5fbb18ba-98d3-4073-ab43-9395f32b975c - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001011347 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Emerging evidence suggests that an increased density of pre-treatment CD8+ tumor-infiltrating lymphocytes (TILs) is associated with good response to chemoradiotherapy (CRT) in patients with locally advanced rectal cancer. However, the significance of T-cell complexity in the clinical setting remains unknown. High-throughput T-cell receptor (TCR) β sequencing was applied to quantify the TCR repertoire of pre-treatment biopsies from 67 patients with advanced rectal cancer receiving preoperative CRT. Changes in TCR repertoire before and after CRT were also analysed in 23 patients.
2022-11-22 | GSE218181 | GEO
Project description:Immune checkpoint inhibitors (CPI) have dramatically changed the treatment landscape of advanced HCC (aHCC), but factors associated with response/resistance to CPI remain to be elucidated. The main aim of this project was to identify features associated with response and/or resistance to checkpoint inhibitors in advanced HCC at the single-cell resolution. We subjected both pre-treatment tissue biopsies and serial peripheral blood mononuclear cell (PBMC) samples of aHCC patients (n=44) treated with systemic therapy to droplet-based single-cell transcriptome (scRNAseq) and T-cell receptor sequencing (scTCRseq) using Chromium Single Cell V(D)J Solution. Doing so, we obtained high quality transcriptomic data for tissue biopsies and PBMC samples.
| EGAS00001007547 | EGA
Project description:The addition of aPD1 to 5-FU/platinum in advanced gastric cancer (GC) yields variable responses. To understand cooperativity between chemotherapy and immunotherapy, we previously reported a phase II trial sequentially adding pembrolizumab to 5-FU/platinum. In this study, we use single-cell RNA- and TCR-sequencing to analyze 66,813 T cells from primary tumor biopsies pre-treatment, post-chemotherapy, and post-immunotherapy in 33 patients. We observed greater abundance, persistence, and recruitment of T cells with predicted tumor-reactivity in patients with prolonged progression-free survival (slow progressors). Increased B cell abundance and predicted B cell to T cell interactions supported T cell memory and co-stimulation, providing a mechanism for increased abundance and persistence of progenitor-exhausted and tumor-reactive T cells in slow progressors. T cell clones emerging in the tumor after immunotherapy were in the blood before treatment only in slow progressors. Our study thus highlights pre-treatment and early chemotherapy-induced T cell dynamics and B cell to T cell interactions that may drive durable response to chemoimmunotherapy in GC.
2026-04-01 | GSE315929 | GEO
Project description:The addition of aPD1 to 5-FU/platinum in advanced gastric cancer (GC) yields variable responses. To understand cooperativity between chemotherapy and immunotherapy, we previously reported a phase II trial sequentially adding pembrolizumab to 5-FU/platinum. In this study, we use single-cell RNA- and TCR-sequencing to analyze 66,813 T cells from primary tumor biopsies pre-treatment, post-chemotherapy, and post-immunotherapy in 33 patients. We observed greater abundance, persistence, and recruitment of T cells with predicted tumor-reactivity in patients with prolonged progression-free survival (slow progressors). Increased B cell abundance and predicted B cell to T cell interactions supported T cell memory and co-stimulation, providing a mechanism for increased abundance and persistence of progenitor-exhausted and tumor-reactive T cells in slow progressors. T cell clones emerging in the tumor after immunotherapy were in the blood before treatment only in slow progressors. Our study thus highlights pre-treatment and early chemotherapy-induced T cell dynamics and B cell to T cell interactions that may drive durable response to chemoimmunotherapy in GC.
2026-04-01 | GSE315928 | GEO
Project description:The GPC3-specific TGFBRII dominant-negative (DN) armored CAR-T cell therapy demonstrated promising clinical efficacy in phase I trials for advanced hepatocellular carcinoma (HCC). To investigate the spatial mechanisms of tumor response and resistance, we performed Xenium in situ spatial transcriptomic analysis on 18 samples from 13 patients of longitudinally collected FFPE tumor biopsies, enabling single-cell resolution mapping of tumor-immune interactions throughout the treatment course.
2026-05-26 | GSE332850 | GEO
Project description:The study aims to evaluate the efficacy and safety of a novel cell-based therapy for advanced hepatocellular carcinoma (HCC). Current guidelines for advanced HCC recommend systemic therapies, such as tyrosine kinase inhibitors (TKIs) and immune checkpoint inhibitors (ICIs); however, their combined efficacy as first-line treatments remains suboptimal. This study reports findings from a first-in-human phase I clinical trial involving 3 patients with advanced HCC who had previously demonstrated poor responses to first-line therapies. The treatment involved local intratumoral injection of CRISPR-edited, PD1-deleted T lymphocytes, engineered to enhance antitumor immunity (ClinicalTrials.gov NCT04417764). Key outcomes include a treatment response rate of 90% among assessable patients, with a median survival after enrolment of 17.2 months and an overall median survival after HCC diagnosis of 46.9 months. As of December 31, 2023, the three-year survival rate was 20%, and one patient exhibited an exceptional survival duration of 43.6 months. Secondary outcomes revealed that patients receiving the engineered T-cell therapy reported a significantly improved quality of life compared to the observation group. The tumor immune microenvironment was analyzed pre- and post-therapy using single-cell RNA sequencing, which demonstrated that tumor-infiltrating lymphocytes (TILs) developed an effector-like phenotype following therapy. In conclusion, this study provides strong evidence supporting the viability of CRISPR-edited, PD1-deleted T lymphocytes as a therapeutic option for advanced HCC, addressing an urgent need for more effective treatment strategies in this patient population.
2026-01-18 | GSE287386 | GEO
Project description:We provide 5' and/or 3' single cell and single nuclei RNA sequencing data for matched comparisons of profiling from fresh (single cells) and frozen (single nuclei) samples of a non small cell lung cancer sample, a cutaneous melanoma sample , and a primary uveal melanoma sample. We also provide matched samples processed with published dissociation protocols (*TST and *CST) for two samples as comparison. Next, we profiled three sequential biopsies (one pre-treatment and two on-treatment) from the KEYNOTE-001 trial by 5' single-nuclei RNA sequencing from frozen specimens. For these three datapoints we provide matched SlideSeq V2 spatial transcriptomic data. Finally, we provide 5' single nuclei RNA-sequencing data for 7 liver-metastatic uveal melanoma samples profiled at pre, on, and post treatment timepoints with MEK-inhibitor selumetinib. For all samples profiled with 5' capture we also provide TCR receptor information. This study provides a framework for the application of single nuclei RNA-sequencing on clinical grade specimens, and demonstrates the feasibility of this approach to dissect the biology of archival specimens or rare diseases.
2022-10-19 | GSE216069 | GEO
Project description:We provide 5' and/or 3' single cell and single nuclei RNA sequencing data for matched comparisons of profiling from fresh (single cells) and frozen (single nuclei) samples of a non small cell lung cancer sample, a cutaneous melanoma sample , and a primary uveal melanoma sample. We also provide matched samples processed with published dissociation protocols (*TST and *CST) for two samples as comparison. Next, we profiled three sequential biopsies (one pre-treatment and two on-treatment) from the KEYNOTE-001 trial by 5' single-nuclei RNA sequencing from frozen specimens. For these three datapoints we provide matched SlideSeq V2 spatial transcriptomic data. Finally, we provide 5' single nuclei RNA-sequencing data for 7 liver-metastatic uveal melanoma samples profiled at pre, on, and post treatment timepoints with MEK-inhibitor selumetinib. For all samples profiled with 5' capture we also provide TCR receptor information. This study provides a framework for the application of single nuclei RNA-sequencing on clinical grade specimens, and demonstrates the feasibility of this approach to dissect the biology of archival specimens or rare diseases.
2022-10-19 | GSE216055 | GEO
Project description:Mass spectrometry-based phosphoproteomics of tumor tissue lysates provides a potential personalized medicine approach based on its ability to identify activated signaling pathways and novel drug targets. We performed a pilot study (NCT01636908) to determine the effect of protein kinase inhibitors (PKIs) on tyrosine-(pTyr)-phosphoproteomic profiles of serial tumor biopsies in patients with advanced cancer. Tumor needle biopsies were analyzed from 31 patients with advanced cancer before and after 2 weeks treatment with sorafenib (SOR), erlotinib (ERL), dasatinib (DAS), vemurafenib (VEM), sunitinib (SUN) or everolimus (EVE). pTyr-Phosphoproteomics of pre- and on-treatment biopsies was performed by phosphotyrosine immunoprecipitation followed by LC-MS/MS.
2019-04-18 | PXD008032 | Pride
Project description:The lack of an appropriate preclinical model of metabolic dysfunction-associated steatotic liver disease (MASLD) that recapitulates the whole disease spectrum impedes exploration of disease pathophysiology and the development of effective treatment strategies. Considering the fact that MASLD patients accompanying type 2 diabetes mellitus (T2DM) have high risk of developing metabolic dysfunction-associated steatohepatitis (MASH), advanced fibrosis, and HCC, we treated low-dose streptozotocin (STZ; 40 mg/kg) for 5 consecutive days and subsequently fed a high-fat diet (HFD) to male C57BL/6J mice at 7 weeks of age (STZ+HFD). STZ+HFD mice gradually developed fatty liver, MASH, hepatic fibrosis, and hepatocellular carcinoma (HCC) in the context of metabolic dysfunction. In particular, from 20 weeks of age, MASH was evident, and from 32 weeks of age, advanced fibrosis was developed. At 38 weeks, a proportion of STZ+HFD mice developed HCC, which was subsequently observed in all mice up to 68 weeks of age. Furthermore, the hepatic transcriptomic features of STZ+HFD mice closely reflected those of obese patients with T2DM, MASH and MASLD-related HCC. Notably, dietary changes and tirzepatide administration alleviated MASH, hepatic fibrosis, and hepatic tumorigenesis in STZ+HFD mice. In conclusion, a murine model recapitulating the main histopathologic, transcriptomic, and metabolic alterations observed in MASLD patients with metabolic dysfunction was successfully established.
2024-06-17 | GSE246221 | GEO