51
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Budzinska MA, Shackel NA, Urban S, Tu T. Cellular Genomic Sites of Hepatitis B Virus DNA Integration. Genes (Basel) 2018; 9:E365. [PMID: 30037029 PMCID: PMC6071206 DOI: 10.3390/genes9070365] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022] Open
Abstract
Infection with the Hepatitis B Virus (HBV) is one of the strongest risk-factors for liver cancer (hepatocellular carcinoma, HCC). One of the reported drivers of HCC is the integration of HBV DNA into the host cell genome, which may induce pro-carcinogenic pathways. These reported pathways include: induction of chromosomal instability; generation of insertional mutagenesis in key cancer-associated genes; transcription of downstream cancer-associated cellular genes; and/or formation of a persistent source of viral protein expression (particularly HBV surface and X proteins). The contribution of each of these specific mechanisms towards carcinogenesis is currently unclear. Here, we review the current knowledge of specific sites of HBV DNA integration into the host genome, which sheds light on these mechanisms. We give an overview of previously-used methods to detect HBV DNA integration and the enrichment of integration events in specific functional and structural cellular genomic sites. Finally, we posit a theoretical model of HBV DNA integration during disease progression and highlight open questions in the field.
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Affiliation(s)
| | - Nicholas A Shackel
- Centenary Institute, University of Sydney, Sydney NSW 2050, Australia.
- South Western Sydney Clinical School, University of New South Wales, Liverpool NSW 2170, Australia.
- Gastroenterology, Liverpool Hospital, Liverpool NSW 2170, Australia.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
- German Center for Infection Research (DZIF), Partner Site Heidelberg, D-69120 Heidelberg, Germany.
| | - Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
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52
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Aldose reductase inhibitor protects mice from alcoholic steatosis by repressing saturated fatty acid biosynthesis. Chem Biol Interact 2018; 287:41-48. [PMID: 29630881 DOI: 10.1016/j.cbi.2018.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/18/2018] [Accepted: 04/05/2018] [Indexed: 01/18/2023]
Abstract
Alcoholic liver injury results in morbidity and mortality worldwide, but there are currently no effective and safe therapeutics. Previously we demonstrated that aldose reductase (AR) inhibitor ameliorated alcoholic hepatic steatosis. To clarify the mechanism whereby AR inhibitor improves alcoholic hepatic steatosis, herein we investigated the effect of AR inhibitor on hepatic metabolism in mice fed a Lieber-DeCarli liquid diet with 5% ethanol. Nontargeted metabolomics showed carbohydrates and lipids were characteristic categories in ethanol diet-fed mice with or without AR inhibitor treatment, whereas AR inhibitor mainly affected carbohydrates and peptides. Ethanol-induced galactose metabolism and fatty acid biosynthesis are important for the induction of hepatic steatosis, while AR inhibitor impaired galactose metabolism without perturbing fatty acid biosynthesis. In parallel with successful treatment of steatosis, AR inhibitor suppressed ethanol-activated galactose metabolism and saturated fatty acid biosynthesis. Sorbitol in galactose metabolism and stearic acid in saturated fatty acid biosynthesis were potential biomarkers responsible for ethanol or ethanol plus AR inhibitor treatment. In vitro analysis confirmed that exogenous addition of sorbitol augmented ethanol-induced steatosis and stearic acid. These findings not only reveal metabolic patterns associated with disease and treatment, but also shed light on functional biomarkers contribute to AR inhibition therapy.
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53
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O'Donnell KA. Advances in functional genetic screening with transposons and CRISPR/Cas9 to illuminate cancer biology. Curr Opin Genet Dev 2018; 49:85-94. [PMID: 29587177 PMCID: PMC6312197 DOI: 10.1016/j.gde.2018.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/18/2022]
Abstract
Large-scale genome sequencing studies have identified a wealth of mutations in human tumors and have dramatically advanced the field of cancer genetics. However, the functional consequences of an altered gene in tumor progression cannot always be inferred from mutation status alone. This underscores the critical need for complementary methods to assign functional significance to mutated genes in cancer. Transposons are mobile genetic elements that serve as powerful tools for insertional mutagenesis. Over the last decade, investigators have employed mouse models with ondemand transposon-mediated mutagenesis to perform unbiased genetic screens to identify clinically relevant genes that participate in the pathogenesis of human cancer. Two distinct DNA transposon mutagenesis systems, Sleeping Beauty (SB) and PiggyBac (PB), have been applied extensively in vivo and more recently, in ex vivo settings. These studies have informed our understanding of the genes and pathways that drive cancer initiation, progression, and metastasis. This review highlights the latest progress on cancer gene identification for specific cancer subtypes, as well as new technological advances and incorporation of the CRISPR/Cas9 toolbox into transposon-mediated functional genetic studies.
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Affiliation(s)
- Kathryn A O'Donnell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390-9148, United States.
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54
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Wang T, Qin ZY, Wen LZ, Guo Y, Liu Q, Lei ZJ, Pan W, Liu KJ, Wang XW, Lai SJ, Sun WJ, Wei YL, Liu L, Guo L, Chen YQ, Wang J, Xiao HL, Bian XW, Chen DF, Wang B. Epigenetic restriction of Hippo signaling by MORC2 underlies stemness of hepatocellular carcinoma cells. Cell Death Differ 2018; 25:2086-2100. [PMID: 29555977 DOI: 10.1038/s41418-018-0095-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/14/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
The evolutionarily conserved Hippo signaling pathway is a key regulator of stem cell self-renewal, differentiation, and organ size. While alterations in Hippo signaling are causally linked to uncontrolled cell growth and a broad range of malignancies, genetic mutations in the Hippo pathway are uncommon and it is unclear how the tumor suppressor function of the Hippo pathway is disrupted in human cancers. Here, we report a novel epigenetic mechanism of Hippo inactivation in the context of hepatocellular carcinoma (HCC). We identify a member of the microrchidia (MORC) protein family, MORC2, as an inhibitor of the Hippo pathway by controlling upstream Hippo regulators, neurofibromatosis 2 (NF2) and kidney and brain protein (KIBRA). Mechanistically, MORC2 forms a complex with DNA methyltransferase 3A (DNMT3A) at the promoters of NF2 and KIBRA, leading to their DNA hyper-methylation and transcriptional repression. As a result, NF2 and KIBRA are crucial targets of MORC2 to regulate confluence-induced activation of Hippo signaling and contact inhibition of cell growth under both physiological and pathological conditions. The MORC2-NF2/KIBRA axis is critical for maintaining self-renewal, sorafenib resistance, and oncogenicity of HCC cells in vitro and in nude mice. Furthermore, MORC2 expression is elevated in HCC tissues, associated with stem-like properties of cancer cells, and disease progression in patients. Collectively, MORC2 promotes cancer stemness and tumorigenesis by facilitating DNA methylation-dependent silencing of Hippo signaling and could be a potential molecular target for cancer therapeutics.
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Affiliation(s)
- Tao Wang
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Zhong-Yi Qin
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Liang-Zhi Wen
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Yan Guo
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Qin Liu
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Zeng-Jie Lei
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, Jiangsu Province, China
| | - Wei Pan
- Department of Medical Genetics, Second Military Medical University (Navy Medical University), 200433, Shanghai, China
| | - Kai-Jun Liu
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Xing-Wei Wang
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Shu-Jie Lai
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Wen-Jing Sun
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Yan-Ling Wei
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Lei Liu
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Ling Guo
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Yu-Qin Chen
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Jun Wang
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Hua-Liang Xiao
- Department of Pathology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Key Laboratory of Tumor Immunopathology of Ministry of Education of China, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Dong-Feng Chen
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China.
| | - Bin Wang
- Department of Gastroenterology, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), 400042, Chongqing, China.
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55
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Riordan JD, Feddersen CR, Tschida BR, Jackson P, Keng VW, Linden MA, Amin K, Stipp CS, Largaespada DA, Dupuy AJ. Chronic liver injury alters driver mutation profiles in hepatocellular carcinoma in mice. Hepatology 2018; 67:924-939. [PMID: 28961327 PMCID: PMC5826818 DOI: 10.1002/hep.29565] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/31/2017] [Accepted: 09/27/2017] [Indexed: 02/06/2023]
Abstract
Most hepatocellular carcinomas (HCCs) develop in a chronically injured liver, yet the extent to which this microenvironment promotes neoplastic transformation or influences selective pressures for genetic drivers of HCC remains unclear. We sought to determine the impact of hepatic injury in an established mouse model of HCC induced by Sleeping Beauty transposon mutagenesis. Chemically induced chronic liver injury dramatically increased tumor penetrance and significantly altered driver mutation profiles, likely reflecting distinct selective pressures. In addition to established human HCC genes and pathways, we identified several injury-associated candidates that represent promising loci for further study. Among them, we found that FIGN is overexpressed in human HCC and promotes hepatocyte invasion. We also validated Gli2's oncogenic potential in vivo, providing direct evidence that Hedgehog signaling can drive liver tumorigenesis in the context of chronic injury. Finally, we show that a subset of injury-associated candidate genes identifies two distinct classes of human HCCs. Further analysis of these two subclasses revealed significant trends among common molecular classification schemes of HCC. The genes and mechanisms identified here provide functional insights into the origin of HCC in a chronic liver damage environment. CONCLUSION A chronically damaged liver microenvironment influences the genetic mechanisms that drive hepatocarcinogenesis. (Hepatology 2018;67:924-939).
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Affiliation(s)
- Jesse D. Riordan
- Department of Anatomy & Cell Biology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
| | - Charlotte R. Feddersen
- Department of Anatomy & Cell Biology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
| | - Barbara R. Tschida
- Masonic Cancer Center, Department of Pediatrics & Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Pauline Jackson
- Masonic Cancer Center, Department of Pediatrics & Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vincent W. Keng
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Michael A. Linden
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Khalid Amin
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher S. Stipp
- Department of Biology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
| | - David A. Largaespada
- Masonic Cancer Center, Department of Pediatrics & Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Adam J. Dupuy
- Department of Anatomy & Cell Biology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
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56
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Zhang S, Zhou K, Luo X, Li L, Tu HC, Sehgal A, Nguyen LH, Zhang Y, Gopal P, Tarlow BD, Siegwart DJ, Zhu H. The Polyploid State Plays a Tumor-Suppressive Role in the Liver. Dev Cell 2018; 44:447-459.e5. [PMID: 29429824 DOI: 10.1016/j.devcel.2018.01.010] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/06/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
Most cells in the liver are polyploid, but the functional role of polyploidy is unknown. Polyploidization occurs through cytokinesis failure and endoreduplication around the time of weaning. To interrogate polyploidy while avoiding irreversible manipulations of essential cell-cycle genes, we developed orthogonal mouse models to transiently and potently alter liver ploidy. Premature weaning, as well as knockdown of E2f8 or Anln, allowed us to toggle between diploid and polyploid states. While there was no detectable impact of ploidy alterations on liver function, metabolism, or regeneration, mice with more polyploid hepatocytes suppressed tumorigenesis and mice with more diploid hepatocytes accelerated tumorigenesis in mutagen- and high-fat-induced models. Mechanistically, the diploid state was more susceptible to Cas9-mediated tumor-suppressor loss but was similarly susceptible to MYC oncogene activation, indicating that polyploidy differentially protected the liver from distinct genomic aberrations. This suggests that polyploidy evolved in part to prevent malignant outcomes of liver injury.
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Affiliation(s)
- Shuyuan Zhang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kejin Zhou
- Simmons Comprehensive Cancer Center, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xin Luo
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Li
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ho-Chou Tu
- Alnylam Pharmaceuticals, Cambridge, MA 02142, USA
| | | | - Liem H Nguyen
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu Zhang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Purva Gopal
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Branden D Tarlow
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel J Siegwart
- Simmons Comprehensive Cancer Center, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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57
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Lu H, Bhoopatiraju S, Wang H, Schmitz NP, Wang X, Freeman MJ, Forster CL, Verneris MR, Linden MA, Hallstrom TC. Loss of UHRF2 expression is associated with human neoplasia, promoter hypermethylation, decreased 5-hydroxymethylcytosine, and high proliferative activity. Oncotarget 2018; 7:76047-76061. [PMID: 27738314 PMCID: PMC5340178 DOI: 10.18632/oncotarget.12583] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 09/24/2016] [Indexed: 12/31/2022] Open
Abstract
Ubiquitin-like with PHD and ring finger domains 2 (UHRF2) binds to 5-hydroxymethylcytosine (5hmC), a DNA base involved in tissue development, but it is unknown how their distribution compares with each other in normal and malignant human tissues. We used IHC on human tumor specimens (160 from 19 tumor types) or normal tissue to determine the expression and distribution of UHRF2, Ki-67, and 5hmC. We also examined UHRF2 expression in cord blood progenitors and compared its expression to methylation status in 6 leukemia cell lines and 15 primary human leukemias. UHRF2 is highly expressed, paralleling that of 5hmC, in most non-neoplastic, differentiated tissue with low Ki-67 defined proliferative activity. UHRF2 is expressed in common lymphoid progenitors and mature lymphocytes but not common myeloid progenitors or monocytes. In contrast, UHRF2 immunostaining in human cancer tissues revealed widespread reduction or abnormal cytoplasmic localization which correlated with a higher Ki-67 and reduced 5hmC. UHRF2 expression is reduced in some leukemia cell lines, this correlates with promoter hypermethylation, and similar UHRF2 methylation profiles are seen in primary human leukemia samples. Thus, UHRF2 and 5hmC are widely present in differentiated human tissues, and UHRF2 protein is poorly expressed or mislocalized in diverse human cancers.
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Affiliation(s)
- Huarui Lu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sweta Bhoopatiraju
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hongbo Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nolan P Schmitz
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiaohong Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew J Freeman
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Colleen L Forster
- BioNet, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael R Verneris
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael A Linden
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy C Hallstrom
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
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58
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Woo CC, Chen WC, Teo XQ, Radda GK, Lee PTH. Downregulating serine hydroxymethyltransferase 2 (SHMT2) suppresses tumorigenesis in human hepatocellular carcinoma. Oncotarget 2018; 7:53005-53017. [PMID: 27391339 PMCID: PMC5288164 DOI: 10.18632/oncotarget.10415] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/29/2016] [Indexed: 12/29/2022] Open
Abstract
Serine-glycine biosynthetic pathway diverts the glycolytic intermediate 3-phosphoglycerate to synthesize serine and glycine, of which the latter was found to correlate with cancer cell proliferation. Increased de novo biosynthesis of glycine by serine hydroxymethyltransferase 2 (SHMT2) is the central mechanism to fuel one-carbon pools supporting tumorigenesis. However, the therapeutic potential in targeting SHMT2 in hepatocellular carcinoma (HCC) is unknown. In this study we showed that SHMT2 inhibition significantly suppressed liver tumorigenesis. In vitro, SHMT2-knockdown was found to reduce cell growth and tumorigenicity in Huh-7 and HepG2 liver cancer cells. Moreover SHMT2-knockdown Huh-7 cells failed to form tumor xenograft after subcutaneous inoculation into nude mice. Similarly, inducible SHMT2 inhibition, via doxycycline-added drinking water, was found to reduce tumor incidence and tumor growth in a human tumor xenograft mouse model. SHMT2-knockdown increased the susceptibility of Huh-7 cells to doxorubicin suggesting its potential in combination chemotherapy. Through isotopomer tracing of [2–13C] glycine metabolism, we demonstrated that SHMT2 activity is associated with cancer phenotype. However, overexpression of SHMT2 was insufficient to transform immortalized hepatic cells to malignancy, suggesting that SHMT2 is one of the building blocks in liver cancer metabolism but does not initiate malignant transformation. Moreover, our results suggest that glycine, but not 5,10-methylenetetrahydrofolate, from the SHMT2-mediated enzymatic reaction is instrumental in tumorigenesis. Indeed, we found that SHMT2-knockdown cells exhibited increased glycine uptake. Taken together, our data suggest that SHMT2 may be a potential target in the treatment of human HCC.
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59
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Li Y, Zhai Y, Song Q, Zhang H, Cao P, Ping J, Liu X, Guo B, Liu G, Song J, Zhang Y, Yang A, Yan H, Yang L, Cui Y, Ma Y, Xing J, Shen X, Liu T, Zhang H, An J, Bei JX, Jia W, Kang L, Liu L, Yuan D, Hu Z, Shen H, Lu L, Wang X, Li H, He F, Zhang H, Zhou G. Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus-Related Hepatocellular Carcinoma. Clin Cancer Res 2017; 24:906-915. [PMID: 29246937 DOI: 10.1158/1078-0432.ccr-17-2537] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/20/2017] [Accepted: 12/05/2017] [Indexed: 12/17/2022]
Abstract
Purpose: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. In China, chronic hepatitis B virus (HBV) infection remains the major risk factor for HCC. In this study, we performed a genome-wide association study (GWAS) among Chinese populations to identify novel genetic loci contributing to susceptibility to HBV-related HCC.Experimental Design: GWAS scan is performed in a collection of 205 HBV-related HCC trios (each trio includes an affected proband and his/her both parents), and 355 chronic HBV carriers with HCC (cases) and 360 chronic HBV carriers without HCC (controls), followed by two rounds of replication studies totally consisting of 3,796 cases and 2,544 controls.Results: We identified a novel association signal within the CDK14 gene at 7q21.13 (index rs10272859, OR = 1.28, P = 9.46 × 10-10). Furthermore, we observed that the at-risk rs10272859[G] allele was significantly associated with higher mRNA expression levels of CDK14 in liver tissues. Chromosome conformation capture assays in liver cells confirmed that a physical interaction exists between the promoter region of CDK14 and the risk-associated SNPs in strong linkage disequilibrium with the index rs10272859 at 7q21.13. This index rs10272859 also showed significant association with the survival of HCC patients.Conclusions: Our findings highlight a novel locus at 7q21.13 conferring both susceptibility and prognosis to HBV-related HCC, and suggest the CDK14 gene to be the functional target of the 7q21.13 locus. Clin Cancer Res; 24(4); 906-15. ©2017 AACR.
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Affiliation(s)
- Yuanfeng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Yun Zhai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Qingfeng Song
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Haitao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Pengbo Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Jie Ping
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Xinyi Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Bingqian Guo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Guanjun Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Jin Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Ying Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Aiqing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Hongbo Yan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Liang Yang
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Ying Cui
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Yilong Ma
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, P.R. China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi'an, Shaanxi, P.R. China
| | - Xizhong Shen
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Taotao Liu
- Department of Gastroenterology, Zhongshan Hospital of Fudan University, Shanghai, P.R. China
| | - Hongxin Zhang
- Department of Pain Treatment, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, P.R. China
| | - Jiaze An
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, P.R. China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in Southern China, Guangzhou, Guangdong, P.R. China
| | - Weihua Jia
- State Key Laboratory of Oncology in Southern China, Guangzhou, Guangdong, P.R. China.,Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, P.R. China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, P.R. China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, P.R. China
| | - Lijun Liu
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, P.R. China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, P.R. China
| | - Dongya Yuan
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, P.R. China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, P.R. China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Ministry of Education (MOE) Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Ministry of Education (MOE) Key Laboratory of Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Lei Lu
- Department of Surgical Oncology, Bayi Hospital Affiliated Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
| | - Xuan Wang
- Department of Surgical Oncology, Bayi Hospital Affiliated Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
| | - Hua Li
- Department of Oncology, Chengdu Military General Hospital, Chengdu, Sichuan, P.R. China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China. .,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Hongxing Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China. .,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China. .,National Engineering Research Center for Protein Drugs, Beijing, P.R. China.,National Center for Protein Sciences at Beijing, Beijing, P.R. China
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60
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Johnston JR, Chase PB, Pinto JR. Troponin through the looking-glass: emerging roles beyond regulation of striated muscle contraction. Oncotarget 2017; 9:1461-1482. [PMID: 29416706 PMCID: PMC5787451 DOI: 10.18632/oncotarget.22879] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/20/2017] [Indexed: 01/03/2023] Open
Abstract
Troponin is a heterotrimeric Ca2+-binding protein that has a well-established role in regulating striated muscle contraction. However, mounting evidence points to novel cellular functions of troponin, with profound implications in cancer, cardiomyopathy pathogenesis and skeletal muscle aging. Here, we highlight the non-canonical roles and aberrant expression patterns of troponin beyond the sarcomeric milieu. Utilizing bioinformatics tools and online databases, we also provide pathway, subcellular localization, and protein-protein/DNA interaction analyses that support a role for troponin in multiple subcellular compartments. This emerging knowledge challenges the conventional view of troponin as a sarcomere-specific protein exclusively involved in muscle contraction and may transform the way we think about sarcomeric proteins, particularly in the context of human disease and aging.
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Affiliation(s)
- Jamie R Johnston
- Department of Biomedical Sciences, The Florida State University College of Medicine, Tallahassee, FL, 32306-4300, USA
| | - P Bryant Chase
- Department of Biological Science, The Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Jose Renato Pinto
- Department of Biomedical Sciences, The Florida State University College of Medicine, Tallahassee, FL, 32306-4300, USA
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61
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Wang C, Bernards R. In vivo veritas: Finding novel genes involved in liver cancer through in vivo genetic screens. Hepatology 2017; 66:2078-2080. [PMID: 28718890 DOI: 10.1002/hep.29382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/22/2017] [Accepted: 07/06/2017] [Indexed: 12/07/2022]
Affiliation(s)
- Cun Wang
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - René Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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62
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Class III phosphatidylinositol-3-OH kinase controls epithelial integrity through endosomal LKB1 regulation. Nat Cell Biol 2017; 19:1412-1423. [DOI: 10.1038/ncb3631] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/18/2017] [Indexed: 12/18/2022]
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63
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Benthani FA, Herrmann D, Tran PN, Pangon L, Lucas MC, Allam AH, Currey N, Al-Sohaily S, Giry-Laterriere M, Warusavitarne J, Timpson P, Kohonen-Corish MRJ. 'MCC' protein interacts with E-cadherin and β-catenin strengthening cell-cell adhesion of HCT116 colon cancer cells. Oncogene 2017; 37:663-672. [PMID: 29035389 DOI: 10.1038/onc.2017.362] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 08/14/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023]
Abstract
E-cadherin and β-catenin are key proteins that are essential in the formation of the epithelial cell layer in the colon but their regulatory pathways that are disrupted in cancer metastasis are not completely understood. Mutated in colorectal cancer (MCC) is a tumour suppressor gene that is silenced by promoter methylation in colorectal cancer and particularly in patients with increased lymph node metastasis. Here, we show that MCC methylation is found in 45% of colon and 24% of rectal cancers and is associated with proximal colon, poorly differentiated, circumferential and mucinous tumours as well as increasing T stage and larger tumour size. Knockdown of MCC in HCT116 colon cancer cells caused a reduction in E-cadherin protein level, which is a hallmark of epithelial-mesenchymal transition in cancer, and consequently diminished the E-cadherin/β-catenin complex. MCC knockdown disrupted cell-cell adhesive strength and integrity in the dispase and transepithelial electrical resistance assays, enhanced hepatocyte growth factor-induced cell scatter and increased tumour cell invasiveness in an organotypic assay. The Src/Abl inhibitor dasatinib, a candidate anti-invasive drug, abrogated the invasive properties induced by MCC deficiency. Mechanistically, we establish that MCC interacts with the E-cadherin/β-catenin complex. These data provide a significant advance in the current understanding of cell-cell adhesion in colon cancer cells.
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Affiliation(s)
- F A Benthani
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - D Herrmann
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - P N Tran
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - L Pangon
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - M C Lucas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - A H Allam
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - N Currey
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - S Al-Sohaily
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - M Giry-Laterriere
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - J Warusavitarne
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - P Timpson
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - M R J Kohonen-Corish
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia.,School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
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64
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The convergent roles of the nuclear factor I transcription factors in development and cancer. Cancer Lett 2017; 410:124-138. [PMID: 28962832 DOI: 10.1016/j.canlet.2017.09.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/11/2017] [Accepted: 09/16/2017] [Indexed: 02/07/2023]
Abstract
The nuclear factor I (NFI) transcription factors play important roles during normal development and have been associated with developmental abnormalities in humans. All four family members, NFIA, NFIB, NFIC and NFIX, have a homologous DNA binding domain and function by regulating cell proliferation and differentiation via the transcriptional control of their target genes. More recently, NFI genes have also been implicated in cancer based on genomic analyses and studies of animal models in a variety of tumours across multiple organ systems. However, the association between their functions in development and in cancer is not well described. In this review, we summarise the evidence suggesting a converging role for the NFI genes in development and cancer. Our review includes all cancer types in which the NFI genes are implicated, focusing predominantly on studies demonstrating their oncogenic or tumour-suppressive potential. We conclude by presenting the challenges impeding our understanding of NFI function in cancer biology, and demonstrate how a developmental perspective may contribute towards overcoming such hurdles.
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65
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Kawakami K, Largaespada DA, Ivics Z. Transposons As Tools for Functional Genomics in Vertebrate Models. Trends Genet 2017; 33:784-801. [PMID: 28888423 DOI: 10.1016/j.tig.2017.07.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
Abstract
Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes. For example, the Sleeping Beauty transposon has become highly instrumental to induce tumors in experimental animals in a tissue-specific manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mice, and rats.
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Affiliation(s)
- Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan; These authors contributed equally to this work
| | - David A Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN, USA; These authors contributed equally to this work
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany; These authors contributed equally to this work..
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66
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Feuerecker B, Durst M, Michalik M, Schneider G, Saur D, Menzel M, Schwaiger M, Schilling F. Hyperpolarized 13C Diffusion MRS of Co-Polarized Pyruvate and Fumarate to Measure Lactate Export and Necrosis. J Cancer 2017; 8:3078-3085. [PMID: 28928899 PMCID: PMC5604459 DOI: 10.7150/jca.20250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/04/2017] [Indexed: 02/06/2023] Open
Abstract
Background: Non-invasive tumor characterization and monitoring are among the key goals of medical imaging. Using hyperpolarized 13C-labelled metabolic probes fast metabolic pathways can be probed in real-time, providing new opportunities for tumor characterization. In this in vitro study, we investigated whether measurement of apparent diffusion coefficient (ADC) measurements and magnetic resonance spectroscopy (MRS) of co-polarized 13C-labeled pyruvic acid and fumaric acid can non-invasively detect both necrosis and changes in lactate export, which are parameters indicative of tumor aggressiveness. Methods:13C-labeled pyruvic acid and fumaric acid were co-polarized in a preclinical hyperpolarizer and the dissolved compounds were added to prepared samples of 8932 pancreatic cancer and MCF-7 breast carcinoma cells. Extracellular lactate concentrations and cell viability were measured in separate assays. Results: The mean ratios of the ADC values of lactate and pyruvate (ADClac/ADCpyr) between MCF-7 (0.533 ± 0.015, n = 3) and 8932 pancreatic cancer cells (0.744 ± 0.064, n = 3) showed a statistically significant difference (p = 0.048). 8932 cells had higher extracellular lactate concentrations in the extracellular medium (22.97 ± 2.53 ng/µl) compared with MCF-7 cells (7.52 ± 0.59 ng/µl; p < 0.001). Fumarate-to-malate conversion was only detectable in necrotic cells, thereby allowing clear differentiation between necrotic and viable cells. Conclusion: We provide evidence that MRS of hyperpolarized 13C-labelled pyruvic acid and fumaric acid, with their respective conversions to lactate and malate, are useful for characterization of necrosis and lactate efflux in tumor cells.
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Affiliation(s)
- Benedikt Feuerecker
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Markus Durst
- Institute of Medical Engineering, Technische Universität München, Garching, Germany.,GE Global Research, Munich, Germany
| | - Michael Michalik
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Günter Schneider
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Garching, Germany
| | - Dieter Saur
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Garching, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Markus Schwaiger
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Franz Schilling
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
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67
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Masson JJ, Billings HW, Palmer CS. Metabolic reprogramming during hepatitis B disease progression offers novel diagnostic and therapeutic opportunities. Antivir Chem Chemother 2017; 25:53-57. [PMID: 28768434 PMCID: PMC5890528 DOI: 10.1177/2040206617701372] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Metabolic remodeling occurs in immune cells during an infection. Host cells must upregulate energy production for growth, proliferation, and effector functions to limit the damage imposed by pathogens. One example, the hepatitis B virus, induces hepatic injury in human hepatocytes through dysregulation of aerobic glycolysis and lipid metabolism. Increased glycolytic metabolism mediated by elevated expression of Glut1, glucose influx, and lactate secretion is associated with this Warburg phenotype, a classic metabolic signature also observed in cancer cells. This article brings into focus the tight interaction between HBV infection and metabolic dysfunction and how these processes facilitate the progression of end-stage liver diseases, such as hepatocellular carcinoma. We also provide evidence and models by which other viruses such as HIV and Zika disrupt their host metabolic machinery. The emergence of the immunometabolism field provides novel opportunities to take advantage of intermediary metabolites and key metabolic pathways for diagnostic and therapeutic purposes.
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Affiliation(s)
- Jesse Jr Masson
- 1 Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Hugh Ww Billings
- 1 Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Clovis S Palmer
- 1 Centre for Biomedical Research, Burnet Institute, Melbourne, Australia.,2 Department of Infectious Diseases, Monash University, Melbourne, Australia.,3 Department of Microbiology and Immunology, University of, Melbourne, Melbourne, Australia
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68
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Rangel R, Guzman-Rojas L, Kodama T, Kodama M, Newberg JY, Copeland NG, Jenkins NA. Identification of New Tumor Suppressor Genes in Triple-Negative Breast Cancer. Cancer Res 2017; 77:4089-4101. [DOI: 10.1158/0008-5472.can-17-0785] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/28/2017] [Accepted: 06/05/2017] [Indexed: 11/16/2022]
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69
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Guo C, Ma J, Zhong Q, Zhao M, Hu T, Chen T, Qiu L, Wen L. Curcumin improves alcoholic fatty liver by inhibiting fatty acid biosynthesis. Toxicol Appl Pharmacol 2017; 328:1-9. [PMID: 28476407 DOI: 10.1016/j.taap.2017.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/01/2017] [Accepted: 05/01/2017] [Indexed: 12/19/2022]
Abstract
Alcoholic fatty liver is a threat to human health. It has been long known that abstinence from alcohol is the most effective therapy, other effective therapies are not available for the treatment in humans. Curcumin has a great potential for anti-oxidation and anti-inflammation, but the effect on metabolic reconstruction remains little known. Here we performed metabolomic analysis by gas chromatography/mass spectrometry and explored ethanol pathogenic insight as well as curcumin action pattern. We identified seventy-one metabolites in mouse liver. Carbohydrates and lipids were characteristic categories. Pathway analysis results revealed that ethanol-induced pathways including biosynthesis of unsaturated fatty acids, fatty acid biosynthesis and pentose and glucuronate interconversions were suppressed by curcumin. Additionally, ethanol enhanced galactose metabolism and pentose phosphate pathway. Glyoxylate and dicarboxylate metabolism and pyruvate metabolism were inhibited in mice fed ethanol diet plus curcumin. Stearic acid, oleic acid and linoleic acid were disease biomarkers and therapical biomarkers. These results reflect the landscape of hepatic metabolism regulation. Our findings illustrate ethanol pathological pathway and metabolic mechanism of curcumin therapy.
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Affiliation(s)
- Chang Guo
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China; Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan 364012, People's Republic of China; Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University, Longyan 364012, People's Republic of China
| | - Jingfan Ma
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China; Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan 364012, People's Republic of China; Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University, Longyan 364012, People's Republic of China
| | - Qionghong Zhong
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China
| | - Mengyuan Zhao
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China
| | - Tianxing Hu
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China
| | - Tong Chen
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China; Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan 364012, People's Republic of China; Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University, Longyan 364012, People's Republic of China
| | - Longxin Qiu
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China; Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan 364012, People's Republic of China; Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University, Longyan 364012, People's Republic of China.
| | - Longping Wen
- School of Life Sciences, Longyan University, Longyan 364012, People's Republic of China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.
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70
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Siddiqui S, Kadlecek S, Pourfathi M, Xin Y, Mannherz W, Hamedani H, Drachman N, Ruppert K, Clapp J, Rizi R. The use of hyperpolarized carbon-13 magnetic resonance for molecular imaging. Adv Drug Deliv Rev 2017; 113:3-23. [PMID: 27599979 PMCID: PMC5783573 DOI: 10.1016/j.addr.2016.08.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/25/2016] [Accepted: 08/27/2016] [Indexed: 02/06/2023]
Abstract
Until recently, molecular imaging using magnetic resonance (MR) has been limited by the modality's low sensitivity, especially with non-proton nuclei. The advent of hyperpolarized (HP) MR overcomes this limitation by substantially enhancing the signal of certain biologically important probes through a process known as external nuclear polarization, enabling real-time assessment of tissue function and metabolism. The metabolic information obtained by HP MR imaging holds significant promise in the clinic, where it could play a critical role in disease diagnosis and therapeutic monitoring. This review will provide a comprehensive overview of the developments made in the field of hyperpolarized MR, including advancements in polarization techniques and delivery, probe development, pulse sequence optimization, characterization of healthy and diseased tissues, and the steps made towards clinical translation.
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Affiliation(s)
- Sarmad Siddiqui
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen Kadlecek
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mehrdad Pourfathi
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xin
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Mannherz
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hooman Hamedani
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas Drachman
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kai Ruppert
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Justin Clapp
- Department of Anesthesiology and Critical Care, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahim Rizi
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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71
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Song CQ, Li Y, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte D, Zender L, Wang XW, Thorgeirsson S, Weng Z, Xue W. Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice. Gastroenterology 2017; 152:1161-1173.e1. [PMID: 27956228 PMCID: PMC6204228 DOI: 10.1053/j.gastro.2016.12.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/22/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS It has been a challenge to identify liver tumor suppressors or oncogenes due to the genetic heterogeneity of these tumors. We performed a genome-wide screen to identify suppressors of liver tumor formation in mice, using CRISPR-mediated genome editing. METHODS We performed a genome-wide CRISPR/Cas9-based knockout screen of P53-null mouse embryonic liver progenitor cells that overexpressed MYC. We infected p53-/-;Myc;Cas9 hepatocytes with the mGeCKOa lentiviral library of 67,000 single-guide RNAs (sgRNAs), targeting 20,611 mouse genes, and transplanted the transduced cells subcutaneously into nude mice. Within 1 month, all the mice that received the sgRNA library developed subcutaneous tumors. We performed high-throughput sequencing of tumor DNA and identified sgRNAs increased at least 8-fold compared to the initial cell pool. To validate the top 10 candidate tumor suppressors from this screen, we collected data from patients with hepatocellular carcinoma (HCC) using the Cancer Genome Atlas and COSMIC databases. We used CRISPR to inactivate candidate tumor suppressor genes in p53-/-;Myc;Cas9 cells and transplanted them subcutaneously into nude mice; tumor formation was monitored and tumors were analyzed by histology and immunohistochemistry. Mice with liver-specific disruption of p53 were given hydrodynamic tail-vein injections of plasmids encoding Myc and sgRNA/Cas9 designed to disrupt candidate tumor suppressors; growth of tumors and metastases was monitored. We compared gene expression profiles of liver cells with vs without tumor suppressor gene disrupted by sgRNA/Cas9. Genes found to be up-regulated after tumor suppressor loss were examined in liver cancer cell lines; their expression was knocked down using small hairpin RNAs, and tumor growth was examined in nude mice. Effects of the MEK inhibitors AZD6244, U0126, and trametinib, or the multi-kinase inhibitor sorafenib, were examined in human and mouse HCC cell lines. RESULTS We identified 4 candidate liver tumor suppressor genes not previously associated with liver cancer (Nf1, Plxnb1, Flrt2, and B9d1). CRISPR-mediated knockout of Nf1, a negative regulator of RAS, accelerated liver tumor formation in mice. Loss of Nf1 or activation of RAS up-regulated the liver progenitor cell markers HMGA2 and SOX9. RAS pathway inhibitors suppressed the activation of the Hmga2 and Sox9 genes that resulted from loss of Nf1 or oncogenic activation of RAS. Knockdown of HMGA2 delayed formation of xenograft tumors from cells that expressed oncogenic RAS. In human HCCs, low levels of NF1 messenger RNA or high levels of HMGA2 messenger RNA were associated with shorter patient survival time. Liver cancer cells with inactivation of Plxnb1, Flrt2, and B9d1 formed more tumors in mice and had increased levels of mitogen-activated protein kinase phosphorylation. CONCLUSIONS Using a CRISPR-based strategy, we identified Nf1, Plxnb1, Flrt2, and B9d1 as suppressors of liver tumor formation. We validated the observation that RAS signaling, via mitogen-activated protein kinase, contributes to formation of liver tumors in mice. We associated decreased levels of NF1 and increased levels of its downstream protein HMGA2 with survival times of patients with HCC. Strategies to inhibit or reduce HMGA2 might be developed to treat patients with liver cancer.
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MESH Headings
- Animals
- Benzimidazoles/pharmacology
- Blotting, Western
- Butadienes/pharmacology
- CRISPR-Cas Systems
- Carcinoma, Hepatocellular/genetics
- Cell Line, Tumor
- Cytoskeletal Proteins
- DNA, Neoplasm/genetics
- Enzyme Inhibitors
- Gene Expression Regulation, Neoplastic
- Genes, Neurofibromatosis 1
- Genome-Wide Association Study
- HMGA Proteins/genetics
- HMGA2 Protein/genetics
- Hepatocytes/metabolism
- High-Throughput Nucleotide Sequencing
- Humans
- Immunohistochemistry
- Liver Neoplasms/genetics
- Liver Neoplasms, Experimental/genetics
- Membrane Glycoproteins/genetics
- Mice
- Mice, Knockout
- Mice, Nude
- Mitogen-Activated Protein Kinases/genetics
- Nerve Tissue Proteins/genetics
- Niacinamide/analogs & derivatives
- Niacinamide/pharmacology
- Nitriles/pharmacology
- Phenylurea Compounds/pharmacology
- Prognosis
- Protein Kinase Inhibitors/pharmacology
- Proto-Oncogene Proteins c-myc/genetics
- Pyridones/pharmacology
- Pyrimidinones/pharmacology
- Real-Time Polymerase Chain Reaction
- Receptors, Cell Surface/genetics
- Sequence Analysis, DNA
- Sorafenib
- Survival Analysis
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Proteins/genetics
- ras Proteins/genetics
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Affiliation(s)
- Chun-Qing Song
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Yingxiang Li
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jill Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Angela Park
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Yotsawat Pomyen
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Soren Hough
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Zachary Kennedy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Andrew Fischer
- Department of Pathology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts; Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Darryl Conte
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Lars Zender
- Department of Internal Medicine VIII, University Department of Medicine, University Hospital Tübingen, Tübingen, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University, Tübingen, Germany
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Snorri Thorgeirsson
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China.
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts; Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
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72
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de la Rosa J, Weber J, Friedrich MJ, Li Y, Rad L, Ponstingl H, Liang Q, de Quirós SB, Noorani I, Metzakopian E, Strong A, Li MA, Astudillo A, Fernández-García MT, Fernández-García MS, Hoffman GJ, Fuente R, Vassiliou GS, Rad R, López-Otín C, Bradley A, Cadiñanos J. A single-copy Sleeping Beauty transposon mutagenesis screen identifies new PTEN-cooperating tumor suppressor genes. Nat Genet 2017; 49:730-741. [PMID: 28319090 PMCID: PMC5409503 DOI: 10.1038/ng.3817] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/24/2017] [Indexed: 12/11/2022]
Abstract
The overwhelming number of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. Here we developed a novel whole-body insertional mutagenesis screen in mice, which was designed for the discovery of Pten-cooperating tumor suppressors. Toward this aim, we coupled mobilization of a single-copy inactivating Sleeping Beauty transposon to Pten disruption within the same genome. The analysis of 278 transposition-induced prostate, breast and skin tumors detected tissue-specific and shared data sets of known and candidate genes involved in cancer. We validated ZBTB20, CELF2, PARD3, AKAP13 and WAC, which were identified by our screens in multiple cancer types, as new tumor suppressor genes in prostate cancer. We demonstrated their synergy with PTEN in preventing invasion in vitro and confirmed their clinical relevance. Further characterization of Wac in vivo showed obligate haploinsufficiency for this gene (which encodes an autophagy-regulating factor) in a Pten-deficient context. Our study identified complex PTEN-cooperating tumor suppressor networks in different cancer types, with potential clinical implications.
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Affiliation(s)
- Jorge de la Rosa
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Julia Weber
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, München, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Yilong Li
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Lena Rad
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Hannes Ponstingl
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Qi Liang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Imran Noorani
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Alexander Strong
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Meng Amy Li
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Aurora Astudillo
- Servicio de Anatomía Patológica, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | | | - Gary J Hoffman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,School of Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Rocío Fuente
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - George S Vassiliou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Roland Rad
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, München, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Spain
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Juan Cadiñanos
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), Oviedo, Spain
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73
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Resistance mechanisms to TP53-MDM2 inhibition identified by in vivo piggyBac transposon mutagenesis screen in an Arf -/- mouse model. Proc Natl Acad Sci U S A 2017; 114:3151-3156. [PMID: 28265066 DOI: 10.1073/pnas.1620262114] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Inhibitors of double minute 2 protein (MDM2)-tumor protein 53 (TP53) interaction are predicted to be effective in tumors in which the TP53 gene is wild type, by preventing TP53 protein degradation. One such setting is represented by the frequent CDKN2A deletion in human cancer that, through inactivation of p14ARF, activates MDM2 protein, which in turn degrades TP53 tumor suppressor. Here we used piggyBac (PB) transposon insertional mutagenesis to anticipate resistance mechanisms occurring during treatment with the MDM2-TP53 inhibitor HDM201. Constitutive PB mutagenesis in Arf-/- mice provided a collection of spontaneous tumors with characterized insertional genetic landscapes. Tumors were allografted in large cohorts of mice to assess the pharmacologic effects of HDM201. Sixteen out of 21 allograft models were sensitive to HDM201 but ultimately relapsed under treatment. A comparison of tumors with acquired resistance to HDM201 and untreated tumors identified 87 genes that were differentially and significantly targeted by the PB transposon. Resistant tumors displayed a complex clonality pattern suggesting the emergence of several resistant subclones. Among the most frequent alterations conferring resistance, we observed somatic and insertional loss-of-function mutations in transformation-related protein 53 (Trp53) in 54% of tumors and transposon-mediated gain-of-function alterations in B-cell lymphoma-extra large (Bcl-xL), Mdm4, and two TP53 family members, resulting in expression of the TP53 dominant negative truncations ΔNTrp63 and ΔNTrp73. Enhanced BCL-xL and MDM4 protein expression was confirmed in resistant tumors, as well as in HDM201-resistant patient-derived tumor xenografts. Interestingly, concomitant inhibition of MDM2 and BCL-xL demonstrated significant synergy in p53 wild-type cell lines in vitro. Collectively, our findings identify several potential mechanisms by which TP53 wild-type tumors may escape MDM2-targeted therapy.
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74
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Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification. Proc Natl Acad Sci U S A 2017; 114:E2215-E2224. [PMID: 28251929 PMCID: PMC5358385 DOI: 10.1073/pnas.1701512114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite concerted efforts to identify causal genes that drive breast cancer (BC) initiation and progression, we have yet to establish robust signatures to stratify patient risk. Here we used in vivo transposon-based forward genetic screening to identify potentially relevant BC driver genes. Integrating this approach with survival prediction analysis, we identified six gene pairs that could prognose human BC subtypes into high-, intermediate-, and low-risk groups with high confidence and reproducibility. Furthermore, we identified susceptibility gene sets for basal and claudin-low subtypes (21 and 16 genes, respectively) that stratify patients into three relative risk subgroups. These signatures offer valuable prognostic insight into the genetic basis of BC and allow further exploration of the interconnectedness of BC driver genes during disease progression. Robust prognostic gene signatures and therapeutic targets are difficult to derive from expression profiling because of the significant heterogeneity within breast cancer (BC) subtypes. Here, we performed forward genetic screening in mice using Sleeping Beauty transposon mutagenesis to identify candidate BC driver genes in an unbiased manner, using a stabilized N-terminal truncated β-catenin gene as a sensitizer. We identified 134 mouse susceptibility genes from 129 common insertion sites within 34 mammary tumors. Of these, 126 genes were orthologous to protein-coding genes in the human genome (hereafter, human BC susceptibility genes, hBCSGs), 70% of which are previously reported cancer-associated genes, and ∼16% are known BC suppressor genes. Network analysis revealed a gene hub consisting of E1A binding protein P300 (EP300), CD44 molecule (CD44), neurofibromin (NF1) and phosphatase and tensin homolog (PTEN), which are linked to a significant number of mutated hBCSGs. From our survival prediction analysis of the expression of human BC genes in 2,333 BC cases, we isolated a six-gene-pair classifier that stratifies BC patients with high confidence into prognostically distinct low-, moderate-, and high-risk subgroups. Furthermore, we proposed prognostic classifiers identifying three basal and three claudin-low tumor subgroups. Intriguingly, our hBCSGs are mostly unrelated to cell cycle/mitosis genes and are distinct from the prognostic signatures currently used for stratifying BC patients. Our findings illustrate the strength and validity of integrating functional mutagenesis screens in mice with human cancer transcriptomic data to identify highly prognostic BC subtyping biomarkers.
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75
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Xu C, Qi X, Du X, Zou H, Gao F, Feng T, Lu H, Li S, An X, Zhang L, Wu Y, Liu Y, Li N, Capecchi MR, Wu S. piggyBac mediates efficient in vivo CRISPR library screening for tumorigenesis in mice. Proc Natl Acad Sci U S A 2017; 114:722-727. [PMID: 28062688 PMCID: PMC5278437 DOI: 10.1073/pnas.1615735114] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas9 is becoming an increasingly important tool to functionally annotate genomes. However, because genome-wide CRISPR libraries are mostly constructed in lentiviral vectors, in vivo applications are severely limited as a result of difficulties in delivery. Here, we examined the piggyBac (PB) transposon as an alternative vehicle to deliver a guide RNA (gRNA) library for in vivo screening. Although tumor induction has previously been achieved in mice by targeting cancer genes with the CRISPR/Cas9 system, in vivo genome-scale screening has not been reported. With our PB-CRISPR libraries, we conducted an in vivo genome-wide screen in mice and identified genes mediating liver tumorigenesis, including known and unknown tumor suppressor genes (TSGs). Our results demonstrate that PB can be a simple and nonviral choice for efficient in vivo delivery of CRISPR libraries.
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Affiliation(s)
- Chunlong Xu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaolan Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Huiying Zou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fei Gao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tao Feng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengxing Lu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shenglan Li
- Department of Neurosurgery, Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030
- Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Xiaomeng An
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lijun Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuanyuan Wu
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Ying Liu
- Department of Neurosurgery, Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030
- Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030
- The Senator Lloyd & B. A. Bentsen Center for Stroke Research, the Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Mario R Capecchi
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112;
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China;
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76
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Multi-omics analyses reveal metabolic alterations regulated by hepatitis B virus core protein in hepatocellular carcinoma cells. Sci Rep 2017; 7:41089. [PMID: 28112229 PMCID: PMC5253728 DOI: 10.1038/srep41089] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is partly responsible for hepatitis, fatty liver disease and hepatocellular carcinoma (HCC). HBV core protein (HBc), encoded by the HBV genome, may play a significant role in HBV life cycle. However, the function of HBc in the occurrence and development of liver disease is still unclear. To investigate the underlying mechanisms, HBc-transfected HCC cells were characterized by multi-omics analyses. Combining proteomics and metabolomics analyses, our results showed that HBc promoted the expression of metabolic enzymes and the secretion of metabolites in HCC cells. In addition, glycolysis and amino acid metabolism were significantly up-regulated by HBc. Moreover, Max-like protein X (MLX) might be recruited and enriched by HBc in the nucleus to regulate glycolysis pathways. This study provides further insights into the function of HBc in the molecular pathogenesis of HBV-induced diseases and indicates that metabolic reprogramming appears to be a hallmark of HBc transfection.
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77
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Rangel R, Lee SC, Hon-Kim Ban K, Guzman-Rojas L, Mann MB, Newberg JY, Kodama T, McNoe LA, Selvanesan L, Ward JM, Rust AG, Chin KY, Black MA, Jenkins NA, Copeland NG. Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression. Proc Natl Acad Sci U S A 2016; 113:E7749-E7758. [PMID: 27849608 PMCID: PMC5137755 DOI: 10.1073/pnas.1613859113] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) has the worst prognosis of any breast cancer subtype. To better understand the genetic forces driving TNBC, we performed a transposon mutagenesis screen in a phosphatase and tensin homolog (Pten) mutant mice and identified 12 candidate trunk drivers and a much larger number of progression genes. Validation studies identified eight TNBC tumor suppressor genes, including the GATA-like transcriptional repressor TRPS1 Down-regulation of TRPS1 in TNBC cells promoted epithelial-to-mesenchymal transition (EMT) by deregulating multiple EMT pathway genes, in addition to increasing the expression of SERPINE1 and SERPINB2 and the subsequent migration, invasion, and metastasis of tumor cells. Transposon mutagenesis has thus provided a better understanding of the genetic forces driving TNBC and discovered genes with potential clinical importance in TNBC.
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Affiliation(s)
- Roberto Rangel
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Song-Choon Lee
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Kenneth Hon-Kim Ban
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
- Deparment of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138673
| | - Liliana Guzman-Rojas
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Michael B Mann
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Justin Y Newberg
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Takahiro Kodama
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Leslie A McNoe
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | | | - Jerrold M Ward
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Alistair G Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, United Kingdom
| | - Kuan-Yew Chin
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Nancy A Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
| | - Neal G Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030;
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore 138673
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78
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Han C, Yang L, Choi HH, Baddour J, Achreja A, Liu Y, Li Y, Li J, Wan G, Huang C, Ji G, Zhang X, Nagrath D, Lu X. Amplification of USP13 drives ovarian cancer metabolism. Nat Commun 2016; 7:13525. [PMID: 27892457 PMCID: PMC5133706 DOI: 10.1038/ncomms13525] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 10/12/2016] [Indexed: 12/25/2022] Open
Abstract
Dysregulated energetic metabolism has been recently identified as a hallmark of cancer. Although mutations in metabolic enzymes hardwire metabolism to tumourigenesis, they are relatively infrequent in ovarian cancer. More often, cancer metabolism is re-engineered by altered abundance and activity of the metabolic enzymes. Here we identify ubiquitin-specific peptidase 13 (USP13) as a master regulator that drives ovarian cancer metabolism. USP13 specifically deubiquitinates and thus upregulates ATP citrate lyase and oxoglutarate dehydrogenase, two key enzymes that determine mitochondrial respiration, glutaminolysis and fatty acid synthesis. The USP13 gene is co-amplified with PIK3CA in 29.3% of high-grade serous ovarian cancers and its overexpression is significantly associated with poor clinical outcome. Inhibiting USP13 remarkably suppresses ovarian tumour progression and sensitizes tumour cells to the treatment of PI3K/AKT inhibitor. Our results reveal an important metabolism-centric role of USP13, which may lead to potential therapeutics targeting USP13 in ovarian cancers. Cancer cells need to reprogramme their metabolism to allow rapid cell proliferation. Here, the authors show that USP13 is amplified in ovarian cancer and its protein product, a deubiquitinase, drives tumour progression by rewiring the metabolism of cancer cells by stabilising two critical metabolic enzymes.
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Affiliation(s)
- Cecil Han
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lifeng Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Hyun Ho Choi
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Joelle Baddour
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Abhinav Achreja
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Yunhua Liu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yujing Li
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jiada Li
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, Changsha 410008, China
| | - Guohui Wan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Cheng Huang
- Drug Discovery Laboratory, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xinna Zhang
- Department of Gynaecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Deepak Nagrath
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA.,Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Xiongbin Lu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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79
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Narayanavari SA, Chilkunda SS, Ivics Z, Izsvák Z. Sleeping Beauty transposition: from biology to applications. Crit Rev Biochem Mol Biol 2016; 52:18-44. [PMID: 27696897 DOI: 10.1080/10409238.2016.1237935] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.
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Affiliation(s)
- Suneel A Narayanavari
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Shreevathsa S Chilkunda
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Zoltán Ivics
- b Division of Medical Biotechnology , Paul Ehrlich Institute , Langen , Germany
| | - Zsuzsanna Izsvák
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
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80
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Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic disease with a high mortality rate. Genetic and biochemical studies have shown that RAS signaling mediated by KRAS plays a pivotal role in disease initiation, progression and drug resistance. RAS signaling affects several cellular processes in PDAC, including cellular proliferation, migration, cellular metabolism and autophagy. 90% of pancreatic cancer patients harbor somatic oncogenic point mutations in KRAS, which lead to constitutive activation of the molecule. Pancreatic cancers lacking KRAS mutations show activation of RAS via upstream signaling through receptor mediated tyrosine kinases, like EGFR, and in a small fraction of patients, oncogenic activation of the downstream B-RAF molecule is detected. RAS-stimulated signaling of RAF/MEK/ERK, PI3K/AKT/mTOR and RalA/B is active in human pancreatic cancers, cancer cell lines and mouse models of PDAC, although activation levels of each signaling arm appear to be variable across different tumors and perhaps within different subclones of single tumors. Recently, several targeted therapies directed towards MEK, ERK, PI3K and mTOR have been assayed in pancreatic cancer cell lines and in mouse models of the disease with promising results for their ability to impede cellular growth or delay tumor formation, and several inhibitors are currently in clinical trials. However, therapy-induced cross activation of RAS effector molecules has elucidated the complexities of targeting RAS signaling. Combinatorial therapies are now being explored as an approach to overcome RAS-induced therapeutic resistance in pancreatic cancer.
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Affiliation(s)
- Karen M Mann
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph Juan
- Molecular Oncology Department, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Nancy A Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Neal G Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA
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81
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Teufel A, Dufour JF. Two-Step Forward Genetic Screen in Mice Identifies the Ral Pathway as a Central Drug Target in Hepatocellular Carcinoma. Gastroenterology 2016; 151:231-3. [PMID: 27371877 DOI: 10.1053/j.gastro.2016.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Andreas Teufel
- Department of Medicine I, University Medical Center, Regensburg, Germany.
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82
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Kodama T, Bard-Chapeau EA, Newberg JY, Kodama M, Rangel R, Yoshihara K, Ward JM, Jenkins NA, Copeland NG. Two-Step Forward Genetic Screen in Mice Identifies Ral GTPase-Activating Proteins as Suppressors of Hepatocellular Carcinoma. Gastroenterology 2016; 151:324-337.e12. [PMID: 27178121 DOI: 10.1053/j.gastro.2016.04.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/24/2016] [Accepted: 04/27/2016] [Indexed: 01/16/2023]
Abstract
BACKGROUND & AIMS High-throughput sequencing technologies have identified thousands of infrequently mutated genes in hepatocellular carcinomas (HCCs). However, high intratumor and intertumor heterogeneity, combined with large numbers of passenger mutations, have made it difficult to identify driver mutations that contribute to the development of HCC. We combined transposon mutagenesis with a high-throughput screen of a small-hairpin RNA (shRNA) library to identify genes and pathways that contribute to HCC development. METHODS Sleeping beauty transposons were mobilized in livers of transgenic mice predisposed to develop hepatocellular adenoma and HCC owing to expression of the hepatitis B virus surface antigen. This whole-genome mutagenesis technique was used to generate an unbiased catalogue of candidate cancer genes (CCGs). Pooled shRNA libraries targeting 250 selected CCGs then were introduced into immortalized mouse liver cells and the cells were monitored for their tumor-forming ability after injection into nude mice. RESULTS Transposon-mediated mutagenesis identified 1917 high-confident CCGs and highlighted the importance of Ras signaling in the development of HCC. Subsequent pooled shRNA library screening of 250 selected CCGs validated 27 HCC tumor-suppressor genes. Individual shRNA knockdown of 4 of these genes (Acaa2, Hbs1l, Ralgapa2, and Ubr2) increased the proliferation of multiple human HCC cell lines in culture and accelerated the formation of xenograft tumors in nude mice. The ability of Ralgapa2 to promote HCC cell proliferation and tumor formation required its inhibition of Rala and Ralb. Dual inhibition of Ras signaling via Ral and Raf, using a combination of small-molecule inhibitor RBC8 and sorafenib, reduced the proliferation of HCC cells in culture and completely inhibited their growth as xenograft tumors in nude mice. CONCLUSIONS In a 2-step forward genetic screen in mice, we identified members of the Ral guanosine triphosphatase-activating protein pathway and other proteins as suppressors of HCC cell proliferation and tumor growth. These proteins might serve as therapeutic targets for liver cancer.
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Affiliation(s)
- Takahiro Kodama
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Emilie A Bard-Chapeau
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Justin Y Newberg
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Michiko Kodama
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Roberto Rangel
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jerrold M Ward
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Nancy A Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Neal G Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas.
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83
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Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq. Nat Commun 2016; 7:12144. [PMID: 27385103 PMCID: PMC4941052 DOI: 10.1038/ncomms12144] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 06/04/2016] [Indexed: 12/18/2022] Open
Abstract
Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration and utilizes already available gene expression profiles to determine chromosomal aberrations. Chromosomal aberrations can be detected by global gene expression analysis. Here, the authors report eSNP-Karyotyping, a new method that can detect chromosomal aberrations by measuring the ratio of expression between the two alleles without comparison to a matched diploid sample.
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84
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Transposon mutagenesis identifies genes and cellular processes driving epithelial-mesenchymal transition in hepatocellular carcinoma. Proc Natl Acad Sci U S A 2016; 113:E3384-93. [PMID: 27247392 DOI: 10.1073/pnas.1606876113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is thought to contribute to metastasis and chemoresistance in patients with hepatocellular carcinoma (HCC), leading to their poor prognosis. The genes driving EMT in HCC are not yet fully understood, however. Here, we show that mobilization of Sleeping Beauty (SB) transposons in immortalized mouse hepatoblasts induces mesenchymal liver tumors on transplantation to nude mice. These tumors show significant down-regulation of epithelial markers, along with up-regulation of mesenchymal markers and EMT-related transcription factors (EMT-TFs). Sequencing of transposon insertion sites from tumors identified 233 candidate cancer genes (CCGs) that were enriched for genes and cellular processes driving EMT. Subsequent trunk driver analysis identified 23 CCGs that are predicted to function early in tumorigenesis and whose mutation or alteration in patients with HCC is correlated with poor patient survival. Validation of the top trunk drivers identified in the screen, including MET (MET proto-oncogene, receptor tyrosine kinase), GRB2-associated binding protein 1 (GAB1), HECT, UBA, and WWE domain containing 1 (HUWE1), lysine-specific demethylase 6A (KDM6A), and protein-tyrosine phosphatase, nonreceptor-type 12 (PTPN12), showed that deregulation of these genes activates an EMT program in human HCC cells that enhances tumor cell migration. Finally, deregulation of these genes in human HCC was found to confer sorafenib resistance through apoptotic tolerance and reduced proliferation, consistent with recent studies showing that EMT contributes to the chemoresistance of tumor cells. Our unique cell-based transposon mutagenesis screen appears to be an excellent resource for discovering genes involved in EMT in human HCC and potentially for identifying new drug targets.
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85
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Koso H, Yi H, Sheridan P, Miyano S, Ino Y, Todo T, Watanabe S. Identification of RNA-Binding Protein LARP4B as a Tumor Suppressor in Glioma. Cancer Res 2016; 76:2254-64. [PMID: 26933087 DOI: 10.1158/0008-5472.can-15-2308] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
Transposon-based insertional mutagenesis is a valuable method for conducting unbiased forward genetic screens to identify cancer genes in mice. We used this system to elucidate factors involved in the malignant transformation of neural stem cells into glioma-initiating cells. We identified an RNA-binding protein, La-related protein 4b (LARP4B), as a candidate tumor-suppressor gene in glioma. LARP4B expression was consistently decreased in human glioma stem cells and cell lines compared with normal neural stem cells. Moreover, heterozygous deletion of LARP4B was detected in nearly 80% of glioblastomas in The Cancer Genome Atlas database. LARP4B loss was also associated with low expression and poor patient survival. Overexpression of LARP4B in glioma cell lines strongly inhibited proliferation by inducing mitotic arrest and apoptosis in four of six lines as well as in two patient-derived glioma stem cell populations. The expression levels of CDKN1A and BAX were also upregulated upon LARP4B overexpression, and the growth-inhibitory effects were partially dependent on p53 (TP53) activity in cells expressing wild-type, but not mutant, p53. We further found that the La module, which is responsible for the RNA chaperone activity of LARP4B, was important for the growth-suppressive effect and was associated with BAX mRNA. Finally, LARP4B depletion in p53 and Nf1-deficient mouse primary astrocytes promoted cell proliferation and led to increased tumor size and invasiveness in xenograft and orthotopic models. These data provide strong evidence that LARP4B serves as a tumor-suppressor gene in glioma, encouraging further exploration of the RNA targets potentially involved in LARP4B-mediatd growth inhibition. Cancer Res; 76(8); 2254-64. ©2016 AACR.
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Affiliation(s)
- Hideto Koso
- Division of Molecular and Developmental Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hungtsung Yi
- Division of Molecular and Developmental Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Paul Sheridan
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Ino
- Division of Innovative Cancer Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomoki Todo
- Division of Innovative Cancer Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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86
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Wang X, Zhang W, Tang J, Huang R, Li J, Xu D, Xie Y, Jiang R, Deng L, Zhang X, Chai Y, Qin X, Sun B. LINC01225 promotes occurrence and metastasis of hepatocellular carcinoma in an epidermal growth factor receptor-dependent pathway. Cell Death Dis 2016; 7:e2130. [PMID: 26938303 PMCID: PMC4823934 DOI: 10.1038/cddis.2016.26] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 12/17/2022]
Abstract
The long noncoding RNAs (lncRNAs) have long been clarified to participate in hepatocellular carcinoma (HCC) as a biomarker. We carried out the present study in order to identify HCC-related lncRNAs and elucidate the functional roles in the development and progression of HCC. Our previous study has provided that LINC01225 may be an HCC-related gene. Here, we verified that LINC01225 was upregulated in HCC. Knockdown of LINC01225 resulted in inhibited cell proliferation and invasion with activated apoptosis and cell cycle arrest in vitro. Overexpression of LINC01225 in LINC01225 knockdown cells presented that attenuated cell proliferation and invasion were restored and enhanced. Subcutaneous and tail vein/intraperitoneal injection xenotransplantation model in vivo validated reduced tumor progression and metastasis. Investigation of mechanism found that LINC01225 could bind to epidermal growth factor receptor (EGFR) and increase the protein level of EGFR, and subsequently fine tune the EGFR/Ras/Raf-1/MEK/MAPK signaling pathway. Analysis with clinicopathological information suggested a high expression of LINC01225 is positively associated with poor prognosis. We also proved that LINC01225 was stably expressed in serum and can act as a novel biomarker in predicting the diagnosis of HCC. As a conclusion, LINC01225 plays a crucial role in HCC and can act as a biomarker for the diagnosis and prognosis of HCC.
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Affiliation(s)
- X Wang
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - W Zhang
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - J Tang
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - R Huang
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - J Li
- Department of General Surgery, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - D Xu
- Department of Rheumatology, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, P.R. China
| | - Y Xie
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - R Jiang
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - L Deng
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - X Zhang
- The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, P.R. China
| | - Y Chai
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
| | - X Qin
- The Affiliated Changzhou NO.2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, P.R. China
| | - B Sun
- Liver Transplantation Center of the First Affiliated Hospital and Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, P.R. China
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87
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Heqing Y, Bin L, Xuemei Y, Linfa L. The role and mechanism of autophagy in sorafenib targeted cancer therapy. Crit Rev Oncol Hematol 2016; 100:137-40. [PMID: 26920575 DOI: 10.1016/j.critrevonc.2016.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/14/2016] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
Targeting kinase inhibitors (TKIs) are effective tools for treating advanced cancer. However, acquired resistance represents a roadblock in the use of TKIs, such as sorafenib, for cancer therapy. Understanding the acquisition of resistance to sorafenib will help doctors to cope with acquired resistance to TKIs in general and to develop personalized medicine strategies for cancer patients. Autophagy is a biological process that occurs in normal organisms. However, it is also a component of multiple disease processes, including cancer development and progression. However, the roles of autophagy in cancer and in response to cancer therapy are controversial. In this review, we summarize the progress in autophagy and sorafenib resistance research, which is representative of acquired resistance to targeted cancer therapy.
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Affiliation(s)
- Yi Heqing
- Department of Nuclear Medicine, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, Zhejiang Province 310021, PR China
| | - Long Bin
- Department of Nuclear Medicine, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, Zhejiang Province 310021, PR China
| | - Ye Xuemei
- Department of Nuclear Medicine, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, Zhejiang Province 310021, PR China
| | - Li Linfa
- Department of Nuclear Medicine, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, Zhejiang Province 310021, PR China.
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88
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Lévy P, Bartosch B. Metabolic reprogramming: a hallmark of viral oncogenesis. Oncogene 2015; 35:4155-64. [DOI: 10.1038/onc.2015.479] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/11/2015] [Accepted: 11/14/2015] [Indexed: 02/07/2023]
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89
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Chiu AP, Tschida BR, Lo LH, Moriarity BS, Rowlands DK, Largaespada DA, Keng VW. Transposon mouse models to elucidate the genetic mechanisms of hepatitis B viral induced hepatocellular carcinoma. World J Gastroenterol 2015; 21:12157-12170. [PMID: 26576100 PMCID: PMC4641133 DOI: 10.3748/wjg.v21.i42.12157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/18/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
The major type of human liver cancer is hepatocellular carcinoma (HCC), and there are currently many risk factors that contribute to this deadly disease. The majority of HCC occurrences are associated with chronic hepatitis viral infection, and hepatitis B viral (HBV) infection is currently a major health problem in Eastern Asia. Elucidating the genetic mechanisms associated with HBV-induced HCC has been difficult due to the heterogeneity and genetic complexity associated with this disease. A repertoire of animal models has been broadly used to study the pathophysiology and to develop potential treatment regimens for HBV-associated HCC. The use of these animal models has provided valuable genetic information and has been an important contributor to uncovering the factors involved in liver malignant transformation, invasion and metastasis. Recently, transposon-based mouse models are becoming more widely used in liver cancer research to interrogate the genome by forward genetics and also used to validate genes rapidly in a reverse genetic manner. Importantly, these transposon-based rapid reverse genetic mouse models could become crucial in testing potential therapeutic agents before proceeding to clinical trials in human. Therefore, this review will cover the use of transposon-based mouse models to address the problems of liver cancer, especially HBV-associated HCC occurrences in Asia.
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90
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Chen WC, Teo XQ, Lee MY, Radda GK, Lee P. Robust hyperpolarized (13)C metabolic imaging with selective non-excitation of pyruvate (SNEP). NMR IN BIOMEDICINE 2015; 28:1021-1030. [PMID: 26119950 DOI: 10.1002/nbm.3346] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/22/2015] [Accepted: 05/22/2015] [Indexed: 06/04/2023]
Abstract
In vivo metabolic imaging using hyperpolarized [1-(13)C]pyruvate provides localized biochemical information and is particularly useful in detecting early disease changes, as well as monitoring disease progression and treatment response. However, a major limitation of hyperpolarized magnetization is its unrecoverable decay, due not only to T1 relaxation but also to radio-frequency (RF) excitation. RF excitation schemes used in metabolic imaging must therefore be able to utilize available hyperpolarized magnetization efficiently and robustly for the optimal detection of substrate and metabolite activities. In this work, a novel RF excitation scheme called selective non-excitation of pyruvate (SNEP) is presented. This excitation scheme involves the use of a spectral selective RF pulse to specifically exclude the excitation of [1-(13)C]pyruvate, while uniformly exciting the key metabolites of interest (namely [1-(13)C]lactate and [1-(13)C]alanine) and [1-(13)C]pyruvate-hydrate. By eliminating the loss of hyperpolarized [1-(13)C]pyruvate magnetization due to RF excitation, the signal from downstream metabolite pools is increased together with enhanced dynamic range. Simulation results, together with phantom measurements and in vivo experiments, demonstrated the improvement in signal-to-noise ratio (SNR) and the extension of the lifetime of the [1-(13)C]lactate and [1-(13)C]alanine pools when compared with conventional non-spectral selective (NS) excitation. SNEP has also been shown to perform comparably well with multi-band (MB) excitation, yet SNEP possesses distinct advantages, including ease of implementation, less stringent demands on gradient performance, increased robustness to frequency drifts and B0 inhomogeneity as well as easier quantification involving the use of [1-(13)C]pyruvate-hydrate as a proxy for the actual [1-(13)C] pyruvate signal. SNEP is therefore a promising alternative for robust hyperpolarized [1-(13)C]pyruvate metabolic imaging with high fidelity.
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Affiliation(s)
- Way Cherng Chen
- Functional Metabolism Group, Singapore Bioimaging Consortium (A*STAR), Singapore
| | - Xing Qi Teo
- Functional Metabolism Group, Singapore Bioimaging Consortium (A*STAR), Singapore
| | - Man Ying Lee
- Functional Metabolism Group, Singapore Bioimaging Consortium (A*STAR), Singapore
| | - George K Radda
- Functional Metabolism Group, Singapore Bioimaging Consortium (A*STAR), Singapore
| | - Philip Lee
- Functional Metabolism Group, Singapore Bioimaging Consortium (A*STAR), Singapore
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91
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Bermejo-Rodríguez C, Pérez-Mancera PA. Use of DNA transposons for functional genetic screens in mouse models of cancer. Curr Opin Biotechnol 2015; 35:103-10. [PMID: 26073851 DOI: 10.1016/j.copbio.2015.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/14/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022]
Abstract
Cancer is a very heterogeneous disease with complex genetic interactions. In recent years, the systematic sequencing of cancer genomes has provided information to design personalized therapeutic interventions. However, the complexity of cancer genomes commonly makes it difficult to identify specific genes involved in tumour development or therapeutic responsiveness. The generation of mouse models of cancer using transposon-mediated approaches has provided a powerful tool to unveil the role of key genes during cancer development. Here we will discuss how the use of forward and reverse genetic approaches mediated by DNA transposons can support the investigation of cancer pathogenesis, including the identification of cancer promoting mechanisms and potential therapeutic targets.
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Affiliation(s)
- Camino Bermejo-Rodríguez
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Pedro A Pérez-Mancera
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Molecular and Clinical Cancer Medicine, National Institute for Health Research Liverpool Pancreas Biomedical Research Unit, University of Liverpool, Daulby Street, Liverpool L69 3GA, UK.
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92
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LaFave MC, Varshney GK, Burgess SM. GeIST: a pipeline for mapping integrated DNA elements. Bioinformatics 2015; 31:3219-21. [PMID: 26049161 DOI: 10.1093/bioinformatics/btv350] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/29/2015] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED There are several experimental contexts in which it is important to identify DNA integration sites, such as insertional mutagenesis screens, gene and enhancer trap applications, and gene therapy. We previously developed an assay to identify millions of integrations in multiplexed barcoded samples at base-pair resolution. The sheer amount of data produced by this approach makes the mapping of individual sites non-trivial without bioinformatics support. This article presents the Genomic Integration Site Tracker (GeIST), a command-line pipeline designed to map the integration sites produced by this assay and identify the samples from which they came. GeIST version 2.1.0, a more adaptable version of our original pipeline, can identify integrations of murine leukemia virus, adeno-associated virus, Tol2 transposons or Ac/Ds transposons, and can be adapted for other inserted elements. It has been tested on experimental data for each of these delivery vectors and fine-tuned to account for sequencing and cloning artifacts. AVAILABILITY AND IMPLEMENTATION GeIST uses a combination of Bash shell scripting and Perl. GeIST is available at http://research.nhgri.nih.gov/software/GeIST/. CONTACT burgess@mail.nih.gov.
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Affiliation(s)
- Matthew C LaFave
- Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA
| | - Gaurav K Varshney
- Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-8004, USA
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93
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Moriarity BS, Largaespada DA. Sleeping Beauty transposon insertional mutagenesis based mouse models for cancer gene discovery. Curr Opin Genet Dev 2015; 30:66-72. [PMID: 26051241 DOI: 10.1016/j.gde.2015.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 01/04/2023]
Abstract
Large-scale genomic efforts to study human cancer, such as the cancer gene atlas (TCGA), have identified numerous cancer drivers in a wide variety of tumor types. However, there are limitations to this approach, the mutations and expression or copy number changes that are identified are not always clearly functionally relevant, and only annotated genes and genetic elements are thoroughly queried. The use of complimentary, nonbiased, functional approaches to identify drivers of cancer development and progression is ideal to maximize the rate at which cancer discoveries are achieved. One such approach that has been successful is the use of the Sleeping Beauty (SB) transposon-based mutagenesis system in mice. This system uses a conditionally expressed transposase and mutagenic transposon allele to target mutagenesis to somatic cells of a given tissue in mice to cause random mutations leading to tumor development. Analysis of tumors for transposon common insertion sites (CIS) identifies candidate cancer genes specific to that tumor type. While similar screens have been performed in mice with the PiggyBac (PB) transposon and viral approaches, we limit extensive discussion to SB. Here we discuss the basic structure of these screens, screens that have been performed, methods used to identify CIS.
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Affiliation(s)
- Branden S Moriarity
- Department of Pediatrics, University of Minnesota Minneapolis, MN 55455, United States; Center for Genome Engineering, University of Minnesota Minneapolis, MN 55455, United States; Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455, United States
| | - David A Largaespada
- Department of Pediatrics, University of Minnesota Minneapolis, MN 55455, United States; Center for Genome Engineering, University of Minnesota Minneapolis, MN 55455, United States; Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455, United States; Department of Genetics, Cell Biology, and Development, University of Minnesota Minneapolis, MN 55455, United States.
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94
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Song S, Honjo S, Jin J, Chang SS, Scott AW, Chen Q, Kalhor N, Correa AM, Hofstetter WL, Albarracin CT, Wu TT, Johnson RL, Hung MC, Ajani JA. The Hippo Coactivator YAP1 Mediates EGFR Overexpression and Confers Chemoresistance in Esophageal Cancer. Clin Cancer Res 2015; 21:2580-90. [PMID: 25739674 DOI: 10.1158/1078-0432.ccr-14-2191] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 02/13/2015] [Indexed: 01/12/2023]
Abstract
PURPOSE Esophageal cancer is an aggressive malignancy and often resistant to therapy. Overexpression of EGFR has been associated with poor prognosis of patients with esophageal cancer. However, clinical trials using EGFR inhibitors have not provided benefit for patients with esophageal cancer. Failure of EGFR inhibition may be due to crosstalk with other oncogenic pathways. EXPERIMENTAL DESIGN In this study, expression of YAP1 and EGFR were examined in EAC-resistant tumor tissues versus sensitive tissues by IHC. Western blot analysis, immunofluorescence, real-time PCR, promoter analysis, site-directed mutagenesis, and in vitro and in vivo functional assays were performed to elucidate the YAP1-mediated EGFR expression and transcription and the relationship with chemoresistance in esophageal cancer. RESULTS We demonstrate that Hippo pathway coactivator YAP1 can induce EGFR expression and transcription in multiple cell systems. Both YAP1 and EGFR are overexpressed in resistant esophageal cancer tissues compared with sensitive esophageal cancer tissues. Furthermore, we found that YAP1 increases EGFR expression at the level of transcription requiring an intact TEAD-binding site in the EGFR promoter. Most importantly, exogenous induction of YAP1 induces resistance to 5-fluorouracil and docetaxcel, whereas knockdown of YAP1 sensitizes esophageal cancer cells to these cytotoxics. Verteporfin, a YAP1 inhibitor, effectively inhibits both YAP1 and EGFR expression and sensitizes cells to cytotoxics. CONCLUSIONS Our data provide evidence that YAP1 upregulation of EGFR plays an important role in conferring therapy resistance in esophageal cancer cells. Targeting YAP1-EGFR axis may be more efficacious than targeting EGFR alone in esophageal cancer.
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Affiliation(s)
- Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Soichiro Honjo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiankang Jin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shih-Shin Chang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ailing W Scott
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qiongrong Chen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, MD Anderson Cancer Center, The University of Texas, Houston, Texas
| | - Arlene M Correa
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Constance T Albarracin
- Department of Pathology, MD Anderson Cancer Center, The University of Texas, Houston, Texas
| | - Tsung-Teh Wu
- Department of Pathology, Mayo Clinic, Rochester, Minnesota
| | - Randy L Johnson
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Center for Molecular Medicine and Graduate Institute of Cancer Biology, China Medical University, Taichung, Taiwan
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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95
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Takeda H, Wei Z, Koso H, Rust AG, Yew CCK, Mann MB, Ward JM, Adams DJ, Copeland NG, Jenkins NA. Transposon mutagenesis identifies genes and evolutionary forces driving gastrointestinal tract tumor progression. Nat Genet 2015; 47:142-50. [PMID: 25559195 DOI: 10.1038/ng.3175] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 12/04/2014] [Indexed: 12/14/2022]
Abstract
To provide a more comprehensive understanding of the genes and evolutionary forces driving colorectal cancer (CRC) progression, we performed Sleeping Beauty (SB) transposon mutagenesis screens in mice carrying sensitizing mutations in genes that act at different stages of tumor progression. This approach allowed us to identify a set of genes that appear to be highly relevant for CRC and to provide a better understanding of the evolutionary forces and systems properties of CRC. We also identified six genes driving malignant tumor progression and a new human CRC tumor-suppressor gene, ZNF292, that might also function in other types of cancer. Our comprehensive CRC data set provides a resource with which to develop new therapies for treating CRC.
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Affiliation(s)
- Haruna Takeda
- 1] Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore. [2] Department of Oncologic Pathology, School of Medicine, Kanazawa Medical University, Ishikawa, Japan
| | - Zhubo Wei
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
| | - Hideto Koso
- 1] Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore. [2] Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Alistair G Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Christopher Chin Kuan Yew
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Michael B Mann
- 1] Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore. [2] Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jerrold M Ward
- Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Neal G Copeland
- 1] Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore. [2] Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
| | - Nancy A Jenkins
- 1] Division of Genomics and Genetics, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore. [2] Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
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96
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Riordan JD, Drury LJ, Smith RP, Brett BT, Rogers LM, Scheetz TE, Dupuy AJ. Sequencing methods and datasets to improve functional interpretation of sleeping beauty mutagenesis screens. BMC Genomics 2014; 15:1150. [PMID: 25526783 PMCID: PMC4378557 DOI: 10.1186/1471-2164-15-1150] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animal models of cancer are useful to generate complementary datasets for comparison to human tumor data. Insertional mutagenesis screens, such as those utilizing the Sleeping Beauty (SB) transposon system, provide a model that recapitulates the spontaneous development and progression of human disease. This approach has been widely used to model a variety of cancers in mice. Comprehensive mutation profiles are generated for individual tumors through amplification of transposon insertion sites followed by high-throughput sequencing. Subsequent statistical analyses identify common insertion sites (CISs), which are predicted to be functionally involved in tumorigenesis. Current methods utilized for SB insertion site analysis have some significant limitations. For one, they do not account for transposon footprints - a class of mutation generated following transposon remobilization. Existing methods also discard quantitative sequence data due to uncertainty regarding the extent to which it accurately reflects mutation abundance within a heterogeneous tumor. Additionally, computational analyses generally assume that all potential insertion sites have an equal probability of being detected under non-selective conditions, an assumption without sufficient relevant data. The goal of our study was to address these potential confounding factors in order to enhance functional interpretation of insertion site data from tumors. RESULTS We describe here a novel method to detect footprints generated by transposon remobilization, which revealed minimal evidence of positive selection in tumors. We also present extensive characterization data demonstrating an ability to reproducibly assign semi-quantitative information to individual insertion sites within a tumor sample. Finally, we identify apparent biases for detection of inserted transposons in several genomic regions that may lead to the identification of false positive CISs. CONCLUSION The information we provide can be used to refine analyses of data from insertional mutagenesis screens, improving functional interpretation of results and facilitating the identification of genes important in cancer development and progression.
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Affiliation(s)
| | | | | | | | | | | | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City IA 52242, USA.
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97
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Vyazunova I, Maklakova VI, Berman S, De I, Steffen MD, Hong W, Lincoln H, Morrissy AS, Taylor MD, Akagi K, Brennan CW, Rodriguez FJ, Collier LS. Sleeping Beauty mouse models identify candidate genes involved in gliomagenesis. PLoS One 2014; 9:e113489. [PMID: 25423036 PMCID: PMC4244117 DOI: 10.1371/journal.pone.0113489] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 10/27/2014] [Indexed: 01/01/2023] Open
Abstract
Genomic studies of human high-grade gliomas have discovered known and candidate tumor drivers. Studies in both cell culture and mouse models have complemented these approaches and have identified additional genes and processes important for gliomagenesis. Previously, we found that mobilization of Sleeping Beauty transposons in mice ubiquitously throughout the body from the Rosa26 locus led to gliomagenesis with low penetrance. Here we report the characterization of mice in which transposons are mobilized in the Glial Fibrillary Acidic Protein (GFAP) compartment. Glioma formation in these mice did not occur on an otherwise wild-type genetic background, but rare gliomas were observed when mobilization occurred in a p19Arf heterozygous background. Through cloning insertions from additional gliomas generated by transposon mobilization in the Rosa26 compartment, several candidate glioma genes were identified. Comparisons to genetic, epigenetic and mRNA expression data from human gliomas implicates several of these genes as tumor suppressor genes and oncogenes in human glioblastoma.
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Affiliation(s)
- Irina Vyazunova
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Vilena I. Maklakova
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Samuel Berman
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ishani De
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Megan D. Steffen
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Won Hong
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Hayley Lincoln
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - A. Sorana Morrissy
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Keiko Akagi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States of America
| | - Cameron W. Brennan
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Fausto J. Rodriguez
- Department of Pathology, Division of Neuropathology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Lara S. Collier
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
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98
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Takai A, Dang HT, Wang XW. Identification of drivers from cancer genome diversity in hepatocellular carcinoma. Int J Mol Sci 2014; 15:11142-60. [PMID: 24955791 PMCID: PMC4100204 DOI: 10.3390/ijms150611142] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers with a dismal outcome. The complicated molecular pathogenesis of HCC caused by tumor heterogeneity makes it difficult to identify druggable targets useful for treating HCC patients. One approach that has a potential for the improvement of patient prognosis is the identification of cancer driver genes that play a critical role in the development of HCC. Recent technological advances of high-throughput methods, such as gene expression profiles, DNA copy number alterations and somatic mutations, have expanded our understanding of the comprehensive genetic profiles of HCC. Integrative analysis of these omics profiles enables us to classify the molecular subgroups of HCC patients. As each subgroup classified according to genetic profiles has different clinical features, such as recurrence rate and prognosis, the tumor subclassification tools are useful in clinical practice. Furthermore, a global genetic analysis, including genome-wide RNAi functional screening, makes it possible to identify cancer vulnerable genes. Identification of common cancer driver genes in HCC leads to the development of an effective molecular target therapy.
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Affiliation(s)
- Atsushi Takai
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hien T Dang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Xin W Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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99
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Roessler S, Budhu A, Wang XW. Deciphering cancer heterogeneity: the biological space. Front Cell Dev Biol 2014; 2:12. [PMID: 25364720 PMCID: PMC4207029 DOI: 10.3389/fcell.2014.00012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/17/2014] [Indexed: 01/15/2023] Open
Abstract
Most lethal solid tumors including hepatocellular carcinoma (HCC) are considered incurable due to extensive heterogeneity in clinical presentation and tumor biology. Tumor heterogeneity may result from different cells of origin, patient ethnicity, etiology, underlying disease, and diversity of genomic and epigenomic changes which drive tumor development. Cancer genomic heterogeneity thereby impedes treatment options and poses a significant challenge to cancer management. Studies of the HCC genome have revealed that although various genomic signatures identified in different HCC subgroups share a common prognosis, each carries unique molecular changes which are linked to different sets of cancer hallmarks whose misregulation has been proposed by Hanahan and Weinberg to be essential for tumorigenesis. We hypothesize that these specific sets of cancer hallmarks collectively occupy different tumor biological space representing the misregulation of different biological processes. In principle, a combination of different cancer hallmarks can result in new convergent molecular networks that are unique to each tumor subgroup and represent ideal druggable targets. Due to the ability of the tumor to adapt to external factors such as treatment or changes in the tumor microenvironment, the tumor biological space is elastic. Our ability to identify distinct groups of cancer patients with similar tumor biology who are most likely to respond to a specific therapy would have a significant impact on improving patient outcome. It is currently a challenge to identify a particular hallmark or a newly emerged convergent molecular network for a particular tumor. Thus, it is anticipated that the integration of multiple levels of data such as genomic mutations, somatic copy number aberration, gene expression, proteomics, and metabolomics, may help us grasp the tumor biological space occupied by each individual, leading to improved therapeutic intervention and outcome.
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Affiliation(s)
- Stephanie Roessler
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Xin W Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
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