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Lee OW, Rodrigues C, Lin SH, Luo W, Jones K, Brown DW, Zhou W, Karlins E, Khan SM, Baulande S, Raynal V, Surdez D, Reynaud S, Rubio RA, Zaidi S, Grossetête S, Ballet S, Lapouble E, Laurence V, Pierron G, Gaspar N, Corradini N, Marec-Bérard P, Rothman N, Dagnall CL, Burdett L, Manning M, Wyatt K, Yeager M, Chari R, Leisenring WM, Kulozik AE, Kriebel J, Meitinger T, Strauch K, Kirchner T, Dirksen U, Mirabello L, Tucker MA, Tirode F, Armstrong GT, Bhatia S, Robison LL, Yasui Y, Romero-Pérez L, Hartmann W, Metzler M, Diver WR, Lori A, Freedman ND, Hoover RN, Morton LM, Chanock SJ, Grünewald TGP, Delattre O, Machiela MJ. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding. Am J Hum Genet 2023; 110:427-441. [PMID: 36787739 PMCID: PMC10027473 DOI: 10.1016/j.ajhg.2023.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.
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Affiliation(s)
- Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Calvin Rodrigues
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Virginie Raynal
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Didier Surdez
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Stephanie Reynaud
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Sakina Zaidi
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sandrine Grossetête
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Stelly Ballet
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Eve Lapouble
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | | | - Gaelle Pierron
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Institut Gustave Roussy, 94800 Villejuif, France
| | - Nadège Corradini
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Perrine Marec-Bérard
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Michelle Manning
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Raj Chari
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Genome Modification Core Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andreas E Kulozik
- University Children's Hospital of Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, 80539 Munich, Germany
| | - Thomas Kirchner
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Uta Dirksen
- University Children's Hospital of Essen, 45147 Essen, Germany
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Franck Tirode
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama, Birmingham, AL 35294, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard- Domagk Institute of Pathology, University Hospital of Münster, 48149 Münster, Germany
| | - Markus Metzler
- University Children's Hospital of Erlangen, 91054 Erlangen, Germany
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olivier Delattre
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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2
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circXRCC5 foster gastric cancer growth and metastasis by the HNRNPC/circXRCC5/miR-655-3p/RREB1/UBA2 positive feedback loop. Cancer Gene Ther 2022; 29:1648-1661. [PMID: 35661832 DOI: 10.1038/s41417-022-00482-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/22/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023]
Abstract
Gastric cancer (GC) is one of the most common malignancies, leading to millions of deaths each year. Here, we investigated the molecular mechanisms of GC, with a focus on circXRCC5/miR-655-3p/RREB1/UBA2 axis. circXRCC5 was identified in 62 paired cancer specimens and adjacent normal tissues by genome-wide bioinformatics analysis and verified by qRT-PCR and Sanger sequencing. Knockdown or exogenous expression of circXRCC5 was performed to validate the functional significance of circXRCC5 using both in vitro and in vivo assays, including CCK-8, colony formation, EdU incorporation, transwell system, as well as animal experiments. RNA immunoprecipitation, biotinylated RNA pull-down, ChIP, and dual-luciferase assays were employed to validate the regulatory network of circXRCC5/miR-655-3p/RREB1/UBA2. Frequently elevated circXRCC5 in GC tissues and cell lines was associated with poor prognosis of GC patients. Functionally, circXRCC5 overexpression facilitated GC cell proliferation, migration, and invasion, as well as promoted tumor growth and metastasis in vivo. Mechanistically, circXRCC5 served as a sponge of miR-655-3p to induce upregulation of RREB1. RREB1 was identified as a transcriptional activator of UBA2, thus contributing to GC tumorigenesis. Moreover, RNA binding protein (RBP) HNRNPC was proved to interact with circXRCC5 to promote circXRCC5 biogenesis. Collectively, circXRCC5 facilitates GC progression through the HNRNPC/circXRCC5/miR-655-3p/RREB1/UBA2 axis, which might bring novel therapeutic strategies for GC treatment.
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3
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Gao Q, Wu Y, Lu C, Kai W, Xie W, Wang Q, Wang L, Liu S, Pan Y. Knockdown of RREB1 inhibits cell proliferation via enhanced p16 expression in gastric cancer. Cell Cycle 2021; 20:2465-2475. [PMID: 34666611 DOI: 10.1080/15384101.2021.1987676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Gastric cancer (GC) is the most common gastrointestinal malignancy worldwide. However, the molecular mechanisms of the progression of GC are not fully understood. Ras-responsive element binding protein 1 (RREB1) is an oncogene in many types of cancer that is involved in various biological processes, such as DNA damage repair, cell growth and proliferation, cell differentiation, fat development, and fasting glucose balance. In this study, we demonstrate the role of RREB1 in gastric cancer. First, by immunohistochemistry staining (IHC) and bioinformatics analysis, we demonstrated the expression of RREB1 in gastric cancer and paired normal gastric tissues. Then, we established RREB1 overexpression and knockdown cell lines via lentiviral transfection and detected cell proliferation by using MTT, colony-forming, cell cycle and apoptosis assays in vitro. We demonstrated the effect of RREB1 on cell proliferation in vivo by using a subcutaneous xenograft tumor model in nude mice. Finally, by using Western blotting and IHC, we demonstrated the possible mechanism by which RREB1 affects cell proliferation. The IHC and bioinformatics analyses demonstrated that RREB1 was highly expressed in gastric cancer and showed that RREB1-expressing patients had a larger tumor size and more lymphovascular invasion than RREB1-negative patients. Knockdown of RREB1 inhibited cell proliferation in vivo and in vitro. Knockdown of RREB1 enhanced p16 expression in vivo and in vitro, and p16 expression was negatively related to RREB1 in gastric cancer tissue. RREB1 was highly expressed in gastric cancer, and knockdown of RREB1 inhibited cell proliferation via enhanced p16 expression.
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Affiliation(s)
- Qi Gao
- Department of General Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi, China.,Department of General Surgery, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yunhua Wu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chaoxiang Lu
- Department of General Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi, China.,Department of General Surgery, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wang Kai
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Weike Xie
- Department of General Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi, China.,Department of General Surgery, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qi Wang
- Department of General Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi, China.,Department of General Surgery, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lei Wang
- Department of General Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi, China.,Department of General Surgery, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shiqi Liu
- Department of General Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi, China.,Department of General Surgery, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yongkang Pan
- Department of General Surgery, Xi'an Children's Hospital, Xi'an, Shaanxi, China.,Department of General Surgery, The Affiliated Children Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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4
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Kikutake C, Yoshihara M, Suyama M. Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis. NAR Cancer 2021; 3:zcab008. [PMID: 34316701 PMCID: PMC8210231 DOI: 10.1093/narcan/zcab008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/21/2021] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer-related mutations have been mainly identified in protein-coding regions. Recent studies have demonstrated that mutations in non-coding regions of the genome could also be a risk factor for cancer. However, the non-coding regions comprise 98% of the total length of the human genome and contain a huge number of mutations, making it difficult to interpret their impacts on pathogenesis of cancer. To comprehensively identify cancer-related non-coding mutations, we focused on recurrent mutations in non-coding regions using somatic mutation data from COSMIC and whole-genome sequencing data from The Cancer Genome Atlas (TCGA). We identified 21 574 recurrent mutations in non-coding regions that were shared by at least two different samples from both COSMIC and TCGA databases. Among them, 580 candidate cancer-related non-coding recurrent mutations were identified based on epigenomic and chromatin structure datasets. One of such mutation was located in RREB1 binding site that is thought to interact with TEAD1 promoter. Our results suggest that mutations may disrupt the binding of RREB1 to the candidate enhancer region and increase TEAD1 expression levels. Our findings demonstrate that non-coding recurrent mutations and coding mutations may contribute to the pathogenesis of cancer.
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Affiliation(s)
- Chie Kikutake
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Minako Yoshihara
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mikita Suyama
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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5
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Chen R, Sugiyama A, Kataoka N, Sugimoto M, Yokoyama S, Fukuda A, Takaishi S, Seno H. Promoter-Level Transcriptome Identifies Stemness Associated With Relatively High Proliferation in Pancreatic Cancer Cells. Front Oncol 2020; 10:316. [PMID: 32266133 PMCID: PMC7099289 DOI: 10.3389/fonc.2020.00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/21/2020] [Indexed: 11/13/2022] Open
Abstract
Both pancreatic intraepithelial neoplasia (PanIN), a frequent precursor of pancreatic cancer, and intraductal papillary mucinous neoplasm (IPMN), a less common precursor, undergo several phases of molecular conversions and finally develop into highly malignant solid tumors with negative effects on the quality of life. We approached this long-standing issue by examining the following PanIN/IPMN cell lines derived from mouse models of pancreatic cancer: Ptf1a-Cre; KrasG12D; p53f/+ and Ptf1a-Cre; KrasG12D; and Brg1f/f pancreatic ductal adenocarcinomas (PDAs). The mRNA from these cells was subjected to a cap analysis of gene expression (CAGE) to map the transcription starting sites and quantify the expression of promoters across the genome. Two RNA samples extracted from three individual subcutaneous tumors generated by the transplantation of PanIN or IPMN cancer cell lines were used to generate libraries and Illumina Seq, with four RNA samples in total, to depict discrete transcriptional network between IPMN and PanIN. Moreover, in IPMN cells, the transcriptome tended to be enriched for suppressive and inhibitory biological processes. In contrast, the transcriptome of PanIN cells exhibited properties of stemness. Notably, the proliferation capacity of the latter cells in culture was only minimally constrained by well-known chemotherapy drugs such as GSK690693 and gemcitabine. The various transcriptional factor network systems detected in PanIN and IPMN cells reflect the distinct molecular profiles of these cell types. Further, we hope that these findings will enhance our mechanistic understanding of the characteristic molecular alterations underlying pancreatic cancer precursors. These data may provide a promising direction for therapeutic research.
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Affiliation(s)
- Ru Chen
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aiko Sugiyama
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoyuki Kataoka
- Laboratory of Cell Regulation, Department of Applied Animal Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies Health Promotion and Preemptive Medicine, Tokyo Medical University, Tokyo, Japan
| | - Shoko Yokoyama
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akihisa Fukuda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigeo Takaishi
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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6
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Deng YN, Xia Z, Zhang P, Ejaz S, Liang S. Transcription Factor RREB1: from Target Genes towards Biological Functions. Int J Biol Sci 2020; 16:1463-1473. [PMID: 32210733 PMCID: PMC7085234 DOI: 10.7150/ijbs.40834] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/06/2020] [Indexed: 02/05/2023] Open
Abstract
The Ras-responsive element binding protein 1(RREB1) is a member of zinc finger transcription factors, which is widely involved in biological processes including cell proliferation, transcriptional regulation and DNA damage repair. New findings reveal RREB1 functions as both transcriptional repressors and transcriptional activators for transcriptional regulation of target genes. The activation of RREB1 is regulated by MAPK pathway. We have summarized the target genes of RREB1 and discussed RREB1 roles in the cancer development. In addition, increasing evidences suggest that RREB1 is a potential risk gene for type 2 diabetes and obesity. We also review the current clinical application of RREB1 as a biomarker for melanoma detection. In conclusion, RREB1 is a promising diagnostic biomarker or new drug target for cancers and metabolic diseases.
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Affiliation(s)
- Ya-Nan Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China
| | - Zijing Xia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China.,Department of Rheumatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, P. R. China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, P. R. China
| | - Samina Ejaz
- Department of Biochemistry and Biotechnology, Baghdad Campus, The Islamia University of Bahawalpur, Pakistan
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, P.R. China
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7
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Yao J, Zhong L, Zhong P, Liu D, Yuan Z, Liu J, Yao S, Zhao Y, Chen M, Li L, Liu L, Liu B. RAS-Responsive Element-Binding Protein 1 Blocks the Granulocytic Differentiation of Myeloid Leukemia Cells. Oncol Res 2019; 27:809-818. [PMID: 30982491 PMCID: PMC7848438 DOI: 10.3727/096504018x15451301487729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
RAS-responsive element-binding protein 1 (RREB1) is a transcription factor that is implicated in RAS signaling and multiple tumors. However, the role of RREB1 in acute myeloid leukemia has not been studied. We found that RREB1 is overexpressed in AML patients and myeloid leukemia cell lines (NB4 and HL-60), and RREB1 expression was significantly decreased during granulocytic differentiation of myeloid leukemia cells induced by all-trans retinoic acid (ATRA). Then we performed a RREB1 knockdown assay in NB4 and HL-60 cells; the results showed that knockdown of RREB1 upregulated expression of CD11b, CEBPβ, and microRNA-145 (miR-145), which hinted that knockdown of RREB1 enhanced granulocytic differentiation of myeloid leukemia cells. In addition, inhibitor of miR-145 can offset the enhanced effect on granulocytic differentiation mediated by downregulation of RREB1. These collective findings demonstrated that RREB1 blocks granulocytic differentiation of myeloid leukemia cells by inhibiting the expression of miR-145 and downstream targets of the RAS signal pathway. These may provide a promising therapeutic target for AML patients.
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Affiliation(s)
- Juanjuan Yao
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Liang Zhong
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Pengqiang Zhong
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Dongdong Liu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Zhen Yuan
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Junmei Liu
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Shifei Yao
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Yi Zhao
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Min Chen
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Lianwen Li
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Lu Liu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, P.R. China
| | - Beizhong Liu
- Central Laboratory of Yong Chuan Hospital, Chongqing Medical University, Chongqing, P.R. China
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8
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Rahrmann EP, Wolf NK, Otto GM, Heltemes-Harris L, Ramsey LB, Shu J, LaRue RS, Linden MA, Rathe SK, Starr TK, Farrar MA, Moriarity BS, Largaespada DA. Sleeping Beauty Screen Identifies RREB1 and Other Genetic Drivers in Human B-cell Lymphoma. Mol Cancer Res 2019; 17:567-582. [PMID: 30355676 DOI: 10.1158/1541-7786.mcr-18-0582] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/13/2018] [Accepted: 10/15/2018] [Indexed: 11/16/2022]
Abstract
Follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) are the most common non-Hodgkin lymphomas distinguishable by unique mutations, chromosomal rearrangements, and gene expression patterns. Here, it is demonstrated that early B-cell progenitors express 2',3'-cyclic-nucleotide 3' phosphodiesterase (CNP) and that when targeted with Sleeping Beauty (SB) mutagenesis, Trp53R270H mutation or Pten loss gave rise to highly penetrant lymphoid diseases, predominantly follicular lymphoma and DLBCL. In efforts to identify the genetic drivers and signaling pathways that are functionally important in lymphomagenesis, SB transposon insertions were analyzed from splenomegaly specimens of SB-mutagenized mice (n = 23) and SB-mutagenized mice on a Trp53R270H background (n = 7) and identified 48 and 12 sites with statistically recurrent transposon insertion events, respectively. Comparison with human data sets revealed novel and known driver genes for B-cell development, disease, and signaling pathways: PI3K-AKT-mTOR, MAPK, NFκB, and B-cell receptor (BCR). Finally, functional data indicate that modulating Ras-responsive element-binding protein 1 (RREB1) expression in human DLBCL cell lines in vitro alters KRAS expression, signaling, and proliferation; thus, suggesting that this proto-oncogene is a common mechanism of RAS/MAPK hyperactivation in human DLBCL. IMPLICATIONS: A forward genetic screen identified new genetic drivers of human B-cell lymphoma and uncovered a RAS/MAPK-activating mechanism not previously appreciated in human lymphoid disease. Overall, these data support targeting the RAS/MAPK pathway as a viable therapeutic target in a subset of human patients with DLBCL.
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Affiliation(s)
- Eric P Rahrmann
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota.
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Natalie K Wolf
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - George M Otto
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Lynn Heltemes-Harris
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Lab Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, University of Minnesota, Minneapolis, Minnesota
| | - Laura B Ramsey
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, University of Minnesota, Minneapolis, Minnesota
| | - Jingmin Shu
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Rebecca S LaRue
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Michael A Linden
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota
| | - Susan K Rathe
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Timothy K Starr
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Department of Ob-Gyn and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Michael A Farrar
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Lab Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, University of Minnesota, Minneapolis, Minnesota
| | - Branden S Moriarity
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota
| | - David A Largaespada
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota
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9
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Liu Y, Guan J, Chen X. Identification of Differentially Expressed Genes under the Regulation of Transcription Factors in Osteosarcoma. Pathol Oncol Res 2018; 25:1091-1102. [PMID: 30411296 DOI: 10.1007/s12253-018-0519-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022]
Abstract
The present study was to investigate and identify the differentially expressed genes (DEGs) in the transcriptional regulatory network of osteosarcoma (OS). The gene expression dataset from Gene Expression Omnibus (GEO) datasets was downloaded. DEGs were identified and their functional annotation was also conducted. In addition, differentially expressed transcription factors (TFs) and the regulatory genes were identified. The electronic validation was used to verify the expression of selected genes. The integrated analysis led to 932 DEGs. The results of functional annotation indicated that these DEGs significantly enriched in the p53 signaling pathway, Jak-STAT signaling pathway and Wnt signaling pathway. ZNF354C, NFIC, NFATC2, SP2, FOXO3, EGR1, ZEB1, RREB1, EGR2 and SRF were covered by most TFs. The expression levels of NFIC and EGR2 in electronic validation were compatible with our bio-informatics result. In conclusion, the deregulation of these genes may provide valuable information in understanding the underlying molecular mechanism in the OS.
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Affiliation(s)
- Yang Liu
- Department of Orthopaedics, The First Affiliated Hospital of Bengbu Medical College, No. 287, ChangHuai Road, Bengbu, 233004, Anhui Province, China
| | - Jianzhong Guan
- Department of Orthopaedics, The First Affiliated Hospital of Bengbu Medical College, No. 287, ChangHuai Road, Bengbu, 233004, Anhui Province, China.
| | - Xiaotian Chen
- Department of Orthopaedics, The First Affiliated Hospital of Bengbu Medical College, No. 287, ChangHuai Road, Bengbu, 233004, Anhui Province, China
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10
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Siegfried A, Romary C, Escudié F, Nicaise Y, Grand D, Rochaix P, Barres B, Vergez S, Chevreau C, Coindre JM, Uro-Coste E, Le Guellec S. RREB1-MKL2 fusion in biphenotypic "oropharyngeal" sarcoma: New entity or part of the spectrum of biphenotypic sinonasal sarcomas? Genes Chromosomes Cancer 2018; 57:203-210. [PMID: 29266774 DOI: 10.1002/gcc.22521] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/17/2017] [Accepted: 12/17/2017] [Indexed: 02/03/2023] Open
Abstract
An increasing number of sarcomas displaying a primitive, monomorphic spindle cell phenotype have been shown to harbor recurrent gene fusions, including biphenotypic sinonasal sarcoma (SNS). Occurring in the sinonasal area of middle-aged patients, SNS is a locally aggressive tumor harboring in 90% of cases recurrent gene fusions involving the PAX3 gene, in which the chimeric transcription factor induces an aberrant dual myogenic and neural phenotype. Here, we report an unusual oropharyngeal monomorphic spindle cell sarcoma in a 53-year-old man that revealed a novel RREB1-MKL2 gene fusion by RNA sequencing with the Illumina TruSight RNA Fusion Panel. The gene fusion was validated by RT-PCR. Although the tumor location is unusual (but head and neck seated), most of the other clinical, morphologic, immunophenotypic (focal combined expression of S100 protein, SMA, desmin, and myogenin) and oncogenic data suggest that this biphenotypic "oropharyngeal" sarcoma is closely related to the biphenotypic SNS spectrum. Notably, the RREB1-MKL2 chimeric transcription factor encoded by this fusion gene produced an increase in MKL2 expression, which regulates both neural and myogenic differentiation, mimicking the crucial role of PAX3 reported in SNS oncogenesis. NGS and especially RNA sequencing may be used to identify new candidate fusion oncogenes in soft tissue tumors, which would help in updating the existing classification. In turn, this would lead to better therapeutic management of patients.
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Affiliation(s)
- Aurore Siegfried
- Department of Pathology, Toulouse University Hospital, Toulouse, France.,INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France
| | - Claire Romary
- Department of Pathology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Fréderic Escudié
- Department of Pathology, Toulouse University Hospital, Toulouse, France
| | - Yvan Nicaise
- Department of Pathology, Toulouse University Hospital, Toulouse, France
| | - David Grand
- Department of Pathology, Toulouse University Hospital, Toulouse, France
| | - Philippe Rochaix
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Pathology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Béatrice Barres
- Department of Pathology, Toulouse University Hospital, Toulouse, France
| | - Sébastien Vergez
- Department of ENT-Head and Neck Surgery, Regional Hospital University Centre of Toulouse, Toulouse, France
| | - Christine Chevreau
- Department of Oncology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Jean-Michel Coindre
- Department of Biopathology, Institut Bergonié, Bordeaux, France.,INSERM U916, Institut Bergonié, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - Emmanuelle Uro-Coste
- Department of Pathology, Toulouse University Hospital, Toulouse, France.,INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France
| | - Sophie Le Guellec
- INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France.,Department of Pathology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
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11
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Watson G, Ronai ZA, Lau E. ATF2, a paradigm of the multifaceted regulation of transcription factors in biology and disease. Pharmacol Res 2017; 119:347-357. [PMID: 28212892 PMCID: PMC5457671 DOI: 10.1016/j.phrs.2017.02.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 01/16/2023]
Abstract
Stringent transcriptional regulation is crucial for normal cellular biology and organismal development. Perturbations in the proper regulation of transcription factors can result in numerous pathologies, including cancer. Thus, understanding how transcription factors are regulated and how they are dysregulated in disease states is key to the therapeutic targeting of these factors and/or the pathways that they regulate. Activating transcription factor 2 (ATF2) has been studied in a number of developmental and pathological conditions. Recent findings have shed light on the transcriptional, post-transcriptional, and post-translational regulatory mechanisms that influence ATF2 function, and thus, the transcriptional programs coordinated by ATF2. Given our current knowledge of its multiple levels of regulation and function, ATF2 represents a paradigm for the mechanistic complexity that can regulate transcription factor function. Thus, increasing our understanding of the regulation and function of ATF2 will provide insights into fundamental regulatory mechanisms that influence how cells integrate extracellular and intracellular signals into a genomic response through transcription factors. Characterization of ATF2 dysfunction in the context of pathological conditions, particularly in cancer biology and response to therapy, will be important in understanding how pathways controlled by ATF2 or other transcription factors might be therapeutically exploited. In this review, we provide an overview of the currently known upstream regulators and downstream targets of ATF2.
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Affiliation(s)
- Gregory Watson
- Department of Tumor Biology and Program in Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Ze'ev A Ronai
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA; Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion, Haifa, 3109601, Israel
| | - Eric Lau
- Department of Tumor Biology and Program in Chemical Biology and Molecular Medicine, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
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12
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Xu SQ, Buraschi S, Morcavallo A, Genua M, Shirao T, Peiper SC, Gomella LG, Birbe R, Belfiore A, Iozzo RV, Morrione A. A novel role for drebrin in regulating progranulin bioactivity in bladder cancer. Oncotarget 2016; 6:10825-39. [PMID: 25839164 PMCID: PMC4484422 DOI: 10.18632/oncotarget.3424] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/23/2015] [Indexed: 01/13/2023] Open
Abstract
We recently established a critical role for the growth factor progranulin in bladder cancer insofar as progranulin promotes urothelial cancer cell motility and contributes, as an autocrine growth factor, to the transformed phenotype by modulating invasion and anchorage-independent growth. In addition, progranulin expression is upregulated in invasive bladder cancer tissues compared to normal controls. However, the molecular mechanisms of progranulin action in bladder cancer have not been fully elucidated. In this study, we searched for novel progranulin-interacting proteins using pull-down assays with recombinant progranulin and proteomics. We discovered that drebrin, an F-actin binding protein, bound progranulin in urothelial cancer cells. We characterized drebrin function in urothelial cancer cell lines and showed that drebrin is critical for progranulin-dependent activation of the Akt and MAPK pathways and modulates motility, invasion and anchorage-independent growth. In addition, drebrin regulates tumor formation in vivo and its expression is upregulated in bladder cancer tissues compared to normal tissue controls. Our data are translationally relevant as indicate that drebrin exerts an essential functional role in the regulation of progranulin action and may constitute a novel target for therapeutic intervention in bladder tumors. In addition, drebrin may serve as novel biomarker for bladder cancer.
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Affiliation(s)
- Shi-Qiong Xu
- Department of Urology and Biology of Prostate Cancer Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Simone Buraschi
- Department of Pathology, Anatomy and Cell Biology and Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alaide Morcavallo
- Department of Urology and Biology of Prostate Cancer Program, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Health and Endocrinology, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Marco Genua
- Department of Urology and Biology of Prostate Cancer Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Tomoaki Shirao
- Department of Neurobiology and Behavior, Gunma University School of Medicine, Showamachi, Maebashi, Japan
| | - Stephen C Peiper
- Department of Pathology, Anatomy and Cell Biology and Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leonard G Gomella
- Department of Urology and Biology of Prostate Cancer Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ruth Birbe
- Department of Pathology, Anatomy and Cell Biology and Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Antonino Belfiore
- Department of Health and Endocrinology, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Renato V Iozzo
- Department of Pathology, Anatomy and Cell Biology and Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrea Morrione
- Department of Urology and Biology of Prostate Cancer Program, Thomas Jefferson University, Philadelphia, PA, USA
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13
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Bonomo JA, Guan M, Ng MCY, Palmer ND, Hicks PJ, Keaton JM, Lea JP, Langefeld CD, Freedman BI, Bowden DW. The ras responsive transcription factor RREB1 is a novel candidate gene for type 2 diabetes associated end-stage kidney disease. Hum Mol Genet 2014; 23:6441-7. [PMID: 25027322 DOI: 10.1093/hmg/ddu362] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Familial clustering and presumed genetic risk for type 2 diabetic (T2D) and non-diabetic end-stage kidney disease (ESKD) appear strong in African Americans. Examination of exome sequencing data in African American T2D-ESKD cases and non-diabetic non-nephropathy controls identified two low-frequency variants in the RREB1 gene, a repressor of the angiotensinogen (AGT) gene previously associated with kidney function, as being associated with T2D-ESKD: rs9379084 (P = 0.00087, OR = 0.26; D1171N) and rs41302867 (P = 0.00078, OR = 0.21; splice site variant). Rs41302867 replicated association in an independent sample of African Americans with T2D-ESKD [rs41302867 P = 0.033 (OR = 0.50)], and a trend towards rs9379084 association was observed (P = 0.070). In European Americans with T2D-ESKD compared with European American population based controls, both RREB1 variants replicated association [rs9379084 P = 1.67 × 10(-4) (OR = 0.54) and rs41302867 P = 0.013 (OR = 0.69)]. Rs9379084 was not associated with non-T2D-ESKD or T2D in African Americans (P = 0.55 and P = 0.37, respectively), but was associated with T2D in European Americans (P = 0.014, OR = 0.65). In African Americans, rs41302867 was associated with non-T2D-ESKD [P = 0.036 (OR = 0.54)] and hypertension attributed ESKD [H-ESKD, P = 0.029 (OR = 0.50)]. A meta-analysis combining African American and European American T2D-ESKD data revealed P = 3.52 × 10(-7) and 3.70 × 10(-5) for rs9379084 and rs41302867 association, respectfully. A locus-wide analysis evaluating putatively functional SNPs revealed several nominal associations with T2D-ESKD, non-T2D-ESKD and T2D in African and European Americans. RREB1 is a large, complex gene which codes a multidomain zinc finger binding protein and transcription factor. We posit that variants in RREB1 modulate seemingly disparate phenotypes (i.e. T2D, T2D-ESKD and non-T2D-ESKD) through altered activity resulting from splice site and missense variants.
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Affiliation(s)
- Jason A Bonomo
- Department of Molecular Medicine and Translational Science, Center for Genomics and Personalized Medicine Research
| | - Meijian Guan
- Center for Genomics and Personalized Medicine Research
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research
| | - Nicholette D Palmer
- Center for Genomics and Personalized Medicine Research, Department of Biochemistry
| | | | | | - Janice P Lea
- Department of Internal Medicine - Nephrology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl D Langefeld
- Center for Genomics and Personalized Medicine Research, Department of Biostatistical Sciences
| | - Barry I Freedman
- Center for Genomics and Personalized Medicine Research, Department of Internal Medicine - Nephrology, Wake Forest School of Medicine, Winston Salem, NC 27157, USA and
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Department of Biochemistry,
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14
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Guin S, Pollard C, Ru Y, Ritterson Lew C, Duex JE, Dancik G, Owens C, Spencer A, Knight S, Holemon H, Gupta S, Hansel D, Hellerstein M, Lorkiewicz P, Lane AN, Fan TWM, Theodorescu D. Role in tumor growth of a glycogen debranching enzyme lost in glycogen storage disease. J Natl Cancer Inst 2014; 106:dju062. [PMID: 24700805 DOI: 10.1093/jnci/dju062] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bladder cancer is the most common malignancy of the urinary system, yet our molecular understanding of this disease is incomplete, hampering therapeutic advances. METHODS Here we used a genome-wide functional short-hairpin RNA (shRNA) screen to identify suppressors of in vivo bladder tumor xenograft growth (n = 50) using bladder cancer UMUC3 cells. Next-generation sequencing was used to identify the most frequently occurring shRNAs in tumors. Genes so identified were studied in 561 patients with bladder cancer for their association with stratification of clinical outcome by Kaplan-Meier analysis. The best prognostic marker was studied to determine its mechanism in tumor suppression using anchorage-dependent and -independent growth, xenograft (n = 20), and metabolomic assays. Statistical significance was determined using two-sided Student t test and repeated-measures statistical analysis. RESULTS We identified the glycogen debranching enzyme AGL as a prognostic indicator of patient survival (P = .04) and as a novel regulator of bladder cancer anchorage-dependent (P < .001), anchorage-independent (mean ± standard deviation, 180 ± 23.1 colonies vs 20±9.5 in control, P < .001), and xenograft growth (P < .001). Rescue experiments using catalytically dead AGL variants revealed that this effect is independent of AGL enzymatic functions. We demonstrated that reduced AGL enhances tumor growth by increasing glycine synthesis through increased expression of serine hydroxymethyltransferase 2. CONCLUSIONS Using an in vivo RNA interference screen, we discovered that AGL, a glycogen debranching enzyme, has a biologically and statistically significant role in suppressing human cancer growth.
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Affiliation(s)
- Sunny Guin
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Courtney Pollard
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Yuanbin Ru
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Carolyn Ritterson Lew
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Jason E Duex
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Garrett Dancik
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Charles Owens
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Andrea Spencer
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Scott Knight
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Heather Holemon
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Sounak Gupta
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Donna Hansel
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Marc Hellerstein
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Pawel Lorkiewicz
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Andrew N Lane
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Teresa W-M Fan
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD)
| | - Dan Theodorescu
- Affiliations of authors: Department of Surgery (SGui, CP, YR, CRL, JED, GD, CO, DT) and Department of Pharmacology (SGui, CP, YR, CRL, JED, GD, CO, DT), University of Colorado, Denver, CO; Sigma-Aldrich Research Biotech, Saint Louis, MO (AS, SK, HH); Department of Pathology, Cleveland Clinic, Cleveland, OH (SGup, DH); Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA (MH); Department of Medicine, University of California at San Francisco, San Francisco, CA (MH); Center for Regulatory and Environmental Analytical Metabolomics, Department of Chemistry, University of Louisville, Louisville, KY (PL); Graduate Center of Toxicology, Biopharm Complex, University of Kentucky, Lexington, KY (ANL, TW-MF); University of Colorado Comprehensive Cancer Center, Denver, CO (DT). Present affiliations: Department of Biomedical Informatics, Windber Research Institute, Windber, PA (YR); Mathematics and Computer Science Department, Eastern Connecticut State University, Willimantic, CT (GD).
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15
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Liu CT, Monda KL, Taylor KC, Lange L, Demerath EW, Palmas W, Wojczynski MK, Ellis JC, Vitolins MZ, Liu S, Papanicolaou GJ, Irvin MR, Xue L, Griffin PJ, Nalls MA, Adeyemo A, Liu J, Li G, Ruiz-Narvaez EA, Chen WM, Chen F, Henderson BE, Millikan RC, Ambrosone CB, Strom SS, Guo X, Andrews JS, Sun YV, Mosley TH, Yanek LR, Shriner D, Haritunians T, Rotter JI, Speliotes EK, Smith M, Rosenberg L, Mychaleckyj J, Nayak U, Spruill I, Garvey WT, Pettaway C, Nyante S, Bandera EV, Britton AF, Zonderman AB, Rasmussen-Torvik LJ, Chen YDI, Ding J, Lohman K, Kritchevsky SB, Zhao W, Peyser PA, Kardia SLR, Kabagambe E, Broeckel U, Chen G, Zhou J, Wassertheil-Smoller S, Neuhouser ML, Rampersaud E, Psaty B, Kooperberg C, Manson JE, Kuller LH, Ochs-Balcom HM, Johnson KC, Sucheston L, Ordovas JM, Palmer JR, Haiman CA, McKnight B, Howard BV, Becker DM, Bielak LF, Liu Y, Allison MA, Grant SFA, Burke GL, Patel SR, Schreiner PJ, Borecki IB, Evans MK, Taylor H, Sale MM, Howard V, Carlson CS, Rotimi CN, Cushman M, Harris TB, Reiner AP, Cupples LA, North KE, Fox CS. Genome-wide association of body fat distribution in African ancestry populations suggests new loci. PLoS Genet 2013; 9:e1003681. [PMID: 23966867 PMCID: PMC3744443 DOI: 10.1371/journal.pgen.1003681] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 06/13/2013] [Indexed: 01/18/2023] Open
Abstract
Central obesity, measured by waist circumference (WC) or waist-hip ratio (WHR), is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS) of fat distribution among those of predominantly African ancestry (AA). We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1). Overall, 25 SNPs with single genomic control (GC)-corrected p-values<5.0 × 10(-6) were followed-up (stage 2) in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA) WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10(-8) for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10(-8) for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5 × 10(-8); RREB1: p = 5.7 × 10(-8)). Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region) in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN). Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02). In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce the concept that there are fat distribution loci that are independent of generalized adiposity.
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Affiliation(s)
- Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Keri L. Monda
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kira C. Taylor
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology and Population Health, University of Louisville, Louisville, Kentucky, United States of America
| | - Leslie Lange
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ellen W. Demerath
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, New York, United States of America
| | - Mary K. Wojczynski
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jaclyn C. Ellis
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Mara Z. Vitolins
- Department of Epidemiology & Prevention, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Simin Liu
- Departments of Epidemiology, Medicine, and Obstetrics and Gynecology and Center for Metabolic Disease Prevention, Los Angeles, California, United States of America
| | - George J. Papanicolaou
- Division of Cardiovascular Sciences, Prevention and Population Sciences Program, National Heart, Lung, & Blood Institute, Bethesda, Maryland, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, UAB, Birmingham, Alabama, United States of America
| | - Luting Xue
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Paula J. Griffin
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Jiankang Liu
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Guo Li
- University of Washington, Seattle, Washington, United States of America
| | - Edward A. Ruiz-Narvaez
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Wei-Min Chen
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Fang Chen
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Sara S. Strom
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Xiuqing Guo
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jeanette S. Andrews
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yan V. Sun
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas H. Mosley
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Talin Haritunians
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | | | - Megan Smith
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Lynn Rosenberg
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Josyf Mychaleckyj
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Uma Nayak
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ida Spruill
- Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - W. Timothy Garvey
- Department of Epidemiology, UAB School of Public Health, Birmingham, Alabama, United States of America
| | - Curtis Pettaway
- Department of Urology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
| | - Angela F. Britton
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan B. Zonderman
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health, NIH Biomedical Center, Baltimore, Maryland, United States of America
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yii-Der Ida Chen
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jingzhong Ding
- Department of Internal Medicine/Geriatrics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Kurt Lohman
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Stephen B. Kritchevsky
- Department of Internal Medicine/Geriatrics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Wei Zhao
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patricia A. Peyser
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Edmond Kabagambe
- Department of Epidemiology, UAB, Birmingham, Alabama, United States of America
| | - Ulrich Broeckel
- Department of Pediatrics, Medicine and Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Marian L. Neuhouser
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Evadnie Rampersaud
- Miami Institute for Human Genomics, Miami, Florida, United States of America
- John T. McDonald Department of Human Genetics, University of Miami, Miami, Florida, United States of America
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, Washington, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lewis H. Kuller
- Department of Epidemiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Heather M. Ochs-Balcom
- Department of Social and Preventive Medicine, University at Buffalo, Buffalo, New York, United States of America
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lara Sucheston
- Department of Biostatistics, University of Buffalo School of Public Health and Health Professions, New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York, United States of America
| | - Jose M. Ordovas
- Tufts University, Boston, Massachusetts, United States of America
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Barbara V. Howard
- MedStar Health Research Institute and Georgetown University, Hyattsville, Maryland, United States of America
| | - Diane M. Becker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Matthew A. Allison
- University of California at San Diego Department of Preventive Medicine, La Jolla, California, United States of America
| | - Struan F. A. Grant
- Division of Human Genetics, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Gregory L. Burke
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Sanjay R. Patel
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Pamela J. Schreiner
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ingrid B. Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michele K. Evans
- Health Disparities Research Section, Clinical Research Branch, National Institute on Aging, National Institutes of Health, NIH Biomedical Center, Baltimore, Maryland, United States of America
| | - Herman Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Michele M. Sale
- Center for Public Genomics, Department of Biochemistry and Molecular Genetics and Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Virginia Howard
- Department of Epidemiology, UAB School of Public Health, Birmingham, Alabama, United States of America
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Mary Cushman
- Department of Medicine, University of Vermont, Colchester, Vermont, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland, United States of America
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- NHLBI's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Caroline S. Fox
- NHLBI's Framingham Heart Study, Framingham, Massachusetts, United States of America
- NHLBI's Center for Population Studies, Framingham, Massachusetts, United States of America
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
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16
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Kent OA, Fox-Talbot K, Halushka MK. RREB1 repressed miR-143/145 modulates KRAS signaling through downregulation of multiple targets. Oncogene 2012; 32:2576-85. [PMID: 22751122 DOI: 10.1038/onc.2012.266] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A lack of expression of miR-143 and miR-145 has been demonstrated to be a frequent feature of colorectal tumors. Activating KRAS mutations have been reported in 30-60% of colorectal cancers and an inverse correlation between Kras and miR-143/145 expression has been observed. Previously, we have demonstrated that oncogenic Kras leads to repression of the miR-143/145 cluster in pancreatic cancer and is dependent on the Ras responsive element (RRE) binding protein (RREB1), which negatively regulates miR-143/145 expression. In the present study, we have found that RREB1 is overexpressed in colorectal adenocarcinoma tumors and cell lines, and the expression of the miR-143/145 primary transcript is inversely related to RREB1 expression. In colorectal cancer cell lines, the miR-143/145 cluster is repressed by RREB1 downstream of constitutively active KRAS. RREB1 is activated by the MAPK pathway and negatively represses the miR-143/145 promoter through interaction with two RREs. In addition, overexpression of miR-143 or miR-145 in HCT116 cells abrogates signaling through the MAPK, PI3K and JNK pathways by downregulation of both KRAS and RREB1 in addition to downregulation of a cohort of genes in the MAPK signaling cascade. These results establish a complex network of regulation through which the miR-143/145 cluster is able to modulate KRAS signaling in colorectal cancer.
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Affiliation(s)
- O A Kent
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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17
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Smith SC, Baras AS, Owens CR, Dancik G, Theodorescu D. Transcriptional signatures of Ral GTPase are associated with aggressive clinicopathologic characteristics in human cancer. Cancer Res 2012; 72:3480-91. [PMID: 22586063 DOI: 10.1158/0008-5472.can-11-3966] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
RalA and RalB are small GTPases that support malignant development and progression in experimental models of bladder, prostate, and squamous cancer. However, demonstration of their clinical relevance in human tumors remains lacking. Here, we developed tools to evaluate Ral protein expression, activation, and transcriptional output and evaluated their association with clinicopathologic parameters in common human tumor types. To evaluate the relevance of Ral activation and transcriptional output, we correlated RalA and RalB activation with the mutational status of key human bladder cancer genes. We also identified and evaluated a transcriptional signature of genes that correlates with depletion of RalA and RalB in vivo. The Ral transcriptional signature score, but not protein expression as evaluated by immunohistochemistry, predicted disease stage, progression to muscle invasion, and survival in human bladder cancers and metastatic and stem cell phenotypes in bladder cancer models. In prostate cancer, the Ral transcriptional signature score was associated with seminal vesicle invasion, androgen-independent progression, and reduced survival. In squamous cell carcinoma, this score was decreased in cancer tissues compared with normal mucosa, validating the experimental findings that Ral acts as a tumor suppressor in this tumor type. Together, our findings show the clinical relevance of Ral in human cancer and provide a rationale for the development of Ral-directed therapies.
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Affiliation(s)
- Steven C Smith
- Department of Urology, University of Virginia, Charlottesville, Virginia, USA
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