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Transcriptomic Profiling of anti-CD276/NKG2DLs CAR-T Cells Stimulated by A549 Cells

ABSTRACT: 1. we performed a bulk RNA-seq analysis after 24-hour co-culture with A549 cells. Compared with untransduced T cells, CAR-T cells presented broad transcriptomic differences. Pathway enrichment analysis of the differentially expressed genes (DEGs) revealed significantly upregulated cytokine-receptor cross-talk pathway, as well as TNF, JAK-STAT, NF-κB, and IL-17 signaling pathways in CAR-T cells compared with that in UTD. All these pathways are critical for T cell activation, proliferation, differentiation, and effector functions. 2. We also carried out continuous antigen exposure (CAE) wherein CAR-T cells were induced into an exhaustion state. We observed substantial transcriptomic differences and thousands of DEGs among distinct CAR-T cell groups and the UTD group. To better understand the specific advantages of Bicephali CAR-T cells over two single-targeting CAR-T cells, we employed Venn diagrams to visualize the DEGs among the three groups and revealed 346 unique DEGs of multi-targeting Bicephali CAR-T cells. We further subjected these 346 DEGs to Gene Ontology (GO) pathway enrichment analysis and found that positive regulation of T cell function and oxidative stress were among the top enriched pathways.

ORGANISM(S): Homo sapiens

PROVIDER: GSE302681 | GEO | 2025/12/12

REPOSITORIES: GEO

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Project description:The research hypothesis was that the unique expression profile of monocytes in response to Interferon-beta (IFN-Î²) might be masked by the response profile of the more abundant T cells. The analysis of monocytes response may highlight novel IFN-Î² functions and pathways that have not been recognized previously. The aim of this study was to characterized the IFN-Î² transcriptional response in monocytes, a small but influential cell-subset, using gene expression profile and pathway analysis. The expression profiles of purified human monocytes and T cells pulse with IFN-Î² overnight were compared, and revealed 276 and 42 Differentially Expressed Genes (DEGs) in monocytes and T cells respectively, with only 5 genes common to both sets. Many of the DEGs detected in monocytes were novel with respect to the recognized IFN-Î² response, and included genes involved in immune-specific activities, communication between cells, regulation of apoptosis, cell migration, and protein translation. Network and pathway analysis of the T cells response revealed the familiar immune pathways, response to virus pathways, and IFN canonical pathway. In monocytes, however, we detected along with known IFN-Î²-related pathways, such as cell migration also pathways that had not been previously described in the context of IFN-Î² response, such as the High-Mobility Group Box-1 (HMGB1) signaling pathway. However, most DEGs in monocytes did not cluster to specific networks or canonical pathways. The monocyte-specific DEGs and pathways described herein are beyond the current knowledge regarding the biology of the IFN-Î² response and the differential response to IFN-Î² of monocytes versus T cells described emphasizes the importance of cell-specific studies for elucidating the spectrum of cytokine-mediated immunomodulation. Monocytes and T lymphocytes were isolated from 3 healthy volunteers. For each sample the expression profile of untreated cells was compared to the profile of IFN-Î² treated cells, i.e. 4 samples from each donor (2 cell types, with and without treatment), 12 samples total.

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Transcriptomic Profiling of anti-CD276/NKG2DLs CAR-T Cells Stimulated by A549 Cells

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