Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies

Li Song, Zhangyi Ouyang, David Cohen, Yang Cao, Jennifer Altreuter, Gali Bai, Xihao Hu, Kenneth J. Livak, Heng Li, Ming Tang, Bo Li, X. Shirley Liu

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

We applied our computational algorithm TRUST4 to assemble immune receptor (T-cell receptor/B-cell receptor) repertoires from approximately 12,000 RNA sequencing samples from The Cancer Genome Atlas and seven immunotherapy studies. From over 35 million assembled complete complementary-determining region 3 sequences, we observed that the expression of CCL5 and MZB1 is the most positively correlated genes with T-cell clonal expansion and B-cell clonal expansion, respectively. We analyzed amino acid evolution during B-cell receptor somatic hypermutation and identified tyrosine as the preferred residue. We found that IgG1+IgG3 antibodies together with FcRn were associated with complementdependent cytotoxicity and antibody-dependent cellular cytotoxicity or phagocytosis. In addition to B-cell infiltration, we discovered that B-cell clonal expansion and IgG1+IgG3 antibodies are also correlated with better patient outcomes. Finally, we created a website, VisualizIRR, for users to interactively explore and visualize the immune repertoires in this study.

Original languageEnglish (US)
Pages (from-to)788-799
Number of pages12
JournalCancer Immunology Research
Volume10
Issue number7
DOIs
StatePublished - Jul 2022

ASJC Scopus subject areas

  • Immunology
  • Cancer Research

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