Mechanisms by which whole genome doubling drives breast tumor evolution [scRNA-seq]
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE274140 | GEO | 2026/03/15
REPOSITORIES: GEO
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Project description:Whole genome doubling (WGD) is one of the most common genetic alterations in human cancer generally associated with poor clinical outcome, yet the underlying mechanisms have not been delineated. Here we developed an experimental model of WGD using murine mammary tumor cell lines in immunocompetent mice and found that WGD triggers immune evasion characterized by reduced infiltration of CD8+ T cells. Via comprehensive cellular and molecular characterization of WGD+ and WGD- tumors at the single cell level, we determined that WGD+ cancer cells have diminished antigen presentation due to muted response to IFN stimulation in part due to epigenetic silencing of transcriptional regulators of MHCI genes via the PRC2 complex. WGD+ tumors also have lower alpha-ketoglutarate/succinate ratio that might lead to the observed increase in histone H3 lysine 27 trimethyl levels associated with repressive chromatin. Lastly, WGD+ tumors are more responsive to anti-PD-L1 blockade and to EED inhibitors and this is associated with increased antigen presentation and CD8+ T cell infiltration. Our results have important implications for the treatment of patients with WGD+ breast cancer.
2026-03-15 | GSE274224 | GEO
Project description:Whole genome doubling (WGD) is one of the most common genetic alterations in human cancer generally associated with poor clinical outcome, yet the underlying mechanisms have not been delineated. Here we developed an experimental model of WGD using murine mammary tumor cell lines in immunocompetent mice and found that WGD triggers immune evasion characterized by reduced infiltration of CD8+ T cells. Via comprehensive cellular and molecular characterization of WGD+ and WGD- tumors at the single cell level, we determined that WGD+ cancer cells have diminished antigen presentation due to muted response to IFN stimulation in part due to epigenetic silencing of transcriptional regulators of MHCI genes via the PRC2 complex. WGD+ tumors also have lower alpha-ketoglutarate/succinate ratio that might lead to the observed increase in histone H3 lysine 27 trimethyl levels associated with repressive chromatin. Lastly, WGD+ tumors are more responsive to anti-PD-L1 blockade and to EED inhibitors and this is associated with increased antigen presentation and CD8+ T cell infiltration. Our results have important implications for the treatment of patients with WGD+ breast cancer.
2026-03-15 | GSE274160 | GEO
Project description:Triple-negative breast cancers (TNBC) account for 10-15% of all breast cancers. The combination of chemotherapy and Immunotherapy (ICI: immune checkpoint inhibitor) is now a standard in stages II-III TNBC while this regimen is used only in a subset of advanced TNBC tumors presenting a high expression of PD-L1. However, whole exome sequencing of tumors in clinical trials investigating ICI for treatment of various solid tumors other than breast cancer indicate that tumors which undergone a WGD (whole genome doubling) are more sensitive to immune checkpoints inhibitors. Almost all human cells are diploid. Nevertheless, a WGD happens when regulation system maintaining the diploid status fail. The WGD+ cells are tetraploid, oncogenic and facilitate tumorigenesis. The WGD occurs in 44% of breast cancers and has been correlated to advanced cases, lower survival and higher resistance to chemotherapies and targeted therapies. Therefore it is crucial todefine the role of WGD towards the immune escape/control of TNBC and response to ICI. The first step of this work was to generate different cells line in both WGD- and WGD+ status. Using a technique of membrane homofusion of parentals cells, we obtained a WGD in three different basal murine mammary tumor cell lines (67NR, 168fARN, TA3Hauschka) and one human TNBC cell (SUM 159). The acquisition of WGD was then confirmed by flow cytometry (FACS) (DNA quantity by Hoechst staining) and karyotyping. The TA3Hauschka cell line is of particular interest since it is the only murine cell line which is diploid in parental state. By injection of WGD+ or parental DP cells in mammary fat pads of syngeneic immunocompetent strain or immunocompromised (NSG) mice, we observed a plateau of tumoral growth only for immunocompetent mice injected with WGD- cells while the WGD+ tumors escaped to spontaneous immune control. No difference of growth was seen in NSG mice between WGD- and WGD+ tumors. On tumor sections, a much more pronounced necrosis was seen in WGD- tumors comparatively to WGD+ tumors in syngeneic mice while the necrosis was mild and similar for both WGD+ and WGD- tumors in NSG mice. Immunofluorescence staining demonstrated an important neutrophilic infiltration of WGD+ while the WGD- tumors had strong T-cell lymphoid infiltrates frankly superior to the lymphoid infiltration of WGD+ tumors. These differences of infiltrates have been confirmed on digested tumors by both FACS and single cells RNA expression (scRNA) analyses. The FACS analysis also showed that the WGD+ tumors had an immunosuppressive pattern with notably higher levels of Tregs cells. To validate the hypothesis that WGD- are controlled by the infiltration of cytotoxic CD8 cells (leading to higher necrosis) while WGD+ tumors induce an immunosuppressive field, we performed an in vivo experiment investigating depletion of CD8 and neutrophils (anti-CD8 and anti-Ly6G antibodies) and a treatment by anti-PD-L1 antibodies (ICI). The treatment by isotypes antibodies confirmed the immune control of only the WGD- tumors. Anti-CD8 treatment led to an important increase in WGD- tumors growth but hadn’t any impact on WGD+ tumors while anti-Ly6G antibodies had no significative impact on WGD- and WGD+ tumors. The treatment by anti-PD-L1 antibodies was significantly more efficient to reduce the growth of WGD+ tumors than WGD- tumors. ScRNA analysis of WGD- and WGD+ untreated tumors revealed that WGD+ tumors have a significative decrease of presentation of MHCI complex. Therefore, this study highlights the potential role of biomarker of response to immune checkpoint inhibitor of whole genome doubling in TNBC.
2026-03-15 | GSE273085 | GEO
Project description:Triple-negative breast cancers (TNBC) account for 10-15% of all breast cancers. The combination of chemotherapy and Immunotherapy (ICI: immune checkpoint inhibitor) is now a standard in stages II-III TNBC while this regimen is used only in a subset of advanced TNBC tumors presenting a high expression of PD-L1. However, whole exome sequencing of tumors in clinical trials investigating ICI for treatment of various solid tumors other than breast cancer indicate that tumors which undergone a WGD (whole genome doubling) are more sensitive to immune checkpoints inhibitors. Almost all human cells are diploid. Nevertheless, a WGD happens when regulation system maintaining the diploid status fail. The WGD+ cells are tetraploid, oncogenic and facilitate tumorigenesis. The WGD occurs in 44% of breast cancers and has been correlated to advanced cases, lower survival and higher resistance to chemotherapies and targeted therapies. Therefore it is crucial todefine the role of WGD towards the immune escape/control of TNBC and response to ICI. The first step of this work was to generate different cells line in both WGD- and WGD+ status. Using a technique of membrane homofusion of parentals cells, we obtained a WGD in three different basal murine mammary tumor cell lines (67NR, 168fARN, TA3Hauschka) and one human TNBC cell (SUM 159). The acquisition of WGD was then confirmed by flow cytometry (FACS) (DNA quantity by Hoechst staining) and karyotyping. The TA3Hauschka cell line is of particular interest since it is the only murine cell line which is diploid in parental state. By injection of WGD+ or parental DP cells in mammary fat pads of syngeneic immunocompetent strain or immunocompromised (NSG) mice, we observed a plateau of tumoral growth only for immunocompetent mice injected with WGD- cells while the WGD+ tumors escaped to spontaneous immune control. No difference of growth was seen in NSG mice between WGD- and WGD+ tumors. On tumor sections, a much more pronounced necrosis was seen in WGD- tumors comparatively to WGD+ tumors in syngeneic mice while the necrosis was mild and similar for both WGD+ and WGD- tumors in NSG mice. Immunofluorescence staining demonstrated an important neutrophilic infiltration of WGD+ while the WGD- tumors had strong T-cell lymphoid infiltrates frankly superior to the lymphoid infiltration of WGD+ tumors. These differences of infiltrates have been confirmed on digested tumors by both FACS and single cells RNA expression (scRNA) analyses. The FACS analysis also showed that the WGD+ tumors had an immunosuppressive pattern with notably higher levels of Tregs cells. To validate the hypothesis that WGD- are controlled by the infiltration of cytotoxic CD8 cells (leading to higher necrosis) while WGD+ tumors induce an immunosuppressive field, we performed an in vivo experiment investigating depletion of CD8 and neutrophils (anti-CD8 and anti-Ly6G antibodies) and a treatment by anti-PD-L1 antibodies (ICI). The treatment by isotypes antibodies confirmed the immune control of only the WGD- tumors. Anti-CD8 treatment led to an important increase in WGD- tumors growth but hadn’t any impact on WGD+ tumors while anti-Ly6G antibodies had no significative impact on WGD- and WGD+ tumors. The treatment by anti-PD-L1 antibodies was significantly more efficient to reduce the growth of WGD+ tumors than WGD- tumors. ScRNA analysis of WGD- and WGD+ untreated tumors revealed that WGD+ tumors have a significative decrease of presentation of MHCI complex. Therefore, this study highlights the potential role of biomarker of response to immune checkpoint inhibitor of whole genome doubling in TNBC.
2026-03-15 | GSE273031 | GEO
Project description:Loss of antigen presentation by MHCI is a common mechanism of tumor immune evasion. Mitochondrial oxidative phosphorylation (OXPHOS) capacity influences MHCI expression, but the underlying molecular mechanisms remain unclear. Here, we demonstrate that the relative flow of electrons through complex I or II of the mitochondrial electron transport chain (ETC) regulates MHCI expression and antigen presentation in cancer cells. Specifically, reducing electron flow from complex II increases mitochondrial succinate which activates transcription of MHCI and antigen processing and presentation (APP) genes. These phenotypes are independent of the interferon (IFN) signaling pathway and driven by succinate-mediated enzymatic inhibition of lysine-specific demethylases, KDM5A/B and destabilization of polycomb repressor complex 2 (PRC2). Finally, knockout of the mitochondrial Complex I inhibitor protein, MCJ, preferentially reduces electron flow through Complex II and increases succinate which drives an enhanced antigen-dependent CD8+ T cell response to mouse melanoma tumors in vivo. These findings suggest that the mitochondrial ETC can be manipulated therapeutically to enhance antitumor immune responses independently of IFNγ.
2022-12-31 | GSE198346 | GEO
Project description:The infiltration of effector CD8+ T cells into tumors is one of the major predictors of clinical outcome for epithelial ovarian cancer (EOC) patients. Immune cell infiltration is a complex process that could be affected by the epigenetic makeup of the tumor. Here, we demonstrate that a lysine 4 histone H3 (H3K4) demethylase KDM5A impairs immune cell infiltration and inhibits anti-tumor immune response. Mechanistically, KDM5A silences genes involved in antigen processing and presentation pathway. Antigen processing and presentation is a critical step that is required for CD8+ T cells infiltration and activation of CD8+ T cell mediated anti-tumor immune response. KDM5A inhibition restores the expression of antigen presentation pathway in vitro and promotes anti-tumor immune response mediated by CD8+ T cells in vivo in a syngeneic EOC mouse model. Notably, a negative correlation between expression of KDM5A and genes involved in antigen processing and presentation pathway such as HLA-A and HLA-B is observed in the majority of cancer types. In summary, our results establish KDM5A as a regulator of CD8+ T cells tumor infiltration and demonstrate that KDM5A inhibition is a novel therapeutic strategy aiming to boost anti-tumor immune response.
2022-05-02 | GSE194359 | GEO
Project description:The infiltration of effector CD8+ T cells into tumors is one of the major predictors of clinical outcome for epithelial ovarian cancer (EOC) patients. Immune cell infiltration is a complex process that could be affected by the epigenetic makeup of the tumor. Here, we demonstrate that a lysine 4 histone H3 (H3K4) demethylase KDM5A impairs immune cell infiltration and inhibits anti-tumor immune response. Mechanistically, KDM5A silences genes involved in antigen processing and presentation pathway. Antigen processing and presentation is a critical step that is required for CD8+ T cells infiltration and activation of CD8+ T cell mediated anti-tumor immune response. KDM5A inhibition restores the expression of antigen presentation pathway in vitro and promotes anti-tumor immune response mediated by CD8+ T cells in vivo in a syngeneic EOC mouse model. Notably, a negative correlation between expression of KDM5A and genes involved in antigen processing and presentation pathway such as HLA-A and HLA-B is observed in the majority of cancer types. In summary, our results establish KDM5A as a regulator of CD8+ T cells tumor infiltration and demonstrate that KDM5A inhibition is a novel therapeutic strategy aiming to boost anti-tumor immune response.
2022-05-02 | GSE194358 | GEO
Project description:Pro-inflammatory microglia contribute to disease progression in neuroinflammatory and neurodegenerative diseases. We identify novel Kv1.3 channel-dependent molecular and cellular mechanisms during microglial activation and unravel a Kv1.3-dependent pathway for MHCI-restricted antigen presentation by microglia to CD8+ T cells.
2018-10-24 | PXD006753 | Pride
Project description:Immune evasion is an important hallmark of cancer ensured by diverse strategies, including immunosuppression and downregulation of antigen presentation. Here, to restore immunogenicity of cancer cells, we employed the minimal gene regulatory network of highly immunogenic type 1 conventional dendritic cells (cDC1) to reprogram cancer cells into professional antigen presenting cells (APCs). We showed that enforced expression of PU.1, IRF8 and BATF3 (PIB) was sufficient to induce cDC1 phenotype in 33 cell lines derived from human and mouse hematological and solid tumors. PIB gradually modified the cancer cell transcriptional and epigenetic program imposing global antigen presentation and cDC1 gene signatures within 9 days. cDC1 reprogramming restored the expression of antigen presentation complexes as well as co-stimulatory molecules at the cell surface, leading to the presentation of endogenous antigens on MHC-I, and to CD8+ T cell mediated killing. Functionally, tumor- APCs acquired the ability to uptake and process exogenous proteins and dead cells, secreted inflammatory cytokines and cross-presented antigens to naïve CD8+ T cells. Importantly, tumor-APCs were efficiently generated at the single cell level from primary cancer cells of 7 solid tumors that presented antigens to memory and naïve T-cells, as well as to activated patient-specific intra-tumoral lymphocytes. Alongside antigen presentation, tumor-APCs harboring TP53, KRAS and PTEN mutations showed impaired tumorigenicity in vitro and in vivo. Finally, using in vivo mouse models of melanoma, we showed that intra-tumoral injection of tumor-APCs promoted lymphoid infiltration, delayed tumor growth and increased survival. The anti-tumor immunity elicited by tumor-APCs was synergistic with immune checkpoint inhibitors enabling tumor eradication. Our approach combines cDC1’s antigen processing and presenting abilities with endogenous generation of tumor antigens and serves as a platform for the development of novel immunotherapies based on endowed antigen presentation in cancer cells.
2023-10-24 | PXD039789 | Pride
Project description:Whole genome doubling (WGD) is a frequent event in cancer evolution associated with chromosomal instability, metastasis, and poor prognosis. While the genomic consequences of WGD are well documented, the effects of non-genetic alterations that accompany WGD, such as changes to cell and nuclear size, on tetraploid (4N) cancer cell physiology are less understood. Here, we show that cell and nuclear volume do not always scale with DNA content after WGD in cancer cells, resulting in 4N cells that differ in size. We find that small size is associated with enhanced cell fitness, mitotic fidelity, and tumorigenicity in 4N cancer cells and with poor patient survival in WGD-positive human cancers. Overall, these results suggest that cell and nuclear size contribute to the tumorigenic potential of 4N cancer cells and could be an important prognostic marker in human tumors that undergo WGD.
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