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CD47 masks pro-phagocytic ligands in cis on tumor cells to suppress antitumor immunity

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Abstract

Cancer cells often overexpress CD47, which triggers the inhibitory receptor SIRPα expressed on macrophages, to elude phagocytosis and antitumor immunity. Pharmacological blockade of CD47 or SIRPα is showing promise as anticancer therapy, although CD47 blockade has been associated with hematological toxicities that may reflect its broad expression pattern on normal cells. Here we found that, in addition to triggering SIRPα, CD47 suppressed phagocytosis by a SIRPα-independent mechanism. This mechanism prevented phagocytosis initiated by the pro-phagocytic ligand, SLAMF7, on tumor cells, due to a cis interaction between CD47 and SLAMF7. The CD47–SLAMF7 interaction was disrupted by CD47 blockade and by a first-in-class agonist SLAMF7 antibody, but not by SIRPα blockade, thereby promoting antitumor immunity. Hence, CD47 suppresses phagocytosis not only by engaging SIRPα, but also by masking cell-intrinsic pro-phagocytic ligands on tumor cells and knowledge of this mechanism may influence the decision between CD47 blockade or SIRPα blockade for therapeutic purposes.

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Fig. 1: CD47, but not SIRPα, inhibits phagocytosis by SLAMF7.
Fig. 2: Lack of CD47 or SIRPα phenocopies the effects of blockade.
Fig. 3: Both CD47 and SIRPα inhibit FcR-mediated phagocytosis.
Fig. 4: CD47 interacts in cis with SLAMF7 on tumor cells.
Fig. 5: Freeing SLAMF7 from CD47 promotes phagocytosis.
Fig. 6: First-in-class SLAMF7 mAb Z10 promotes phagocytosis.
Fig. 7: mAb Z10 frees SLAMF7 from CD47.

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Data availability

RNA-seq data supporting the findings of this study have been deposited into the Gene Expression Omnibus under accession no. GSE223059. All other relevant data are available from the corresponding author upon reasonable request. Source data are provided with this paper.

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Acknowledgements

We thank members of the Veillette laboratory for useful discussions. We also acknowledge T. van den Berg (Amsterdam) and T. Matozaki (Kobe) for providing hybridomas. This work was supported by grants from the Canadian Institutes of Health Research (MT-14429, MOP-82906, FDN-143338, PJT-178314 and PJT-183593), the Terry Fox Research Institute (1190-02) and the Ministère de l’économie et de l’innovation (Québec) to A.V.; and US National Institutes of Health grant R37 CA239072 to E.H. A.V. received a contract from Bristol Myers-Squibb to study the mechanism of action of SLAMF7 monoclonal antibody elotuzumab against multiple myeloma. Z.T. received a Fellowship from the Cole Foundation; C.C.G. received a Studentship from the Fonds de la recherche en santé – Québec; J.L. receives a Studentship from the Chinese Science Council; and A.V. holds the Canada Research Chair on Signaling in the Immune System.

Author information

Authors and Affiliations

Authors

Contributions

Z.T., M.C.-Z., J.Q., D.D., Y.Z., E.H. and A.V. designed experiments. Z.T., M.C.-Z., J.Q., C.C.G., J.L. and Y.Z. performed experiments. All authors interpreted the results. Z.T. and A.V. wrote the manuscript. All authors commented on the manuscript. A.V. and E.H. provided funding.

Corresponding author

Correspondence to André Veillette.

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Competing interests

Members of the Veillette laboratory will file a patent on the use of monoclonal antibody Z10 for the treatment of SLAMF7-positive human tumors. The authors declare no other competing interests.

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Nature Immunology thanks David Raulet and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Ioana Visan, in collaboration with the Nature Immunology team. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Generation of Fc-silent mAbs.

a, The three mutations (‘LALAPG’) introduced in the Fc portion of mAbs to render them Fc-silent are depicted. LALAPG is L234A (‘LA’), L235A (‘LA’), and P329G (‘PG’). b, Binding assay of Fc-intact and Fc-silent variants of mIgG2a (mAb MOPC21) or hIgG1 (mAb Z10) to FcRs on BMDMs assessed by flow cytometry. c, Binding of Fc-silent mSIRPα mAbs #23, #27 and MY-1 to EL-4 cells and EL-4 cells expressing full-length mSIRPα or a variant of mSIRPα containing only the first Ig-like variable (V) domain assessed by flow cytometry. d, Binding of a soluble mCD47-Fc fusion protein to EL-4 cells, expressing or not expressing mSIRPα, studied by flow cytometry. MFI, mean fluorescence intensity. e, Binding of Fc-silent mSIRPα mAbs #23, #27 and MY-1 to mSIRPα-Fc, mSIRPβ1a-Fc, mSIRPβ1b-Fc and mSIRPβ1c-Fc, determined by ELISA. f, Binding of Fc-silent Ctrl IgG MOPC21, hCD47 mAbs B6H12 and AO-176 or hSIRPα-Fc fusion proteins TTI-621 and ALX148 to WT and CD47−/− Daudi cells evaluated by flow cytometry. g, Binding of Fc-silent hSIRPα mAbs to Sirpa-/- BMDMs, transduced with retroviruses encoding or not encoding the V1 or V2 version of hSIRPα, studied by flow cytometry. All data are means ± s.e.m. ****p < 0.0001. Flow cytometry profiles are representative of 3 (c,f, g) or 2 (b) independent experiments. Results are pooled from 5 (d) and 3 (e) independent experiments.

Extended Data Fig. 2 CD47, but not SIRPα, inhibits SLAMF7-mediated phagocytosis.

a,b, Representative flow cytometry profiles (a) and compiled data from 3 independent experiments (b) of phagocytosis assays of L1210 cells by WT BMDMs, assessed by flow cytometry using the pHrodo dye as in Fig. 1b. c, Phagocytosis assays of L1210 cells by WT BMDMs as in Fig. 1b. BMDMs and L1210 cells were pre-treated with indicated mAbs, followed or not by extensive washing, prior to the phagocytosis assay. d, Tumors from the experiment depicted in Fig. 1e were dissected, weighed, measured, and analyzed by flow cytometry. e, Phagocytosis of Raji cells by Sirpa-/- BMDMs, expressing or not expressing hSIRPα version V1 or V2 as in Fig. 1f. f,g, Representative flow cytometry profiles (f) and compiled data from 4 independent experiments (g) of phagocytosis assays of WT and Cd47-/- L1210 cells by WT or Sirpa-/- BMDMs, assessed by flow cytometry using the pHrodo dye as in Fig. 2a. h, Phagocytosis assays of WT and Cd47-/- L1210 cells by WT or Sirpa-/- BMDMs, with or without pre-treatment of lipopolysaccharide (LPS), as in Fig. 2a. i, Tumors from the experiment depicted in Fig. 2e were dissected, weighed, measured and analyzed by flow cytometry. One mouse from ‘Rag1-/- mice + Cd47-/- L1210’ group showed no clinically detectable tumor on day 17. All data are means ± s.e.m. ns, not significant; *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001. Flow cytometry profiles are representative of 3 (a) or 4 (f) independent experiments. Results are pooled from 3 (b,c,e) or 4 (g,h) mice studied in 3 (b,c,e) or 4 (g,h) independent experiments, 14 (d) mice from 3 independent experiments, and 11 (WT L1210) or 10 (Cd47-/- L1210) mice from 2 independent experiments (i). Each symbol represents one mouse.

Extended Data Fig. 3 Loss of SIRPa does not alter macrophage differentiation.

a, RNA sequence of Sirpa-/- vs WT BMDMs was analyzed. b, expression of various cell surface markers (red lines) in WT and Sirpa-/- BMDMs assayed by flow cytometry. Filled curves, Ctrl IgG. c, expression of various cell surface markers (red lines) in WT and Sirpa-/- BMDMs from a second Sirpa-/- C57BL/6 mouse strain (#54) assayed by flow cytometry. Filled curves, Ctrl IgG. d,e, Phagocytosis of L1210 cells (d) and Raji cells (e), expressing or not expressing CD47, by WT or Sirpa-/- BMDMs as in Fig. 2a. All data are means ± s.e.m. ns, not significant; **p < 0.01, ***p < 0.001, and ****p < 0.0001. 3 pairs of mice were studied in one experiment (a). Flow cytometry profiles are representative of 3 (b,c) independent experiments. Results are pooled from a total of 3 (d,e) mice studied in 3 independent experiments. Each symbol represents one mouse.

Extended Data Fig. 4 Both CD47 and SIRPα inhibit FcR-mediated tumor growth.

Tumors from the experiment depicted in Fig. 3d were dissected, weighed, measured and analysed by flow cytometry. One mouse from ‘Rag1-/- mice + Ctrl IgG (C1.18.4)’ group showed no clinically detectable tumor on day 18. All data are means ± s.e.m. ns, not significant; ****p < 0.0001. Results are pooled from a total of 15 mice [16 mice for ‘Rag1-/- mice + Tac mAb (7G7)’ group] from 3 independent experiments. Each symbol represents one mouse.

Extended Data Fig. 5 CD47 interacts in cis with SLAMF7.

a, Expression of Flag or CD47 (red lines) on L1210 cells and Cd47-/- L1210 cells, expressing or not expressing mCD47-Flag, assessed by flow cytometry. Permeabilization was used for the Flag staining. Filled curves, Ctrl IgG. b, Means of the normalized total ion current (TIC) for the potential interactors of CD47. c, Expression of hCD47 (red lines) on WT or CD47-/- 293 T cells was assessed by flow cytometry. Filled curves, Ctrl IgG. d, Fluorescence intensity of Dye 647 and Dye 547 in CD47-/- 293 T cells, transfected with tagged versions of mCD47 and mSLAMF7 and treated with or without Ctrl IgG, mCD47 mAb and mSLAMF7 mAb, assayed by flow cytometry. e, Binding of soluble mSIRPα-Fc fusion protein and expression of mCD47 on transfected CD47-/- 293 T cells assessed by flow cytometry. f, Binding of soluble mSLAMF7-Fc fusion protein and expression of mSLAMF7 on transfected BI-141 cells assessed by flow cytometry. g,h, Representative confocal microscopy images (g) and compiled data from 18 cells in 3 independent experiments (h) of FRET assays as in Fig. 4d,e. All data are means ± s.e.m. ns, not significant; ****p < 0.0001. Flow cytometry profiles are representative of 3 (a,c-f) independent experiments. Results are representative of 3 (g) independent experiments. Results are pooled from 3 (b,h) independent experiments.

Extended Data Fig. 6 Structure-function analyses of CD47 and SLAMF7.

a, Expression of mCD47 and mSLAMF7 and binding of mSIRPα-Fc (red lines) in L1210 derivatives assessed by flow cytometry. Filled curves, Ctrl IgG or Ctrl Fc fusion protein. b, Phagocytosis assays of L1210 derivatives by WT or Sirpa-/- BMDMs as in Fig. 2a. c, Expression of mSLAMF7 (red lines) in Slamf7-/- conA-activated CD4+ T cells, transduced with variants of mSLAMF7 constructs, assessed by flow cytometry. Filled curves, Ctrl IgG. d, Phagocytosis assays of conA-activated CD4+ T cells by WT or Sirpa-/- BMDMs as in Fig. 2a. e,f, Schematic representation (e) and time-course of normalized dye 505 fluorescence intensity (f) of LUV-based FRET assay of mSLAMF7 (donor) or hPD-L1 (donor) with mCD47 (acceptor) or hPD-1 (acceptor) monitored by a real time plate reader. g, Time-course of normalized dye 505 fluorescence intensity of LUV-based FRET assay of mSLAMF7 (donor) with mCD47 (acceptor), pre-treated with Ctrl IgG MOPC21, mSLAMF7 mAb 4G2 and mCD47 mAb Miap301, monitored by a real time plate reader. h, Binding of soluble hCD47-Fc fusion protein to WT or CD47-/- Raji cells assessed by flow cytometry. All data are means ± s.e.m. ns, not significant; **p < 0.01 and ***p < 0.001. Flow cytometry profiles are representative of 3 (a,c) or 2 (h) independent experiments. Results are representative of 3 (f) or 2 (g) independent experiments. Results are pooled from 4 (b) or 4 (d; for all variants, except 3 for SLAMF7R75A) independent experiments. Each symbol represents one mouse.

Extended Data Fig. 7 mAb Z10 promotes phagocytosis with SIRPα blockade.

a,b, Phagocytosis assay of Daudi (a, left), MM.1 S (a, right), and Fc-silent CD3 + CD28 mAbs activated mouse CD8+ T cells expressing (b, right) or not expressing (b, left) hSLAMF7 by WT or Sirpa-/- BMDMs assayed by fluorescence microscopy. c, Schematic representations of the impact of mAb Z10 on macrophages or target cells. d, Tumors from experiment depicted in Fig. 6g were dissected, weighed, measured, and analysed by flow cytometry. One mouse showed no detectable tumor in the ‘SIRPα mAb (#27) + SLAMF7 mAb (Z10)’ group on day 24. All data are means ± s.e.m. ns, not significant; **p < 0.01, ***p < 0.001, and ****p < 0.0001. Results are pooled from 3 (a,b) mice studied in 3 (a,b) independent experiments; 8 [except 7 for ‘SLAMF7 mAb (Z10)’ and ‘SIRPα mAb (#27)’ groups] mice from 2 independent experiments (d). Each symbol represents one mouse.

Extended Data Fig. 8 Z10 disrupts CD47-SLAMF7 interaction and does not affect conjugate formation.

a, Co-immunoprecipitation assay of CD47 and SLAMF7 in CD47-/- 293 T cells expressing a Flag-tagged variant of hCD47 and a Myc-tagged variant of hSLAMF7, in the presence of Ctrl IgG MOPC21 or hSLAMF7 mAb Z10. b, Representative flow cytometry profiles (b, left) and compiled data from 3 independent experiments (b, right) of conjugate formation assays of Sirpa-/- BMDMs with Raji cells for the indicated time points, in the presence of Ctrl IgG or hSLAMF7 mAb Z10, detected by flow cytometry. c, Conjugate formation assays of Sirpa-/- BMDMs with Raji cells for 20 minutes, assessed by confocal microscopy. All data are means ± s.e.m. ns, not significant. Results are representative of 2 (a) independent experiments. Flow cytometry profiles are representative of 3 independent experiments (b). Results are pooled from a total of 3 (b,c) mice studied in 3 (b,c) independent experiments. Each symbol represents one mouse.

Source data

Extended Data Fig. 9 Z10 does not interfere with phagocytosis of CD47-deficient targets.

a,b, Phagocytosis of Raji (a) and Daudi (b), expressing or not expressing CD47 by WT or Sirpa-/- BMDMs in the presence of Ctrl IgG MOPC21 and hSLAMF7 mAb Z10 assayed by fluorescence microscopy. All data are means ± s.e.m. ns, not significant; **p < 0.01 and ****p < 0.0001. Results are pooled from 3 (a,b) mice studied in 3 independent experiments. Each symbol represents one mouse.

Extended Data Fig. 10 Z10 binds to the second Ig-like domain of SLAMF7.

a,b, Binding of hSLAMF7 mAbs Z10, Elo and Z8 to CD47-/- 293 T cells expressing various chimeras between hSLAMF7 and mSLAMF7 (a) or various mutants of hSLAMF7 (b), assayed by flow cytometry. For the chimeras, the residues in hSLAMF7 (numbered) were replaced by the equivalent residues in mSLAMF7. Flow cytometry profiles are representative of 3 (a,b, except 2 for hSLAMF7N177A, hSLAMF7P178A, hSLAMF7V179A, hSLAMF7S180A) independent experiments.

Supplementary information

Source data

Source Data Fig. 4

Unprocessed immunoblots.

Source Data Extended Data Fig. 8

Unprocessed immunoblots.

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Tang, Z., Zhong, MC., Qian, J. et al. CD47 masks pro-phagocytic ligands in cis on tumor cells to suppress antitumor immunity. Nat Immunol 24, 2032–2041 (2023). https://doi.org/10.1038/s41590-023-01671-2

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