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Rahi H, Olave MC, Fritchie KJ, Greipp PT, Halling KC, Kipp BR, Graham RP. Gene Fusions in Gastrointestinal Tract cancers. Genes Chromosomes Cancer 2022; 61:285-297. [PMID: 35239225 DOI: 10.1002/gcc.23035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/10/2022] Open
Abstract
Fusion genes have been identified a wide array of human neoplasms including hematologic and solid tumors, including gastrointestinal tract neoplasia. A fusion gene is the product of parts of two genes which are joined together following a deletion, translocation or chromosomal inversion. Together with single nucleotide variants, insertions, deletions, and amplification, fusion genes represent one of the key genomic mechanisms for tumor development. Detecting fusions in the clinic is accomplished by a variety of techniques including break-apart fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR), and next-generation sequencing (NGS). Some recurrent gene fusions have been successfully targeted by small molecule or monoclonal antibody therapies (i.e. targeted therapies), while others are used for as biomarkers for diagnostic and prognostic purposes. The purpose of this review article is to discuss the clinical utility of detection of gene fusions in carcinomas and neoplasms arising primarily in the digestive system. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hamed Rahi
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Maria C Olave
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karen J Fritchie
- Division of Anatomic Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Patricia T Greipp
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R Kipp
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rondell P Graham
- Division of Laboratory of Genetics and Genomics, Mayo Clinic, Rochester, MN, USA.,Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
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52
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Kim SS, Kycia I, Karski M, Ma RK, Bordt EA, Kwan J, Karki A, Winter E, Aktas RG, Wu Y, Emili A, Bauer DE, Sethupathy P, Vakili K. DNAJB1-PRKACA in HEK293T cells induces LINC00473 overexpression that depends on PKA signaling. PLoS One 2022; 17:e0263829. [PMID: 35167623 PMCID: PMC8846505 DOI: 10.1371/journal.pone.0263829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Fibrolamellar carcinoma (FLC) is a primary liver cancer that most commonly arises in adolescents and young adults in a background of normal liver tissue and has a poor prognosis due to lack of effective chemotherapeutic agents. The DNAJB1-PRKACA gene fusion (DP) has been reported in the majority of FLC tumors; however, its oncogenic mechanisms remain unclear. Given the paucity of cellular models, in particular FLC tumor cell lines, we hypothesized that engineering the DP fusion gene in HEK293T cells would provide insight into the cellular effects of the fusion gene. We used CRISPR/Cas9 to engineer HEK293T clones expressing DP fusion gene (HEK-DP) and performed transcriptomic, proteomic, and mitochondrial studies to characterize this cellular model. Proteomic analysis of DP interacting partners identified mitochondrial proteins as well as proteins in other subcellular compartments. HEK-DP cells demonstrated significantly elevated mitochondrial fission, which suggests a role for DP in altering mitochondrial dynamics. Transcriptomic analysis of HEK-DP cells revealed a significant increase in LINC00473 expression, similar to what has been observed in primary FLC samples. LINC00473 overexpression was reversible with siRNA targeting of PRKACA as well as pharmacologic targeting of PKA and Hsp40 in HEK-DP cells. Therefore, our model suggests that LINC00473 is a candidate marker for DP activity.
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Affiliation(s)
- Stephanie S. Kim
- Department of Surgery, Boston Children’s Hospital, Boston, MA, United States of America
| | - Ina Kycia
- Department of Surgery, Boston Children’s Hospital, Boston, MA, United States of America
| | - Michael Karski
- Department of Surgery, Boston Children’s Hospital, Boston, MA, United States of America
| | - Rosanna K. Ma
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Evan A. Bordt
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Julian Kwan
- Department of Biochemistry, Center for Networks Systems Biology, Boston University School of Medicine, Boston, MA, United States of America
| | - Anju Karki
- Department of Surgery, Boston Children’s Hospital, Boston, MA, United States of America
| | - Elle Winter
- Department of Surgery, Boston Children’s Hospital, Boston, MA, United States of America
| | - Ranan G. Aktas
- Department of Surgery, Boston Children’s Hospital, Boston, MA, United States of America
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Boston, MA, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States of America
| | - Andrew Emili
- Department of Biochemistry, Center for Networks Systems Biology, Boston University School of Medicine, Boston, MA, United States of America
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Boston, MA, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States of America
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Khashayar Vakili
- Department of Surgery, Boston Children’s Hospital, Boston, MA, United States of America
- * E-mail:
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53
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Roles of fusion genes in digestive system cancers: dawn for cancer precision therapy. Crit Rev Oncol Hematol 2022; 171:103622. [PMID: 35124200 DOI: 10.1016/j.critrevonc.2022.103622] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
For advanced and advanced tumors of the digestive system, personalized, precise treatment could be a lifesaving medicine. With the development of next-generation sequencing technology, detection of fusion genes in solid tumors has become more extensive. Some fusion gene targeting therapies have been written into the guidelines for digestive tract tumors, such as for neurotrophic receptor tyrosine kinase, fibroblast growth factor receptor 2. There are also many fusion genes being investigated as potential future therapeutic targets. This review focuses on the current detection methods for fusion genes, fusion genes written into the digestive system tumor guidelines, and potential fusion gene therapy targets in different organs to discuss the possibility of clinical treatments for these targets in digestive system tumors.
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54
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Chang WI, Lin C, Liguori N, Honeyman JN, DeNardo B, El-Deiry W. Molecular Targets for Novel Therapeutics in Pediatric Fusion-Positive Non-CNS Solid Tumors. Front Pharmacol 2022; 12:747895. [PMID: 35126101 PMCID: PMC8811504 DOI: 10.3389/fphar.2021.747895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/03/2021] [Indexed: 12/31/2022] Open
Abstract
Chromosomal fusions encoding novel molecular drivers have been identified in several solid tumors, and in recent years the identification of such pathogenetic events in tumor specimens has become clinically actionable. Pediatric sarcomas and other rare tumors that occur in children as well as adults are a group of heterogeneous tumors often with driver gene fusions for which some therapeutics have already been developed and approved, and others where there is opportunity for progress and innovation to impact on patient outcomes. We review the chromosomal rearrangements that represent oncogenic events in pediatric solid tumors outside of the central nervous system (CNS), such as Ewing Sarcoma, Rhabdomyosarcoma, Fibrolamellar Hepatocellular Carcinoma, and Renal Cell Carcinoma, among others. Various therapeutics such as CDK4/6, FGFR, ALK, VEGF, EGFR, PDGFR, NTRK, PARP, mTOR, BRAF, IGF1R, HDAC inhibitors are being explored among other novel therapeutic strategies such as ONC201/TIC10.
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Affiliation(s)
- Wen-I Chang
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- Pediatric Hematology/Oncology, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
- *Correspondence: Wen-I Chang, ; Wafik El-Deiry,
| | - Claire Lin
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Nicholas Liguori
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Joshua N. Honeyman
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
- Pediatric Surgery, The Warren Alpert Medical School, Brown University, Providence, RI, United States
| | - Bradley DeNardo
- Pediatric Hematology/Oncology, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
| | - Wafik El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI, United States
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- Cancer Center at Brown University, The Warren Alpert Medical School, Brown University, Providence, RI, United States
- Hematology/Oncology Division, Department of Medicine, Lifespan Health System and Brown University, Providence, RI, United States
- *Correspondence: Wen-I Chang, ; Wafik El-Deiry,
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55
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Bolger GB. The cAMP-signaling cancers: Clinically-divergent disorders with a common central pathway. Front Endocrinol (Lausanne) 2022; 13:1024423. [PMID: 36313756 PMCID: PMC9612118 DOI: 10.3389/fendo.2022.1024423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/27/2022] [Indexed: 12/01/2022] Open
Abstract
The cAMP-signaling cancers, which are defined by functionally-significant somatic mutations in one or more elements of the cAMP signaling pathway, have an unexpectedly wide range of cell origins, clinical manifestations, and potential therapeutic options. Mutations in at least 9 cAMP signaling pathway genes (TSHR, GPR101, GNAS, PDE8B, PDE11A, PRKARA1, PRKACA, PRKACB, and CREB) have been identified as driver mutations in human cancer. Although all cAMP-signaling pathway cancers are driven by mutation(s) that impinge on a single signaling pathway, the ultimate tumor phenotype reflects interactions between five critical variables: (1) the precise gene(s) that undergo mutation in each specific tumor type; (2) the effects of specific allele(s) in any given gene; (3) mutations in modifier genes (mutational "context"); (4) the tissue-specific expression of various cAMP signaling pathway elements in the tumor stem cell; and (5) and the precise biochemical regulation of the pathway components in tumor cells. These varying oncogenic mechanisms reveal novel and important targets for drug discovery. There is considerable diversity in the "druggability" of cAMP-signaling components, with some elements (GPCRs, cAMP-specific phosphodiesterases and kinases) appearing to be prime drug candidates, while other elements (transcription factors, protein-protein interactions) are currently refractory to robust drug-development efforts. Further refinement of the precise driver mutations in individual tumors will be essential for directing priorities in drug discovery efforts that target these mutations.
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56
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Kaida A, Iwakuma T. Regulation of p53 and Cancer Signaling by Heat Shock Protein 40/J-Domain Protein Family Members. Int J Mol Sci 2021; 22:13527. [PMID: 34948322 PMCID: PMC8706882 DOI: 10.3390/ijms222413527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/27/2022] Open
Abstract
Heat shock proteins (HSPs) are molecular chaperones that assist diverse cellular activities including protein folding, intracellular transportation, assembly or disassembly of protein complexes, and stabilization or degradation of misfolded or aggregated proteins. HSP40, also known as J-domain proteins (JDPs), is the largest family with over fifty members and contains highly conserved J domains responsible for binding to HSP70 and stimulation of the ATPase activity as a co-chaperone. Tumor suppressor p53 (p53), the most frequently mutated gene in human cancers, is one of the proteins that functionally interact with HSP40/JDPs. The majority of p53 mutations are missense mutations, resulting in acquirement of unexpected oncogenic activities, referred to as gain of function (GOF), in addition to loss of the tumor suppressive function. Moreover, stability and levels of wild-type p53 (wtp53) and mutant p53 (mutp53) are crucial for their tumor suppressive and oncogenic activities, respectively. However, the regulatory mechanisms of wtp53 and mutp53 are not fully understood. Accumulating reports demonstrate regulation of wtp53 and mutp53 levels and/or activities by HSP40/JDPs. Here, we summarize updated knowledge related to the link of HSP40/JDPs with p53 and cancer signaling to improve our understanding of the regulation of tumor suppressive wtp53 and oncogenic mutp53 GOF activities.
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Affiliation(s)
- Atsushi Kaida
- Department of Oral Radiation Oncology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan;
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Tomoo Iwakuma
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pediatrics, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
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57
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Identification of pyroptosis-related signature for cervical cancer predicting prognosis. Aging (Albany NY) 2021; 13:24795-24814. [PMID: 34837692 PMCID: PMC8660613 DOI: 10.18632/aging.203716] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/28/2021] [Indexed: 12/21/2022]
Abstract
Cervical cancer (CC) is one of the most common malignancies encountered in gynecology practice. However, there is a paucity of information about specific biomarkers that assist in the diagnosis and prognosis of CC. Pyroptosis is a form of programmed cell death whose different elements are related to the occurrence, invasion, and metastasis of tumors. However, the role of pyroptosis phenomena in the progression of CC has not yet been elucidated. This study focuses on the development of a pyroptosis-associated prognostic signature for CC using integrated bioinformatics to delineate the relationships among the signature, tumor microenvironment, and immune response of the patients. In this respect, we identified a prognostic signature that depends on eight pyroptosis-related genes (PRGs) that designate with better prognostic survival in the low-risk group (P<0.05) and where AUC values were greater than 0.7. A multi-factor Cox regression analysis indicated that such a signature could be used as an independent prognostic factor, and both the DCA and the Nomogram suggested that the proposed prognostic signature had good predictive capabilities. Interestingly, this prognostic signature can be applied to multiple tumors and thus, is versatile from a clinical point of view. In addition, there were significant differences in the tumor microenvironment and immune infiltration status between the high- and low-risk groups (P<0. 05). The core gene granzyme B (GZMB) was screened and the CC-associated regulatory axis, GZMB/ miR-378a/TRIM52-AS1, was constructed, which may promote CC progression, and further experimentation is needed to validate these results.
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58
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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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59
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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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60
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Ramms DJ, Raimondi F, Arang N, Herberg FW, Taylor SS, Gutkind JS. G αs-Protein Kinase A (PKA) Pathway Signalopathies: The Emerging Genetic Landscape and Therapeutic Potential of Human Diseases Driven by Aberrant G αs-PKA Signaling. Pharmacol Rev 2021; 73:155-197. [PMID: 34663687 PMCID: PMC11060502 DOI: 10.1124/pharmrev.120.000269] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many of the fundamental concepts of signal transduction and kinase activity are attributed to the discovery and crystallization of cAMP-dependent protein kinase, or protein kinase A. PKA is one of the best-studied kinases in human biology, with emphasis in biochemistry and biophysics, all the way to metabolism, hormone action, and gene expression regulation. It is surprising, however, that our understanding of PKA's role in disease is largely underappreciated. Although genetic mutations in the PKA holoenzyme are known to cause diseases such as Carney complex, Cushing syndrome, and acrodysostosis, the story largely stops there. With the recent explosion of genomic medicine, we can finally appreciate the broader role of the Gαs-PKA pathway in disease, with contributions from aberrant functioning G proteins and G protein-coupled receptors, as well as multiple alterations in other pathway components and negative regulators. Together, these represent a broad family of diseases we term the Gαs-PKA pathway signalopathies. The Gαs-PKA pathway signalopathies encompass diseases caused by germline, postzygotic, and somatic mutations in the Gαs-PKA pathway, with largely endocrine and neoplastic phenotypes. Here, we present a signaling-centric review of Gαs-PKA-driven pathophysiology and integrate computational and structural analysis to identify mutational themes commonly exploited by the Gαs-PKA pathway signalopathies. Major mutational themes include hotspot activating mutations in Gαs, encoded by GNAS, and mutations that destabilize the PKA holoenzyme. With this review, we hope to incite further study and ultimately the development of new therapeutic strategies in the treatment of a wide range of human diseases. SIGNIFICANCE STATEMENT: Little recognition is given to the causative role of Gαs-PKA pathway dysregulation in disease, with effects ranging from infectious disease, endocrine syndromes, and many cancers, yet these disparate diseases can all be understood by common genetic themes and biochemical signaling connections. By highlighting these common pathogenic mechanisms and bridging multiple disciplines, important progress can be made toward therapeutic advances in treating Gαs-PKA pathway-driven disease.
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Affiliation(s)
- Dana J Ramms
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Francesco Raimondi
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Nadia Arang
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Friedrich W Herberg
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Susan S Taylor
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - J Silvio Gutkind
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
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61
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Tavakoli S, Adili A, Akbari M, Tamjidifar R, Tarzi S, Saadat M, Hatamnezhad LS, Shotorbani BS, Shotorbani SS. Inhibition effect of Hsp90 on TLR2, TLR4, and MAPK signaling pathway in melanoma in-vitro. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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62
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Abstract
The identification of large chromosomal rearrangements in cancers has multiplied exponentially over the last decade. These complex and often rare genomic events have traditionally been challenging to study, in part owing to lack of tools that efficiently engineer disease-associated inversions, deletions and translocations in model systems. The emergence and refinement of genome editing technologies, such as CRISPR, have significantly expanded our ability to generate and interrogate chromosomal aberrations to better understand the networks that govern cancer growth. Here we review how existing technologies are employed to faithfully model cancer-associated chromosome rearrangements in the laboratory, with the ultimate goal of developing more accurate pre-clinical models of and therapeutic strategies for cancers driven by these genomic events. Summary: Chromosome rearrangements can be potent cancer drivers and effective therapeutic targets. Here, we review how genome-editing technologies can be exploited to engineer and study complex structural variants, and identify new treatment options.
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Affiliation(s)
- Salvador Alonso
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
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63
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Glenfield C, Innan H. Gene Duplication and Gene Fusion Are Important Drivers of Tumourigenesis during Cancer Evolution. Genes (Basel) 2021; 12:1376. [PMID: 34573358 PMCID: PMC8466788 DOI: 10.3390/genes12091376] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently observed in human malignancies and many of the products of these events are pathogenic, representing significant drivers of tumourigenesis and cancer evolution. In certain subsets of cancers duplicated and fused genes appear to be essential for initiation of tumour formation, and some even have the capability of transforming normal cells, highlighting the importance of understanding the events that result in their formation. The mechanisms that drive gene duplication and fusion are unregulated in cancer and they facilitate rapid evolution by selective forces akin to Darwinian survival of the fittest on a cellular level. In this review, we examine current knowledge of the landscape and prevalence of gene duplication and gene fusion in human cancers.
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Affiliation(s)
| | - Hideki Innan
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawar 240-0193, Japan;
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64
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Rare variants of primary liver cancer: Fibrolamellar, combined, and sarcomatoid hepatocellular carcinomas. Eur J Med Genet 2021; 64:104313. [PMID: 34418585 DOI: 10.1016/j.ejmg.2021.104313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/21/2021] [Accepted: 07/22/2021] [Indexed: 01/07/2023]
Abstract
Hepatocellular carcinoma (HCC) constitutes 80% of all primary liver cancers. Based on key developments in the understanding of its carcinogenesis and the advancement of treatment options, detailed algorithms and practice guidelines have been published to guide the clinical management of HCC. Furthermore, several subclasses of HCC have been described based on molecular profiles and linked to pathological characteristics, clinical features, and disease aggressiveness. Most recently, the combination of the checkpoint inhibitor atezolizumab plus bevacizumab has significantly increased treatment response in the first line systemic treatment of HCC. Unfortunately, rare HCC variants, in particular fibrolamellar liver cancer (FLC), combined hepatocellular carcinoma and cholangiocarcinoma (cHCC-CCA), and sarcomatoid hepatocellular carcinoma (sHCC), were excluded from phase III studies. Therefore, data for decision-making and treatment allocation for these distinct entities, representing 1-5% of all primary liver cancers, is scarce. Moreover, most of the knowledge available for these rare HCC variants is based on registry data and retrospective studies. In this position paper, we briefly summarize the current clinical knowledge regarding FLC, cHCC-CCA, and sHCC. Based on our summary, we propose future clinical research activities within the framework of the European Reference Network on Hepatological Diseases (ERN RARE-LIVER).
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65
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Liquid-liquid phase separation: a principal organizer of the cell's biochemical activity architecture. Trends Pharmacol Sci 2021; 42:845-856. [PMID: 34373114 DOI: 10.1016/j.tips.2021.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022]
Abstract
Numerous processes occur simultaneously in the cell both for normal function and in response to changes in the environment. The ability of cells to segregate biochemical reactions into separate compartments is essential to ensure specificity and efficiency in cellular processes. The discovery of liquid-liquid phase separation as a mechanism of compartmentalization has revised our thinking regarding the intracellular organization of molecular pathways such as signal transduction. Here, we highlight recent studies that advance our understanding of how phase separation impacts the organization of biochemical processes, with a particular focus on the tools used to study the functional impact of phase separation. In addition, we offer some of our perspectives on the pathological consequences of dysregulated phase separation in biochemical pathways.
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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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67
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Samdanci ET, Akatli AN, Soylu NK. Clinicopathological Features of Two Extremely Rare Hepatocellular Carcinoma Variants: a Brief Review of Fibrolamellar and Scirrhous Hepatocellular Carcinoma. J Gastrointest Cancer 2021; 51:1187-1192. [PMID: 32860202 DOI: 10.1007/s12029-020-00500-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE We aimed to distinguish between fibrolamellar hepatocellular carcinoma and scirrhous hepatocellular carcinoma histopathologically. METHODS AND RESULTS In this review, fibrolamellar hepatocellular carcinoma and scirrhous hepatocellular carcinoma two specific and rare variants of hepatocellular carcinoma, which are difficult to diagnose histopathologically are discussed. CONCLUSION The clinical, radiological, gross, histopathological, immunohistochemical, and molecular features of these two tumors, which are defined by the World Health Organization (WHO), are mentioned.
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Affiliation(s)
- Emine Turkmen Samdanci
- Liver Institute, Pathology Department, Inonu University, School of Medicine, Malatya, Turkey.
| | - Ayse Nur Akatli
- Liver Institute, Pathology Department, Inonu University, School of Medicine, Malatya, Turkey
| | - Nese Karadag Soylu
- Liver Institute, Pathology Department, Inonu University, School of Medicine, Malatya, Turkey
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68
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MicroRNA-27a promotes tumorigenesis in tongue squamous cell carcinoma by enhancing proliferation, migration and suppressing apoptosis. Eur Arch Otorhinolaryngol 2021; 278:4557-4567. [PMID: 33912994 DOI: 10.1007/s00405-021-06837-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Tongue squamous cell carcinoma (TSCC) is a major subtype of head and neck squamous cell carcinoma (HNSCC), which is an intractable cancer with a poor prognosis. Studies have shown that microRNAs (miRNAs) play an important role in TSCC biology. However, the expression and functions of miRNAs in TSCC remain unclear. METHODS The non-coding RNA profiles of TSCC were downloaded from the GEO database. WGCNA (Weighted gene co-expression network analysis) and differential expression miRNA (DE-miRNA) analyses were employed to identify key candidate miRNAs. miRNA expression was detected using RT-qPCR analysis. The target genes of key miRNAs were predicted. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to explore the potential functions and pathways of key miRNA. miRNA inhibitor was transfected to detect the function of miRNA. The effect of miRNA deregulation on TSCC cell proliferation and apoptosis was investigated using MTS, Annexin V-FITC/PI double staining, and flow cytometry assays. RESULTS miR-27a was a key miRNA in TSCC, which was significantly up-regulated in both Cal-27 cells and malignant tissues from the TSCC patients. In addition, functional analysis showed that miR-27a was involved in the regulation of the MAPK, ERBB, and Jak-STAT signaling pathways. Moreover, RHOA and PRKACA were potential target genes of miR-27a, suggesting them as possible mediators of the tumor-promoting effect of miR-27a. Moreover, downregulation of miR-27a inhibited cell proliferation and facilitated cell apoptosis in Cal-27 cells. CONCLUSION Our findings strongly suggest that miR-27a could promote the tumorigenesis and development of TSCC, which makes it a potential new diagnostic marker and therapeutic target for TSCC.
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69
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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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70
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Help for Sick Kids: New Insights Into Hepatoblastoma. Cell Mol Gastroenterol Hepatol 2021; 12:350-351. [PMID: 33775655 PMCID: PMC8257457 DOI: 10.1016/j.jcmgh.2021.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023]
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71
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Olivieri C, Walker C, Karamafrooz A, Wang Y, Manu VS, Porcelli F, Blumenthal DK, Thomas DD, Bernlohr DA, Simon SM, Taylor SS, Veglia G. Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A. Commun Biol 2021; 4:321. [PMID: 33692454 PMCID: PMC7946884 DOI: 10.1038/s42003-021-01819-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023] Open
Abstract
An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-CDNAJB1) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-CDNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera's allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-CDNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adak Karamafrooz
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Yingjie Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
- Chemistry, University of Minnesota, Minneapolis, MN, USA
- Shenzhen Bay Laboratory, Shenzhen, China
| | - V S Manu
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Fernando Porcelli
- DIBAF - University of Tuscia - Largo dell' Università, Viterbo, Italy
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - David A Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry and Pharmacology, University of California at San Diego, La Jolla, CA, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.
- Chemistry, University of Minnesota, Minneapolis, MN, USA.
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72
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Lee MW, Miljanic M, Triplett T, Ramirez C, Aung KL, Eckhardt SG, Capasso A. Current methods in translational cancer research. Cancer Metastasis Rev 2021; 40:7-30. [PMID: 32929562 PMCID: PMC7897192 DOI: 10.1007/s10555-020-09931-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022]
Abstract
Recent developments in pre-clinical screening tools, that more reliably predict the clinical effects and adverse events of candidate therapeutic agents, has ushered in a new era of drug development and screening. However, given the rapid pace with which these models have emerged, the individual merits of these translational research tools warrant careful evaluation in order to furnish clinical researchers with appropriate information to conduct pre-clinical screening in an accelerated and rational manner. This review assesses the predictive utility of both well-established and emerging pre-clinical methods in terms of their suitability as a screening platform for treatment response, ability to represent pharmacodynamic and pharmacokinetic drug properties, and lastly debates the translational limitations and benefits of these models. To this end, we will describe the current literature on cell culture, organoids, in vivo mouse models, and in silico computational approaches. Particular focus will be devoted to discussing gaps and unmet needs in the literature as well as current advancements and innovations achieved in the field, such as co-clinical trials and future avenues for refinement.
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Affiliation(s)
- Michael W Lee
- Department of Medical Education, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Mihailo Miljanic
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Todd Triplett
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Craig Ramirez
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Kyaw L Aung
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - S Gail Eckhardt
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Anna Capasso
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
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73
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Postler TS. A most versatile kinase: The catalytic subunit of PKA in T-cell biology. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 361:301-318. [PMID: 34074497 DOI: 10.1016/bs.ircmb.2021.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cAMP-dependent protein kinase, more commonly referred to as protein kinase A (PKA), is one of the most-studied enzymes in biology. PKA is ubiquitously expressed in mammalian cells, can be activated in response to a plethora of biological stimuli, and phosphorylates more than 250 known substrates. Indeed, PKA is of central importance to a wide range of organismal processes, including energy homeostasis, memory formation and immunity. It serves as the primary effector of the second-messenger molecule 3',5'-cyclic adenosine monophosphate (cAMP), which is believed to have mostly inhibitory effects on the adaptive immune response. In particular, elevated levels of intracellular cAMP inhibit the activation of conventional T cells by limiting signal transduction through the T-cell receptor and altering gene expression, primarily in a PKA-dependent manner. Regulatory T cells have been shown to increase the cAMP levels in adjacent T cells by direct and indirect means, but the role of cAMP within regulatory T cells themselves remains incompletely understood. Paradoxically, cAMP has been implicated in promoting T-cell activation as well, adding another functional dimension beyond its established immunosuppressive effects. Furthermore, PKA can phosphorylate the NF-κB subunit p65, a transcription factor that is essential for T-cell activation, independently of cAMP. This phosphorylation of p65 drastically enhances NF-κB-dependent transcription and thus is likely to facilitate immune activation. How these immunosuppressive and immune-activating properties of PKA balance in vivo remains to be elucidated. This review provides a brief overview of PKA regulation, its ability to affect NF-κB activation, and its diverse functions in T-cell biology.
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Affiliation(s)
- Thomas S Postler
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY, United States.
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74
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Guo M, Xiao ZD, Dai Z, Zhu L, Lei H, Diao LT, Xiong Y. The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers. Nucleic Acids Res 2021; 48:12618-12631. [PMID: 33275145 PMCID: PMC7736799 DOI: 10.1093/nar/gkaa1119] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
The majority of the human genome encodes long noncoding RNA (lncRNA) genes, critical regulators of various cellular processes, which largely outnumber protein-coding genes. However, lncRNA-involved fusions have not been surveyed and characterized yet. Here, we present a systematic study of the lncRNA fusion landscape across cancer types and identify >30 000 high-confidence tumor-specific lncRNA fusions (using 8284 tumor and 6946 normal samples). Fusions positively correlated with DNA damage and cancer stemness and were specifically low in microsatellite instable (MSI)-High or virus-infected tumors. Moreover, fusions distribute differently among cancer molecular subtypes, but with shared enrichment in tumors that are microsatellite stable (MSS), with high somatic copy number alterations (SCNA), and with poor survival. Importantly, we find a potentially new mechanism, mediated by enhancer RNAs (eRNA), which generates secondary fusions that form densely connected fusion networks with many fusion hubs targeted by FDA-approved drugs. Finally, we experimentally validate functions of two tumor-promoting chimeric proteins derived from mRNA-lncRNA fusions, KDM4B-G039927 and EPS15L1-lncOR7C2-1. The EPS15L1 fusion protein may regulate (Gasdermin E) GSDME, critical in pyroptosis and anti-tumor immunity. Our study completes the fusion landscape in cancers, sheds light on fusion mechanisms, and enriches lncRNA functions in tumorigenesis and cancer progression.
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Affiliation(s)
- Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhen-Dong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Zhiming Dai
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510006, China
| | - Ling Zhu
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Lei
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Li-Ting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
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75
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Van AAN, Kunkel MT, Baffi TR, Lordén G, Antal CE, Banerjee S, Newton AC. Protein kinase C fusion proteins are paradoxically loss of function in cancer. J Biol Chem 2021; 296:100445. [PMID: 33617877 PMCID: PMC8008189 DOI: 10.1016/j.jbc.2021.100445] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/02/2022] Open
Abstract
Within the AGC kinase superfamily, gene fusions resulting from chromosomal rearrangements have been most frequently described for protein kinase C (PKC), with gene fragments encoding either the C-terminal catalytic domain or the N-terminal regulatory moiety fused to other genes. Kinase fusions that eliminate regulatory domains are typically gain of function and often oncogenic. However, several quality control pathways prevent accumulation of aberrant PKC, suggesting that PKC fusions may paradoxically be loss of function. To explore this topic, we used biochemical, cellular, and genome editing approaches to investigate the function of fusions that retain the portion of the gene encoding either the catalytic domain or regulatory domain of PKC. Overexpression studies revealed that PKC catalytic domain fusions were constitutively active but vulnerable to degradation. Genome editing of endogenous genes to generate a cancer-associated PKC fusion resulted in cells with detectable levels of fusion transcript but no detectable protein. Hence, PKC catalytic domain fusions are paradoxically loss of function as a result of their instability, preventing appreciable accumulation of protein in cells. Overexpression of a PKC regulatory domain fusion suppressed both basal and agonist-induced endogenous PKC activity, acting in a dominant-negative manner by competing for diacylglycerol. For both catalytic and regulatory domain fusions, the PKC component of the fusion proteins mediated the effects of the full-length fusions on the parameters examined, suggesting that the partner protein is dispensable in these contexts. Taken together, our findings reveal that PKC gene fusions are distinct from oncogenic fusions and present a mechanism by which loss of PKC function occurs in cancer.
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Affiliation(s)
- An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Maya T Kunkel
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Corina E Antal
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Sourav Banerjee
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, California, USA.
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Lu TW, Aoto PC, Weng JH, Nielsen C, Cash JN, Hall J, Zhang P, Simon SM, Cianfrocco MA, Taylor SS. Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma. PLoS Biol 2020; 18:e3001018. [PMID: 33370777 PMCID: PMC7793292 DOI: 10.1371/journal.pbio.3001018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/08/2021] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
When the J-domain of the heat shock protein DnaJB1 is fused to the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), replacing exon 1, this fusion protein, J-C subunit (J-C), becomes the driver of fibrolamellar hepatocellular carcinoma (FL-HCC). Here, we use cryo-electron microscopy (cryo-EM) to characterize J-C bound to RIIβ, the major PKA regulatory (R) subunit in liver, thus reporting the first cryo-EM structure of any PKA holoenzyme. We report several differences in both structure and dynamics that could not be captured by the conventional crystallography approaches used to obtain prior structures. Most striking is the asymmetry caused by the absence of the second cyclic nucleotide binding (CNB) domain and the J-domain in one of the RIIβ:J-C protomers. Using molecular dynamics (MD) simulations, we discovered that this asymmetry is already present in the wild-type (WT) RIIβ2C2 but had been masked in the previous crystal structure. This asymmetry may link to the intrinsic allosteric regulation of all PKA holoenzymes and could also explain why most disease mutations in PKA regulatory subunits are dominant negative. The cryo-EM structure, combined with small-angle X-ray scattering (SAXS), also allowed us to predict the general position of the Dimerization/Docking (D/D) domain, which is essential for localization and interacting with membrane-anchored A-Kinase-Anchoring Proteins (AKAPs). This position provides a multivalent mechanism for interaction of the RIIβ holoenzyme with membranes and would be perturbed in the oncogenic fusion protein. The J-domain also alters several biochemical properties of the RIIβ holoenzyme: It is easier to activate with cAMP, and the cooperativity is reduced. These results provide new insights into how the finely tuned allosteric PKA signaling network is disrupted by the oncogenic J-C subunit, ultimately leading to the development of FL-HCC.
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Affiliation(s)
- Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Phillip C. Aoto
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Cole Nielsen
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Jennifer N. Cash
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - James Hall
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Ping Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
| | - Sanford M. Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, United States of America
| | - Michael A. Cianfrocco
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
- Department of Pharmacology, University of California, San Diego, La Jolla, California, United States of America
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El Dika I, Mayer RJ, Venook AP, Capanu M, LaQuaglia MP, Kobos R, O'Neill AF, Chou JF, Ly M, Ang C, O'Reilly EM, Gordan JD, Abou‐Alfa GK. A Multicenter Randomized Three-Arm Phase II Study of (1) Everolimus, (2) Estrogen Deprivation Therapy (EDT) with Leuprolide + Letrozole, and (3) Everolimus + EDT in Patients with Unresectable Fibrolamellar Carcinoma. Oncologist 2020; 25:925-e1603. [PMID: 32400000 PMCID: PMC7648371 DOI: 10.1634/theoncologist.2020-0367] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
LESSONS LEARNED FLC is a complex cancer with many implicated oncogenic pathways. Single or dual targeting does not appear to alter the natural history of the cancer, and novel therapeutics are needed. Estrogen deprivation therapy with letrozole and leuprolide, alone or in combination with the mTOR inhibitor, everolimus, did not demonstrate clinical activity in advanced fibrolamellar carcinoma. The study drugs were well tolerated when administered as single agents or in combination in this patient population. This study demonstrates that, despite the rarity of FLC, multicenter therapeutic clinical trials are feasible and support the value of this consortium. BACKGROUND Fibrolamellar carcinoma (FLC) is an uncommon malignancy in young people and is sometimes associated with pregnancy and oral contraceptive use. Immunohistochemical staining and genetic profiling of FLC tumor specimens have revealed aromatase overexpression. The overexpression of mTOR and S6 kinase has been noted in 25% of FLC. On the basis of interaction between estrogen and the PI3K/Akt/mTOR pathway, we hypothesized that suppression of estrogen and mTOR signaling could have antineoplastic activity in FLC. METHODS Patients were randomized to arm A (everolimus), arm B (letrozole/leuprolide; estrogen deprivation therapy [EDT]), or arm C (everolimus/letrozole/leuprolide). Upon disease progression, patients in arm A or B could proceed to part 2 (everolimus/letrozole/leuprolide). The primary endpoint was progression-free survival (PFS) at 6 months (PFS6) assessed using a Simon's minimax two-stage design, hypothesizing an improvement in PFS6 from 40% to 64% with the study regimen. RESULTS Twenty-eight patients were enrolled. An unplanned analysis was performed because of perceived concern for lack of efficacy. Stable disease was observed in 9 of 26 evaluable patients (35%). PFS6 was 0%. Median overall survival (OS) was 12.4 months (95% confidence interval [CI], 7.4-20.9) for the whole study cohort. Grade 3 adverse events in ≥10% of patients were nausea (11%), vomiting (11%), anemia (11%), elevated aspartate transaminase (AST; 32%), alanine transaminase (ALT; 36%), and alkaline phosphatase (14%). All 28 patients experienced an event for PFS outcome, and four deaths were due to disease progression. CONCLUSION Neither EDT nor mTOR inhibition improved outcomes in FLC. Other treatment strategies are needed.
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Affiliation(s)
- Imane El Dika
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - Robert J. Mayer
- Dana‐Farber Cancer Institute, Harvard Medical SchoolBostonMassachusettsUSA
| | - Alan P. Venook
- University of California San FranciscoSan FranciscoCaliforniaUSA
| | | | - Michael P. LaQuaglia
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - Rachel Kobos
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - Allison F. O'Neill
- Dana‐Farber Cancer Institute, Harvard Medical SchoolBostonMassachusettsUSA
| | - Joanne F. Chou
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Michele Ly
- Sidney Kimmel Medical College of Thomas Jefferson UniversityPhiladelphiaPennsylvaniaUSA
| | - Celina Ang
- Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Eileen M. O'Reilly
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
| | - John D. Gordan
- University of California San FranciscoSan FranciscoCaliforniaUSA
| | - Ghassan K. Abou‐Alfa
- Memorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
- Weill Cornell College of MedicineNew YorkNew YorkUSA
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Kong L, Liu P, Fei X, Wu T, Wang Z, Zhang B, Li J, Tan X. A Prognostic Prediction Model Developed Based on Four CpG Sites and Weighted Correlation Network Analysis Identified DNAJB1 as a Novel Biomarker for Pancreatic Cancer. Front Oncol 2020; 10:1716. [PMID: 32984053 PMCID: PMC7477361 DOI: 10.3389/fonc.2020.01716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
Background The prognosis of pancreatic cancer, which is among the solid tumors associated with high mortality, is poor. There is a need to improve the overall survival rate of patients with pancreatic cancer. Materials and Methods The Cancer Genome Atlas (TCGA) dataset with 153 samples and the International Cancer Genome Consortium (ICGC) dataset with 235 samples were used as the discovery and validation cohorts, respectively. The least absolute shrinkage and selection operator regression was used to construct the prognostic prediction model based on the DNA methylation markers. The predictive efficiency of the model was evaluated based on the calibration curve, concordance index, receiver operating characteristic curve, area under the curve, and decision curve. The xenograft model and cellular functional experiments were used to investigate the potential role of DNAJB1 in pancreatic cancer. Results A prognostic prediction model based on four CpG sites (cg00609645, cg13512069, cg23811464, and cg03502002) was developed using TCGA dataset. The model effectively predicted the overall survival rate of patients with pancreatic cancer, which was verified in the ICGC dataset. Next, a nomogram model based on the independent prognostic factors was constructed to predict the overall survival rate of patients with pancreatic cancer. The nomogram model had a higher predictive value than TCGA or ICGC datasets. The low-risk group with improved prognosis exhibited less mutational frequency and high immune infiltration. The brown module with 247 genes derived from the WGCNA analysis was significantly correlated with the prognostic prediction model, tumor grade, clinical stage, and T stage. The bioinformatic analysis indicated that DNAJB1 can serve as a novel biomarker for pancreatic cancer. DNAJB1 knockdown significantly inhibited the proliferation, migration, and invasion of pancreatic cancer cells in vivo and in vitro. Conclusion The prognostic prediction model based on four CpG sites is a new method for predicting the prognosis of patients with pancreatic cancer. The molecular characteristic analyses, including Gene Ontology, Gene Set Enrichment Analysis, mutation spectrum, and immune infiltration of the subgroups, stratified by the model provided novel insights into the initiation and development of pancreatic cancer. DNAJB1 may serve as diagnostic and prognostic biomarkers for pancreatic cancer.
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Affiliation(s)
- Lingming Kong
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Peng Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiang Fei
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tianyu Wu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhongpeng Wang
- Department of Cardiology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Baohui Zhang
- Department of Physiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Jiatong Li
- Department of Orthopedics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaodong Tan
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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Zhang JZ, Lu TW, Stolerman LM, Tenner B, Yang JR, Zhang JF, Falcke M, Rangamani P, Taylor SS, Mehta S, Zhang J. Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling. Cell 2020; 182:1531-1544.e15. [PMID: 32846158 PMCID: PMC7502557 DOI: 10.1016/j.cell.2020.07.043] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/30/2020] [Accepted: 07/30/2020] [Indexed: 12/25/2022]
Abstract
The fidelity of intracellular signaling hinges on the organization of dynamic activity architectures. Spatial compartmentation was first proposed over 30 years ago to explain how diverse G protein-coupled receptors achieve specificity despite converging on a ubiquitous messenger, cyclic adenosine monophosphate (cAMP). However, the mechanisms responsible for spatially constraining this diffusible messenger remain elusive. Here, we reveal that the type I regulatory subunit of cAMP-dependent protein kinase (PKA), RIα, undergoes liquid-liquid phase separation (LLPS) as a function of cAMP signaling to form biomolecular condensates enriched in cAMP and PKA activity, critical for effective cAMP compartmentation. We further show that a PKA fusion oncoprotein associated with an atypical liver cancer potently blocks RIα LLPS and induces aberrant cAMP signaling. Loss of RIα LLPS in normal cells increases cell proliferation and induces cell transformation. Our work reveals LLPS as a principal organizer of signaling compartments and highlights the pathological consequences of dysregulating this activity architecture.
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Affiliation(s)
- Jason Z Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tsan-Wen Lu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lucas M Stolerman
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica R Yang
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Department of Physics, Humboldt University, 12489 Berlin, Germany
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Lamarca A, Frizziero M, Fulton A, McNamara MG, Filobbos R, Hubner RA, Wardell S, Valle JW. Fibrolamellar carcinoma: Challenging the challenge. Eur J Cancer 2020; 137:144-147. [PMID: 32768872 DOI: 10.1016/j.ejca.2020.06.035] [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: 06/15/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022]
Abstract
Fibrolamellar carcinoma (FLC) is a rare and poorly understood malignancy, which seems to be more prevalent in young patients compared with conventional hepatocellular carcinoma (HCC). Performing prospective clinical trials recruiting patients diagnosed with FLC has proven challenging with scarce data available guiding clinical management. The use of a number of chemotherapy compounds in these patients, including cisplatin, epirubicin, 5-fluorouracil (5-FU) and recombinant interferon α-2B (IFN-α-2B), has been reported in the literature, mainly in the form of case reports. The most promising systemic therapy tested so far is the combination of 5-FU infusion and 3-weekly IFN-α-2B, based on results from a phase II clinical trial. This article provides an overview of our own experience with this treatment schedule for patients with FLC, confirming its activity and treatment-derived benefit in the real world. Current challenges being faced by healthcare professionals treating patients with advanced FLC are discussed, especially the increasingly limited access to IFN-α-2B, which could compromise the access to an active therapy in the coming future, and the difficulties in the development of new treatment options for advanced FLC.
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Affiliation(s)
- Angela Lamarca
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom; Division Cancer Sciences, University of Manchester; Manchester, United Kingdom.
| | - Melissa Frizziero
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Alexander Fulton
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Mairéad G McNamara
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom; Division Cancer Sciences, University of Manchester; Manchester, United Kingdom
| | - Rafik Filobbos
- Department of Radiology, North Manchester General Hospital, Manchester, United Kingdom
| | - Richard A Hubner
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom; Division Cancer Sciences, University of Manchester; Manchester, United Kingdom
| | - Steve Wardell
- Department of Pharmacy, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Juan W Valle
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom; Division Cancer Sciences, University of Manchester; Manchester, United Kingdom.
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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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Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, Shue YT, Ko JH, Lee MC, Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NJ, Jackson PK, Narla G, Gordan JD, Shokat KM, Sage J. Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Cancer Cell 2020; 38:129-143.e7. [PMID: 32531271 PMCID: PMC7363571 DOI: 10.1016/j.ccell.2020.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 02/18/2020] [Accepted: 05/04/2020] [Indexed: 12/23/2022]
Abstract
Using unbiased kinase profiling, we identified protein kinase A (PKA) as an active kinase in small cell lung cancer (SCLC). Inhibition of PKA activity genetically, or pharmacologically by activation of the PP2A phosphatase, suppresses SCLC expansion in culture and in vivo. Conversely, GNAS (G-protein α subunit), a PKA activator that is genetically activated in a small subset of human SCLC, promotes SCLC development. Phosphoproteomic analyses identified many PKA substrates and mechanisms of action. In particular, PKA activity is required for the propagation of SCLC stem cells in transplantation studies. Broad proteomic analysis of recalcitrant cancers has the potential to uncover targetable signaling networks, such as the GNAS/PKA/PP2A axis in SCLC.
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Affiliation(s)
- Garry L Coles
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Cristea
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - James T Webber
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rebecca S Levin
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steven M Moss
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andy He
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jaya Sangodkar
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yeonjoo C Hwang
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia Arand
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brandon Mauch
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Vicky Le
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yan Ting Shue
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie H Ko
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Myung Chang Lee
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christina Kong
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Ohlmeyer
- Icahn School of Medicine at Mount Sinai, New York, NY, USA; Atux Iskay LLC, Plainsboro, New Jersey, NJ 08536, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Peter K Jackson
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Goutham Narla
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John D Gordan
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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Mishra A, Emamgholi F, Erlangga Z, Hartleben B, Unger K, Wolff K, Teichmann U, Kessel M, Woller N, Kühnel F, Dow LE, Manns MP, Vogel A, Lowe SW, Saborowski A, Saborowski M. Generation of focal mutations and large genomic deletions in the pancreas using inducible in vivo genome editing. Carcinogenesis 2020; 41:334-344. [PMID: 31170286 PMCID: PMC8204487 DOI: 10.1093/carcin/bgz108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/18/2019] [Accepted: 06/05/2019] [Indexed: 12/31/2022] Open
Abstract
Beyond the nearly uniform presence of KRAS mutations, pancreatic cancer is increasingly recognized as a heterogeneous disease. Preclinical in vivo model systems exist, but with the advent of precision oncology, murine models with enhanced genetic flexibility are needed to functionally annotate genetic alterations found in the human malignancy. Here, we describe the generation of focal gene disruptions and large chromosomal deletions via inducible and pancreas-specific expression of Cas9 in adult mice. Experimental mice are derived on demand directly from genetically engineered embryonic stem cells, without the need for further intercrossing. To provide initial validation of our approach, we show that disruption of the E3 ubiquitin ligase Rnf43 accelerates KrasG12D-dependent tumourigenesis. Moreover, we demonstrate that this system can be used to rapidly interrogate the impact of complex cancer-associated alleles through the generation of a previously unstudied 1.2 megabase deletion surrounding the CDKN2A and CDKN2B tumour suppressors. Thus, our approach is capable of reproducibly generating biallelic and precise loss of large chromosomal fragments that, in conjunction with mutant Kras, leads to development of pancreatic ductal adenocarcinoma with full penetrance.
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Affiliation(s)
- Amrendra Mishra
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Fatemeh Emamgholi
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Zulrahman Erlangga
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Björn Hartleben
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, German Research Center for Environmental Health, Munich, Germany
| | - Katharina Wolff
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | | | - Michael Kessel
- Department for Molecular Cell Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Norman Woller
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Florian Kühnel
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Lukas E Dow
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, USA
| | - Michael P Manns
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, USA
| | - Anna Saborowski
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
| | - Michael Saborowski
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover, Germany
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84
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de Oliveira S, Houseright RA, Korte BG, Huttenlocher A. DnaJ-PKAc fusion induces liver inflammation in a zebrafish model of fibrolamellar carcinoma. Dis Model Mech 2020; 13:dmm042564. [PMID: 32102783 PMCID: PMC7197716 DOI: 10.1242/dmm.042564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
Fibrolamellar carcinoma (FLC) is a rare liver cancer that affects adolescents and young adults. Genomic analysis of FLC has revealed a 400 kb deletion in chromosome 19 that leads to the chimeric transcript DNAJB1-PRKACA (DnaJ-PKAc), comprised of the first exon of heat shock protein 40 (DNAJB1) and exons 2-10 of the catalytic subunit of protein kinase A (PRKACA). Here, we report a new zebrafish model of FLC induced by ectopic expression of zebrafish Dnaja-Pkaca (zfDnaJa-Pkaca) in hepatocytes that is amenable to live imaging of early innate immune inflammation. Expression of zfDnaJa-Pkaca in hepatocytes induces hepatomegaly and increased hepatocyte size. In addition, FLC larvae exhibit early innate immune inflammation characterized by early infiltration of neutrophils and macrophages into the liver microenvironment. Increased Caspase-a (the zebrafish homolog for human caspase-1) activity was also found in the liver of FLC larvae, and pharmacological inhibition of Tnfα and caspase-a decreased liver size and inflammation. Overall, these findings show that innate immune inflammation is an early feature in a zebrafish model of FLC and that pharmacological inhibition of TNFα or caspase-1 activity might be targets to treat inflammation and progression in FLC patients.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sofia de Oliveira
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ruth A Houseright
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Benjamin G Korte
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53792, USA
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85
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Dinh TA, Sritharan R, Smith FD, Francisco AB, Ma RK, Bunaciu RP, Kanke M, Danko CG, Massa AP, Scott JD, Sethupathy P. Hotspots of Aberrant Enhancer Activity in Fibrolamellar Carcinoma Reveal Candidate Oncogenic Pathways and Therapeutic Vulnerabilities. Cell Rep 2020; 31:107509. [PMID: 32294439 PMCID: PMC7474926 DOI: 10.1016/j.celrep.2020.03.073] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Although FLC tumors exhibit a distinct gene expression profile, the chromatin regulatory landscape and the genes most critical for tumor cell survival remain unclear. Here, we use chromatin run-on sequencing to discover ∼7,000 enhancers and 141 enhancer hotspots activated in FLC relative to nonmalignant liver. Bioinformatic analyses reveal aberrant ERK/MEK signaling and candidate master transcriptional regulators. We also define the genes most strongly associated with hotspots of FLC enhancer activity, including CA12 and SLC16A14. Treatment of FLC cell models with inhibitors of CA12 or SLC16A14 independently reduce cell viability and/or significantly enhance the effect of the MEK inhibitor cobimetinib. These findings highlight molecular targets for drug development, as well as drug combination approaches.
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Affiliation(s)
- Timothy A Dinh
- Curriculum in Genetics & Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ramja Sritharan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - F Donelson Smith
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Adam B Francisco
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rosanna K Ma
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rodica P Bunaciu
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Charles G Danko
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Andrew P Massa
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - John D Scott
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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86
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Vyas M, Hechtman JF, Zhang Y, Benayed R, Yavas A, Askan G, Shia J, Klimstra DS, Basturk O. DNAJB1-PRKACA fusions occur in oncocytic pancreatic and biliary neoplasms and are not specific for fibrolamellar hepatocellular carcinoma. Mod Pathol 2020; 33:648-656. [PMID: 31676785 PMCID: PMC7125037 DOI: 10.1038/s41379-019-0398-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
Recently discovered DNAJB1-PRKACA oncogenic fusions have been considered diagnostic for fibrolamellar hepatocellular carcinoma. In this study, we describe six pancreatobiliary neoplasms with PRKACA fusions, five of which harbor the DNAJB1-PRKACA fusion. All neoplasms were subjected to a hybridization capture-based next-generation sequencing assay (MSK-IMPACT), which enables the identification of sequence mutations, copy number alterations, and selected structural rearrangements involving ≥410 genes (n = 6) and/or to a custom targeted, RNA-based panel (MSK-Fusion) that utilizes Archer Anchored Multiplex PCR technology and next-generation sequencing to detect gene fusions in 62 genes (n = 2). Selected neoplasms also underwent FISH analysis, albumin mRNA in-situ hybridization, and arginase-1 immunohistochemical labeling (n = 3). Five neoplasms were pancreatic, and one arose in the intrahepatic bile ducts. All revealed at least focal oncocytic morphology: three cases were diagnosed as intraductal oncocytic papillary neoplasms, and three as intraductal papillary mucinous neoplasms with mixed oncocytic and pancreatobiliary or gastric features. Four cases had an invasive carcinoma component composed of oncocytic cells. Five cases revealed DNAJB1-PRKACA fusions and one revealed an ATP1B1-PRKACA fusion. None of the cases tested were positive for albumin or arginase-1. Our data prove that DNAJB1-PRKACA fusion is neither exclusive nor diagnostic for fibrolamellar hepatocellular carcinoma, and caution should be exercised in diagnosing liver tumors with DNAJB1-PRKACA fusions as fibrolamellar hepatocellular carcinoma, particularly if a pancreatic lesion is present. Moreover, considering DNAJB1-PRKACA fusions lead to upregulated protein kinase activity and that this upregulated protein kinase activity has a significant role in tumorigenesis of fibrolamellar hepatocellular carcinoma, protein kinase inhibition could have therapeutic potential in the treatment of these pancreatobiliary neoplasms as well, once a suitable drug is developed.
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Affiliation(s)
- Monika Vyas
- Memorial Sloan Kettering Cancer Center, NY, US
| | | | | | | | | | - Gokce Askan
- Memorial Sloan Kettering Cancer Center, NY, US
| | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, NY, US
| | | | - Olca Basturk
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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87
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Sindhi R, Rohan V, Bukowinski A, Tadros S, de Ville de Goyet J, Rapkin L, Ranganathan S. Liver Transplantation for Pediatric Liver Cancer. Cancers (Basel) 2020; 12:cancers12030720. [PMID: 32204368 PMCID: PMC7140094 DOI: 10.3390/cancers12030720] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Unresectable hepatocellular carcinoma (HCC) was first removed successfully with total hepatectomy and liver transplantation (LT) in a child over five decades ago. Since then, children with unresectable liver cancer have benefitted greatly from LT and a confluence of several equally important endeavors. Regional and trans-continental collaborations have accelerated the development and standardization of chemotherapy regimens, which provide disease control to enable LT, and also serve as a test of unresectability. In the process, tumor histology, imaging protocols, and tumor staging have also matured to better assess response and LT candidacy. Significant trends include a steady increase in the incidence of and use of LT for hepatoblastoma, and a significant improvement in survival after LT for HCC with each decade. Although LT is curative for most unresectable primary liver sarcomas, such as embryonal sarcoma, the malignant rhabdoid tumor appears relapse-prone despite chemotherapy and LT. Pediatric liver tumors remain rare, and diagnostic uncertainty in some settings can potentially delay treatment or lead to the selection of less effective chemotherapy. We review the current knowledge relevant to diagnosis, LT candidacy, and post-transplant outcomes for these tumors, emphasizing recent observations made from large registries or larger series.
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Affiliation(s)
- Rakesh Sindhi
- Hillman Center for Pediatric Transplantation, UPMC-Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; (A.B.); (S.T.)
- Correspondence: ; Tel.: +1-412-692-7123
| | - Vinayak Rohan
- Medical University of South Carolina, Charleston, SC 29403, USA;
| | - Andrew Bukowinski
- Hillman Center for Pediatric Transplantation, UPMC-Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; (A.B.); (S.T.)
| | - Sameh Tadros
- Hillman Center for Pediatric Transplantation, UPMC-Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; (A.B.); (S.T.)
| | - Jean de Ville de Goyet
- Mediterranean Institute for Transplantation and Advanced Specialized Therapies (ISMETT), 90127 Palermo, Italy;
| | - Louis Rapkin
- Department of Hematology/Oncology, UPMC-Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA;
| | - Sarangarajan Ranganathan
- Department of Pathology, Children’s Hospital Medical Center of Cincinnati, Cincinnati, OH 45229, USA;
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88
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Ranganathan S, Lopez-Terrada D, Alaggio R. Hepatoblastoma and Pediatric Hepatocellular Carcinoma: An Update. Pediatr Dev Pathol 2020; 23:79-95. [PMID: 31554479 DOI: 10.1177/1093526619875228] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hepatoblastomas (HBs) and pediatric hepatocellular carcinomas (HCCs) together account for almost 80% of primary malignant liver tumors in children and adolescents/young adults. Children's Hepatic International Collaboration (CHIC), Children's Oncology Group (COG), SociétéInternationale d'Oncologie Pédiatrique (SIOP), and International Childhood Liver Tumors Strategy Group trials have contributed to define prognostic factors and risk stratification in these tumors. The recently proposed histologic International Consensus classification of HB and HCC in children based on retrospective analysis from CHIC cases represents the base to define entities with homogeneous clinicopathologic and molecular features. This review will provide a morphologic guide for the upcoming International Liver Tumor treatment trial (Pediatric Hepatic International Tumour Trial) to be conducted through several continents. There will be an emphasis on molecular features and immunohistochemical markers for the definition of the individual histologic subtypes of HB and to better characterize the group of liver tumors in the provisional category of hepatocellular neoplasm-not otherwise specified. A brief overview of HCC in children will also be provided.
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Affiliation(s)
- Sarangarajan Ranganathan
- Department of Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Pathology, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas
| | - Dolores Lopez-Terrada
- Department of Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Pathology, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas
| | - Rita Alaggio
- Department of Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Pathology, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas
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89
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Singhi AD, Wood LD, Parks E, Torbenson MS, Felsenstein M, Hruban RH, Nikiforova MN, Wald AI, Kaya C, Nikiforov YE, Favazza L, He J, McGrath K, Fasanella KE, Brand RE, Lennon AM, Furlan A, Dasyam AK, Zureikat AH, Zeh HJ, Lee K, Bartlett DL, Slivka A. Recurrent Rearrangements in PRKACA and PRKACB in Intraductal Oncocytic Papillary Neoplasms of the Pancreas and Bile Duct. Gastroenterology 2020; 158:573-582.e2. [PMID: 31678302 PMCID: PMC7010554 DOI: 10.1053/j.gastro.2019.10.028] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Intraductal oncocytic papillary neoplasms (IOPNs) of the pancreas and bile duct contain epithelial cells with numerous, large mitochondria and are cystic precursors to pancreatic ductal adenocarcinoma (PDAC) and cholangiocarcinoma (CCA), respectively. However, IOPNs do not have the genomic alterations found in other pancreatobiliary neoplasms. In fact, no recurrent genomic alterations have been described in IOPNs. PDACs without activating mutations in KRAS contain gene rearrangements, so we investigated whether IOPNs have recurrent fusions in genes. METHODS We analyzed 20 resected pancreatic IOPNs and 3 resected biliary IOPNs using a broad RNA-based targeted sequencing panel to detect cancer-related fusion genes. Four invasive PDACs and 2 intrahepatic CCAs from the same patients as the IOPNs, were also available for analysis. Samples of pancreatic cyst fluid (n = 5, collected before surgery) and bile duct brushings (n = 2) were analyzed for translocations. For comparison, we analyzed pancreatobiliary lesions from 126 patients without IOPN (controls). RESULTS All IOPNs evaluated were found to have recurring fusions of ATP1B1-PRKACB (n = 13), DNAJB1-PRKACA (n = 6), or ATP1B1-PRKACA (n = 4). These fusions also were found in corresponding invasive PDACs and intrahepatic CCAs, as well as in matched pancreatic cyst fluid and bile duct brushings. These gene rearrangements were absent from all 126 control pancreatobiliary lesions. CONCLUSIONS We identified fusions in PRKACA and PRKACB genes in pancreatic and biliary IOPNs, as well as in PDACs and pancreatic cyst fluid and bile duct cells from the same patients. We did not identify these gene fusions in 126 control pancreatobiliary lesions. These fusions might be used to identify patients at risk for IOPNs and their associated invasive carcinomas.
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Affiliation(s)
- Aatur D Singhi
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Emma Parks
- Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Michael S Torbenson
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, Minnesota
| | - Matthäus Felsenstein
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Surgery, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Marina N Nikiforova
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Abigail I Wald
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Cihan Kaya
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Laura Favazza
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Jin He
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kevin McGrath
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Kenneth E Fasanella
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Randall E Brand
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Anne Marie Lennon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alessandro Furlan
- Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Anil K Dasyam
- Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Amer H Zureikat
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Herbert J Zeh
- Department of Surgery, University of Texas Southwestern, Dallas, Texas
| | - Kenneth Lee
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - David L Bartlett
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Adam Slivka
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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90
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Fan T, Hu Y, Xin J, Zhao M, Wang J. Analyzing the genes and pathways related to major depressive disorder via a systems biology approach. Brain Behav 2020; 10:e01502. [PMID: 31875662 PMCID: PMC7010578 DOI: 10.1002/brb3.1502] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Major depressive disorder (MDD) is a mental disorder caused by the combination of genetic, environmental, and psychological factors. Over the years, a number of genes potentially associated with MDD have been identified. However, in many cases, the role of these genes and their relationship in the etiology and development of MDD remains unclear. Under such situation, a systems biology approach focusing on the function correlation and interaction of the candidate genes in the context of MDD will provide useful information on exploring the molecular mechanisms underlying the disease. METHODS We collected genes potentially related to MDD by screening the human genetic studies deposited in PubMed (https://www.ncbi.nlm.nih.gov/pubmed). The main biological themes within the genes were explored by function and pathway enrichment analysis. Then, the interaction of genes was analyzed in the context of protein-protein interaction network and a MDD-specific network was built by Steiner minimal tree algorithm. RESULTS We collected 255 candidate genes reported to be associated with MDD from available publications. Functional analysis revealed that biological processes and biochemical pathways related to neuronal development, endocrine, cell growth and/or survivals, and immunology were enriched in these genes. The pathways could be largely grouped into three modules involved in biological procedures related to nervous system, the immune system, and the endocrine system, respectively. From the MDD-specific network, 35 novel genes potentially associated with the disease were identified. CONCLUSION By means of network- and pathway-based methods, we explored the molecular mechanism underlying the pathogenesis of MDD at a systems biology level. Results from our work could provide valuable clues for understanding the molecular features of MDD.
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Affiliation(s)
- Ting Fan
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Ying Hu
- Academy of Psychology and Behavior, Tianjin Normal University, Tianjin, China
| | - Juncai Xin
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Mengwen Zhao
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
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91
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Jewell ML, Gibson JR, Guy CD, Hyun J, Du K, Oh SH, Premont RT, Hsu DS, Ribar T, Gregory SG, Diehl AME. Single-Cell RNA Sequencing Identifies Yes-Associated Protein 1-Dependent Hepatic Mesothelial Progenitors in Fibrolamellar Carcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:93-107. [PMID: 31669305 PMCID: PMC10069284 DOI: 10.1016/j.ajpath.2019.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/23/2019] [Accepted: 09/26/2019] [Indexed: 12/29/2022]
Abstract
Fibrolamellar carcinoma (FLC) is characterized by in-frame fusion of DnaJ heat shock protein family (Hsp40) member B1 (DNAJB1) with protein kinase cAMP-activated catalytic subunit α (PRKACA) and by dense desmoplasia. Surgery is the only effective treatment because mechanisms supporting tumor survival are unknown. We used single-cell RNA sequencing to characterize a patient-derived FLC xenograft model and identify therapeutic targets. Human FLC cells segregated into four discrete clusters that all expressed the oncogene Yes-associated protein 1 (YAP1). The two communities most enriched with cells coexpressing FLC markers [CD68, A-kinase anchoring protein 12 (AKAP12), cytokeratin 7, epithelial cell adhesion molecule (EPCAM), and carbamoyl palmitate synthase-1] also had the most cells expressing YAP1 and its proproliferative target genes (AREG and CCND1), suggesting these were proliferative FLC cell clusters. The other two clusters were enriched with cells expressing profibrotic YAP1 target genes, ACTA2, ELN, and COL1A1, indicating these were fibrogenic FLC cells. All clusters expressed the YAP1 target gene and mesothelial progenitor marker mesothelin, and many mesothelin-positive cells coexpressed albumin. Trajectory analysis predicted that the four FLC communities were derived from a single cell type transitioning among phenotypic states. After establishing a novel FLC cell line that harbored the DNAJB1-PRKACA fusion, YAP1 was inhibited, which significantly reduced expression of known YAP1 target genes as well as cell growth and migration. Thus, both FLC epithelial and stromal cells appear to arise from DNAJB1-PRKACA fusion in a YAP1-dependent liver mesothelial progenitor, identifying YAP1 as a target for FLC therapy.
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Affiliation(s)
- Mark L Jewell
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Cynthia D Guy
- Department of Pathology, Duke University, Durham, North Carolina
| | - Jeongeun Hyun
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Kuo Du
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Seh-Hoon Oh
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Richard T Premont
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - David S Hsu
- Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Thomas Ribar
- Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Anna Mae E Diehl
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina.
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92
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Abstract
Cancer arises from a single cell through a series of acquired mutations and epigenetic alterations. Tumors gradually develop into a complex tissue comprised of phenotypically heterogeneous cancer cell populations, as well as noncancer cells that make up the tumor microenvironment. The phenotype, or state, of each cancer and stromal cell is influenced by a plethora of cell-intrinsic and cell-extrinsic factors. The diversity of these cellular states promotes tumor progression, enables metastasis, and poses a challenge for effective cancer treatments. Thus, the identification of strategies for the therapeutic manipulation of tumor heterogeneity would have significant clinical implications. A major barrier in the field is the difficulty in functionally investigating heterogeneity in tumors in cancer patients. Here we review how mouse models of human cancer can be leveraged to interrogate tumor heterogeneity and to help design better therapeutic strategies.
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Affiliation(s)
- Tuomas Tammela
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julien Sage
- Department of Pediatrics and Department of Genetics, Stanford University, Stanford, California 94305, USA
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93
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Alves-Bezerra M, Furey N, Johnson CG, Bissig KD. Using CRISPR/Cas9 to model human liver disease. JHEP Rep 2019; 1:392-402. [PMID: 32039390 PMCID: PMC7005665 DOI: 10.1016/j.jhepr.2019.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/15/2019] [Accepted: 09/19/2019] [Indexed: 02/07/2023] Open
Abstract
CRISPR/Cas9 gene editing has revolutionised biomedical research. The ease of design has allowed many groups to apply this technology for disease modelling in animals. While the mouse remains the most commonly used organism for embryonic editing, CRISPR is now increasingly performed with high efficiency in other species. The liver is also amenable to somatic genome editing, and some delivery methods already allow for efficient editing in the whole liver. In this review, we describe CRISPR-edited animals developed for modelling a broad range of human liver disorders, such as acquired and inherited hepatic metabolic diseases and liver cancers. CRISPR has greatly expanded the repertoire of animal models available for the study of human liver disease, advancing our understanding of their pathophysiology and providing new opportunities to develop novel therapeutic approaches.
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Affiliation(s)
- Michele Alves-Bezerra
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Stem Cells and Regenerative Medicine Center (STAR), Baylor College of Medicine, Houston, TX, USA
| | - Nika Furey
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Stem Cells and Regenerative Medicine Center (STAR), Baylor College of Medicine, Houston, TX, USA.,Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Collin G Johnson
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Stem Cells and Regenerative Medicine Center (STAR), Baylor College of Medicine, Houston, TX, USA
| | - Karl-Dimiter Bissig
- Center for Cell and Gene Therapy, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Stem Cells and Regenerative Medicine Center (STAR), Baylor College of Medicine, Houston, TX, USA.,Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
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94
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Zhang S, Wu X, Diao P, Wang C, Wang D, Li S, Wang Y, Cheng J. Identification of a prognostic alternative splicing signature in oral squamous cell carcinoma. J Cell Physiol 2019; 235:4804-4813. [PMID: 31637730 DOI: 10.1002/jcp.29357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Shuting Zhang
- Jiangsu Key Laboratory of Oral Disease Nanjing Medical University Jiangsu China
| | - Xiang Wu
- Jiangsu Key Laboratory of Oral Disease Nanjing Medical University Jiangsu China
| | - Pengfei Diao
- Jiangsu Key Laboratory of Oral Disease Nanjing Medical University Jiangsu China
| | - Chenxing Wang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China
| | - Dongmiao Wang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China
| | - Sheng Li
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China
| | - Yanling Wang
- Jiangsu Key Laboratory of Oral Disease Nanjing Medical University Jiangsu China
| | - Jie Cheng
- Jiangsu Key Laboratory of Oral Disease Nanjing Medical University Jiangsu China
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology Nanjing Medical University Nanjing China
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95
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96
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Molecular and histological correlations in liver cancer. J Hepatol 2019; 71:616-630. [PMID: 31195064 DOI: 10.1016/j.jhep.2019.06.001] [Citation(s) in RCA: 293] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/22/2019] [Accepted: 06/01/2019] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer, both at the molecular and histological level. High-throughput sequencing and gene expression profiling have identified distinct transcriptomic subclasses and numerous recurrent genetic alterations; several HCC subtypes characterised by histological features have also been identified. HCC phenotype appears to be closely related to particular gene mutations, tumour subgroups and/or oncogenic pathways. Non-proliferative tumours display a well-differentiated phenotype. Among this molecular subgroup, CTNNB1-mutated HCCs constitute a homogeneous subtype, exhibiting cholestasis and microtrabecular and pseudoglandular architectural patterns. Another non-proliferative subtype has a gene expression pattern similar to that of mature hepatocytes (G4) and displays a steatohepatitic phenotype. In contrast, proliferative HCCs are most often poorly differentiated, and notably include tumours with progenitor features. A novel morphological variant of proliferative HCC - designated "macrotrabecular-massive" - was recently shown to be associated with angiogenesis activation and poor prognosis. Altogether, these findings may help to translate our knowledge of HCC biology into clinical practice, resulting in improved precision medicine for patients with this highly aggressive malignancy. This manuscript reviews the most recent data in this exciting field, discussing future directions and challenges.
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97
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Wu H, Li X, Li H. Gene fusions and chimeric RNAs, and their implications in cancer. Genes Dis 2019; 6:385-390. [PMID: 31832518 PMCID: PMC6889028 DOI: 10.1016/j.gendis.2019.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/03/2019] [Accepted: 08/21/2019] [Indexed: 01/26/2023] Open
Abstract
Gene fusions are appreciated as ideal cancer biomarkers and therapeutic targets. Chimeric RNAs are traditionally thought to be products of gene fusions, and thus, also cancer-specific. Recent research has demonstrated that chimeric RNAs can be generated by intergenic splicing in the absence of gene fusion, and such chimeric RNAs are also found in normal physiology. These new findings challenge the traditional theory of chimeric RNAs exclusivity to cancer, and complicates use of chimeric RNAs in cancer detection. Here, we provide an overview of gene fusions and chimeric RNAs, and emphasize their differences. We note that gene fusions are able to generate chimeric RNAs in accordance with the central dogma of biology, and that chimeric RNAs may also be able to influence the generation of the gene fusions per the “horse before the cart” hypothesis. We further expand upon the “horse before the cart” hypothesis, summarizing current evidence in support of the theory and exploring its potential impact on the field.
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Affiliation(s)
- Hao Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA
- Corresponding author. Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, 22908, USA. Fax: +1 434 2437244. http://lilab.medicine.virginia.edu
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98
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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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99
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Cheng JS, Tsai WL, Liu PF, Goan YG, Lin CW, Tseng HH, Lee CH, Shu CW. The MAP3K7-mTOR Axis Promotes the Proliferation and Malignancy of Hepatocellular Carcinoma Cells. Front Oncol 2019; 9:474. [PMID: 31214512 PMCID: PMC6558008 DOI: 10.3389/fonc.2019.00474] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/17/2019] [Indexed: 12/28/2022] Open
Abstract
Targeted therapy is currently limited for patients with hepatocellular carcinoma (HCC) due to the lack of suitable targets. Kinases play pivotal roles in many cellular biological processes, whereas dysregulation of kinases may lead to various diseases, particularly cancer. However, the role of kinases in HCC malignancy remains unclear. In this study, we employed a kinome small interfering RNA (siRNA) library, comprising 710 kinase-related genes, to screen whether any kinases were essential for cell proliferation in various HCC cell lines. Through a kinome siRNA library screening, we found that MAP3K7 was a crucial gene for HCC cell proliferation. Pharmacological or genetic ablation of MAP3K7 diminished the growth, migration, and invasion of HCC cells, including primary HCC cells. Stable knockdown of MAP3K7 attenuated tumor formation in a spheroid cell culture model and tumor xenograft mouse model. In addition, silencing MAP3K7 reduced the phosphorylation and expression of mammalian target of rapamycin (mTOR) in HCC cells. MAP3K7 expression was positively correlated with mTOR expression in tumors of patients with HCC. Higher co-expression of MAP3K7 and mTOR was significantly associated with poor prognosis of HCC. Taken together, our results revealed that the MAP3K7-mTOR axis might promote tumorigenesis and malignancy, which provides a potential marker or therapeutic target for HCC patients.
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Affiliation(s)
- Jin-Shiung Cheng
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wei-Lun Tsai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Pei-Feng Liu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yih-Gang Goan
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Wen Lin
- Division of Gastroenterology and Hepatology, E-Da Dachang Hospital, I-Shou University, Kaohsiung, Taiwan.,School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan
| | - Ho-Hsing Tseng
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Cheng-Hsin Lee
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Wen Shu
- School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan
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100
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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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