@article{54ac29e1f23d4f81ac508c71bb8e3468,
title = "Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies",
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.",
author = "Li Song and Zhangyi Ouyang and David Cohen and Yang Cao and Jennifer Altreuter and Gali Bai and Xihao Hu and Livak, {Kenneth J.} and Heng Li and Ming Tang and Bo Li and Liu, {X. Shirley}",
note = "Funding Information: We acknowledge the following funding sources for supporting this work: NCI grants U01CA226196 (H. Li), U24CA224316 (CIDC at DFCI), 1R01CA245318 (B. Li), 1R01CA258524-01A1 (B. Li), and China Scholarship Council (Z. Ouyang and Y. Cao). Funding Information: L. Song reports grants from NCI during the conduct of the study. D. Cohen reports grants from NCI during the conduct of the study; personal fees from ProFound Therapeutics outside the submitted work. X. Hu reports other support from GV20 Therapeutics outside the submitted work. K.J. Livak reports grants from NIH/NCI during the conduct of the study; other support from Fluidigm Corporation outside the submitted work. X.S. Liu reports grants from NIH during the conduct of the study; and X.S. Liu conducted the work while being a faculty at DFCI, and is currently a board member and shareholder of GV20 Oncotherapy, and the full-time CEO of its subsidiary GV20 Therapeutics. X. Hu conducted the work while being a postdoctoral fellow at DFCI, and is currently a full-time employee of GV20 Therapeutics. No disclosures were reported by the other authors. Publisher Copyright: {\textcopyright} 2022 American Association for Cancer Research.",
year = "2022",
month = jul,
doi = "10.1158/2326-6066.CIR-21-0965",
language = "English (US)",
volume = "10",
pages = "788--799",
journal = "Cancer Immunology Research",
issn = "2326-6066",
publisher = "American Association for Cancer Research Inc.",
number = "7",
}