Gene expression differences between TILs that are reactive to tumor cells and TILs that are not reactive
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ABSTRACT:
PROVIDER: PRJNA1060655 | ENA |
REPOSITORIES: ENA
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Project description:Clinical significance of tumor-infiltrating lymphocytes (TILs) was demonstrated in many tumor types. In the clinical trials, immune check point inhibitors showed significant clinical efficacy in some tumor types with high mutation burden such as melanoma, bladder cancer, and smoking-induced lung cancer, while there were little effects in cancers with lower mutation rates such as breast cancer. Recently, selection and adoptive transfer of autologous mutation-specific TILs showed successful regression of metastatic tumors in an estrogen receptor-positive breast cancer patient. In this study, we analyzed gene expression profiles in cultured TILs that are reactive or non reactive against autologous breast cancer cells. We cultured TILs and cancer cells derived from breast tumor tissues obtained from the surgery. Reactivity of TILs against cancer cells was determined by interferon gamma (IFN-γ) ELISA analysis after co-culture of TILs and cancer cells for 24 hours. The total RNA was purified from cultured TILs (post-REP TILs) using RNeasy kits. The gene expression library is generated by Illumina TruSeq RNA library prep kit and sequenced.
2025-06-30 | GSE252437 | GEO
Project description:Tumor-reactive CD8+ tumor infiltrating lymphocytes (TILs) represent a subtype of T cells that could recognize and destroy tumor specifically. Understanding the regulatory mechanism of tumor-reactive CD8+ T cells has important therapeutic implications. Yet the DNA methylation status of this T cell subtype has not been elucidated. In this study, we segregated tumor-reactive and bystander CD8+ TILs, as well as naïve and effector memory CD8+ T cell subtypes as controls from colorectal cancer (CRC) patients, to compare their transcriptome and methylome characteristics. Transcriptome profiling confirmed previous conclusion that tumor-reactive TILs have an exhausted tissue-resident memory signature. Whole-genome methylation profiling identified a distinct methylome pattern of tumor-reactive CD8+ T cells, with tumor-reactive markers (CD39 and CD103) being specifically demethylated. In addition, dynamic changes were observed during the transition of naïve T cells into tumor-reactive CD8+ T cells. Transcription factor (TF) binding motif enrichment analysis identified several immune-related TFs, including three exhaustion-related genes (NR4A1, BATF and EGR2) and VDR, that potentially play important regulatory role in tumor-reactive CD8+ T cells. Our study supports the involvement of DNA methylation in shaping tumor-reactive and bystander CD8+ TILs, and provides a valuable resource for the development of novel DNA methylation markers and future therapeutics.
2019-12-12 | GSE141878 | GEO
Project description:Reactivation and clonal expansion of tumor specific antigen (TSA)-reactive T cells are key to the success of checkpoint blockade and adoptive transfer of tumor-infiltrating lymphocyte (TIL) based therapies. There are no reliable markers to specifically identify the repertoire of TSA-reactive T cells due to their heterogeneous composition. Here we introduce FucoID as a general platform to detect endogenous antigen-specific T cells and study their biology. Through this interaction dependent labeling approach, TSA-reactive T cells can be detected and separated from bystander T cells in primary tumor digests based on their cell-surface enzymatic fucosyl-biotinylation. Compared to bystander TILs, TSA-reactive TILs possess a unique gene features according to RNA-seq.
2020-10-22 | GSE154604 | GEO
Project description:Reactivation and clonal expansion of tumor specific antigen (TSA)-reactive T cells are key to the success of checkpoint blockade and adoptive transfer of tumor-infiltrating lymphocyte (TIL) based therapies. There are no reliable markers to specifically identify the repertoire of TSA-reactive T cells due to their heterogeneous composition. Here we introduce FucoID as a general platform to detect endogenous antigen-specific T cells and study their biology. Through this interaction dependent labeling approach, TSA-reactive T cells can be detected and separated from bystander T cells in primary tumor digests based on their cell-surface enzymatic fucosyl-biotinylation. Compared to bystander TILs, TSA-reactive TILs possess a unique gene features according to RNA-seq.
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Project description:Purpose: Transcriptome profiling (RNA-seq) was used to compare the expression differences between T in PBMC and TILs Methods:Paired TILs and T in PBMC cells were sorted from fresh patient blood and tumor samples. Then the mRNA were sequeced using xTen platform. The sequence reads that passed quality filters were analyzed. Results: by extract mRNA from tumor infiltrated T cells from ovarian cancer patient sample and T cells from patient bllod samples, we compared the different expressed genes from TIL and T in blood. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to T cell exhausetion. Conclusions: We conclude that T in PBMC and TILs share different transcriptome characterization.
2022-12-18 | GSE157936 | GEO
Project description:Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes and with cell products mostly composed of blood-borne clonotypes that persisted in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost tumor-associated transcriptional signatures, including exhaustion, and responders exhibited an intermediate exhausted effector state after TIL engraftment in the tumor, suggesting functional reinvigoration. Our findings provide insight into the nature and dynamics of tumor-specific clonotypes associated with clinical response to TIL-ACT, with implications for treatment optimization.
2024-09-13 | GSE261023 | GEO
Project description:Tumor-infiltrating lymphocyte (TIL)-therapy has received FDA approval for the treatment of advanced melanoma and shows potential for broader applications in solid tumors, including glioblastoma. In this study, tumor-reactive TILs (tr-TILs) are isolated and enriched for CD137 expression from cavitron ultrasonic aspirator (CUSA) emulsions of 161 adult patients diagnosed with diffuse gliomas. Tr-TILs are successfully expanded in 87 out of the 161 patients, reflecting an expansion rate of 54%. Notably, the presence of IDH1 mutation and the cumulative dose of steroids are identified as significant negative predictors of expansion efficacy. The expanded tr-TILs exhibit distinct phenotypic and molecular dysfunctional features yet show upregulated expression of progenitor/memory-like markers and polyclonal T-cell receptors. Importantly, these tr-TILs demonstrate specific antitumor reactivity against autologous tumor cells in both in vitro and in vivo xenograft models. These findings provide a compelling background for a personalized immunotherapeutic approach while tackling one of the most significant challenges in oncology.
2025-06-23 | GSE299789 | GEO
Project description:Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes and with cell products mostly composed of blood-borne clonotypes that persisted in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost tumor-associated transcriptional signatures, including exhaustion, and responders exhibited an intermediate exhausted effector state after TIL engraftment in the tumor, suggesting functional reinvigoration. Our findings provide insight into the nature and dynamics of tumor-specific clonotypes associated with clinical response to TIL-ACT, with implications for treatment optimization.
2023-08-01 | GSE229860 | GEO
Project description:Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes and with cell products mostly composed of blood-borne clonotypes that persisted in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost tumor-associated transcriptional signatures, including exhaustion, and responders exhibited an intermediate exhausted effector state after TIL engraftment in the tumor, suggesting functional reinvigoration. Our findings provide insight into the nature and dynamics of tumor-specific clonotypes associated with clinical response to TIL-ACT, with implications for treatment optimization.
2023-08-01 | GSE229858 | GEO
Project description:Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. Conversely, lack of clinical responses was associated with tumors devoid of tumor-reactive resident clonotypes and with cell products mostly composed of blood-borne clonotypes that persisted in blood but not in tumors post-ACT. Upon expansion, tumor-specific TILs lost tumor-associated transcriptional signatures, including exhaustion, and responders exhibited an intermediate exhausted effector state after TIL engraftment in the tumor, suggesting functional reinvigoration. Our findings provide insight into the nature and dynamics of tumor-specific clonotypes associated with clinical response to TIL-ACT, with implications for treatment optimization.
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