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Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

Author

Listed:
  • Mahesh Yadav

    (Genentech)

  • Suchit Jhunjhunwala

    (Genentech)

  • Qui T. Phung

    (Genentech)

  • Patrick Lupardus

    (Genentech)

  • Joshua Tanguay

    (Genentech)

  • Stephanie Bumbaca

    (Genentech)

  • Christian Franci

    (Genentech)

  • Tommy K. Cheung

    (Genentech)

  • Jens Fritsche

    (Immatics Biotechnologies GmbH, 72076 Tubingen, Germany)

  • Toni Weinschenk

    (Immatics Biotechnologies GmbH, 72076 Tubingen, Germany)

  • Zora Modrusan

    (Genentech)

  • Ira Mellman

    (Genentech)

  • Jennie R. Lill

    (Genentech)

  • Lélia Delamarre

    (Genentech)

Abstract

A combination of genome-wide exome and transcriptome analysis, mass spectrometry and computational structural modelling are used here to identify immunogenic neo-antigens in two mouse tumour cancer cell lines; mice vaccinated with predicted immunogenic peptides yielded therapeutically useful cytotoxic T-lymphocyte responses.

Suggested Citation

  • Mahesh Yadav & Suchit Jhunjhunwala & Qui T. Phung & Patrick Lupardus & Joshua Tanguay & Stephanie Bumbaca & Christian Franci & Tommy K. Cheung & Jens Fritsche & Toni Weinschenk & Zora Modrusan & Ira M, 2014. "Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing," Nature, Nature, vol. 515(7528), pages 572-576, November.
    • Handle: RePEc:nat:nature:v:515:y:2014:i:7528:d:10.1038_nature14001
    DOI: 10.1038/nature14001
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    Cited by:

    1. Hakimeh Ebrahimi-Nik & Marmar Moussa & Ryan P. Englander & Summit Singhaviranon & Justine Michaux & HuiSong Pak & Hiroko Miyadera & William L. Corwin & Grant L. J. Keller & Adam T. Hagymasi & Tatiana , 2021. "Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    2. Jiefei Han & Yiting Dong & Xiuli Zhu & Alexandre Reuben & Jianjun Zhang & Jiachen Xu & Hua Bai & Jianchun Duan & Rui Wan & Jie Zhao & Jing Bai & Xuefeng Xia & Xin Yi & Chao Cheng & Jie Wang & Zhijie W, 2024. "Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Mehwish Iftikhar & Muhammad Imran Qureshi & Shazia Qayyum & Iram Fatima & Sriyanto Sriyanto & Yasinta Indrianti & Aqeel Khan & Leo-Paul Dana, 2021. "Impact of Multifaceted Workplace Bullying on the Relationships between Technology Usage, Organisational Climate and Employee Physical and Emotional Health," IJERPH, MDPI, vol. 18(6), pages 1-19, March.
    4. Judit Svensson-Arvelund & Sara Cuadrado-Castano & Gvantsa Pantsulaia & Kristy Kim & Mark Aleynick & Linda Hammerich & Ranjan Upadhyay & Michael Yellin & Henry Marsh & Daniel Oreper & Suchit Jhunjhunwa, 2022. "Expanding cross-presenting dendritic cells enhances oncolytic virotherapy and is critical for long-term anti-tumor immunity," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Zhen Lu & Jinyun Chen & Pengfei Yu & Matthew J. Atherton & Jun Gui & Vivek S. Tomar & Justin D. Middleton & Neil T. Sullivan & Sunil Singhal & Subin S. George & Ashley G. Woolfork & Aalim M. Weljie & , 2022. "Tumor factors stimulate lysosomal degradation of tumor antigens and undermine their cross-presentation in lung cancer," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Naomi Hoenisch Gravel & Annika Nelde & Jens Bauer & Lena Mühlenbruch & Sarah M. Schroeder & Marian C. Neidert & Jonas Scheid & Steffen Lemke & Marissa L. Dubbelaar & Marcel Wacker & Anna Dengler & Rei, 2023. "TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Jennifer G. Abelin & Erik J. Bergstrom & Keith D. Rivera & Hannah B. Taylor & Susan Klaeger & Charles Xu & Eva K. Verzani & C. Jackson White & Hilina B. Woldemichael & Maya Virshup & Meagan E. Olive &, 2023. "Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    8. Ashish Goyal & Jens Bauer & Joschka Hey & Dimitris N. Papageorgiou & Ekaterina Stepanova & Michael Daskalakis & Jonas Scheid & Marissa Dubbelaar & Boris Klimovich & Dominic Schwarz & Melanie Märklin &, 2023. "DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    9. Jens Bauer & Natalie Köhler & Yacine Maringer & Philip Bucher & Tatjana Bilich & Melissa Zwick & Severin Dicks & Annika Nelde & Marissa Dubbelaar & Jonas Scheid & Marcel Wacker & Jonas S. Heitmann & S, 2022. "The oncogenic fusion protein DNAJB1-PRKACA can be specifically targeted by peptide-based immunotherapy in fibrolamellar hepatocellular carcinoma," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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