Dataset Information

Single-cell RNA sequencing on TILs from 4T1 mouse model treated with STING agonist deliveredy by PEG biopsy marker shows activation of antigen presenting cells and macrophages but does not show T cell clonality.

ABSTRACT: To better characterize the TME effects of ADU-S100 delivered by the PEG, we performed single cell RNA sequencing (scRNA-seq) on CD45+ immune cells from 4T1 tumors 14 days after treatment. We found that antigen presenting cell (APC) and macrophage clusters exhibited robust upregulation of IFN-induced genes by ADU-S100, as well as significant enrichment for hallmark IFN gene signatures. To explore whether immune escape could be secondary to a failure of STING agonist to induce T-cell clonality and expansion, we further performed T-cell receptor sequencing (TCR-seq) on these CD45+ immune cells from animals treated with PEG markers with PBS or 100 µg ADU-S100. We then analyzed the frequency of unique clonotypes that were expanded following PBS versus ADU-S100 treatment. In both groups, there was no evidence for clonotype expansion.

ORGANISM(S): Mus musculus

PROVIDER: GSE294854 | GEO | 2025/04/21

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Purpose: Next-generation sequencing (NGS)-derived transcriptome profiling (RNA-seq) is a powerful tool for analysing cellular pathways involved in treatment responses. In this study, RNA-seq was used to perform differential gene expression (DEG) and gene ontology (GO) analyses in prostate tumors treated with different immunotherapies and their combination. This was in order to investigate which pathways are activated and mediate the therapeutic effect. Methods: Mice with TRAMP-C2 subcutaneous prostate tumors were treated with either HBSS (control) or cyto-IL-15 or the STING agonist ADU-S100 or combination of ADU-S100 and cyto-IL-15. At day 6, tumors were removed and RNA was harvested to be used for RNA sequencing with Illumina NovaSeq. Using DESeq2, a comparison of gene expression between the treatment cohorts was performed and the Wald test was used to generate p-values and Log2 fold changes. GO analysis was performed on the statistically significant genes by implementing GeneSCF software using Fisher exact test. The mgi GO list was used to cluster the set of genes based on their biological process. Results: DEG analysis shown that more than 1,000 genes were differentially expressed in tumors 6 days after treatment with ADU-S100 or its combination with cyto-IL-15 (1,040 genes for ADU-S100 compared to control; 1,141 genes for combination compared to control). Most of the differentially expressed genes were upregulated (>70% in both comparisons). cyto-IL-15 led to differential expression of 96 genes compared to control. Differential expressed genes included Cxcl11 involved in immune cell recruitment and activation, and genes encoding granzymes a and b, which are proteases released by cytotoxic T cells and natural killer (NK) cells to kill cancer cells. In the control versus ADU-S100 or combination comparisons, GO analysis revealed that the majority of genes were involved in processes such as cellular responses to interferon-γ and β, complement activation, innate immune response, phagocytosis, and B cell signalling and activation. Conclusions: This study provides valuable insights in differential expression and activation of genes and cellular pathways involved in eliciting responses to immunotherapies in mouse prostate tumors. Using NSG and more specifically RNAseq-based transcriptome characterization, a detailed quantitative and qualitative analysis on how novel therapies exert their efficacy in tumors can be achieved and uncover the specific biological processes and functions contributing to the anti-tumor effects.

Project description:In study NCT00594880, we successfully administered weekly doses of pegylated interferon-α-2a (Peg-IFN-α2a) with antiretroviral therapy (ART) for 5 weeks, before continued Peg-IFN-α2a monotherapy to 12 weeks (primary endpoint) in chronic HIV-infected subjects. Subjects maintaining HIV viral load <400 copies/ml by primary endpoint were defined as responders. We now describe innate immune correlates and transcriptional profiles associated with viral control and decrease in integrated HIV DNA after Peg-IFN-α2a immunotherapy. Peripheral blood samples were obtained prior to Peg-IFN-α2a administration (ART), after 5 weeks of ART+Peg-IFN-α2a dual treatment, and after 12 weeks of Peg-IFN-α2a monotherapy. Cell subset modulation, natural killer cell (NK) function and signaling, as well as inflammatory mediators and gene expression were assessed. Results were analyzed using R.2.5.1 or MATLAB 7.10.0. Five weeks of ART+Peg-IFN-α2a preserved the frequency of immune subsets and NK cytotoxicity, while increased the levels of inflammatory mediators, and decreased cell-responsiveness to in vitro IFN-α re-stimulation. Gene expression analysis showed that induction of host restriction factors after ART+Peg-IFN-α2a was not solely predictive of a virologic response, and revealed a 108 gene signature that identified subjects who did not modulate genes after ART+Peg-IFN-α2a. A 29 gene signature along with higher NK cell activation and IFN-γ-induced protein 10 (IP-10) levels on ART, as well as higher in vitro responses to IFN-γ-induced NK cytotoxicity, and decrease in the frequency of NK bearing inhibitory receptors [i.e. killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail 1 (KIR2DL1) or KIR2DL2/DL3] and C-C chemokine receptor type 7+ (CCR7) myeloid dendritic cells after ART+Peg-IFN-α2a distinguished responders from non-responders. Reductions in integrated HIV DNA after immunotherapy were associated with expression patterns of genes that are associated with activated cell-mediated response and NK cytotoxicity. In summary, innate activation and NK cell cytotoxicity are identified as correlates of HIV control and reduction after Peg-IFN-α2a immunotherapy in ART-suppressed subjects.

Project description:Background: PD-1 pathway blockade has revolutionized cancer care, but many patients do not durably benefit from these therapies. Novel treatments to engage anti-tumor immunity in this setting are needed. The stimulator of interferon genes (STING) protein, an innate sensor of cytoplasmic DNA, is a promising target with several agonists in development; however, recent clinical trials of these agents have not demonstrated efficacy for most patients. Here, we present detailed biomarker analyses of a patient with anti-PD-L1 refractory Merkel cell carcinoma that had a durable (~1 year), abscopal response to ADU-S100 (intralesional STING agonist) combined with anti-PD-1 blockade. Methods: Tumor biopsies and peripheral blood acquired pre- and post-treatment were analyzed with single cell RNA sequencing, 27-color flow cytometry, T cell receptor sequencing and multiplexed immunohistochemistry (mIHC; post treatment tumor specimen only). Critically, cancer-specific CD8 T cells were identified using MHC-I tetramers containing peptides from the Merkel cell polyomavirus (MCPyV), the etiologic agent of this cancer. Cell lines and tumor specimens from 76 patients were used to evaluate STING expression and signaling in MCC. Results: High levels of antigen cancer-specific T cells were observed in the tumor prior to ADU-S100 treatment (12% of T cells recognized an MCPyV epitope). These cancer-specific CD8 T cells exhibited characteristics of exhaustion including high TOX and low TCF1. Following STING agonist treatment, MCPyV-specific CD8 T cells expanded 3-fold with minimal phenotypic changes. An increase in antigen presentation on MCC tumor cells was also observed (1.8% of tumor cells MHC-I positive before treatment, 8.2% after treatment). This was not a result of ADU-S100 acting directly on tumor cells as mIHC analysis of 88 tumor samples confirmed little or no STING expression in tumor cells, but high STING expression on infiltrating immune and stromal cells. Further in vitro studies showed MCPyV-positive MCC cell lines are STING deficient, and ADU-S100 did not induce interferon. Conclusions: Our study suggests that STING agonists act on intratumoral immune cells to release interferons, which upregulate tumor cell antigen presentation and reinvigorate the anti-tumor response from pre-existing cancer-specific T cells. Thus, patients with anti-PD-(L)1-refractory disease showing downregulation of antigen-presentation may benefit from intralesional STING agonists.

Dataset Information

Single-cell RNA sequencing on TILs from 4T1 mouse model treated with STING agonist deliveredy by PEG biopsy marker shows activation of antigen presenting cells and macrophages but does not show T cell clonality.

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets