دورية أكاديمية

Pan-cancer proteogenomics characterization of tumor immunity.

التفاصيل البيبلوغرافية
العنوان: Pan-cancer proteogenomics characterization of tumor immunity.
المؤلفون: Petralia F; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: francesca.petralia@mssm.edu., Ma W; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Yaron TM; Meyer Cancer Center, 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; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA., Caruso FP; BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy; Department of Electrical Engineering and Information Technologies, University of Naples 'Federico II', Naples, Italy., Tignor N; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Wang JM; Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA., Charytonowicz D; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Johnson JL; Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA., Huntsman EM; Meyer Cancer Center, 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., Marino GB; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Calinawan A; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Evangelista JE; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Selvan ME; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Chowdhury S; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Rykunov D; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Krek A; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Song X; Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Turhan B; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Christianson KE; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Lewis DA; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Deng EZ; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Clarke DJB; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Whiteaker JR; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA., Kennedy JJ; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA., Zhao L; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA., Segura RL; Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Batra H; Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Raso MG; Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Parra ER; Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Soundararajan R; Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Tang X; Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., 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., Yi X; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Satpathy S; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Wang Y; Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA., Wiznerowicz M; Department of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland; Department of Oncology, Heliodor Swiecicki Clinical Hospital, 60-203 Poznań, Poland., González-Robles TJ; Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA., Iavarone A; Department of Neurological Surgery, Department of Biochemistry, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA., Gosline SJC; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Reva B; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Robles AI; Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA., Nesvizhskii AI; Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Mani DR; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA., Gillette MA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA., Klein RJ; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Cieslik M; Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Zhang B; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Paulovich AG; Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA., Sebra R; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Gümüş ZH; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Hostetter G; Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA., Fenyö D; Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA., Omenn GS; Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & Environmental Health, University of Michigan, Ann Arbor, MI 48109, USA., Cantley LC; Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA., Ma'ayan A; Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Lazar AJ; Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Ceccarelli M; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA; Department of Public Health Sciences, University of Miami, Miami, FL, USA., Wang P; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: pei.wang@mssm.edu.
مؤلفون مشاركون: Clinical Proteomic Tumor Analysis Consortium
المصدر: Cell [Cell] 2024 Feb 29; Vol. 187 (5), pp. 1255-1277.e27. Date of Electronic Publication: 2024 Feb 14.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Cell Press Country of Publication: United States NLM ID: 0413066 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-4172 (Electronic) Linking ISSN: 00928674 NLM ISO Abbreviation: Cell Subsets: MEDLINE
أسماء مطبوعة: Publication: Cambridge, Ma : Cell Press
Original Publication: Cambridge, MIT Press.
مواضيع طبية MeSH: Neoplasms*/genetics , Neoplasms*/immunology , Neoplasms*/therapy , Proteogenomics*, Humans ; Combined Modality Therapy ; Genomics ; Proteomics ; Tumor Escape
مستخلص: Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.
Competing Interests: Declaration of interests R. Sebra is currently a paid consultant and equity holder at GeneDx. L.C.C. is a founder and member of the board of directors of Agios Pharmaceuticals; is a founder and receives research support from Petra Pharmaceuticals; has equity in and consults for Cell Signaling Technologies, Volastra, Larkspur, and 1 Base Pharmaceuticals; and consults for Loxo-Lilly. J.L.J. has received consulting fees from Scorpion Therapeutics and Volastra Therapeutics. T.M.Y. is a co-founder and stockholder of DeStroke.
(Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
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معلومات مُعتمدة: U24 CA210954 United States CA NCI NIH HHS; U01 CA214116 United States CA NCI NIH HHS; U24 CA210985 United States CA NCI NIH HHS; R33 CA263705 United States CA NCI NIH HHS; U24 CA210986 United States CA NCI NIH HHS; HHSN261201500003C United States CA NCI NIH HHS; U24 CA271075 United States CA NCI NIH HHS; U24 CA210955 United States CA NCI NIH HHS; P30 ES017885 United States ES NIEHS NIH HHS; U24 CA210993 United States CA NCI NIH HHS; U24 CA271114 United States CA NCI NIH HHS; U24 CA264250 United States CA NCI NIH HHS; T32 GM136542 United States GM NIGMS NIH HHS; U24 CA210967 United States CA NCI NIH HHS; U24 CA270823 United States CA NCI NIH HHS; F30 CA271622 United States CA NCI NIH HHS; U24 CA210972 United States CA NCI NIH HHS; U54 CA263001 United States CA NCI NIH HHS; HHSN261201500003I United States CA NCI NIH HHS; U24 CA210979 United States CA NCI NIH HHS; U24 CA271012 United States CA NCI NIH HHS; U01 CA214114 United States CA NCI NIH HHS; U01 CA214125 United States CA NCI NIH HHS; F30 CA265288 United States CA NCI NIH HHS; U24 CA224260 United States CA NCI NIH HHS
فهرسة مساهمة: Investigator: J Abelin; F Aguet; Y Akiyama; E An; S Anand; M Anurag; Ö Babur; J Bavarva; C Birger; MJ Birrer; S Cao; SA Carr; DW Chan; AM Chinnaiyan; H Cho; K Clauser; A Colaprico; DC Zhou; F da Veiga Leprevost; C Day; SM Dhanasekaran; L Ding; MJ Domagalski; Y Dou; BJ Druker; N Edwards; MJ Ellis; SM Foltz; A Francis; Y Geffen; G Getz; DI Heiman; R Hong; Y Hu; C Huang; EJ Jaehnig; SD Jewell; J Ji; W Jiang; L Katsnelson; KA Ketchum; I Kolodziejczak; K Krug; C Kumar-Sinha; JT Lei; WW Liang; Y Liao; CM Lindgren; T Liu; W Liu; J McDermott; W McKerrow; M Mesri; MB Mumphrey; CJ Newton; R Oldroyd; SH Payne; P Pugliese; KD Rodland; FM Rodrigues; KV Ruggles; SR Savage; EE Schadt; M Schnaubelt; T Schraink; S Schürer; Z Shi; RD Smith; F Song; Y Song; V Stathias; EP Storrs; J Tan; NV Terekhanova; RR Thangudu; M Thiagarajan; LB Wang; B Wen; Y Wu; MA Wyczalkowski; L Yao; QK Li; H Zhang; Q Zhang; X Zhang; Z Zhang
Keywords: histopathology; immune subtype; immunotherapy; kinase activity; multiomic deconvolution; proteogenomics; tumor immunity
تواريخ الأحداث: Date Created: 20240215 Date Completed: 20240304 Latest Revision: 20240617
رمز التحديث: 20240617
مُعرف محوري في PubMed: PMC10988632
DOI: 10.1016/j.cell.2024.01.027
PMID: 38359819
قاعدة البيانات: MEDLINE
الوصف
تدمد:1097-4172
DOI:10.1016/j.cell.2024.01.027