Tumor microbial burden drives immune responses through regulation of Interferon signaling
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE329919 | GEO | 2026/05/08
REPOSITORIES: GEO
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Project description:Tumor microbial burden drives immune responses through regulation of Interferon signaling
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Project description:Tumor mutation burden is an imperfect proxy of tumor foreignness and has therefore failed to consistently demonstrate clinical utility in predicting responses in the context of immunotherapy. We evaluated mutations in regions of the genome that are unlikely to undergo loss and discovered that clonal mutations in single-copy regions and those present in multiple copies per cell constitute a persistent tumor mutation burden (pTMB) that is linked with therapeutic response to immune checkpoint blockade. Persistent mutations were retained in the context of tumor evolution under selective pressure of immunotherapy and tumors with a high pTMB content were characterized by a more inflamed tumor microenvironment. pTMB imposes an evolutionary bottleneck that cancer cells cannot overcome and may thus drive sustained immunologic tumor control in the context of immunotherapy.
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Project description:The roles of V-ATPase subunits in regulating CRC immune evasion remain unclear. By analyzing the Tumor and Immune System Interaction Database (TISIDB) for correlations between V-ATPases subunits and immune activities, we found that subunit ATP6V0A1 was inversely correlated with immune activities, especially with the proportions of effective or memory T cells in colon adenocarcinoma (COAD), suggesting an immunosuppressive role. With Atp6v0a1/ATP6V0A1 knockdown CRC cells and CRC syngeneic and xenograft mouse models, we confirmed that tumor cell-intrinsic ATP6V0A1 promotes the growth of CRC in an immune-dependent manner. To determine the type of immune cells contributing to ATP6V0A1-mediated immune evasion, we used single-cell transcriptome sequencing (sc-RNA seq) to analyze the ATP6V0A1-edited immune microenvironment in murine MC38 tumors. Holistic immune profiles in Atp6v0a1 knockdown and control MC38 tumors were compared. The results showed that Atp6v0a1 interference in MC38 cells increased the percentages of naïve T, effector T, and memory-like T-2 cells in the total T cell population while decreasing the percentages of exhausted T, Treg, and memory-like T-1 cells. Moreover, the percentages of granulocytes, monocytes, and dendritic cells within the myeloid population were increased in Atp6v0a1 knockdown-derived tumors, whereas the percentage of macrophages was decreased. Of all the immune cell subclusters, memory-like T-2 cells exhibited the most significantly increased cell count ratio in shv0a1 tumors vs. control tumors. In addition, memory-like T-2 cells expressed more effector markers than memory-like T-1 cells. These data suggest that MC38-derived ATP6V0A1 induced immunosuppressive tumor microenvironment (TME) and suppression of the effectiveness of memory-like T cells may play important roles in ATP6V0A1-regulated CRC immune evasion. The study provides directions to investigate the roles and mechanisms of ATP6V0A1 regulating anti-tumor immunity and thus shed light on the potential for ATP6V0A1-targeted immunotherapy in CRC.
2024-01-01 | GSE238084 | GEO
Project description:p53 is a critical tumor suppressor gene that inhibits cancer development by regulating cell cycle arrest, apoptosis, DNA repair, and metabolism. However, recent studies examining TP53 mutations in cancer immunotherapy have yielded inconsistent results, likely due to differences in tumor mutational burden (TMB) and the context-dependent roles of specific p53 mutants. In this study, we assessed the function of G242V and S258I Trp53 mutations in MC38 cells in the context of immunotherapy by generating Trp53 deletion and observed significantly enhanced responses to anti-PD-1 therapy. We next characterized how the Trp53 deletion in MC38 tumor cells alters the immune response. To this end, we performed single-cell RNA and paired single-cell TCR sequencing (scRNAseq and scTCRseq) of anti-PD-1 treated Trp53CON and Trp53KO MC38 tumors on day 11 after tumor cells inoculation.
2025-08-31 | GSE295668 | GEO
Project description:Objective: Bile acids (BAs) not only influence gut microbiome composition but are also metabolized by gut bacteria to form various microbial BAs. Among these, 3-oxo-lithocholic acid (-oxo-LCA) and isoalloLCA have been reported to modulate host immunity, suppress intestinal pathogens, and provide anti-aging benefits. However, their specific effects on intestinal epithelial cells (IECs) and their role in colorectal cancer (CRC) progression remain unclear. Design: To investigate the impact of 3-oxo-LCA on intestinal tumorigenesis, we examined its effects on the growth of mouse and human CRC cell lines (CT26, MC38, HCT116), as well as on primary mouse intestinal organoids and patient-derived CRC organoids (PDCOs). Additionally, we evaluated its role in vivo using APCMin/+ mice and multiple CRC models, including syngeneic CT26 and MC38 models, as well as HCT116 and PDX-derived xenografts in NSG (immunodeficient) mice. Results: Our findings show that 3-oxo-LCA is a potent FXR agonist that restores FXR signaling both in vitro and in vivo. This results in reduced growth of CRC cell lines and suppression of intestinal stem cell (ISC)’s proliferation in both mouse organoids and PDCOs. In APCMin/+ mice, 3-oxo-LCA reduced BA levels, enhanced gut barrier function, decreased tumor burden, and blocked tumor initiation. Furthermore, it significantly inhibited tumor progression in syngeneic and xenograft mouse models and promoted apoptosis within the tumors, enhancing cancer cell death. Conclusion: These results underscore the therapeutic potential of 3-oxo-LCA as a novel FXR agonist for CRC treatment, with its ability to inhibit tumorigenesis and progression by modulating epithelial cell proliferation and inducing apoptosis.
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Project description:We designed a novel intratumoral (IT) IL-12 mRNA therapy to promote local IL-12 tumor production whilst mitigating systemic effects. A single IT dose of mouse (m)IL-12 mRNA induced IFNγ and CD8+ T cell-dependent tumor regression in multiple syngeneic mouse models including MC38-R, and animals with a complete response demonstrated immunity to re-challenge. In order to further investigate the impact of mIL-12 mRNA on the MC38-R TME, we performed tumor transcriptomic evaluation 24h and 7 days after a single IT dose of 0.5 micrograms IL-12 or control mRNA. mRNA was isolated from snap-frozen syngeneic tumors using an RNeasy mini kit (Qiagen) and quantified on the Affymetrix mouse 430 2.0 microarray.
2020-09-01 | E-MTAB-9316 | biostudies-arrayexpress
Project description:Regulatory T cells (Tregs) are a barrier to effective anti-tumor immunity. Neuropilin-1 (Nrp1) is required to maintain intratumoral Treg stability and function but is dispensable for peripheral immune homeostasis, Treg-restricted Nrp1 deletion in mice results in profound tumor resistant due to Treg functional fragility. Drivers of Treg fragility, the mechanistic basis of Nrp1 dependency, and the relevance of these processes for human cancer and immunotherapy remain unknown. NRP1 expression on human Tregs in melanoma and HNSCC was highly heterogeneous and correlated with prognosis. Using a mouse model of melanoma in which mutant Nrp1-deficient (Nrp1–/–) and wild type (WT) Tregs could be assessed in a competitive environment, we found that a high proportion of intratumoral Nrp1–/– Tregs produce interferon-γ (IFNγ), which in turn drove the fragility of surrounding WT Tregs, boosting anti-tumor immunity and facilitating tumor clearance. We also show that IFNγ-induced Treg fragility is required for an effective response to PD1 immunotherapy, suggesting that cancer therapies promoting Treg fragility may be efficacious .
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Project description:To assess the role of Bap1 genes in MC38 colon carcinoma cell linewe knocked out the Bap1 gene in the MC38 cell line through CRISPR-Cas9 technology, MC38-Bap1-Wildtype and MC38-Bap1-Knockout tumor cells expressing BFP fluorescent protein were injected into Rag2-deficient mice subcutaneously. On the 10th day of tumor growth, BFP positive tumor cells were isolated and sorted by flow Cytometer. Bulk RNA-seq was performed on MC38-Bap1-Wildtype and MC38-Bap1-Knockout tumor cells for different gene signatures.
2025-07-06 | E-MTAB-10587 | biostudies-arrayexpress
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.
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