MYC regulates the antitumor immune response through CD47 and PD-L1

Abstract

The MYC oncogene codes for a transcription factor that is overexpressed in many human cancers. Here we show that MYC regulates the expression of two immune checkpoint proteins on the tumor cell surface: the innate immune regulator CD47 (cluster of differentiation 47) and the adaptive immune checkpoint PD-L1 (programmed death-ligand 1). Suppression of MYC in mouse tumors and human tumor cells caused a reduction in the levels of CD47 and PD-L1 messenger RNA and protein. MYC was found to bind directly to the promoters of the Cd47 and Pd-l1 genes. MYC inactivation in mouse tumors down-regulated CD47 and PD-L1 expression and enhanced the antitumor immune response. In contrast, when MYC was inactivated in tumors with enforced expression of CD47 or PD-L1, the immune response was suppressed, and tumors continued to grow. Thus, MYC appears to initiate and maintain tumorigenesis, in part, through the modulation of immune regulatory molecules.

Fig. 1. MYC regulates the expression of CD47 and PD-L1 in murine and human leukemia and lymphomas

(A) Flow cytometry median fluorescence intensity (MFI) was used to determine the relative cell surface expression of CD47 (blue), PD-L1 (green), and other immune proteins following MYC inactivation in MYC T-ALL 4188 cells in vitro (n=3). (B) Tumors were harvested from primary MYC-driven lymphomas 0 or 4 days following MYC inactivation. mRNA and protein levels were quantified by qPCR and flow cytometry MFI (n=3 tumors per condition). Representative flow cytometry histograms are shown to the right. (C) CD47 (blue) and PD-L1 (green) protein levels in Jurkat and CCRF-CEM cells were quantified by flow cytometry MFI following MYC inhibition by conditional shRNA knockdown or 10 µM JQ1 treatment (n=3 biological replicates).

Fig. 2. MYC regulates CD47 and PD-L1 expression in human and mouse tumors and binds to the promoters of the corresponding genes

(A) and (B) The mRNA and protein levels of MYC (gray), CD47 (blue), and PD-L1 (green) in human melanoma SKMEL28 and human NSCLC H1299 cells were determined by qPCR and flow cytometry MFI, respectively, 48 hours after MYC inactivation in vitro. MYC was inactivated by 10 µM JQ1 treatment or MYC shRNA knockdown (n=3 biological and 3 technical replicates for qPCR and 3 biological replicates for flow cytometry). (C) ChIP-seq analysis of MYC binding to the promoter sequence of the genes encoding CD47 and PD-L1 in mouse MYC T-ALL cells. IgG was used as a negative control. ChIP-sequencing traces were generated from GSE44672 (34). Exons are represented as vertical bars, the untranslated region (UTR) is represented by a black line, and arrows indicate the direction of transcription.

Fig. 3. Constitutive expression of CD47 and PD-L1 in mouse MYC T-ALL 4188 cells prevents recruitment of immune effectors after MYC inactivation

(A) Quantification of CD4⁺ T cells in transplanted control (gray) or constitutive CD47 or PD-L1-expressing (colored) tumors before 2, 4, 11 or 21 days after MYC inactivation. Control, CD47-expressing, or PD-L1- expressing MYC T-ALL 4188 tumor cells were transplanted into FVB RAG1-/- mice one week after reconstitution with fLuc⁺ CD4⁺ T cells. Administration of Dox to inactivate MYC in established tumors is day 0. Left panel: representative bioluminescence images of tumor-bearing RAG1−/− animals. Right panel: average bioluminescence signal of the T cells is shown (n=5 tumors per group). (B) Quantification of F4/80⁺ or CD69⁺ cells in transplanted control (gray) or constitutive CD47 or PD-L1-expressing (colored) tumors before or 4 days after MYC inactivation by immunohistochemistry using markers for macrophages (F4/80) and activated T cells (CD69). Tumor cells were transplanted into WT FVB hosts. Administration of Dox to inactivate MYC in established tumors is day 0. The y axis denotes the number of positively staining cells per field. For representative images, see Fig. S13. Data represent mean ± SEM derived from measurements of 3 independent tumors and 3 measurements per tumor.

Fig. 4. Down-Regulation of CD47 or PD-L1 is Required for Tumor Regression, Shutdown of Angiogenesis, and Induction of Senescence upon MYC inactivation

(A) Survival after MYC inactivation of syngeneic FVB/N mice that had been transplanted with either MSCV control (gray), CD47-expressing (blue), or PD-L1-expressing (green) fLuc⁺ MYC T-ALL cells. MYC was inactivated when tumors reached 1.5 cm³ (d0). (n=5 for control, n=10 for CD47, and n=5 for PD-L1). (B) MYC expression before (d0) or after MYC inactivation (d4). (C) Bioluminescence imaging measurement of tumor burden before and after MYC inactivation in control (gray), CD47-expressing (blue), and PD-L1-expressing (green) tumors. Three representative animals are shown per group. (D) Minimal residual disease (remaining tumor cells) after MYC inactivation was measured by bioluminescence imaging. (E) Angiogenesis was measured 0 and 4 days after MYC inactivation in control, CD47-expressing, and PD-L1- expressing tumors growing in WT FVB hosts by immunofluorescence for CD31. For representative images, see Fig. S15. (F) Control, CD47-expressing, and PD-L1-expressing tumors were analyzed by immunostaining for senescence associated β-galactosidease (SA-β- gal) in tumors described in (E). The y axis denotes the number of positively staining microvessels (E) or cells (F) per field. For representative images, see Fig. S15B. Data represent mean ± SEM derived from measurements of 3 independent tumors and 3 measurements per tumor.