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Feng H, Meng G, Lin T, Parikh H, Pan Y, Li Z, Krischer J, Li Q. ISLET: individual-specific reference panel recovery improves cell-type-specific inference. Genome Biol 2023; 24:174. [PMID: 37496087 PMCID: PMC10373385 DOI: 10.1186/s13059-023-03014-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 07/12/2023] [Indexed: 07/28/2023] Open
Abstract
We propose a statistical framework ISLET to infer individual-specific and cell-type-specific transcriptome reference panels. ISLET models the repeatedly measured bulk gene expression data, to optimize the usage of shared information within each subject. ISLET is the first available method to achieve individual-specific reference estimation in repeated samples. Using simulation studies, we show outstanding performance of ISLET in the reference estimation and downstream cell-type-specific differentially expressed genes testing. We apply ISLET to longitudinal transcriptomes profiled from blood samples in a large observational study of young children and confirm the cell-type-specific gene signatures for pancreatic islet autoantibody. ISLET is available at https://bioconductor.org/packages/ISLET .
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Affiliation(s)
- Hao Feng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Guanqun Meng
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Hemang Parikh
- Health Informatics Institute, University of South Florida, Tampa, FL, 33620, USA
| | - Yue Pan
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jeffrey Krischer
- Health Informatics Institute, University of South Florida, Tampa, FL, 33620, USA
| | - Qian Li
- Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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Ferrat LA, Vehik K, Sharp SA, Lernmark Å, Rewers MJ, She JX, Ziegler AG, Toppari J, Akolkar B, Krischer JP, Weedon MN, Oram RA, Hagopian WA, Barbour A, Bautista K, Baxter J, Felipe-Morales D, Driscoll K, Frohnert BI, Stahl M, Gesualdo P, Hoffman M, Karban R, Liu E, Norris J, Peacock S, Shorrosh H, Steck A, Stern M, Villegas E, Waugh K, Simell OG, Adamsson A, Ahonen S, Åkerlund M, Hakola L, Hekkala A, Holappa H, Hyöty H, Ikonen A, Ilonen J, Jäminki S, Jokipuu S, Karlsson L, Kero J, Kähönen M, Knip M, Koivikko ML, Koskinen M, Koreasalo M, Kurppa K, Kytölä J, Latva-aho T, Lindfors K, Lönnrot M, Mäntymäki E, Mattila M, Miettinen M, Multasuo K, Mykkänen T, Niininen T, Niinistö S, Nyblom M, Oikarinen S, Ollikainen P, Othmani Z, Pohjola S, Rajala P, Rautanen J, Riikonen A, Riski E, Pekkola M, Romo M, Ruohonen S, Simell S, Sjöberg M, Stenius A, Tossavainen P, Vähä-Mäkilä M, Vainionpää S, Varjonen E, Veijola R, Viinikangas I, Virtanen SM, Schatz D, Hopkins D, Steed L, Bryant J, Silvis K, Haller M, Gardiner M, McIndoe R, Sharma A, Anderson SW, Jacobsen L, Marks J, Towe PD, Bonifacio E, Gezginci C, Heublein A, Hohoff E, Hummel S, Knopff A, Koch C, Koletzko S, Ramminger C, Roth R, Schmidt J, Scholz M, Stock J, Warncke K, Wendel L, Winkler C, Agardh D, Aronsson CA, Ask M, Bennet R, Cilio C, Dahlberg S, Engqvist H, Ericson-Hallström E, Fors AB, Fransson L, Gard T, Hansen M, Jisser H, Johansen F, Jonsdottir B, Elding Larsson H, Lindström M, Lundgren M, Maziarz M, Månsson-Martinez M, Melin J, Mestan Z, Nilsson C, Ottosson K, Rahmati K, Ramelius A, Salami F, Sjöberg A, Sjöberg B, Törn C, Wimar Å, Killian M, Crouch CC, Skidmore J, Chavoshi M, Meyer A, Meyer J, Mulenga D, Powell N, Radtke J, Romancik M, Roy S, Schmitt D, Zink S, Becker D, Franciscus M, Smith MDE, Daftary A, Klein MB, Yates C, Austin-Gonzalez S, Avendano M, Baethke S, Burkhardt B, Butterworth M, Clasen J, Cuthbertson D, Eberhard C, Fiske S, Garmeson J, Gowda V, Heyman K, Hsiao B, Karges C, Laras FP, Li Q, Liu S, Liu X, Lynch K, Maguire C, Malloy J, McCarthy C, Parikh H, Remedios C, Shaffer C, Smith L, Smith S, Sulman N, Tamura R, Tewey D, Toth M, Uusitalo U, Vijayakandipan P, Wood K, Yang J, Yu L, Miao D, Bingley P, Williams A, Chandler K, Kelland I, Khoud YB, Zahid H, Randell M, Chavoshi M, Radtke J, Zink S, Ke S, Mulholland N, Rich SS, Chen WM, Onengut-Gumuscu S, Farber E, Pickin RR, Davis J, Davis J, Gallo D, Bonnie J, Campolieto P, Petrosino JF, Ajami NJ, Lloyd RE, Ross MC, O’Brien JL, Hutchinson DS, Smith DP, Wong MC, Tian X, Ayvaz T, Tamegnon A, Truong N, Moreno H, Riley L, Moreno E, Bauch T, Kusic L, Metcalf G, Muzny D, Doddapaneni H, Gibbs R, Bourcier K, Briese T, Johnson SB, Triplett E, Ziegler AG, Tamura R, Norris J, Virtanen SM, Frohnert BI, Gesualdo P, Koreasalo M, Miettinen M, Niinistö S, Riikonen A, Silvis K, Hohoff E, Hummel S, Winkler C, Aronsson CA, Skidmore J, Smith MDE, Butterworth M, Li Q, Liu X, Tamura R, Uusitalo U, Yang J, Rich SS, Norris J, Steck A, Ilonen J, Ziegler AG, Törn C, Li Q, Liu X, Parikh H, Erlich H, Chen WM, Onengut-Gumuscu S, Schatz D, Ziegler AG, Cilio C, Bonifacio E, Knip M, Schatz D, Burkhardt B, Lynch K, Yu L, Bingley P, Bourcier K, Hyöty H, Triplett E, Lloyd R, Gesualdo P, Waugh K, Lönnrot M, Agardh D, Cilio C, Larsson HE, Killian M, Burkhardt B, Lynch K, Briese T, Waugh K, Schatz D, Killian M, Johnson SB, Roth R, Baxter J, Driscoll K, Schatz D, Stock J, Fiske S, Liu X, Lynch K, Smith L, Baxter J, Lernmark Å, Baxter J, Killian M, Bautista K, Gesualdo P, Hoffman M, Karban R, Norris J, Waugh K, Adamsson A, Kähönen M, Niininen T, Stenius A, Varjonen E, Hopkins D, Steed L, Bryant J, Gardiner M, Marks J, Ramminger C, Stock J, Winkler C, Aronsson CA, Jonsdottir B, Melin J, Killian M, Crouch CC, Mulenga D, McCarthy C, Smith L, Smith S, Tamura R, Johnson SB, Agardh D, Liu E, Koletzko S, Kurppa K, Stahl M, Hoffman M, Kurppa K, Lindfors K, Simell S, Steed L, Aronsson CA, Killian M, Tamura R, Haller M, Larsson HE, Frohnert BI, Gesualdo P, Hoffman M, Steck A, Kähönen M, Veijola R, Steed L, Jacobsen L, Marks J, Stock J, Warncke K, Lundgren M, Wimar Å, Crouch CC, Liu X, Tamura R. Author Correction: A combined risk score enhances prediction of type 1 diabetes among susceptible children. Nat Med 2022; 28:599. [DOI: 10.1038/s41591-021-01631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Xhonneux LP, Knight O, Lernmark Å, Bonifacio E, Hagopian WA, Rewers MJ, She JX, Toppari J, Parikh H, Smith KGC, Ziegler AG, Akolkar B, Krischer JP, McKinney EF. Transcriptional networks in at-risk individuals identify signatures of type 1 diabetes progression. Sci Transl Med 2021; 13:eabd5666. [PMID: 33790023 PMCID: PMC8447843 DOI: 10.1126/scitranslmed.abd5666] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/24/2020] [Accepted: 03/12/2021] [Indexed: 12/11/2022]
Abstract
Type 1 diabetes (T1D) is a disease of insulin deficiency that results from autoimmune destruction of pancreatic islet β cells. The exact cause of T1D remains unknown, although asymptomatic islet autoimmunity lasting from weeks to years before diagnosis raises the possibility of intervention before the onset of clinical disease. The number, type, and titer of islet autoantibodies are associated with long-term disease risk but do not cause disease, and robust early predictors of individual progression to T1D onset remain elusive. The Environmental Determinants of Diabetes in the Young (TEDDY) consortium is a prospective cohort study aiming to determine genetic and environmental interactions causing T1D. Here, we analyzed longitudinal blood transcriptomes of 2013 samples from 400 individuals in the TEDDY study before both T1D and islet autoimmunity. We identified and interpreted age-associated gene expression changes in healthy infancy and age-independent changes tracking with progression to both T1D and islet autoimmunity, beginning before other evidence of islet autoimmunity was present. We combined multivariate longitudinal data in a Bayesian joint model to predict individual risk of T1D onset and validated the association of a natural killer cell signature with progression and the model's predictive performance on an additional 356 samples from 56 individuals in the independent Type 1 Diabetes Prediction and Prevention study. Together, our results indicate that T1D is characterized by early and longitudinal changes in gene expression, informing the immunopathology of disease progression and facilitating prediction of its course.
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Affiliation(s)
- Louis-Pascal Xhonneux
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Oliver Knight
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC Skåne University Hospital Malmo, Jan Waldenströms gata 35, Malmö, Sweden
| | - Ezio Bonifacio
- Center for Regenerative Therapies, Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - William A Hagopian
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA 98122, USA
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1462 Laney Walker Blvd., Augusta, GA 30912, USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Kiinamyllynkatu 4-8, 20521 Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turun Lyliopisto, Finland
| | - Hemang Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, and Klinikum rechts der Isar, Technische, Universität München, Forschergruppe Diabetes e.V., Arcisstraße 21, 80333 München, Germany
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, 9000 Rockville Pike Bethesda, MD 20892, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
- Cambridge Centre for Artificial Intelligence in Medicine, University of Cambridge, Cambridge, UK
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Li Q, Parikh H, Butterworth MD, Lernmark Å, Hagopian W, Rewers M, She JX, Toppari J, Ziegler AG, Akolkar B, Fiehn O, Fan S, Krischer JP. Longitudinal Metabolome-Wide Signals Prior to the Appearance of a First Islet Autoantibody in Children Participating in the TEDDY Study. Diabetes 2020; 69:465-476. [PMID: 32029481 PMCID: PMC7034190 DOI: 10.2337/db19-0756] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/05/2019] [Indexed: 12/19/2022]
Abstract
Children at increased genetic risk for type 1 diabetes (T1D) after environmental exposures may develop pancreatic islet autoantibodies (IA) at a very young age. Metabolic profile changes over time may imply responses to exposures and signal development of the first IA. Our present research in The Environmental Determinants of Diabetes in the Young (TEDDY) study aimed to identify metabolome-wide signals preceding the first IA against GAD (GADA-first) or against insulin (IAA-first). We profiled metabolomes by mass spectrometry from children's plasma at 3-month intervals after birth until appearance of the first IA. A trajectory analysis discovered each first IA preceded by reduced amino acid proline and branched-chain amino acids (BCAAs), respectively. With independent time point analysis following birth, we discovered dehydroascorbic acid (DHAA) contributing to the risk of each first IA, and γ-aminobutyric acid (GABAs) associated with the first autoantibody against insulin (IAA-first). Methionine and alanine, compounds produced in BCAA metabolism and fatty acids, also preceded IA at different time points. Unsaturated triglycerides and phosphatidylethanolamines decreased in abundance before appearance of either autoantibody. Our findings suggest that IAA-first and GADA-first are heralded by different patterns of DHAA, GABA, multiple amino acids, and fatty acids, which may be important to primary prevention of T1D.
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Affiliation(s)
- Qian Li
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Hemang Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Martha D Butterworth
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
| | | | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Technical University of Munich, Klinikum Rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Oliver Fiehn
- Genome Center, University of California, Davis, Davis, CA
| | - Sili Fan
- Genome Center, University of California, Davis, Davis, CA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
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5
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Mattila M, Erlund I, Lee HS, Niinistö S, Uusitalo U, Andrén Aronsson C, Hummel S, Parikh H, Rich SS, Hagopian W, Toppari J, Lernmark Å, Ziegler AG, Rewers M, Krischer JP, Norris JM, Virtanen SM. Plasma ascorbic acid and the risk of islet autoimmunity and type 1 diabetes: the TEDDY study. Diabetologia 2020; 63:278-286. [PMID: 31728565 PMCID: PMC6946743 DOI: 10.1007/s00125-019-05028-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023]
Abstract
AIMS/HYPOTHESIS We studied the association of plasma ascorbic acid with the risk of developing islet autoimmunity and type 1 diabetes and examined whether SNPs in vitamin C transport genes modify these associations. Furthermore, we aimed to determine whether the SNPs themselves are associated with the risk of islet autoimmunity or type 1 diabetes. METHODS We used a risk set sampled nested case-control design within an ongoing international multicentre observational study: The Environmental Determinants of Diabetes in the Young (TEDDY). The TEDDY study followed children with increased genetic risk from birth to endpoints of islet autoantibodies (350 cases, 974 controls) and type 1 diabetes (102 cases, 282 controls) in six clinical centres. Control participants were matched for family history of type 1 diabetes, clinical centre and sex. Plasma ascorbic acid concentration was measured at ages 6 and 12 months and then annually up to age 6 years. SNPs in vitamin C transport genes were genotyped using the ImmunoChip custom microarray. Comparisons were adjusted for HLA genotypes and for background population stratification. RESULTS Childhood plasma ascorbic acid (mean ± SD 10.76 ± 3.54 mg/l in controls) was inversely associated with islet autoimmunity risk (adjusted OR 0.96 [95% CI 0.92, 0.99] per +1 mg/l), particularly islet autoimmunity, starting with insulin autoantibodies (OR 0.94 [95% CI 0.88, 0.99]), but not with type 1 diabetes risk (OR 0.93 [95% Cl 0.86, 1.02]). The SLC2A2 rs5400 SNP was associated with increased risk of type 1 diabetes (OR 1.77 [95% CI 1.12, 2.80]), independent of plasma ascorbic acid (OR 0.92 [95% CI 0.84, 1.00]). CONCLUSIONS/INTERPRETATION Higher plasma ascorbic acid levels may protect against islet autoimmunity in children genetically at risk for type 1 diabetes. Further studies are warranted to confirm these findings. DATA AVAILABILITY The datasets generated and analysed during the current study will be made available in the NIDDK Central Repository at https://www.niddkrepository.org/studies/teddy.
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Affiliation(s)
- Markus Mattila
- Faculty of Social Sciences/Health Sciences, Tampere University, Tampere, Finland
- Department of Public Health Solutions, National Institute for Health and Welfare, PO Box 30, FI-00271, Helsinki, Finland
| | - Iris Erlund
- Department of Public Health Solutions, National Institute for Health and Welfare, PO Box 30, FI-00271, Helsinki, Finland
- Department of Government Services, National Institute for Health and Welfare, Helsinki, Finland
| | - Hye-Seung Lee
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Sari Niinistö
- Department of Public Health Solutions, National Institute for Health and Welfare, PO Box 30, FI-00271, Helsinki, Finland
| | - Ulla Uusitalo
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | | | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Helmhtoltz Zentrum München, Munich, Germany
| | - Hemang Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | | | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Anette G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Forschergruppe Diabetes e.V., Helmhtoltz Zentrum München, Munich, Germany
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Suvi M Virtanen
- Faculty of Social Sciences/Health Sciences, Tampere University, Tampere, Finland.
- Department of Public Health Solutions, National Institute for Health and Welfare, PO Box 30, FI-00271, Helsinki, Finland.
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland.
- Science Centre, Tampere University Hospital, Tampere, Finland.
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Zook JM, McDaniel J, Olson ND, Wagner J, Parikh H, Heaton H, Irvine SA, Trigg L, Truty R, McLean CY, De La Vega FM, Xiao C, Sherry S, Salit M. An open resource for accurately benchmarking small variant and reference calls. Nat Biotechnol 2019; 37:561-566. [PMID: 30936564 PMCID: PMC6500473 DOI: 10.1038/s41587-019-0074-6] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 02/19/2019] [Indexed: 12/30/2022]
Abstract
Benchmark small variant calls are required for developing, optimizing and assessing the performance of sequencing and bioinformatics methods. Here, as part of the Genome in a Bottle (GIAB) Consortium, we apply a reproducible, cloud-based pipeline to integrate multiple short- and linked-read sequencing datasets and provide benchmark calls for human genomes. We generate benchmark calls for one previously analyzed GIAB sample, as well as six genomes from the Personal Genome Project. These new genomes have broad, open consent, making this a 'first of its kind' resource that is available to the community for multiple downstream applications. We produce 17% more benchmark single nucleotide variations, 176% more indels and 12% larger benchmark regions than previously published GIAB benchmarks. We demonstrate that this benchmark reliably identifies errors in existing callsets and highlight challenges in interpreting performance metrics when using benchmarks that are not perfect or comprehensive. Finally, we identify strengths and weaknesses of callsets by stratifying performance according to variant type and genome context.
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Affiliation(s)
- Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
| | - Jennifer McDaniel
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Hemang Parikh
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Haynes Heaton
- 10x Genomics, Pleasanton, CA, USA
- Wellcome Trust Sanger Institute,, Hinxton, Cambridge, UK
| | | | - Len Trigg
- Real Time Genomics, Hamilton, New Zealand
| | | | - Cory Y McLean
- Verily Life Sciences, South San Francisco, CA, USA
- Google Inc., Mountain View, CA, USA
| | - Francisco M De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stephen Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Marc Salit
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
- Joint Initiative for Metrology in Biology, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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7
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Monach P, Parikh H, Conklin L, Damsker J, Grayson P, Cuthbertson D, Carette S, Khalidi N, Koening C, Langford C, McAlear C, Moreland L, Pagnoux C, Seo P, Specks U, Sreih A, Ytterberg S, Hoffman E, Merkel P. 035. CANDIDATE BIOMARKERS IN ANCA-ASSOCIATED VASCULITIS IDENTIFIED USING A PROTEOMIC APPROACH. Rheumatology (Oxford) 2019. [DOI: 10.1093/rheumatology/kez057.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Philip Seo
- Johns Hopkins University of Baltimore, MD USA
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8
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Conklin LS, Merkel PA, Pachman LM, Parikh H, Tawalbeh S, Damsker JM, Cuthbertson DD, Morgan GA, Monach PA, Hathout Y, Nagaraju K, van den Anker J, McAlear CA, Hoffman EP. Serum biomarkers of glucocorticoid response and safety in anti-neutrophil cytoplasmic antibody-associated vasculitis and juvenile dermatomyositis. Steroids 2018; 140:159-166. [PMID: 30352204 PMCID: PMC6640634 DOI: 10.1016/j.steroids.2018.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 12/25/2022]
Abstract
Glucocorticoids are standard of care for many chronic inflammatory conditions, including juvenile dermatomyositis (JDM) and anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). We sought to define pharmacodynamic biomarkers of therapeutic efficacy and safety concerns of glucocorticoid treatment for these two disorders. Previous proteomic profiling of patients with Duchenne muscular dystrophy (DMD) and inflammatory bowel disease (IBD) treated with glucocorticoids identified candidate biomarkers for efficacy and safety concerns of glucocorticoids. Serial serum samples from patients with AAV (n = 30) and JDM (n = 12) were obtained during active disease, and after treatment with glucocorticoids. For AAV, 8 of 11 biomarkers of the anti-inflammatory response to glucocorticoids were validated (P-value ≤0.05; CD23, macrophage-derived cytokine, interleukin-22 binding protein, matrix metalloproteinase-12, T lymphocyte surface antigen Ly9, fibrinogen gamma chain, angiopoietin-2 [all decreased], and protein C [increased]), as were 5 of 7 safety biomarkers (P-value ≤0.05; afamin, matrix metalloproteinase-3, insulin growth factor binding protein-5, angiotensinogen, leptin [all increased]). For JDM, 10 of 11 efficacy biomarkers were validated (P-value ≤0.05; all proteins except fibrinogen gamma chain) and 6 of 7 safety biomarkers (P-value ≤0.05; AAV proteins plus growth hormone binding protein). The identified efficacy biomarkers may be useful as objective outcome measures for early phase proof-of-concept studies when assessing novel anti-inflammatory drugs in JDM and AAV, and likely in other inflammatory disorders. Similarly, safety biomarkers may also be helpful assessing toxicity of alternatives to glucocorticoids.
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Affiliation(s)
- Laurie S Conklin
- ReveraGen BioPharma, 155 Gibbs St., Suite 433, Rockville, MD 20850, USA; Division of Gastroenterology, George Washington University School of Medicine and Health Sciences, Children's National Health System, 111 Michigan Avenue NW, Washington, DC 20010, USA.
| | - Peter A Merkel
- Division of Rheumatology and the Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania School of Medicine, 3400 Spruce St, Philadelphia, PA 19104, USA.
| | - Lauren M Pachman
- Northwestern University, Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital, 225 E. Chicago Ave., Chicago, IL 60611, USA.
| | - Hemang Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Shefa Tawalbeh
- Department of Biomedical Engineering, Binghamton University - SUNY, 4400 Vestal Pkwy E, Binghamton, NY 13902, USA.
| | - Jesse M Damsker
- ReveraGen BioPharma, 155 Gibbs St., Suite 433, Rockville, MD 20850, USA.
| | - David D Cuthbertson
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Gabrielle A Morgan
- Northwestern University, Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital, 225 E. Chicago Ave., Chicago, IL 60611, USA.
| | - Paul A Monach
- Division of Rheumatology, Boston University School of Medicine, 75 E. Newton St., Boston, MA USA 02118, USA.
| | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University - SUNY, 4400 Vestal Pkwy E, Binghamton, NY 13902, USA.
| | - Kanneboyina Nagaraju
- ReveraGen BioPharma, 155 Gibbs St., Suite 433, Rockville, MD 20850, USA; School of Pharmacy and Pharmaceutical Sciences, Binghamton University - SUNY, 4400 Vestal Pkwy E, Binghamton, NY 13902, USA.
| | - John van den Anker
- ReveraGen BioPharma, 155 Gibbs St., Suite 433, Rockville, MD 20850, USA; Department of Clinical Pharmacology, George Washington University School of Medicine and Health Sciences, Children's National Health System, 111 Michigan Avenue NW, Washington, DC 20010, USA.
| | - Carol A McAlear
- Division of Rheumatology, University of Pennsylvania School of Medicine, 3400 Spruce St, Philadelphia, PA 19104, USA.
| | - Eric P Hoffman
- ReveraGen BioPharma, 155 Gibbs St., Suite 433, Rockville, MD 20850, USA; School of Pharmacy and Pharmaceutical Sciences, Binghamton University - SUNY, 4400 Vestal Pkwy E, Binghamton, NY 13902, USA.
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9
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Grayson PC, Eddy S, Taroni JN, Lightfoot YL, Mariani L, Parikh H, Lindenmeyer MT, Ju W, Greene CS, Godfrey B, Cohen CD, Krischer J, Kretzler M, Merkel PA. Metabolic pathways and immunometabolism in rare kidney diseases. Ann Rheum Dis 2018; 77:1226-1233. [PMID: 29724730 DOI: 10.1136/annrheumdis-2017-212935] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 04/04/2018] [Accepted: 04/16/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVES To characterise renal tissue metabolic pathway gene expression in different forms of glomerulonephritis. METHODS Patients with nephrotic syndrome (NS), antineutrophil cytoplasmic antibody-associated vasculitis (AAV), systemic lupus erythematosus (SLE) and healthy living donors (LD) were studied. Clinically indicated renal biopsies were obtained at time of diagnosis and microdissected into glomerular and tubulointerstitial compartments. Microarray-derived differential gene expression of 88 genes representing critical enzymes of metabolic pathways and 25 genes related to immune cell markers was compared between disease groups. Correlation analyses measured relationships between metabolic pathways, kidney function and cytokine production. RESULTS Reduced steady state levels of mRNA species were enriched in pathways of oxidative phosphorylation and increased in the pentose phosphate pathway (PPP) with maximal perturbation in AAV and SLE followed by NS, and least in LD. Transcript regulation was isozymes specific with robust regulation in hexokinases, enolases and glucose transporters. Intercorrelation networks were observed between enzymes of the PPP (eg, transketolase) and macrophage markers (eg, CD68) (r=0.49, p<0.01). Increased PPP transcript levels were associated with reduced glomerular filtration rate in the glomerular (r=-0.49, p<0.01) and tubulointerstitial (r=-0.41, p<0.01) compartments. PPP expression and tumour necrosis factor activation were tightly co-expressed (r=0.70, p<0.01). CONCLUSION This study demonstrated concordant alterations of the renal transcriptome consistent with metabolic reprogramming across different forms of glomerulonephritis. Activation of the PPP was tightly linked with intrarenal macrophage marker expression, reduced kidney function and increased production of cytokines. Modulation of glucose metabolism may offer novel immune-modulatory therapeutic approaches in rare kidney diseases.
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Affiliation(s)
- Peter C Grayson
- Vasculitis Translational Research Program, Systemic Autoimmunity Branch, National Institutes of Health/NIAMS, Bethesda, Maryland, USA.,Vasculitis Clinical Research Consortium, Philadelphia, Pennsylvania, USA
| | - Sean Eddy
- Division of Nephrology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Nephrotic Syndrome Study Network Consortia, Ann Arbor, Michigan, USA
| | - Jaclyn N Taroni
- Vasculitis Clinical Research Consortium, Philadelphia, Pennsylvania, USA.,Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yaíma L Lightfoot
- Vasculitis Translational Research Program, Systemic Autoimmunity Branch, National Institutes of Health/NIAMS, Bethesda, Maryland, USA
| | - Laura Mariani
- Division of Nephrology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Nephrotic Syndrome Study Network Consortia, Ann Arbor, Michigan, USA
| | - Hemang Parikh
- Vasculitis Clinical Research Consortium, Philadelphia, Pennsylvania, USA.,Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Maja T Lindenmeyer
- Nephrological Center Medical Clinic and Polyclinic IV, University of Munich, Munich, Germany
| | - Wenjun Ju
- Division of Nephrology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Nephrotic Syndrome Study Network Consortia, Ann Arbor, Michigan, USA
| | - Casey S Greene
- Vasculitis Clinical Research Consortium, Philadelphia, Pennsylvania, USA.,Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brad Godfrey
- Division of Nephrology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Nephrotic Syndrome Study Network Consortia, Ann Arbor, Michigan, USA
| | - Clemens D Cohen
- Nephrological Center Medical Clinic and Polyclinic IV, University of Munich, Munich, Germany
| | - Jeffrey Krischer
- Vasculitis Clinical Research Consortium, Philadelphia, Pennsylvania, USA.,Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Matthias Kretzler
- Division of Nephrology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Nephrotic Syndrome Study Network Consortia, Ann Arbor, Michigan, USA
| | - Peter A Merkel
- Vasculitis Clinical Research Consortium, Philadelphia, Pennsylvania, USA.,Division of Rheumatology and Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Zhang M, Lykke-Andersen S, Zhu B, Xiao W, Hoskins JW, Zhang X, Rost LM, Collins I, van de Bunt M, Jia J, Parikh H, Zhang T, Song L, Jermusyk A, Chung CC, Zhu B, Zhou W, Matters GL, Kurtz RC, Yeager M, Jensen TH, Brown KM, Ongen H, Bamlet WR, Murray BA, McCarthy MI, Chanock SJ, Chatterjee N, Wolpin BM, Smith JP, Olson SH, Petersen GM, Shi J, Amundadottir LT. Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues. Gut 2018; 67. [PMID: 28634199 PMCID: PMC5762429 DOI: 10.1136/gutjnl-2016-313146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0.1), with the strongest effects seen near transcriptional start sites. Approximately 23% and 42% of genes with significant cis-eQTLs appeared to be specific for tumour-derived and normal-derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in non-coding regulatory regions, in particular for pancreatic tissues (1.53-fold to 3.12-fold, p≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 (rs687289) was associated with ABO expression in histologically normal (p=5.8×10-8) and tumour-derived (p=8.3×10-5) tissues. The high linkage disequilibrium between this variant and the O blood group generating deletion variant in ABO (exon 6) suggested that nonsense-mediated decay (NMD) of the 'O' mRNA might explain this finding. However, knockdown of crucial NMD regulators did not influence decay of the ABO 'O' mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL. CONCLUSIONS We have identified cis-eQTLs representing potential functional regulatory variants in the pancreas and generated a rich data set for further studies on gene expression and its regulation in pancreatic tissues.
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Affiliation(s)
- Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Soren Lykke-Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Bin Zhu
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Wenming Xiao
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
| | - Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Xijun Zhang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA,Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Lauren M. Rost
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Martijn van de Bunt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK,Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA,Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Lei Song
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Charles C. Chung
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA,Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA,Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA,Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Gail L. Matters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Robert C. Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 20892, USA,Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kevin M. Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - William R. Bamlet
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Bradley A. Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge, Massachusetts 02142, USA
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK,Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford OX3 7LJ, UK,Oxford NIHR Biomedical Research Centre, Churchill Hospital, Old Road, Headington, Oxford OX3 7LE, UK
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Nilanjan Chatterjee
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jill P. Smith
- Division of Gastroenterology & Hepatology, Georgetown University Hospital, Washington, DC 20007, USA
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Gloria M. Petersen
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA,Corresponding author: Laufey Thora Amundadottir, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Advanced Technology Center, 8717 Grovemont Circle, Bethesda, Maryland 20892-4605. Tel: 240-760-6454, Fax: 301-402-3134,
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11
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Mehta M, Puntambekar S, Chitale M, Puntambekar S, Parikh H. Reconstruction of the Distal Ureter Following an Extensive Resection of Ureter for Stage IV Endometriosis. J Minim Invasive Gynecol 2017. [DOI: 10.1016/j.jmig.2017.08.242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Choi J, Xu M, Makowski MM, Zhang T, Law MH, Kovacs MA, Granzhan A, Kim WJ, Parikh H, Gartside M, Trent JM, Teulade-Fichou MP, Iles MM, Newton-Bishop JA, Bishop DT, MacGregor S, Hayward NK, Vermeulen M, Brown KM. A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF. Nat Genet 2017; 49:1326-1335. [PMID: 28759004 DOI: 10.1038/ng.3927] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/07/2017] [Indexed: 12/13/2022]
Abstract
Previous genome-wide association studies have identified a melanoma-associated locus at 1q42.1 that encompasses a ∼100-kb region spanning the PARP1 gene. Expression quantitative trait locus (eQTL) analysis in multiple cell types of the melanocytic lineage consistently demonstrated that the 1q42.1 melanoma risk allele (rs3219090[G]) is correlated with higher PARP1 levels. In silico fine-mapping and functional validation identified a common intronic indel, rs144361550 (-/GGGCCC; r2 = 0.947 with rs3219090), as displaying allele-specific transcriptional activity. A proteomic screen identified RECQL as binding to rs144361550 in an allele-preferential manner. In human primary melanocytes, PARP1 promoted cell proliferation and rescued BRAFV600E-induced senescence phenotypes in a PARylation-independent manner. PARP1 also transformed TERT-immortalized melanocytes expressing BRAFV600E. PARP1-mediated senescence rescue was accompanied by transcriptional activation of the melanocyte-lineage survival oncogene MITF, highlighting a new role for PARP1 in melanomagenesis.
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Affiliation(s)
- Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Mai Xu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Matthew H Law
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michael A Kovacs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Anton Granzhan
- CNRS UMR 9187, INSERM U1196, Institut Curie, PSL Research University and Université Paris Sud, Université Paris Saclay, Orsay, France
| | - Wendy J Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Hemang Parikh
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Michael Gartside
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jeffrey M Trent
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Marie-Paule Teulade-Fichou
- CNRS UMR 9187, INSERM U1196, Institut Curie, PSL Research University and Université Paris Sud, Université Paris Saclay, Orsay, France
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Julia A Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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13
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Amundadottir LT, Andresen SL, Xiao W, Hoskins J, Jermusyk A, Rost L, Collins I, Jia J, Mobaraki M, Zhu B, Kurtz R, Parikh H, Song L, Yeager M, Jensen T, Bamlet W, Chatterjee N, Wolpin B, Smith J, Olson S, Petersen G, Shi J, Zhang M. Abstract 1442: Analysis of cis-eQTLs in normal and tumor-derived pancreatic tissues reveals functional insights, including for the 9q34.1 ABO pancreatic cancer risk locus. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Objective: To elucidate the genetic architecture of gene expression in pancreatic tissues.
Design: We performed expression quantitative trait locus (eQTL) and allele specific expression (ASE) analyses using RNA-sequence data and 1000 Genomes (1000G) imputed GWAS genotypes from 95 fresh frozen histologically normal pancreatic tissue samples. Data from 115 pancreatic tumor-derived tissue samples from The Cancer Genome Atlas (TCGA) was included for comparison.
Results: We identified 38,615 cis-eQTLs (corresponding to 484 Genes) in histologically normal tissues and 39,713 cis-eQTL (corresponding to 237 Genes) in tumor tissues (FDR<0.1), with the strongest effects seen near transcriptional start sites (TSS). Approximately 23% and 42% of genes with significant cis-eQTLs (eGenes) appeared to be specific for tumor and normal derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in noncoding regulatory regions marked by modified histones, DNAse hypersensitivity and bound transcription factors, in particular for pancreatic tissues (1.53-3.12 fold, P≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 in the ABO gene (rs687289) was associated with ABO expression in histologically normal (P=5.8x10-8) and tumor-derived (P=8.3x10-5) pancreatic tissues. The high linkage disequilibrium (LD) between this variant and the O blood group generating deletion variant in exon 6 of ABO suggested that nonsense-mediated decay (NMD) of the “O” mRNA could explain the eQTL. However, knock-down of crucial NMD regulators did not influence decay of the ABO “O” mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL.
Conclusions: We have identified cis-eQTLs representing potential functional regulatory variants in the pancreas and generated a rich dataset for further studies on gene expression and regulation in pancreatic tissues.
Citation Format: Laufey T. Amundadottir, Soren Lykke Andresen, Wenming Xiao, Jason Hoskins, Ashley Jermusyk, Lauren Rost, Irene Collins, Jinping Jia, Michael Mobaraki, Bin Zhu, Robert Kurtz, Hemang Parikh, Lei Song, Meredith Yeager, Torben Jensen, William Bamlet, Nilanjan Chatterjee, Brian Wolpin, Jill Smith, Sara Olson, Gloria Petersen, Jianxin Shi, Mingfeng Zhang. Analysis of cis-eQTLs in normal and tumor-derived pancreatic tissues reveals functional insights, including for the 9q34.1 ABO pancreatic cancer risk locus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1442. doi:10.1158/1538-7445.AM2017-1442
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14
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Hoskins JW, Ibrahim A, Emmanuel MA, Manmiller SM, Wu Y, O’Neill M, Jia J, Collins I, Zhang M, Thomas JV, Rost LM, Das S, Parikh H, Haake JM, Matters GL, Kurtz RC, Bamlet WR, Klein A, Stolzenberg-Solomon R, Wolpin BM, Yarden R, Wang Z, Smith J, Olson SH, Andresson T, Petersen GM, Amundadottir LT. Functional characterization of a chr13q22.1 pancreatic cancer risk locus reveals long-range interaction and allele-specific effects on DIS3 expression. Hum Mol Genet 2016; 25:4726-4738. [PMID: 28172817 PMCID: PMC5815622 DOI: 10.1093/hmg/ddw300] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/08/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple common susceptibility loci for pancreatic cancer. Here we report fine-mapping and functional analysis of one such locus residing in a 610 kb gene desert on chr13q22.1 (marked by rs9543325). The closest candidate genes, KLF5, KLF12, PIBF1, DIS3 and BORA, range in distance from 265-586 kb. Sequencing three sub-regions containing the top ranked SNPs by imputation P-value revealed a 30 bp insertion/deletion (indel) variant that was significantly associated with pancreatic cancer risk (rs386772267, P = 2.30 × 10-11, OR = 1.22, 95% CI 1.15-1.28) and highly correlated to rs9543325 (r2 = 0.97 in the 1000 Genomes EUR population). This indel was the most significant cis-eQTL variant in a set of 222 histologically normal pancreatic tissue samples (β = 0.26, P = 0.004), with the insertion (risk-increasing) allele associated with reduced DIS3 expression. DIS3 encodes a catalytic subunit of the nuclear RNA exosome complex that mediates RNA processing and decay, and is mutated in several cancers. Chromosome conformation capture revealed a long range (570 kb) physical interaction between a sub-region of the risk locus, containing rs386772267, and a region ∼6 kb upstream of DIS3 Finally, repressor regulatory activity and allele-specific protein binding by transcription factors of the TCF/LEF family were observed for the risk-increasing allele of rs386772267, indicating that expression regulation at this risk locus may be influenced by the Wnt signaling pathway. In conclusion, we have identified a putative functional indel variant at chr13q22.1 that associates with decreased DIS3 expression in carriers of pancreatic cancer risk-increasing alleles, and could therefore affect nuclear RNA processing and/or decay.
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Affiliation(s)
- Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abdisamad Ibrahim
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mickey A. Emmanuel
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah M. Manmiller
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yinglun Wu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maura O’Neill
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Janelle V. Thomas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren M. Rost
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jefferson M. Haake
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Gail L. Matters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Robert C. Kurtz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - William R. Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Alison Klein
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology, the Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ronit Yarden
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jill Smith
- Department of Medicine, Georgetown University Hospital, Washington, DC, and Department of Medicine, Penn State University College of Medicine, Hershey PA, USA
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gloria M. Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Choi J, Makowski M, Zhang T, Law M, Kim W, Kovacs M, Parikh H, Aoude L, Gartside M, Trent J, Vermeulen M, Macgregor S, Hayward N, Xu M, Brown K. Abstract 4487: An INDEL variant confers melanoma risk through PARP1 expression regulation. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent genome wide association studies identified several new loci for melanoma susceptibility including chr1q42.1 locus encompassing Poly [ADP-ribose] polymerase 1 (PARP1). As an effort to identify effecter genes and functional risk variants from this locus we performed expression quantitative trait loci (eQTL) analysis in 62 melanoma cell lines. Among the genes in 1Mb area eQTL was identified for PARP1 and subsequently validated by qPCR, where increased PARP1 levels are significantly correlated with the risk allele (p = 0.03, copy number adjusted). Further allele discrimination qPCR of PARP1 transcripts in 14 melanoma cell lines heterozygous and of neutral copy for the lead SNP indicated significantly higher proportion for the risk allele (p = .0001). Same allelic imbalance was also observed in 51 heterozygous melanomas with neutral copy numbers from The Cancer Genome Atlas (p = .028). To identify functional risk variants mediating these effects we annotated this locus using six melanoma relevant cell types available from ENCODE and Roadmap database. Based on recent fine mapping data suggesting single-SNP model for this locus we prioritized high LD variants for nomination. Among 65 SNPs of high LD with the lead SNP or imputed best SNP (r2>0.6 using 1000 Genomes phase3), four exhibited strong evidence as potential transcriptional enhancers. Electro Mobility Shift Assays and luciferase assays on these four variants demonstrated that one of them, a six-base pair INDEL (-/GGGCCC) in the first intron, displayed strong allelic functionality. Consistent with the expression data melanoma-associated deletion allele results in higher luciferase activity while protective insertion allele binds a group of proteins with higher affinity. Subsequent comparative mass-spectrometry for these insertion-binding proteins identified a striking collection of Guanine-quadruplex binding proteins including RECQ1 as potential inhibitors of PARP1 expression. Consistent with this hypothesis over-expression of RECQL results in more pronounced allelic difference in luciferase activities indicating that RECQ1 contributes to allelic PARP1 expression. Further interrogation of RECQ1 and PARP1 expression correlation analysis suggested that RECQ1 levels are inversely correlated with PARP1 in melanomas carrying insertion alleles. These data demonstrate that increased PARP1 expression is correlated with melanoma risk and an INDEL variant mediates differential PARP1 expression possibly through secondary DNA structure binding proteins including RECQ1.
Citation Format: Jiyeon Choi, Matthew Makowski, Tongwu Zhang, Matthew Law, Wendy Kim, Michael Kovacs, Hemang Parikh, Lauren Aoude, Michael Gartside, Jeffrey Trent, Michiel Vermeulen, Stuart Macgregor, Nicholas Hayward, Mai Xu, Kevin Brown. An INDEL variant confers melanoma risk through PARP1 expression regulation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4487.
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Affiliation(s)
| | | | | | - Matthew Law
- 3Queensland Institute of Medical Research, Australia
| | | | | | | | - Lauren Aoude
- 3Queensland Institute of Medical Research, Australia
| | | | - Jeffrey Trent
- 4Translational Genomics Research Institute, Phoenix, AZ
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Parikh H, Mohiyuddin M, Lam HYK, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M. svclassify: a method to establish benchmark structural variant calls. BMC Genomics 2016; 17:64. [PMID: 26772178 PMCID: PMC4715349 DOI: 10.1186/s12864-016-2366-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/05/2016] [Indexed: 01/24/2023] Open
Abstract
Background The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). High-quality benchmark small variant calls for the pilot National Institute of Standards and Technology (NIST) Reference Material (NA12878) have been developed by the Genome in a Bottle Consortium, but no similar high-quality benchmark SV calls exist for this genome. Since SV callers output highly discordant results, we developed methods to combine multiple forms of evidence from multiple sequencing technologies to classify candidate SVs into likely true or false positives. Our method (svclassify) calculates annotations from one or more aligned bam files from many high-throughput sequencing technologies, and then builds a one-class model using these annotations to classify candidate SVs as likely true or false positives. Results We first used pedigree analysis to develop a set of high-confidence breakpoint-resolved large deletions. We then used svclassify to cluster and classify these deletions as well as a set of high-confidence deletions from the 1000 Genomes Project and a set of breakpoint-resolved complex insertions from Spiral Genetics. We find that likely SVs cluster separately from likely non-SVs based on our annotations, and that the SVs cluster into different types of deletions. We then developed a supervised one-class classification method that uses a training set of random non-SV regions to determine whether candidate SVs have abnormal annotations different from most of the genome. To test this classification method, we use our pedigree-based breakpoint-resolved SVs, SVs validated by the 1000 Genomes Project, and assembly-based breakpoint-resolved insertions, along with semi-automated visualization using svviz. Conclusions We find that candidate SVs with high scores from multiple technologies have high concordance with PCR validation and an orthogonal consensus method MetaSV (99.7 % concordant), and candidate SVs with low scores are questionable. We distribute a set of 2676 high-confidence deletions and 68 high-confidence insertions with high svclassify scores from these call sets for benchmarking SV callers. We expect these methods to be particularly useful for establishing high-confidence SV calls for benchmark samples that have been characterized by multiple technologies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2366-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hemang Parikh
- Genome-Scale Measurements Group, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8313, Gaithersburg, MD, 20899, USA. .,Dakota Consulting Inc., 1110 Bonifant Street, Suite 310, Silver Spring, MD, 20910, USA.
| | | | - Hugo Y K Lam
- Bina Technologies, Roche Sequencing, Redwood City, CA, 94065, USA.
| | - Hariharan Iyer
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Desu Chen
- Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD, 20742, USA.
| | - Mark Pratt
- Personalis Inc., 1350 Willow Road, Suite 202, Menlo Park, CA, 94025, USA.
| | - Gabor Bartha
- Personalis Inc., 1350 Willow Road, Suite 202, Menlo Park, CA, 94025, USA.
| | - Noah Spies
- Genome-Scale Measurements Group, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8313, Gaithersburg, MD, 20899, USA. .,Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Wolfgang Losert
- Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD, 20742, USA.
| | - Justin M Zook
- Genome-Scale Measurements Group, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8313, Gaithersburg, MD, 20899, USA.
| | - Marc Salit
- Genome-Scale Measurements Group, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8313, Gaithersburg, MD, 20899, USA. .,Bioengineering Department, Stanford University, Stanford, CA, USA.
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Hoskins JW, Ibrahim A, Emmanuel M, Manmiller S, Jia J, Parikh H, Collins I, Ylaya K, Altekruse SF, Hewitt SM, Petersen GM, Amundadottir LT. Abstract A1-09: Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. Cancer Res 2015. [DOI: 10.1158/1538-7445.transcagen-a1-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A genome-wide association study (GWAS) of pancreatic cancer conducted within the NCI Cohort Consortium (PanScan I and II) identified pancreatic cancer susceptibility loci on chromosomes 1q32.1/NR5A2, 5p15.33/CLPTM1L/TERT, 9q34.2/ABO, and 13q22.1. The most significant single-nucleotide polymorphism (SNP) identified on 13q22.1, rs9543325, lies in a ~600 kb gene desert; the nearest genes are KLF5, KLF12, PIBF1, DIS3, and BORA (265–586 kb away). Imputation using the 1000 Genomes and DCEG reference datasets did not improve the GWAS signal, but produced a set of highly correlated SNPs for functional follow-up. We performed eQTL analysis to test for association between the genotypes of these functional candidate variants and expression of nearby genes. Among 64 normal derived pancreatic tissue samples, DIS3 expression showed the strongest association with a 30 bp indel variant in the risk locus (P = 4.8 × 10-4), indicating risk alleles associate with reduced DIS3 expression. Mutations in DIS3 have previously been identified in acute myeloid leukemia and multiple myeloma, and its expression has been correlated with metastatic potential in colorectal cancer, suggesting DIS3 is relevant to cancer biology. Chromosome conformation capture identified a physical interaction between the indel-containing locus and a region near the DIS3 promoter. Luciferase assay for regulatory function of this indel-containing locus revealed allele-specific silencer activity for the insertion allele. Supershift electromobility shift assay (EMSA) demonstrated binding of LEF1 specifically to the insertion allele of the indel, which contains two in silico predicted LEF1 binding elements. Finally, through immunohistochemical analysis, high DIS3 protein levels associated with better survival for pancreatic cancer patients (hazard ratio = 2.87, 95% CI = 1.49–5.53, P = 0.001). Our results suggest that at least one target gene for the pancreatic cancer risk variants on chr13q22.1 may be DIS3, and that the underlying biology may be mediated by the novel indel through a long-range repressive effect on DIS3 expression.
Citation Format: Jason W. Hoskins, Abdisamad Ibrahim, Mickey Emmanuel, Sarah Manmiller, Jinping Jia, Hemang Parikh, Irene Collins, Kris Ylaya, Sean F. Altekruse, Stephen M. Hewitt, Gloria M. Petersen, Laufey T. Amundadottir. Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-09.
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Affiliation(s)
| | | | | | | | | | | | | | - Kris Ylaya
- 1National Cancer Institute, Bethesda, MD,
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Puntambekar SP, Sugoor D, Joshi G, Puntambekar SP, kumbhare S, Sharma V, Parikh H. Single Institutional Experience of 410 Cases of Type B & Type C (Querleu Morrow Classification) Laparoscopic Radical Hysterectomy. J Minim Invasive Gynecol 2015; 22:S91-S92. [DOI: 10.1016/j.jmig.2015.08.247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ekman C, Elgzyri T, Ström K, Almgren P, Parikh H, Dekker Nitert M, Rönn T, Manderson Koivula F, Ling C, Tornberg ÅB, Wollmer P, Eriksson KF, Groop L, Hansson O. Less pronounced response to exercise in healthy relatives to type 2 diabetic subjects compared with controls. J Appl Physiol (1985) 2015; 119:953-60. [PMID: 26338460 DOI: 10.1152/japplphysiol.01067.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 08/27/2015] [Indexed: 01/03/2023] Open
Abstract
Healthy first-degree relatives with heredity of type 2 diabetes (FH+) are known to have metabolic inflexibility compared with subjects without heredity for diabetes (FH-). In this study, we aimed to test the hypothesis that FH+ individuals have an impaired response to exercise compared with FH-. Sixteen FH+ and 19 FH- insulin-sensitive men similar in age, peak oxygen consumption (V̇o2 peak), and body mass index completed an exercise intervention with heart rate monitored during exercise for 7 mo. Before and after the exercise intervention, the participants underwent a physical examination and tests for glucose tolerance and exercise capacity, and muscle biopsies were taken for expression analysis. The participants attended, on average, 39 training sessions during the intervention and spent 18.8 MJ on exercise. V̇o2 peak/kg increased by 14%, and the participants lost 1.2 kg of weight and 3 cm waist circumference. Given that the FH+ group expended 61% more energy during the intervention, we used regression analysis to analyze the response in the FH+ and FH- groups separately. Exercise volume had a significant effect on V̇o2 peak, weight, and waist circumference in the FH- group, but not in the FH+ group. After exercise, expression of genes involved in metabolism, oxidative phosphorylation, and cellular respiration increased more in the FH- compared with the FH+ group. This suggests that healthy, insulin-sensitive FH+ and FH- participants with similar age, V̇o2 peak, and body mass index may respond differently to an exercise intervention. The FH+ background might limit muscle adaptation to exercise, which may contribute to the increased susceptibility to type 2 diabetes in FH+ individuals.
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Affiliation(s)
- C Ekman
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - T Elgzyri
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - K Ström
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden; Swedish Winter Sports Research Centre, Department of Health Sciences, Mid Sweden University, Östersund, Sweden
| | - P Almgren
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - H Parikh
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden; Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Marloes Dekker Nitert
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - T Rönn
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | | | - C Ling
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - Å B Tornberg
- Department of Health Sciences, Division of Physiotherapy, Lund University, Lund, Sweden; Genetic Molecular Epidemiology Unit, Lund University Diabetes Center, Clinical Research Centre, Malmö, Sweden; and
| | - P Wollmer
- Department of Health Sciences, Division of Physiotherapy, Lund University, Lund, Sweden; Department of Clinical Sciences, Clinical Physiology and Nuclear Medicine Unit, Lund University, Malmö, Sweden
| | - K F Eriksson
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - L Groop
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden
| | - O Hansson
- Department of Clinical Sciences, Clinical Research Centre, Malmö University Hospital, Lund University, Malmö, Sweden;
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Hoskins JW, Ibrahim A, Emmanuel M, Parikh H, Jia J, Collins I, Ylaya K, Altekruse SF, Hewitt SM, Petersen GM, Amundadottir LT. Abstract B111: Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. Cancer Res 2015. [DOI: 10.1158/1538-7445.panca2014-b111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A genome-wide association study (GWAS) of pancreatic cancer conducted within the NCI Cohort Consortium (PanScan I and II) identified pancreatic cancer susceptibility loci on chromosomes 1q32.1/NR5A2, 5p15.33/CLPTM1L/TERT, 9q34.2/ABO, and 13q22.1. The most significant single-nucleotide polymorphism (SNP) identified on 13q22.1, rs9543325, lies in a 600 kb gene desert; the nearest genes are KLF5, KLF12, PIBF1, DIS3, and BORA (265–586 kb). Imputation using the 1000 Genomes and DCEG reference datasets did not improve the GWAS signal, but produced a set of highly correlated SNPs for functional follow-up. We performed eQTL analysis to test for association between the genotypes of these functional candidate variants and expression of nearby genes. Among 100 normal derived pancreatic tissue samples, DIS3 expression showed the strongest association with a novel 30 bp indel variant in the risk locus (P = 4.0 × 104), indicating risk alleles associate with reduced DIS3 expression. Mutations in DIS3 have previously been identified in acute myeloid leukemia and multiple myeloma, and its expression has been correlated with metastatic potential in colorectal cancer, suggesting DIS3 is relevant to cancer biology. Chromosome conformation capture identified a physical interaction between the indel-containing locus and a region near the DIS3 promoter. Luciferase assay for regulatory function of this indel-containing locus revealed allele-specific silencer activity for the insertion allele. Supershift electromobility shift assay (EMSA) demonstrated binding of LEF1 specifically to the insertion allele of the indel, which contains two in silico predicted LEF1 binding elements. Finally, through immunohistochemical analysis, high DIS3 protein levels associated with better survival for pancreatic cancer patients (hazard ratio = 2.87, 95% CI = 1.49–5.53, P = 0.001). Our results suggest that at least one target gene for the pancreatic cancer risk variants on chr13q22.1 may be DIS3, and that the underlying biology may be mediated by the novel indel through a long-range repressive effect on DIS3 expression.
Citation Format: Jason W. Hoskins, Abdisamad Ibrahim, Mickey Emmanuel, Hemang Parikh, Jinping Jia, Irene Collins, Kris Ylaya, Sean F. Altekruse, Stephen M. Hewitt, Gloria M. Petersen, Laufey T. Amundadottir. Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression with prognostic implications. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B111.
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Affiliation(s)
| | | | | | | | | | | | - Kris Ylaya
- 1National Cancer Institute, Bethesda, MD,
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Hoskins JW, Flandez M, Jia J, Parikh H, Collins I, Emmanuel M, Ibrahim A, Xiao W, Powell J, Malats N, Petersen GM, Real FX, Amundadottir LT. Abstract B112: Transcriptome analysis in pancreatic cancer reveals a tumor suppressor function for HNF1A. Cancer Res 2015. [DOI: 10.1158/1538-7445.panca2014-b112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC), as with all cancer, is driven by dysregulation of genetic programs due to accumulation of somatic mutations, epigenetic modifications and changes in the micro-environment. Holistic views of perturbations in gene expression networks could illuminate key regulators and pathways for this highly lethal cancer. Toward this end, we performed massively-parallel mRNA-sequencing in normal (n = 10) and tumor (n = 8) derived pancreatic tissue samples as well as pancreatic cancer cell lines (n = 9), and determined differential gene expression (DE) patterns. Sub-network enrichment analyses of all expressed genes based on magnitude of DE identified HNF1A as the regulator of the most significantly and consistently dysregulated expression sub-network in our pancreatic tumor samples (median P = 7.56 x 10-7, median rank = 1, range = 1-25). To explore the effect of HNF1A expression in pancreatic tumor-derived cells we generated stable HNF1A-inducible clones in two pancreatic cancer cell lines. Induction of HNF1A overexpression caused severe growth inhibition (5.3-fold, P = 4.5x10-5 for MIA PaCa-2 clones; 7.2-fold, P = 2.2x10-5 for PANC-1 clones), and G0/G1 cell cycle arrest. This was accompanied by down-regulation of 49 out of 84 assayed cell cycle genes, while only 1 displayed increased expression. These data, combined with HNF1A’s direct regulation of pancreatic development and homeostasis genes (i.e. PDX1, PTF1A and NR5A2), suggest it may be an important tumor suppressor in pancreatic cells.
Citation Format: Jason W. Hoskins, Marta Flandez, Jinping Jia, Hemang Parikh, Irene Collins, Mickey Emmanuel, Abdisamad Ibrahim, Wenming Xiao, John Powell, Nuria Malats, Gloria M. Petersen, Fransisco X. Real, Laufey T. Amundadottir. Transcriptome analysis in pancreatic cancer reveals a tumor suppressor function for HNF1A. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B112.
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Affiliation(s)
| | - Marta Flandez
- 2CNIO-Spanish National Cancer Research Centre, Madrid, Spain,
| | | | | | | | | | | | | | - John Powell
- 3National Institutes of Health, Bethesda, MD,
| | - Nuria Malats
- 2CNIO-Spanish National Cancer Research Centre, Madrid, Spain,
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Wang Z, Zhu B, Zhang M, Parikh H, Jia J, Chung CC, Sampson JN, Hoskins JW, Hutchinson A, Burdette L, Ibrahim A, Hautman C, Raj PS, Abnet CC, Adjei AA, Ahlbom A, Albanes D, Allen NE, Ambrosone CB, Aldrich M, Amiano P, Amos C, Andersson U, Andriole G, Andrulis IL, Arici C, Arslan AA, Austin MA, Baris D, Barkauskas DA, Bassig BA, Beane Freeman LE, Berg CD, Berndt SI, Bertazzi PA, Biritwum RB, Black A, Blot W, Boeing H, Boffetta P, Bolton K, Boutron-Ruault MC, Bracci PM, Brennan P, Brinton LA, Brotzman M, Bueno-de-Mesquita HB, Buring JE, Butler MA, Cai Q, Cancel-Tassin G, Canzian F, Cao G, Caporaso NE, Carrato A, Carreon T, Carta A, Chang GC, Chang IS, Chang-Claude J, Che X, Chen CJ, Chen CY, Chen CH, Chen C, Chen KY, Chen YM, Chokkalingam AP, Chu LW, Clavel-Chapelon F, Colditz GA, Colt JS, Conti D, Cook MB, Cortessis VK, Crawford ED, Cussenot O, Davis FG, De Vivo I, Deng X, Ding T, Dinney CP, Di Stefano AL, Diver WR, Duell EJ, Elena JW, Fan JH, Feigelson HS, Feychting M, Figueroa JD, Flanagan AM, Fraumeni JF, Freedman ND, Fridley BL, Fuchs CS, Gago-Dominguez M, Gallinger S, Gao YT, Gapstur SM, Garcia-Closas M, Garcia-Closas R, Gastier-Foster JM, Gaziano JM, Gerhard DS, Giffen CA, Giles GG, Gillanders EM, Giovannucci EL, Goggins M, Gokgoz N, Goldstein AM, Gonzalez C, Gorlick R, Greene MH, Gross M, Grossman HB, Grubb R, Gu J, Guan P, Haiman CA, Hallmans G, Hankinson SE, Harris CC, Hartge P, Hattinger C, Hayes RB, He Q, Helman L, Henderson BE, Henriksson R, Hoffman-Bolton J, Hohensee C, Holly EA, Hong YC, Hoover RN, Hosgood HD, Hsiao CF, Hsing AW, Hsiung CA, Hu N, Hu W, Hu Z, Huang MS, Hunter DJ, Inskip PD, Ito H, Jacobs EJ, Jacobs KB, Jenab M, Ji BT, Johansen C, Johansson M, Johnson A, Kaaks R, Kamat AM, Kamineni A, Karagas M, Khanna C, Khaw KT, Kim C, Kim IS, Kim JH, Kim YH, Kim YC, Kim YT, Kang CH, Jung YJ, Kitahara CM, Klein AP, Klein R, Kogevinas M, Koh WP, Kohno T, Kolonel LN, Kooperberg C, Kratz CP, Krogh V, Kunitoh H, Kurtz RC, Kurucu N, Lan Q, Lathrop M, Lau CC, Lecanda F, Lee KM, Lee MP, Le Marchand L, Lerner SP, Li D, Liao LM, Lim WY, Lin D, Lin J, Lindstrom S, Linet MS, Lissowska J, Liu J, Ljungberg B, Lloreta J, Lu D, Ma J, Malats N, Mannisto S, Marina N, Mastrangelo G, Matsuo K, McGlynn KA, McKean-Cowdin R, McNeill LH, McWilliams RR, Melin BS, Meltzer PS, Mensah JE, Miao X, Michaud DS, Mondul AM, Moore LE, Muir K, Niwa S, Olson SH, Orr N, Panico S, Park JY, Patel AV, Patino-Garcia A, Pavanello S, Peeters PHM, Peplonska B, Peters U, Petersen GM, Picci P, Pike MC, Porru S, Prescott J, Pu X, Purdue MP, Qiao YL, Rajaraman P, Riboli E, Risch HA, Rodabough RJ, Rothman N, Ruder AM, Ryu JS, Sanson M, Schned A, Schumacher FR, Schwartz AG, Schwartz KL, Schwenn M, Scotlandi K, Seow A, Serra C, Serra M, Sesso HD, Severi G, Shen H, Shen M, Shete S, Shiraishi K, Shu XO, Siddiq A, Sierrasesumaga L, Sierri S, Loon Sihoe AD, Silverman DT, Simon M, Southey MC, Spector L, Spitz M, Stampfer M, Stattin P, Stern MC, Stevens VL, Stolzenberg-Solomon RZ, Stram DO, Strom SS, Su WC, Sund M, Sung SW, Swerdlow A, Tan W, Tanaka H, Tang W, Tang ZZ, Tardon A, Tay E, Taylor PR, Tettey Y, Thomas DM, Tirabosco R, Tjonneland A, Tobias GS, Toro JR, Travis RC, Trichopoulos D, Troisi R, Truelove A, Tsai YH, Tucker MA, Tumino R, Van Den Berg D, Van Den Eeden SK, Vermeulen R, Vineis P, Visvanathan K, Vogel U, Wang C, Wang C, Wang J, Wang SS, Weiderpass E, Weinstein SJ, Wentzensen N, Wheeler W, White E, Wiencke JK, Wolk A, Wolpin BM, Wong MP, Wrensch M, Wu C, Wu T, Wu X, Wu YL, Wunder JS, Xiang YB, Xu J, Yang HP, Yang PC, Yatabe Y, Ye Y, Yeboah ED, Yin Z, Ying C, Yu CJ, Yu K, Yuan JM, Zanetti KA, Zeleniuch-Jacquotte A, Zheng W, Zhou B, Mirabello L, Savage SA, Kraft P, Chanock SJ, Yeager M, Landi MT, Shi J, Chatterjee N, Amundadottir LT. Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33. Hum Mol Genet 2014; 23:6616-33. [PMID: 25027329 PMCID: PMC4240198 DOI: 10.1093/hmg/ddu363] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/30/2014] [Accepted: 07/08/2014] [Indexed: 02/03/2023] Open
Abstract
Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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Affiliation(s)
- Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics
| | | | | | - Jinping Jia
- Division of Cancer Epidemiology and Genetics
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Christopher Hautman
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Andrew A Adjei
- Korle Bu Teaching Hospital, PO BOX 77, Accra, Ghana, University of Ghana Medical School, PO Box 4236, Accra, Ghana
| | - Anders Ahlbom
- Unit of Epidemiology, Institute of Environmental Medicine
| | | | - Naomi E Allen
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, UK
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Melinda Aldrich
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Pilar Amiano
- Public Health Division of Gipuzkoa, Basque Regional Health Department, San Sebastian, Spain, CIBERESP, CIBER Epidemiologia y Salud Publica, Madrid, Spain
| | | | | | - Gerald Andriole
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Irene L Andrulis
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mt Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Cecilia Arici
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Italy
| | - Alan A Arslan
- Department of Obstetrics and Gynecology and Department of Population Health, New York University School of Medicine, New York, NY, USA, New York University Cancer Institute, New York, NY, USA
| | - Melissa A Austin
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Dalsu Baris
- Division of Cancer Epidemiology and Genetics
| | - Donald A Barkauskas
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine and
| | - Bryan A Bassig
- Division of Cancer Epidemiology and Genetics, Division of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | | | | | | | - Pier Alberto Bertazzi
- Department of Clinical Sciences and Community Health, University of Milan, Department of Preventive Medicine, Fondazione IRCCS Ca' Granda Policlinico Hospital, Milan, Italy
| | - Richard B Biritwum
- Korle Bu Teaching Hospital, PO BOX 77, Accra, Ghana, University of Ghana Medical School, PO Box 4236, Accra, Ghana
| | | | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA, International Epidemiology Institute, Rockville, MD, USA
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition, Potsdam-Rehbruecke, Germany
| | - Paolo Boffetta
- Institute for Translational Epidemiology, Hematology and Medical Oncology, Mount Sinai Hospital School of Medicine, New York, NY, USA
| | - Kelly Bolton
- Division of Cancer Epidemiology and Genetics, Department of Oncology, University of Cambridge, Cambridge CB2 2RE, UK
| | | | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | | | | | - H Bas Bueno-de-Mesquita
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands, Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mary Ann Butler
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Cincinnati, OH, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | | | - Alfredo Carrato
- Medical Oncology Department, Hospital Ramón y Cajal, Madrid, Spain
| | - Tania Carreon
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Cincinnati, OH, USA
| | - Angela Carta
- Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mt Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Gee-Chen Chang
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan, Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | | | - Jenny Chang-Claude
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xu Che
- Department of Abdominal Surgery and
| | - Chien-Jen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, Graduate Institute of Epidemiology, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chih-Yi Chen
- Cancer Center, China Medical University Hospital, Taipei, Taiwan
| | | | | | - Kuan-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yuh-Min Chen
- Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine and Chest Department, Taipei Veterans General Hospital, Taipei, Taiwan, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | | | - Lisa W Chu
- Cancer Prevention Institute of California, Fremont, CA, USA
| | | | | | | | - David Conti
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine and
| | | | - Victoria K Cortessis
- Department of Preventive Medicine, Biostatistics Division, Keck School of Medicine and
| | | | - Olivier Cussenot
- CeRePP, Paris, France, AP-HP, Department of Urology, Tenon Hospital, GHU-Est, Paris, France, UPMC Univ Paris 06, GRC n°5, ONCOTYPE-URO, Paris, France
| | - Faith G Davis
- Department of Public Health Sciences, School of Public Health, University of Alberta, Edmonton, AB, Canada T6G 2R3
| | - Immaculata De Vivo
- Program in Molecular and Genetic Epidemiology, Department of Medicine, Channing Division of Network Medicine and Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Xiang Deng
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, People's Republic of China
| | | | - Anna Luisa Di Stefano
- Service de Neurologie Mazarin, GH Pitie-Salpetriere, APHP, and UMR 975 INSERM-UPMC, CRICM, Paris, France
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Eric J Duell
- Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - Joanne W Elena
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, Bethesda, MD, USA
| | - Jin-Hu Fan
- Shanghai Cancer Institute, Shanghai, People's Republic of China
| | | | | | | | - Adrienne M Flanagan
- UCL Cancer Institute, Huntley Street, London WC1E 6BT, UK, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | | | | | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA, Channing Laboratory, Department of Medicine
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | | | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotaong University School of Medicine, Shanghai, China
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Reina Garcia-Closas
- Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Spain
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, and The Ohio State University Department of Pathology and Pediatrics, Columbus, OH, USA
| | - J Michael Gaziano
- Division of Preventive Medicine, Department of Medicine and Division of Aging, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA, Massachusetts Veteran's Epidemiology, Research and Information Center, Geriatric Research Education and Clinical Center, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Daniela S Gerhard
- Office of Cancer Genomics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carol A Giffen
- Information Management Services Inc., Calverton, MD, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria & Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Victoria, Australia
| | | | | | - Michael Goggins
- Department of Oncology, Department of Pathology and Department of Medicine, The Sol Goldman Pancreatic Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Carlos Gonzalez
- Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Richard Gorlick
- Albert Einstein College of Medicine, The Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Myron Gross
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Robert Grubb
- Department of Urology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Peng Guan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Goran Hallmans
- Department of Public Health and Clinical Medicine/Nutritional Research
| | | | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Claudia Hattinger
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Richard B Hayes
- Division of Cancer Epidemiology and Genetics, Department of Population Health, New York University Langone Medical Center and Department of Environmental Medicine, New York University Langone Medical Center, New York University Cancer Institute, New York, NY, USA
| | - Qincheng He
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | | | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Chancellor Hohensee
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Yun-Chul Hong
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea, Department of Preventive Medicine and
| | | | - H Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Chin-Fu Hsiao
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences and Taiwan Lung Cancer Tissue/Specimen Information Resource Center, National Health Research Institutes, Zhunan, Taiwan
| | - Ann W Hsing
- Cancer Prevention Institute of California, Fremont, CA, USA, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Chao Agnes Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences and
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Ming-Shyan Huang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - David J Hunter
- Program in Molecular and Genetic Epidemiology, Department of Medicine, Channing Division of Network Medicine and Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Kevin B Jacobs
- Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA, Bioinformed, LLC, Gaithersburg, MD, USA
| | - Mazda Jenab
- International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics
| | - Christoffer Johansen
- Department of Oncology, Finsen Center, Rigshospitalet, Copenhagen, Denmark, Unit of Survivorship, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC-WHO), Lyon, France, Department of Public Health and Clinical Medicine
| | | | - Rudolf Kaaks
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | | | - Kay-Tee Khaw
- School of Clinical Medicine, University of Cambridge, UK
| | | | - In-Sam Kim
- Department of Biochemistry and Department of Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jin Hee Kim
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Yeul Hong Kim
- Genomic Research Center for Lung and Breast/Ovarian Cancers, Korea University Anam Hospital, Seoul, Republic of Korea, Department of Internal Medicine and Division of Brain and Division of Oncology/Hematology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Young-Chul Kim
- Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun-eup, Republic of Korea
| | - Young Tae Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Hyun Kang
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoo Jin Jung
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Alison P Klein
- Department of Oncology, Department of Pathology and Department of Medicine, The Sol Goldman Pancreatic Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA, Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Manolis Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain, CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain, National School of Public Health, Athens, Greece
| | - Woon-Puay Koh
- Duke-NUS Graduate Medical School, Singapore, Singapore, Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Vittorio Krogh
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Hideo Kunitoh
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan, Department of Respiratory Medicine, Mitsui Memorial Hospital, Tokyo, Japan
| | | | - Nilgun Kurucu
- Department of Pediatric Oncology, A.Y. Ankara Oncology Training and Research Hospital, Yenimahalle- Ankara, Turkey
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics
| | - Mark Lathrop
- Centre National de Genotypage, IG/CEA, Evry Cedex, France, Centre d'Étude du Polymorphism Humain (CEPH), Paris, France
| | - Ching C Lau
- Texas Children's Cancer and Hematology Centers
| | - Fernando Lecanda
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Kyoung-Mu Lee
- Department of Preventive Medicine and Department of Environmental Health, Korea National Open University, Seoul, Republic of Korea
| | | | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Donghui Li
- Department of Gastrointestinal Medical Oncology
| | | | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Dongxin Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore, School of Life Sciences, Anhui Medical University, Hefei, China
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology and
| | - Josep Lloreta
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Daru Lu
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jing Ma
- Department of Medicine, Channing Division of Network Medicine and Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nuria Malats
- Centro Nacional de Investigaciones Oncologicas, Melchor Fernández Almagro, 3, Madrid E-28029, Spain
| | - Satu Mannisto
- National Institute for Health and Welfare, Helsinki, Finland
| | - Neyssa Marina
- Lucile Packard Children's Hospital, Stanford University, Palo Alto, CA, USA
| | - Giuseppe Mastrangelo
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padua, Italy
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan, Department of Preventive Medicine, Kyushu University Faculty of Medical Scicence, Fukuoka, Japan
| | | | | | - Lorna H McNeill
- Department of Health Disparities Research, Division of OVP, Cancer Prevention and Population Sciences, and Center for Community-Engaged Translational Research, Duncan Family Institute and
| | | | | | | | - James E Mensah
- Korle Bu Teaching Hospital, PO BOX 77, Accra, Ghana, University of Ghana Medical School, PO Box 4236, Accra, Ghana
| | - Xiaoping Miao
- Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Dominique S Michaud
- Department of Epidemiology, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | | | - Lee E Moore
- Division of Cancer Epidemiology and Genetics
| | - Kenneth Muir
- Health Sciences Research Institute, University of Warwick, Coventry, UK
| | | | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Nick Orr
- Complex Traits Genetics Team and
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Jae Yong Park
- Department of Biochemistry and Department of Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea, Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Alpa V Patel
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Ana Patino-Garcia
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Sofia Pavanello
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padua, Italy
| | - Petra H M Peeters
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, Utrecht, The Netherlands, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | | | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Piero Picci
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA, Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Stefano Porru
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Italy
| | - Jennifer Prescott
- Program in Molecular and Genetic Epidemiology, Department of Medicine, Channing Division of Network Medicine and Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Xia Pu
- Department of Epidemiology
| | | | - You-Lin Qiao
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | | | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | | | - Rebecca J Rodabough
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Avima M Ruder
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Cincinnati, OH, USA
| | - Jeong-Seon Ryu
- Department of Internal Medicine, Inha University College of Medicine, Incheon, Korea
| | - Marc Sanson
- Service de Neurologie Mazarin, GH Pitie-Salpetriere, APHP, and UMR 975 INSERM-UPMC, CRICM, Paris, France
| | - Alan Schned
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute and Department of Oncology and
| | - Kendra L Schwartz
- Karmanos Cancer Institute and Department of Family Medicine and Public Health Sciences, Wayne State University School of Medicine, Detroit, MI, USA
| | | | - Katia Scotlandi
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Adeline Seow
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Consol Serra
- Centre for Research in Occupational Health, Universitat Pompeu Fabra, Barcelona, Spain, CIBER of Epidemiology and Public Health (CIBERESP)
| | - Massimo Serra
- Laboratory of Experimental Oncology, Orthopaedic Rizzoli Institute, Bologna, Italy
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council Victoria & Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Victoria, Australia
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Min Shen
- Division of Cancer Epidemiology and Genetics
| | - Sanjay Shete
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX, USA
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Afshan Siddiq
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK
| | - Luis Sierrasesumaga
- Department of Pediatrics, University Clinic of Navarra, Universidad de Navarra, Pamplona, Spain
| | - Sabina Sierri
- Nutritional Epidemiology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alan Dart Loon Sihoe
- Department of Surgery, Division of Cardiothoracic Surgery, Queen Mary Hospital, Hong Kong, China
| | | | - Matthias Simon
- Department of Neurosurgery, University of Bonn Medical Center, Bonn, Germany
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | | | - Margaret Spitz
- Dan L. Duncan Center, Baylor College of Medicine, Houston, TX, USA
| | - Meir Stampfer
- Department of Medicine, Channing Division of Network Medicine and Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Par Stattin
- Department of Surgical and Perioperative Sciences, Urology and Andrology and
| | - Mariana C Stern
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Victoria L Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | | | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sara S Strom
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Malin Sund
- Department of Surgical and Perioperative Sciences/Surgery, Umeå University, Umeå, Sweden
| | - Sook Whan Sung
- Department of Thoracic and Cardiovascular Surgery, Seoul St Mary's Hospital, Seoul, South Korea
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK, Division of Breast Cancer Research, Institute of Cancer Research, London, UK
| | - Wen Tan
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hideo Tanaka
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Wei Tang
- Division of Cancer Epidemiology and Genetics
| | - Ze-Zhang Tang
- Shanxi Cancer Hospital, Taiyuan, Shanxi, People's Republic of China
| | - Adonina Tardon
- Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Evelyn Tay
- Korle Bu Teaching Hospital, PO BOX 77, Accra, Ghana, University of Ghana Medical School, PO Box 4236, Accra, Ghana
| | | | - Yao Tettey
- Korle Bu Teaching Hospital, PO BOX 77, Accra, Ghana, University of Ghana Medical School, PO Box 4236, Accra, Ghana
| | - David M Thomas
- Sir Peter MacCallum Department of Oncology, University of Melbourne, St Andrew's Place, East Melbourne, VIC, Australia
| | - Roberto Tirabosco
- Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | | | | | | | - Ruth C Travis
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, UK
| | | | | | | | - Ying-Huang Tsai
- Department of Pulmonary Medicine, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | | | - Rosario Tumino
- Cancer Registry Associazione Iblea Ricerca Epidemiologica, Onlus and Asp Ragusa, Ragusa Italy
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Paolo Vineis
- Imperial College, London, UK, Human Genetics Foundation (HuGeF), Torino Italy
| | - Kala Visvanathan
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark, National Food Institute, Technical University of Denmark, Soborg, Denmark
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics
| | | | - Junwen Wang
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA, Department of Biochemistry and Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sophia S Wang
- Division of Cancer Etiology, Department of Population Sciences, City of Hope and the Beckman Research Institute, Duarte, CA, USA
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway, Department of Research, Cancer Registry of Norway, Oslo, Norway, Department of Medical Epidemiology and Biostatistics and Samfundet Folkhälsan, Helsinki, Finland
| | | | | | | | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John K Wiencke
- University of California San Francisco, San Francisco, CA, USA
| | - Alicja Wolk
- Unit of Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA, Channing Laboratory, Department of Medicine
| | | | | | - Chen Wu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tangchun Wu
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padua, Italy
| | | | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Medical Research Center and Cancer Center of Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jay S Wunder
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotaong University School of Medicine, Shanghai, China
| | - Jun Xu
- School of Public Health, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | | | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital and
| | | | - Edward D Yeboah
- Korle Bu Teaching Hospital, PO BOX 77, Accra, Ghana, University of Ghana Medical School, PO Box 4236, Accra, Ghana
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Chen Ying
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chong-Jen Yu
- Department of Internal Medicine, National Cheng Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics
| | - Jian-Min Yuan
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA and
| | - Krista A Zanetti
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, Bethesda, MD, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA, New York University Cancer Institute, New York, NY, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | | | | | - Peter Kraft
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory, National Cancer Institute, Division of Cancer Epidemiology and Genetics, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics
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Planck T, Shahida B, Parikh H, Ström K, Åsman P, Brorson H, Hallengren B, Lantz M. Smoking induces overexpression of immediate early genes in active Graves' ophthalmopathy. Thyroid 2014; 24:1524-32. [PMID: 25135760 DOI: 10.1089/thy.2014.0153] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Cigarette smoking is a risk factor for the development of Graves' ophthalmopathy (GO). In a previous study of gene expression in intraorbital fat, adipocyte-related immediate early genes (IEGs) were overexpressed in patients with GO compared to controls. We investigated whether IEGs are upregulated by smoking, and examined other pathways that may be affected by smoking. METHODS Gene expression in intraorbital fat was studied in smokers (n=8) and nonsmokers (n=8) with severe active GO, as well as in subcutaneous fat in thyroid-healthy smokers (n=5) and nonsmokers (n=5) using microarray and real-time polymerase chain reaction (PCR). RESULTS With microarray, eight IEGs were upregulated more than 1.5-fold in smokers compared to nonsmokers with GO. Five were chosen for confirmation and were also overexpressed with real-time PCR. Interleukin-1 beta/IL-1B/(2.3-fold) and interleukin-6/IL-6/(2.4-fold) were upregulated both with microarray and with real-time PCR in smokers with GO compared to nonsmokers. Major histocompatibility complex, class II, DR beta 1/HLA-DRB1/was upregulated with microarray (2.1-fold) and with borderline significance with real-time PCR. None of these genes were upregulated in smokers compared to nonsmokers in subcutaneous fat. CONCLUSIONS IEGs, IL-1B, and IL-6 were overexpressed in smokers with severe active GO compared to nonsmokers, suggesting that smoking activates pathways associated with adipogenesis and inflammation. This study underlines the importance of IEGs in the pathogenesis of GO, and provides evidence for possible novel therapeutic interventions in GO. The mechanisms activated by smoking may be shared with other conditions such as rheumatoid arthritis.
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Affiliation(s)
- Tereza Planck
- 1 Department of Endocrinology, Skåne University Hospital , Malmö, Sweden
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25
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Hoskins JW, Jia J, Flandez M, Parikh H, Xiao W, Collins I, Emmanuel MA, Ibrahim A, Powell J, Zhang L, Malats N, Bamlet WR, Petersen GM, Real FX, Amundadottir LT. Transcriptome analysis of pancreatic cancer reveals a tumor suppressor function for HNF1A. Carcinogenesis 2014; 35:2670-8. [PMID: 25233928 DOI: 10.1093/carcin/bgu193] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is driven by the accumulation of somatic mutations, epigenetic modifications and changes in the micro-environment. New approaches to investigating disruptions of gene expression networks promise to uncover key regulators and pathways in carcinogenesis. We performed messenger RNA-sequencing in pancreatic normal (n = 10) and tumor (n = 8) derived tissue samples, as well as in pancreatic cancer cell lines (n = 9), to determine differential gene expression (DE) patterns. Sub-network enrichment analyses identified HNF1A as the regulator of the most significantly and consistently dysregulated expression sub-network in pancreatic tumor tissues and cells (median P = 7.56×10(-7), median rank = 1, range = 1-25). To explore the effects of HNF1A expression in pancreatic tumor-derived cells, we generated stable HNF1A-inducible clones in two pancreatic cancer cell lines (PANC-1 and MIA PaCa-2) and observed growth inhibition (5.3-fold, P = 4.5×10(-5) for MIA PaCa-2 clones; 7.2-fold, P = 2.2×10(-5) for PANC-1 clones), and a G0/G1 cell cycle arrest and apoptosis upon induction. These effects correlated with HNF1A-induced down-regulation of 51 of 84 cell cycle genes (e.g. E2F1, CDK2, CDK4, MCM2/3/4/5, SKP2 and CCND1), decreased expression of anti-apoptotic genes (e.g. BIRC2/5/6 and AKT) and increased expression of pro-apoptotic genes (e.g. CASP4/9/10 and APAF1). In light of the established role of HNF1A in the regulation of pancreatic development and homeostasis, our data suggest that it also functions as an important tumor suppressor in the pancreas.
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Affiliation(s)
- Jason W Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA, Department of Laboratory Medicine and Pathology and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA, Department of Laboratory Medicine and Pathology and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Marta Flandez
- Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA, Department of Laboratory Medicine and Pathology and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Wenming Xiao
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA, Department of Laboratory Medicine and Pathology and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Mickey A Emmanuel
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA, Department of Laboratory Medicine and Pathology and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Abdisamad Ibrahim
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA, Department of Laboratory Medicine and Pathology and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - John Powell
- Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lizhi Zhang
- Department of Laboratory Medicine and Pathology and
| | - Nuria Malats
- Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - William R Bamlet
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and
| | - Gloria M Petersen
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and
| | - Francisco X Real
- Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, Epithelial Carcinogenesis Group, CNIO-Spanish National Cancer Research Centre, E-28029 Madrid, Spain, Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute and Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA, Department of Laboratory Medicine and Pathology and Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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Lebdai S, Verhoest G, Parikh H, Jacquet SF, Bensalah K, Chautard D, Rioux Leclercq N, Azzouzi AR, Bigot P. Identification and validation of TGFBI as a promising prognosis marker of clear cell renal cell carcinoma. Urol Oncol 2014; 33:69.e11-8. [PMID: 25035170 DOI: 10.1016/j.urolonc.2014.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To identify prognostic biomarkers in clear cell renal cell carcinoma (ccRCC) using a proteomic approach. MATERIAL AND METHODS We performed a comparative proteomic profiling of ccRCC and normal renal tissues from 9 different human specimens. We assessed differential protein expression by iTRAQ (isobaric tagging reagent for absolute quantify) labeling with regard to tumor aggressiveness according to the stage, size, grade, and necrosis (SSIGN) score and confirmed our results using Western blot (9 patients) and immunohistochemistry (135 patients) analysis. RESULTS After proteomic analysis, 928 constitutive proteins were identified. Among these proteins, 346 had a modified expression in tumor compared with that of normal tissue. Pathway and integrated analyses indicated the presence of an up-regulation of the pentose phosphate pathway in aggressive tumors. In total, 14 proteins were excreted and could potentially become biomarkers. Overexpression of transforming growth factor, beta-induced (TGFBI) in ccRCC was confirmed using Western blot and immunohistochemistry analysis. A significant association was found between the presence of TGFBI expression with tumor category T3-4 (P<0.0001), Fuhrman grades III and IV (P<0.0001), tumor size>4cm (P<0.0001), presence of tumor necrosis (P<0.0001), nodal involvement (n = 0.009), metastasis (P = 0.012), SSIGN score≥5 (P<0.0001), cancer progression (P<0.0001), and cancer-specific death (P<0.0001). Cancer-specific survival was significantly better for patients with no cytoplasmic TGFBI expression (1-, 3-, 5-y cancer-specific survival of 94.7%, 87.8%, and 73.4% vs. 92.9%, 71.2%, and 49.8%, respectively; P<0.0001). CONCLUSION We identified 346 proteins involved in renal carcinogenesis and confirmed the presence of a metabolic shift in aggressive tumors. TGFBI was overexpressed in tumors with high SSIGN scores and was significantly associated with oncologic outcomes.
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Affiliation(s)
- Souhil Lebdai
- Department of Urology, Angers University Hospital, Angers, France
| | - Gregory Verhoest
- Department of Urology, Pontchaillou University Hospital, Rennes, France
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Karim Bensalah
- Department of Urology, Pontchaillou University Hospital, Rennes, France
| | - Denis Chautard
- Department of Urology, Angers University Hospital, Angers, France
| | | | | | - Pierre Bigot
- Department of Urology, Angers University Hospital, Angers, France; Université Pierre et Marie Currie, Paris, France.
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27
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Jia J, Bosley AD, Thompson A, Hoskins JW, Cheuk A, Collins I, Parikh H, Xiao Z, Ylaya K, Dzyadyk M, Cozen W, Hernandez BY, Lynch CF, Loncarek J, Altekruse SF, Zhang L, Westlake CJ, Factor VM, Thorgeirsson S, Bamlet WR, Hewitt SM, Petersen GM, Andresson T, Amundadottir LT. CLPTM1L promotes growth and enhances aneuploidy in pancreatic cancer cells. Cancer Res 2014; 74:2785-95. [PMID: 24648346 DOI: 10.1158/0008-5472.can-13-3176] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) of 10 different cancers have identified pleiotropic cancer predisposition loci across a region of chromosome 5p15.33 that includes the TERT and CLPTM1L genes. Of these, susceptibility alleles for pancreatic cancer have mapped to the CLPTM1L gene, thus prompting an investigation of the function of CLPTM1L in the pancreas. Immunofluorescence analysis indicated that CLPTM1L localized to the endoplasmic reticulum where it is likely embedded in the membrane, in accord with multiple predicted transmembrane domains. Overexpression of CLPTM1L enhanced growth of pancreatic cancer cells in vitro (1.3-1.5-fold; PDAY7 < 0.003) and in vivo (3.46-fold; PDAY68 = 0.039), suggesting a role in tumor growth; this effect was abrogated by deletion of two hydrophilic domains. Affinity purification followed by mass spectrometry identified an interaction between CLPTM1L and non-muscle myosin II (NMM-II), a protein involved in maintaining cell shape, migration, and cytokinesis. The two proteins colocalized in the cytoplasm and, after treatment with a DNA-damaging agent, at the centrosomes. Overexpression of CLPTM1L and depletion of NMM-II induced aneuploidy, indicating that CLPTM1L may interfere with normal NMM-II function in regulating cytokinesis. Immunohistochemical analysis revealed enhanced staining of CLPTM1L in human pancreatic ductal adenocarcinoma (n = 378) as compared with normal pancreatic tissue samples (n = 17; P = 1.7 × 10(-4)). Our results suggest that CLPTM1L functions as a growth-promoting gene in the pancreas and that overexpression may lead to an abrogation of normal cytokinesis, indicating that it should be considered as a plausible candidate gene that could explain the effect of pancreatic cancer susceptibility alleles on chr5p15.33.
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Affiliation(s)
- Jinping Jia
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Allen D Bosley
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Abbey Thompson
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jason W Hoskins
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Adam Cheuk
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Irene Collins
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Hemang Parikh
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Zhen Xiao
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kris Ylaya
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Marta Dzyadyk
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Wendy Cozen
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Brenda Y Hernandez
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Charles F Lynch
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jadranka Loncarek
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Sean F Altekruse
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lizhi Zhang
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Christopher J Westlake
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Valentina M Factor
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Snorri Thorgeirsson
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - William R Bamlet
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Stephen M Hewitt
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Gloria M Petersen
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Thorkell Andresson
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Laufey T Amundadottir
- Authors' Affiliations: Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics; Pediatric Oncology Branch; Laboratory of Pathology; Division of Cancer Control and Population Sciences; Laboratory of Experimental Carcinogenesis, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda; Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research; Laboratory of Protein Dynamics and Signaling and Laboratory of Cell & Developmental Signaling, NCI-Frederick, Frederick, Maryland; Keck School of Medicine, University of Southern California, Los Angeles, California; University of Hawaii Cancer Center, Honolulu, Hawaii; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa; and Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
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Jia J, Parikh H, Xiao W, Hoskins JW, Pflicke H, Liu X, Collins I, Zhou W, Wang Z, Powell J, Thorgeirsson SS, Rudloff U, Petersen GM, Amundadottir LT. An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer. BMC Med Genomics 2013; 6:33. [PMID: 24053169 PMCID: PMC3849454 DOI: 10.1186/1755-8794-6-33] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/16/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Pancreatic cancer is a highly lethal cancer with limited diagnostic and therapeutic modalities. METHODS To begin to explore the genomic landscape of pancreatic cancer, we used massively parallel sequencing to catalog and compare transcribed regions and potential regulatory elements in two human cell lines derived from normal and cancerous pancreas. RESULTS By RNA-sequencing, we identified 2,146 differentially expressed genes in these cell lines that were enriched in cancer related pathways and biological processes that include cell adhesion, growth factor and receptor activity, signaling, transcription and differentiation. Our high throughput Chromatin immunoprecipitation (ChIP) sequence analysis furthermore identified over 100,000 regions enriched in epigenetic marks, showing either positive (H3K4me1, H3K4me3, RNA Pol II) or negative (H3K27me3) correlation with gene expression. Notably, an overall enrichment of RNA Pol II binding and depletion of H3K27me3 binding were seen in the cancer derived cell line as compared to the normal derived cell line. By selecting genes for further assessment based on this difference, we confirmed enhanced expression of aldehyde dehydrogenase 1A3 (ALDH1A3) in two larger sets of pancreatic cancer cell lines and in tumor tissues as compared to normal derived tissues. CONCLUSIONS As aldehyde dehydrogenase (ALDH) activity is a key feature of cancer stem cells, our results indicate that a member of the ALDH superfamily, ALDH1A3, may be upregulated in pancreatic cancer, where it could mark pancreatic cancer stem cells.
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Affiliation(s)
- Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Hoskins J, Ibrahim A, Jia J, Collins I, Parikh H, Petersen GM, Amundadottir L. Abstract 3137: Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic cancer is the 10th most common cancer and 4th most common cause of cancer mortality in the United States. A genome wide association study has revealed pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. The chr13q22.1 region contains the most significant of all risk SNPs, rs9543325, (P= 3.27 x 10−11) which is located in a gene desert. The nearest genes are KLF5, KLF12, PIBF1, DIS3 and BORA, which range in distance from 265kb to 586kb, respectively, from the most significant variants. Given the high linkage disequilibrium across this risk locus, there are many candidate functional variants to consider. Imputation in the region did not improve the signal but gave a set of highly correlated SNPs which likely includes the functional variant(s). In an effort to identify the functional variant(s) we performed eQTL analyses to test the association between the genotypes of these candidate SNPs and expression of nearby genes. Among 100 normal pancreatic tissue samples, DIS3 showed the strongest association with SNPs in our risk locus (P-values as low as 0.0004). Mutations in DIS3 have been identified in acute myeloid leukemia and multiple myeloma, and its expression has been correlated with metastatic potential in colorectal cancer, suggesting this gene could be important in pancreatic cancer biology. Chromosome Conformation Capture (3C) was performed to test for physical interactions between the risk locus and nearby genes. This assay confirmed the three dimensional proximity of the risk locus and DIS3 promoter. Sub-regions of the risk locus were then cloned upstream of a minimal promoter controlling luciferase expression to assay for potential allele specific enhancer/silencer activity. This assay revealed a sub-region downstream of rs9543325 that causes allele-specific silencing. These results suggest that a sub-region of the chr13q22.1 risk locus has allele-specific effects on DIS3 expression, which may have implications in the susceptibility to pancreatic cancer.
Citation Format: Jason Hoskins, Abdisamad Ibrahim, Jinping Jia, Irene Collins, Hemang Parikh, Gloria M. Petersen, Laufey Amundadottir. Functional analysis of the chr13q22.1 pancreatic cancer risk locus suggests allele-specific effects on DIS3 expression. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3137. doi:10.1158/1538-7445.AM2013-3137
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Affiliation(s)
| | | | - Jinping Jia
- 1National Cancer Institute, Gaithersburg, MD
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Jia J, Collins I, Dzyadyk M, Thompson A, Cheuk A, Parikh H, Wang Z, Westlake C, Bosley A, Petersen G, Andresson T, Amundadottir L. Abstract 2556: Functional characterization of the pancreatic cancer TERT-CLPTM1L risk locus on chr5p15.33. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-2556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic cancer is a highly lethal cancer with few well established risk factors. PanScan, a genome wide association study (GWAS) of pancreatic cancer has identified four pancreatic cancer susceptibility loci in populations of European ancestry. One of these is in a multi cancer locus on chr5p15.33 where the most significant SNP from the GWAS (rs401681, P=3.7x10-7, ORAllele=1.19) lies in a region containing two genes, TERT and CLPTM1L. The TERT gene encodes the catalytic subunit of telomerase, well known for its essential role in maintaining telomere ends. The function of CLPTM1L is not as clear, although it has been proposed to play a role in apoptosis. It is predicted to encode a protein with 6 transmembrane (TM) domains and two large hydrophilic domains: a loop of 253 aa between the first and second TM domains, and a C-terminal tail of 89 aa.
We have performed imputation to fine-map the signal to a SNP three orders of magnitude more significant than the GWAS SNP (PImputed=1.4x10-10, ORAllele=1.30). As this SNP is located in the CLPTM1L gene we have performed a series of experiments to investigate the function of the CLPTM1L gene and its encoded protein. Immunofluorescence analysis in pancreatic cancer cells (PANC-1) indicates that it localizes to the endoplasmic reticulum. Affinity purification and mass spectrometry (HEK-293T, hTERT-HPNE and PANC-1 cells) identified MYH9, a non-muscle heavy chain myosin, as a potential interacting protein. The interaction has been validated by co-immunoprecipitation and co-localization experiments. To examine if CLPTM1L plays a role in growth control, we created stable PANC-1 cell lines overexpressing the full length CLPTM1L gene as well as two deletions, a C-terminal deletion and a loop deletion, and assayed growth in vitro and in vivo. Cell lines overexpressing full length CLPTM1L grow faster in vitro and in vivo as compared to cells containing empty vector. Interestingly, the two CLPTM1L mutants abolish this effect. Furthermore, we have shown by RNA-seq that the CLPTM1L gene is overexpressed in pancreatic tumors as compared to normal pancreatic tissues. Our results indicate that CLPTM1L may play a role in the control of cell growth and oncogenesis in the pancreas. Our current efforts aim at further characterizing the function of CLPTM1L and to correlate pancreatic cancer risk variants on 5p15.33 to molecular phenotypes to attempt to explain the underlying biology of the risk.
Citation Format: Jinping Jia, Irene Collins, Marta Dzyadyk, Abbey Thompson, Adam Cheuk, Hemang Parikh, Zhaoming Wang, Chris Westlake, Allen Bosley, Gloria Petersen, Thorkell Andresson, Laufey Amundadottir. Functional characterization of the pancreatic cancer TERT-CLPTM1L risk locus on chr5p15.33. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2556. doi:10.1158/1538-7445.AM2013-2556
Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.
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Affiliation(s)
| | | | | | | | - Adam Cheuk
- 2NCI-pediatric onology branch, Gaithersburg, MD
| | | | | | | | - Allen Bosley
- 5NCI-Laboratory of proteimics and Analytical Technologies, Frederick, MD
| | | | - Thorkell Andresson
- 5NCI-Laboratory of proteimics and Analytical Technologies, Frederick, MD
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Agalliu I, Wang Z, Wang T, Dunn A, Parikh H, Myers T, Burk RD, Amundadottir L. Characterization of SNPs associated with prostate cancer in men of Ashkenazic descent from the set of GWAS identified SNPs: impact of cancer family history and cumulative SNP risk prediction. PLoS One 2013; 8:e60083. [PMID: 23573233 PMCID: PMC3616024 DOI: 10.1371/journal.pone.0060083] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 02/24/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified multiple SNPs associated with prostate cancer (PrCa). Population isolates may have different sets of risk alleles for PrCa constituting unique population and individual risk profiles. METHODS To test this hypothesis, associations between 31 GWAS SNPs of PrCa were examined among 979 PrCa cases and 1,251 controls of Ashkenazic descent using logistic regression. We also investigated risks by age at diagnosis, pathological features of PrCa, and family history of cancer. Moreover, we examined associations between cumulative number of risk alleles and PrCa and assessed the utility of risk alleles in PrCa risk prediction by comparing the area under the curve (AUC) for different logistic models. RESULTS Of the 31 genotyped SNPs, 8 were associated with PrCa at p ≤ 0.002 (corrected p-value threshold) with odds ratios (ORs) ranging from 1.22 to 1.42 per risk allele. Four SNPs were associated with aggressive PrCa, while three other SNPs showed potential interactions for PrCa by family history of PrCa (rs8102476; 19q13), lung cancer (rs17021918; 4q22), and breast cancer (rs10896449; 11q13). Men in the highest vs. lowest quartile of cumulative number of risk alleles had ORs of 3.70 (95% CI 2.76-4.97); 3.76 (95% CI 2.57-5.50), and 5.20 (95% CI 2.94-9.19) for overall PrCa, aggressive cancer and younger age at diagnosis, respectively. The addition of cumulative risk alleles to the model containing age at diagnosis and family history of PrCa yielded a slightly higher AUC (0.69 vs. 0.64). CONCLUSION These data define a set of risk alleles associated with PrCa in men of Ashkenazic descent and indicate possible genetic differences for PrCa between populations of European and Ashkenazic ancestry. Use of genetic markers might provide an opportunity to identify men at highest risk for younger age of onset PrCa; however, their clinical utility in identifying men at highest risk for aggressive cancer remains limited.
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Affiliation(s)
- Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America.
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Nitert MD, Dayeh T, Volkov P, Elgzyri T, Hall E, Nilsson E, Yang BT, Lang S, Parikh H, Wessman Y, Weishaupt H, Attema J, Abels M, Wierup N, Almgren P, Jansson PA, Rönn T, Hansson O, Eriksson KF, Groop L, Ling C. Impact of an exercise intervention on DNA methylation in skeletal muscle from first-degree relatives of patients with type 2 diabetes. Diabetes 2012; 61:3322-32. [PMID: 23028138 PMCID: PMC3501844 DOI: 10.2337/db11-1653] [Citation(s) in RCA: 267] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To identify epigenetic patterns, which may predispose to type 2 diabetes (T2D) due to a family history (FH) of the disease, we analyzed DNA methylation genome-wide in skeletal muscle from individuals with (FH(+)) or without (FH(-)) an FH of T2D. We found differential DNA methylation of genes in biological pathways including mitogen-activated protein kinase (MAPK), insulin, and calcium signaling (P ≤ 0.007) and of individual genes with known function in muscle, including MAPK1, MYO18B, HOXC6, and the AMP-activated protein kinase subunit PRKAB1 in skeletal muscle of FH(+) compared with FH(-) men. We further validated our findings from FH(+) men in monozygotic twin pairs discordant for T2D, and 40% of 65 analyzed genes exhibited differential DNA methylation in muscle of both FH(+) men and diabetic twins. We further examined if a 6-month exercise intervention modifies the genome-wide DNA methylation pattern in skeletal muscle of the FH(+) and FH(-) individuals. DNA methylation of genes in retinol metabolism and calcium signaling pathways (P < 3 × 10(-6)) and with known functions in muscle and T2D including MEF2A, RUNX1, NDUFC2, and THADA decreased after exercise. Methylation of these human promoter regions suppressed reporter gene expression in vitro. In addition, both expression and methylation of several genes, i.e., ADIPOR1, BDKRB2, and TRIB1, changed after exercise. These findings provide new insights into how genetic background and environment can alter the human epigenome.
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Affiliation(s)
- Marloes Dekker Nitert
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Tasnim Dayeh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Peter Volkov
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Targ Elgzyri
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Elin Hall
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Emma Nilsson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Beatrice T. Yang
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Stefan Lang
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ylva Wessman
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Holger Weishaupt
- Immunology Unit, Institute for Experimental Medical Science, Lund University, Lund, Sweden
| | - Joanne Attema
- Immunology Unit, Institute for Experimental Medical Science, Lund University, Lund, Sweden
| | - Mia Abels
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Nils Wierup
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Peter Almgren
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Per-Anders Jansson
- Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Tina Rönn
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Ola Hansson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Leif Groop
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, CRC, Scania University Hospital, Malmö, Sweden
- Corresponding author: Charlotte Ling,
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Agalliu I, Wang Z, Dunn A, Parikh H, Myers T, Burk R, Amundadottir L. Abstract 28: Characterization of SNPs associated with prostate cancer in men of Ashkenazic descent from the set of GWAS identified SNPs: Impact of cancer family history. Cancer Epidemiol Biomarkers Prev 2012. [DOI: 10.1158/1055-9965.gwas-28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background: Genome-wide association studies (GWAS) have identified several SNPs that are independently associated with prostate cancer (PrCa) in Caucasian men. Population isolates with unique allele frequencies are likely to have different sets of risk alleles for PrCa constituting personalized population risk stratification in addition to individual risk profiles.
Methods: To test this hypothesis, we examined associations between 31 GWAS SNPs and PrCa among 979 cases and 1,251 controls of Ashkenazic descent. Odds ratios (OR) and 95% confidence intervals (CIs) were estimated for each SNP using logistic regression models adjusted for age. We also investigated risk in strata by age at diagnosis, pathological features of PrCa, as well as family history of PrCa and other cancers.
Results: Of 31 SNPs, 19 (62%) were associated with PrCa at p<0.05 in one or more genetic risk models. The strongest associations with PrCa were for rs6983267 at 8q24 (OR=1.78, p=5.7 x 10−7;comparison of GG vs. TT genotype), and rs1465618 at 2p21 (OR=2.19; p=0.003; AA vs. AG/GG). Six SNPs were associated with aggressive PrCa, while six others with less aggressive cancer. Four SNPs showed statistically significant interactions between PrCa and family history of PrCa (rs8102476 at 19q13), lung cancer (rs17021918 at 4q22), colorectal cancer (rs6983267 at 8q24), and breast cancer (rs10896449 at 11q13).
Conclusion: These data define a specific set of risk alleles associated with PrCa in Ashkenazic men. Results demonstrate differences between men of European and Ashkenazic ancestry in relation to genetic susceptibility of PrCa. Interactions of genetic variants with family history of specific cancers indicate a complex network of inherited cancer risk syndromes still to be defined. Use of genetic markers to identify men at higher risk of PrCa will provide an opportunity for personalized care of PrCa prevention through screening of high-risk individuals, independent of family history information.
Citation Format: Ilir Agalliu, Zhaoming Wang, Anne Dunn, Hemang Parikh, Timothy Myers, Robert Burk, Laufey Amundadottir. Characterization of SNPs associated with prostate cancer in men of Ashkenazic descent from the set of GWAS identified SNPs: Impact of cancer family history. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr 28.
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Affiliation(s)
- Ilir Agalliu
- 1Albert Einstein College of Medicine, Bronx, NY, 2National Institutes of Health, Bethesda, MD
| | - Zhaoming Wang
- 1Albert Einstein College of Medicine, Bronx, NY, 2National Institutes of Health, Bethesda, MD
| | - Anne Dunn
- 1Albert Einstein College of Medicine, Bronx, NY, 2National Institutes of Health, Bethesda, MD
| | - Hemang Parikh
- 1Albert Einstein College of Medicine, Bronx, NY, 2National Institutes of Health, Bethesda, MD
| | - Timothy Myers
- 1Albert Einstein College of Medicine, Bronx, NY, 2National Institutes of Health, Bethesda, MD
| | - Robert Burk
- 1Albert Einstein College of Medicine, Bronx, NY, 2National Institutes of Health, Bethesda, MD
| | - Laufey Amundadottir
- 1Albert Einstein College of Medicine, Bronx, NY, 2National Institutes of Health, Bethesda, MD
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Planck T, Parikh H, Groop L, Hallengren B, Lantz M. Intraorbital deiodinase type 2 expression is downregulated in chronic phase of Graves' ophthalmopathy. Clin Endocrinol (Oxf) 2012; 77:486-7. [PMID: 22288557 DOI: 10.1111/j.1365-2265.2012.04350.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Taneera J, Lang S, Sharma A, Fadista J, Zhou Y, Ahlqvist E, Jonsson A, Lyssenko V, Vikman P, Hansson O, Parikh H, Korsgren O, Soni A, Krus U, Zhang E, Jing XJ, Esguerra JLS, Wollheim CB, Salehi A, Rosengren A, Renström E, Groop L. A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets. Cell Metab 2012; 16:122-34. [PMID: 22768844 DOI: 10.1016/j.cmet.2012.06.006] [Citation(s) in RCA: 271] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 02/05/2012] [Accepted: 06/18/2012] [Indexed: 12/13/2022]
Abstract
Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors. Using 48 genes located near T2D risk variants, we identified gene coexpression and protein-protein interaction networks that were strongly associated with islet insulin secretion and HbA(1c). We integrated our data to form a rank list of putative T2D genes, of which CHL1, LRFN2, RASGRP1, and PPM1K were validated in INS-1 cells to influence insulin secretion, whereas GPR120 affected apoptosis in islets. Expression variation of the top 20 genes explained 24% of the variance in HbA(1c) with no claim of the direction. The data present a global map of genes associated with islet dysfunction and demonstrate the value of systems genetics for the identification of genes potentially involved in T2D.
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Affiliation(s)
- Jalal Taneera
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital Malmö, Lund University, Malmö 20502, Sweden.
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Elgzyri T, Parikh H, Zhou Y, Dekker Nitert M, Rönn T, Segerström ÅB, Ling C, Franks PW, Wollmer P, Eriksson KF, Groop L, Hansson O. First-degree relatives of type 2 diabetic patients have reduced expression of genes involved in fatty acid metabolism in skeletal muscle. J Clin Endocrinol Metab 2012; 97:E1332-7. [PMID: 22547424 DOI: 10.1210/jc.2011-3037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
CONTEXT First-degree relatives of patients with type 2 diabetes (FH+) have been shown to have decreased energy expenditure and decreased expression of mitochondrial genes in skeletal muscle. In previous studies, it has been difficult to distinguish whether mitochondrial dysfunction and differential regulation of genes are primary (genetic) or due to reduced physical activity, obesity, or other correlated factors. OBJECTIVE The aim of this study was to investigate whether mitochondrial dysfunction is a primary defect or results from an altered metabolic state. DESIGN We compared gene expression in skeletal muscle from 24 male subjects with FH and 26 without FH matched for age, glucose tolerance, VO(2peak) (peak oxygen uptake), and body mass index using microarrays. Additionally, type fiber composition, mitochondrial DNA content, and citrate synthase activity were measured. The results were followed up in an additional cohort with measurements of in vivo metabolism. RESULTS FH+ vs. FH- subjects showed reduced expression of mitochondrial genes (P = 2.75 × 10(-6)), particularly genes involved in fatty acid metabolism (P = 4.08 × 10(-7)), despite similar mitochondrial DNA content. Strikingly, a 70% reduced expression of the monoamine oxidase A (MAOA) gene was found in FH+ vs. FH- individuals (P = 0.0009). Down-regulation of the genes involved in fat metabolism was associated with decreased in vivo fat oxidation and increased glucose oxidation examined in an additional cohort of elderly men. CONCLUSIONS These results suggest that genetically altered fatty acid metabolism predisposes to type 2 diabetes and propose a role for catecholamine-metabolizing enzymes like MAOA in the regulation of energy metabolism.
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Affiliation(s)
- T Elgzyri
- Department of Clinical Sciences, Clinical Research Center, Malmö University Hospital, Lund University, 20502 Malmö, Sweden
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Johansson LE, Danielsson APH, Parikh H, Klintenberg M, Norström F, Groop L, Ridderstråle M. Differential gene expression in adipose tissue from obese human subjects during weight loss and weight maintenance. Am J Clin Nutr 2012; 96:196-207. [PMID: 22648723 DOI: 10.3945/ajcn.111.020578] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Differential gene expression in adipose tissue during diet-induced weight loss followed by a weight stability period is poorly characterized. Markers of these processes may provide a deeper understanding of underlying mechanisms. OBJECTIVE We aimed to identify differentially expressed genes in human adipose tissue during weight loss and weight maintenance after weight loss. DESIGN RNA from subcutaneous abdominal adipose tissue from 9 obese subjects was analyzed by using a complementary DNA microarray at baseline after weight loss on a low-calorie diet and after weight maintenance. RESULTS Subjects lost 18.8 ± 1.8% of weight and maintained this loss during weight maintenance (1.1 ± 2.1%; range: -9.3 to 10.6%). Most differentially expressed genes exhibited a reciprocal regulation and returned to baseline after weight loss (2163 genes) and weight maintenance (3175 genes). CETP and ABCG1, both of which participate in the HDL-mediated reverse cholesterol transport (RCT), were among the most upregulated of the 750 genes that were differentially expressed after both processes. Several genes involved in inflammation were downregulated. The use of real-time polymerase chain reaction confirmed or partially confirmed the previously implicated genes TNMD and MMP9 (both downregulated), PNPLA3 (upregulated), and CIDEA and SCD (both reciprocally regulated). CONCLUSIONS The beneficial effects of weight loss should be investigated after long-term weight maintenance. The processes of weight loss and weight maintenance should be viewed as biologically distinct. CETP and ABCG1 may be important mediators of these effects through HDL-mediated RCT.
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Affiliation(s)
- Lovisa E Johansson
- Department of Clinical Sciences Malmö, Clinical Obesity, Lund University Diabetes Centre, Lund University, Malmö, Sweden
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Wang Z, Parikh H, Jia J, Myers T, Yeager M, Jacobs KB, Hutchinson A, Burdett L, Ghosh A, Thun MJ, Gapstur SM, Ryan Diver W, Virtamo J, Albanes D, Cancel-Tassin G, Valeri A, Cussenot O, Offit K, Giovannucci E, Ma J, Stampfer MJ, Michael Gaziano J, Hunter DJ, Dutra-Clarke A, Kirchhoff T, Alavanja M, Freeman LB, Koutros S, Hoover R, Berndt SI, Hayes RB, Agalliu I, Burk RD, Wacholder S, Thomas G, Amundadottir L. Y chromosome haplogroups and prostate cancer in populations of European and Ashkenazi Jewish ancestry. Hum Genet 2012; 131:1173-85. [PMID: 22271044 PMCID: PMC3374121 DOI: 10.1007/s00439-012-1139-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/04/2012] [Indexed: 12/15/2022]
Abstract
Genetic variation on the Y chromosome has not been convincingly implicated in prostate cancer risk. To comprehensively analyze the role of inherited Y chromosome variation in prostate cancer risk in individuals of European ancestry, we genotyped 34 binary Y chromosome markers in 3,995 prostate cancer cases and 3,815 control subjects drawn from four studies. In this set, we identified nominally significant association between a rare haplogroup, E1b1b1c, and prostate cancer in stage I (P = 0.012, OR = 0.51; 95% confidence interval 0.30–0.87). Population substructure of E1b1b1c carriers suggested Ashkenazi Jewish ancestry, prompting a replication phase in individuals of both European and Ashkenazi Jewish ancestry. The association was not significant for prostate cancer overall in studies of either Ashkenazi Jewish (1,686 cases and 1,597 control subjects) or European (686 cases and 734 control subjects) ancestry (Pmeta = 0.078), but a meta-analysis of stage I and II studies revealed a nominally significant association with prostate cancer risk (Pmeta = 0.010, OR = 0.77; 95% confidence interval 0.62–0.94). Comparing haplogroup frequencies between studies, we noted strong similarities between those conducted in the US and France, in which the majority of men carried R1 haplogroups, resembling Northwestern European populations. On the other hand, Finns had a remarkably different haplogroup distribution with a preponderance of N1c and I1 haplogroups. In summary, our results suggest that inherited Y chromosome variation plays a limited role in prostate cancer etiology in European populations but warrant follow-up in additional large and well characterized studies of multiple ethnic backgrounds.
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Affiliation(s)
- Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702 USA
| | - Hemang Parikh
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20877 USA
| | - Jinping Jia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20877 USA
| | - Timothy Myers
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702 USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20877 USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702 USA
| | - Kevin B. Jacobs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702 USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702 USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Core Genotyping Facility, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702 USA
| | - Arpita Ghosh
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Michael J. Thun
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303 USA
| | - Susan M. Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303 USA
| | - W. Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303 USA
| | - Jarmo Virtamo
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, 00300 Helsinki, Finland
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Geraldine Cancel-Tassin
- Centre de Recherche pour les Pathologies Prostatiques (CeRePP), Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, 75020 Paris, France
| | - Antoine Valeri
- Centre de Recherche pour les Pathologies Prostatiques (CeRePP), Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, 75020 Paris, France
| | - Olivier Cussenot
- Centre de Recherche pour les Pathologies Prostatiques (CeRePP), Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, 75020 Paris, France
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, Box 192, 1275 York Avenue, New York, NY 10065 USA
| | - Ed Giovannucci
- Channing Laboratory, Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Jing Ma
- Channing Laboratory, Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Meir J. Stampfer
- Channing Laboratory, Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - J. Michael Gaziano
- Channing Laboratory, Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - David J. Hunter
- Program in Molecular and Genetic Epidemiology, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115 USA
| | - Ana Dutra-Clarke
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, Box 192, 1275 York Avenue, New York, NY 10065 USA
| | - Tomas Kirchhoff
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, Box 192, 1275 York Avenue, New York, NY 10065 USA
- Division of Epidemiology, Department of Environmental Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Michael Alavanja
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Laura B. Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Richard B. Hayes
- Division of Epidemiology, Department of Environmental Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Ilir Agalliu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NewYork, NY 10461 USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NewYork, NY 10461 USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NewYork, NY 10461 USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NewYork, NY 10461 USA
- Department of Obstetrics, Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NewYork, NY 10461 USA
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Gilles Thomas
- Synergie-Lyon-Cancer, Universite Lyon 1, Centre Leon Berard, 69373 Lyon Cedex 08, France
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20877 USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, MD 20877 USA
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Yazdan-Shahmorad A, Lehmkuhle MJ, Gage GJ, Marzullo TC, Parikh H, Miriani RM, Kipke DR. Estimation of electrode location in a rat motor cortex by laminar analysis of electrophysiology and intracortical electrical stimulation. J Neural Eng 2011; 8:046018. [PMID: 21690656 DOI: 10.1088/1741-2560/8/4/046018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
While the development of microelectrode arrays has enabled access to disparate regions of a cortex for neurorehabilitation, neuroprosthetic and basic neuroscience research, accurate interpretation of the signals and manipulation of the cortical neurons depend upon the anatomical placement of the electrode arrays in a layered cortex. Toward this end, this report compares two in vivo methods for identifying the placement of electrodes in a linear array spaced 100 µm apart based on in situ laminar analysis of (1) ketamine-xylazine-induced field potential oscillations in a rat motor cortex and (2) an intracortical electrical stimulation-induced movement threshold. The first method is based on finding the polarity reversal in laminar oscillations which is reported to appear at the transition between layers IV and V in laminar 'high voltage spindles' of the rat cortical column. Analysis of histological images in our dataset indicates that polarity reversal is detected 150.1 ± 104.2 µm below the start of layer V. The second method compares the intracortical microstimulation currents that elicit a physical movement for anodic versus cathodic stimulation. It is based on the hypothesis that neural elements perpendicular to the electrode surface are preferentially excited by anodic stimulation while cathodic stimulation excites those with a direction component parallel to its surface. With this method, we expect to see a change in the stimulation currents that elicits a movement at the beginning of layer V when comparing anodic versus cathodic stimulation as the upper cortical layers contain neuronal structures that are primarily parallel to the cortical surface and lower layers contain structures that are primarily perpendicular. Using this method, there was a 78.7 ± 68 µm offset in the estimate of the depth of the start of layer V. The polarity reversal method estimates the beginning of layer V within ±90 µm with 95% confidence and the intracortical stimulation method estimates it within ±69.3 µm. We propose that these methods can be used to estimate the in situ location of laminar electrodes implanted in the rat motor cortex.
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Affiliation(s)
- A Yazdan-Shahmorad
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, USA.
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Planck T, Parikh H, Brorson H, Mårtensson T, Åsman P, Groop L, Hallengren B, Lantz M. Gene expression in Graves' ophthalmopathy and arm lymphedema: similarities and differences. Thyroid 2011; 21:663-74. [PMID: 21510802 DOI: 10.1089/thy.2010.0217] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Graves' ophthalmopathy (GO) and lymphedema share some pathogenetic mechanisms, such as edema, inflammation, and adipogenesis. The aim of this study was to examine similarities and differences between chronic GO and chronic lymphedema. METHODS Intraorbital adipose tissue was collected from patients with active (n = 10) or chronic GO (n = 10) and thyroid-healthy controls (n = 10). Arm subcutaneous adipose tissue was obtained from patients with chronic arm lymphedema (n = 10), where the unaffected arm served as a control. Gene expression was studied using microarray and real-time polymerase chain reaction. RESULTS The following genes were significantly upregulated (p < 0.05) in lymphedema but not in GO and have functions in wound healing, fibrosis, fat metabolism, inflammation, differentiation, development, adhesion, and the cytoskeleton: ATP-binding cassette, sub-family G (WHITE), member 1 (ABCG1), actin, alpha 2, smooth muscle, aorta (ACTA2), secreted frizzled-related protein 2 (SFRP2), tenascin C (TNC), pentraxin-related gene, rapidly induced by IL-1 beta (PTX3), and carboxypeptidase X (M14 family), member 1 (CPMX1). In chronic GO, but not in lymphedema, adipocyte-related immediate early genes known to be overexpressed in patients with active GO were upregulated but at a lower level than previously shown for the active phase. Genes of the Wnt pathway, such as secreted frizzled-related protein 1, 2, and 3, were up- and downregulated in both chronic GO and lymphedema. Parathyroid hormone-like hormone (PTHLH) was downregulated (p = 0.01) and apolipoprotein L domain containing 1 (APOLD1) was upregulated (p = 0.05) in both active and chronic GO. CONCLUSIONS There are more differences than similarities between chronic ophthalmopathy and chronic lymphedema, but both conditions exhibit less inflammation and adipogenesis compared to the active phases. In lymphedema, fibrosis dominates. PTHLH, which can inhibit adipogenesis, is downregulated both in active and chronic ophthalmopathy, indicating the possibility of an increased risk of adipogenesis.
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Affiliation(s)
- Tereza Planck
- Department of Endocrinology, Skåne University Hospital, CRC, Malmö, Sweden.
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Olsson AH, Rönn T, Ladenvall C, Parikh H, Isomaa B, Groop L, Ling C. Two common genetic variants near nuclear-encoded OXPHOS genes are associated with insulin secretion in vivo. Eur J Endocrinol 2011; 164:765-71. [PMID: 21325017 PMCID: PMC3080761 DOI: 10.1530/eje-10-0995] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
CONTEXT Mitochondrial ATP production is important in the regulation of glucose-stimulated insulin secretion. Genetic factors may modulate the capacity of the β-cells to secrete insulin and thereby contribute to the risk of type 2 diabetes. OBJECTIVE The aim of this study was to identify genetic loci in or adjacent to nuclear-encoded genes of the oxidative phosphorylation (OXPHOS) pathway that are associated with insulin secretion in vivo. DESIGN AND METHODS To find polymorphisms associated with glucose-stimulated insulin secretion, data from a genome-wide association study (GWAS) of 1467 non-diabetic individuals, including the Diabetes Genetic Initiative (DGI), was examined. A total of 413 single nucleotide polymorphisms with a minor allele frequency ≥0.05 located in or adjacent to 76 OXPHOS genes were included in the DGI GWAS. A more extensive population-based study of 4323 non-diabetics, the PPP-Botnia, was used as a replication cohort. Insulinogenic index during an oral glucose tolerance test was used as a surrogate marker of glucose-stimulated insulin secretion. Multivariate linear regression analyses were used to test genotype-phenotype associations. RESULTS Two common variants were identified in the DGI, where the major C-allele of rs606164, adjacent to NADH dehydrogenase (ubiquinone) 1 subunit C2 (NDUFC2), and the minor G-allele of rs1323070, adjacent to cytochrome c oxidase subunit VIIa polypeptide 2 (COX7A2), showed nominal associations with decreased glucose-stimulated insulin secretion (P=0.0009, respective P=0.003). These associations were replicated in PPP-Botnia (P=0.002 and P=0.05). CONCLUSION Our study shows that genetic variation near genes involved in OXPHOS may influence glucose-stimulated insulin secretion in vivo.
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Affiliation(s)
- Anders H Olsson
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Tina Rönn
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Claes Ladenvall
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Hemang Parikh
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, National Institutes of HealthBethesda, MarylandUSA
| | - Bo Isomaa
- Folkhälsan Research CenterHelsinkiFinland
- Department of Social Services and Health CareJakobstadFinland
| | - Leif Groop
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
| | - Charlotte Ling
- Department of Clinical SciencesLund University Diabetes Center, CRC, Scania University Hospital, Lund UniversityMalmöSweden
- (Correspondence should be addressed to C Ling; )
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Jia J, Frank N, Parikh H, Flandez M, Collins I, Hussain P, Lo K, Petersen GM, Real F, Ammundadottir L. Abstract 4965: Genome analysis of a pancreatic cancer susceptibility locus in the NR5A2 gene on chromosome 1q32.1. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic cancer is highly lethal with an estimated 5-year relative survival rate of less than 5%. A genome wide association study (GWAS) of pancreatic cancer (PanScan) conducted within the NCI Cohort Consortium and the Pancreatic Cancer Case-Control Consortium (PANC4) recently identified four common susceptibility loci for pancreatic cancer on chromosomes 1q32.1, 5p15.33, 9q34.2 and 13q22.1. To investigate how these germline variants influence pancreatic cancer risk, we are employing both genome wide and targeted approaches. For the former, we are characterizing the epigenome and transcriptome of pancreatic cell lines and tissue samples for genomic annotation and prioritization of methods to use in targeted approaches with the aim of directly linking pancreatic cancer risk variants to molecular phenotypes and mechanisms that underlie the association signals.
As an example of our approach we will present results in a pancreatic cancer susceptibility locus on chromosome 1q32.2 marked by SNP (single nucleotide polymorphism) rs3790844. This SNP is located in the first intron of the NR5A2 gene that encodes a nuclear receptor of the Ftz-F1 family known to be involved in pancreatic development, cholesterol and bile acid homeostasis, steroidogenesis and cell proliferation. In ChIP-sequencing and MeDIP-chip experiments, we observed repressive histone modification marks (H3K27me3) and regions of DNA methylation in the NR5A2 gene locus in pancreatic cell lines whereas only a few weak positive histone modification marks were observed (H3K4me1 and H3K4me3). This pattern of epigenetic marks correlates well with low expression of NR5A2 in the same cell lines. Expression of the NR5A2 gene at the RNA level is high in normal pancreatic tissue samples as compared to stage I-III pancreatic adenocarcinoma, most islet cell and neuroendocrine tumors. Using immunohistochemistry, nuclear NR5A2 was detected in normal acinar cells and – at lower levels – in normal ductal cells. The protein was also expressed in low and high grade PanINs and in the majority of PDAC analyzed. Our analysis of the tissue specific expression of NR5A2 shows that it is mainly expressed in normal pancreas, colon, small intestine, liver and breast but detected at low levels or not at all in most other tissue types and cancer cell lines. Furthermore we have identified a novel NR5A2 transcript by rapid amplification of cDNA ends (RACE) and mapped a promoter in front of this transcript in the genomic region corresponding to first intron of the two annotated Refseq transcripts.
Establishing a comprehensive catalog of epigenetic patterns coupled with targeted analysis to correlate risk variants to molecular phenotypes could provide functional plausibility for known pancreatic cancer association signals discovered by GWAS findings.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4965. doi:10.1158/1538-7445.AM2011-4965
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Affiliation(s)
- Jinping Jia
- 1Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD
| | - Naomi Frank
- 1Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD
| | - Hemang Parikh
- 1Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD
| | - Marta Flandez
- 2Molecular Pathyology Programme Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Irene Collins
- 1Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD
| | - Perwez Hussain
- 3Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD
| | - Ken Lo
- 4Roche Nimblegen, Madison, WI
| | | | - Francisco Real
- 2Molecular Pathyology Programme Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Laufey Ammundadottir
- 1Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD
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Koeck T, Olsson AH, Nitert MD, Sharoyko VV, Ladenvall C, Kotova O, Reiling E, Rönn T, Parikh H, Taneera J, Eriksson JG, Metodiev MD, Larsson NG, Balhuizen A, Luthman H, Stančáková A, Kuusisto J, Laakso M, Poulsen P, Vaag A, Groop L, Lyssenko V, Mulder H, Ling C. A common variant in TFB1M is associated with reduced insulin secretion and increased future risk of type 2 diabetes. Cell Metab 2011; 13:80-91. [PMID: 21195351 DOI: 10.1016/j.cmet.2010.12.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 06/12/2010] [Accepted: 11/10/2010] [Indexed: 01/07/2023]
Abstract
Type 2 diabetes (T2D) evolves when insulin secretion fails. Insulin release from the pancreatic β cell is controlled by mitochondrial metabolism, which translates fluctuations in blood glucose into metabolic coupling signals. We identified a common variant (rs950994) in the human transcription factor B1 mitochondrial (TFB1M) gene associated with reduced insulin secretion, elevated postprandial glucose levels, and future risk of T2D. Because islet TFB1M mRNA levels were lower in carriers of the risk allele and correlated with insulin secretion, we examined mice heterozygous for Tfb1m deficiency. These mice displayed lower expression of TFB1M in islets and impaired mitochondrial function and released less insulin in response to glucose in vivo and in vitro. Reducing TFB1M mRNA and protein in clonal β cells by RNA interference impaired complexes of the mitochondrial oxidative phosphorylation system. Consequently, nutrient-stimulated ATP generation was reduced, leading to perturbed insulin secretion. We conclude that a deficiency in TFB1M and impaired mitochondrial function contribute to the pathogenesis of T2D.
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Affiliation(s)
- Thomas Koeck
- Department of Clinical Sciences, Lund University Diabetes Centre, CRC, Scania University Hospital, 205 02 Malmö, Sweden
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Lo KC, Holster H, Jia J, Parikh H, Collins I, Brazas R, Selzer R, Amundadottir L. Abstract 164: High-throughput epigenetic analysis of susceptibility loci identified by GWAS in pancreatic cancer. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic cancer is a highly lethal cancer with few well established risk factors. A genome wide association study (GWAS) of pancreatic cancer (PanScan) is being conducted within the framework of the NCI-sponsored Cohort Consortium and the Pancreatic Cancer Case-Control Consortium (PANC4). Susceptibility loci discovered to date in PanScan are non-coding variants that lie in intronic or intergenic regions, suggesting that the underlying signals may function through regulatory mechanisms that influence gene expression or splicing. Alternatively, these may lie in unannotated transcripts and directly affect their function.
Epigenetic mechanisms, such as DNA methylation, can affect the regulation of gene expression and plays a critical role in the development of many human diseases including cancer. Powerful methods exist to analyze DNA methylation patterns in higher eukaryotes including methylated DNA immunoprecipitation (MeDIP), an affinity based approach to enrich methylated DNA regions from genomic DNA, which can be combined with microarrays to profile genomic DNA methylation patterns. We created a new semi-custom MeDIP-optimized array design based on our Human DNA Methylation 3×720K CpG Island Plus RefSeq Promoter array by tiling additional regions associated with pancreatic cancer that were identified in the PanScan study. To complement DNA methylation data a genome-wide transcriptome analysis was performed with RNA-sequencing (RNA-seq). Here we describe a comprehensive genome wide analysis of 8 pancreatic cancer cell lines to examine methylation patterns of Refseq promoters and annotated CpG islands as well as transcribed sequences.
One of the susceptibility loci from PanScan is in the vicinity of the ABO gene on Chr9q34 where four SNPs (rs505922, rs495828, rs657152 and rs630014) are associated with a significantly increased risk of pancreatic cancer. As a pilot study, DNA methylation patterns and expressed sequences in this locus were investigated in cell lines derived from pancreatic tumors and normal pancreatic tissues. Our genome wide DNA methylation and RNA-seq analysis aims at establishing a comprehensive catalog of epigenetic patterns in pancreatic cell lines that could provide plausibility for the association signal in the ABO gene and other GWAS regions and thereby, initiate the characterization of the molecular phenotype of the susceptibility alleles for pancreatic cancer risk.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 164.
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Parikh H, Lyssenko V, Groop LC. Prioritizing genes for follow-up from genome wide association studies using information on gene expression in tissues relevant for type 2 diabetes mellitus. BMC Med Genomics 2009; 2:72. [PMID: 20043853 PMCID: PMC2815699 DOI: 10.1186/1755-8794-2-72] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 12/31/2009] [Indexed: 02/08/2023] Open
Abstract
Background Genome-wide association studies (GWAS) have emerged as a powerful approach for identifying susceptibility loci associated with polygenetic diseases such as type 2 diabetes mellitus (T2DM). However, it is still a daunting task to prioritize single nucleotide polymorphisms (SNPs) from GWAS for further replication in different population. Several recent studies have shown that genetic variation often affects gene-expression at proximal (cis) as well as distal (trans) genomic locations by different mechanisms such as altering rate of transcription or splicing or transcript stability. Methods To prioritize SNPs from GWAS, we combined results from two GWAS related to T2DM, the Diabetes Genetics Initiative (DGI) and the Wellcome Trust Case Control Consortium (WTCCC), with genome-wide expression data from pancreas, adipose tissue, liver and skeletal muscle of individuals with or without T2DM or animal models thereof to identify T2DM susceptibility loci. Results We identified 1,170 SNPs associated with T2DM with P < 0.05 in both GWAS and 243 genes that were located in the vicinity of these SNPs. Out of these 243 genes, we identified 115 differentially expressed in publicly available gene expression profiling data. Notably five of them, IGF2BP2, KCNJ11, NOTCH2, TCF7L2 and TSPAN8, have subsequently been shown to be associated with T2DM in different populations. To provide further validation of our approach, we reversed the approach and started with 26 known SNPs associated with T2DM and related traits. We could show that 12 (57%) (HHEX, HNF1B, IGF2BP2, IRS1, KCNJ11, KCNQ1, NOTCH2, PPARG, TCF7L2, THADA, TSPAN8 and WFS1) out of 21 genes located in vicinity of these SNPs were showing aberrant expression in T2DM from the gene expression profiling studies. Conclusions Utilizing of gene expression profiling data from different tissues of individuals with or without T2DM or animal models thereof is a powerful tool for prioritizing SNPs from WGAS for further replication studies.
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Affiliation(s)
- Hemang Parikh
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden.
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Parikh H, Nilsson E, Ling C, Poulsen P, Almgren P, Nittby H, Eriksson KF, Vaag A, Groop LC. Molecular correlates for maximal oxygen uptake and type 1 fibers. Am J Physiol Endocrinol Metab 2008; 294:E1152-9. [PMID: 18445752 DOI: 10.1152/ajpendo.90255.2008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Maximal oxygen uptake (Vo(2max)) and the amount of type 1 fibers are interrelated, but the underlying unifying molecular mechanisms are poorly understood. To explore these mechanisms, we related gene expression profiles in skeletal muscle biopsies of 43 age-matched men from published datasets with Vo(2max) and the amount of type 1 fibers and replicated some of the findings in muscle biopsies from 154 young and elderly individuals using real-time PCR. We identified 66 probe sets (genes or expressed sequence tags) positively and 83 probe sets inversely correlated with Vo(2max) and 171 probe sets positively and 217 probe sets inversely correlated with percentage of type 1 fibers in human skeletal muscle. Genes involved in oxidative phosphorylation (OXPHOS) showed high expression in individuals with high Vo(2max), whereas the opposite was not the case in individuals with low Vo(2max). Instead, genes such as AHNAK and BCL6 were associated with low Vo(2max). Also, expression of the OXPHOS genes NDUFB5 and ATP5C1 increased with exercise training and decreased with aging. In contrast, expression of AHNAK in skeletal muscle decreased with exercise training and increased with aging. Eleven genes (NDUFB4, COX5A, UQCRB, ATP5C1, ATP5G3, ETHE1, FABP3, ISCA1, MYST4, C9orf3, and PKIA) were positively correlated with both Vo(2max) and the percentage of type 1 fibers. Vo(2max) closely reflects expression of OXPHOS genes, particularly that of NDUFB5 and ATP5C1, in skeletal muscle, suggesting good muscle fitness. In contrast, a high expression of AHNAK was associated with a low Vo(2max) and poor muscle fitness.
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Affiliation(s)
- Hemang Parikh
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden.
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Hirte HW, Raghunadharao D, Baetz T, Hotte S, Rajappa S, Iacobucci A, Sharma S, Parikh H, Kulkarni S, Patil S, Gaston S. A phase 1 study of the selective cyclin dependent kinase inhibitor P276–00 in patients with advanced refractory neoplasms. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.14117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
14117 Background: In human cancers, genetic and epigenetic events result in over-expression of cyclins or absence or diminished levels of Cdk inhibitors, providing tumor cells with selective growth advantage. This has prompted the development of pharmacological Cdk inhibitors that could potentially produce anti-tumor effect. P276–00 is a selective Cdk4-D1 and Cdk1-B inhibitor. This study was designed to determine the maximum tolerated dose (MTD), toxicity profile, pharmacokinetics, and antitumour activity of P276–00 given intravenously to patients with advanced refractory solid tumours. Methods: P276–00 was administered in escalating doses to cohorts of eligible patients (pts), starting with a dose of 9 mg/m2 as a 30 minute iv infusion day 1 to 5, and day 8 to 12, q 3 weekly. To date 22 pts have been entered on the study (cohort 1 - 4 pts at 9 mg/m2, cohort 2 - 4 pts at 12.6 mg/m2, cohort 3 - 6 pts at 17.6 mg/m2, cohort 4 - 8 pts at 24.6 mg/m2) with PS 0–2, and mean age of 56 years. Pharmacokinetic profiles were obtained on cycle 1 days 1 and 5. Skin biopsies were obtained immediately prior to starting study treatment and on day 21 of cycle 2 and will be analyzed for Ki67, cleaved caspase 3, phospho-Rb, cyclin D1 and cdk4, and microarray. Results: To date dose limiting toxicity has occurred in one pt. Grade 3 fatigue occurred in 1 pt at 17.6 mg/m2. The most common drug-related adverse events, which were all grade 1 or 2, were fatigue, nausea, hypotension, sweating, and dry mouth. No Grade 3 biochemical toxicities have been reported so far. There have been no responses noted to date. 4 pts have stable disease after 2 cycles. Pharmacokinetic results: The Cmax, t1/2, and AUC0–8 on day 1 were as follows: 9 mg/m2- 315 ng/mL, 6.6 hr, 883 ng.h/mL; 12.6 mg/m2- 402 ng/mL, 5.5 hr, 848 ng.h/mL; 17.6 mg/m2- 589 ng/mL, 5.3 hr, 1289 ng.h/mL; 24.6 mg/m2- 621 ng/mL, 5.6 hr, 1286 ng.h/mL. Conclusions: P276–00 is well tolerated, but grade 3 fatigue has been noted in 1 pt at 17.6 mg/m2 dose level. We have observed confirmed stable disease in one patient. PK results indicate that at 9 mg/m2,12.6 mg/m2, 17.6 mg/m2 and 24.6 mg/m2 we are able to cross the cdk4 enzyme IC50 approximately 10, 13, 19 and 20 times and cross the anti-proliferative IC50 1.1, 1.4, 2.1 and 2.2 times respectively. Accrual continues at the 34.4 mg/m2 dose level. No significant financial relationships to disclose.
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Affiliation(s)
- H. W. Hirte
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - D. Raghunadharao
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - T. Baetz
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Hotte
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Rajappa
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - A. Iacobucci
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Sharma
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - H. Parikh
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Kulkarni
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Patil
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
| | - S. Gaston
- Juravinski Cancer Centre, Hamilton, ON, Canada; Nizam’s Institute of Medical Science, Hyderabad, India; Cancer Centre of Southeastern Ontario, Kingston, ON, Canada; Nicholas Piramal India Ltd., Mumbai, India; Endpoint Research Ltd, Mississauga, ON, Canada
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Vondrichova T, de Capretz A, Parikh H, Frenander C, Asman P, Aberg M, Groop L, Hallengren B, Lantz M. COX-2 and SCD, markers of inflammation and adipogenesis, are related to disease activity in Graves' ophthalmopathy. Thyroid 2007; 17:511-7. [PMID: 17614770 DOI: 10.1089/thy.2007.0028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
CONTEXT Inflammation and adipogenesis are two parallel processes with increased activity in severe Graves' ophthalmopathy. OBJECTIVE The aim of this work was to define target genes for therapeutic intervention in adipogenesis and inflammation in Graves' ophthalmopathy. DESIGN Orbital tissue was obtained from patients with ophthalmopathy in acute or chronic phase undergoing orbital surgery to study gene expression followed by the study of potential intervention mechanisms in preadipocytes. SETTING Clinic of Endocrinology, University Hospital, Malmö, Sweden. PARTICIPANTS Patients in acute severe or in chronic phase of ophthalmopathy. INTERVENTIONS Lateral orbital decompression in acute phase and restorative surgery in chronic phase. In vitro treatment of preadipocytes with rosiglitazone and diclofenac. MAIN OUTCOME MEASURE Gene expression in intraorbital tissue or preadipocytes and differentiation of preadipocytes. RESULTS A marker of adipose tissue, stearoyl-coenzyme A desaturase (SCD), and the proinflammatory gene, cyclooxygenase-2 (COX-2), were overexpressed in patients in active phase compared to the chronic phase of ophthalmopathy. In growth-arrested preadipocytes stimulated with rosiglitazone, COX-2 expression increased temporarily within 1 hour and decreased to undetectable levels after 48 hours. In contrast, SCD and peroxisome proliferator-activated receptor-gamma (PPAR-gamma) expression increased continuously from day 2 to day 7 during adipogenesis. Diclofenac, an inhibitor of cyclooxygenases with antagonistic effects on PPAR-gamma, reduced the number of mature adipocytes by approximately 50%. CONCLUSION We conclude that inflammation and adipogenesis decrease with a decrease in activity of ophthalmopathy and that the nonsteroidal antiinflammatory drug diclofenac inhibits adipogenesis. This may represent a putative future treatment of endocrine ophthalmopathy.
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Affiliation(s)
- Tereza Vondrichova
- Division of Diabetes and Endocrinology, Department of Clinical Sciences, Lund University, Malmö University Hospital, Malmö, Sweden
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Parikh H, Carlsson E, Chutkow WA, Johansson LE, Storgaard H, Poulsen P, Saxena R, Ladd C, Schulze PC, Mazzini MJ, Jensen CB, Krook A, Björnholm M, Tornqvist H, Zierath JR, Ridderstråle M, Altshuler D, Lee RT, Vaag A, Groop LC, Mootha VK. TXNIP regulates peripheral glucose metabolism in humans. PLoS Med 2007; 4:e158. [PMID: 17472435 PMCID: PMC1858708 DOI: 10.1371/journal.pmed.0040158] [Citation(s) in RCA: 367] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 03/01/2007] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is characterized by defects in insulin secretion and action. Impaired glucose uptake in skeletal muscle is believed to be one of the earliest features in the natural history of T2DM, although underlying mechanisms remain obscure. METHODS AND FINDINGS We combined human insulin/glucose clamp physiological studies with genome-wide expression profiling to identify thioredoxin interacting protein (TXNIP) as a gene whose expression is powerfully suppressed by insulin yet stimulated by glucose. In healthy individuals, its expression was inversely correlated to total body measures of glucose uptake. Forced expression of TXNIP in cultured adipocytes significantly reduced glucose uptake, while silencing with RNA interference in adipocytes and in skeletal muscle enhanced glucose uptake, confirming that the gene product is also a regulator of glucose uptake. TXNIP expression is consistently elevated in the muscle of prediabetics and diabetics, although in a panel of 4,450 Scandinavian individuals, we found no evidence for association between common genetic variation in the TXNIP gene and T2DM. CONCLUSIONS TXNIP regulates both insulin-dependent and insulin-independent pathways of glucose uptake in human skeletal muscle. Combined with recent studies that have implicated TXNIP in pancreatic beta-cell glucose toxicity, our data suggest that TXNIP might play a key role in defective glucose homeostasis preceding overt T2DM.
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Affiliation(s)
- Hemang Parikh
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden
| | - Emma Carlsson
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden
- Steno Diabetes Center, Gentofte, Denmark
| | - William A Chutkow
- Cardiovascular Division, Brigham and Women's Hospital, Cambridge, Massachusetts, United States of America
| | - Lovisa E Johansson
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden
| | | | | | - Richa Saxena
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christine Ladd
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - P. Christian Schulze
- Cardiovascular Division, Brigham and Women's Hospital, Cambridge, Massachusetts, United States of America
| | - Michael J Mazzini
- Cardiovascular Division, Brigham and Women's Hospital, Cambridge, Massachusetts, United States of America
| | | | - Anna Krook
- Department of Physiology and Pharmacology, Section Integrative Physiology, Karolinska Institute, Stockholm, Sweden
| | - Marie Björnholm
- Department of Molecular Medicine and Surgical Sciences, Section Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | | | - Juleen R Zierath
- Department of Molecular Medicine and Surgical Sciences, Section Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Ridderstråle
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden
| | - David Altshuler
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard T Lee
- Cardiovascular Division, Brigham and Women's Hospital, Cambridge, Massachusetts, United States of America
| | - Allan Vaag
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden
- Steno Diabetes Center, Gentofte, Denmark
| | - Leif C Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Malmö, Malmö, Sweden
- Program in Molecular Medicine, Helsinki University, Helsinki, Finland
- * To whom correspondence should be addressed. E-mail: (LCG); (VKM)
| | - Vamsi K Mootha
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail: (LCG); (VKM)
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Shaat N, Lernmark A, Karlsson E, Ivarsson S, Parikh H, Berntorp K, Groop L. A variant in the transcription factor 7-like 2 (TCF7L2) gene is associated with an increased risk of gestational diabetes mellitus. Diabetologia 2007; 50:972-9. [PMID: 17342473 DOI: 10.1007/s00125-007-0623-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Accepted: 01/21/2007] [Indexed: 12/18/2022]
Abstract
AIMS/HYPOTHESIS Genetic and epidemiological studies suggest an association between gestational diabetes mellitus and type 2 diabetes. Both are polygenic multifactorial disorders characterised by beta cell dysfunction and insulin resistance. Our aim was to investigate whether common genetic variants that have previously been associated with type 2 diabetes or related phenotypes would also confer risk for gestational diabetes mellitus. MATERIALS AND METHODS In 1,881 unrelated pregnant Scandinavian women (649 women with gestational diabetes mellitus, 1,232 non-diabetic control subjects) we genotyped the transcription factor 7-like 2 (TCF7L2 rs7903146), adiponectin (ADIPOQ +276G > T), peroxisome-proliferator activated receptor, gamma 2 (PPARG Pro12Ala), PPARG-coactivator, 1 alpha (PPARGC1A Gly482Ser), forkhead box C2 (FOXC2 -512C > T) and beta3-adrenergic receptor (ADRB3 Trp64Arg) polymorphisms using TaqMan allelic discrimination assay or RFLP. RESULTS The CC, CT and TT genotype frequencies of the TCF7L2 rs7903146 variant differed significantly between women with gestational diabetes mellitus and control women (46.3, 43.6 and 10.1% vs 58.5, 35.3 and 6.2%, p = 3.7 x 10(-6), corrected p value [Pc] for multiple testing Pc = 2.2 x 10(-5)). The T-allele was associated with an increased risk of gestational diabetes mellitus (odds ratio 1.49 [95% CI 1.28-1.75], p = 4.9 x 10(-7) [Pc = 2.8 x 10(-6)]). Compared with wild-type CC-genotype carriers, heterozygous (CT-genotype) and homozygous (TT-genotype) carriers had a 1.6-fold (95% CI 1.26-1.93, p = 3.7 x 10(-5) [Pc = 0.0002]) and a 2.1-fold (95% CI 1.41-2.99, p = 0.0001 [Pc = 0.0008]) increased risk of gestational diabetes mellitus, respectively. The other polymorphisms studied were not significantly associated with gestational diabetes mellitus (ADIPOQ +276G > T: 1.17 [1.01-1.36], p = 0.039 [Pc = 0.23]; PPARG Pro12Ala: 1.06 [0.87-1.29], p = 0.53; PPARGC1A Gly482Ser: 0.96 [0.83-1.10], p = 0.54; FOXC2 -512C > T: 1.01 [0.87-1.16], p = 0.94; and ADRB3 Trp64Arg: 1.22 [0.95-1.56], p = 0.12). CONCLUSIONS/INTERPRETATION The TCF7L2 rs7903146 variant is associated with an increased risk of gestational diabetes mellitus in Scandinavian women.
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Affiliation(s)
- N Shaat
- Department of Clinical Sciences/Diabetes & Endocrinology, Malmö University Hospital, Lund University, Malmö, Sweden.
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