{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T00:48:49Z","timestamp":1793148529121,"version":"4.5.0"},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T00:00:00Z","timestamp":1725321600000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100009812","name":"Princess Margaret Cancer Foundation","doi-asserted-by":"publisher","award":["886012001223"],"award-info":[{"award-number":["886012001223"]}],"id":[{"id":"10.13039\/100009812","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Gouvernement du Canada | Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["142246, 152863,152864,159567,438793"],"award-info":[{"award-number":["142246, 152863,152864,159567,438793"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Gouvernement du Canada | Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["FDN-148395"],"award-info":[{"award-number":["FDN-148395"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004376","name":"Terry Fox Research Institute","doi-asserted-by":"publisher","award":["1090, 1124"],"award-info":[{"award-number":["1090, 1124"]}],"id":[{"id":"10.13039\/501100004376","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31801111"],"award-info":[{"award-number":["31801111"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Genet"],"published-print":{"date-parts":[[2024,9]]},"DOI":"10.1038\/s41588-024-01874-9","type":"journal-article","created":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T10:02:01Z","timestamp":1725357721000},"page":"1890-1902","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["In vivo CRISPR screens identify a dual function of MEN1 in regulating tumor\u2013microenvironment interactions"],"prefix":"10.1038","volume":"56","author":[{"given":"Peiran","family":"Su","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yibo","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5719-1272","authenticated-orcid":false,"given":"Yong","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1495-4238","authenticated-orcid":false,"given":"Guanghui","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1941-3951","authenticated-orcid":false,"given":"Sujun","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona","family":"Teng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinpei","family":"Ci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengdi","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2235-2758","authenticated-orcid":false,"given":"Michael Y.","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8989-8771","authenticated-orcid":false,"given":"Jun","family":"Hao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vivian","family":"Chu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenxi","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiyan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4476-9925","authenticated-orcid":false,"given":"Parinaz","family":"Mehdipour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4670-1243","authenticated-orcid":false,"given":"Xin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1046-9852","authenticated-orcid":false,"given":"Sajid A.","family":"Marhon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3977-7939","authenticated-orcid":false,"given":"Fraser","family":"Soares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3063-0292","authenticated-orcid":false,"given":"Nhu-An","family":"Pham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bell Xi","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter Hyunwuk","family":"Her","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengrui","family":"Feng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Najd","family":"Alshamlan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryam","family":"Khalil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rehna","family":"Krishnan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangyou","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2841-1250","authenticated-orcid":false,"given":"Chang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francis","family":"Burrows","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Razqallah","family":"Hakem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathieu","family":"Lupien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shane","family":"Harding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin H.","family":"Lok","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"O\u2019Brien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1880-6905","authenticated-orcid":false,"given":"Alejandro","family":"Berlin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel D.","family":"De Carvalho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David G.","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9977-2104","authenticated-orcid":false,"given":"Daniel","family":"Schramek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9160-5405","authenticated-orcid":false,"given":"Ming-Sound","family":"Tsao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2898-3363","authenticated-orcid":false,"given":"Housheng Hansen","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,9,3]]},"reference":[{"key":"1874_CR1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/s41392-020-00280-x","volume":"5","author":"M-Z Jin","year":"2020","unstructured":"Jin, M.-Z. & Jin, W.-L. The updated landscape of tumor microenvironment and drug repurposing. Signal Transduct. Target Ther. 5, 166 (2020).","journal-title":"Signal Transduct. Target Ther."},{"key":"1874_CR2","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nature07205","volume":"454","author":"A Mantovani","year":"2008","unstructured":"Mantovani, A., Allavena, P., Sica, A. & Balkwill, F. Cancer-related inflammation. Nature 454, 436\u2013444 (2008).","journal-title":"Nature"},{"key":"1874_CR3","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","volume":"144","author":"D Hanahan","year":"2011","unstructured":"Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646\u2013674 (2011).","journal-title":"Cell"},{"key":"1874_CR4","doi-asserted-by":"crossref","first-page":"5591","DOI":"10.1242\/jcs.116392","volume":"125","author":"FR Balkwill","year":"2012","unstructured":"Balkwill, F. R., Capasso, M. & Hagemann, T. The tumor microenvironment at a glance. J. Cell Sci. 125, 5591\u20135596 (2012).","journal-title":"J. Cell Sci."},{"key":"1874_CR5","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/s41422-020-0355-0","volume":"30","author":"J Qian","year":"2020","unstructured":"Qian, J. et al. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res. 30, 745\u2013762 (2020).","journal-title":"Cell Res."},{"key":"1874_CR6","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1038\/s41588-021-00911-1","volume":"53","author":"SZ Wu","year":"2021","unstructured":"Wu, S. Z. et al. A single-cell and spatially resolved atlas of human breast cancers. Nat. Genet. 53, 1334\u20131347 (2021).","journal-title":"Nat. Genet."},{"key":"1874_CR7","doi-asserted-by":"crossref","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"},{"key":"1874_CR8","doi-asserted-by":"crossref","first-page":"5811","DOI":"10.2147\/IJN.S321416","volume":"16","author":"L Tang","year":"2021","unstructured":"Tang, L. et al. Nanoparticle-mediated targeted drug delivery to remodel tumor microenvironment for cancer therapy. Int. J. Nanomed. 16, 5811\u20135829 (2021).","journal-title":"Int. J. Nanomed."},{"key":"1874_CR9","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1126\/science.1247005","volume":"343","author":"O Shalem","year":"2014","unstructured":"Shalem, O. et al. Genome-scale CRISPR\u2013Cas9 knockout screening in human cells. Science 343, 84\u201387 (2014).","journal-title":"Science"},{"key":"1874_CR10","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1126\/science.1246981","volume":"343","author":"T Wang","year":"2014","unstructured":"Wang, T., Wei, J. J., Sabatini, D. M. & Lander, E. S. Genetic screens in human cells using the CRISPR\u2013Cas9 system. Science 343, 80\u201384 (2014).","journal-title":"Science"},{"key":"1874_CR11","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1016\/j.cell.2018.11.044","volume":"176","author":"J Henriksson","year":"2019","unstructured":"Henriksson, J. et al. Genome-wide CRISPR screens in T helper cells reveal pervasive crosstalk between activation and differentiation. Cell 176, 882\u2013896.e18 (2019).","journal-title":"Cell"},{"key":"1874_CR12","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nature23270","volume":"547","author":"RT Manguso","year":"2017","unstructured":"Manguso, R. T. et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature 547, 413\u2013418 (2017).","journal-title":"Nature"},{"key":"1874_CR13","doi-asserted-by":"crossref","first-page":"1958","DOI":"10.1016\/j.cell.2018.10.024","volume":"175","author":"E Shifrut","year":"2018","unstructured":"Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators of immune function. Cell 175, 1958\u20131971 (2018).","journal-title":"Cell"},{"key":"1874_CR14","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1016\/j.cell.2017.06.010","volume":"170","author":"A Tsherniak","year":"2017","unstructured":"Tsherniak, A. et al. Defining a cancer dependency map. Cell 170, 564\u2013576.e16 (2017).","journal-title":"Cell"},{"key":"1874_CR15","doi-asserted-by":"crossref","unstructured":"Jin, V., Wang, J. & Tang, B. Integration of Multisource Heterogenous Omics Information in Cancer (Frontiers Media SA, 2020).","DOI":"10.3389\/978-2-88963-448-4"},{"key":"1874_CR16","volume":"12","author":"C Pacini","year":"2021","unstructured":"Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021).","journal-title":"Nat. Commun."},{"key":"1874_CR17","doi-asserted-by":"crossref","first-page":"5357","DOI":"10.1016\/j.cell.2021.09.006","volume":"184","author":"X Wang","year":"2021","unstructured":"Wang, X. et al. In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. Cell 184, 5357\u20135374.e22 (2021).","journal-title":"Cell"},{"key":"1874_CR18","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1158\/2159-8290.CD-19-0780","volume":"10","author":"F Li","year":"2020","unstructured":"Li, F. et al. In vivo epigenetic CRISPR screen identifies Asf1a as an immunotherapeutic target in Kras-mutant lung adenocarcinoma. Cancer Discov. 10, 270\u2013287 (2020).","journal-title":"Cancer Discov."},{"key":"1874_CR19","doi-asserted-by":"crossref","first-page":"6601","DOI":"10.1038\/s41388-021-01882-7","volume":"40","author":"S Gao","year":"2021","unstructured":"Gao, S. et al. CRISPR screens identify cholesterol biosynthesis as a therapeutic target on stemness and drug resistance of colon cancer. Oncogene 40, 6601\u20136613 (2021).","journal-title":"Oncogene"},{"key":"1874_CR20","doi-asserted-by":"crossref","first-page":"2171","DOI":"10.1182\/blood.2019004108","volume":"137","author":"F Soares","year":"2021","unstructured":"Soares, F. et al. CRISPR screen identifies genes that sensitize AML cells to double-negative T-cell therapy. Blood 137, 2171\u20132181 (2021).","journal-title":"Blood"},{"key":"1874_CR21","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1016\/j.cell.2015.02.038","volume":"160","author":"S Chen","year":"2015","unstructured":"Chen, S. et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 160, 1246\u20131260 (2015).","journal-title":"Cell"},{"key":"1874_CR22","volume":"15","author":"W Li","year":"2014","unstructured":"Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR\/Cas9 knockout screens. Genome Biol. 15, 554 (2014).","journal-title":"Genome Biol."},{"key":"1874_CR23","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1038\/ng.3984","volume":"49","author":"RM Meyers","year":"2017","unstructured":"Meyers, R. M. et al. Computational correction of copy number effect improves specificity of CRISPR\u2013Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779\u20131784 (2017).","journal-title":"Nat. Genet."},{"key":"1874_CR24","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":"1874_CR25","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1038\/s41586-023-05755-9","volume":"615","author":"F Perner","year":"2023","unstructured":"Perner, F. et al. MEN1 mutations mediate clinical resistance to menin inhibition. Nature 615, 913\u2013919 (2023).","journal-title":"Nature"},{"key":"1874_CR26","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1038\/s41586-023-05812-3","volume":"615","author":"GC Issa","year":"2023","unstructured":"Issa, G. C. et al. The menin inhibitor revumenib in KMT2A-rearranged or NPM1-mutant leukaemia. Nature 615, 920\u2013924 (2023).","journal-title":"Nature"},{"key":"1874_CR27","first-page":"258","volume":"25","author":"CE Sparbier","year":"2023","unstructured":"Sparbier, C. E. et al. Targeting Menin disrupts the KMT2A\/B and polycomb balance to paradoxically activate bivalent genes. Nat. Cell Biol. 25, 258\u2013272 (2023).","journal-title":"Nat. Cell Biol."},{"key":"1874_CR28","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1158\/2159-8290.CD-22-0416","volume":"13","author":"YM Soto-Feliciano","year":"2023","unstructured":"Soto-Feliciano, Y. M. et al. A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition. Cancer Discov. 13, 146\u2013169 (2023).","journal-title":"Cancer Discov."},{"key":"1874_CR29","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1126\/science.adc9318","volume":"379","author":"J Lin","year":"2023","unstructured":"Lin, J. et al. Menin \u2018reads\u2019 H3K79me2 mark in a nucleosomal context. Science 379, 717\u2013723 (2023).","journal-title":"Science"},{"key":"1874_CR30","doi-asserted-by":"crossref","first-page":"3537","DOI":"10.1038\/sj.onc.1209400","volume":"25","author":"P La","year":"2006","unstructured":"La, P. et al. Tumor suppressor menin: the essential role of nuclear localization signal domains in coordinating gene expression. Oncogene 25, 3537\u20133546 (2006).","journal-title":"Oncogene"},{"key":"1874_CR31","doi-asserted-by":"crossref","first-page":"e21856","DOI":"10.7554\/eLife.21856","volume":"6","author":"PJ Skene","year":"2017","unstructured":"Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017).","journal-title":"eLife"},{"key":"1874_CR32","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"1874_CR33","doi-asserted-by":"crossref","first-page":"2502","DOI":"10.1038\/nprot.2013.150","volume":"8","author":"S Wang","year":"2013","unstructured":"Wang, S. et al. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat. Protoc. 8, 2502\u20132515 (2013).","journal-title":"Nat. Protoc."},{"key":"1874_CR34","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1158\/2159-8290.CD-22-0416","volume":"13","author":"YM Soto-Feliciano","year":"2023","unstructured":"Soto-Feliciano, Y. M. et al. Molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition. Cancer Discov. 13, 146\u2013169 (2023).","journal-title":"Cancer Discov."},{"key":"1874_CR35","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-20830-9","volume":"12","author":"SA Madani Tonekaboni","year":"2021","unstructured":"Madani Tonekaboni, S. A., Haibe-Kains, B. & Lupien, M. Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations. Nat. Commun. 12, 499 (2021).","journal-title":"Nat. Commun."},{"key":"1874_CR36","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1158\/2159-8290.CD-21-0506","volume":"11","author":"R Chen","year":"2021","unstructured":"Chen, R., Ishak, C. A. & De Carvalho, D. D. Endogenous retroelements and the viral mimicry response in cancer therapy and cellular homeostasis. Cancer Discov. 11, 2707\u20132725 (2021).","journal-title":"Cancer Discov."},{"key":"1874_CR37","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1126\/science.1240933","volume":"341","author":"D Gao","year":"2013","unstructured":"Gao, D. et al. Cyclic GMP\u2013AMP synthase is an innate immune sensor of HIV and other retroviruses. Science 341, 903\u2013906 (2013).","journal-title":"Science"},{"key":"1874_CR38","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/j.cell.2015.07.056","volume":"162","author":"D Roulois","year":"2015","unstructured":"Roulois, D. et al. DNA-demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts. Cell 162, 961\u2013973 (2015).","journal-title":"Cell"},{"key":"1874_CR39","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/s43018-021-00185-w","volume":"2","author":"KL Morel","year":"2021","unstructured":"Morel, K. L. et al. EZH2 inhibition activates a dsRNA\u2013STING\u2013interferon stress axis that potentiates response to PD-1 checkpoint blockade in prostate cancer. Nat. Cancer 2, 444\u2013456 (2021).","journal-title":"Nat. Cancer"},{"key":"1874_CR40","volume":"347","author":"S Liu","year":"2015","unstructured":"Liu, S. et al. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science 347, aaa2630 (2015).","journal-title":"Science"},{"key":"1874_CR41","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.ccell.2015.02.016","volume":"27","author":"D Borkin","year":"2015","unstructured":"Borkin, D. et al. Pharmacologic inhibition of the Menin-MLL interaction blocks progression of MLL leukemia in vivo. Cancer Cell 27, 589\u2013602 (2015).","journal-title":"Cancer Cell"},{"key":"1874_CR42","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/s41556-020-00613-6","volume":"23","author":"S Chen","year":"2021","unstructured":"Chen, S. et al. Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression. Nat. Cell Biol. 23, 87\u201398 (2021).","journal-title":"Nat. Cell Biol."},{"key":"1874_CR43","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.immuni.2021.01.003","volume":"54","author":"W Xu","year":"2021","unstructured":"Xu, W. et al. Early innate and adaptive immune perturbations determine long-term severity of chronic virus and Mycobacterium tuberculosis coinfection. Immunity 54, 526\u2013541.e7 (2021).","journal-title":"Immunity"},{"key":"1874_CR44","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1016\/j.ccell.2019.11.001","volume":"36","author":"AV Krivtsov","year":"2019","unstructured":"Krivtsov, A. V. et al. A Menin-MLL inhibitor induces specific chromatin changes and eradicates disease in models of MLL-rearranged leukemia. Cancer Cell 36, 660\u2013673.e11 (2019).","journal-title":"Cancer Cell"},{"key":"1874_CR45","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1038\/nchembio.773","volume":"8","author":"J Grembecka","year":"2012","unstructured":"Grembecka, J. et al. Menin-MLL inhibitors reverse oncogenic activity of MLL fusion proteins in leukemia. Nat. Chem. Biol. 8, 277\u2013284 (2012).","journal-title":"Nat. Chem. Biol."},{"key":"1874_CR46","doi-asserted-by":"crossref","first-page":"3357","DOI":"10.1182\/blood-2021-149831","volume":"138","author":"JA Davis","year":"2021","unstructured":"Davis, J. A. et al. Clinical-stage menin inhibitor KO-539 is synergistically active with multiple classes of targeted agents in KMT2A-r and NPM1-mutant AML models. Blood 138, 3357 (2021).","journal-title":"Blood"},{"key":"1874_CR47","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/s41574-021-00468-3","volume":"17","author":"A Al-Salameh","year":"2021","unstructured":"Al-Salameh, A., Cadiot, G., Calender, A., Goudet, P. & Chanson, P. Clinical aspects of multiple endocrine neoplasia type 1. Nat. Rev. Endocrinol. 17, 207\u2013224 (2021).","journal-title":"Nat. Rev. Endocrinol."},{"key":"1874_CR48","volume":"11","author":"H Qiu","year":"2020","unstructured":"Qiu, H. et al. MEN1 deficiency leads to neuroendocrine differentiation of lung cancer and disrupts the DNA damage response. Nat. Commun. 11, 1009 (2020).","journal-title":"Nat. Commun."},{"key":"1874_CR49","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1126\/science.276.5311.404","volume":"276","author":"SC Chandrasekharappa","year":"1997","unstructured":"Chandrasekharappa, S. C. et al. Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science 276, 404\u2013407 (1997).","journal-title":"Science"},{"key":"1874_CR50","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1126\/science.1200609","volume":"331","author":"Y Jiao","year":"2011","unstructured":"Jiao, Y. et al. DAXX\/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 331, 1199\u20131203 (2011).","journal-title":"Science"},{"key":"1874_CR51","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.ccr.2008.05.003","volume":"14","author":"A Yokoyama","year":"2008","unstructured":"Yokoyama, A. & Cleary, M. L. Menin critically links MLL proteins with LEDGF on cancer-associated target genes. Cancer Cell 14, 36\u201346 (2008).","journal-title":"Cancer Cell"},{"key":"1874_CR52","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"ES Lander","year":"2001","unstructured":"Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860\u2013921 (2001).","journal-title":"Nature"},{"key":"1874_CR53","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1038\/s41576-019-0165-8","volume":"20","author":"LM Payer","year":"2019","unstructured":"Payer, L. M. & Burns, K. H. Transposable elements in human genetic disease. Nat. Rev. Genet. 20, 760\u2013772 (2019).","journal-title":"Nat. Rev. Genet."},{"key":"1874_CR54","doi-asserted-by":"crossref","DOI":"10.1186\/s13100-016-0080-x","volume":"7","author":"A Babaian","year":"2016","unstructured":"Babaian, A. & Mager, D. L. Endogenous retroviral promoter exaptation in human cancer. Mob. DNA 7, 24 (2016).","journal-title":"Mob. DNA"},{"key":"1874_CR55","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1158\/2159-8290.CD-19-1493","volume":"10","author":"G Deblois","year":"2020","unstructured":"Deblois, G. et al. Epigenetic switch-induced viral mimicry evasion in chemotherapy-resistant breast cancer. Cancer Discov. 10, 1312\u20131329 (2020).","journal-title":"Cancer Discov."},{"key":"1874_CR56","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/j.cell.2018.05.052","volume":"174","author":"W Sheng","year":"2018","unstructured":"Sheng, W. et al. LSD1 ablation stimulates anti-tumor immunity and enables checkpoint blockade. Cell 174, 549\u2013563.e19 (2018).","journal-title":"Cell"},{"key":"1874_CR57","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1016\/j.cell.2015.07.011","volume":"162","author":"KB Chiappinelli","year":"2015","unstructured":"Chiappinelli, K. B. et al. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell 162, 974\u2013986 (2015).","journal-title":"Cell"},{"key":"1874_CR58","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1038\/s41588-021-00934-8","volume":"53","author":"R Linares-Saldana","year":"2021","unstructured":"Linares-Saldana, R. et al. BRD4 orchestrates genome folding to promote neural crest differentiation. Nat. Genet. 53, 1480\u20131492 (2021).","journal-title":"Nat. Genet."},{"key":"1874_CR59","volume":"14","author":"Z Wei","year":"2023","unstructured":"Wei, Z. et al. MYC reshapes CTCF-mediated chromatin architecture in prostate cancer. Nat. Commun. 14, 1787 (2023).","journal-title":"Nat. Commun."},{"key":"1874_CR60","doi-asserted-by":"crossref","first-page":"D1091","DOI":"10.1093\/nar\/gkt1068","volume":"42","author":"V Law","year":"2014","unstructured":"Law, V. et al. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 42, D1091\u2013D1097 (2014).","journal-title":"Nucleic Acids Res."},{"key":"1874_CR61","doi-asserted-by":"crossref","first-page":"3336","DOI":"10.1093\/bioinformatics\/btw476","volume":"32","author":"J Ma","year":"2016","unstructured":"Ma, J. et al. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics 32, 3336\u20133338 (2016).","journal-title":"Bioinformatics"},{"key":"1874_CR62","doi-asserted-by":"crossref","first-page":"db.prot090811","DOI":"10.1101\/pdb.prot090811","volume":"2016","author":"T Wang","year":"2016","unstructured":"Wang, T., Lander, E. S. & Sabatini, D. M. Viral packaging and cell culture for CRISPR-based screens. Cold Spring Harb. Protoc. 2016, db.prot090811 (2016).","journal-title":"Cold Spring Harb. Protoc."},{"key":"1874_CR63","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"1874_CR64","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","volume":"28","author":"L Wang","year":"2012","unstructured":"Wang, L., Wang, S. & Li, W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28, 2184\u20132185 (2012).","journal-title":"Bioinformatics"},{"key":"1874_CR65","volume":"17","author":"L Wang","year":"2016","unstructured":"Wang, L. et al. Measure transcript integrity using RNA-seq data. BMC Bioinformatics 17, 58 (2016).","journal-title":"BMC Bioinformatics"},{"key":"1874_CR66","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","volume":"31","author":"S Anders","year":"2015","unstructured":"Anders, S., Pyl, P. T. & Huber, W. HTSeq\u2014a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166\u2013169 (2015).","journal-title":"Bioinformatics"},{"key":"1874_CR67","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1101\/gr.248658.119","volume":"29","author":"SAM Tonekaboni","year":"2019","unstructured":"Tonekaboni, S. A. M., Mazrooei, P., Kofia, V., Haibe-Kains, B. & Lupien, M. Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks. Genome Res. 29, 1733\u20131743 (2019).","journal-title":"Genome Res."},{"key":"1874_CR68","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284\u2013287 (2012).","journal-title":"OMICS"},{"key":"1874_CR69","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"1874_CR70","doi-asserted-by":"crossref","first-page":"e1005112","DOI":"10.1371\/journal.pcbi.1005112","volume":"12","author":"H Chen","year":"2016","unstructured":"Chen, H. et al. Cytofkit: a bioconductor package for an integrated mass cytometry data analysis pipeline. PLoS Comput. Biol. 12, e1005112 (2016).","journal-title":"PLoS Comput. Biol."},{"key":"1874_CR71","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.cell.2015.05.047","volume":"162","author":"JH Levine","year":"2015","unstructured":"Levine, J. H. et al. Data-driven phenotypic dissection of aml reveals progenitor-like cells that correlate with prognosis. Cell 162, 184\u2013197 (2015).","journal-title":"Cell"},{"key":"1874_CR72","doi-asserted-by":"crossref","first-page":"861","DOI":"10.21105\/joss.00861","volume":"3","author":"L McInnes","year":"2018","unstructured":"McInnes, L., Healy, J., Saul, N. & Gro\u00dfberger, L. UMAP: uniform manifold approximation and projection. J. Open Source Softw. 3, 861 (2018).","journal-title":"J. Open Source Softw."},{"key":"1874_CR73","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/s42003-019-0415-5","volume":"2","author":"LM Weber","year":"2019","unstructured":"Weber, L. M., Nowicka, M., Soneson, C. & Robinson, M. D. diffcyt: differential discovery in high-dimensional cytometry via high-resolution clustering. Commun. Biol. 2, 183 (2019).","journal-title":"Commun. Biol."}],"container-title":["Nature Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01874-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01874-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01874-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,12]],"date-time":"2025-02-12T15:30:21Z","timestamp":1739374221000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41588-024-01874-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9]]},"references-count":73,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2024,9]]}},"alternative-id":["1874"],"URL":"https:\/\/doi.org\/10.1038\/s41588-024-01874-9","relation":{},"ISSN":["1061-4036","1546-1718"],"issn-type":[{"value":"1061-4036","type":"print"},{"value":"1546-1718","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9]]},"assertion":[{"value":"10 November 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 September 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"F.B. is Vice President of Translational Research of Kura Oncology, Inc. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}