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Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy

ABSTRACT: Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy

PROVIDER: PRJNA580251 | ENA |

REPOSITORIES: ENA

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Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy

Project description:We performed single-cell RNA sequencing (scRNA-seq) and deep analysis of T cell receptor (TCR) clonotypes (scTCR-seq) in cancer patients across several indications, assessing the profiles of TCRs in the various populations of T cells in tumours, normal adjacent tissue (NAT), and peripheral blood. In a subset of patients, we find clear evidence of clonotypic expansion of T effector-like cells not only within the tumour but also in NAT.

2019-12-09 | GSE139555 | GEO

Responders to immune checkpoint therapy display early clonal expansion of tumour-infiltrating lymphocytes

Project description:Responders to immune checkpoint therapy display early clonal expansion of tumour-infiltrating lymphocytes

| PRJNA922553 | ENA

Responders to immune checkpoint therapy display early clonal expansion of tumour-infiltrating lymphocytes

Project description:Using murine models that exclude variation in host genetics, environmental factors and tumour mutation burden, limiting variation between animals to naturally diverse TCRβ repertoires, we applied bulk TCRseq to study TCRβ repertoire dynamics in ICT responders and non-responders

2024-05-08 | GSE222575 | GEO

WISP2/CCN5 is a prognostic biomarker influenced by tumour purity and fibroblast infiltration in hepatocellular carcinoma

Project description:Background Hepatocellular carcinoma (HCC) is the second leading cause of cancer death worldwide. The dismal outcome is attributable to high frequency of recurrence and metastasis. Therefore, identification of effective biomarkers is a key strategy to inform prognosis and improve survival of HCC patients Methods We analysed expression of WNT-1-induced signalling protein-2 (WISP2) and the prognostic correlation in HCC patients using Oncomine, Kaplan Meier plotter, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) . We explored the role of WISP2 in HCC using the Cancer Cell Line Encyclopedia (CCLE) and gene microarrays and then assessed the correlation between WISP2 and stromal cells in tumour tissues using the Tumor IMmune Estimation Resource (TIMER). Finally, the role of WISP2 and its relationship with tumour purity and fibroblast infiltration were examined both in vitro and in vivo. Results WISP2 was downregulated in HCC tissues, and high expression of WISP2 was associated with better prognosis in patients with certain clinicopathologic characteristics. Upregulation of WISP2 in HCC was related to inhibition of the malignant phenotype in vitro, but these alterations were not observed in vivo . WISP2 also negatively correlated with tumour purity, and increased infiltration of fibroblasts promoted malignant progression in HCC tissues. The enhanced infiltration ability of fibroblasts was related to upregulated high-mobility group protein 1 (HMGB1) after overexpression of WISP2 in HCC. Conclusions The findings shed light on the anticancer role of WISP2 in HCC, suggest that WISP2 overexpression may serve as a biomarker for better prognosis, and indicate that WISP2 expression is influenced by tumour purity and fibroblast infiltration.

2019-07-20 | GSE134563 | GEO

RNA-seq analysis of CD8 tumour infiltrating lymphocytes from GFP-Egr2 Knockin and hCD2-Cre Egr2loxP/loxP Egr3-/- mice

Project description:To determine the effect of Egr2 and Egr3 on tumour infiltrating lymphocyte gene expression, GFP-Egr2 knockin (Egr2 Kin) and hCD2-Cre Egr2loxP/loxP Egr3-/- (Egr2/3 DKO) mice were inoculated with MC38 or B16 tumour cells. Fourteen days later, GFP-Egr2high and Egr2-/-Egr3-/- CD8+ tumour infiltrating lymphocytes were isolated from Egr2 Kin and Egr2/3 DKO mice, respectively, and analysed by RNA-seq.

2023-01-31 | E-MTAB-11672 | biostudies-arrayexpress

SPP1+ macrophages in HR+ breast cancer are associated with tumour-infiltrating lymphocytes.

Project description:SPP1+ macrophages in HR+ breast cancer are associated with tumour-infiltrating lymphocytes.

| PRJNA1088841 | ENA

microRNAs of thymocytes and of peripheral and pancreas-infiltrating T lymphocytes

Project description:As early as one month of age, nonobese diabetic (NOD) mice feature pancreatic infiltration of autoreactive T lymphocytes, which destruct insulin-producing beta cells, producing autoimmune diabetes mellitus (T1D) within eightmonths. Thus, we hypothesized that during the development of T1D, the transcriptional modulation of immune reactivity genes may occur as thymocytes mature into peripheral T lymphocytes. The transcriptome of thymocytes and peripheral CD3+ T lymphocytes from prediabetic or diabetic mice analyzed through microarray hybridizations identified the differentially expressed genes.

2012-07-31 | E-MEXP-3572 | biostudies-arrayexpress

mRNAs of thymocytes and of peripheral and pancreas-infiltrating T lymphocytes

Project description:As early as one month of age, nonobese diabetic (NOD) mice feature pancreatic infiltration of autoreactive T lymphocytes, which destruct insulin-producing beta cells, producing autoimmune diabetesmellitus (T1D) within eight months. Thus, we hypothesized that during the development of T1D, the transcriptional modulation of immune reactivity genes may occur as thymocytes mature into peripheral T lymphocytes. The transcriptome of thymocytes and peripheral CD3+ T lymphocytes from prediabetic or diabetic mice analyzed through microarray hybridizations identified the differentially expressed genes.

2012-07-31 | E-MEXP-3573 | biostudies-arrayexpress

WISP2/CCN5 is a prognostic biomarker influenced by tumour purity and fibroblast infiltration in hepatocellular carcinoma

Project description:WISP2/CCN5 is a prognostic biomarker influenced by tumour purity and fibroblast infiltration in hepatocellular carcinoma

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Therapy induced tumour secretomes promote resistance and tumour progression

Project description:Drug resistance invariably limits the clinical efficacy of targeted therapy with kinase inhibitors against cancer. We found that targeted therapy with BRAF, ALK, or EGFR inhibitors induces a complex network of secreted signals in drug-stressed melanoma and lung adenocarcinoma cells. This therapy-induced secretome (TIS) stimulates the outgrowth, infiltration and metastasis of drug-resistant cancer clones in the tumour. Additionally, the TIS supports the survival of drug-sensitive cells, contributing to incomplete tumour regression. We used transcriptomic analysis of sensitive tumour cells and xenograft tumours treated with vehicle, vemurafenib, or crizotinib to identify the transcriptional drivers and to dissect the TIS in melanoma (A375, Colo800, UACC62) and lung adenocarcinoma (H3122). In addition, we utilize cell type–specific mRNA purification by translating ribosome affinity purification (TRAP) to identify pathways that are up-regulated in resistant cells (A375R) in response to the regressing tumour microenvironment.

2015-03-26 | GSE64741 | GEO

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