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RNA sequencing of CD19-directed chimeric antigen receptor T (CART19) cells with and without TP-0903 treatment

ABSTRACT: TP-0903 was obtained from Tolero Pharmaceuticals. CART19 cells from five biological replicates were thawed and stimulated with irradiated Jeko-1 cells (120 Gy) for 5 days. Jeko-1 is a human mantle cell lymphoma cell line that expresses the CD19 antigen (ATCC). Each sample was treated with either 30 nM TP0903 (treated condition) or DMSO (untreated control). CART19 were isolated to a purity of 100% using CD19 microbeads (Miltenyi). RNA was isolated from the CART19 using QIAGEN RNeasy Plus Mini Kit (Cat. No. 74134). RNA was further treated with DNase I and purified using Zymo Research RNA Clean & Concentrator (Cat. No. R1015).

ORGANISM(S): Homo sapiens

PROVIDER: GSE199257 | GEO | 2023/10/04

REPOSITORIES: GEO

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Project description:We performed single-cell RNA sequencing of a lymphoma (OCI-Ly18) subcutaneous tumor harvested from NSG mice two weeks after infusion with CART19 plus DMSO or CART19 plus Venetoclax (Suppl. Fig. 3A). Lymphoma cells with shared gene expression profiles were clustered using uniform manifold and approximation (UMAP) analysis. We identified six clusters characterized by different cell-cycle phases (Suppl. Fig. 3B), including one G1-dominant cluster, two S clusters, one G1/G2 cluster, one G2/M cluster, and an M cluster with high Ki67 expression. First, we observed a substantially lower proportion of cells assigned to G1-dom in the CART19/venetoclax-treated condition (8.4%) than in the CART19-treated condition (24%). These indicated a prevalent depletion of the G1-dom cluster by the addition of venetoclax (Suppl. Fig. 4C). In accordance with recent reports that venetoclax can induce cell cycle arrest and death in tumor cells in G1 39, these results suggest that venetoclax treatment also enhances CART’s anti-tumor efficacy by hindering the progression of cell cycle. Interestingly, the “G1-dominant (G1-dom)” and the additional “MKI67hi” cluster (high proliferative cells) showed significant enrichment of genes corresponding to interferon-gamma responsiveness, suggesting that the cells of these two clusters might have been interacting with CART cells (Suppl. Fig. 4D). Of note, by performing GO enrichment analysis with differentially expressed genes (DEGs) between CART19 and CART19/venetoclax combination in the MKI67hi cluster that represent a rapidly proliferating tumor subpopulation, we identified several pathways, including enrichment of the negative regulation of the G2/M phase transition in the CART19/venetoclax-treatment condition in the MKI67hi cluster (Suppl. Fig. 4E and 4F). Taken together, these data implicate that venetoclax treatment enhances CART-mediated tumor killing by promoting tumor apoptosis and inhibiting the cell cycle in cancer cells while also enhancing the interferon responses in neoplastic B-cells when engaging CART cells.

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RNA sequencing of CD19-directed chimeric antigen receptor T (CART19) cells with and without TP-0903 treatment

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