|
1
|
Chiou SH, Tseng D, Reuben A, Mallajosyula V, Molina IS, Conley S, Wilhelmy J, McSween AM, Yang X, Nishimiya D, Sinha R, Nabet BY, Wang C, Shrager JB, Berry MF, Backhus L, Lui NS, Wakelee HA, Neal JW, Padda SK, Berry GJ, Delaidelli A, Sorensen PH, Sotillo E, Tran P, Benson JA, Richards R, Labanieh L, Klysz DD, Louis DM, Feldman SA, Diehn M, Weissman IL, Zhang J, Wistuba II, Futreal PA, Heymach JV, Garcia KC, Mackall CL, Davis MM. Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. Immunity 2021; 54:586-602.e8. [PMID: 33691136 PMCID: PMC7960510 DOI: 10.1016/j.immuni.2021.02.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/08/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
To identify disease-relevant T cell receptors (TCRs) with shared antigen specificity, we analyzed 778,938 TCRβ chain sequences from 178 non-small cell lung cancer patients using the GLIPH2 (grouping of lymphocyte interactions with paratope hotspots 2) algorithm. We identified over 66,000 shared specificity groups, of which 435 were clonally expanded and enriched in tumors compared to adjacent lung. The antigenic epitopes of one such tumor-enriched specificity group were identified using a yeast peptide-HLA A∗02:01 display library. These included a peptide from the epithelial protein TMEM161A, which is overexpressed in tumors and cross-reactive epitopes from Epstein-Barr virus and E. coli. Our findings suggest that this cross-reactivity may underlie the presence of virus-specific T cells in tumor infiltrates and that pathogen cross-reactivity may be a feature of multiple cancers. The approach and analytical pipelines generated in this work, as well as the specificity groups defined here, present a resource for understanding the T cell response in cancer.
Collapse
Affiliation(s)
- Shin-Heng Chiou
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Diane Tseng
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Irene S Molina
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Stephanie Conley
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Julie Wilhelmy
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Alana M McSween
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Xinbo Yang
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Daisuke Nishimiya
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chunlin Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Mark F Berry
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Leah Backhus
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Natalie S Lui
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Heather A Wakelee
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Joel W Neal
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Sukhmani K Padda
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Patrick Tran
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Jalen A Benson
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Rebecca Richards
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dorota D Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - David M Louis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Jianjun Zhang
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|