Pan-cancer proteogenomics connects oncogenic drivers to functional states.

Autor: Li Y; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Porta-Pardo E; Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain., Tokheim C; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA., Bailey MH; Department of Biology and Simmons Center for Cancer Research, Brigham Young University, Provo, UT 84602, USA., Yaron TM; Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA., Stathias V; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA., Geffen Y; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA., Imbach KJ; Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain., Cao S; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Anand S; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Akiyama Y; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Liu W; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA., Wyczalkowski MA; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Song Y; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Storrs EP; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Wendl MC; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA., Zhang W; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Sibai M; Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain., Ruiz-Serra V; Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Spain; Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain., Liang WW; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Terekhanova NV; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Rodrigues FM; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Clauser KR; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Heiman DI; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Zhang Q; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Aguet F; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Calinawan AP; Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Dhanasekaran SM; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA., Birger C; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Satpathy S; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Zhou DC; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Wang LB; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Baral J; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA., Johnson JL; Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Huntsman EM; Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Pugliese P; Department of Science and Technology, University of Sannio, 82100 Benevento, Italy., Colaprico A; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA., Iavarone A; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Neurological Surgery, Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA., Chheda MG; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Neurology, Washington University in St. Louis, St. Louis, MO 63130, USA., Ricketts CJ; Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA., Fenyö D; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA., Payne SH; Department of Biology, Brigham Young University, Provo, UT 84602, USA., Rodriguez H; Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA., Robles AI; Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA., Gillette MA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA., Kumar-Sinha C; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA., Lazar AJ; Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Cantley LC; Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA. Electronic address: lewis_cantley@dfci.harvard.edu., Getz G; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA. Electronic address: gadgetz@broadinstitute.org., Ding L; Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA. Electronic address: lding@wustl.edu.

Publikováno v: Cell [Cell] 2023 Aug 31; Vol. 186 (18), pp. 3921-3944.e25. Date of Electronic Publication: 2023 Aug 14.

Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.

Autor: Sahu A; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, Colorado., Wang X; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China., Munson P; Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts., Klomp JPG; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Wang X; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Cardiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China., Gu SS; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Han Y; School of Life Sciences and Technology, Tongji University, Shanghai, China., Qian G; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Nicol P; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Zeng Z; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Wang C; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Tokheim C; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Zhang W; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Fu J; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Wang J; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Nair NU; Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland., Rens JAP; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Bourajjaj M; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Jansen B; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Leenders I; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Lemmers J; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Musters M; Lead Pharma, Kloosterstraat, Oss, the Netherlands., van Zanten S; Lead Pharma, Kloosterstraat, Oss, the Netherlands., van Zelst L; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Worthington J; Axis Bioservices, Coleraine, United Kingdom., Liu JS; Department of Statistics, Harvard University, Cambridge, Massachusetts., Juric D; Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts., Meyer CA; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Oubrie A; Lead Pharma, Kloosterstraat, Oss, the Netherlands., Liu XS; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Fisher DE; Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts.; Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts., Flaherty KT; Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, Massachusetts.

Publikováno v: Cancer discovery [Cancer Discov] 2023 Mar 01; Vol. 13 (3), pp. 672-701.

Genetic fusions favor tumorigenesis through degron loss in oncogenes.

Autor: Liu J; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA., Tokheim C; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA., Lee JD; Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.; Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA., Gan W; Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA., North BJ; Department of Biomedical Sciences, Creighton University, Omaha, NE, 68178, USA., Liu XS; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. xsliu@ds.dfci.harvard.edu.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. xsliu@ds.dfci.harvard.edu., Pandolfi PP; Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA. PierPaolo.PandolfiDeRinaldis@renown.org.; Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10124, Italy. PierPaolo.PandolfiDeRinaldis@renown.org.; Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, 89502, USA. PierPaolo.PandolfiDeRinaldis@renown.org., Wei W; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA. wwei2@bidmc.harvard.edu.

Publikováno v: Nature communications [Nat Commun] 2021 Nov 18; Vol. 12 (1), pp. 6704. Date of Electronic Publication: 2021 Nov 18.

Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network.

Autor: Zeng Z; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Fu J; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, China., Cibulskis C; Broad Institute of MIT and Harvard, Cambridge, Massachusetts., Jhaveri A; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Gumbs C; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Das B; Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland., Sanchez-Espiridion B; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Janssens S; The Emmes Company, LLC, Rockville, Maryland., Taing L; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts., Wang J; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, China., Lindsay J; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Vilimas T; Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland., Zhang J; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Tokheim C; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Sahu A; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Jiang P; Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland., Yan C; Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland., Duose DY; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Cerami E; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Chen L; Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland., Cohen D; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Chen Q; Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland., Enos R; The Emmes Company, LLC, Rockville, Maryland., Huang X; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Lee JJ; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas., Liu Y; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Neuberg DS; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Nguyen C; Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland., Patterson C; Broad Institute of MIT and Harvard, Cambridge, Massachusetts., Sarkar S; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Shukla S; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts., Tang M; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts., Tsuji J; Broad Institute of MIT and Harvard, Cambridge, Massachusetts., Uduman M; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts., Wang X; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Weirather JL; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.; Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts., Yu J; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Yu J; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts., Zhang J; Department of Thoracic/Head and Neck Medical Oncology and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Zhang J; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas., Meerzaman D; Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland., Thurin M; Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland., Futreal A; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Karlovich C; Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland., Gabriel SB; Broad Institute of MIT and Harvard, Cambridge, Massachusetts., Wistuba II; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.; Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas., Liu XS; Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts. cwu@partners.org xsliu@ds.dfci.harvard.edu.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts., Wu CJ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts. cwu@partners.org xsliu@ds.dfci.harvard.edu.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.

Publikováno v: Clinical cancer research : an official journal of the American Association for Cancer Research [Clin Cancer Res] 2021 Sep 15; Vol. 27 (18), pp. 5049-5061. Date of Electronic Publication: 2020 Dec 15.

pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection.

Autor: Xia, Huiming^1,2 (AUTHOR), Hoang, My H.¹ (AUTHOR), Schmidt, Evelyn¹ (AUTHOR), Kiwala, Susanna¹ (AUTHOR), McMichael, Joshua² (AUTHOR), Skidmore, Zachary L.^1,2 (AUTHOR), Fisk, Bryan^1,2 (AUTHOR), Song, Jonathan J.^1,2 (AUTHOR), Hundal, Jasreet² (AUTHOR), Mooney, Thomas² (AUTHOR), Walker, Jason R.² (AUTHOR), Goedegebuure, S. Peter^3,4 (AUTHOR), Miller, Christopher A.^1,4 (AUTHOR), Gillanders, William E.^3,4 (AUTHOR), Griffith, Obi L.^1,2,4,5 (AUTHOR) obigriffith@wustl.edu, Griffith, Malachi^1,2,4,5 (AUTHOR) mgriffit@wustl.edu

Publikováno v: Genome Medicine. 11/14/2024, Vol. 16 Issue 1, p1-12. 12p.