Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma.

• Authors: Moon Hee Lee, University of Helsinki; Jason Theodoropoulos, University of Helsinki; Jani Huuhtanen, University of Helsinki; Dipabarna Bhattacharya, University of Helsinki; Petrus Järvinen, Helsinki University; Sara Tornberg, Helsinki University; Harry Nísen, Helsinki University; Tuomas Mirtti, Emory University; Ilona Uski, University of Helsinki; Anita Kumari, University of Helsinki; Karita Peltonen, University of Helsinki; Arianna Draghi, Copenhagen University; Marco Donia, Copenhagen University; Anna Kreutzman, University of Helsinki; Satu Mustjoki, University of Helsinki
• Journal Title: Cancer Res Commun
• Volume: Volume 3, Number 7
• Publisher: American Association for Cancer Research | 2023-07, Pages 1260-1276
• Type of Work: Article | Final Publisher PDF
• Publisher DOI: http://doi.org/10.1158/2767-9764.CRC-22-0514
• Subjects: Health Sciences, Immunology; Chemistry, General; Health Sciences, Pathology; Engineering, Biomedical; Health Sciences, Oncology
• Keywords: Humans; Lymphocytes, Tumor-Infiltrating; Carcinoma, Renal Cell; CD8-Positive T-Lymphocytes; Kidney Neoplasms; Receptors, Antigen, T-Cell; Receptors, Antigen, T-Cell, alpha-beta; Tumor Microenvironment

Abstract

UNLABELLED: The successful use of expanded tumor-infiltrating lymphocytes (TIL) in adoptive TIL therapies has been reported, but the effects of the TIL expansion, immunophenotype, function, and T cell receptor (TCR) repertoire of the infused products relative to the tumor microenvironment (TME) are not well understood. In this study, we analyzed the tumor samples (n = 58) from treatment-naïve patients with renal cell carcinoma (RCC), "pre-rapidly expanded" TILs (pre-REP TIL, n = 15) and "rapidly expanded" TILs (REP TIL, n = 25) according to a clinical-grade TIL production protocol, with single-cell RNA (scRNA)+TCRαβ-seq (TCRαβ sequencing), TCRβ-sequencing (TCRβ-seq), and flow cytometry. REP TILs encompassed a greater abundance of CD4+ than CD8+ T cells, with increased LAG-3 and low PD-1 expressions in both CD4+ and CD8+ T cell compartments compared with the pre-REP TIL and tumor T cells. The REP protocol preferentially expanded small clones of the CD4+ phenotype (CD4, IL7R, KLRB1) in the TME, indicating that the largest exhausted T cell clones in the tumor do not expand during the expansion protocol. In addition, by generating a catalog of RCC-associated TCR motifs from >1,000 scRNA+TCRαβ-seq and TCRβ-seq RCC, healthy and other cancer sample cohorts, we quantified the RCC-associated TCRs from the expansion protocol. Unlike the low-remaining amount of anti-viral TCRs throughout the expansion, the quantity of the RCC-associated TCRs was high in the tumors and pre-REP TILs but decreased in the REP TILs. Our results provide an in-depth understanding of the origin, phenotype, and TCR specificity of RCC TIL products, paving the way for a more rationalized production of TILs. SIGNIFICANCE: TILs are a heterogenous group of immune cells that recognize and attack the tumor, thus are utilized in various clinical trials. In our study, we explored the TILs in patients with kidney cancer by expanding the TILs using a clinical-grade protocol, as well as observed their characteristics and ability to recognize the tumor using in-depth experimental and computational tools.