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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ScRNA and TCRalpha-beta-seq data from 3 dissociated renal cell carcinoma samples that were CD45 positive sorted, enriched for lymphocytes and sequenced

ABSTRACT: In our study, we have characterized the non-expanded and expanded tumor-infiltrating lymphocytes (TILs) from treatment-naive renal cell carcinoma (RCC) patients (n=3), as well as the minimally cultured pre-REP TILs and rapidly expanded REP TILs with a clinical-grade TIL expansion protocol. We observed that the REP TILs encompassed an abundance of CD4positive T-cells, together with increased LAG-3 and low PD-1 expression in the CD4positive and CD8positive T-cells. In addition, we observed that the TIL expansion protocol expanded small CD4positive T-cell clonotypes in the tumor microenvironment (TME), and that the large, exhausted tumor T-cell clonotypes do not expand. We further identified RCC-associated TCR motifs that were validated in multiple TCRalpha-beta-seq and scRNAand TCRalpha-beta-seq datasets, as well as quantified the RCC-associated TCRs from the REP protocol. Overall, the T-cells carrying the RCC-associated TCRs remained high in the tumors and corresponding pre-REP TILs, but the frequency was reduced in the REP TILs. Furthermore, the overall anti-viral TCRs remained low throughout the REP protocol. Our results provide an in-depth understanding of the origin, immunophenotype, and specificity of the TCRs in RCC TILs.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Moon Hee Lee

PROVIDER: E-MTAB-12910 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The immunological characterization of expanded tumor-infiltrating lymphocytes in renal cell carcinoma patients

Project description:In this study, we comprehensively characterized the non-expanded and expanded tumor-infiltrating lymphocytes (TILs) from treatment-naÃƒÂ¯ve RCC patients, as well as the corresponding Ã¢Â€ÂœyoungÃ¢Â€Â TILs (pre-REP TILs) and Ã¢Â€Âœrapidly expandedÃ¢Â€Â TILs (REP TILs) following a clinical-grade TIL production protocol. From our scRNA+TCRÃŽÂ±ÃŽÂ²-seq and TCRÃŽÂ²-seq analyses, we show that the REP protocol preferentially favors the expansion CD4+ T-cells that originate from small T-cell clones in the tumor microenvironment (TME), indicating that the large, exhausted T-cell clones in the tumor do not expand during the protocol. We further identified RCC-associated TCR motifs that were validated in multiple TCRÃŽÂ±ÃŽÂ²-seq and scRNA+TCRÃŽÂ±ÃŽÂ²-seq datasets, as well as quantified the RCC-associated TCRs from the REP protocol. Overall, the T-cells carrying the RCC-associated TCRs remained high in the tumors and corresponding pre-REP TILs, but the frequency was reduced in the REP TILs. Furthermore, the overall anti-viral TCRs remained low throughout the REP protocol. Our results provide an in-depth understanding of the origin, phenotype, and specificity of the TCRs in RCC TILs.

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Fluidigm single-cell RNA-seq analysis for gene signatures associated with T-cell persistence

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Single-cell transcriptome analysis reveals gene signatures associated with T-cell persistence following adoptive cell therapy

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2019-10-15 | GSE135852 | GEO

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