1
|
Teng YHF, Quah HS, Suteja L, Dias JML, Mupo A, Bashford-Rogers RJM, Vassiliou GS, Chua MLK, Tan DSW, Lim DWT, Iyer NG. Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures. Cancer Immunol Immunother 2022; 71:989-998. [PMID: 34580764 PMCID: PMC8476067 DOI: 10.1007/s00262-021-03047-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 08/25/2021] [Indexed: 12/02/2022]
Abstract
Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias toward the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood, but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus-driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (i.e., viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer but, in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages, and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific pattern motifs, and these motifs were uniquely found to each cancer type. This suggests that they may be enriched for specificity to common antigens found in the tumor microenvironment of different cancers. The identification of shared TCRs in infiltrating tumor T cells not only adds to our understanding of the tumor-adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.
Collapse
Affiliation(s)
- Yvonne H. F. Teng
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Hong Sheng Quah
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Lisda Suteja
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - João M. L. Dias
- Hutchison/MRC Research Centre, MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ UK
| | | | | | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, CB2 0AW UK
| | - Melvin L. K. Chua
- Duke-NUS Medical School, Singapore, Singapore
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Daniel S. W. Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Darren W. T. Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
| | - N. Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore, Singapore
| |
Collapse
|
2
|
Abstract
Despite the extreme diversity of T-cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely shared sequences, often referred to as "public," have been suggested to be over-represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here, we show that even for large cohorts, the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection. Whether a sequence is shared by many individuals is predicted to depend on the number of queried individuals and the sampling depth, as well as on the sequence itself, in agreement with the data. We introduce the degree of publicness conditional on the queried cohort size and the size of the sampled repertoires. Based on these observations, we propose a public/private sequence classifier, "PUBLIC" (Public Universal Binary Likelihood Inference Classifier), based on the generation probability, which performs very well even for small cohort sizes.
Collapse
Affiliation(s)
- Yuval Elhanati
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | - Zachary Sethna
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | | | - Thierry Mora
- Laboratoire de physique statistiqueCNRSSorbonne UniversitéUniversité Paris‐Diderot, and École Normale Supérieure (PSL University)ParisFrance
| | - Aleksandra M. Walczak
- Laboratoire de physique théoriqueCNRSSorbonne Université, and École Normale Supérieure (PSL University)ParisFrance
| |
Collapse
|