Published in Nat Commun. 2017 Apr 5;8:14802
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 SEs to drive CD47 overexpression to escape immune surveillance.
CD47 is an immunoglobulin-like transmembrane ligand that inhibits phagocytosis by binding to the extracellular region of SIRP-alpha on macrophages. Prior studies have shown that cancer cells overexpress CD47 to protect themselves from immunosurveilance, however, not all types of cancer express high levels of CD47 and those that do seem to be more resistant to drug therapies. In recent years, it was discovered that using specific antibodies against CD47, blocks the interaction between CD47 and SIRP-alpha, inducing macrophages to engulf malignant cells and hence, decreasing the growth rate of tumors successfully. This study is designed to uncover the transcription factor(s) directly binding to CD47 active enhancers that are responsible for the increased CD47 expression on cancer cells, with the goal of finding alternative upstream targets to disrupt CD47’s antiphagocytic function. By analyzing the CD47 regulatory genomic landscape, we discovered that: i) CD47 is regulated by super-enhancers (SEs) in cancer cell types where CD47 protein levels are the highest. ii) a set of active constituent enhancers located within two distinct super-enhancers, dynamically regulate CD47 expression in different cancer cell types tested. iii) the TNF-NFKB1 signaling pathway is directly involved in the regulation of CD47 through the specific activation of a distal downstream constituent enhancers in breast cancer. In conclusion, our data describes for the first time, the CD47 cis-regulatory architecture across different cancer and tumor types, which includes the formation of CD47 SEs. Furthermore, through the characterization of two CD47 SEs, we were able to identify an inflammatory component involved in the direct upregulation of CD47 in breast cancer. This information will help us in the future to generate target therapies, to disrupt the identified pathways upstream CD47 or super-enhancers regulating CD47 to combine with the CD47 antibody therapy for the treatment of cancer.