{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T19:20:28Z","timestamp":1793215228513,"version":"4.5.0"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T00:00:00Z","timestamp":1738713600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T00:00:00Z","timestamp":1738713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Data"],"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:p>Pseudomyxoma peritonei (PMP), a rare condition characterized by mucinous ascites in the peritoneal cavity, often leads to a poor prognosis. However, omics profiling of this disease remains significantly underexplored. Here, we present single-cell transcriptomic profiling of five PMP cases to identify cell type-specific gene features associated with PMP pathogenesis. Additionally, we provide bulk RNA-seq datasets from two independent cohorts: 19 fresh frozen tissue samples (12 PMPs) and 34 formalin-fixed paraffin-embedded (FFPE) samples (25 PMPs). We also offer protein expression data from a tissue microarray (TMA) analysis of 90 samples (45 PMPs). Our single-cell and bulk transcriptomic profiles, along with TMA verifications, reveal the cellular diversity of PMP, highlighting the coexistence of epithelial and mesenchymal characteristics within PMP cells. These datasets enhance our understanding of PMP pathogenesis and provide a valuable resource for uncovering the intricate molecular landscape of PMP, with the potential to improve clinical utility through further research.<\/jats:p>","DOI":"10.1038\/s41597-025-04561-4","type":"journal-article","created":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T13:39:44Z","timestamp":1738762784000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Molecular characterization of Pseudomyxoma peritonei with single-cell and bulk RNA sequencing"],"prefix":"10.1038","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2001-7435","authenticated-orcid":false,"given":"Ye Jin","family":"Ha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seong-Hwan","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4176-5187","authenticated-orcid":false,"given":"Seon-Kyu","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ka Hee","family":"Tak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeong-Hwan","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chan Wook","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong Sik","family":"Yoon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1030-7730","authenticated-orcid":false,"given":"Seon-Young","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jong Lyul","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,2,5]]},"reference":[{"key":"4561_CR1","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1016\/S1055-3207(03)00026-7","volume":"12","author":"BJ Moran","year":"2003","unstructured":"Moran, B. J. & Cecil, T. D. The etiology, clinical presentation, and management of pseudomyxoma peritonei. Surg Oncol Clin N Am 12, 585\u2013603 (2003).","journal-title":"Surg Oncol Clin N Am"},{"key":"4561_CR2","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1080\/00365521.2017.1284896","volume":"52","author":"U Darr","year":"2017","unstructured":"Darr, U. et al. Diagnosis of Pseudomyxoma peritonei via endoscopic ultrasound guided fine needle aspiration: a case report and review of literature. Scand J Gastroenterol 52, 609\u2013612 (2017).","journal-title":"Scand J Gastroenterol"},{"key":"4561_CR3","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1080\/02656736.2017.1310938","volume":"33","author":"R Mittal","year":"2017","unstructured":"Mittal, R., Chandramohan, A. & Moran, B. Pseudomyxoma peritonei: natural history and treatment. 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Int J Gynecol Cancer 13, 413\u2013418 (2003).","journal-title":"Int J Gynecol Cancer"},{"key":"4561_CR6","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-020-06787-4","volume":"20","author":"R Ma","year":"2020","unstructured":"Ma, R., Wang, B., Zhai, X., Lu, Y. & Xu, H. Management and prognostic prediction of appendiceal mucinous adenocarcinoma with peritoneal metastasis: a single center study in China. BMC Cancer 20, 280 (2020).","journal-title":"BMC Cancer"},{"key":"4561_CR7","doi-asserted-by":"publisher","first-page":"425","DOI":"10.3393\/ac.2021.00920.0131","volume":"37","author":"YJ Kim","year":"2021","unstructured":"Kim, Y. J. & Kim, C. H. Treatment for Peritoneal Metastasis of Patients With Colorectal Cancer. 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Single\u2010cell transcriptomics provides new insights into the role of fibroblasts during peritoneal fibrosis. Clinical and Translational Medicine 11 (2021).","DOI":"10.1002\/ctm2.321"},{"key":"4561_CR11","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010).","journal-title":"Bioinformatics"},{"key":"4561_CR12","doi-asserted-by":"publisher","first-page":"lqaa078","DOI":"10.1093\/nargab\/lqaa078","volume":"2","author":"Y Zhang","year":"2020","unstructured":"Zhang, Y., Parmigiani, G. & Johnson, W. E. ComBat-seq: batch effect adjustment for RNA-seq count data. 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