{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T19:54:06Z","timestamp":1792439646795,"version":"4.5.0"},"reference-count":71,"publisher":"Springer Science and Business Media LLC","issue":"10","license":[{"start":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T00:00:00Z","timestamp":1725408000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T00:00:00Z","timestamp":1725408000000},"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":["Nat Cell Biol"],"published-print":{"date-parts":[[2024,10]]},"DOI":"10.1038\/s41556-024-01498-5","type":"journal-article","created":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T06:02:55Z","timestamp":1725429775000},"page":"1759-1772","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Wnt-deficient and hypoxic environment orchestrates squamous reprogramming of human pancreatic ductal adenocarcinoma"],"prefix":"10.1038","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2712-1123","authenticated-orcid":false,"given":"Hiroki","family":"Tamagawa","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8745-5478","authenticated-orcid":false,"given":"Masayuki","family":"Fujii","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Togasaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takashi","family":"Seino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shintaro","family":"Kawasaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ai","family":"Takano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kohta","family":"Toshimitsu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1115-2117","authenticated-orcid":false,"given":"Sirirat","family":"Takahashi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuki","family":"Ohta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mami","family":"Matano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenta","family":"Kawasaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujiro","family":"Machida","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shigeki","family":"Sekine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9552-8806","authenticated-orcid":false,"given":"Akihito","family":"Machinaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken","family":"Sasai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuzo","family":"Kodama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4893-5414","authenticated-orcid":false,"given":"Nobuyuki","family":"Kakiuchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7778-5374","authenticated-orcid":false,"given":"Seishi","family":"Ogawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomonori","family":"Hirano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroshi","family":"Seno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minoru","family":"Kitago","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuko","family":"Kitagawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eisuke","family":"Iwasaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1466-4532","authenticated-orcid":false,"given":"Takanori","family":"Kanai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8353-8137","authenticated-orcid":false,"given":"Toshiro","family":"Sato","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,9,4]]},"reference":[{"key":"1498_CR1","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/s41568-023-00648-5","volume":"24","author":"M Fujii","year":"2024","unstructured":"Fujii, M., Sekine, S. & Sato, T. Decoding the basis of histological variation in human cancer. Nat. Rev. Cancer 24, 141\u2013158 (2024).","journal-title":"Nat. Rev. Cancer"},{"key":"1498_CR2","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/nature16965","volume":"531","author":"P Bailey","year":"2016","unstructured":"Bailey, P. et al. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature 531, 47\u201352 (2016).","journal-title":"Nature"},{"key":"1498_CR3","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/nm.2344","volume":"17","author":"EA Collisson","year":"2011","unstructured":"Collisson, E. A. et al. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat. Med. 17, 500\u2013503 (2011).","journal-title":"Nat. Med."},{"key":"1498_CR4","doi-asserted-by":"publisher","first-page":"1168","DOI":"10.1038\/ng.3398","volume":"47","author":"RA Moffitt","year":"2015","unstructured":"Moffitt, R. A. et al. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat. Genet. 47, 1168\u20131178 (2015).","journal-title":"Nat. Genet."},{"key":"1498_CR5","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nature14169","volume":"518","author":"N Waddell","year":"2015","unstructured":"Waddell, N. et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature 518, 495\u2013501 (2015).","journal-title":"Nature"},{"key":"1498_CR6","unstructured":"Cancer Genome Atlas Research Network. Integrated genomic characterization of pancreatic ductal adenocarcinoma. Cancer Cell 32, 185\u2013203 (2017)."},{"key":"1498_CR7","doi-asserted-by":"crossref","unstructured":"Puleo, F. et al. Stratification of pancreatic ductal adenocarcinomas based on tumor and microenvironment features. Gastroenterology 155, 1999\u20132013.e3 (2018).","DOI":"10.1053\/j.gastro.2018.08.033"},{"key":"1498_CR8","doi-asserted-by":"crossref","unstructured":"Connor, A. A. et al. Integration of genomic and transcriptional features in pancreatic cancer reveals increased cell cycle progression in metastases. Cancer Cell 35, 267\u2013282.e267 (2019).","DOI":"10.1016\/j.ccell.2018.12.010"},{"key":"1498_CR9","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/s41575-019-0109-y","volume":"16","author":"EA Collisson","year":"2019","unstructured":"Collisson, E. A., Bailey, P., Chang, D. K. & Biankin, A. V. Molecular subtypes of pancreatic cancer. Nat. Rev. Gastroenterol. Hepatol. 16, 207\u2013220 (2019).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"1498_CR10","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/s43018-019-0010-1","volume":"1","author":"A Hayashi","year":"2020","unstructured":"Hayashi, A. et al. A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma. Nat. Cancer 1, 59\u201374 (2020).","journal-title":"Nat. Cancer"},{"key":"1498_CR11","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/s41588-019-0566-9","volume":"52","author":"M Chan-Seng-Yue","year":"2020","unstructured":"Chan-Seng-Yue, M. et al. Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat. Genet. 52, 231\u2013240 (2020).","journal-title":"Nat. Genet."},{"key":"1498_CR12","doi-asserted-by":"crossref","unstructured":"Raghavan, S. et al. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell 184, 6119\u20136137.e6126 (2021).","DOI":"10.1016\/j.cell.2021.11.017"},{"key":"1498_CR13","doi-asserted-by":"publisher","first-page":"1566","DOI":"10.1158\/2159-8290.CD-20-0133","volume":"10","author":"K Miyabayashi","year":"2020","unstructured":"Miyabayashi, K. et al. Intraductal transplantation models of human pancreatic ductal adenocarcinoma reveal progressive transition of molecular subtypes. Cancer Discov. 10, 1566\u20131589 (2020).","journal-title":"Cancer Discov."},{"key":"1498_CR14","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1038\/nature25459","volume":"554","author":"S Mueller","year":"2018","unstructured":"Mueller, S. et al. Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes. Nature 554, 62\u201368 (2018).","journal-title":"Nature"},{"key":"1498_CR15","doi-asserted-by":"publisher","first-page":"e45313","DOI":"10.7554\/eLife.45313","volume":"8","author":"CR Adams","year":"2019","unstructured":"Adams, C. R. et al. Transcriptional control of subtype switching ensures adaptation and growth of pancreatic cancer. ELife 8, e45313 (2019).","journal-title":"ELife"},{"key":"1498_CR16","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.cell.2014.06.003","volume":"158","author":"A Kapoor","year":"2014","unstructured":"Kapoor, A. et al. Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer. Cell 158, 185\u2013197 (2014).","journal-title":"Cell"},{"key":"1498_CR17","doi-asserted-by":"publisher","first-page":"e130811","DOI":"10.1172\/jci.insight.130811","volume":"4","author":"B Tu","year":"2019","unstructured":"Tu, B. et al. YAP1 oncogene is a context-specific driver for pancreatic ductal adenocarcinoma. JCI Insight 4, e130811 (2019).","journal-title":"JCI Insight"},{"key":"1498_CR18","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1136\/gutjnl-2015-311256","volume":"66","author":"P Martinelli","year":"2017","unstructured":"Martinelli, P. et al. GATA6 regulates EMT and tumour dissemination, and is a marker of response to adjuvant chemotherapy in pancreatic cancer. Gut 66, 1665\u20131676 (2017).","journal-title":"Gut"},{"key":"1498_CR19","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1016\/j.stem.2017.12.009","volume":"22","author":"T Seino","year":"2018","unstructured":"Seino, T. et al. Human pancreatic tumor organoids reveal loss of stem cell niche factor dependence during disease progression. Cell Stem Cell 22, 454\u2013467 e456 (2018).","journal-title":"Cell Stem Cell"},{"key":"1498_CR20","doi-asserted-by":"publisher","first-page":"107625","DOI":"10.1016\/j.celrep.2020.107625","volume":"31","author":"H Brunton","year":"2020","unstructured":"Brunton, H. et al. HNF4A and GATA6 loss reveals therapeutically actionable subtypes in pancreatic cancer. Cell Rep. 31, 107625 (2020).","journal-title":"Cell Rep."},{"key":"1498_CR21","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1136\/gutjnl-2020-321397","volume":"71","author":"B Kloesch","year":"2022","unstructured":"Kloesch, B. et al. A GATA6-centred gene regulatory network involving HNFs and DeltaNp63 controls plasticity and immune escape in pancreatic cancer. Gut 71, 766\u2013777 (2022).","journal-title":"Gut"},{"key":"1498_CR22","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2019102808","volume":"39","author":"M Kalisz","year":"2020","unstructured":"Kalisz, M. et al. HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer. EMBO J. 39, e102808 (2020).","journal-title":"EMBO J."},{"key":"1498_CR23","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1016\/j.ccell.2018.02.003","volume":"33","author":"J Andricovich","year":"2018","unstructured":"Andricovich, J. et al. Loss of KDM6A activates super-enhancers to induce gender-specific squamous-like pancreatic cancer and confers sensitivity to BET inhibitors. Cancer Cell 33, 512\u2013526 e518 (2018).","journal-title":"Cancer Cell"},{"key":"1498_CR24","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1002\/ijc.32072","volume":"145","author":"S Watanabe","year":"2019","unstructured":"Watanabe, S. et al. Loss of KDM6A characterizes a poor prognostic subtype of human pancreatic cancer and potentiates HDAC inhibitor lethality. Int. J. Cancer 145, 192\u2013205 (2019).","journal-title":"Int. J. Cancer"},{"key":"1498_CR25","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1002\/1097-0142(197205)29:5<1133::AID-CNCR2820290503>3.0.CO;2-4","volume":"29","author":"RW Cihak","year":"1972","unstructured":"Cihak, R. W., Kawashima, T. & Steer, A. Adenoacanthoma (adenosquamous carcinoma) of the pancreas. Cancer 29, 1133\u20131140 (1972).","journal-title":"Cancer"},{"key":"1498_CR26","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.humpath.2009.07.012","volume":"41","author":"KR Voong","year":"2010","unstructured":"Voong, K. R. et al. Resected pancreatic adenosquamous carcinoma: clinicopathologic review and evaluation of adjuvant chemotherapy and radiation in 38 patients. Hum. Pathol. 41, 113\u2013122 (2010).","journal-title":"Hum. Pathol."},{"key":"1498_CR27","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.jss.2011.06.015","volume":"174","author":"CA Boyd","year":"2012","unstructured":"Boyd, C. A., Benarroch-Gampel, J., Sheffield, K. M., Cooksley, C. D. & Riall, T. S. 415 patients with adenosquamous carcinoma of the pancreas: a population-based analysis of prognosis and survival. J. Surg. Res. 174, 12\u201319 (2012).","journal-title":"J. Surg. Res."},{"key":"1498_CR28","first-page":"75","volume":"6","author":"CG Simone","year":"2013","unstructured":"Simone, C. G. et al. Characteristics and outcomes of adenosquamous carcinoma of the pancreas. Gastrointest. Cancer Res. 6, 75\u201379 (2013).","journal-title":"Gastrointest. Cancer Res."},{"key":"1498_CR29","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1038\/ncb2992","volume":"16","author":"G Whissell","year":"2014","unstructured":"Whissell, G. et al. The transcription factor GATA6 enables self-renewal of colon adenoma stem cells by repressing BMP gene expression. Nat. Cell Biol. 16, 695\u2013707 (2014).","journal-title":"Nat. Cell Biol."},{"key":"1498_CR30","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms4150","volume":"5","author":"S Tsuji","year":"2014","unstructured":"Tsuji, S. et al. The miR-363-GATA6-Lgr5 pathway is critical for colorectal tumourigenesis. Nat. Commun. 5, 3150 (2014).","journal-title":"Nat. Commun."},{"key":"1498_CR31","doi-asserted-by":"crossref","unstructured":"Somerville, T. D. D. et al. TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma. Cell Rep. 25, 1741\u20131755 e1747 (2018).","DOI":"10.1016\/j.celrep.2018.10.051"},{"key":"1498_CR32","doi-asserted-by":"publisher","first-page":"e53381","DOI":"10.7554\/eLife.53381","volume":"9","author":"TD Somerville","year":"2020","unstructured":"Somerville, T. D. et al. Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation. ELife 9, e53381 (2020).","journal-title":"ELife"},{"key":"1498_CR33","doi-asserted-by":"publisher","first-page":"E12343","DOI":"10.1073\/pnas.1812915116","volume":"115","author":"FH Hamdan","year":"2018","unstructured":"Hamdan, F. H. & Johnsen, S. A. DeltaNp63-dependent super enhancers define molecular identity in pancreatic cancer by an interconnected transcription factor network. Pro. Natl Acad. Sci. USA 115, E12343\u2013E12352 (2018).","journal-title":"Pro. Natl Acad. Sci. USA"},{"key":"1498_CR34","doi-asserted-by":"publisher","first-page":"1217","DOI":"10.1126\/science.aaw1026","volume":"363","author":"AA Chakraborty","year":"2019","unstructured":"Chakraborty, A. A. et al. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science 363, 1217\u20131222 (2019).","journal-title":"Science"},{"key":"1498_CR35","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1158\/1541-7786.MCR-12-0511","volume":"11","author":"HT Su","year":"2013","unstructured":"Su, H. T. et al. Stem cell marker nestin is critical for TGF-\u03b21-mediated tumor progression in pancreatic cancer. Mol. Cancer Res. 11, 768\u2013779 (2013).","journal-title":"Mol. Cancer Res."},{"key":"1498_CR36","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1158\/0008-5472.CAN-09-3269","volume":"71","author":"P Papageorgis","year":"2011","unstructured":"Papageorgis, P. et al. Smad4 inactivation promotes malignancy and drug resistance of colon cancer. Cancer Res. 71, 998\u20131008 (2011).","journal-title":"Cancer Res."},{"key":"1498_CR37","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1136\/gutjnl-2018-317706","volume":"68","author":"C Maurer","year":"2019","unstructured":"Maurer, C. et al. Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Gut 68, 1034\u20131043 (2019).","journal-title":"Gut"},{"key":"1498_CR38","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1016\/j.cell.2015.07.013","volume":"162","author":"HW Park","year":"2015","unstructured":"Park, H. W. et al. Alternative Wnt signaling activates YAP\/TAZ. Cell 162, 780\u2013794 (2015).","journal-title":"Cell"},{"key":"1498_CR39","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1146\/annurev.cellbio.042308.113344","volume":"25","author":"AM Zorn","year":"2009","unstructured":"Zorn, A. M. & Wells, J. M. Vertebrate endoderm development and organ formation. Annu. Rev. Cell Dev. Biol. 25, 221\u2013251 (2009).","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"1498_CR40","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1038\/nature06145","volume":"449","author":"K Agger","year":"2007","unstructured":"Agger, K. et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449, 731\u2013734 (2007).","journal-title":"Nature"},{"key":"1498_CR41","doi-asserted-by":"crossref","unstructured":"Su, W. et al. 18F-FDG PET\/CT feature of pancreatic adenosquamous carcinoma with pathological correlation. Abdom. Radiol. 45, 743\u2013749.","DOI":"10.1007\/s00261-019-02393-6"},{"key":"1498_CR42","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1038\/s41568-020-00303-3","volume":"20","author":"JA Losman","year":"2020","unstructured":"Losman, J. A., Koivunen, P. & Kaelin, W. G. Jr. 2-Oxoglutarate-dependent dioxygenases in cancer. Nat. Rev. Cancer 20, 710\u2013726 (2020).","journal-title":"Nat. Rev. Cancer"},{"key":"1498_CR43","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1038\/nature13981","volume":"518","author":"BW Carey","year":"2015","unstructured":"Carey, B. W., Finley, L. W., Cross, J. R., Allis, C. D. & Thompson, C. B. Intracellular \u03b1-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature 518, 413\u2013416 (2015).","journal-title":"Nature"},{"key":"1498_CR44","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1016\/j.celrep.2017.09.078","volume":"21","author":"T Ezponda","year":"2017","unstructured":"Ezponda, T. et al. UTX\/KDM6A loss enhances the malignant phenotype of multiple myeloma and sensitizes cells to EZH2 inhibition. Cell Rep. 21, 628\u2013640 (2017).","journal-title":"Cell Rep."},{"key":"1498_CR45","doi-asserted-by":"publisher","first-page":"eaai8312","DOI":"10.1126\/scitranslmed.aai8312","volume":"9","author":"LD Ler","year":"2017","unstructured":"Ler, L. D. et al. Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Sci. Transl. Med. 9, eaai8312 (2017).","journal-title":"Sci. Transl. Med."},{"key":"1498_CR46","doi-asserted-by":"crossref","unstructured":"Kawasaki, K. et al. An organoid biobank of neuroendocrine neoplasms enables genotype\u2013phenotype mapping. Cell 183, 1420\u20131435.e1421 (2020).","DOI":"10.1016\/j.cell.2020.10.023"},{"key":"1498_CR47","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1126\/science.aat5749","volume":"362","author":"JW Park","year":"2018","unstructured":"Park, J. W. et al. Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage. Science 362, 91\u201395 (2018).","journal-title":"Science"},{"key":"1498_CR48","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1126\/science.aah4307","volume":"355","author":"P Mu","year":"2017","unstructured":"Mu, P. et al. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science 355, 84\u201388 (2017).","journal-title":"Science"},{"key":"1498_CR49","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nature12213","volume":"499","author":"MS Lawrence","year":"2013","unstructured":"Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214\u2013218 (2013).","journal-title":"Nature"},{"key":"1498_CR50","doi-asserted-by":"publisher","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. https:\/\/doi.org\/10.14806\/ej.17.1.200 (2011).","DOI":"10.14806\/ej.17.1.200"},{"key":"1498_CR51","doi-asserted-by":"publisher","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":"1498_CR52","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1186\/s12859-018-2435-4","volume":"19","author":"M Foroutan","year":"2018","unstructured":"Foroutan, M. et al. Single sample scoring of molecular phenotypes. BMC Bioinform. 19, 404 (2018).","journal-title":"BMC Bioinform."},{"key":"1498_CR53","doi-asserted-by":"publisher","unstructured":"Hao, Y. et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/s41587-023-01767-y (2023).","DOI":"10.1038\/s41587-023-01767-y"},{"key":"1498_CR54","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27729-z","volume":"13","author":"GC Linderman","year":"2022","unstructured":"Linderman, G. C. et al. Zero-preserving imputation of single-cell RNA-seq data. Nat. Commun. 13, 192 (2022).","journal-title":"Nat. Commun."},{"key":"1498_CR55","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4772-0","volume":"19","author":"K Street","year":"2018","unstructured":"Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genom. 19, 477 (2018).","journal-title":"BMC Genom."},{"key":"1498_CR56","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14766-3","volume":"11","author":"K Van den Berge","year":"2020","unstructured":"Van den Berge, K. et al. Trajectory-based differential expression analysis for single-cell sequencing data. Nat. Commun. 11, 1201 (2020).","journal-title":"Nat. Commun."},{"key":"1498_CR57","doi-asserted-by":"publisher","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":"1498_CR58","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-01684-6","volume":"7","author":"LN Randolph","year":"2017","unstructured":"Randolph, L. N., Bao, X., Zhou, C. & Lian, X. An all-in-one, Tet-On 3G inducible PiggyBac system for human pluripotent stem cells and derivatives. Sci. Rep. 7, 1549 (2017).","journal-title":"Sci. Rep."},{"key":"1498_CR59","doi-asserted-by":"publisher","unstructured":"Matano, M. et al. Modeling colorectal cancer using CRISPR-Cas9-mediated engineering of human intestinal organoids. Nat. Med. https:\/\/doi.org\/10.1038\/nm.3802 (2015).","DOI":"10.1038\/nm.3802"},{"key":"1498_CR60","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/nmeth.1802","volume":"9","author":"BK Koo","year":"2012","unstructured":"Koo, B. K. et al. Controlled gene expression in primary Lgr5 organoid cultures. Nat. Methods 9, 81\u201383 (2012).","journal-title":"Nat. Methods"},{"key":"1498_CR61","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1038\/nprot.2015.088","volume":"10","author":"M Fujii","year":"2015","unstructured":"Fujii, M., Matano, M., Nanki, K. & Sato, T. Efficient genetic engineering of human intestinal organoids using electroporation. Nat. Protoc. 10, 1474\u20131485 (2015).","journal-title":"Nat. Protoc."},{"key":"1498_CR62","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-20358-5","volume":"8","author":"Q Guo","year":"2018","unstructured":"Guo, Q. et al. \u2018Cold shock\u2019 increases the frequency of homology directed repair gene editing in induced pluripotent stem cells. Sci. Rep. 8, 2080 (2018).","journal-title":"Sci. Rep."},{"key":"1498_CR63","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nmeth.2688","volume":"10","author":"JD Buenrostro","year":"2013","unstructured":"Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213\u20131218 (2013).","journal-title":"Nat. Methods"},{"key":"1498_CR64","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1038\/nmeth.4396","volume":"14","author":"MR Corces","year":"2017","unstructured":"Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959\u2013962 (2017).","journal-title":"Nat. Methods"},{"key":"1498_CR65","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"1498_CR66","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"1498_CR67","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","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":"1498_CR68","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576\u2013589 (2010).","journal-title":"Mol. Cell"},{"key":"1498_CR69","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1038\/nmeth.3542","volume":"12","author":"C Schmidl","year":"2015","unstructured":"Schmidl, C., Rendeiro, A. F., Sheffield, N. C. & Bock, C. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat. Methods 12, 963\u2013965 (2015).","journal-title":"Nat. Methods"},{"key":"1498_CR70","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29857-6","volume":"13","author":"X Shi","year":"2022","unstructured":"Shi, X. et al. Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity. Nat. Commun. 13, 2169 (2022).","journal-title":"Nat. Commun."},{"key":"1498_CR71","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1158\/2159-8290.CD-18-0349","volume":"8","author":"H Tiriac","year":"2018","unstructured":"Tiriac, H. et al. Organoid profiling identifies common responders to chemotherapy in pancreatic cancer. Cancer Discov. 8, 1112\u20131129 (2018).","journal-title":"Cancer Discov."}],"container-title":["Nature Cell Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41556-024-01498-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41556-024-01498-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41556-024-01498-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,11]],"date-time":"2024-10-11T12:04:22Z","timestamp":1728648262000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41556-024-01498-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,4]]},"references-count":71,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2024,10]]}},"alternative-id":["1498"],"URL":"https:\/\/doi.org\/10.1038\/s41556-024-01498-5","relation":{},"ISSN":["1465-7392","1476-4679"],"issn-type":[{"value":"1465-7392","type":"print"},{"value":"1476-4679","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,4]]},"assertion":[{"value":"12 October 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 September 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"T.S. is an inventor on several patents related to organoid culture. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}