{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T00:46:15Z","timestamp":1774399575673,"version":"3.50.1"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["CA274234, CA275712, CA278758"],"award-info":[{"award-number":["CA274234, CA275712, CA278758"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>CD47 is a key innate immune checkpoint that enables tumor cells to evade macrophage-mediated clearance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods\/Results<\/jats:title>\n                    <jats:p>To systematically identify genetic regulators of CD47 surface expression,  we performed FACS-based genome-wide CRISPR screens in three murine cancer cell lines B16 (melanoma), MC38 (colon adenocarcinoma), and EMT6 (breast carcinoma).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Comparative analysis of cells with high or low CD47 surface expression using DrugZ revealed CD47 itself as the top hit, validating the screens. Notably, DNAJC13 emerged as a consistent and robust regulator of CD47 expression across all three cell lines. Functional validation using DNAJC13-knockout cells confirmed a significant reduction in CD47 surface levels. Furthermore, in co-culture assays with macrophages, DNAJC13-deficient tumor cells exhibited increased susceptibility to phagocytosis, supporting a functional role for DNAJC13 in innate immune evasion. Finally, we verify that DNAJC13-knockout decrease tumor burden when treated with CD47 blockade.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Overall, this study highlights a previously unrecognized regulator of CD47 and demonstrates the utility of high-throughput FACS-based CRISPR screening to uncover modulators of key immune checkpoint pathways.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2025.1684539","type":"journal-article","created":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T07:57:40Z","timestamp":1768204660000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["FACS-based genome-wide CRISPR screening platform identifies modulators of CD47"],"prefix":"10.3389","volume":"16","author":[{"given":"Ling","family":"Yin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yifan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huimin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuelong","family":"Yan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siting","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xu","family":"Feng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francisco","family":"Saenz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dandan","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chang","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiantian","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jialing","family":"Fu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junjie","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1246981","article-title":"Genetic screens in human cells using the CRISPR-Cas9 system","volume":"343","author":"Wang","year":"2014","journal-title":"Science"},{"key":"B2","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/nrg3899","article-title":"High-throughput functional genomics using CRISPR-Cas9","volume":"16","author":"Shalem","year":"2015","journal-title":"Nat Rev Genet"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1126\/science.1258096","article-title":"Genome editing. The new frontier of genome engineering with CRISPR-Cas9","volume":"346","author":"Doudna","year":"2014","journal-title":"Science"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.05.010","article-title":"Development and applications of CRISPR-Cas9 for genome engineering","volume":"157","author":"Hsu","year":"2014","journal-title":"Cell"},{"key":"B5","doi-asserted-by":"publisher","first-page":"2810","DOI":"10.1016\/j.molcel.2023.07.004","article-title":"FACS-based genome-wide CRISPR screens define key regulators of DNA damage signaling pathways","volume":"83","author":"Huang","year":"2023","journal-title":"Mol Cell"},{"key":"B6","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/s43586-022-00098-7","article-title":"High-content CRISPR screening","volume":"2","author":"Bock","year":"2022","journal-title":"Nat Rev Methods Primers"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1016\/j.iotech.2022.100070","article-title":"CD47-SIRPalpha-targeted therapeutics: status and prospects","volume":"13","author":"Maute","year":"2022","journal-title":"Immunooncol Technol"},{"key":"B8","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s40364-023-00456-x","article-title":"The landscape overview of CD47-based immunotherapy for hematological Malignancies","volume":"11","author":"Yang","year":"2023","journal-title":"biomark Res"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.22.01794","article-title":"Magrolimab in combination with azacitidine in patients with higher-risk myelodysplastic syndromes: final results of a phase ib study","volume":"41","author":"Sallman","year":"2023","journal-title":"J Clin Oncol"},{"key":"B10","doi-asserted-by":"publisher","first-page":"2249","DOI":"10.3390\/cells11142249","article-title":"Immune checkpoint inhibition in acute myeloid leukemia and myelodysplastic syndromes","volume":"11","author":"Abaza","year":"2022","journal-title":"Cells"},{"key":"B11","doi-asserted-by":"publisher","first-page":"49","DOI":"10.32604\/or.2023.042383","article-title":"Opportunities and challenges of CD47-targeted therapy in cancer immunotherapy","volume":"32","author":"Chen","year":"2023","journal-title":"Oncol Res"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1016\/j.coi.2012.01.010","article-title":"The CD47-SIRPalpha pathway in cancer immune evasion and potential therapeutic implications","volume":"24","author":"Chao","year":"2012","journal-title":"Curr Opin Immunol"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2746-2","article-title":"Functional genomic landscape of cancer-intrinsic evasion of killing by T cells","volume":"586","author":"Lawson","year":"2020","journal-title":"Nature"},{"key":"B14","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1186\/s13073-019-0665-3","article-title":"Identifying chemogenetic interactions from CRISPR screens with drugZ","volume":"11","author":"Colic","year":"2019","journal-title":"Genome Med"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1002\/1878-0261.13263","article-title":"Targeted inhibition of STAT3 induces immunogenic cell death of hepatocellular carcinoma cells via glycolysis","volume":"16","author":"Li","year":"2022","journal-title":"Mol Oncol"},{"key":"B16","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s13045-022-01292-6","article-title":"Hypoxia-inducible factors: master regulators of hypoxic tumor immune escape","volume":"15","author":"Wu","year":"2022","journal-title":"J Hematol Oncol"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.semcancer.2023.01.001","article-title":"The complex network of transcription factors, immune checkpoint inhibitors and stemness features in colorectal cancer: A recent update","volume":"89","author":"Merhi","year":"2023","journal-title":"Semin Cancer Biol"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac194","article-title":"DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)","volume":"50","author":"Sherman","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.622602","article-title":"Mitochondrial regulation of macrophage response against pathogens","volume":"11","author":"Choudhuri","year":"2020","journal-title":"Front Immunol"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.734229","article-title":"Reactive oxygen species in macrophages: sources and targets","volume":"12","author":"Canton","year":"2021","journal-title":"Front Immunol"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbadis.2020.165845","article-title":"Mitochondrial function in immune cells in health and disease","volume":"1866","author":"Faas","year":"2020","journal-title":"Biochim Biophys Acta Mol Basis Dis"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"B23","doi-asserted-by":"publisher","first-page":"W98","DOI":"10.1093\/nar\/gkx247","article-title":"GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses","volume":"45","author":"Tang","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-17-0307","article-title":"TIMER: A web server for comprehensive analysis of tumor-infiltrating immune cells","volume":"77","author":"Li","year":"2017","journal-title":"Cancer Res"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.5114\/wo.2014.47136","article-title":"The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge","volume":"19","author":"Tomczak","year":"2015","journal-title":"Contemp Oncol (Pozn)"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1038\/nm.3931","article-title":"CD47 blockade triggers T cell\u2013mediated destruction of immunogenic tumors","volume":"21","author":"Liu","year":"2015","journal-title":"Nat Med"},{"key":"B27","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1126\/science.1238856","article-title":"Engineered SIRP\u03b1 variants as immunotherapeutic adjuvants to anticancer antibodies","volume":"341","author":"Weiskopf","year":"2013","journal-title":"Science"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3001375","article-title":"Calreticulin is the dominant pro-phagocytic signal on multiple human cancers and is counterbalanced by CD47","volume":"2","author":"Chao","year":"2010","journal-title":"Sci Trans Med"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1534\/g3.117.041277","article-title":"Evaluation and design of genome-wide CRISPR\/SpCas9 knockout screens","volume":"7","author":"Hart","year":"2017","journal-title":"G3: Genes Genomes Genet"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab540","article-title":"Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2","volume":"49","author":"Tang","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"B31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0554-4","article-title":"MAGeCK enables robust identification of essential genes from genome-scale CRISPR\/Cas9 knockout screens","volume":"15","author":"Li","year":"2014","journal-title":"Genome Biol"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.11.015","article-title":"High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities","volume":"163","author":"Hart","year":"2015","journal-title":"Cell"},{"key":"B33","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1038\/s41419-019-1621-2","article-title":"Cyclin-dependent kinase 1-mediated phosphorylation of SET at serine 7 is essential for its oncogenic activity","volume":"10","author":"Yin","year":"2019","journal-title":"Cell Death Dis"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1684539\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T07:57:41Z","timestamp":1768204661000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1684539\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,12]]},"references-count":33,"alternative-id":["10.3389\/fimmu.2025.1684539"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2025.1684539","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,12]]},"article-number":"1684539"}}