A Super-enhancer Associated with CD47 Links Pro-inflammatory Signaling in CD47 Upregulation in Breast Cancer
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PROVIDER: PRJNA360117 | ENA |
REPOSITORIES: ENA
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Project description:CD47 is a cell surface molecule that inhibits phagocytosis of cells that express it by binding to its receptor, SIRPα, on macrophages and other immune cells. CD47 is expressed at different levels by neoplastic and normal cells. Here, to reveal mechanisms by which different neoplastic cells generate this dominant 'don't eat me' signal, we analyse the CD47 regulatory genomic landscape. We identify two distinct super-enhancers (SEs) associated with CD47 in certain cancer cell types. We show that a set of active constituent enhancers, located within the two CD47 SEs, regulate CD47 expression in different cancer cell types and that disruption of CD47 SEs reduces CD47 gene expression. Finally we report that the TNF-NFKB1 signalling pathway directly regulates CD47 by interacting with a constituent enhancer located within a CD47-associated SE specific to breast cancer. These results suggest that cancers can evolve SE to drive CD47 overexpression to escape immune surveillance.
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Project description:Highly accessible genomic super-enhancers often upregulate tumor-promoting genes in cancer, yet the role of genomic variation within them remains unclear. We identified a bifunctional super-enhancer that regulates the expression of cancer-promoting genes LINC00636 and CD47 in breast cancer. Our study revealed that a common germline insertion variant within the super-enhancer is associated with better progression-free survival in breast cancer patients and reduced chromatin accessibility at the super-enhancer locus. By deleting the insertion allele in breast cancer cells, we observed increased chromatin accessibility, leading to upregulation of LINC00636 and CD47, delayed cell death, and reduced infiltration of CD80+ pro-inflammatory macrophages—events that promote tumor growth. The absence of the insertion also activated a protumoral transcriptional program through LINC00636 overexpression. Our findings highlight an insertion/deletion variant that fine-tunes the regulatory function of a bifunctional super-enhancer and suggest a protective role for the insertion in breast cancer.
2026-02-26 | GSE290710 | GEO
Project description:Highly accessible genomic super-enhancers often upregulate tumor-promoting genes in cancer, yet the role of genomic variation within them remains unclear. We identified a bifunctional super-enhancer that regulates the expression of cancer-promoting genes LINC00636 and CD47 in breast cancer. Our study revealed that a common germline insertion variant within the super-enhancer is associated with better progression-free survival in breast cancer patients and reduced chromatin accessibility at the super-enhancer locus. By deleting the insertion allele in breast cancer cells, we observed increased chromatin accessibility, leading to upregulation of LINC00636 and CD47, delayed cell death, and reduced infiltration of CD80+ pro-inflammatory macrophages—events that promote tumor growth. The absence of the insertion also activated a protumoral transcriptional program through LINC00636 overexpression. Our findings highlight an insertion/deletion variant that fine-tunes the regulatory function of a bifunctional super-enhancer and suggest a protective role for the insertion in breast cancer.
2026-02-26 | GSE290709 | GEO
Project description:A Super-enhancer Associated with CD47 Links Pro-inflammatory Signaling in CD47 Upregulation in Breast Cancer
| PRJNA360118 | ENA
Project description:Cytokines are key regulators of tumor immune surveillance by controlling immune cell activity. Here, we investigated whether interleukin 4 (IL4) has antileukemic activity via immune-mediated mechanisms in an in vivo murine model of acute myeloid leukemia driven by the MLL-AF9 fusion gene. Although IL4 strongly inhibited leukemia development in immunocompetent mice, the effect was diminished in immune-deficient recipient mice, demonstrating that the antileukemic effect of IL4 in vivo is dependent on the host immune system. Using flow cytometric analysis and immunohistochemistry, we revealed that the antileukemic effect of IL4 coincided with an expansion of F4/80+ macrophages in the bone marrow and spleen. To elucidate whether this macrophage expansion was responsible of the antileukemic effect, we depleted macrophages in vivo with clodronate liposomes. Macrophage depletion eliminated the antileukemic effect of IL4, showing that macrophages mediated the IL4-induced killing of leukemia cells. In addition, IL4 enhanced murine macrophage-mediated phagocytosis of leukemia cells in vitro. Global transcriptomic analysis of macrophages revealed an enrichment of signatures associated with alternatively activated macrophages and increased phagocytosis upon IL4 stimulation. Notably, IL4 concurrently induced Stat6-dependent upregulation of CD47 on leukemia cells, which suppressed macrophage activity. Consistent with this finding, combining CD47 blockade with IL4 stimulation enhanced macrophage-mediated phagocytosis of leukemia cells. Thus, IL4 has two counteracting roles in regulating phagocytosis in mice; enhancing macrophage-mediated killing of leukemia cells, but also inducing CD47 expression that protects target cells from excessive phagocytosis. Taken together, our data suggests that combined strategies that activate macrophages and block CD47 have therapeutic potential in AML.
2021-07-14 | GSE155048 | GEO
Project description:IL4 promotes phagocytosis of murine leukemia cells counteracted by CD47 upregulation
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Project description:Elevated CD47 expression in some cancers is associated with decreased survival and limits phagocytic clearance by engaging its counter-receptor SIRPα, but elevated CD47 mRNA expression in human melanomas is associated with improved survival. Gene expression data suggested that recruitment of natural killer (NK) cells, which highly express CD47, into the tumor microenvironment contribute to this correlation. The CD47 ligand thrombospondin-1 inhibited wildtype but not Cd47-/- murine NK cell proliferation and granzyme B and interferon-γ expression in vitro. Cd47-/- NK cells correspondingly showed augmented effector phenotypes. Although, wildtype and Cd47-/- NK cells were equally effective for killing B16 melanoma cells in vitro, Cd47-/- mice exhibited enhanced B16 tumor growth in vivo. Consistent with the human data, tumor-bearing Cd47-/- mice had decreased splenic NK numbers with impaired effector protein expression and elevated exhaustion markers. A pro-apoptotic signature in Cd47-/- NK cells was associated with stress-mediated elevation of mitochondrial proton leak, increased reactive oxygen species and apoptosis. Gene expression profiling identified CD47-dependent transcriptional responses in in NK cells from tumor-bearing mice that regulate systemic NK activation and exhaustion. Treating wildtype mice with a CD47 antibody that blocks thrombospondin-1 binding delayed tumor growth and was associated with increased NK recruitment and increased granzyme B- and interferon-γ levels in intratumoral NK but not CD8+ T cells. Therefore, CD47 in the tumor microenvironment regulates NK-mediated tumor immunity, and therapeutic blockade enhances NK immune function.
2020-04-13 | GSE113876 | GEO
Project description:CD47 is a “don’t eat me” signal that is frequently overexpressed in tumors to evade phagocytosis by tumor associated macrophages (TAM). Investigational agents targeting CD47, such as magrolimab, aim to induce phagocytosis of tumor cells by TAMs. Previously, two functionally defined key TAM subsets have been identified: complement C1q C chain positive (C1QC) TAMs, which display pro-phagocytic activity, and secreted phosphoprotein 1 positive (SPP1) TAMs that express pro-angiogenic markers. Here we characterize CD47 expression and its relationship with tumor macrophages in solid tumor samples.
2025-09-04 | GSE296861 | GEO
Project description:To identify candidate genes regulated by CD47 Affymetrix Human Genome U133 Plus GeneChip 2.0 HCC cell line Huh7 cells with or without CD47 repressed
2014-06-01 | E-GEOD-47563 | biostudies-arrayexpress
Project description:Although KRAS G12C inhibitors have altered the treatment strategy of patients with KRAS G12C mutant lung cancer, their efficacy is insufficient to eliminate tumors. Here, we identified that inhibition of mutant KRAS promotes escape from macrophage phagocytosis by upregulating the expression of ‘don’t eat me’ signal proteins, including CD47. CD47 was induced by the binding of FOXA1 to the super-enhancer of CD47. The addition of an anti-CD47 antibody restored macrophage phagocytosis and phenotype of macrophages.
2025-07-15 | GSE291687 | GEO