Scott, A. M., Wolchok, J. D. & Old, L. J. Antibody therapy of cancer. Nat. Rev. Cancer 12, 278–287 (2012).
Sliwkowski, M. X. & Mellman, I. Antibody therapeutics in cancer. Science 341, 1192–1198 (2013).
Weiskopf, K. & Weissman, I. L. Macrophages are critical effectors of antibody therapies for cancer. mAbs 7, 303–310 (2015).
Tsao, L.-C. et al. CD47 blockade augmentation of trastuzumab antitumor efficacy dependent on antibody-dependent cellular phagocytosis. JCI Insight 4, e131882 (2019).
Brodsky, F. M. Monoclonal antibodies as magic bullets. Pharm. Res. 5, 1–9 (1988).
Maleki, L. A., Baradaran, B., Majidi, J., Mohammadian, M. & Shahneh, F. Z. Future prospects of monoclonal antibodies as magic bullets in immunotherapy. Hum. Antibodies 22, 9–13 (2013).
Glennie, M. J., French, R. R., Cragg, M. S. & Taylor, R. P. Mechanisms of killing by anti-CD20 monoclonal antibodies. Mol. Immunol. 44, 3823–3837 (2007).
Chao, M. P. et al. Anti-CD47 antibody synergizes with rituximab to promote phagocytosis and eradicate non-Hodgkin lymphoma. Cell 142, 699–713 (2010).
Logtenberg, M. E. W. et al. Glutaminyl cyclase is an enzymatic modifier of the CD47–SIRPα axis and a target for cancer immunotherapy. Nat. Med. 25, 612–619 (2019).
Macauley, M. S., Crocker, P. R. & Paulson, J. C. Siglec-mediated regulation of immune cell function in disease. Nat. Rev. Immunol. 14, 653–666 (2014).
Northcott, P. A. et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428–434 (2014).
Gao, S. et al. The oncogenic role of MUC12 in RCC progression depends on c‐Jun/TGF‐β signalling. J. Cell. Mol. Med. 24, 8789–8802 (2020).
Taylor-Papadimitriou, J. et al. MUC1 and the immunobiology of cancer. J. Mammary Gland Biol. Neoplasia 7, 209–221 (2002).
O’Prey, J., Wilkinson, S. & Ryan, K. M. Tumor antigen LRRC15 impedes adenoviral infection: implications for virus-based cancer therapy. J. Virol. 82, 5933–5939 (2008).
Purcell, J. W. et al. LRRC15 is a novel mesenchymal protein and stromal target for antibody–drug conjugates. Cancer Res. 78, 4059–4072 (2018).
Itoh, Y. et al. Identification and expression of human epiglycanin/MUC21: a novel transmembrane mucin. Glycobiology 18, 74–83 (2008).
Snyder, K. A. et al. Podocalyxin enhances breast tumor growth and metastasis and is a target for monoclonal antibody therapy. Breast Cancer Res. 17, 46 (2015).
Tarbé, N. G., Rio, M.-C., Hummel, S., Weidle, U. H. & Zöller, M. Overexpression of the small transmembrane and glycosylated protein SMAGP supports metastasis formation of a rat pancreatic adenocarcinoma line. Int. J. Cancer 117, 913–922 (2005).
Ajona, D. et al. Blockade of the complement C5a/C5aR1 axis impairs lung cancer bone metastasis by CXCL16-mediated effects. Am. J. Respir. Crit. Care Med. 197, 1164–1176 (2018).
Hollingsworth, M. A. & Swanson, B. J. Mucins in cancer: protection and control of the cell surface. Nat. Rev. Cancer 4, 45–60 (2004).
Jiang, S. et al. Cholesterol induces epithelial-to-mesenchymal transition of prostate cancer cells by suppressing degradation of EGFR through APMAP. Cancer Res. 79, 3063–3075 (2019).
Gerber, H. et al. The APMAP interactome reveals new modulators of APP processing and beta-amyloid production that are altered in Alzheimer’s disease. Acta Neuropathol. Commun. 7, 13 (2019).
Ilhan, A. et al. Localization and characterization of the novel protein encoded by C20orf3. Biochem. J. 414, 485–495 (2008).
Barkal, A. A. et al. Engagement of MHC class I by the inhibitory receptor LILRB1 suppresses macrophages and is a target of cancer immunotherapy. Nat. Immunol. 19, 76–84 (2018).
Clynes, R., Takechi, Y., Moroi, Y., Houghton, A. & Ravetch, J. V. Fc receptors are required in passive and active immunity to melanoma. Proc. Natl Acad. Sci. USA 95, 652–656 (1998).
Lattin, J. E. et al. Expression analysis of G protein-coupled receptors in mouse macrophages. Immunome Res. 4, 5 (2008).
Recio, C. et al. Activation of the immune-metabolic receptor GPR84 enhances inflammation and phagocytosis in macrophages. Front. Immunol. 9, 1419 (2018).
Wang, J., Wu, X., Simonavicius, N., Tian, H. & Ling, L. Medium-chain fatty acids as ligands for orphan G protein-coupled receptor GPR84. J. Biol. Chem. 281, 34457–34464 (2006).
Gont, A., Daneshmand, M., Woulfe, J. & Lorimer, I. PREX1 integrates G protein-coupled receptor and phosphoinositide 3-kinase signaling to promote glioblastoma invasion. Eur. J. Cancer 61, S171–S172 (2016).
Noy, R. & Pollard, J. W. Tumor-associated macrophages: from mechanisms to therapy. Immunity 41, 49–61 (2014).
Cunha, L. D. et al. LC3-associated phagocytosis in myeloid Cells Promotes Tumor Immune Tolerance. Cell 175, 429–441.e16 (2018).
Su, S. et al. Immune checkpoint inhibition overcomes ADCP-induced immunosuppression by macrophages. Cell 175, 442–457.e23 (2018).
Pathria, P., Louis, T. L. & Varner, J. A. Targeting tumor-associated macrophages in cancer. Trends Immunol. 40, 310–327 (2019).
Ruffell, B. & Coussens, L. M. Macrophages and therapeutic resistance in cancer. Cancer Cell 27, 462–472 (2015).
Hicks, M. A. et al. The evolution of function in strictosidine synthase-like proteins. Proteins Struct. Funct. Bioinf. 79, 3082–3098 (2011).
Khersonsky, O. & Tawfik, D. S. Structure-reactivity studies of serum paraoxonase PON1 suggest that its native activity is lactonase. Biochemistry 44, 6371–6382 (2005).
Flannagan, R. S., Jaumouillé, V. & Grinstein, S. The cell biology of phagocytosis. Annu. Rev. Pathol. 7, 61–98 (2012).
Manguso, R. T. et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 547, 413–418 (2017).
Lawson, K. A. et al. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature 586, 120–126 (2020).
Morgens, D. W. et al. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nat. Commun. 8, 15178 (2017).
Horlbeck, M. A. et al. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. eLife 5, e19760 (2016).
Morgens, D. W., Deans, R. M., Li, A. & Bassik, M. C. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat. Biotechnol. 34, 634–636 (2016).
Liu, N. et al. Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature 553, 228–232 (2018).
Jeng, E. E. et al. Systematic identification of host cell regulators of Legionella pneumophila pathogenesis using a genome-wide CRISPR screen. Cell Host Microbe 26, 551–563.e6 (2019).
Haney, M. S. et al. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nat. Genet. 50, 1716–1727 (2018).
Reimand, J. et al. g:Profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 44, W83–W89 (2016).
Schutze, M.-P., Peterson, P. A. & Jackson, M. R. An N-terminal double-arginine motif maintains type II membrane proteins in the endoplasmic reticulum. EMBO J. 13, 1696–1705 (1994).
Delaveris, C. S., Chiu, S. H., Riley, N. M. & Bertozzi, C. R. Modulation of immune cell reactivity with cis-binding Siglec agonists. Proc. Natl Acad. Sci. USA 118, e2012408118 (2021).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2014).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113–1120 (2013).
Jerby-Arnon, L. et al. Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma. Nat. Med. 27, 289–300 (2021).
Jerby-Arnon, L. et al. A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade. Cell 175, 984–997.e24 (2018).
Sade-Feldman, M. et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell 175, 998–1013.e20 (2018).
Neftel, C. et al. An integrative model of cellular states, plasticity, and genetics for glioblastoma. Cell 178, 835–849.e21 (2019).
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).
Shi, J., Blundell, T. L. & Mizuguchi, K. FUGUE: sequence–structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243–257 (2001).
Ben-David, M. et al. Catalytic versatility and backups in enzyme active sites: the case of serum paraoxonase 1. J. Mol. Biol. 418, 181–196 (2012).
Tanaka, Y. et al. Structural and mutational analyses of Drp35 from Staphylococcus aureus: a possible mechanism for its lactonase activity. J. Biol. Chem. 282, 5770–5780 (2007).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011).
Sockolosky, J. T. et al. Durable antitumor responses to CD47 blockade require adaptive immune stimulation. Proc. Natl Acad. Sci. USA 113, E2646–E2654 (2016).
More News
Could bird flu in cows lead to a human outbreak? Slow response worries scientists
US halts funding to controversial virus-hunting group: what researchers think
How high-fat diets feed breast cancer