ABSTRACT: bulk TCR-seq data IMCISION on the PBMCs of responding patients bulkTCR-seq data generated with the immunoSEQ platform (Adaptive Biotechnologies) on PBMCs of responding patients, pre- and post-treatment.
Project description:We performed bulk TCR sequencing (Adaptive Biotechnologies, Seattle, WA) on peripheral blood monocytic cells (PBMCs) from 9 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021) that responded to anti-PD-1 and anti-CTLA4 combination immunotherapy. DNA was extracted from PBMCs that were isolated from pre-treatment and on-treatment blood.
Project description:We performed single cell RNA- and TCR-sequencing (10x Genomics) on immune infiltrates (CD45+ cells) from 18 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021). Viable immune cells were isolated from pre-treatment and post-treatment primary tumor biopsies of 10 patients responding (1 partial pathological response and 9 major pathological responses) and 7 patients non-responding to anti-PD-1 and anti-CTLA4 combination immunotherapy. One patient treated with anti-PD-1 monotherapy (1 major pathological response) was included in the dataset. Bulk TCR-seq was performed on the PBMCs of responding patients, pre- and post-treatment.
Project description:In the clinical trial, we evaluated the immunological efficacy of the vaccination of GBM6-AD, a tumor-cell lysate, assisted with poly-ICLC in low grade glioma. To characterize the gene expression, subset proportions, and T-cell receptor (TCR) profile of T-cells in PBMCs, we analyzed pre- and post-neoadjuvant vaccinated PBMCs from four immunological responders (103-018, -26, -29, -51), using droplet-based 5’ single-cell RNA-sequencing (scRNA-seq) and single-cell T-cell receptor-sequencing (scTCR-seq) with 10x GENOMICS platform. Further, we analyzed the gene expression profiles in resected tumor specimens by bulk RNA-seq analyses.
Project description:T-cell receptor (TCR) diversity is generated through V(D)J recombination, which are essential for adaptive immunity. Although many methods have been applied, a simple method to detect TCR rearrangement at the DNA level remains lacking. Here we introduce HTGTS-TCR-seq, a novel approach derived from high-throughput genome-wide translocation sequencing (HTGTS), to comprehensively and unbiasedly analyze TCR recombination. Unlike multiplex PCR requiring extensive V-J segment primers, HTGTS-TCR-seq enables unbiased TCR profiling through targeted enrichment and deep sequencing by a single primer. This method identifies biased V(D)J segment usage in developing T cells through V/J primer-based amplification and provides unique complementarity determining region 3 (CDR3) profiles in mature T cells via J primers. HTGTS-TCR-seq detects rearrangement at both alleles, enabling quantification of DJβ and VβDJβ rearrangement products with productive and nonproductive profile. Applied to human peripheral blood mononuclear cells (PBMCs), HTGTS-TCR-seq reveals a shared CDR3 motif between humans and mice. HTGTS-TCR-seq is a robust tool for T cell immunity research, with potential application in immune responses analysis, cancer research, and autoimmune diseases investigation.
Project description:We used the latest technology, BD Rhapsody, to analyze the pairing of α and β chains that constitute the TCR of PBMCs from patients with type 1 diabetes at the single-cell level.
Project description:We utilized RNA-seq to identify differential gene expression in Vγ9 Vδ2 gdT cells isolated from human PBMCs upon TCR stimulation. We find that ~30% genes are commonly up- and down-regulated between different phosphoantigen treatments (p<0.05). Inhibition of Notch signaling alongside TCR activation results in downregulation of many effector genes in Vγ9 Vδ2 T cells.
