Peptide Driven Identification of TCRs (PDI-TCR) reveals dynamics and phenotypes of CD4 T cells in tuberculosis [TCR-Seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE301489 | GEO | 2025/07/07
REPOSITORIES: GEO
Similar Datasets
Project description:Accurately assigning antigen specificity to T cell receptor (TCR) sequences is challenging due to the complexity of the TCR-antigen recognition process in humans. We developed the Peptide-Driven Identification of TCRs (PDI-TCR) assay, a novel method combining in vitro expansion with peptide pools, bulk TCR sequencing, and statistical analysis to identify antigen-specific TCRs from human blood. A key feature of PDI-TCR is its ability to account for bystander T cell expansion using both antigen-specific and non-specific peptide pools, distinguishing true antigen-specific TCRs from the unspecific ones. We applied PDI-TCR to Tuberculosis (TB) patients, sampling blood at diagnosis and throughout therapy, and Mycobacterium tuberculosis (Mtb)-sensitized healthy individuals (IGRA+). We identified hundreds of Mtb-specific and unspecific TCRs, and in combination with single-cell mRNA and TCR sequencing of CD4 T cells, we characterized the transcriptome of Mtb-specific and unspecific T cells in each cohort. Mtb-specific T cells were highly diverse, with the presence of short-lived effector phenotypes only in TB at diagnosis and memory phenotypes maintained through treatment. In contrast, unspecific T cells were more clonally restricted and expanded, cytotoxic, and maintained through treatment. Thus, PDI-TCR is a powerful tool for identifying antigen-specific TCRs. Combined with single-cell sequencing of T cell populations, it enables direct ex vivo monitoring of antigen-specific T cells.
2025-04-30 | GSE293807 | GEO
Project description:HLA-E molecules can present self and pathogen-derived peptides to both NK-cells and T-cells. T-cells that recognize HLA-E peptides via their T-cell receptor (TCR) are termed donor-unrestricted T-cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T-cells from 21 individuals recognizing HLA-E tetramers (TM) folded with 2 Mtb HLA-E restricted peptides. We sorted HLA-E Mtb TM+ and TMCD8+ T-cells directly ex vivo and performed bulk RNA-sequencing and single cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E Mtb specific T-cells have a highly diverse TCR repertoire.
2024-02-04 | GSE236154 | GEO
Project description:We introduced single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation that can be used for screening antigen specific CD8+ T cells. We compared the diversity of T cell receptor repertoire captured by SCT and folded peptide-MHC multimer presenting HLA-A02:01 restricted CMV peptide. We then constructed SCT libraries designed to capture SARS-CoV-2 spike specific CD8+ T cells from COVID-19 participants and healthy donors. TCR sequencing with antigen specificity was analyzed. The immunogenicity of these epitopes was validated by functional assays of T cells with cloned TCRs captured using SCT libraries.
2022-01-01 | E-MTAB-11229 | biostudies-arrayexpress
Project description:HLA-DR-lacking HSPCs [HLA-DR(-) HSPCs] were detected in aplastic anemia (AA) patients with HLA-DR15. HLA-DR(-) HSPCs may evade the attack by CD4+ T-cells recognizing the autoantigen presented by HLA-DR15. The goal of this study is to clarify the immune escape mechanisms from antigen-specific T-cells by comparing the trranscriptome profile of HLA-DR(+) HSPCs and HLA-DR(-) HSPCs.
2022-05-31 | GSE183768 | GEO
Project description:Immunological mechanisms of susceptibility to NTM disease are poorly understood. We evaluated innate and antigen-specific adaptive immune responses to Mycobacterium avium complex in individuals with MAC lung disease. We investigated the gene expression changes induced in PBMCs by polyclonal stimulation (anti-CD3, anti-CD28), Mav and Mtb lysates and a peptide pool (MTB300) in individuals with MAC lung disease (MACDZ), and healthy controls (IGRA+ and IGRA-).
2022-09-23 | GSE199403 | GEO
Project description:We hypothesized that individuals with immunological sensitization to Mycobacterium tuberculosis (Mtb), conventionally regarded as evidence of latent tuberculosis infection (LTBI), would demonstrate binary responses to preventive therapy. This would reflect the differential immunological consequences of the sterilization of viable infection in those with an active Mtb infection versus no Mtb killing in those who, despite T cell recognition of Mtb antigens, did not harbor viable Mtb bacilli. We investigated the blood transcriptional profiles of 18 individuals with a positive IGRA result and known recent exposure to an index person with isoniazid and rifampicin susceptible pulmonary tuberculosis, at baseline, 2 weeks after initiating combined rifampicin/isoniazid (RH) preventive therapy and at treatment completion. Healthy control volunteers with no history of TB exposure and negative IGRA results were also included. RNA from unstimulated and M. tuberculosis peptide stimulated whole blood (from QuantiFERON TB1 and TB2 tubes) was measured using Agilent microarrays. A set of 474 genes showed the greatest interpersonal and temporal expression variability in antigen-stimulated blood. By performing longitudinal unsupervised clustering analysis with the subset of most variable genes, the IGRA+ participants were separated into two distinct groups. The IGRA-negative controls clustered within one of these groups suggesting that, in contrast to the other subgroup of IGRA+ individuals, RH had no discernible effect in this subgroup. 117 genes were significantly differentially expressed over time between these two groups, with the majority of them associated with immunological pathways known to be important in mycobacterial control. We contend that the different host RNA response reflects lack of Mtb viability in the group that clustered with the IGRA- unexposed healthy controls, and Mtb viability in the one that clustered away. Gene expression patterns in the blood of IGRA+ individuals emerging during the course of RH treatment which reflect Mtb viability could have major implications in the identification of risk of progression/reactivation, treatment stratification and clinical trials for LTBI therapy.
2021-01-19 | GSE153340 | GEO
Project description:We hypothesized that individuals with immunological sensitization to Mycobacterium tuberculosis (Mtb), conventionally regarded as evidence of latent tuberculosis infection (LTBI), would demonstrate binary responses to preventive therapy. This would reflect the differential immunological consequences of the sterilization of viable infection in those with an active Mtb infection versus no Mtb killing in those who, despite T cell recognition of Mtb antigens, did not harbor viable Mtb bacilli. We investigated the blood transcriptional profiles of 18 individuals with a positive IGRA result and known recent exposure to an index person with isoniazid and rifampicin susceptible pulmonary tuberculosis, at baseline, 2 weeks after initiating combined rifampicin/isoniazid (RH) preventive therapy and at treatment completion. Healthy control volunteers with no history of TB exposure and negative IGRA results were also included. RNA from unstimulated and M. tuberculosis peptide stimulated whole blood (from QuantiFERON TB1 and TB2 tubes) was measured using Agilent microarrays. A set of 474 genes showed the greatest interpersonal and temporal expression variability in antigen-stimulated blood. By performing longitudinal unsupervised clustering analysis with the subset of most variable genes, the IGRA+ participants were separated into two distinct groups. The IGRA-negative controls clustered within one of these groups suggesting that, in contrast to the other subgroup of IGRA+ individuals, RH had no discernible effect in this subgroup. 117 genes were significantly differentially expressed over time between these two groups, with the majority of them associated with immunological pathways known to be important in mycobacterial control. We contend that the different host RNA response reflects lack of Mtb viability in the group that clustered with the IGRA- unexposed healthy controls, and Mtb viability in the one that clustered away. Gene expression patterns in the blood of IGRA+ individuals emerging during the course of RH treatment which reflect Mtb viability could have major implications in the identification of risk of progression/reactivation, treatment stratification and clinical trials for LTBI therapy.
2021-01-19 | GSE153326 | GEO
Project description:Discovering antigen-reactive T cell receptors (TCRs) is central to developing effective engineered T cell immunotherapies. However, the conventional technologies for isolating antigen-reactive TCRs (i.e., major histocompatibility complex (MHC) multimer staining) focus on high-affinity interactions between the TCR and MHC-antigen complex, and may fail to identify TCRs with high efficacy for activating T cells. Here, we develop a microfluidic single-cell screening method for antigen-reactive T cells named ATLAS-seq (Aptamer-based T Lymphocyte Activity Screening and SEQuencing). This technology isolates and characterizes activated T cells via an aptamer-based fluorescent molecular sensor, which monitors the cytotoxic cytokine IFNγ secretion from single T cells upon antigen stimulation, followed by single-cell RNA and single-cell TCR sequencing. We use ATLAS-seq to screen TCRs reactive to cytomegalovirus (CMV) or prostate specific antigen (PSA) from peripheral blood mononuclear cells (PBMCs). ATLAS-seq identifies distinct TCR clonotype populations with higher T cell activation levels compared to TCRs recovered by MHC multimer staining. Select TCR clonotypes from ATLAS-seq are more efficient in target cell killing than those from MHC multimer staining. Collectively, ATLAS-seq provides an efficient and broadly applicable technology to screen antigen-reactive TCRs for engineered T cell immunotherapy.
2024-10-11 | GSE234359 | GEO
Project description:T cell receptors (TCRs) recognize specific peptides presented by human leukocyte antigens (HLAs) on the surface of antigen presenting cells and are involved in fighting pathogens and cancer surveillance. Canonical docking orientation of TCRs to their target peptide-HLAs (pHLAs) is essential for T cell activation, with reverse binding TCRs lacking functionality. TCR binding geometry and molecular interaction footprint with pHLAs is typically obtained by determining the crystal structure. Here, we describe the use of a cross-linking tandem mass spectrometry (XL-MS/MS) method to decipher the binding orienta-tion of several TCRs to their target pHLAs. Cross-linking sites were localized to specific residues and their molecular interac-tions showed differentiation between TCRs binding in canonical or reverse orientations. Structural prediction and crystal structure determination of two TCR-pHLA complexes validated these findings. The XL-MS/MS method described herein offers a faster and simpler approach for elucidating TCR-pHLA binding orientation and interactions.
2025-05-07 | PXD056652 | Pride
Project description:The investigators recently identified promiscuous HLA-DR-derived epitopes from the human telomerase reverse transcriptase (TERT) called universal cancer peptides (UCP), to study tumor-specific CD4+ T cell responses.
The investigators found high frequency of naturally occuring UCP-specific TH1 cells in long term survival of metastatic colorectal cancer (CRC) previously treated by 5 fluoro-uracil -oxaliplatin (Folfox) +/- bevacizumab regiment (Godet et al. OncoImmunology 2012 and unpublished data).
Epitopes-CRC02 is a French prospective multicenter study which will evaluate the post chemotherapy and post surgery modulation of host tumor-specific CD4 TH1 cell responses in metastatic colorectal cancer patients and their correlation with progression-free survival.
| 2218590 | ecrin-mdr-crc