Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes

Tianshi Lu, Shidan Wang, Lin Xu, Qinbo Zhou, Nirmish Singla, Jianjun Gao, Subrata Manna, Laurentiu Pop, Zhiqun Xie, Mingyi Chen, Jason J. Luke, James Brugarolas, Raquibul Hannan, Tao Wang

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Lack of responsiveness to checkpoint inhibitors is a central problem in the modern era of cancer immunotherapy. Tumor neoantigens are critical targets of the host antitumor immune response, and their presence correlates with the efficacy of immunotherapy treatment. Many studies involving assessment of tumor neoantigens principally focus on total neoantigen load, which simplistically treats all neoantigens equally. Neoantigen load has been linked with treatment response and prognosis in some studies but not others. We developed a Cauchy-Schwarz index of Neoantigens (CSiN) score to better account for the degree of concentration of immunogenic neoantigens in truncal mutations. Unlike total neoantigen load determinations, CSiN incorporates the effect of both clonality and MHC binding affinity of neoantigens when characterizing tumor neoantigen profiles. By analyzing the clinical responses in 501 treated patients with cancer (with most receiving checkpoint inhibitors) and the overall survival of 1978 patients with cancer at baseline, we showed that CSiN scores predict treatment response to checkpoint inhibitors and prognosis in patients with melanoma, lung cancer, and kidney cancer. CSiN score substantially outperformed prior genetics-based prediction methods of responsiveness and fills an important gap in research involving assessment of tumor neoantigen burden.

Original languageEnglish (US)
JournalScience Immunology
Volume5
Issue number44
DOIs
StatePublished - Feb 21 2020

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

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