Ontology highlight
ABSTRACT:
PROVIDER: PRJNA544699 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We analyzed 778,938 T cell receptor (TCR) CDR3b sequences from 178 non-small cell lung cancer (NSCLC) patients using GLIPH2 (Grouping of Lymphocyte Interactions with Paratope Hotspots 2). We identified over 66,000 TCR shared specificity groups, of which over 400 were enriched in tumor vs. adjacent lung. We focused on one tumor-enriched specificity group and used a yeast display library to identify the peptide epitopes. These include peptides from TMEM161A, which is an overexpressed antigen in NSCLC, and homologous peptides from Epstein-Barr virus (EBV) and E. coli, aligning with recent reports of virus-specific T cells in tumor infiltrates. Overall, we analyzed a very large dataset of TCR sequences from NSCLC patients and found thousands of specificities shared by three or more patients. This creates a database of TCR shared specificity groups in NSCLC, and also a template for mining and understanding the specificity of infiltrating T cells for any cancer.
2021-03-11 | GSE151531 | GEO
Project description:We analyzed 778,938 T cell receptor (TCR) CDR3b sequences from 178 non-small cell lung cancer (NSCLC) patients using GLIPH2 (Grouping of Lymphocyte Interactions with Paratope Hotspots 2). We identified over 66,000 TCR shared specificity groups, of which over 400 were enriched in tumor vs. adjacent lung. We focused on one tumor-enriched specificity group and used a yeast display library to identify the peptide epitopes. These include peptides from TMEM161A, which is an overexpressed antigen in NSCLC, and homologous peptides from Epstein-Barr virus (EBV) and E. coli, aligning with recent reports of virus-specific T cells in tumor infiltrates. Overall, we analyzed a very large dataset of TCR sequences from NSCLC patients and found thousands of specificities shared by three or more patients. This creates a database of TCR shared specificity groups in NSCLC, and also a template for mining and understanding the specificity of infiltrating T cells for any cancer.
2021-03-11 | GSE151537 | GEO
Project description:T cell responses within pediatric brain tumors (PBT) remain poorly understood. We performed single-cell RNA-seq (scRNA-seq) and paired T cell receptor sequencing (TCR-Seq) of patient-derived brain tumor-infiltrating T cells to map T cell molecular profile with TCR repertoire and clonality. We demonstrate marked clonal expansion of intra-tumoral T cells and reveal their differential phenotype, transcriptional state and functional properties within brain tumors. To understand T cell responses within highly immunogenic tumors that respond to checkpoint blockers, we undertook analysis of human non-small cell lung cancer (NSCLC). We performed single-cell RNA-seq (scRNA-seq) and paired T cell receptor sequencing (TCR-Seq) of patient-derived lung tumor-infiltrating T cells to map T cell molecular profile with clonality.
2024-01-16 | GSE221776 | GEO
Project description:We launched an investigator-initiated, Simon’s two-stage design trial of neoadjuvant sintilimab combined with carboplatin and nab-paclitaxel (nab-PC) in early-stage EGFR-mutant NSCLC (Clinicaltrial.gov number NCT05244213). Here we report the first interim results of stage 1 cohort which met the overall primary endpoint in advance, and multi-omics profiling of neoadjuvant immunotherapy combination in early-stage EGFR-mutant patients. We performed in-depth single-cell RNA/TCR sequencing (scRNA/TCR-seq) of cells derived from 11 resected tumors as well as 34 tumors from real-world cohort which were all confirmed wild-type lung adenocarcinoma (LUAD) or adeno-squamous carcinoma (ASC) and received neoadjuvant immunochemotherapy as control. By associating the tumor microenvironment (TME) and with responses, we uncovered heterogeneous mechanisms of primary resistance, providing insights into further strategic developments of combination regimens to improve the clinical outcome of EGFR-mutant NSCLC patients.
2024-05-17 | GSE241934 | GEO
Project description:Whole exome sequencing was performed on set of 48 DNA samples obtained from 16 EGFR mutated NSCLC patients whose tumors progressed following EGFR-TKI treatment. The DNA samples included baseline biopsy, rebiopsy and blood from the same patient. By comparing the variants in rebiopsy tumors and baseline tumors we aim to understand the genomic alterations responsible for the development of EGFR-TKI resistance in NSCLC patients.
2022-02-11 | E-MTAB-11404 | biostudies-arrayexpress
Project description:Considerable progress has recently been made in cancer immunotherapy, including immune checkpoint blockade, cancer vaccine, and adoptive T cell methods. The lack of effective targets is a major cause of the low immunotherapy response rate in colorectal cancer (CRC). Here, we used a proteogenomic strategy comprising immunopeptidomics, whole exome sequencing, and 16S ribosomal DNA sequencing analyses of 8 patients with CRC to identify neoantigens and bacterial immunopeptides that can serve as antitumor targets. This study directly identified several personalized neoantigens and bacterial immunopeptides. Immunoassays showed that all neoantigens and 5 of 8 bacterial immunopeptides could be recognized by autologous T cells. Additionally, T cell receptor (TCR) αβ sequencing revealed the TCR repertoire of epitope-reactive CD8+ T cells. Functional studies showed that T cell receptor -T (TCR-T) could be activated by epitope pulsed lymphoblastoid cells. Overall, this study comprehensively profiled the CRC immunopeptidome, revealing several neoantigens and bacterial immunopeptides with potential to serve as immunotherapy targets in CRC.
2023-11-28 | PXD047311 | iProX
Project description:Purpose: The goal of this study is to delineate the processes of CD8+ T cell differentiation in primary NSCLC by integrating transcriptomic and tcr profiles. Methods: A combination of single cell RNA and TCR sequencing (scRNA-seq and scTCR- seq) was used, in tumors, normal tissues adjacent to the tumor (juxta-tumor), and circulating blood derived from 11 patients with untreated, primary NSCLC. Results: We show that precursor, memory-like CD8+ TILs include 2 main populations: one is also present in the blood (circulating precursors); the other is also present in juxta-tumor tissue and bears markers of memory resident T cells (resident precursors). Both precursor subtypes differentiate into a main population of terminal effectors through a similar “transitional” stage. Terminal effectors are not observed in blood or juxta-tumor tissue, are more clonally expanded, and express signatures of exhaustion. A significant proportion of transitional and terminal effectors also express cell cycle signatures and Ki67, suggesting that clonal expansion occurs in situ is part of the terminal differentiation process.
2021-01-29 | GSE162498 | GEO
Project description:Purpose: The goal of this study is to delineate the processes of CD8+ T cell differentiation in primary NSCLC by integrating transcriptomic and tcr profiles. Methods: A combination of single cell RNA and TCR sequencing (scRNA-seq and scTCR- seq) was used, in tumors, normal tissues adjacent to the tumor (juxta-tumor), and circulating blood derived from 11 patients with untreated, primary NSCLC. Results: We show that precursor, memory-like CD8+ TILs include 2 main populations: one is also present in the blood (circulating precursors); the other is also present in juxta-tumor tissue and bears markers of memory resident T cells (resident precursors). Both precursor subtypes differentiate into a main population of terminal effectors through a similar “transitional” stage. Terminal effectors are not observed in blood or juxta-tumor tissue, are more clonally expanded, and express signatures of exhaustion. A significant proportion of transitional and terminal effectors also express cell cycle signatures and Ki67, suggesting that clonal expansion occurs in situ is part of the terminal differentiation process.
2021-01-29 | GSE162499 | GEO
Project description:Background: T-cell receptor (TCR) stimulation is essential to complete differentiation of tumor-infiltrating regulatory T cells (T-Tregs). Therefore, elucidation of TCR-dependent regulatory network involved in activation and proliferation of T-Tregs will facilitate discovery of novel antitumor remedy. Here, we investigated transcriptional features specific for antigen-reactive Tregs by harnessing single-cell RNA and TCR analyses of human Tregs derived from patients with non-small cell lung cancer (NSCLC). Methods: Assuming Tregs undergo clonal expansion in response to antigens, we sought for transcriptional features specific for antigen-reactive Tregs by comparing gene expression of Tregs with unique TCR clonotypes and those with expanded TCR clonotypes. To verify the identified molecule, multiplex immunohistochemistry and flow cytometry were used. Results: We found that the proportion of Tregs with expanded clonotypes was much higher in the tumor than in the periphery blood. We also found that T-Tregs with shared clonotypes were transcriptionally more similar to each other than to those with different clonotypes. Finally, we identified SYNGR2, TNFRSF18, DUSP4, and CTLA4 as core signature genes for T-Tregs with expanded clonotypes and confirmed their existences expressed on human T-Tregs. Interestingly, T-Treg-specific co-regulatory network revealed that SYNGR2, TNFRSF18 and DUSP4 are potential coordinators between TCR-dependent activation and cell proliferation. Conclusions: Our study shed light on regulatory insights of TCR-dependent Treg activation and differentiation in tumor and therapeutic strategies for patients with NSCLC.
2023-01-01 | GSE164146 | GEO
Project description:We had previously demonstrated the role of CD103 integrin on lung tumor-infiltrating lymphocyte (TIL) clones in promoting specific TCR-mediated epithelial tumor cell cytotoxicity. However, the contribution of CD103 on intratumoral T-cell distribution and functions, and the prognosis significance of TIL subpopulations in non-small cell lung carcinoma (NSCLC) have thus far not been systematically addressed. Here we investigate the transcriptomic profil of these cell population, using PBMC cells as control.
2015-06-29 | E-MTAB-3266 | biostudies-arrayexpress