Project description:This study examines the T cell landscape in head and neck squamous cell carcinoma (HNSCC) using single-cell RNA sequencing combined with T cell receptor and protein profiling. By analyzing tumor-infiltrating T cells from 28 patients, we identified diverse T cell subsets, characterized their transcriptional states, and mapped their clonal dynamics. These findings provide a detailed view of the immune microenvironment in HNSCC and offer insights into T cell-mediated immunity and potential targets for immunotherapy and are patient-matched to PBMC TCR sequencing and Xenium spatial transcriptomics in separate GEO submissions.
Project description:We collected HNSCC primary tumor from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for single cell RNA seq analysis.
Project description:To obtain an unbiased characterization of the resident and infiltrating immune cell populations of mouse kidneys in healthy and diseased states, we performed single cell RNA-seq of facs-sorted CD45+ immune cells and CD4+ T cells from naïve and injured kidneys, at selected time points.
Project description:High-throughput single-cell RNA-seq of tumor-infiltrating NK cells uncovered an NK subset, exhibiting elevated expression of activation markers, cytolytic molecules, chemokines and cytokines when Hif1a was absent in NK cells.
Project description:Metastatic uveal melanoma generally responds poorly to immunotherapy. The aim here was to sequence tumor-infiltrating lymphocytes from uveal melanoma metastases to study their phenotypes and T-cell receptor (TCR) clonotypes. We performed paired single-cell transcriptome and TCR sequencing using the 10x Genomics platform of IL2-expanded tumor-infiltrating lymphocytes from 7 liver and 1 subcutaneous metastasis.
Project description:Single-cell RNA-sequencing and single-cell TCR-sequencing was used to characterize PGE2-mediated changes in the gene expression profile of tumor-infiltrating CD8+ T cells.
Project description:Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. HPV-negative HNSCC, which arises in the upper airway mucosa, is particularly aggressive, with nearly half of patients succumbing to the disease within five years and limited response to immune checkpoint inhibitors compared to other cancers. There is a need to further explore the complex immune landscape in HPV-negative HNSCC to identify potential therapeutic targets. Here, we integrated two single-cell RNA sequencing datasets from 29 samples and nearly 300,000 immune cells to investigate immune cell dynamics across tumor progression and lymph node metastasis. Notable shifts toward adaptative immune cell populations were observed in the 14 distinct HNSCC-associated peripheral blood mononuclear (PBMCs) and 21 tumor-infiltrating immune cells (TICs) considering disease stages. All PBMCs and TICs revealed unique molecular signatures correlating with lymph node involvement; however, broadly, TICs increased ligand expression among effector cytokines, growth factors, and interferon-related genes. Pathway analysis comparing PBMCs and TICs further confirmed active cell signaling among Monocyte-Macrophage, Dendritic cell, Natural Killer (NK), and T cell populations. Receptor-ligand analysis revealed significant communication patterns shifts among TICs, between CD8+ T cells and NK cells, showing heightened immunosuppressive signaling that correlated with disease progression. In locally invasive HPV-negative HNSCC samples, highly multiplexed immunofluorescence assays highlighted peri-tumoral clustering of exhausted CD8+ T and NK cells, alongside their exclusion from intra-tumoral niches. These findings emphasize cytotoxic immune cells as valuable biomarkers and therapeutic targets, shedding light on the mechanisms by which the HNSCC sustainably evades immune responses.