TY - JOUR

T1 - Targeting Precision in Cancer Immunotherapy: Naturally-Occurring Antigen-Specific TCR Discovery with Single-Cell Sequencing

AU - Alrhmoun, Saleh

AU - Fisher, Marina

AU - Lopatnikova, Julia

AU - Perik-Zavodskaia, Olga

AU - Volynets, Marina

AU - Perik-Zavodskii, Roman

AU - Shevchenko, Julia

AU - Nazarov, Kirill

AU - Philippova, Julia

AU - Alsalloum, Alaa

AU - Kurilin, Vasily

AU - Silkov, Alexander

AU - Sennikov, Sergey

N1 - This work was carried out with the support of the Russian Science Foundation, project number 21-65-00004

PY - 2024/12

Y1 - 2024/12

N2 - Background: Adoptive cell therapy is the most promising approach for battling cancer, with T cell receptor-engineered T (TCR-T) cell therapy emerging as the most viable option for treating solid tumors. Current techniques for preparing TCR-T cell therapy provide a limited number of candidates TCRs, missing the comprehensive view of the repertoire, which may hinder the identification of the most effective TCRs. Methods: Dendritic cells were primed with immunogenic peptides of the antigen of interest to expand antigen-specific CD8 T lymphocytes from peripheral blood. Following that, the entire repertoire of naturally occurring antigen-specific TCRs was analyzed using single-cell RNA sequencing, alongside the assessment of the dominancy, transcriptome, and binding specificity of the obtained clonotypes, utilizing the TCRscape tool and ERGO-II neural network to identify the most effective candidate for TCR-T cell therapy development. Finally, TCR-T cells with the candidate TCR were obtained, followed by assessing their functionality and selectivity. Results: The developed protocol achieved a remarkable increase in the percentage of antigen-specific T cells by more than 200-fold, with more than 100 antigen-specific TCR clonotypes identified. The resulting TCR-T cells demonstrated high cytotoxicity and selectivity for the targeted antigen, indicating their potential to preferentially target tumor cells. Conclusions: This study offers a comprehensive approach for the discovery and analysis of not only few, but the entire repertoire of naturally occurring antigen-specific TCRs for TCR-T cell therapy development. Additionally, the proposed approach can be tailored to accommodate different types of antigens and MHC variants, making it a highly versatile tool for both research and clinical applications.

AB - Background: Adoptive cell therapy is the most promising approach for battling cancer, with T cell receptor-engineered T (TCR-T) cell therapy emerging as the most viable option for treating solid tumors. Current techniques for preparing TCR-T cell therapy provide a limited number of candidates TCRs, missing the comprehensive view of the repertoire, which may hinder the identification of the most effective TCRs. Methods: Dendritic cells were primed with immunogenic peptides of the antigen of interest to expand antigen-specific CD8 T lymphocytes from peripheral blood. Following that, the entire repertoire of naturally occurring antigen-specific TCRs was analyzed using single-cell RNA sequencing, alongside the assessment of the dominancy, transcriptome, and binding specificity of the obtained clonotypes, utilizing the TCRscape tool and ERGO-II neural network to identify the most effective candidate for TCR-T cell therapy development. Finally, TCR-T cells with the candidate TCR were obtained, followed by assessing their functionality and selectivity. Results: The developed protocol achieved a remarkable increase in the percentage of antigen-specific T cells by more than 200-fold, with more than 100 antigen-specific TCR clonotypes identified. The resulting TCR-T cells demonstrated high cytotoxicity and selectivity for the targeted antigen, indicating their potential to preferentially target tumor cells. Conclusions: This study offers a comprehensive approach for the discovery and analysis of not only few, but the entire repertoire of naturally occurring antigen-specific TCRs for TCR-T cell therapy development. Additionally, the proposed approach can be tailored to accommodate different types of antigens and MHC variants, making it a highly versatile tool for both research and clinical applications.

KW - HER2/neu

KW - TCR-T cell therapy

KW - adoptive cell therapy

KW - cancer immunotherapy

KW - naturally occurring TCRs

KW - single-cell sequencing

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85211798100&origin=inward&txGid=60ac87aed15fd3d8303fb0ee457436dd

UR - https://www.mendeley.com/catalogue/713fff97-00b3-372d-a2c1-a3222095eb38/

U2 - 10.3390/cancers16234020

DO - 10.3390/cancers16234020

M3 - Article

C2 - 39682207

VL - 16

JO - Cancers

JF - Cancers

SN - 2072-6694

IS - 23

M1 - 4020

ER -