to Translating Next-Generation Sequencing Research into Patient Care Improvement for Hepatobiliary and Pancreatic Cancers. Int J Mol Sci 2017; 18:E180. [PMID: 28106782 PMCID: PMC5297812 DOI: 10.3390/ijms18010180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 12/19/2016] [Accepted: 12/27/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatobiliary and pancreatic (HBP) cancers are associated with high cancer-related death rates. Surgery aiming for complete tumor resection (R0) remains the cornerstone of the treatment for HBP cancers. The current progress in the adjuvant treatment is quite slow, with gemcitabine chemotherapy available only for pancreatic ductal adenocarcinoma (PDA). In the advanced and metastatic setting, only two targeted drugs have been approved by the Food & Drug Administration (FDA), which are sorafenib for hepatocellular carcinoma and erlotinib for PDA. It is a pity that multiple Phase III randomized control trials testing the efficacy of targeted agents have negative results. Failure in the development of effective drugs probably reflects the poor understanding of genome-wide alterations and molecular mechanisms orchestrating therapeutic resistance and recurrence. In the post-ENCODE (Encyclopedia of DNA Elements) era, cancer is referred to as a highly heterogeneous and systemic disease of the genome. The unprecedented potential of next-generation sequencing (NGS) technologies to accurately identify genetic and genomic variations has attracted major research and clinical interest. The applications of NGS include targeted NGS with potential clinical implications, while whole-exome and whole-genome sequencing focus on the discovery of both novel cancer driver genes and therapeutic targets. These advances dictate new designs for clinical trials to validate biomarkers and drugs. This review discusses the findings of available NGS studies on HBP cancers and the limitations of genome sequencing analysis to translate genome-based biomarkers and drugs into patient care in the clinic.
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Affiliation(s)
- Ioannis D Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
| | | | - Demosthenes E Ziogas
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, 'G. Hatzikosta' General Hospital, 45001 Ioannina, Greece.
| | | | - Dimitrios Schizas
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Efstathios G Lykoudis
- Department of Plastic Surgery, Ioannina University School of Medicine, 45110 Ioannina, Greece.
| | - Evangelos Felekouras
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Anastasios Machairas
- Third Department of Surgery, Attikon General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece.
| | - Christos Katsios
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
| | - Theodoros Liakakos
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China.
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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42
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Affiliation(s)
- Miral Sadaria Grandhi
- Department of Surgery, Division of Surgical Oncology, Section of Gastrointestinal Surgical Oncology, Rutgers Cancer Institute of New Jersey/Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Timothy M. Pawlik
- Department of Surgery, The Urban Meyer III and Shelley Meyer Chair for Cancer Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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43
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Riggle KM, Turnham R, Scott JD, Yeung RS, Riehle KJ. Fibrolamellar Hepatocellular Carcinoma: Mechanistic Distinction From Adult Hepatocellular Carcinoma. Pediatr Blood Cancer 2016; 63:1163-7. [PMID: 26990031 PMCID: PMC4877189 DOI: 10.1002/pbc.25970] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 02/17/2016] [Indexed: 12/19/2022]
Abstract
Fibrolamellar hepatocellular carcinoma (FL-HCC) has historically been classified as a rare subtype of HCC. However, unlike "classic" HCC, it occurs in children and young adults without underlying liver disease. The recent discovery of a deletion mutation in all FL-HCCs represented a major advancement in understanding the pathogenesis of this disease. This deletion results in the fusion of the genes encoding a heat shock protein (DNAJB1) and the catalytic subunit of protein kinase A (PKA, PRKACA), and overexpression of PRKACA and enhanced cAMP-dependent PKA activity. This review summarizes recent advancements in FL-HCC pathogenesis and characteristics of the HSP40-PKA C protein.
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Affiliation(s)
- Kevin M. Riggle
- Department of SurgeryUniversity of WashingtonSeattleWashington,Division of General and Thoracic SurgerySeattle Children's HospitalSeattleWashington
| | - Rigney Turnham
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleWashington,Department of PharmacologyUniversity of WashingtonSeattleWashington
| | - John D. Scott
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleWashington,Department of PharmacologyUniversity of WashingtonSeattleWashington
| | - Raymond S. Yeung
- Department of SurgeryUniversity of WashingtonSeattleWashington,Northwest Liver Research ProgramUniversity of WashingtonSeattleWashington
| | - Kimberly J. Riehle
- Department of SurgeryUniversity of WashingtonSeattleWashington,Division of General and Thoracic SurgerySeattle Children's HospitalSeattleWashington,Northwest Liver Research ProgramUniversity of WashingtonSeattleWashington,Department of PathologyUniversity of WashingtonSeattleWashington
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44
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Graham RP, Terracciano LM, Meves A, Vanderboom PM, Dasari S, Yeh MM, Torbenson MS, Cruise MW. Hepatic adenomas with synchronous or metachronous fibrolamellar carcinomas: both are characterized by LFABP loss. Mod Pathol 2016; 29:607-15. [PMID: 27015136 DOI: 10.1038/modpathol.2016.59] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/11/2016] [Accepted: 02/11/2016] [Indexed: 02/05/2023]
Abstract
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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Affiliation(s)
- Rondell P Graham
- Division of Anatomic Pathology, Department of Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Matthew M Yeh
- Department of Anatomic Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Michael S Torbenson
- Division of Anatomic Pathology, Department of Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael W Cruise
- Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
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45
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Reid LM, Sethupathy P. The DNAJB1-PRKACA chimera: Candidate biomarker and therapeutic target for fibrolamellar carcinomas. Hepatology 2016; 63:662-4. [PMID: 26505878 DOI: 10.1002/hep.28307] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lola M Reid
- Department of Cell Biology and Physiology, UNC School of Medicine, Chapel Hill, NC.,Program in Molecular Biology and Biotechnology, UNC School of Medicine, Chapel Hill, NC.,Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC
| | - Praveen Sethupathy
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC.,Department of Genetics, UNC School of Medicine, Chapel Hill, NC
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46
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Sergi CM. Hepatocellular Carcinoma, Fibrolamellar Variant: Diagnostic Pathologic Criteria and Molecular Pathology Update. A Primer. Diagnostics (Basel) 2015; 6:diagnostics6010003. [PMID: 26838800 PMCID: PMC4808818 DOI: 10.3390/diagnostics6010003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 12/13/2022] Open
Abstract
Fibrolamellar hepatocellular carcinoma (FL-HCC) is generally a fairly rare event in routine pathology practice. This variant of hepatocellular carcinoma (HCC) is peculiarly intriguing and,in addition, poorly understood. Young people or children are often the target individuals with this type of cancer. Previously, I highlighted some pathology aspects of FL-HCC, but in this review, the distinctive clinico-pathologic features of FL-HCC and the diagnostic pathologic criteria of FL-HCC are fractionally reviewed and expanded upon. Further, molecular genetics update data with reference to this specific tumor are particularly highlighted as a primer for general pathologists and pediatric histopathologists. FL-HCC may present with metastases, and regional lymph nodes may be sites of metastatic spread. However, peritoneal and pulmonary metastatic foci have also been reported. To the best of our knowledge, FL-HCC was initially considered having an indolent course, but survival outcomes have recently been updated reconsidering the prognosis of this tumor. Patients seem to respond well to surgical resection, but recurrences are common. Thus, alternative therapies, such as chemotherapy and radiation, are ongoing. Overall, it seems that this aspect has not been well-studied for this variant of HCC and should be considered as target for future clinical trials. Remarkably, FL-HCC data seem to point to a liver neoplasm of uncertain origin and unveiled outcome. A functional chimeric transcript incorporating DNAJB1 and PRKACA was recently added to FL-HCC. This sensational result may give remarkable insights into the understanding of this rare disease and potentially provide the basis for its specific diagnostic marker. Detection of DNAJB1-PRKACA seems to be, indeed, a very sensitive and specific finding in supporting the diagnosis of FL-HCC. In a quite diffuse opinion, prognosis of this tumor should be reconsidered following the potentially mandatory application of new molecular biological tools.
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Affiliation(s)
- Consolato M Sergi
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, 8440 112 St., AB T6G2B7, Canada.
- Department of Pediatrics, Stollery Children's Hospital, Edmonton, AB T6G2B7, Canada.
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47
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Marquardt JU, Andersen JB, Thorgeirsson SS. Functional and genetic deconstruction of the cellular origin in liver cancer. Nat Rev Cancer 2015; 15:653-67. [PMID: 26493646 DOI: 10.1038/nrc4017] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the past decade, research on primary liver cancers has particularly highlighted the uncommon plasticity of differentiated parenchymal liver cells (that is, hepatocytes and cholangiocytes (also known as biliary epithelial cells)), the role of liver progenitor cells in malignant transformation, the importance of the tumour microenvironment and the molecular complexity of liver tumours. Whereas other reviews have focused on the landscape of genetic alterations that promote development and progression of primary liver cancers and the role of the tumour microenvironment, the crucial importance of the cellular origin of liver cancer has been much less explored. Therefore, in this Review, we emphasize the importance and complexity of the cellular origin in tumour initiation and progression, and attempt to integrate this aspect with recent discoveries in tumour genomics and the contribution of the disrupted hepatic microenvironment to liver carcinogenesis.
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Affiliation(s)
- Jens U Marquardt
- Department of Medicine I, Johannes Gutenberg University, Langenbeckstrasse 1, 55131 Mainz, Germany
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Snorri S Thorgeirsson
- Laboratory of Experimental Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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48
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Transcriptomic characterization of fibrolamellar hepatocellular carcinoma. Proc Natl Acad Sci U S A 2015; 112:E5916-25. [PMID: 26489647 DOI: 10.1073/pnas.1424894112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
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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49
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Lafaro KJ, Pawlik TM. Fibrolamellar hepatocellular carcinoma: current clinical perspectives. J Hepatocell Carcinoma 2015; 2:151-7. [PMID: 27508204 PMCID: PMC4918295 DOI: 10.2147/jhc.s75153] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fibrolamellar carcinoma (FLC) is a variant of hepatocellular carcinoma (HCC), which comprises ∼1%–9% of all HCCs. Although FLC is a variant of HCC, it is distinct from HCC in that it most often affects younger patients (10–35 years of age) with no underlying liver disease. FLC often presents with vague abdominal pain, nausea, abdominal fullness, malaise, and weight loss. Surgery is the current mainstay of treatment for FLC and remains the only potentially curative option. While FLCs are considered less responsive to chemotherapy than their classic HCC counterparts, there have been suggestions that multimodality treatments may be effective, especially in advanced cases. Further research is necessary to determine effective systemic therapies as an adjunct to surgery for FLC.
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Affiliation(s)
- Kelly J Lafaro
- Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timothy M Pawlik
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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50
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Affiliation(s)
- Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
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