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STARTRAC analyses of scRNAseq data from a mouse tumor model reveal T cell dynamics and therapeutic targets in cancer

ABSTRACT: To understand anti-tumor immune response, we performed single cell RNA-Seq and paired single cell TCR sequencing on T cells derived from multiple tissues of MC38-tumor-bearing mice

ORGANISM(S): Mus musculus

PROVIDER: GSE168944 | GEO | 2021/04/01

REPOSITORIES: GEO

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STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets.

Project description:Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human and mouse tumors. STARTRAC analyses demonstrated peripheral T cell subsets that were developmentally connected with tumor-infiltrating CD8+ cells, CD4+ Th1 cells, and T reg cells. In addition, large amounts of paired TCRα/β sequences enabled us to identify a specific enrichment of paired public TCR clones in tumor. Finally, we identified CCR8 as a tumor-associated T reg cell marker that could preferentially deplete tumor-associated T reg cells. We showed that CCR8-depleting antibody treatment provided therapeutic benefit in CT26 tumors and synergized with anti-PD-1 treatment in MC38 and B16F10 tumor models.

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Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:We investigate the single-cell landscape of the inflammatory mouse tumor model MC38, a C57BL/6 tumor cell line derived from colon adenocarcinoma. MC38 (diluted in HBSS and matrigel) was inoculated in the right unilateral flank (in the border of positions B2 and B3) of C57BL/6 mice (ref Study 16-3384 AV). Draining lymph nodes were taken one day after group-out (average 150-250 mm3 tumor size at day 0), approximately 14-19 days. Draining lymph nodes were dissociated and flow sorted accordingly to obtain the cells for 10x Chromium 5' Gene Expression Profiling and TCR sequencing.

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Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

Project description:Single cell TCR-seq profiling of T cells isolated from LNs of MC38 tumor-bearing mice

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Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T-cells [SMART-Seq]

Project description:To identify the role of KLF4 on exhausted CD8 T-cells in vivo, we adoptively transferred PmelI CD8 T-cells transduced with MigRI/Klf4 into MC38-gp100 tumor-bearing Rag2 KO mice on day7. We then isolated tumor-infiltrating PmelI CD8 T-cells on day15 and their gene expression profiles were analyzed by SMART-seq. Also, to investigate the effect of KLF4 deficiency, we isolated PD1+ CD8+ TILs from MC38 tumor-bearing control and Klf4 cKO mice on day14, and SMART-seq was performed.

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Transcriptome of tumor tissues from MC38 bearing mice

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Project description:Through forward genetic screening, we found a gene called LDL receptor Related Protein 10 (Lrp10) that plays an important role in the homeostasis and differentiation of peripheral CD8 T cells through its effects on the interleukin 7 receptor (IL7R). Lrp10 knockout mice exhibit enhanced resistance to MC38 tumor growth, and we sought to better define the tumor infiltrating Lrp10+/+ and Lrp10-/- CD8T cells using single cell RNA seq and paired single cell TCR sequencing.

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Gene expression of MC38 tumor tissues from WT or TLR4 deletion mice during Salmonella treatment.

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High baseline tumor burden-associated macrophages promote an immunosuppressive microenvironment and reduce the efficacy of immune checkpoint inhibitors through the IGFBP2-STAT3-PD-L1 pathway

Project description:In order to study the difference between high tumor burden and low tumor burden, we established MC38 tumor-bearing mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

2023-03-14 | GSE227270 | GEO

Tim-4+ Cavity-Resident Macrophages Impair Anti-Tumor CD8+ T cell Immunity [RNA-Seq]

Project description:Here we report RNA sequencing data from sorted Tim-4low vs Tim-4high macrophages in steady-state (no tumor) mice and also MC38-LG-tumor-bearing animals that were treated with isotype or anti-Tim-4 antibody.

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