{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T23:25:53Z","timestamp":1793489153358,"version":"4.5.0"},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"8029","license":[{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T00:00:00Z","timestamp":1722988800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2024,9,12]]},"DOI":"10.1038\/s41586-024-07787-1","type":"journal-article","created":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T16:14:48Z","timestamp":1723047288000},"page":"451-458","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":105,"title":["Glycosphingolipid synthesis mediates immune evasion in KRAS-driven cancer"],"prefix":"10.1038","volume":"633","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1637-0802","authenticated-orcid":false,"given":"Mariluz","family":"Soula","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2704-2724","authenticated-orcid":false,"given":"Gokhan","family":"Unlu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Welch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksey","family":"Chudnovskiy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0528-9099","authenticated-orcid":false,"given":"Beste","family":"Uygur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6874-5285","authenticated-orcid":false,"given":"Vyom","family":"Shah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4946-1436","authenticated-orcid":false,"given":"Hanan","family":"Alwaseem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Bunk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vishvak","family":"Subramanyam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsi-Wen","family":"Yeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1240-8674","authenticated-orcid":false,"given":"Artem","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2692-5602","authenticated-orcid":false,"given":"S\u00f8ren","family":"Heissel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9648-8949","authenticated-orcid":false,"given":"Hani","family":"Goodarzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8807-348X","authenticated-orcid":false,"given":"Gabriel D.","family":"Victora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4730-4012","authenticated-orcid":false,"given":"Semir","family":"Beyaz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7579-9895","authenticated-orcid":false,"given":"K\u0131van\u00e7","family":"Birsoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,8,7]]},"reference":[{"key":"7787_CR1","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/s41586-020-2623-z","volume":"585","author":"JM Ubellacker","year":"2020","unstructured":"Ubellacker, J. M. et al. Lymph protects metastasizing melanoma cells from ferroptosis. Nature 585, 113\u2013118 (2020).","journal-title":"Nature"},{"key":"7787_CR2","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1101\/gad.198630.112","volume":"27","author":"RM Young","year":"2013","unstructured":"Young, R. M. et al. Dysregulated mTORC1 renders cells critically dependent on desaturated lipids for survival under tumor-like stress. Genes Dev. 27, 1115\u20131131 (2013).","journal-title":"Genes Dev."},{"key":"7787_CR3","doi-asserted-by":"publisher","first-page":"2596","DOI":"10.1016\/j.celrep.2018.08.015","volume":"24","author":"D Ackerman","year":"2018","unstructured":"Ackerman, D. et al. Triglycerides promote lipid homeostasis during hypoxic stress by balancing fatty acid saturation. Cell Rep. 24, 2596\u20132605.e5 (2018).","journal-title":"Cell Rep."},{"key":"7787_CR4","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/nrm.2017.138","volume":"19","author":"T Harayama","year":"2018","unstructured":"Harayama, T. & Riezman, H. Understanding the diversity of membrane lipid composition. Nat. Rev. Mol. Cell Biol. 19, 281\u2013296 (2018).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"7787_CR5","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1038\/nrm2335","volume":"9","author":"MP Wymann","year":"2008","unstructured":"Wymann, M. P. & Schneiter, R. Lipid signalling in disease. Nat. Rev. Mol. Cell Biol. 9, 162\u2013176 (2008).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"7787_CR6","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.cmet.2019.11.010","volume":"31","author":"MT Snaebjornsson","year":"2020","unstructured":"Snaebjornsson, M. T., Janaki-Raman, S. & Schulze, A. Greasing the wheels of the cancer machine: the role of lipid metabolism in cancer. Cell Metab. 31, 62\u201376 (2020).","journal-title":"Cell Metab."},{"key":"7787_CR7","doi-asserted-by":"publisher","first-page":"8882","DOI":"10.1073\/pnas.1307237110","volume":"110","author":"JJ Kamphorst","year":"2013","unstructured":"Kamphorst, J. J. et al. Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids. Proc. Natl Acad. Sci. USA 110, 8882\u20138887 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7787_CR8","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1038\/nature17173","volume":"531","author":"S Beyaz","year":"2016","unstructured":"Beyaz, S. et al. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature 531, 53\u201358 (2016).","journal-title":"Nature"},{"key":"7787_CR9","doi-asserted-by":"publisher","first-page":"1988","DOI":"10.1158\/0008-5472.CAN-20-1954","volume":"81","author":"LA Broadfield","year":"2021","unstructured":"Broadfield, L. A. et al. Fat induces glucose metabolism in nontransformed liver cells and promotes liver tumorigenesis. Cancer Res. 81, 1988\u20132001 (2021).","journal-title":"Cancer Res."},{"key":"7787_CR10","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1038\/s41586-021-04075-0","volume":"599","author":"G Pascual","year":"2021","unstructured":"Pascual, G. et al. Dietary palmitic acid promotes a prometastatic memory via Schwann cells. Nature 599, 485\u2013490 (2021).","journal-title":"Nature"},{"key":"7787_CR11","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1038\/s43018-023-00513-2","volume":"4","author":"P Altea-Marzano","year":"2023","unstructured":"Altea-Marzano, P. et al. A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in pro-metastatic NF-\u03baB signaling. Nat. Cancer 4, 344\u2013364 (2023).","journal-title":"Nat. Cancer"},{"key":"7787_CR12","doi-asserted-by":"publisher","first-page":"1848","DOI":"10.1016\/j.cell.2020.11.009","volume":"183","author":"AE Ringel","year":"2020","unstructured":"Ringel, A. E. et al. Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity. Cell 183, 1848\u20131866.e26 (2020).","journal-title":"Cell"},{"key":"7787_CR13","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1016\/j.cmet.2022.09.023","volume":"34","author":"M Martin-Perez","year":"2022","unstructured":"Martin-Perez, M., Urdiroz-Urricelqui, U., Bigas, C. & Benitah, S. A. The role of lipids in cancer progression and metastasis. Cell Metab. 34, 1675\u20131699 (2022).","journal-title":"Cell Metab."},{"key":"7787_CR14","doi-asserted-by":"publisher","first-page":"1922","DOI":"10.1016\/j.stem.2021.08.007","volume":"28","author":"S Beyaz","year":"2021","unstructured":"Beyaz, S. et al. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell 28, 1922\u20131935.e5 (2021).","journal-title":"Cell Stem Cell"},{"key":"7787_CR15","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1016\/j.immuni.2021.05.003","volume":"54","author":"S Xu","year":"2021","unstructured":"Xu, S. et al. Uptake of oxidized lipids by the scavenger receptor CD36 promotes lipid peroxidation and dysfunction in CD8+ T cells in tumors. Immunity 54, 1561\u20131577.e7 (2021).","journal-title":"Immunity"},{"key":"7787_CR16","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1038\/nrc.2017.96","volume":"18","author":"B Ogretmen","year":"2018","unstructured":"Ogretmen, B. Sphingolipid metabolism in cancer signalling and therapy. Nat. Rev. Cancer 18, 33\u201350 (2018).","journal-title":"Nat. Rev. Cancer"},{"key":"7787_CR17","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1038\/nrm.2017.107","volume":"19","author":"YA Hannun","year":"2018","unstructured":"Hannun, Y. A. & Obeid, L. M. Sphingolipids and their metabolism in physiology and disease. Nat. Rev. Mol. Cell Biol. 19, 175\u2013191 (2018).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"7787_CR18","doi-asserted-by":"crossref","unstructured":"Gault, C., Obeid, L. & Hannun, Y. in Sphingolipids as Signaling and Regulatory Molecules (eds Chalfant, C. & Del Poeta, M.) 1\u201323 (Springer, 2010).","DOI":"10.1007\/978-1-4419-6741-1_1"},{"key":"7787_CR19","doi-asserted-by":"publisher","first-page":"726","DOI":"10.3390\/ijms22020726","volume":"22","author":"M Codini","year":"2021","unstructured":"Codini, M., Garcia-Gil, M. & Albi, E. Cholesterol and sphingolipid enriched lipid rafts as therapeutic targets in cancer. Int. J. Mol. Sci. 22, 726 (2021).","journal-title":"Int. J. Mol. Sci."},{"key":"7787_CR20","doi-asserted-by":"publisher","first-page":"2832","DOI":"10.1016\/j.molcel.2022.05.024","volume":"82","author":"G Unlu","year":"2022","unstructured":"Unlu, G. et al. Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability. Mol. Cell 82, 2832\u20132843.e7 (2022).","journal-title":"Mol. Cell"},{"key":"7787_CR21","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nature13475","volume":"510","author":"M Maceyka","year":"2014","unstructured":"Maceyka, M. & Spiegel, S. Sphingolipid metabolites in inflammatory disease. Nature 510, 58\u201367 (2014).","journal-title":"Nature"},{"key":"7787_CR22","doi-asserted-by":"publisher","first-page":"5775","DOI":"10.1021\/acs.chemrev.8b00451","volume":"119","author":"V Corradi","year":"2019","unstructured":"Corradi, V. et al. Emerging diversity in lipid\u2013protein interactions. Chem. Rev. 119, 5775\u20135848 (2019).","journal-title":"Chem. Rev."},{"key":"7787_CR23","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1091\/mbc.e06-01-0076","volume":"17","author":"M Marchetti","year":"2006","unstructured":"Marchetti, M. et al. Stat-mediated signaling induced by type I and type II interferons (IFNs) is differentially controlled through lipid microdomain association and clathrin-dependent endocytosis of IFN receptors. Mol. Biol. Cell 17, 2896\u20132909 (2006).","journal-title":"Mol. Biol. Cell"},{"key":"7787_CR24","doi-asserted-by":"publisher","first-page":"267","DOI":"10.3389\/fimmu.2013.00267","volume":"4","author":"CM Blouin","year":"2013","unstructured":"Blouin, C. M. & Lamaze, C. Interferon gamma receptor: the beginning of the journey. Front. Immunol. 4, 267 (2013).","journal-title":"Front. Immunol."},{"key":"7787_CR25","doi-asserted-by":"publisher","first-page":"e78861","DOI":"10.7554\/eLife.78861","volume":"11","author":"A Kuo","year":"2022","unstructured":"Kuo, A. et al. Murine endothelial serine palmitoyltransferase 1 (SPTLC1) is required for vascular development and systemic sphingolipid homeostasis. eLife 11, e78861 (2022).","journal-title":"eLife"},{"key":"7787_CR26","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1002\/ajh.25300","volume":"94","author":"E Lukina","year":"2019","unstructured":"Lukina, E. et al. Outcomes after 8 years of eliglustat therapy for Gaucher disease type 1: final results from the phase 2 trial. Am. J. Hematol. 94, 29\u201338 (2019).","journal-title":"Am. J. Hematol."},{"key":"7787_CR27","doi-asserted-by":"publisher","first-page":"3329","DOI":"10.1073\/pnas.70.12.3329","volume":"70","author":"CG Gahmberg","year":"1973","unstructured":"Gahmberg, C. G. & Hakomori, S. I. Altered growth behavior of malignant cells associated with changes in externally labeled glycoprotein and glycolipid. Proc. Natl Acad. Sci. USA 70, 3329\u20133333 (1973).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7787_CR28","doi-asserted-by":"publisher","first-page":"138","DOI":"10.4161\/cbt.11.2.14624","volume":"11","author":"LK Ryland","year":"2011","unstructured":"Ryland, L. K., Fox, T. E., Liu, X., Loughran, T. P. & Kester, M. Dysregulation of sphingolipid metabolism in cancer. Cancer Biol. Ther. 11, 138\u2013149 (2011).","journal-title":"Cancer Biol. Ther."},{"key":"7787_CR29","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36128-5","volume":"14","author":"J Liu","year":"2023","unstructured":"Liu, J. et al. Glycolysis regulates KRAS plasma membrane localization and function through defined glycosphingolipids. Nat. Commun. 14, 465 (2023).","journal-title":"Nat. Commun."},{"key":"7787_CR30","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1158\/2159-8290.CD-22-0535","volume":"13","author":"V Jain","year":"2023","unstructured":"Jain, V. et al. Targeting UGCG overcomes resistance to lysosomal autophagy inhibition. Cancer Discov. 13, 454\u2013473 (2023).","journal-title":"Cancer Discov."},{"key":"7787_CR31","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1038\/nature12138","volume":"497","author":"C Commisso","year":"2013","unstructured":"Commisso, C. et al. Macropinocytosis of protein is an amino acid supply route in Ras-transformed cells. Nature 497, 633\u2013637 (2013).","journal-title":"Nature"},{"key":"7787_CR32","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/nature14587","volume":"524","author":"RM Perera","year":"2015","unstructured":"Perera, R. M. et al. Transcriptional control of the autophagy-lysosome system in pancreatic cancer. Nature 524, 361\u2013365 (2015).","journal-title":"Nature"},{"key":"7787_CR33","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1016\/j.cmet.2020.10.017","volume":"33","author":"XG Zhu","year":"2021","unstructured":"Zhu, X. G. et al. Functional genomics in vivo reveal metabolic dependencies of pancreatic cancer cells. Cell Metab. 33, 211\u2013221.e6 (2021).","journal-title":"Cell Metab."},{"key":"7787_CR34","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41586-020-2229-5","volume":"581","author":"K Yamamoto","year":"2020","unstructured":"Yamamoto, K. et al. Autophagy promotes immune evasion of pancreatic cancer by degrading MHC-I. Nature 581, 100\u2013105 (2020).","journal-title":"Nature"},{"key":"7787_CR35","doi-asserted-by":"publisher","first-page":"1495","DOI":"10.1038\/s41590-022-01315-x","volume":"23","author":"J Dubrot","year":"2022","unstructured":"Dubrot, J. et al. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Nat. Immunol. 23, 1495\u20131506 (2022).","journal-title":"Nat. Immunol."},{"key":"7787_CR36","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41586-020-2746-2","volume":"586","author":"KA Lawson","year":"2020","unstructured":"Lawson, K. A. et al. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature 586, 120\u2013126 (2020).","journal-title":"Nature"},{"key":"7787_CR37","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/s41586-022-04585-5","volume":"604","author":"RC Larson","year":"2022","unstructured":"Larson, R. C. et al. CAR T cell killing requires the IFN\u03b3R pathway in solid but not liquid tumours. Nature 604, 563\u2013570 (2022).","journal-title":"Nature"},{"key":"7787_CR38","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nature10742","volume":"481","author":"F-X Contreras","year":"2012","unstructured":"Contreras, F.-X. et al. Molecular recognition of a single sphingolipid species by a protein\u2019s transmembrane domain. Nature 481, 525\u2013529 (2012).","journal-title":"Nature"},{"key":"7787_CR39","doi-asserted-by":"publisher","first-page":"475","DOI":"10.3390\/cancers12020475","volume":"12","author":"P Dubot","year":"2020","unstructured":"Dubot, P. et al. Are glucosylceramide-related sphingolipids involved in the increased risk for cancer in Gaucher disease patients? Review and hypotheses. Cancers 12, 475 (2020).","journal-title":"Cancers"},{"key":"7787_CR40","doi-asserted-by":"publisher","first-page":"5947","DOI":"10.1073\/pnas.0601273103","volume":"103","author":"N Bardeesy","year":"2006","unstructured":"Bardeesy, N. et al. Both p16Ink4a and the p19Arf-p53 pathway constrain progression of pancreatic adenocarcinoma in the mouse. Proc. Natl Acad. Sci. USA 103, 5947\u20135952 (2006).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7787_CR41","doi-asserted-by":"publisher","first-page":"2628","DOI":"10.1093\/bioinformatics\/btz931","volume":"36","author":"SX Ge","year":"2020","unstructured":"Ge, S. X., Jung, D. & Yao, R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36, 2628\u20132629 (2020).","journal-title":"Bioinformatics"},{"key":"7787_CR42","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1038\/s41589-020-0613-y","volume":"16","author":"M Soula","year":"2020","unstructured":"Soula, M. et al. Metabolic determinants of cancer cell sensitivity to canonical ferroptosis inducers. Nat. Chem. Biol. 16, 1351\u20131360 (2020).","journal-title":"Nat. Chem. Biol."},{"key":"7787_CR43","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1038\/nature13589","volume":"514","author":"W Xue","year":"2014","unstructured":"Xue, W. et al. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature 514, 380\u2013384 (2014).","journal-title":"Nature"},{"key":"7787_CR44","doi-asserted-by":"publisher","first-page":"1800","DOI":"10.1101\/gad.244368.114","volume":"28","author":"C-H Huang","year":"2014","unstructured":"Huang, C.-H. et al. CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma. Genes Dev. 28, 1800\u20131814 (2014).","journal-title":"Genes Dev."},{"key":"7787_CR45","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417\u2013419 (2017).","journal-title":"Nat. Methods"},{"key":"7787_CR46","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"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).","journal-title":"Genome Biol."},{"key":"7787_CR47","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1093\/bioinformatics\/btn615","volume":"25","author":"S Carbon","year":"2009","unstructured":"Carbon, S. et al. AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288\u2013289 (2009).","journal-title":"Bioinformatics"},{"key":"7787_CR48","doi-asserted-by":"publisher","first-page":"e8746","DOI":"10.15252\/msb.20188746","volume":"15","author":"MD Luecken","year":"2019","unstructured":"Luecken, M. D. & Theis, F. J. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol. Syst. Biol. 15, e8746 (2019).","journal-title":"Mol. Syst. Biol."},{"key":"7787_CR49","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","volume":"17","author":"RA Amezquita","year":"2020","unstructured":"Amezquita, R. A. et al. Orchestrating single-cell analysis with Bioconductor. Nat. Methods 17, 137\u2013145 (2020).","journal-title":"Nat. Methods"},{"key":"7787_CR50","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","volume":"36","author":"A Butler","year":"2018","unstructured":"Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411\u2013420 (2018).","journal-title":"Nat. Biotechnol."},{"key":"7787_CR51","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888\u20131902.e21 (2019).","journal-title":"Cell"},{"key":"7787_CR52","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1016\/j.cell.2018.05.061","volume":"174","author":"D van Dijk","year":"2018","unstructured":"van Dijk, D. et al. Recovering gene interactions from single-cell data using data diffusion. Cell 174, 716\u2013729.e27 (2018).","journal-title":"Cell"},{"key":"7787_CR53","doi-asserted-by":"publisher","first-page":"eabe6474","DOI":"10.1126\/science.abe6474","volume":"374","author":"L Zheng","year":"2021","unstructured":"Zheng, L. et al. Pan-cancer single-cell landscape of tumor-infiltrating T cells. Science 374, eabe6474 (2021).","journal-title":"Science"},{"key":"7787_CR54","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0844-5","volume":"16","author":"G Finak","year":"2015","unstructured":"Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015).","journal-title":"Genome Biol."},{"key":"7787_CR55","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-17204-5","volume":"7","author":"P Bankhead","year":"2017","unstructured":"Bankhead, P. et al. QuPath: open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).","journal-title":"Sci. Rep."},{"key":"7787_CR56","unstructured":"The Cancer Genome Atlas Consortium. The Pan-Cancer Atlas http:\/\/www.cell.com\/pb-assets\/consortium\/pancanceratlas\/pancani3\/index.html (Cell Press, 2018)."},{"key":"7787_CR57","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","volume":"2","author":"E Cerami","year":"2012","unstructured":"Cerami, E. et al. The cBio Cancer Genomics Portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401\u2013404 (2012).","journal-title":"Cancer Discov."},{"key":"7787_CR58","unstructured":"Kassambara, A., Kosinski, M., Biecek, P. & Fabian, S. survminer: Drawing survival curves using \u2018ggplot2\u2019. https:\/\/CRAN.R-project.org\/package=survminer (2021)."},{"key":"7787_CR59","unstructured":"Hothorn, T. maxstat: Maximally selected rank statistics. https:\/\/CRAN.R-project.org\/package=maxstat (2017)."},{"key":"7787_CR60","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nmeth.3337","volume":"12","author":"AM Newman","year":"2015","unstructured":"Newman, A. M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12, 453\u2013457 (2015).","journal-title":"Nat. Methods"},{"key":"7787_CR61","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1016\/j.immuni.2018.03.023","volume":"48","author":"V Thorsson","year":"2018","unstructured":"Thorsson, V. et al. The immune landscape of cancer. Immunity 48, 812\u2013830.e14 (2018).","journal-title":"Immunity"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07787-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07787-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07787-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T16:06:12Z","timestamp":1726070772000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07787-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,7]]},"references-count":61,"journal-issue":{"issue":"8029","published-print":{"date-parts":[[2024,9,12]]}},"alternative-id":["7787"],"URL":"https:\/\/doi.org\/10.1038\/s41586-024-07787-1","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,7]]},"assertion":[{"value":"29 January 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 August 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"K.B. is a scientific advisor to Nanocare Pharmaceuticals and Atavistik Bio. M.S. is an employee of Lime Therapeutics. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}