Discriminating Th17.1 cell driven sarcoidosis-like inflammation from relapse after anti-BCMA CAR T cells in multiple myeloma
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001006133 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Background: Autologous CD19 CAR T cell therapy leads to durable responses and improved survival in patients with relapsed or refractory large B cell lymphoma (R/R LBCL). Among approved CAR T cell products, axicabtagene ciloleucel (axi-cel; CD19/CD28) has greater real-world efficacy and cytokine-associated toxicity than tisagenlecleucel (tisa-cel; CD19/4-1BB), for reasons that are poorly understood. Methods: Here we report single cell RNA sequencing (scRNA-seq) of 57 pre-infusion CAR T cell products from axi-cel (n=39) and tisa-cel (n=18) patients treated as standard-of-care for R/R LBCL, and their biological associations with clinical outcomes. In vitro CAR manufacturing conditions mimicking those known for axi-cel and tisa-cel were performed using CD19/CD28z or CD19/4-1BBz constructs. Results: ScRNA-seq revealed that axi-cel and tisa-cel are markedly different products. Axi-cel is comprised of more CD4 central memory, CD8 central memory, and CD8 effectors, whereas tisa-cel is comprised of more proliferative CD4 and CD8 cells. Across multiple T cell subsets, axi-cel had greater expression of immune response pathways and protein synthesis and trafficking pathways vs. tisa-cel. On comparison of infusion product CAR transgene-positive (CAR+) cells to CAR transgene-negative (CAR-) T cells, axi-cel CAR+ cells had vastly different gene expression than axi-cel CAR- cells. Unexpectedly, tisa-cel CAR+ cells were highly similar to tisa-cel CAR- cells. Under recapitulated CAR-T manufacturing conditions known to be utilized for axi-cel and tisa-cel, we found that CAR+ cells differed from CAR- cells early after manufacturing yet became more similar to CAR- cells after prolonged expansion. Prolonged time in expansion culture, as utilized during tisa-cel manufacturing, greatly decreased naïve and central memory T cell subsets. Conclusions: Following manufacture, axi-cel is less differentiated and has greater immune activation compared to tisa-cel, potentially accounting for its greater efficacy and toxicity in patients. Our data support the conclusion that tisa-cel is adversely affected by its manufacturing rather than by the CAR construct.
2025-07-30 | GSE297676 | GEO
Project description:Ciltacabtagene autoleucel (cilta-cel) and idecabtagene vicleucel (ide-cel) are FDA-approved BCMA-directed CAR T cells for multiple myeloma. The increased efficacy of cilta-cel compared to ide-cel may be related to its unique nanobody binding domain, but the constructs also differ in their use of EF1α and MND promoters, respectively, to drive CAR expression. To elucidate the basis of cilta-cel’s superior efficacy, we analyzed CAR T cells from 87 patients (50 cilta-cel, 37 ide-cel) using flow cytometry and single-cell multi-omics. Cilta-cel showed a 10-fold higher peak expansion and greater persistence, driven by an inflammatory GZMK⁺ T cell subset marked by EOMES expression and motif accessibility, but not exhaustion profile. Animal modeling revealed that the EF1α promoter (cilta-cel) rather than binder recapitulated increased tumor control, enhanced expansion and GZMK transcriptional profile compared to the MND promoter (ide-cel). Cilta-cel’s efficacy is therefore linked to EF1α-driven GZMK⁺ transcriptional trajectory that supports both persistence and effector function.
2026-05-18 | GSE330627 | GEO
Project description:We performed the first in-depth, comparative and prospective biomonitoring of Multiple Myeloma (MM) patients (N=39) receiving ciltacabtagene autoleucel (cilta-cel) or idecabtagene vicleucel (ide-cel) chimeric antigen receptor T cells (CAR T) in the real-world setting. In cilta-cel patients response rates were higher and atypical neurotoxicities/infections more frequent. Peak CAR T counts were significantly higher in cilta-cel patients, driven by CD4+ CAR expansion, correlating with clinical responses. Expansion of cilta-cel cells was associated with higher CAR and CD27 expression while, in contrast to ide-cel, there was no correlation between TIM3 expression and CAR T proliferation. Cilta-cel CAR T expansion was followed by a CAR-specific switch from proliferation-associated genes to genes/surface markers indicating effector/memory function. The longer persistence of cilta-cel CAR T was associated with increased IL-7R expression; in vitro data showed persistent antigen-independent activation and higher metabolic activity of cilta-cel vs. ide-cel CAR T. Among cilta-cel-treated patients experiencing atypical neurotoxicities, central nervous system (CNS)-infiltrating, effector-type CAR T presented a distinct inflammatory phenotypic/cytokine-expression profile. This in-depth biomonitoring report following real-world cilta-cel or ide-cel highlights intrinsic biological differences between BCMA-targeting CAR T products, potentially explaining differences in clinical activity and toxicity. Our findings may guide optimization of cellular immunotherapy strategies in MM.
2025-05-28 | GSE298011 | GEO
Project description:We performed the first in-depth, comparative and prospective biomonitoring of Multiple Myeloma (MM) patients (N=39) receiving ciltacabtagene autoleucel (cilta-cel) or idecabtagene vicleucel (ide-cel) chimeric antigen receptor T cells (CAR T) in the real-world setting. In cilta-cel patients response rates were higher and atypical neurotoxicities/infections more frequent. Peak CAR T counts were significantly higher in cilta-cel patients, driven by CD4+ CAR expansion, correlating with clinical responses. Expansion of cilta-cel cells was associated with higher CAR and CD27 expression while, in contrast to ide-cel, there was no correlation between TIM3 expression and CAR T proliferation. Cilta-cel CAR T expansion was followed by a CAR-specific switch from proliferation-associated genes to genes/surface markers indicating effector/memory function. The longer persistence of cilta-cel CAR T was associated with increased IL-7R expression; in vitro data showed persistent antigen-independent activation and higher metabolic activity of cilta-cel vs. ide-cel CAR T. Among cilta-cel-treated patients experiencing atypical neurotoxicities, central nervous system (CNS)-infiltrating, effector-type CAR T presented a distinct inflammatory phenotypic/cytokine-expression profile. This in-depth biomonitoring report following real-world cilta-cel or ide-cel highlights intrinsic biological differences between BCMA-targeting CAR T products, potentially explaining differences in clinical activity and toxicity. Our findings may guide optimization of cellular immunotherapy strategies in MM.
2025-05-28 | GSE298012 | GEO
Project description:This submission contains de-identified Olink NPX affinity proteomics data from longitudinal peripheral blood samples collected from patients with relapsed/refractory multiple myeloma treated with BCMA-directed CAR-T therapy (ide-cel or cilta-cel) in a prospective single-center pilot study. Samples were analyzed using the Olink Target 92 Immuno-Oncology panel to characterize inflammatory protein dynamics associated with cytokine release syndrome (CRS). In the associated study, these proteomic data were integrated with wearable physiologic monitoring to evaluate early CRS detection and to identify candidate biomarkers, including IFN-γ.
2026-04-28 | PAD000041 | Pride
Project description:Chimeric antigen receptor (CAR)-T cell therapy has become the standard treatment for refractory and relapsed (r/r) DLBCL in recent years. However, more than half of these patients develop primary or secondary resistance. Given that CAR Tregs are crucial in driving resistant and relapse to CAR-T therapy, but the strategies to overcome are limited. Here, we established a Treg functional high-throughput screening system and identified a natural product, currently in clinical trials, Timosaponin AIII (TAIII), impairs Treg function while activating T cell immune response during CAR-T therapy. Mechanistically, TAIII recruits and blocks the A2AR signaling in CAR-T cells as a novel allosteric inhibitor of A2AR, thereby eliminating CAR-Tregs by suppressing CREB-mediated FoxP3 transcription. Furthermore, TAIII suppresses tumor growth and improves the efficacy of PD-1 immunotherapy by reducing intratumoral Tregs in solid tumor models. Importantly, TAIII increases the Tcm percentage and enhances cytotoxic cytokine secretion of CAR-T cells post-infusion, improving their function. Combining or pretreating CAR-T cells with TAIII enhances their antitumor activity, thereby overcoming late relapses in lymphoma models. These results identify TAIII as a potent adjuvant for CAR-T cell function and manufacturing through eliminating CAR-Tregs proportion, thereby enabling CAR-T therapy to be applied with a broader perspective.
2026-02-11 | GSE289388 | GEO
Project description:Chimeric antigen receptor (CAR)-T cell therapy has become the standard treatment for refractory and relapsed (r/r) DLBCL in recent years. However, more than half of these patients develop primary or secondary resistance. Given that CAR Tregs are crucial in driving resistant and relapse to CAR-T therapy, but the strategies to overcome are limited. Here, we established a Treg functional high-throughput screening system and identified a natural product, currently in clinical trials, Timosaponin AIII (TAIII), impairs Treg function while activating T cell immune response during CAR-T therapy. Mechanistically, TAIII recruits and blocks the A2AR signaling in CAR-T cells as a novel allosteric inhibitor of A2AR, thereby eliminating CAR-Tregs by suppressing CREB-mediated FoxP3 transcription. Furthermore, TAIII suppresses tumor growth and improves the efficacy of PD-1 immunotherapy by reducing intratumoral Tregs in solid tumor models. Importantly, TAIII increases the Tcm percentage and enhances cytotoxic cytokine secretion of CAR-T cells post-infusion, improving their function. Combining or pretreating CAR-T cells with TAIII enhances their antitumor activity, thereby overcoming late relapses in lymphoma models. These results identify TAIII as a potent adjuvant for CAR-T cell function and manufacturing through eliminating CAR-Tregs proportion, thereby enabling CAR-T therapy to be applied with a broader perspective.
2026-02-20 | GSE302847 | GEO
Project description:Although chimeric antigen receptor (CAR) T cell therapy has revolutionised individualised cancer therapies for relapsed/refractory lymphomas, low long-term retention due to basal signalling (antigen-independent activation in the absence of cognate antigen) and off-target toxicity limit the broad applicability of CAR-T products. During CAR development, researchers use model systems, like Jurkat T cells (Jurkats), to screen intracellular signalling arrangements based on their ability to activate (e.g., CD69 expression) and withstand repeated antigen encounters. Although Jurkats are standard for CAR screening, the mapping of CAR generations to Jurkat-specific pTyr networks relative to key TCR nodes and CD69 readouts is not well defined, blurring how hierarchical signalling drives activation. Here, we investigated how costimulation influenced tyrosine phosphorylation cascades using LC-MS/MS based phosphotyrosine (pY) proteomics and CD69 expression in the presence of small molecule inhibitors of key TCR signalling regulators. We found that including TCRζ (CD3ζ; gene CD247) in first (ζ-CAR), second (28ζ-CAR and BBζ-CAR), and third (28BBζ-CAR) generation CARs largely determined pY signalling, irrespective of costimulation. Further, we showed that the phosphatase activity of PTPN22 and SHP-1 were largely negligible for activation of CARs, but indiscriminate inhibition of phosphatases using pervanadate (PV) selectively activated BBζ-CARs without antigen encounter. Finally, we found that selective, partial inhibition of Itk using Soquelitinib reduced basal CD69 expression in CAR-Jurkat cells while maintaining their ability to activate in response to antigen. These data suggest that TCRζ determines the pY signalling profile and that Itk drives basal activation of CD19-CAR Jurkats, which may impact evaluation of new CAR designs in CAR-Jurkat screens.
2025-11-21 | PXD065669 | Pride
Project description:Purpose: To compare cell states amoung three populations of interest among circulating CAR T cells in patients with lymphoma. Methods: Nine patients with large B-cell lymphoma (LBCL) were treated with axicabtagene ciloleucel (axi-cel), a commercial CD19-targeted CAR T-cell therapy. On day 7, fresh peripheral blood mononuclear cells were stained with an antibody panel for fluorescence-activated cell sorting (FACS), a panel for cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and a viability dye. Single live CAR+ T cells were sorted from each patient, counted, processed for 5' single-cell RNA-sequencing with feature barcoding and TCR clonotype analysis on the 10X Genomics platform, and sequenced by the Stanford Genomics Facility (HighSeq 4000) or Novogene (NovaSeq 6000). Results: We found that circulating CD4+ and CD8+ CAR T cells that express CD57 and T-bet are clonally expanded and display features of effector T cells. In contrast, CD4+ CD57- CAR T cells that express Helios expand polyclonally and display features of T regulatory cells. Conclusions: This study provides insights into cell states of circulating CAR T cells on day 7 that associate with clinical response or toxicity in LBCL patients treated with axi-cel.
2022-07-28 | GSE168940 | GEO
Project description:Chimeric antigen receptor (CAR) T cell therapies have revolutionized B cell malignancy treatment, but subsets of patients with large B cell lymphoma (LBCL) experience primary resistance or relapse after CAR T cell treatment. To uncover tumor microenvironment (TME)-induced resistance mechanisms, we examined patients’ intratumoral immune infiltrates and observed that elevated levels of immunoregulatory macrophages in pre-infusion tumor biopsies are correlated with poor clinical responses. In murine models, CAR T cell-produced interferon-gamma (IFN-g) promotes the expression of inducible nitric oxide synthase (iNOS, NOS2) in immunoregulatory macrophages, impairing CAR T cell function. Mechanistically, proteomics analysis of CAR T cells revealed that iNOS-expressing macrophages promote the upregulation of genes mediating apoptosis and cell cycle arrest in CAR T cells, while downregulating ribosome biogenesis and protein synthesis. Furthermore, CAR T cell metabolism is compromised by the depletion of glycolytic intermediates and rewiring of the TCA cycle. Pharmacological inhibition of iNOS enhances the CAR T cell treatment efficacy in B cell tumor-bearing mice. Notably, elevated levels of iNOS+CD14+ monocytes were observed in leukaphereses of patients with non-durable response to CAR T cell therapy. These findings suggest that mitigating iNOS in tumor-associated macrophages (TAMs), potentially by modulating IFN-g expression in CAR T cells, could improve outcomes for LBCL patients.
2026-05-30 | PXD079073 | Pride