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Argmann C, Hou R, Ungaro RC, Irizar H, Al-Taie Z, Huang R, Kosoy R, Venkat S, Song WM, Di'Narzo AF, Losic B, Hao K, Peters L, Comella PH, Wei G, Atreja A, Mahajan M, Iuga A, Desai PT, Branigan P, Stojmirovic A, Perrigoue J, Brodmerkel C, Curran M, Friedman JR, Hart A, Lamousé-Smith E, Wehkamp J, Mehandru S, Schadt EE, Sands BE, Dubinsky MC, Colombel JF, Kasarskis A, Suárez-Fariñas M. Biopsy and blood-based molecular biomarker of inflammation in IBD. Gut 2022:gutjnl-2021-326451. [PMID: 36109152 PMCID: PMC10014487 DOI: 10.1136/gutjnl-2021-326451] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Received: 10/29/2021] [Accepted: 08/22/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE IBD therapies and treatments are evolving to deeper levels of remission. Molecular measures of disease may augment current endpoints including the potential for less invasive assessments. DESIGN Transcriptome analysis on 712 endoscopically defined inflamed (Inf) and 1778 non-inflamed (Non-Inf) intestinal biopsies (n=498 Crohn's disease, n=421 UC and 243 controls) in the Mount Sinai Crohn's and Colitis Registry were used to identify genes differentially expressed between Inf and Non-Inf biopsies and to generate a molecular inflammation score (bMIS) via gene set variance analysis. A circulating MIS (cirMIS) score, reflecting intestinal molecular inflammation, was generated using blood transcriptome data. bMIS/cirMIS was validated as indicators of intestinal inflammation in four independent IBD cohorts. RESULTS bMIS/cirMIS was strongly associated with clinical, endoscopic and histological disease activity indices. Patients with the same histologic score of inflammation had variable bMIS scores, indicating that bMIS describes a deeper range of inflammation. In available clinical trial data sets, both scores were responsive to IBD treatment. Despite similar baseline endoscopic and histologic activity, UC patients with lower baseline bMIS levels were more likely treatment responders compared with those with higher levels. Finally, among patients with UC in endoscopic and histologic remission, those with lower bMIS levels were less likely to have a disease flare over time. CONCLUSION Transcriptionally based scores provide an alternative objective and deeper quantification of intestinal inflammation, which could augment current clinical assessments used for disease monitoring and have potential for predicting therapeutic response and patients at higher risk of disease flares.
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Affiliation(s)
- Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan C Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zainab Al-Taie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruiqi Huang
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Antonio F Di'Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Phillip H Comella
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gabrielle Wei
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ashish Atreja
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Alina Iuga
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | - Mark Curran
- Janssen R&D, Spring House, Pennsylvania, USA
| | | | - Amy Hart
- Janssen R&D, Spring House, Pennsylvania, USA
| | | | - Jan Wehkamp
- Janssen R&D, Spring House, Pennsylvania, USA
| | - Saurabh Mehandru
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marla C Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA .,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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2
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Schaniel C, Dhanan P, Hu B, Xiong Y, Raghunandan T, Gonzalez DM, Dariolli R, D'Souza SL, Yadaw AS, Hansen J, Jayaraman G, Mathew B, Machado M, Berger SI, Tripodig J, Najfeld V, Garg J, Miller M, Surlyn CS, Michelis KC, Tangirala NC, Weerahandi H, Thomas DC, Beaumont KG, Sebra R, Mahajan M, Schadt E, Vidovic D, Schürer SC, Goldfarb J, Azeloglu EU, Birtwistle MR, Sobie EA, Kovacic JC, Dubois NC, Iyengar R. A library of induced pluripotent stem cells from clinically well-characterized, diverse healthy human individuals. Stem Cell Reports 2021; 16:3036-3049. [PMID: 34739849 PMCID: PMC8693622 DOI: 10.1016/j.stemcr.2021.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/14/2022] Open
Abstract
A library of well-characterized human induced pluripotent stem cell (hiPSC) lines from clinically healthy human subjects could serve as a useful resource of normal controls for in vitro human development, disease modeling, genotype-phenotype association studies, and drug response evaluation. We report generation and extensive characterization of a gender-balanced, racially/ethnically diverse library of hiPSC lines from 40 clinically healthy human individuals who range in age from 22 to 61 years. The hiPSCs match the karyotype and short tandem repeat identities of their parental fibroblasts, and have a transcription profile characteristic of pluripotent stem cells. We provide whole-genome sequencing data for one hiPSC clone from each individual, genomic ancestry determination, and analysis of mendelian disease genes and risks. We document similar transcriptomic profiles, single-cell RNA-sequencing-derived cell clusters, and physiology of cardiomyocytes differentiated from multiple independent hiPSC lines. This extensive characterization makes this hiPSC library a valuable resource for many studies on human biology. A library of induced pluripotent stem cells from 40 healthy human subjects Racially/ethnically diverse subjects of clinically well-characterized health Whole-genome sequencing identifies variants of mild common phenotypes or incomplete penetrance Similar physiology of cardiomyocytes from independent hiPSC clones and individuals
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Affiliation(s)
- Christoph Schaniel
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Priyanka Dhanan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Bin Hu
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuguang Xiong
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Teeya Raghunandan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David M Gonzalez
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael Dariolli
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sunita L D'Souza
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; St. Jude's Children's Research Hospital, Memphis, TN, USA
| | - Arjun S Yadaw
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jens Hansen
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gomathi Jayaraman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Seth I Berger
- Center for Genetic Medicine Research & Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Joseph Tripodig
- Sema4, Stamford, CT, USA; Department of Pathology, Tumor Cytogenomics Laboratory, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vesna Najfeld
- Department of Pathology, Tumor Cytogenomics Laboratory, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jalaj Garg
- Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, and The Mount Sinai Hospital, New York, NY, USA; Division of Cardiology, Cardiac Arrhythmia Service, Loma Linda University Health, Loma Linda, CA, USA
| | - Marc Miller
- Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, and The Mount Sinai Hospital, New York, NY, USA
| | - Colleen S Surlyn
- Department of Medicine, Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, The Mount Sinai Hospital, New York, NY, USA; Southeast Health Center, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Katherine C Michelis
- Department of Medicine, Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, The Mount Sinai Hospital, New York, NY, USA; Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern, Dallas, TX, USA
| | - Neelima C Tangirala
- Department of Medicine, Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, The Mount Sinai Hospital, New York, NY, USA
| | - Himali Weerahandi
- Department of Medicine, Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, The Mount Sinai Hospital, New York, NY, USA; Department of Medicine, Division of General Internal Medicine and Clinical Innovation, NYU Grossman School of Medicine, New York, NY, USA
| | - David C Thomas
- Department of Medicine, Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, The Mount Sinai Hospital, New York, NY, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Milind Mahajan
- St. Jude's Children's Research Hospital, Memphis, TN, USA
| | - Eric Schadt
- St. Jude's Children's Research Hospital, Memphis, TN, USA
| | - Dusica Vidovic
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL, USA
| | - Stephan C Schürer
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL, USA
| | - Joseph Goldfarb
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evren U Azeloglu
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marc R Birtwistle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Eric A Sobie
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason C Kovacic
- Center for Genetic Medicine Research & Rare Disease Institute, Children's National Hospital, Washington, DC, USA; Department of Pathology, Tumor Cytogenomics Laboratory, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Nicole C Dubois
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, MA, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Ravi Iyengar
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Crouchet E, Bandiera S, Fujiwara N, Li S, El Saghire H, Fernández-Vaquero M, Riedl T, Sun X, Hirschfield H, Jühling F, Zhu S, Roehlen N, Ponsolles C, Heydmann L, Saviano A, Qian T, Venkatesh A, Lupberger J, Verrier ER, Sojoodi M, Oudot MA, Duong FHT, Masia R, Wei L, Thumann C, Durand SC, González-Motos V, Heide D, Hetzer J, Nakagawa S, Ono A, Song WM, Higashi T, Sanchez R, Kim RS, Bian CB, Kiani K, Croonenborghs T, Subramanian A, Chung RT, Straub BK, Schuppan D, Ankavay M, Cocquerel L, Schaeffer E, Goossens N, Koh AP, Mahajan M, Nair VD, Gunasekaran G, Schwartz ME, Bardeesy N, Shalek AK, Rozenblatt-Rosen O, Regev A, Felli E, Pessaux P, Tanabe KK, Heikenwälder M, Schuster C, Pochet N, Zeisel MB, Fuchs BC, Hoshida Y, Baumert TF. A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery. Nat Commun 2021; 12:5525. [PMID: 34535664 PMCID: PMC8448834 DOI: 10.1038/s41467-021-25468-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/03/2021] [Indexed: 12/25/2022] Open
Abstract
Chronic liver disease and hepatocellular carcinoma (HCC) are life-threatening diseases with limited treatment options. The lack of clinically relevant/tractable experimental models hampers therapeutic discovery. Here, we develop a simple and robust human liver cell-based system modeling a clinical prognostic liver signature (PLS) predicting long-term liver disease progression toward HCC. Using the PLS as a readout, followed by validation in nonalcoholic steatohepatitis/fibrosis/HCC animal models and patient-derived liver spheroids, we identify nizatidine, a histamine receptor H2 (HRH2) blocker, for treatment of advanced liver disease and HCC chemoprevention. Moreover, perturbation studies combined with single cell RNA-Seq analyses of patient liver tissues uncover hepatocytes and HRH2+, CLEC5Ahigh, MARCOlow liver macrophages as potential nizatidine targets. The PLS model combined with single cell RNA-Seq of patient tissues enables discovery of urgently needed targets and therapeutics for treatment of advanced liver disease and cancer prevention.
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Grants
- K01 CA140861 NCI NIH HHS
- R21 CA209940 NCI NIH HHS
- R01 DK099558 NIDDK NIH HHS
- R03 AI131066 NIAID NIH HHS
- R01 CA233794 NCI NIH HHS
- ERC CoG grant (HepatoMetaboPath) and EOS grant and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 272983813 – TRR 179, and Project-ID 314905040 SFB TR209.
- NIH CA140861
- NIH DK099558 Irma T. Hirschl/Monique Weill-Caulier Trust
- This work was supported by ARC, Paris and Institut Hospitalo-Universitaire, Strasbourg (TheraHCC1.0 and 2.0 IHUARC IHU201301187 and IHUARC2019 to T.F.B.), the European Union (ERC-AdG-2014-671231-HEPCIR to T.F.B. and Y.H., EU H2020-667273-HEPCAR to T.F.B. and M.H., INTERREG-IV-Rhin Supérieur-FEDER-Hepato-Regio-Net 2012 to T.F.B. and M.B.Z), ANRS, Paris (2013/108 and ECTZ103701 to T.F.B), NIH (DK099558 to Y. H. and CA233794 to Y.H. and T. F. B; CA140861 to B.C.F., CA209940, R21CA209940 and R03AI131066 to N.P. and T.F.B.), Cancer Prevention and Research Institute of Texas (RR180016 to Y.H), US Department of Defense (W81XWH-16-1-0363 to T.F.B. and Y.H.), the Irma T. Hirschl/Monique Weill-Caulier Trust (Y.H.) and the Foundation of the University of Strasbourg (HEPKIN to T. F. B. and Y. H.) and the Institut Universitaire de France (IUF; T. F. B.). M.H. is supported by an ERC CoG grant (HepatoMetaboPath) and EOS grant and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) –Project-ID 272983813 – TRR 179, and Project-ID 314905040 SFB TR209. This work has been published under the framework of the LABEX ANR-10-LABX-0028_HEPSYS and Inserm Plan Cancer and benefits from funding from the state managed by the French National Research Agency as part of the Investments for the future program.
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Affiliation(s)
- Emilie Crouchet
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Simonetta Bandiera
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shen Li
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hussein El Saghire
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Mirian Fernández-Vaquero
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Xiaochen Sun
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hadassa Hirschfield
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Frank Jühling
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Shijia Zhu
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Natascha Roehlen
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Clara Ponsolles
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Laura Heydmann
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Antonio Saviano
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Tongqi Qian
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anu Venkatesh
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joachim Lupberger
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Eloi R Verrier
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Mozhdeh Sojoodi
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marine A Oudot
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - François H T Duong
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ricard Masia
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Lan Wei
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christine Thumann
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Sarah C Durand
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Victor González-Motos
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Jenny Hetzer
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Shigeki Nakagawa
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Takaaki Higashi
- Department of Gastroenterological Surgery, Kumamoto University, Kumamoto, Japan
| | - Roberto Sanchez
- Department of Pharmacological Sciences and Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Rosa S Kim
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - C Billie Bian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Karun Kiani
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tom Croonenborghs
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- KU Leuven Technology Campus Geel, AdvISe, Geel, Belgium
| | | | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Beate K Straub
- Institute of Pathology, University Medicine, Johannes Gutenberg University, Mainz, Germany
| | - Detlef Schuppan
- Institute for Translational Immunology and Research Center for Immunotherapy (FZI), Johannes Gutenberg University (JGU) Medical Center, Mainz, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Maliki Ankavay
- University of Lille, CNRS, Inserm, CHU Lille, Pasteur Institute of Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Laurence Cocquerel
- University of Lille, CNRS, Inserm, CHU Lille, Pasteur Institute of Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Evelyne Schaeffer
- CNRS UPR3572 Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), Strasbourg, France
| | - Nicolas Goossens
- Division of Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland
| | - Anna P Koh
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ganesh Gunasekaran
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Myron E Schwartz
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center; Harvard Medical School, Cambridge St. CPZN 4216, Boston, MA, USA
| | - Alex K Shalek
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering Science & Department of Chemistry, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Emanuele Felli
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Patrick Pessaux
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Kenneth K Tanabe
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Catherine Schuster
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Nathalie Pochet
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mirjam B Zeisel
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 CNRS 5286 Mixte CLB, Université de Lyon 1 (UCBL1), Lyon, France
| | - Bryan C Fuchs
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Ferring Pharmaceuticals Inc 4245 Sorrento Valley Blvd, San Diego, CA, USA.
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Thomas F Baumert
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France.
- Université de Strasbourg, Strasbourg, France.
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France.
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4
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Uzilov AV, Taik P, Cheesman KC, Javanmard P, Ying K, Roehnelt A, Wang H, Fink MY, Lau CY, Moe AS, Villar J, Bederson JB, Stewart AF, Donovan MJ, Mahajan M, Sebra R, Post KD, Chen R, Geer EB. USP8 and TP53 Drivers are Associated with CNV in a Corticotroph Adenoma Cohort Enriched for Aggressive Tumors. J Clin Endocrinol Metab 2021; 106:826-842. [PMID: 33221858 DOI: 10.1210/clinem/dgaa853] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Indexed: 12/18/2022]
Abstract
CONTEXT Pituitary corticotroph adenomas are rare tumors that can be associated with excess adrenocorticotropin (ACTH) and adrenal cortisol production, resulting in the clinically debilitating endocrine condition Cushing disease. A subset of corticotroph tumors behave aggressively, and genomic drivers behind the development of these tumors are largely unknown. OBJECTIVE To investigate genomic drivers of corticotroph tumors at risk for aggressive behavior. DESIGN Whole-exome sequencing of patient-matched corticotroph tumor and normal deoxyribonucleic acid (DNA) from a patient cohort enriched for tumors at risk for aggressive behavior. SETTING Tertiary care center. PATIENTS Twenty-seven corticotroph tumors from 22 patients were analyzed. Twelve tumors were macroadenomas, of which 6 were silent ACTH tumors, 2 were Crooke's cell tumors, and 1 was a corticotroph carcinoma. INTERVENTION Whole-exome sequencing. MAIN OUTCOME MEASURE Somatic mutation genomic biomarkers. RESULTS We found recurrent somatic mutations in USP8 and TP53 genes, both with higher allelic fractions than other somatic mutations. These mutations were mutually exclusive, with TP53 mutations occurring only in USP8 wildtype (WT) tumors, indicating they may be independent driver genes. USP8-WT tumors were characterized by extensive somatic copy number variation compared with USP8-mutated tumors. Independent of molecular driver status, we found an association between invasiveness, macroadenomas, and aneuploidy. CONCLUSIONS Our data suggest that corticotroph tumors may be categorized into a USP8-mutated, genome-stable subtype versus a USP8-WT, genome-disrupted subtype, the latter of which has a TP53-mutated subtype with high level of chromosome instability. These findings could help identify high risk corticotroph tumors, namely those with widespread CNV, that may need closer monitoring and more aggressive treatment.
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Affiliation(s)
- Andrew V Uzilov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | | | - Khadeen C Cheesman
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pedram Javanmard
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Alessia Roehnelt
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Marc Y Fink
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Chun Yee Lau
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Joshua B Bederson
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew F Stewart
- Diabetes, Obesity, and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael J Donovan
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Kalmon D Post
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rong Chen
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Eliza B Geer
- Multidisciplinary Pituitary and Skull Base Tumor Center, Departments of Medicine and Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York
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5
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Kandel-Kfir M, Garcia-Milan R, Gueta I, Lubitz I, Ben-Zvi I, Shaish A, Shir L, Harats D, Mahajan M, Canaan A, Kamari Y. IFNγ potentiates TNFα/TNFR1 signaling to induce FAT10 expression in macrophages. Mol Immunol 2020; 117:101-109. [DOI: 10.1016/j.molimm.2019.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/22/2023]
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6
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Affiliation(s)
- S Kapoor
- Department of Internal Medicine, Max Super Speciality Hospital, New Delhi, India
| | - R Upreti
- Department of Internal Medicine, Max Super Speciality Hospital, New Delhi, India
| | - M Mahajan
- Department of Internal Medicine, Max Super Speciality Hospital, New Delhi, India
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7
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Blazquez A, Rubinsteyn A, Kodysh J, Finnigan JP, Marron TU, Meseck M, O'Donnell T, Hammerbacher J, Donovan MJ, Mahajan M, Miles BA, Irie H, Tiersten A, Tewari A, Parekh SS, Nair S, Galsky MD, Schadt EE, Friedlander PA, Bhardwaj N. A phase I study of the safety and immunogenicity of a multi-peptide personalized genomic vaccine in the adjuvant treatment of solid tumors and hematological malignancies. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e14307] [Citation(s) in RCA: 2] [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
e14307 Background: Mutation-derived tumor antigens (MTAs) arise as a direct result of somatic variations that occur during carcinogenesis and can be characterized via genetic sequencing and used to identify MTAs. We developed a platform for a fully-personalized MTA-based vaccine in the adjuvant treatment of solid and hematological malignancies. Methods: This is a single-arm, open label, proof-of-concept phase I study designed to test the safety and immunogenicity of Personalized Genomic Vaccine 001 (PGV001) that targets up to 10 predicted personal tumor neoantigens based on patient’s HLA profile (ClinicalTrials.gov: NCT02721043). Results: Patients who completed vaccination with PGV001_002 (head and neck squamous cell cancer) received 10 doses of vaccine comprising 10 long peptides (LP) combined with poly-ICLC (toll-like receptor-3 agonist) intradermally. Vaccine-induced T-cell responses were determined at weeks 0 and 27 (before and after treatment, respectively), ex vivo by interferon (IFN)-g enzyme-linked immunospot assay and after expansion by intracellular cytokine staining. Overlapping 15-mer peptides (OLPs) spanning the entirety of each LP and 9-10-mer peptides corresponding to each predicted class I epitope (Min) were pooled. Ex vivo responses to these peptide pools were undetectable at week 0 but were evident at week 27 against 2 OLPs out of 10 (20%) and in 5 Min out of 10 (50%). After in vitro expansion, neoantigen-specific CD4+ and CD8+ T-cell responses were found in 5 out of 10 pooled peptides (50%). 7 out of 10 (70%) epitopes elicited polyfunctional T-cell responses (secretion of INF-g, TNF-a, and/or IL-2) from either CD4+ or CD8+ T cells. Conclusions: The PGV001 vaccine in our first patient showed both safety and immunogenicity, eliciting CD4+ and CD8+ responses to the vaccine peptides. As we enroll additional patients in this clinical trial, and perform deeper phenotyping of their tumor-reactive T cells, we will learn the determinants necessary for the successful generation of MTA-based vaccines, while informing future immunotherapeutic approaches and rational combinations. Clinical trial information: NCT02721043.
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Affiliation(s)
- Ana Blazquez
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Julia Kodysh
- Icah School of Medicine at Mount Sinai, New York, NY
| | | | | | - Marcia Meseck
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | | | - Brett A. Miles
- Department of Otolaryngology, Mount Sinai Medical Center, New York, NY
| | - Hanna Irie
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Amy Tiersten
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - Sujit Nair
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matt D. Galsky
- Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY
| | | | | | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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8
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Blazquez AB, Rubinsteyn A, Kodysh J, Finnigan JP, Marron T, Sabado RL, Meseck M, O'Donnell TJ, Hammerbacher J, Donovan M, Holt J, Mahajan M, Mandeli J, Misiukiewicz K, Genden EM, Milles BA, Khorasani H, Dottino PR, Irie H, Tiersten AB, Port ER, Wolf AS, Cho HJ, Tewari A, Parekh SS, Nair S, Galsky MD, Oh WK, Gnjatic S, Schadt EE, Friedlander PA, Bhardwaj N. Abstract A005: A phase I study of the safety and immunogenicity of a multipeptide personalized genomic vaccine in the adjuvant treatment of solid cancers. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-a005] [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
Introduction: Mutation-derived tumor antigens (MTAs) arise as a direct result of somatic variations, including nucleotide substitutions, insertions, and deletions that occur during carcinogenesis. These somatic variations can be characterized via genetic sequencing and used to identify MTAs. We developed a platform for a fully-personalized MTA-based vaccine in the adjuvant treatment of solid and hematologic malignanicies. Methods: This is a single-arm, open label, proof-of-concept phase I study designed to test the safety and immunogenicity of Personalized Genomic Vaccine 001 (PGV001) that targets up to 10 predicted personal tumor neoantigens. The single-center study will enroll 20 eligible subjects with histologic diagnosis of solid and hematologic malignancies. Subjects must have no measurable disease at time of first vaccine administration, and 5-year disease recurrence risk of > 30%. Toxicity will be defined by CTCAE v5.0. Blood samples will be collected at various time points for immune response monitoring. Each patient’s vaccine peptides are selected by identifying somatic mutations from comparison of tumor and normal exome sequencing data, phasing somatic variants with co-occurring germline variants using tumor RNA sequencing data, and ranking mutated peptide sequences ”Openvax pipeline.” The process for determining somatic variants hews closely to the Broad Institute’s “Best Practices” for cancer SNVs and indels. The phasing of somatic and germline variants is implemented in a custom bioinformatics tool called Isovar. Mutated protein sequences containing phased variants are ranked according to two criteria: expression of the mutant allele in tumor RNA and aggregated predicted affinity to the patient’s Class I MHCs. Both quantities are normalized and multiplied together to create single ranked ordering of the candidate mutant sequences. Results: PGV001_002 (head and neck squamous cell cancer), who has completed vaccination, received 10 doses of vaccine comprising 10 long peptides (25 amino acid length) combined with poly-ICLC (toll-like receptor-3 agonist) intradermally. Vaccine-induced blood T-cell responses were determined, at weeks 0 (before-treatment) and 27 (after-treatment), ex vivo by interferon (IFN)-g enzyme-linked immunospot (ELISPOT) assay and after in vitro expansion by intracellular cytokine staining (ICS). Overlapping 15-16-mer assays peptides (OLPs) spanning the entirety of each ILP and 9-10-mer peptides corresponding to each predicted class I epitope (Min) were pooled and used to monitor immunogenicity. Ex vivo responses to these peptide pools were undetectable at week 0 but were evident at week 27 against 2 OLPs out of 10 (20%) and in 5 Min out of 10 (50%). After in vitro expansion, neoantigen-specific CD4+ and CD8+ T-cell responses were found in 5 out of 10 pooled peptides (50%). 7 out of 10 (70%) epitopes elicited polyfunctional T-cell responses (secretion of INF-α, TNF-α, and/or IL-2) from either CD4+ or CD8+ T-cells. Conclusion: To identify which predicted epitopes within the peptides pools stimulated the T-cell responses, we deconvoluted all the pools by either ex vivo and in vitro expansion. Ex vivo IFN-α production was detected in 1 (15-mer) peptide out of 15 (6.7%) and in 4 (9-10-mer) peptides out of 22 (18.2%). After expansion with single peptides, of 22 (9-10-mer) peptides tested, CD8+ T-cells were reactive against 13 peptides (59%), while CD4+ responses were seen in response to 11 of 15 (15-16-mer) peptides tested. Both CD4+ and CD8+ T-cell responses were polyfunctional. The PGV001 vaccine in our first patient showed both safety and immunogenicity, eliciting both CD4+ and CD8+ responses to the vaccine peptides. As we are enrolling additional patients, the information learned from this clinical trial will instruct the next generation of MTA-based vaccines, future development of immunotherapeutic approaches and rational combinations.
Citation Format: Ana B. Blazquez, Alex Rubinsteyn, Julia Kodysh, John P. Finnigan, Thomas Marron, Rachel L. Sabado, Marcia Meseck, Timothy J. O'Donnell, Jeffrey Hammerbacher, Michael Donovan, John Holt, Milind Mahajan, John Mandeli, Krysztof Misiukiewicz, Eric M. Genden, Brett A. Milles, Hooman Khorasani, Peter R. Dottino, Hanna Irie, Amy B. Tiersten, Elisa R. Port, Andrea S. Wolf, Hern J. Cho, Ashutosh Tewari, Samir S. Parekh, Sujit Nair, Matthew D. Galsky, William K. Oh, Sacha Gnjatic, Eric E. Schadt, Phillip A. Friedlander, Nina Bhardwaj. A phase I study of the safety and immunogenicity of a multipeptide personalized genomic vaccine in the adjuvant treatment of solid cancers [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A005.
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Affiliation(s)
- Ana B. Blazquez
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Alex Rubinsteyn
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Julia Kodysh
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - John P. Finnigan
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Thomas Marron
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Rachel L. Sabado
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Marcia Meseck
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Timothy J. O'Donnell
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Jeffrey Hammerbacher
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Michael Donovan
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - John Holt
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Milind Mahajan
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - John Mandeli
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | | | - Eric M. Genden
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Brett A. Milles
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Hooman Khorasani
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Peter R. Dottino
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Hanna Irie
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Amy B. Tiersten
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Elisa R. Port
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Andrea S. Wolf
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Hern J. Cho
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Ashutosh Tewari
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Samir S. Parekh
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Sujit Nair
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Matthew D. Galsky
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - William K. Oh
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | - Eric E. Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
| | | | - Nina Bhardwaj
- Icahn School of Medicine at Mount Sinai, New York, NY; Genentech, San Francisco, CA
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9
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Wang M, Beckmann ND, Roussos P, Wang E, Zhou X, Wang Q, Ming C, Neff R, Ma W, Fullard JF, Hauberg ME, Bendl J, Peters MA, Logsdon B, Wang P, Mahajan M, Mangravite LM, Dammer EB, Duong DM, Lah JJ, Seyfried NT, Levey AI, Buxbaum JD, Ehrlich M, Gandy S, Katsel P, Haroutunian V, Schadt E, Zhang B. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease. Sci Data 2018; 5:180185. [PMID: 30204156 PMCID: PMC6132187 DOI: 10.1038/sdata.2018.185] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [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] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/20/2018] [Indexed: 12/30/2022] Open
Abstract
Alzheimer's disease (AD) affects half the US population over the age of 85 and is universally fatal following an average course of 10 years of progressive cognitive disability. Genetic and genome-wide association studies (GWAS) have identified about 33 risk factor genes for common, late-onset AD (LOAD), but these risk loci fail to account for the majority of affected cases and can neither provide clinically meaningful prediction of development of AD nor offer actionable mechanisms. This cohort study generated large-scale matched multi-Omics data in AD and control brains for exploring novel molecular underpinnings of AD. Specifically, we generated whole genome sequencing, whole exome sequencing, transcriptome sequencing and proteome profiling data from multiple regions of 364 postmortem control, mild cognitive impaired (MCI) and AD brains with rich clinical and pathophysiological data. All the data went through rigorous quality control. Both the raw and processed data are publicly available through the Synapse software platform.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Ryan Neff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - John F. Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Mads E. Hauberg
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus 8000, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Aarhus, 8000, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, 8000, Denmark
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Mette A. Peters
- Sage Bionetworks, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Ben Logsdon
- Sage Bionetworks, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | | | - Eric B. Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joseph D. Buxbaum
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Michelle Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York NY 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
| | - Sam Gandy
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York NY 10029, USA
- The Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Psychiatry, JJ Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
- The Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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10
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Labgaa I, Villacorta-Martin C, D’Avola D, Craig A, von Felden J, Martins-Filho SN, Sia D, Stueck A, Ward SC, Fiel MI, Mahajan M, Tabrizian P, Thung SN, Ang C, Friedman SL, Llovet JM, Schwartz M, Villanueva A. A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma. Oncogene 2018; 37:3740-3752. [PMID: 29628508 PMCID: PMC6035113 DOI: 10.1038/s41388-018-0206-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [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: 07/04/2017] [Revised: 01/12/2018] [Accepted: 02/16/2018] [Indexed: 01/28/2023]
Abstract
Cellular components of solid tumors including DNA are released into the bloodstream, but data on circulating-free DNA (cfDNA) in hepatocellular carcinoma (HCC) are still scarce. This study aimed at analyzing mutations in cfDNA and their correlation with tissue mutations in patients with HCC. We included 8 HCC patients treated with surgical resection for whom we collected paired tissue and plasma/serum samples. We analyzed 45 specimens, including multiregional tumor tissue sampling (n = 24), peripheral blood mononuclear cells (PMBC, n = 8), plasma (n = 8) and serum (n = 5). Ultra-deep sequencing (5500× coverage) of all exons was performed in a targeted panel of 58 genes, including frequent HCC driver genes and druggable mutations. Mutations detected in plasma included known HCC oncogenes and tumor suppressors (e.g., TERT promoter, TP53, and NTRK3) as well as a candidate druggable mutation (JAK1). This approach increased the detection rates previously reported for mutations in plasma of HCC patients. A thorough characterization of cis mutations found in plasma confirmed their tumoral origin, which provides definitive evidence of the release of HCC-derived DNA fragments into the bloodstream. This study demonstrates that ultra-deep sequencing of cfDNA is feasible and can confidently detect somatic mutations found in tissue; these data reinforce the role of plasma DNA as a promising minimally invasive tool to interrogate HCC genetics.
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Affiliation(s)
- Ismail Labgaa
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Visceral Surgery, Lausanne University Hospital CHUV, Switzerland
| | - Carlos Villacorta-Martin
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Delia D’Avola
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Liver Unit and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Clinica Universidad de Navarra, Pamplona, Spain
| | - Amanda Craig
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Johann von Felden
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastiao N. Martins-Filho
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Pathology, University of Sao Paulo School of Medicine. Sao Paulo, Brazil,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Daniela Sia
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Ashley Stueck
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US),Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Stephen C. Ward
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US)
| | - M. Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Parissa Tabrizian
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Surgery, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Swan N. Thung
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Celina Ang
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Scott L. Friedman
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Josep M. Llovet
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Liver Cancer Translational Research Laboratory, BCLC Group, IDIBAPS, CIBEREHD, Hospital Clinic, Universitat de Barcelona, Catalonia (Spain),Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Myron Schwartz
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Surgery, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York (US),Correspondence should be addressed to: Augusto Villanueva, MD, PhD, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Box 1123, Room 11-70E, New York, NY 10029,
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11
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Koduru SV, Leberfinger AN, Kawasawa YI, Mahajan M, Gusani NJ, Sanyal AJ, Ravnic DJ. Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. Sci Rep 2018; 8:7967. [PMID: 29789629 PMCID: PMC5964116 DOI: 10.1038/s41598-018-26360-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 01/09/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) was the fifth leading cause of cancer death in men and eighth leading cause of death in women in the United States in 2017. In our study, we sought to identify sncRNAs in various stages of development of HCC. We obtained publicly available small RNA-seq data derived from patients with cirrhosis (n = 14), low-grade dysplastic nodules (LGDN, n = 9), high grade dysplastic nodules (HGDN, n = 6), early hepatocellular carcinoma (eHCC, n = 6), and advanced hepatocellular carcinoma (HCC, n = 20), along with healthy liver tissue samples (n = 9). All samples were analyzed for various types of non-coding RNAs using PartekFlow software. We remapped small RNA-seq to miRBase to obtain differential expressions of miRNAs and found 87 in cirrhosis, 106 in LGDN, 59 in HGDN, 80 in eHCC, and 133 in HCC. Pathway analysis of miRNAs obtained from diseased samples compared to normal samples showed signaling pathways in the microRNA dependent EMT, CD44, and others. Additionally, we analyzed the data sets for piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. We validated the in silico data using human HCC samples with NanoString miRNA global expression. Our results suggest that publically available data is a valuable resource for sncRNA identification in HCC progression (FDR set to <0.05 for all samples) and that a data mining approach is useful for biomarker development.
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Affiliation(s)
- Srinivas V Koduru
- Division of Plastic Surgery, Department of Surgery, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
| | - Ashley N Leberfinger
- Division of Plastic Surgery, Department of Surgery, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Yuka I Kawasawa
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, and Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Milind Mahajan
- Genomics Facility, Department of Genetics and Genomics Sciences, Icahn School of Medicine, Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Niraj J Gusani
- Program for Liver, Pancreas, & Foregut Tumors, Department of Surgery, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Arun J Sanyal
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, Virginia Commonwealth University, 1201 E Marshall St, Richmond, VA, 23298, USA
| | - Dino J Ravnic
- Division of Plastic Surgery, Department of Surgery, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA.
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12
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Linderman MD, Sanderson SC, Bashir A, Diaz GA, Kasarskis A, Zinberg R, Mahajan M, Suckiel SA, Zweig M, Schadt EE. Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years. BMC Med Genomics 2018; 11:5. [PMID: 29382336 PMCID: PMC5791365 DOI: 10.1186/s12920-018-0319-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To address the need for more effective genomics training, beginning in 2012 the Icahn School of Medicine at Mount Sinai has offered a unique laboratory-style graduate genomics course, "Practical Analysis of Your Personal Genome" (PAPG), in which students optionally sequence and analyze their own whole genome. We hypothesized that incorporating personal genome sequencing (PGS) into the course pedagogy could improve educational outcomes by increasing student motivation and engagement. Here we extend our initial study of the pilot PAPG cohort with a report on student attitudes towards genome sequencing, decision-making, psychological wellbeing, genomics knowledge and pedagogical engagement across three course years. METHODS Students enrolled in the 2013, 2014 and 2015 course years completed questionnaires before (T1) and after (T2) a prerequisite workshop (n = 110) and before (T3) and after (T4) PAPG (n = 66). RESULTS Students' interest in PGS was high; 56 of 59 eligible students chose to sequence their own genome. Decisional conflict significantly decreased after the prerequisite workshop (T2 vs. T1 p < 0.001). Most, but not all students, reported low levels of decision regret and test-related distress post-course (T4). Each year baseline decisional conflict decreased (p < 0.001) suggesting, that as the course became more established, students increasingly made their decision prior to enrolling in the prerequisite workshop. Students perceived that analyzing their own genome enhanced the genomics pedagogy, with students self-reporting being more persistent and engaged as a result of analyzing their own genome. More than 90% of respondents reported spending additional time outside of course assignments analyzing their genome. CONCLUSIONS Incorporating personal genome sequencing in graduate medical education may improve student motivation and engagement. However, more data will be needed to quantitatively evaluate whether incorporating PGS is more effective than other educational approaches.
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Affiliation(s)
- Michael D. Linderman
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Computer Science, Middlebury College, Middlebury, VT USA
| | - Saskia C. Sanderson
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Health Behaviour Research Centre, Department of Epidemiology and Public Health, University College London, London, UK
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Ali Bashir
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - George A. Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Andrew Kasarskis
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Randi Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Milind Mahajan
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Sabrina A. Suckiel
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Micol Zweig
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Eric E. Schadt
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
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13
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Yang J, Hagen J, Guntur KV, Allette K, Schuyler S, Ranjan J, Petralia F, Gesta S, Sebra R, Mahajan M, Zhang B, Zhu J, Houten S, Kasarskis A, Vishnudas VK, Akmaev VR, Sarangarajan R, Narain NR, Schadt EE, Argmann CA, Tu Z. A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells. BMC Genomics 2017; 18:987. [PMID: 29273013 PMCID: PMC5741891 DOI: 10.1186/s12864-017-4359-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 11/29/2017] [Indexed: 02/08/2023] Open
Abstract
Background Exosomes and other extracellular vesicles (EVs) have emerged as an important mechanism of cell-to-cell communication. However, previous studies either did not fully resolve what genetic materials were shuttled by exosomes or only focused on a specific set of miRNAs and mRNAs. A more systematic method is required to identify the genetic materials that are potentially transferred during cell-to-cell communication through EVs in an unbiased manner. Results In this work, we present a novel next generation of sequencing (NGS) based approach to identify EV mediated mRNA exchanges between co-cultured adipocyte and macrophage cells. We performed molecular and genomic profiling and jointly considered data from RNA sequencing (RNA-seq) and genotyping to track the “sequence varying mRNAs” transferred between cells. We identified 8 mRNAs being transferred from macrophages to adipocytes and 21 mRNAs being transferred in the opposite direction. These mRNAs represented biological functions including extracellular matrix, cell adhesion, glycoprotein, and signal peptides. Conclusions Our study sheds new light on EV mediated RNA communications between adipocyte and macrophage cells, which may play a significant role in developing insulin resistance in diabetic patients. This work establishes a new method that is applicable to examining genetic material exchanges in many cellular systems and has the potential to be extended to in vivo studies as well. Electronic supplementary material The online version of this article (10.1186/s12864-017-4359-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jialiang Yang
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jacob Hagen
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Kimaada Allette
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Schuyler
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Francesca Petralia
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Robert Sebra
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Milind Mahajan
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sander Houten
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | | | | | - Eric E Schadt
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carmen A Argmann
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Zhidong Tu
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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14
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Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR. A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries. Sci Rep 2017; 7:14626. [PMID: 29116112 PMCID: PMC5676863 DOI: 10.1038/s41598-017-14892-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 02/14/2017] [Accepted: 10/18/2017] [Indexed: 11/26/2022] Open
Abstract
Creating a cDNA library for deep mRNA sequencing (mRNAseq) is generally done by random priming, creating multiple sequencing fragments along each transcript. A 3'-end-focused library approach cannot detect differential splicing, but has potentially higher throughput at a lower cost, along with the ability to improve quantification by using transcript molecule counting with unique molecular identifiers (UMI) that correct PCR bias. Here, we compare an implementation of such a 3'-digital gene expression (3'-DGE) approach with "conventional" random primed mRNAseq. Given our particular datasets on cultured human cardiomyocyte cell lines, we find that, while conventional mRNAseq detects ~15% more genes and needs ~500,000 fewer reads per sample for equivalent statistical power, the resulting differentially expressed genes, biological conclusions, and gene signatures are highly concordant between two techniques. We also find good quantitative agreement at the level of individual genes between two techniques for both read counts and fold changes between given conditions. We conclude that, for high-throughput applications, the potential cost savings associated with 3'-DGE approach are likely a reasonable tradeoff for modest reduction in sensitivity and inability to observe alternative splicing, and should enable many larger scale studies focusing on not only differential expression analysis, but also quantitative transcriptome profiling.
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Affiliation(s)
- Yuguang Xiong
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magali Soumillon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Berkeley Lights, Inc. 5858 Horton St., Emeryville, CA, 94608, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
| | - Jens Hansen
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Hu
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan G C van Hasselt
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gomathi Jayaraman
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Lim
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
| | - Mehdi Bouhaddou
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Loren Ornelas
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | | | - Lindsay Lenaeus
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | | | - Jaehee Shim
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilda Gomez
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Clive Svendsen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leslie M Thompson
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
- Department of Psychiatry and Human Behavior, Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Milind Mahajan
- Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric A Sobie
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evren U Azeloglu
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Marc R Birtwistle
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
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15
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Wang H, Bender A, Wang P, Karakose E, Inabnet WB, Libutti SK, Arnold A, Lambertini L, Stang M, Chen H, Kasai Y, Mahajan M, Kinoshita Y, Fernandez-Ranvier G, Becker TC, Takane KK, Walker LA, Saul S, Chen R, Scott DK, Ferrer J, Antipin Y, Donovan M, Uzilov AV, Reva B, Schadt EE, Losic B, Argmann C, Stewart AF. Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas. Nat Commun 2017; 8:767. [PMID: 28974674 PMCID: PMC5626682 DOI: 10.1038/s41467-017-00992-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [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: 03/27/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022] Open
Abstract
Although diabetes results in part from a deficiency of normal pancreatic beta cells, inducing human beta cells to regenerate is difficult. Reasoning that insulinomas hold the “genomic recipe” for beta cell expansion, we surveyed 38 human insulinomas to obtain insights into therapeutic pathways for beta cell regeneration. An integrative analysis of whole-exome and RNA-sequencing data was employed to extensively characterize the genomic and molecular landscape of insulinomas relative to normal beta cells. Here, we show at the pathway level that the majority of the insulinomas display mutations, copy number variants and/or dysregulation of epigenetic modifying genes, most prominently in the polycomb and trithorax families. Importantly, these processes are coupled to co-expression network modules associated with cell proliferation, revealing candidates for inducing beta cell regeneration. Validation of key computational predictions supports the concept that understanding the molecular complexity of insulinoma may be a valuable approach to diabetes drug discovery. Diabetes results in part from a deficiency of functional pancreatic beta cells. Here, the authors study the genomic and epigenetic landscapes of human insulinomas to gain insight into possible pathways for therapeutic beta cell regeneration, highlighting epigenetic genes and pathways.
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Affiliation(s)
- Huan Wang
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,The Graduate School, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Aaron Bender
- The Graduate School, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peng Wang
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esra Karakose
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - William B Inabnet
- The Department of Surgery, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Steven K Libutti
- The Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Andrew Arnold
- Center for Molecular Medicine, University of Connecticut School of Medicine, Farmington, CT, 06030, USA
| | - Luca Lambertini
- The Departments of Environmental Medicine and Public Health and Obstetrics, Gynecology, and Reproductive Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Micheal Stang
- The Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Herbert Chen
- The Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Yumi Kasai
- The New York Genome Center, New York, NY, 10013, USA
| | - Milind Mahajan
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yayoi Kinoshita
- The Department of Pathology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Thomas C Becker
- The Sarah W. Stedman Center for Nutrition and Metabolism, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Karen K Takane
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Laura A Walker
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shira Saul
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rong Chen
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Donald K Scott
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jorge Ferrer
- The Department of Genetics in Medicine, Imperial College, London, W12 0NN, UK
| | - Yevgeniy Antipin
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Michael Donovan
- The Department of Pathology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew V Uzilov
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Boris Reva
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Bojan Losic
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carmen Argmann
- The Department of Genetics and Genomic Sciences and The Icahn Institute for Genomics and Multiscale Biology, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew F Stewart
- The Diabetes Obesity and Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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16
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Torrecilla S, Sia D, Harrington AN, Zhang Z, Camprecios G, Moeini A, Sara T, Fiel I, Hao K, Higuera M, Cabellos L, Cornella H, Mahajan M, Hoshida Y, Villanueva A, Florman S, Schwartz M, Llovet J. Abstract 3944: Characterization of molecular heterogeneity in hepatocellular carcinoma: Trunk and branch drivers. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3944] [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
Introduction: Molecular heterogeneity occurs in Hepatocellular carcinoma (HCC), but its implications in clinical decision-making are unknown. The clonal evolution model explains that trunk alterations arise at early stages and are shared by all malignant cells, whereas branch alterations occur in subclonal tumoral cells. We aim to characterize the genomic landscape of HCC through the identification of trunk driver alterations and the study of its distribution in intra- and inter-tumor heterogeneity.
Methods: 153 HCC samples representing the multiple steps of hepatocarcinogenesis were analyzed by deep targeted-sequencing covering exonic and promoter regions of the most frequently mutated drivers in HCC. Genes mutated in early lesions [39 dysplastic nodules and 54 early HCCs (eHCC) defined as <2cm, without satellites or vascular invasion] were classified as candidate trunk genes. Candidate trunk genes were further explored in two additional cohorts: a) intra-tumor heterogeneity cohort: 42 tumor regions of 21 tumors >4cm (2-3 regions/tumor); and 2) inter-tumor heterogeneity cohort: 39 tumors from 17 patients with multinodular lesions (2-3 nodules/patient). Transcriptome and copy-number variations (CNVs) were analyzed using expression and SNP arrays, respectively.
Results: A total of 46 mutations were identified in the cohort of early lesions. Average number of mutations and CNV aberrations were higher in eHCCs than in dysplastic nodules [1.1 vs 0.5, mutations/patient (p=0.03), and 8% vs 0.6% of aberrant chromosomal arms (p<0.0003), respectively]. Overall, 72% (23/32) of the sequenced eHCCs presented at least 1 trunk mutation, being TERT, TP53 and CTNNB1 the most frequent (21/23, 91%). In the intra-tumor heterogeneity cohort, 81% (17/21) tumors showed at least 1 shared mutation in TERT, TP53 and/or CTNNB1 between different tumor regions (trunk drivers). In the inter-tumor heterogeneity cohort, the similarity of the CNV-profile of multinodular tumors was used to classify them as clonal (intra-hepatic metastasis) or non-clonal (synchronic tumors). 6/17 (35%) of patients harbored clonal tumors according to their CNV profiles (Pearson p<0.05). Clonality classification was further confirmed by gene expression-based hierarchical clustering. 82% (9/11) of the sequenced clonal tumors shared TERT, TP53 and/or CTNNB1 as trunk alterations. In contrast, no trunk mutations were shared across non-clonal tumors.
Conclusions: TERT, TP53 and CTNNB1 are trunk drivers mutated in early HCC tumors that remained as trunk aberrations across different regions of the same tumor and between primary and metastatic nodules. These mutations are early trunk drivers that can be captured with single biopsies and could represent ideal therapeutic targets in the future.
Citation Format: Sara Torrecilla, Daniela Sia, Andrew N. Harrington, Zhongyang Zhang, Genis Camprecios, Agrin Moeini, Toffanin Sara, Isabel Fiel, Ke Hao, Monica Higuera, Laia Cabellos, Helena Cornella, Milind Mahajan, Yujin Hoshida, Augusto Villanueva, Sander Florman, Myron Schwartz, Josep Llovet. Characterization of molecular heterogeneity in hepatocellular carcinoma: Trunk and branch drivers [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 3944. doi:10.1158/1538-7445.AM2017-3944
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Affiliation(s)
| | - Daniela Sia
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Agrin Moeini
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Toffanin Sara
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Isabel Fiel
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ke Hao
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Laia Cabellos
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - Yujin Hoshida
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Josep Llovet
- Icahn School of Medicine at Mount Sinai, New York, NY
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17
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Koduru SV, Tiwari AK, Leberfinger A, Hazard SW, Kawasawa YI, Mahajan M, Ravnic DJ. Abstract 3499: Differentially expressed small noncoding RNAs in triple-negative breast cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3499] [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
Cancer is the second leading cause of death in the United States and is a major public health concern worldwide. Basic, clinical and epidemiological research is leading to improved cancer detection, prevention, and outcomes. Recent technological advances have allowed unbiased and comprehensive screening of genome-wide gene expression. Small non-coding RNAs (sncRNAs) have been shown to play an important role in biological processes and could serve as a diagnostic, prognostic and therapeutic biomarker for specific diseases. Recent findings have begun to reveal and enhance our understanding of the complex architecture of sncRNA expression including miRNAs, piRNAs, sn/snoRNAs and their relationships with biological systems. We used publicly available small RNA sequencing data that was derived from 24 triple negative breast cancers (TNBC) and 14 adjacent normal tissue samples to remap various types of sncRNAs. We found a total of 55 miRNAs were aberrantly expressed (p<0.005) in TNBC samples (8 miRNAs upregulated; 47 downregulated) compared to adjacent normal tissues whereas the original study reported only 25 novel miRs. In this study, we used pathway analysis of differentially expressed miRNAs which revealed TGF-beta signaling pathways to be profoundly affected in the TNBC samples. Furthermore, our comprehensive re-mapping strategy allowed us to discover a number of other differentially expressed sncRNAs including piRNAs, sn/snoRNAs, rRNAs, miscRNAs and nonsense-mediated decay RNAs. We believe that our sncRNA analysis workflow is extremely comprehensive and suitable for discovery of novel sncRNAs changes, which may lead to the development of innovative diagnostic and therapeutic tools for TNBC.
Citation Format: Srinivas V. Koduru, Amit K. Tiwari, Ashley Leberfinger, Sprague W. Hazard, Yuka Imamura Kawasawa, Milind Mahajan, Dino J. Ravnic. Differentially expressed small noncoding RNAs in triple-negative breast cancer [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 3499. doi:10.1158/1538-7445.AM2017-3499
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18
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Uzilov AV, Cheesman KC, Fink MY, Newman LC, Pandya C, Lalazar Y, Hefti M, Fowkes M, Deikus G, Lau CY, Moe AS, Kinoshita Y, Kasai Y, Zweig M, Gupta A, Starcevic D, Mahajan M, Schadt EE, Post KD, Donovan MJ, Sebra R, Chen R, Geer EB. Identification of a novel RASD1 somatic mutation in a USP8-mutated corticotroph adenoma. Cold Spring Harb Mol Case Stud 2017; 3:a001602. [PMID: 28487882 PMCID: PMC5411693 DOI: 10.1101/mcs.a001602] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/15/2017] [Indexed: 12/30/2022] Open
Abstract
Cushing's disease (CD) is caused by pituitary corticotroph adenomas that secrete excess adrenocorticotropic hormone (ACTH). In these tumors, somatic mutations in the gene USP8 have been identified as recurrent and pathogenic and are the sole known molecular driver for CD. Although other somatic mutations were reported in these studies, their contribution to the pathogenesis of CD remains unexplored. No molecular drivers have been established for a large proportion of CD cases and tumor heterogeneity has not yet been investigated using genomics methods. Also, even in USP8-mutant tumors, a possibility may exist of additional contributing mutations, following a paradigm from other neoplasm types where multiple somatic alterations contribute to neoplastic transformation. The current study utilizes whole-exome discovery sequencing on the Illumina platform, followed by targeted amplicon-validation sequencing on the Pacific Biosciences platform, to interrogate the somatic mutation landscape in a corticotroph adenoma resected from a CD patient. In this USP8-mutated tumor, we identified an interesting somatic mutation in the gene RASD1, which is a component of the corticotropin-releasing hormone receptor signaling system. This finding may provide insight into a novel mechanism involving loss of feedback control to the corticotropin-releasing hormone receptor and subsequent deregulation of ACTH production in corticotroph tumors.
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Affiliation(s)
- Andrew V Uzilov
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Khadeen C Cheesman
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Marc Y Fink
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Leah C Newman
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Chetanya Pandya
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Yelena Lalazar
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Marco Hefti
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Mary Fowkes
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Chun Yee Lau
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Aye S Moe
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Yayoi Kinoshita
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Yumi Kasai
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Micol Zweig
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Arpeta Gupta
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Daniela Starcevic
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Kalmon D Post
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Michael J Donovan
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Rong Chen
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Eliza B Geer
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Multidisciplinary Pituitary and Skull Base Tumor Center, Memorial Sloan Kettering, New York, New York 10065, USA
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19
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Bhatheja S, Johnson K, Vengrenyuk Y, Khader S, Yoshimura T, Benjamin G, Maehara A, Purushothaman M, Mahajan M, Moreno P, Mehran R, Baber U, Dudley J, Narula J, Sharma S, Kini A. ATHEROSCLEROTIC PLAQUE MORPHOLOGY IN RESPONSE TO HIGH INTENSITY LIPID LOWERING THERAPY BY MULTIMODALITY IMAGING AMONG WOMEN AND MEN: A YELLOW-II SUB-STUDY. J Am Coll Cardiol 2017. [DOI: 10.1016/s0735-1097(17)34445-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Abstract
Background: Improved healthcare and recent breakthroughs in technology have substantially reduced cancer mortality rates worldwide. Recent advancements in next-generation sequencing (NGS) have allowed genomic analysis of the human transcriptome. Now, using NGS we can further look into small non-coding regions of RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs), and small nuclear/nucleolar RNAs (sn/snoRNAs) among others. Recent studies looking at sncRNAs indicate their role in important biological processes such as cancer progression and predict their role as biomarkers for disease diagnosis, prognosis, and therapy. Results: In the present study, we data mined publically available small RNA sequencing data from colorectal tissue samples of eight matched patients (benign, tumor, and metastasis) and remapped the data for various small RNA annotations. We identified aberrant expression of 13 miRNAs in tumor and metastasis specimens [tumor vs benign group (19 miRNAs) and metastasis vs benign group (38 miRNAs)] of which five were upregulated, and eight were downregulated, during disease progression. Pathway analysis of aberrantly expressed miRNAs showed that the majority of miRNAs involved in colon cancer were also involved in other cancers. Analysis of piRNAs revealed six to be over-expressed in the tumor vs benign cohort and 24 in the metastasis vs benign group. Only two piRNAs were shared between the two cohorts. Examining other types of small RNAs [sn/snoRNAs, mt_rRNA, miscRNA, nonsense mediated decay (NMD), and rRNAs] identified 15 sncRNAs in the tumor vs benign group and 104 in the metastasis vs benign group, with only four others being commonly expressed. Conclusion: In summary, our comprehensive analysis on publicly available small RNA-seq data identified multiple differentially expressed sncRNAs during colorectal cancer progression at different stages compared to normal colon tissue. We speculate that deciphering and validating the roles of sncRNAs may prove useful in colorectal cancer prognosis, diagnosis, and therapy.
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Affiliation(s)
- Srinivas V Koduru
- Division of Plastic Surgery, Department of Surgery, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Amit K Tiwari
- Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, University of Toledo - Health Sciences Campus, Toledo, OH, USA
| | - Sprague W Hazard
- Department of Anesthesia, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Milind Mahajan
- Genomics Facility, Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dino J Ravnic
- Division of Plastic Surgery, Department of Surgery, College of Medicine, Pennsylvania State University, Hershey, PA, USA
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21
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Koduru SV, Tiwari AK, Leberfinger A, Hazard SW, Kawasawa YI, Mahajan M, Ravnic DJ. A Comprehensive NGS Data Analysis of Differentially Regulated miRNAs, piRNAs, lncRNAs and sn/snoRNAs in Triple Negative Breast Cancer. J Cancer 2017; 8:578-596. [PMID: 28367238 PMCID: PMC5370502 DOI: 10.7150/jca.17633] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/06/2016] [Indexed: 12/12/2022] Open
Abstract
Cancer is the second leading cause of death in the United States and is a major public health concern worldwide. Basic, clinical and epidemiological research is leading to improved cancer detection, prevention, and outcomes. Recent technological advances have allowed unbiased and comprehensive screening of genome-wide gene expression. Small non-coding RNAs (sncRNAs) have been shown to play an important role in biological processes and could serve as a diagnostic, prognostic and therapeutic biomarker for specific diseases. Recent findings have begun to reveal and enhance our understanding of the complex architecture of sncRNA expression including miRNAs, piRNAs, lncRNAs, sn/snoRNAs and their relationships with biological systems. We used publicly available small RNA sequencing data that was derived from 24 triple negative breast cancers (TNBC) and 14 adjacent normal tissue samples to remap various types of sncRNAs. We found a total of 55 miRNAs were aberrantly expressed (p<0.005) in TNBC samples (8 miRNAs upregulated; 47 downregulated) compared to adjacent normal tissues whereas the original study reported only 25 novel miRs. In this study, we used pathway analysis of differentially expressed miRNAs which revealed TGF-beta signaling pathways to be profoundly affected in the TNBC samples. Furthermore, our comprehensive re-mapping strategy allowed us to discover a number of other differentially expressed sncRNAs including piRNAs, lncRNAs, sn/snoRNAs, rRNAs, miscRNAs and nonsense-mediated decay RNAs. We believe that our sncRNA analysis workflow is extremely comprehensive and suitable for discovery of novel sncRNAs changes, which may lead to the development of innovative diagnostic and therapeutic tools for TNBC.
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Affiliation(s)
- Srinivas V Koduru
- Division of Plastic Surgery, Department of Surgery, College of Medicine, Pennsylvania State University, 500 University Drive, Hershey, PA 17033
| | - Amit K Tiwari
- Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, University of Toledo - Health Sciences Campus, 300 Arlington Ave, Toledo, OH 43614
| | - Ashley Leberfinger
- Division of Plastic Surgery, Department of Surgery, College of Medicine, Pennsylvania State University, 500 University Drive, Hershey, PA 17033
| | - Sprague W Hazard
- Department of Anesthesia, College of Medicine, Pennsylvania State University, 500 University Drive, Hershey, PA 17033
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, Department of Biochemistry and Molecular Biology, and Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA17033
| | - Milind Mahajan
- Genomics Facility, Department of Genetics and Genomics Sciences, Icahn School of Medicine, Mount Sinai, 1425 Madison Ave, New York, NY 10029
| | - Dino J Ravnic
- Division of Plastic Surgery, Department of Surgery, College of Medicine, Pennsylvania State University, 500 University Drive, Hershey, PA 17033
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Tiwari M, Rawat N, Vats P, Nagoorvali D, Mahajan M, Chauhan MS, Manik RS, Singla SK, Palta P, Singh MK. 89 METHYLATION STATUS OF IGF2/H19 DMR3 REGION AFFECTS IN VITRO BLASTOCYST PRODUCTION IN GOAT (CAPRA HIRCUS). Reprod Fertil Dev 2017. [DOI: 10.1071/rdv29n1ab89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Parthenogenesis has been observed in lower animals but no known instance has been reported in mammals because both maternal and paternal genomes are a fundamental prerequisite for embryogenesis. A major reason for developmental failure of uniparental zygotes is expression of certain genes in a parent-of-origin-specific manner, i.e. genomic imprinting of genes. Out of many imprinted genes identified so far, IGF2/H19 have been extensively studied and known to play an important role in fetal and placental development. Gene IGF2 is expressed by the paternal allele, H19 is transcribed from the maternal allele, and the reciprocal expression of both genes is regulated by the DMR3 region placed upstream of the H19 gene. In the present study we compared the methylation status of IGF2/H19 DMR in parthenogenetic activated (PA) and IVF goat (Capra hircus) blastocyst through bisulphite sequencing. For this, immature oocytes of usable quality were subjected to in vitro maturation and subsequently used for embryo production through parthenogenesis (n = 993) (by calcium ionophore and 6-DMAP activation) and IVF (n = 1096). It was found that embryo production rate at all the embryonic stages (2-cell, 4-cell, 8–16-cell, morula, and blastocyst) was significantly higher (P < 0.05) in parthenogenesis (74.66 ± 3.35%, 61.90 ± 2.73%, 47.83 ± 2.95%, 38.13 ± 5.28%, and 21.11 ± 2.51%, respectively) as compared with IVF (55.21 ± 2.02%, 38.12 ± 2.48%, 28.53 ± 1.67%, 21.57 ± 1.59%, and 8.23 ± 1.02%, respectively). When blastocysts (n = 6 each) were subjected to TUNEL, it was found that PA blastocyst showed significantly higher (P < 0.05) total cell number (217.83 ± 18.80 v. 159.67 ± 13.94) and significantly low (P < 0.05) apoptotic index (2.04 ± 0.25 v. 4.03 ± 0.29) as compared with IVF blastocysts. For the methylation pattern study, we analysed 17 CpG sites on the DMR3 region of the IGF2/H19 gene. Variable methylation pattern was observed within these CpG sites in different clones (n = 15) of PA and IVF blastocyst. The DMR3 region of the IGF2/H19 gene was significantly hypermethylated (P < 0.05) in PA blastocysts as compared with IVF blastocysts (80.39 ± 2.96, 32.55 ± 4.37, respectively), which suggests higher expression of IGF2 in parthenotes. The result suggests IGF2 might play different roles in different species; the same expression pattern of IGF2 is observed in ovine, but a contrary result is found in porcine species. Our results signify the hypermethylation of IGF2/H19 DMR3, which leads to higher expression of IGF2 to support embryonic development at the blastocyst stage.
This work was supported by the NFBSFARA Project on Parthenogenetic Goat (CA-4002), New Delhi, India.
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23
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Mahajan M, Nagoorvali D, Rawat N, Chauhan MS, Manik RS, Singla SK, Palta P, Singh MK. 90 OVIDUCTAL EPITHELIAL CELLS Co-CULTURE PROMOTES GOAT (CAPRA HIRCUS) IN VITRO PARTHENOGENETIC EMBRYO DEVELOPMENT. Reprod Fertil Dev 2017. [DOI: 10.1071/rdv29n1ab90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Co-culture of pre-implantation embryos with oviducal epithelial cells mimics the in vivo conditions, thus, playing a crucial role in embryo metabolism and gene expression and finally supporting embryonic developmental competence in several ways. Hence, the objective of the present study was to evaluate the effect of goat oviducal epithelial cells (GOEC) co-culture on goat parthenogenetic embryonic development, quality, and relative mRNA abundance of genes related to developmental competence and oxidative stress. The GOEC were obtained from goat oviducts by squeezing and thorough washing with TCM-199 + 10% fetal bovine serum. Goat cumulus–oocyte complexes were collected from slaughterhouse ovaries and matured in TCM-199 + 10% fetal bovine serum supplemented with 5 μg mL−1 of FSH, 10 μg mL−1 of LH, and 1 μg mL−1 of β-oestradiol for 27 h in CO2 incubator with 5% CO2 and at 38.5°C with >95% RH. In vitro matured cumulus–oocyte complexes were denuded and activated with 5 μM calcium ionophore and 2 mM 6-DMAP. Following activation, embryos were co-cultured with and without GOEC (control) in mCR2aa media. The blastocyst development rate was significantly (P < 0.05) higher (23.00 ± 1.15% v. 17.33 ± 1.45%) in the media cultured with GOEC than in control. The total cell number of blastocysts (n = 4) was also found to be significantly more (167.25 ± 17.51 v. 110.25 ± 12.02) than that of control (P < 0.05). However, the apoptotic index (3.76 ± 0.23% v. 7.97 ± 1.99%) was not significantly different in both groups. Further, RNA was isolated from both groups (20 each) of blastocysts on Day 8, and cDNA was prepared. Analysis by qPCR revealed that the relative mRNA abundance of development related genes, i.e. VEGF, BMP4, and CCNB1, showed significantly high (P < 0.05) expression, whereas the expression of CRABP1 was significantly low (P < 0.05) in GOEC co-culture than control. Oxidative stress related genes GPX-1 and SOD2 had comparable expression in both the culture systems, whereas a nonsignificant (P < 0.05) increase in expression of PRDX1 was observed in GOEC co-culture group. In conclusion, co-culture of embryos with GOEC in the simple culture media like mCR2aa helps in improving developmental competence and quality of parthenogenetic embryos.
This work was supported by the NFBSFARA Project on Parthenogenetic Goat (CA-4002), New Delhi, India.
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Nakagawa S, Wei L, Song WM, Higashi T, Ghoshal S, Kim RS, Bian CB, Yamada S, Sun X, Venkatesh A, Goossens N, Bain G, Lauwers GY, Koh AP, El-Abtah M, Ahmad NB, Hoshida H, Erstad DJ, Gunasekaran G, Lee Y, Yu ML, Chuang WL, Dai CY, Kobayashi M, Kumada H, Beppu T, Baba H, Mahajan M, Nair VD, Lanuti M, Villanueva A, Sangiovanni A, Iavarone M, Colombo M, Llovet JM, Subramanian A, Tager AM, Friedman SL, Baumert TF, Schwarz ME, Chung RT, Tanabe KK, Zhang B, Fuchs BC, Hoshida Y. Molecular Liver Cancer Prevention in Cirrhosis by Organ Transcriptome Analysis and Lysophosphatidic Acid Pathway Inhibition. Cancer Cell 2016; 30:879-890. [PMID: 27960085 PMCID: PMC5161110 DOI: 10.1016/j.ccell.2016.11.004] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 09/28/2016] [Accepted: 11/11/2016] [Indexed: 11/22/2022]
Abstract
Cirrhosis is a milieu that develops hepatocellular carcinoma (HCC), the second most lethal cancer worldwide. HCC prediction and prevention in cirrhosis are key unmet medical needs. Here we have established an HCC risk gene signature applicable to all major HCC etiologies: hepatitis B/C, alcohol, and non-alcoholic steatohepatitis. A transcriptome meta-analysis of >500 human cirrhotics revealed global regulatory gene modules driving HCC risk and the lysophosphatidic acid pathway as a central chemoprevention target. Pharmacological inhibition of the pathway in vivo reduced tumors and reversed the gene signature, which was verified in organotypic ex vivo culture of patient-derived fibrotic liver tissues. These results demonstrate the utility of clinical organ transcriptome to enable a strategy, namely, reverse-engineering precision cancer prevention.
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Affiliation(s)
- Shigeki Nakagawa
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Lan Wei
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Won Min Song
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Takaaki Higashi
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Sarani Ghoshal
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Rosa S Kim
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - C Billie Bian
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suguru Yamada
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Xiaochen Sun
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anu Venkatesh
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas Goossens
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Gastroenterology and Hepatology, Geneva University Hospital, 41205 Geneva, Switzerland
| | | | - Gregory Y Lauwers
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Anna P Koh
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mohamed El-Abtah
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noor B Ahmad
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hiroki Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Derek J Erstad
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Ganesh Gunasekaran
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Youngmin Lee
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ming-Lung Yu
- Hepatobiliary Division, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, and Faculty of Medicine, College of Medicine, and Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan; Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Wan-Long Chuang
- Hepatobiliary Division, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, and Faculty of Medicine, College of Medicine, and Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Yen Dai
- Hepatobiliary Division, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, and Faculty of Medicine, College of Medicine, and Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | | | - Hiromitsu Kumada
- Department of Hepatology, Toranomon Hospital, Tokyo 105-0001, Japan
| | - Toru Beppu
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Lanuti
- Division of Thoracic Surgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angelo Sangiovanni
- M. & A. Migliavacca Center for Liver Disease and 1st Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, 20122 Milan, Italy
| | - Massimo Iavarone
- M. & A. Migliavacca Center for Liver Disease and 1st Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, 20122 Milan, Italy
| | - Massimo Colombo
- M. & A. Migliavacca Center for Liver Disease and 1st Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, 20122 Milan, Italy
| | - Josep M Llovet
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Liver Cancer Translational Research Laboratory, Barcelona Clinic Liver Cancer Group, Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, CIBERehd, Universitat de Barcelona, Institució Catalana de Recerca i Estudis Avançats, Catalonia, 08036 Barcelona, Spain
| | - Aravind Subramanian
- Cancer Program, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Andrew M Tager
- Pulmonary and Critical Care Unit, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Scott L Friedman
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas F Baumert
- Institut National de la Santé et de la Recherche Médicale, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67081 Strasbourg, France; Institut Hospitalo-Universitaire, Pôle hépato-digestif, Nouvel Hôpital Civil, 67000 Strasbourg, France; Liver Center, Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Myron E Schwarz
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raymond T Chung
- Liver Center, Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kenneth K Tanabe
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bryan C Fuchs
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Sia D, Harrington AN, Torrecilla S, Zhang Z, Camprecios G, Moeini A, Toffanin S, Fiel MI, Hao K, Higuera M, Cabellos L, Cornella H, Mahajan M, Hoshida Y, Villanueva A, Florman S, Schwartz M, Llovet JM. Abstract 2388: Molecular heterogeneity and trunk driver mutations in hepatocellular carcinoma. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2388] [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
Background and aims: Molecular heterogeneity in hepatocellular carcinoma (HCC) is ill-defined since trunk drivers (early events; common to all cells), branch drivers (later events; present in a subset of cells) and passenger mutations (not relevant), have not been thoroughly described. Most FDA/EMA approved molecular drugs target trunk drivers. We explored heterogeneity by analyzing trunk vs branch mutations in different HCC regions within single and multinodular tumours.
Methods: Intra-tumoral heterogeneity was assessed in 21 patients with single HCCs (size > 4cm; 2 regions/tumour: 42 samples) and inter-tumoral heterogeneity was studied in 17 patients with multinodular HCCs (2-3 nodules/patient; total: 39 samples). Gene expression profiling, SNP array and deep-sequencing (coverage ∼850x) assessing 6 oncodrivers (TERT promoter, TP53, CTNNB1, ARID1A, AXIN1-2 by TruSeqAmplicon, validated by sanger) were explored. Clonality differentiating metastatic (clonal) vs synchronic (non-clonal) tumours was defined by SNP profiles. Trunk mutations were defined as present in a) all regions of a given tumour, or b) in all nodules of metastatic-clonal tumours; all other were considered as branch.
Results: Intra-tumoral heterogeneity assessed by sequencing identified at least 1 oncodriver in 19/21 patients with single tumours. Among those, trunk mutations accounted for 17/19 (90%), and branch for 2/19 cases. Overall 63 mutations were identified, 56 (90%) were identical in different tumoral regions (i.e. truncal; TERT promoter most prevalent). Inter-tumoral heterogeneity explored by SNP profiles defined metastases in 35% (6/17 multinodular cases) and synchronous tumors in 65% (11/17 cases). Genetic proximity confirmed clonality in all metastatic nodules. Regarding molecular subclasses, half of clonal tumours retained identical molecular fingerprint, but the other half switched to more aggressive subclass. All non-clonal tumours belonged to distinct molecular subclasses. Driver oncogenes were explored in 9 patients (5 metastasis and 4 synchronic). Metastatic tumours showed 13 mutations, among which 11 (85%) were truncal. Mutations in non-clonal synchronic tumours were distinct.
Conclusions: Single large HCCs shared common trunk drivers at distinct regions (90%). Similarly, 40% of multinodular tumours were clonal (metastasis) and shared common trunk oncodrivers, while 60% were synchronic, with distinct genomic profile/oncodrivers. Further studies at single-cell sequencing level are recommended.
Citation Format: Daniela Sia, Andrew Neelis Harrington, Sara Torrecilla, Zhongyang Zhang, Genis Camprecios, Agrin Moeini, Sara Toffanin, Maria Isabel Fiel, Ke Hao, Monica Higuera, Laia Cabellos, Helena Cornella, Milind Mahajan, Yujin Hoshida, Augusto Villanueva, Sander Florman, Myron Schwartz, Josep Maria Llovet. Molecular heterogeneity and trunk driver mutations in hepatocellular carcinoma. [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 2388.
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Affiliation(s)
- Daniela Sia
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Andrew Neelis Harrington
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sara Torrecilla
- 2Barcelona-Clínic Liver Cancer Group (HCC Translational Research Laboratory, Liver Unit, Hepato-biliary Surgery), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, CIBERehd, Universitat de Barcelona, Barcelona, Spain
| | - Zhongyang Zhang
- 3Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Genis Camprecios
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Agrin Moeini
- 2Barcelona-Clínic Liver Cancer Group (HCC Translational Research Laboratory, Liver Unit, Hepato-biliary Surgery), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, CIBERehd, Universitat de Barcelona, Barcelona, Spain
| | - Sara Toffanin
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Maria Isabel Fiel
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ke Hao
- 3Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monica Higuera
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laia Cabellos
- 2Barcelona-Clínic Liver Cancer Group (HCC Translational Research Laboratory, Liver Unit, Hepato-biliary Surgery), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, CIBERehd, Universitat de Barcelona, Barcelona, Spain
| | - Helena Cornella
- 2Barcelona-Clínic Liver Cancer Group (HCC Translational Research Laboratory, Liver Unit, Hepato-biliary Surgery), Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, CIBERehd, Universitat de Barcelona, Barcelona, Spain
| | - Milind Mahajan
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yujin Hoshida
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Augusto Villanueva
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sander Florman
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Myron Schwartz
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Josep Maria Llovet
- 1Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Med 2016; 8:62. [PMID: 27245685 PMCID: PMC4888213 DOI: 10.1186/s13073-016-0313-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/04/2016] [Indexed: 12/20/2022] Open
Abstract
Background Personalized therapy provides the best outcome of cancer care and its implementation in the clinic has been greatly facilitated by recent convergence of enormous progress in basic cancer research, rapid advancement of new tumor profiling technologies, and an expanding compendium of targeted cancer therapeutics. Methods We developed a personalized cancer therapy (PCT) program in a clinical setting, using an integrative genomics approach to fully characterize the complexity of each tumor. We carried out whole exome sequencing (WES) and single-nucleotide polymorphism (SNP) microarray genotyping on DNA from tumor and patient-matched normal specimens, as well as RNA sequencing (RNA-Seq) on available frozen specimens, to identify somatic (tumor-specific) mutations, copy number alterations (CNAs), gene expression changes, gene fusions, and also germline variants. To provide high sensitivity in known cancer mutation hotspots, Ion AmpliSeq Cancer Hotspot Panel v2 (CHPv2) was also employed. We integrated the resulting data with cancer knowledge bases and developed a specific workflow for each cancer type to improve interpretation of genomic data. Results We returned genomics findings to 46 patients and their physicians describing somatic alterations and predicting drug response, toxicity, and prognosis. Mean 17.3 cancer-relevant somatic mutations per patient were identified, 13.3-fold, 6.9-fold, and 4.7-fold more than could have been detected using CHPv2, Oncomine Cancer Panel (OCP), and FoundationOne, respectively. Our approach delineated the underlying genetic drivers at the pathway level and provided meaningful predictions of therapeutic efficacy and toxicity. Actionable alterations were found in 91 % of patients (mean 4.9 per patient, including somatic mutations, copy number alterations, gene expression alterations, and germline variants), a 7.5-fold, 2.0-fold, and 1.9-fold increase over what could have been uncovered by CHPv2, OCP, and FoundationOne, respectively. The findings altered the course of treatment in four cases. Conclusions These results show that a comprehensive, integrative genomic approach as outlined above significantly enhanced genomics-based PCT strategies. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0313-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew V Uzilov
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wei Ding
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marc Y Fink
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Biomedical Sciences, Long Island University Post, Brookville, NY, 11548, USA
| | - Yevgeniy Antipin
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew S Brohl
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sarcoma Department, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Claire Davis
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chun Yee Lau
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chetanya Pandya
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yumi Kasai
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - James Powell
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mark Micchelli
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rafael Castellanos
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Linderman
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yayoi Kinoshita
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Micol Zweig
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Katie Raustad
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kakit Cheung
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Diane Castillo
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa Wooten
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Imane Bourzgui
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Leah C Newman
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bino Mathew
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aye S Moe
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jun Liao
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert G Maki
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Randall F Holcombe
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Janina Longtine
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniela Starcevic
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael J Donovan
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shuyu Li
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Rong Chen
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Tan PS, Nakagawa S, Goossens N, Venkatesh A, Huang T, Ward SC, Sun X, Song WM, Koh A, Canasto-Chibuque C, Deshmukh M, Nair V, Mahajan M, Zhang B, Fiel MI, Kobayashi M, Kumada H, Hoshida Y. Clinicopathological indices to predict hepatocellular carcinoma molecular classification. Liver Int 2016; 36:108-18. [PMID: 26058462 PMCID: PMC4674393 DOI: 10.1111/liv.12889] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [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] [Received: 02/27/2015] [Accepted: 06/01/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Hepatocellular carcinoma (HCC) is the second most lethal cancer caused by lack of effective therapies. Although promising, HCC molecular classification, which enriches potential responders to specific therapies, has not yet been assessed in clinical trials of anti-HCC drugs. We aimed to overcome these challenges by developing clinicopathological surrogate indices of HCC molecular classification. METHODS Hepatocellular carcinoma classification defined in our previous transcriptome meta-analysis (S1, S2 and S3 subclasses) was implemented in an FDA-approved diagnostic platform (Elements assay, NanoString). Ninety-six HCC tumours (training set) were assayed to develop molecular subclass-predictive indices based on clinicopathological features, which were independently validated in 99 HCC tumours (validation set). Molecular deregulations associated with the histopathological features were determined by pathway analysis. Sample sizes for HCC clinical trials enriched with specific molecular subclasses were determined. RESULTS Hepatocellular carcinoma subclass-predictive indices were steatohepatitic (SH)-HCC variant and immune cell infiltrate for S1 subclass, macrotrabecular/compact pattern, lack of pseudoglandular pattern, and high serum alpha-foetoprotein (>400 ng/ml) for S2 subclass, and microtrabecular pattern, lack of SH-HCC and clear cell variants, and lower histological grade for S3 subclass. Macrotrabecular/compact pattern, a predictor of S2 subclass, was associated with the activation of therapeutically targetable oncogene YAP and stemness markers EPCAM/KRT19. BMP4 was associated with pseudoglandular pattern. Subclass-predictive indices-based patient enrichment reduced clinical trial sample sizes from 121, 184 and 53 to 30, 43 and 22 for S1, S2 and S3 subclass-targeting therapies respectively. CONCLUSIONS Hepatocellular carcinoma molecular subclasses can be enriched by clinicopathological indices tightly associated with deregulation of therapeutically targetable molecular pathways.
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Affiliation(s)
- Poh Seng Tan
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S,Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Health System, Singapore
| | - Shigeki Nakagawa
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Nicolas Goossens
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S,Division of Gastroenterology and Hepatology, Geneva University Hospital, Switzerland
| | - Anu Venkatesh
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Tiangui Huang
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Stephen C. Ward
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Xiaochen Sun
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Anna Koh
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Claudia Canasto-Chibuque
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Manjeet Deshmukh
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Venugopalan Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, U.S
| | - Maria Isabel Fiel
- Division of Gastroenterology and Hepatology, Geneva University Hospital, Switzerland
| | | | | | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, U.S
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Linderman MD, Bashir A, Diaz GA, Kasarskis A, Sanderson SC, Zinberg RE, Mahajan M, Shah H, Suckiel S, Zweig M, Schadt EE. Preparing the next generation of genomicists: a laboratory-style course in medical genomics. BMC Med Genomics 2015; 8:47. [PMID: 26264128 PMCID: PMC4534145 DOI: 10.1186/s12920-015-0124-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/27/2015] [Indexed: 11/17/2022] Open
Abstract
The growing gap between the demand for genome sequencing and the supply of trained genomics professionals is creating an acute need to develop more effective genomics education. In response we developed “Practical Analysis of Your Personal Genome”, a novel laboratory-style medical genomics course in which students have the opportunity to obtain and analyze their own whole genome. This report describes our motivations for and the content of a “practical” genomics course that incorporates personal genome sequencing and the lessons we learned during the first three iterations of this course.
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Affiliation(s)
- Michael D Linderman
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Ali Bashir
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Andrew Kasarskis
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Saskia C Sanderson
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Milind Mahajan
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Hardik Shah
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Sabrina Suckiel
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Micol Zweig
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Eric E Schadt
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
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29
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King LY, Canasto-Chibuque C, Johnson KB, Yip S, Chen X, Kojima K, Deshmukh M, Venkatesh A, Tan PS, Sun X, Villanueva A, Sangiovanni A, Nair V, Mahajan M, Kobayashi M, Kumada H, Iavarone M, Colombo M, Fiel MI, Friedman SL, Llovet JM, Chung RT, Hoshida Y. A genomic and clinical prognostic index for hepatitis C-related early-stage cirrhosis that predicts clinical deterioration. Gut 2015; 64:1296-302. [PMID: 25143343 PMCID: PMC4336233 DOI: 10.1136/gutjnl-2014-307862] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [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] [Received: 06/17/2014] [Accepted: 07/29/2014] [Indexed: 12/08/2022]
Abstract
OBJECTIVE The number of patients with HCV-related cirrhosis is increasing, leading to a rising risk of complications and death. Prognostic stratification in patients with early-stage cirrhosis is still challenging. We aimed to develop and validate a clinically useful prognostic index based on genomic and clinical variables to identify patients at high risk of disease progression. DESIGN We developed a prognostic index, comprised of a 186-gene signature validated in our previous genome-wide profiling study, bilirubin (>1 mg/dL) and platelet count (<100,000/mm(3)), in an Italian HCV cirrhosis cohort (training cohort, n=216, median follow-up 10 years). The gene signature test was implemented using a digital transcript counting (nCounter) assay specifically developed for clinical use and the prognostic index was evaluated using archived specimens from an independent cohort of HCV-related cirrhosis in the USA (validation cohort, n=145, median follow-up 8 years). RESULTS In the training cohort, the prognostic index was associated with hepatic decompensation (HR=2.71, p=0.003), overall death (HR=6.00, p<0.001), hepatocellular carcinoma (HR=3.31, p=0.001) and progression of Child-Turcotte-Pugh class (HR=6.70, p<0.001). The patients in the validation cohort were stratified into high-risk (16%), intermediate-risk (42%) or low-risk (42%) groups by the prognostic index. The high-risk group had a significantly increased risk of hepatic decompensation (HR=7.36, p<0.001), overall death (HR=3.57, p=0.002), liver-related death (HR=6.49, p<0.001) and all liver-related adverse events (HR=4.98, p<0.001). CONCLUSIONS A genomic and clinical prognostic index readily available for clinical use was successfully validated, warranting further clinical evaluation for prognostic prediction and clinical trial stratification and enrichment for preventive interventions.
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Affiliation(s)
- Lindsay Y. King
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, U.S
| | - Claudia Canasto-Chibuque
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | - Kara B. Johnson
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, U.S
| | - Shun Yip
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | - Xintong Chen
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | - Kensuke Kojima
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | - Manjeet Deshmukh
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | - Anu Venkatesh
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | - Poh Seng Tan
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S,Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Health System, Singapore
| | - Xiaochen Sun
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | | | - Angelo Sangiovanni
- M. & A. Migliavacca Center for Liver Disease and 1st Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, Italy
| | - Venugopalan Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, U.S
| | - Milind Mahajan
- Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, U.S
| | | | | | - Massimo Iavarone
- M. & A. Migliavacca Center for Liver Disease and 1st Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, Italy
| | - Massimo Colombo
- M. & A. Migliavacca Center for Liver Disease and 1st Division of Gastroenterology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, University of Milan, Italy
| | - Maria Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, U.S
| | - Scott L. Friedman
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
| | - Josep M. Llovet
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S,HCC Translational Research Laboratory, Barcelona Clinic Liver Cancer Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer Centro de Investigaciones en Red de Enfermedades Hepáticas y Digestivas, Hosptial Clínic Barcelona, Catalonia, Spain,Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Catalonia, Spain
| | - Raymond T. Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, U.S
| | - Yujin Hoshida
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, U.S
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30
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Sanderson SC, Linderman MD, Zinberg R, Bashir A, Kasarskis A, Zweig M, Suckiel S, Shah H, Mahajan M, Diaz GA, Schadt EE. How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study. Genet Med 2015; 17:866-74. [PMID: 25634025 DOI: 10.1038/gim.2014.203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 12/12/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Health-care professionals need to be trained to work with whole-genome sequencing (WGS) in their practice. Our aim was to explore how students responded to a novel genome analysis course that included the option to analyze their own genomes. METHODS This was an observational cohort study. Questionnaires were administered before (T3) and after the genome analysis course (T4), as well as 6 months later (T5). In-depth interviews were conducted at T5. RESULTS All students (n = 19) opted to analyze their own genomes. At T5, 12 of 15 students stated that analyzing their own genomes had been useful. Ten reported they had applied their knowledge in the workplace. Technical WGS knowledge increased (mean of 63.8% at T3, mean of 72.5% at T4; P = 0.005). In-depth interviews suggested that analyzing their own genomes may increase students' motivation to learn and their understanding of the patient experience. Most (but not all) of the students reported low levels of WGS results-related distress and low levels of regret about their decision to analyze their own genomes. CONCLUSION Giving students the option of analyzing their own genomes may increase motivation to learn, but some students may experience personal WGS results-related distress and regret. Additional evidence is required before considering incorporating optional personal genome analysis into medical education on a large scale.
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Affiliation(s)
- Saskia C Sanderson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael D Linderman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Randi Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Micol Zweig
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sabrina Suckiel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Rehmani K, Raju K, Patnaik S, Naik V, Rajagopalan R, Pawar S, Mahajan M, Rayani B, Murthy S, Rao T. S. 125. Minimally Invasive Esophagectomy (MIE) – adequacy and short term perioperative outcomes – our experience. Eur J Surg Oncol 2014. [DOI: 10.1016/j.ejso.2014.08.121] [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: 11/25/2022] Open
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Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, Mahajan M, Shah H, Kasarskis A, Schadt EE. Analytical validation of whole exome and whole genome sequencing for clinical applications. BMC Med Genomics 2014; 7:20. [PMID: 24758382 PMCID: PMC4022392 DOI: 10.1186/1755-8794-7-20] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [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: 01/08/2014] [Accepted: 04/10/2014] [Indexed: 12/30/2022] Open
Abstract
Background Whole exome and genome sequencing (WES/WGS) is now routinely offered as a clinical test by a growing number of laboratories. As part of the test design process each laboratory must determine the performance characteristics of the platform, test and informatics pipeline. This report documents one such characterization of WES/WGS. Methods Whole exome and whole genome sequencing was performed on multiple technical replicates of five reference samples using the Illumina HiSeq 2000/2500. The sequencing data was processed with a GATK-based genome analysis pipeline to evaluate: intra-run, inter-run, inter-mode, inter-machine and inter-library consistency, concordance with orthogonal technologies (microarray, Sanger) and sensitivity and accuracy relative to known variant sets. Results Concordance to high-density microarrays consistently exceeds 97% (and typically exceeds 99%) and concordance between sequencing replicates also exceeds 97%, with no observable differences between different flow cells, runs, machines or modes. Sensitivity relative to high-density microarray variants exceeds 95%. In a detailed study of a 129 kb region, sensitivity was lower with some validated single-base insertions and deletions “not called”. Different variants are "not called" in each replicate: of all variants identified in WES data from the NA12878 reference sample 74% of indels and 89% of SNVs were called in all seven replicates, in NA12878 WGS 52% of indels and 88% of SNVs were called in all six replicates. Key sources of non-uniformity are variance in depth of coverage, artifactual variants resulting from repetitive regions and larger structural variants.
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Affiliation(s)
- Michael D Linderman
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, Georgieva L, Rees E, Palta P, Ruderfer DM, Carrera N, Humphreys I, Johnson JS, Roussos P, Barker DD, Banks E, Milanova V, Grant SG, Hannon E, Rose SA, Chambert K, Mahajan M, Scolnick EM, Moran JL, Kirov G, Palotie A, McCarroll SA, Holmans P, Sklar P, Owen MJ, Purcell SM, O'Donovan MC. De novo mutations in schizophrenia implicate synaptic networks. Nature 2014; 506:179-84. [PMID: 24463507 DOI: 10.1038/nature12929] [Citation(s) in RCA: 1188] [Impact Index Per Article: 118.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 12/03/2013] [Indexed: 01/04/2023]
Abstract
Inherited alleles account for most of the genetic risk for schizophrenia. However, new (de novo) mutations, in the form of large chromosomal copy number changes, occur in a small fraction of cases and disproportionally disrupt genes encoding postsynaptic proteins. Here we show that small de novo mutations, affecting one or a few nucleotides, are overrepresented among glutamatergic postsynaptic proteins comprising activity-regulated cytoskeleton-associated protein (ARC) and N-methyl-d-aspartate receptor (NMDAR) complexes. Mutations are additionally enriched in proteins that interact with these complexes to modulate synaptic strength, namely proteins regulating actin filament dynamics and those whose messenger RNAs are targets of fragile X mental retardation protein (FMRP). Genes affected by mutations in schizophrenia overlap those mutated in autism and intellectual disability, as do mutation-enriched synaptic pathways. Aligning our findings with a parallel case-control study, we demonstrate reproducible insights into aetiological mechanisms for schizophrenia and reveal pathophysiology shared with other neurodevelopmental disorders.
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Affiliation(s)
- Menachem Fromer
- 1] Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Andrew J Pocklington
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - David H Kavanagh
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Hywel J Williams
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Sarah Dwyer
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Padhraig Gormley
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Lyudmila Georgieva
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Elliott Rees
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Priit Palta
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK [2] Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia [3] Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290 Helsinki, Finland
| | - Douglas M Ruderfer
- 1] Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Noa Carrera
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Isla Humphreys
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Jessica S Johnson
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Panos Roussos
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Douglas D Barker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Eric Banks
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Vihra Milanova
- Department of Psychiatry, Medical University, Sofia 1431, Bulgaria
| | - Seth G Grant
- Centre for Neuroregeneration, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Eilis Hannon
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Samuel A Rose
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Milind Mahajan
- Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Edward M Scolnick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - George Kirov
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Aarno Palotie
- 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [3] Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290 Helsinki, Finland
| | - Steven A McCarroll
- 1] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Pamela Sklar
- 1] Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Michael J Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
| | - Shaun M Purcell
- 1] Division of Psychiatric Genomics in the Department of Psychiatry, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [3] Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Michael C O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK
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Panda AK, Mahajan M. Unusual cause of asymptomatic neck swelling. Ann Med Health Sci Res 2014; 4:S67. [PMID: 25031917 PMCID: PMC4083713 DOI: 10.4103/2141-9248.131729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Zhang B, Gaiteri C, Bodea LG, Wang Z, McElwee J, Podtelezhnikov AA, Zhang C, Xie T, Tran L, Dobrin R, Fluder E, Clurman B, Melquist S, Narayanan M, Suver C, Shah H, Mahajan M, Gillis T, Mysore J, MacDonald ME, Lamb JR, Bennett DA, Molony C, Stone DJ, Gudnason V, Myers AJ, Schadt EE, Neumann H, Zhu J, Emilsson V. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell 2013; 153:707-20. [PMID: 23622250 DOI: 10.1016/j.cell.2013.03.030] [Citation(s) in RCA: 1161] [Impact Index Per Article: 105.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 10/17/2012] [Accepted: 03/22/2013] [Indexed: 12/11/2022]
Abstract
The genetics of complex disease produce alterations in the molecular interactions of cellular pathways whose collective effect may become clear through the organized structure of molecular networks. To characterize molecular systems associated with late-onset Alzheimer's disease (LOAD), we constructed gene-regulatory networks in 1,647 postmortem brain tissues from LOAD patients and nondemented subjects, and we demonstrate that LOAD reconfigures specific portions of the molecular interaction structure. Through an integrative network-based approach, we rank-ordered these network structures for relevance to LOAD pathology, highlighting an immune- and microglia-specific module that is dominated by genes involved in pathogen phagocytosis, contains TYROBP as a key regulator, and is upregulated in LOAD. Mouse microglia cells overexpressing intact or truncated TYROBP revealed expression changes that significantly overlapped the human brain TYROBP network. Thus the causal network structure is a useful predictor of response to gene perturbations and presents a framework to test models of disease mechanisms underlying LOAD.
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Affiliation(s)
- Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Bandyopadhyay U, Cotney J, Nagy M, Oh S, Leng J, Mahajan M, Mane S, Fenton WA, Noonan JP, Horwich AL. RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse. PLoS One 2013; 8:e53575. [PMID: 23301088 PMCID: PMC3536741 DOI: 10.1371/journal.pone.0053575] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [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: 08/27/2012] [Accepted: 12/03/2012] [Indexed: 12/12/2022] Open
Abstract
Mechanisms involved with degeneration of motor neurons in amyotrophic lateral sclerosis (ALS; Lou Gehrig's Disease) are poorly understood, but genetically inherited forms, comprising ~10% of the cases, are potentially informative. Recent observations that several inherited forms of ALS involve the RNA binding proteins TDP43 and FUS raise the question as to whether RNA metabolism is generally disturbed in ALS. Here we conduct whole transcriptome profiling of motor neurons from a mouse strain, transgenic for a mutant human SOD1 (G85R SOD1-YFP), that develops symptoms of ALS and paralyzes at 5-6 months of age. Motor neuron cell bodies were laser microdissected from spinal cords at 3 months of age, a time when animals were presymptomatic but showed aggregation of the mutant protein in many lower motor neuron cell bodies and manifested extensive neuromuscular junction morphologic disturbance in their lower extremities. We observed only a small number of transcripts with altered expression levels or splicing in the G85R transgenic compared to age-matched animals of a wild-type SOD1 transgenic strain. Our results indicate that a major disturbance of polyadenylated RNA metabolism does not occur in motor neurons of mutant SOD1 mice, suggesting that the toxicity of the mutant protein lies at the level of translational or post-translational effects.
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Affiliation(s)
- Urmi Bandyopadhyay
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Justin Cotney
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Maria Nagy
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Sunghee Oh
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jing Leng
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Milind Mahajan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Wayne A. Fenton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - James P. Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Arthur L. Horwich
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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Mahajan M, Joshi R, Gulati A, Yadav SK. Increase in flavan-3-ols by silencing flavonol synthase mRNA affects the transcript expression and activity levels of antioxidant enzymes in tobacco. Plant Biol (Stuttg) 2012; 14:725-33. [PMID: 22324650 DOI: 10.1111/j.1438-8677.2011.00550.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Flavonoids are plant secondary metabolites widespread throughout the plant kingdom involved in many physiological and biochemical functions. Amongst the flavonoids, flavan-3-ols (catechin and epicatechin) are known for their direct free radical scavenging activity in vitro, but studies on their antioxidant potential and interaction with antioxidant enzymes in vivo are lacking. Here, the flavonoid pathway was engineered by silencing a gene encoding flavonol synthase (FLS) in tobacco to direct the flow of metabolites towards production of flavan-3-ols. FLS silencing reduced flavonol content 17-53%, while it increased catechin and epicatechin content 51-93% and 18-27%, respectively. The silenced lines showed a significant increase in expression of genes for dihydroflavonol reductase and anthocyanidin synthase, a downstream gene towards epicatechin production, with no significant change in expression of other genes of the flavonoid pathway. Effects of accumulation of flavan-3-ols in FLS silenced lines on transcript level and activities of antioxidant enzymes were studied. Transcripts of the antioxidant enzymes glutathione reductase (GR), ascorbate peroxidase (APx), and catalase (CAT) increased, while glutathione-S-transferase (GST), decreased in FLS silenced lines. Enhanced activity of all the antioxidant enzymes was observed in silenced tobacco lines. To validate the affect of flavan-3-ols on the antioxidant system, in vitro experiments were conducted with tobacco seedlings exposed to two concentrations of catechin (10 and 50 μm) for 2 days. In vitro exposed seedlings produced similar levels of transcripts and activity of antioxidant enzymes as FLS silenced seedlings. Results suggest that flavan-3-ols (catechin) might be increasing activity of GR, Apx and CAT by elevating their mRNAs levels. Since these enzymes are involved in scavenging of reactive oxygen species, this strategy would help in tailoring crops for enhanced catechin production as well as making them tolerant to oxidative stresses.
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Affiliation(s)
- M Mahajan
- Plant Metabolic Engineering Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, India
| | - R Joshi
- Plant Metabolic Engineering Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, India
| | - A Gulati
- Plant Metabolic Engineering Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, India
| | - S K Yadav
- Plant Metabolic Engineering Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, India
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Sharma R, Mahajan M, Singh B, Singh G, Singh P. Role of the APOB Gene Polymorphism (c.12669G>A, p. Gln4154Lys) in Coronary Artery Disease in the Indian Punjabi Population. Balkan J Med Genet 2011; 14:35-40. [PMID: 24052710 PMCID: PMC3776703 DOI: 10.2478/v10034-011-0045-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
High concentration of apolipoprotein B (apoB) is a risk factor for coronary artery disease (CAD). The association of the APOB gene polymorphism c.12669G>A, p.Gln4154Lys with the risk of CAD varies considerably in different populations. The present study represents the first investigation regarding the role of this APOB gene polymorphism with CAD in the Indian Punjabi population. We have studied the APOB gene polymorphism c.12669G>A, p.Gln4154Lys and its relationship with lipid, apoB, low-density lipoprotein (LDL) heterogeneity and oxidation in subjects suffering from CAD. The study was conducted on 87 patients with CAD; 75 healthy subjects served as controls. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to determine the DNA polymorphism in the APOB gene. Frequency of R- (mutant) allele was significantly high (p <0.05) in CAD patients when compared to controls. Variations in serum lipid levels in the R+R+ and R+R- APOB genotypes were insignificant (p >0.05). However, serum apoB levels were significantly raised (p <0.05) in CAD patients with the R+R- genotype as compared to those with the R+R+ APOB genotype. Coronary artery disease patients had raised significantly raised (p <0.01) Log triglyceride/high density lipoprotein-cholesterol (HDL-C) ratio, apoB carbonyl content and increased malondialdehyde-low density lipoprotein (MDA-LDL levels, irrespective of APOB genotype as compared to controls. Carriers of the R- allele are at higher risk of CAD, probably because of elevated serum apoB levels in the Indian Punjabi population. Overall, it may be concluded that the R- allele might be associated with increased susceptibility towards CAD development in the Indian Punjabi population, and one of the linking factor is the elevation in serum apoB levels. However, this association needs further evaluation in a larger population. Secondly, the robust mechanism behind the positive association of the R- allele with raised serum apoB levels needs to be explored, which might be helpful in the strengthening the observed results.
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Affiliation(s)
- R Sharma
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - M Mahajan
- Department of Biochemistry, Government Medical College, Amritsar, India
| | - B Singh
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India
| | - G Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
| | - P Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
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Tanaka Y, Kawahashi K, Katagiri ZI, Nakayama Y, Mahajan M, Kioussis D. Dual function of histone H3 lysine 36 methyltransferase ASH1 in regulation of Hox gene expression. PLoS One 2011; 6:e28171. [PMID: 22140534 PMCID: PMC3225378 DOI: 10.1371/journal.pone.0028171] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/02/2011] [Indexed: 11/24/2022] Open
Abstract
Hox genes play important roles in haematopoietic development in mammals. ASH1 is a member of the trithorax group (trxG) that is required for proper expression of Hox genes and is preferentially expressed in haematopoietic stem cells. We have recently reported that ASH1 methylates histone H3 at lysine 36 (K36) but its biological function has remained elusive. Here we show that ASH1 regulates Hox gene expression positively and negatively in a leukemic cell line K562 and is required for myelomonocytic differentiation of murine haematopoietic stem cells. ASH1 binds to endogenous Hox loci in K562 cells and its knockdown causes reduced expression of Hox genes. In addition, ASH1 and MLL1 induce more than 100-fold activation of Hox promoters in HeLa cells if expressed simultaneously but not individually. Notably, ASH1 harbouring a point mutation that kills methyltransferase activity is more efficient than wild type ASH1 in Hox gene activation, indicating that K36 methylation is not a prerequisite for Hox gene expression. Moreover, tethering wild type or catalytically inactive methyltransferase domain of ASH1 to a heterologous promoter causes downregulation or upregulation, respectively, of transcription, supporting a hypothesis that K36 methylation imparts repression. Knockdown of ASH1 in K562 cells in vitro causes increased expression of ε-globin gene and reduced expression of myelomonocytic markers GPIIb and GPIIIa, whereas knockdown of ASH1 in murine haematopoietic stem cells in vivo results in decreased number of macrophages and granulocytes, a phenotype similar to that induced by loss of mll1 function. Taken together, our data suggest that ASH1 and MLL1 synergize in activation of Hox genes and thereby regulate development of myelomonocytic lineages from haematopoietic stem cells.
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Affiliation(s)
- Yujiro Tanaka
- Genome Structure and Regulation, School of Biomedical Science and Biochemical Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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Alam M, Mahajan M, Raziuddin M, Singh TP, Yadav S. Proteomics-based approach for identification and purification of human phosphate binding apolipoprotein from amniotic fluid. Genet Mol Res 2009; 8:929-37. [PMID: 19731215 DOI: 10.4238/vol8-3gmr620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Human amniotic fluid is of both maternal and fetal origin; it protects the fetus and provides the environment for growth and development of the fetus. We used a proteomics-based approach for targeting and purifying human phosphate binding protein, a member of the DING family of proteins from amniotic fluid, using Blue Sepharose CL-6B, DEAE-Sephacel and gel filtration chromatography. The protein had earlier been reported to be serendipitously purified along with PON1 (paraoxonase 1). It was identified using electro-spray-ionization-time-of-flight mass spectrometry and was found to be human phosphate binding protein. Human phosphate binding proteins have been reported to play a role as phosphate scavengers and may have a protective function against phosphate-related disorders, such as atherosclerosis, diabetes and kidney stones.
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Affiliation(s)
- M Alam
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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Canaan A, Schulz V, Mahajan M, Urban A, Weissman S. EBNA1—A virally encoded protein binds cellular host promoters in a unique sequence and directly interferes with cellular gene expression. Implications for genomics approaches in drug design. Antiviral Res 2009. [DOI: 10.1016/j.antiviral.2009.02.171] [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: 10/20/2022]
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Gautam V, Ray P, Vandamme P, Chatterjee SS, Das A, Sharma K, Rana S, Garg RK, Madhup SK, Mahajan M, Sharma M. IDENTIFICATION OF LYSINE POSITIVE NON-FERMENTING GRAM NEGATIVE BACILLI (STENOTROPHOMONAS MALTOPHILIA AND BURKHOLDERIA CEPACIA COMPLEX). Indian J Med Microbiol 2009; 27:128-33. [DOI: 10.4103/0255-0857.49425] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Lee JM, Carson R, Arce C, Mahajan M, Lobst S. Development of a minimally invasive epidermal abrasion device for clinical skin sampling and its applications in molecular biology. Int J Cosmet Sci 2009; 31:27-39. [DOI: 10.1111/j.1468-2494.2008.00486.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mahajan M, Kumar V, Anand A. SeO 2-Mediated Oxidation of 1,3-Diazabuta-1,3-dienes: A Single-Pot Synthesis of Functionalized 4-Hydroxyimidazoles. Synlett 2006. [DOI: 10.1055/s-2006-949631] [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: 10/23/2022]
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Li Deng, Kuansan Wang, Acero A, Hsiao-Wuen Hon, Droppo J, Boulis C, Ye-Yi Wang, Jacoby D, Mahajan M, Chelba C, Huang X. Distributed speech processing in miPad's multimodal user interface. ACTA ACUST UNITED AC 2002. [DOI: 10.1109/tsa.2002.804538] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Pillai S, Mahajan M, Carlomusto M. Ceramide potentiates, but sphingomyelin inhibits, vitamin D-induced keratinocyte differentiation: comparison between keratinocytes and HL-60 cells. Arch Dermatol Res 1999; 291:284-9. [PMID: 10367711 DOI: 10.1007/s004030050409] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Differentiation of epidermal keratinocytes and leukemia HL-60 cells induced by 1,25-dihydroxyvitamin D [1,25(OH)2D] has been reported to be mediated, at least in part, by increases in cellular ceramide levels. Ceramides produced by 1,25(OH)2D-induced sphingomyelin (SM) hydrolysis also contribute to the permeability barrier lipids in keratinocytes. Exogenously supplied SM is taken up by mammalian cells, including keratinocytes, and is incorporated into cellular pools. However, the effects of exogenously added SM on keratinocyte differentiation have not been studied. Therefore, in this study, we compared exogenously added SM with a cell-permeable ceramide for their ability to stimulate keratinocyte differentiation induced by 1,25(OH)2D. Both short-chain ceramide (C2-cer) and SM stimulated the differentiation and inhibited the proliferation of HL-60 cells. As expected, this effect was potentiated by 1,25(OH)2D. However, SM inhibited the differentiation and stimulated the proliferation of keratinocytes. While C2-cer potentiated the effects of 1,25(OH)2D, SM reversed the effects of 1,25(OH)2D on keratinocytes. The ratio of SM to ceramide was significantly different between keratinocytes and HL-60 cells. While the SM level of HL-60 cells were twice that of keratinocytes, keratinocytes contained ten times more ceramides than HL-60 cells, resulting in a ceramide/SM ratio 17 times higher in keratinocytes. Thus, we identified similarities and significant differences in the sphingolipid-mediated cell signaling pathway between keratinocytes and HL-60 cells. While SM stimulated HL-60 cell differentiation, presumably by incorporation into SMase-accessible membrane pools, it inhibited keratinocyte differentiation. In keratinocytes, SM was possibly incorporated into a different cellular pool (barrier lipid pool) or altered membrane phospholipid metabolism and membrane fluidity.
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Affiliation(s)
- S Pillai
- Unilever Research, Edgewater, New Jersey 07020, USA.
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Mahajan M, Rohtagi D. Microbiological assay versus spectrophotometry for determination of rifampicin in serum and cerebrospinal fluid. J Commun Dis 1998; 30:293-4. [PMID: 10810573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- M Mahajan
- Department of Microbiology and Pharmacology, UCMS and GTB Hospital, Delhi
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