Single cell RNA sequencing of TSCM predominnant allogeneic anti-BCMA CAR-T cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE280754 | GEO | 2025/10/01
REPOSITORIES: GEO
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Project description:Stem cell memory T cells can be defined as the memory T cell subsets with naïve T cell phenotypes and stem cell-like properties. We find that Notch signaling converts activated T cells into stem cell memory T (TSCM) cells by OP9-DL1 feeder cell coculture. Based on gene expression profile analysis, we provide evidence that these cells represent distinct characters with central memory T (TCM) cells and naïve T cells with effector molecules and transcription factors. TSCM cells induced by Notch cluster closer to TCM cells than naïve T cells, and display similar phenotypes to TCM phenotype in terms of effector molecules and transcription factors, but the gene expressions of TSCM cells are entirely lower than that of TCM cells.
2016-12-15 | GSE92381 | GEO
Project description:Adoptive T-cell immunotherapy provides a promising approach to cancer therapy. Stem cell memory T (TSCM) cells have been proposed as a new class of memory T cells that possess longevity and a high proliferative potential. It has been shown that CD8+ TSCM cells can be generated in vitro from naïve CD8+ T cells via Wnt signaling; however, the methods for inducing TSCM cells from activated or memory T cells remain to be developed. Here, we established a new strategy for generating TSCM-like cells in vitro (designated as “iTSCM” cells) from activated CD4+ and CD8+ T cells in mice and humans by coculturing with stromal cells expressing a Notch ligand. These iTSCM cells lost PD-1 and CTLA-4 expression and produced a large number of tumor-specific effector cells after restimulation. The present study illustrates a novel approach to generating a large number of antigen-specific effector T cells for adoptive immunotherapy.
2017-01-06 | GSE93211 | GEO
Project description:An early-differentiated CD8+ memory T cell subset with stem cell-like properties (TSCM) can be identified within the naïve-like T cell population by the expression of CD95/Fas. Based on experiments including exon- and gene-level expression analysis, we provide evidence that this subset of antigen-specific cells represents an early precursor of conventional central (TCM) and effector (TEM) memory CD8+ T cells with enhanced self-renewal capacity and proliferative potential. We identified 900 genes differentially expressed between major T cell subsets defined along with memory T cell commitment. Based on the analysis of these genes, CD95+ naïve T cells (TSCM) cluster closer to the CD8+ T memory compartment than to classical (CD95-) naïve T (TN) cells, and display an intermittent phenotype between classical TN and TCM cells in terms of all major T cell differentiation markers analyzed.
2011-07-13 | GSE23321 | GEO
Project description:An early-differentiated CD8+ memory T cell subset with stem cell-like properties (TSCM) can be identified within the naïve-like T cell population by the expression of CD95/Fas. Based on experiments including exon- and gene-level expression analysis, we provide evidence that this subset of antigen-specific cells represents an early precursor of conventional central (TCM) and effector (TEM) memory CD8+ T cells with enhanced self-renewal capacity and proliferative potential. We identified 900 genes differentially expressed between major T cell subsets defined along with memory T cell commitment. Based on the analysis of these genes, CD95+ naïve T cells (TSCM) cluster closer to the CD8+ T memory compartment than to classical (CD95-) naïve T (TN) cells, and display an intermittent phenotype between classical TN and TCM cells in terms of all major T cell differentiation markers analyzed. Three healthy human blood donors provided lymphocyte-enriched apheresis blood for this study after informed consent. From all samples, total RNA was isolated using an RNEasy Micro kit (Qiagen), processed by Ambion’s WT expression kit, fragmented and labeled with a WT Terminal Labeling Kit (Affymetrix), hybridized to WT Human Gene 1.0 ST arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), all according to the respective manufacturer's instructions. Samples represent "exon-level" and "gene-level" analyses.
2011-07-12 | E-GEOD-23321 | biostudies-arrayexpress
Project description:Mass spectrometric analysis of MM cell-purified B-cell maturation antigen (BCMA) protein to identify ubiquitylation sites.
2025-07-29 | PXD056372 | Pride
Project description:Chimeric antigen receptor T-cells (CAR-T) targeting B-cell-maturating-antigen (TNRFSF17, BCMA) show unprecedented overall response rates of up to 100% in heavily pretreated relapsed-refractory Multiple Myeloma (RRMM). However, the efficiency of the treatment is hindered by the rapid emergence of tumor-intrinsic mechanisms of resistance. We herein describe a patient with RRMM and extramedullary disease (EMD) who underwent Idecabtagene vicleucel BCMA CAR-T therapy. The patient rapidly achieved very good partial response including full resolution of EMD, but aggressively relapsed 5 months after CAR T cell infusion. Single cell RNA sequencing and immunohistochemistry on the re-emerging tumor cells demonstrated loss of target expression on mRNA and protein levels, and whole genome sequencing revealed the homozygous deletion of Chr 16p1313, including the BCMA locus. Clonal heterogeneity of BCMA could be observed in 32 RRMM patients from our institution. In three of them heterozygous deletion of BCMA could be confirmed, with none of them having underwent prior anti-BCMA therapy. Thus, our report not only provides first evidence of BCMA loss as the underlying mechanism of disease relapse following BCMA targeted immunotherapy in MM. It furthermore identifies a subset of patients at risk to develop biallelic BCMA inactivation thus linking genomic instability in MM to relapse from targeted immunotherapies.
2020-12-30 | GSE143317 | GEO
Project description:Although it is recognised that CD8+ T memory stem cells (Tscm) are heterogeneous in phenotype and function, very few studies have sought to systematically examine these characteristics, particularly in human samples, as the population as a whole is rare and antigen-specific cells even more so. For each T cell subsets investigated, we have performed optimized RNAseq for small number of cells by adapting the Smartseq2 protocol from scRNAseq. The mini-bulk number of cells was chosen to reduce heterogeneity but also maintain an adequate transcriptomics signal. Adapted from Smartseq2 protocol from scRNAseq described by Picelli et al, cell lysis buffer was prepared by adding 1 μl RNase inhibitor (Clontech, Mountain View, USA) to 19 μl Triton X‐100 solution (0.2% v/v). CD8 T cell subpopulations (TN, TSCM, TCM and TEM together with TSCM CXCR3hi/lo and CD122hi/lo) were bulk sorted (50 cells/sample, with replicates) directly into 96-well PCR plates containing 2 μl lysis buffer, 1 μl dNTP mix (10 mM) and 1 μl oligo‐dT primer at 5 μM. Plates were stored at -80 °C until ready to perform the assay. Reverse-transcription and PCR amplifications were performed as described, with the exception of reducing the IS PCR primer to a 50 nM final concentration and increasing the number of cycles to 28. Sequencing libraries were prepared using the Nextera XT Library Preparation Kit (Illumina; San Diego, USA) and sequencing was performed on Illumina NextSeq500 sequencing platforms with 2×150bp paired-end read output, the read depth was approximately 1.3 million reads per sample.
2022-03-10 | E-MTAB-10208 | biostudies-arrayexpress
Project description:Allogeneic chimeric antigen receptor (CAR)-T cell therapies hold the potential to overcome many of the challenges associated with patient-derived (autologous) CAR-T cells. Key considerations in the development of allogeneic CAR-T cell therapies include prevention of GvHD and suppression of allograft rejection. Here we describe preclinical data supporting the ongoing first-in-human clinical trial (CaMMouflage) in relapsed/refractory multiple myeloma patients evaluating CB-011, a hypoimmunogenic, allogeneic anti–B cell maturation antigen (BCMA) CAR-T cell therapy candidate. CB-011 cells feature 4 genomic alterations and were engineered from healthy donor-derived T cells using a Cas12a CRISPR hybrid RNA-DNA (chRDNA) genome-editing technology platform. To address allograft rejection, CAR-T cells were engineered to prevent endogenous human leukocyte antigen (HLA) class I complex expression and overexpress a single-chain polyprotein complex composed of beta-2 microglobulin (B2M) tethered to HLA-E. Additionally, T cell receptor expression was disrupted at the T cell receptor alpha constant locus in combination with the site-specific insertion of a humanized BCMA-specific CAR. CB-011 cells exhibited robust plasmablast cytotoxicity in vitro in a mixed lymphocyte reaction in cell co-cultures derived from patients with multiple myeloma. Additionally, CB-011 cells demonstrated suppressed recognition by and cytotoxicity from HLA-mismatched T cells. CB-011 cells were protected from natural killer (NK) cell–mediated cytotoxicity in vitro and in vivo due to endogenous promoter-driven expression of B2M–HLA-E. Potent antitumor efficacy, when combined with an immune-cloaking armoring strategy to dampen allograft rejection, offers optimized therapeutic potential in multiple myeloma.
2024-02-12 | GSE249316 | GEO
Project description:Plasma cells provide protective antibodies following an infection or vaccination. A network of intrinsic and extrinsic factors fine-tunes the generation of a heterogenous plasma cell pool with varying metabolic requirements, transcriptional profiles and lifespans. Among these intrinsic factors, the B cell maturation antigen (BCMA) has been implicated in APRIL-mediated survival of long-lived plasma cells. Therefore, we introduced a tdTomato reporter into the Tnfrsf17 (BCMA) locus, to decode the developmental steps behind the generation of mature plasma cell subsets. We demonstrate that the BCMA:Tom reporter is exclusively detected in plasma cells, with its expression differing between IgH isotypes and increasing with plasma cell maturity. Combined with a Blimp1-GFP reporter, the BCMA:Tom reporter allowed us to track the step-wise maturation from newly formed to late plasma cells in various plasma cell subpopulations. Notably, in vitro-stimulated B cells induce BCMA only after adoptive transfer into recipient mice, emphasizing the impact of the in vivo microenvironment in establishing a mature plasma cell compartment. The BCMA:Tom reporter mouse provides a robust tool for tracking plasma cell development and maturation with flow cytometry or advanced imaging techniques, enabling a deeper understanding of the mechanisms regulating plasma cell heterogeneity and longevity.
2025-04-02 | GSE276846 | GEO
Project description:Chimeric antigen receptor T cells (CAR-Ts) with T-stem cell (TSCM)-like phenotypic characteristics promote sustained antitumor effects. We performed an unbiased and automated high-throughput screen of a kinase-focused compound set to identify kinase inhibitors (KIs) that preserve human TSCM-like CAR-Ts. We identified three KIs UNC10225387B, UNC10225263A and UNC10112761A that combined in vitro increased the frequency of CD45RA+CCR7+TCF1high TSCM-like CAR-Ts from both healthy donors and cancer patients. KIs-treated CAR-Ts showed enhanced antitumor effects both in vitro and in vivo. The KI cocktail maintains TSCM-like phenotype preferentially in CAR-Ts originating from naïve T cells, and promotes dynamic transcriptomic changes without arresting T-cell activation or modulating the chromatin organization. Specific kinases ITK, ADCK3, MAP3K4 and CDK13 targeted by the KI cocktail in a dose-dependent manner are directly associated with the preservation of TSCM-like CAR-Ts. While individual knockdown of these kinases or their combination enriched in TSCM-like CAR-Ts, only CAR-Ts generated in the presence of the KI cocktail show robust expansion and differentiation upon stimulation with tumor cells. Overall, transient pharmacologic inhibition of strategically targeted kinases maintains stem-like features of CAR-Ts and improves their antitumor activity.
2025-01-20 | GSE261127 | GEO