{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T05:04:41Z","timestamp":1784610281758,"version":"3.55.0"},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T00:00:00Z","timestamp":1784592000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T00:00:00Z","timestamp":1784592000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100004775","name":"Natural Science Foundation of Gansu Province","doi-asserted-by":"crossref","award":["No. 25JRRA584"],"award-info":[{"award-number":["No. 25JRRA584"]}],"id":[{"id":"10.13039\/501100004775","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Gansu Province Health Commission Major Scientific Research Project for Scientific and Technological Innovation in the Health Industry","award":["No. GSWSQNPY2025-15"],"award-info":[{"award-number":["No. GSWSQNPY2025-15"]}]},{"name":"The Key Incubation Project Funds of the second hospital & clinical medical school","award":["2025-22-zdfy-005"],"award-info":[{"award-number":["2025-22-zdfy-005"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Funct Integr Genomics"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1007\/s10142-026-01988-9","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T04:26:15Z","timestamp":1784607975000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single-cell and spatial transcriptomics identify CAPG as a key driver of cisplatin resistance in bladder cancer"],"prefix":"10.1007","volume":"26","author":[{"given":"Jianwei","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoran","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shun","family":"Wan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunpeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyu","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanhui","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,21]]},"reference":[{"key":"1988_CR28","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1038\/s41586-023-06234-x","volume":"619","author":"HA Abdel-Hafiz","year":"2023","unstructured":"Abdel-Hafiz HA, Schafer JM, Chen X, Xiao T, Gauntner TD, Li Z, Theodorescu D (2023) Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature 619:624\u2013631. https:\/\/doi.org\/10.1038\/s41586-023-06234-x","journal-title":"Nature"},{"key":"1988_CR7","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1016\/j.eururo.2016.06.020","volume":"71","author":"J Alfred Witjes","year":"2017","unstructured":"Alfred Witjes J, Lebret T, Comp\u00e9rat EM, Cowan NC, De Santis M, Bruins HM, Hern\u00e1ndez V, Espin\u00f3s EL, Dunn J, Rouanne M, Neuzillet Y, Veskim\u00e4e E, van der Heijden AG, Gakis G, Ribal MJ (2017) Updated 2016 EAU Guidelines on Muscle-invasive and Metastatic Bladder Cancer. Eur Urol 71:462\u2013475. https:\/\/doi.org\/10.1016\/j.eururo.2016.06.020","journal-title":"Eur Urol"},{"key":"1988_CR29","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 (2018) Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 36:411\u2013420. https:\/\/doi.org\/10.1038\/nbt.4096","journal-title":"Nat Biotechnol"},{"key":"1988_CR6","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1016\/j.eururo.2005.04.006","volume":"48","author":"Advanced Bladder Cancer (ABC) Meta-analysis Collaboration","year":"2005","unstructured":"Advanced Bladder Cancer (ABC) Meta-analysis Collaboration (2005) Neoadjuvant chemotherapy in invasive bladder cancer: update of a systematic review and meta-analysis of individual patient data advanced bladder cancer (ABC) meta-analysis collaboration. Eur Urol 48:202\u2013205. https:\/\/doi.org\/10.1016\/j.eururo.2005.04.006 discussion 205\u2013206","journal-title":"Eur Urol"},{"key":"1988_CR42","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1007\/978-1-4419-7046-6_19","volume":"696","author":"D Che","year":"2011","unstructured":"Che D, Liu Q, Rasheed K, Tao X (2011) Decision tree and ensemble learning algorithms with their applications in bioinformatics. Adv Exp Med Biol 696:191\u2013199. https:\/\/doi.org\/10.1007\/978-1-4419-7046-6_19","journal-title":"Adv Exp Med Biol"},{"key":"1988_CR53","doi-asserted-by":"publisher","first-page":"4136","DOI":"10.3390\/ijms20174136","volume":"20","author":"S-H Chen","year":"2019","unstructured":"Chen S-H, Chang J-Y (2019) New Insights into Mechanisms of Cisplatin Resistance: From Tumor Cell to Microenvironment. Int J Mol Sci 20:4136. https:\/\/doi.org\/10.3390\/ijms20174136","journal-title":"Int J Mol Sci"},{"key":"1988_CR12","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1016\/j.ccr.2014.01.009","volume":"25","author":"W Choi","year":"2014","unstructured":"Choi W, Porten S, Kim S, Willis D, Plimack ER, Hoffman-Censits J, Roth B, Cheng T, Tran M, Lee I-L, Melquist J, Bondaruk J, Majewski T, Zhang S, Pretzsch S, Baggerly K, Siefker-Radtke A, Czerniak B, Dinney CPN, McConkey DJ (2014) Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. Cancer Cell 25:152\u2013165. https:\/\/doi.org\/10.1016\/j.ccr.2014.01.009","journal-title":"Cancer Cell"},{"key":"1988_CR43","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1007\/s10238-025-01701-3","volume":"25","author":"Y Fu","year":"2025","unstructured":"Fu Y, Zhao J, Wang Y (2025) LASSO regression and Boruta algorithm to explore the relationship between neutrophil percentage to albumin ratio and asthma: results from the NHANES 2001 to 2018. Clin Exp Med 25:149. https:\/\/doi.org\/10.1007\/s10238-025-01701-3","journal-title":"Clin Exp Med"},{"key":"1988_CR36","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1126\/science.aax0249","volume":"367","author":"GS Gulati","year":"2020","unstructured":"Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, Ilagan F, Kuo AH, Hsieh RW, Cai S, Zabala M, Scheeren FA, Lobo NA, Qian D, Yu FB, Dirbas FM, Clarke MF, Newman AM (2020) Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367:405\u2013411. https:\/\/doi.org\/10.1126\/science.aax0249","journal-title":"Science"},{"key":"1988_CR38","doi-asserted-by":"publisher","unstructured":"H\u00e4nzelmann S, Castelo R, Guinney J (2013) BMC Bioinformatics 14:7. https:\/\/doi.org\/10.1186\/1471-2105-14-7. GSVA: gene set variation analysis for microarray and RNA-seq data","DOI":"10.1186\/1471-2105-14-7"},{"key":"1988_CR40","doi-asserted-by":"publisher","first-page":"bbad002","DOI":"10.1093\/bib\/bbad002","volume":"24","author":"J Hu","year":"2023","unstructured":"Hu J, Szymczak S (2023) A review on longitudinal data analysis with random forest. Brief Bioinform 24:bbad002. https:\/\/doi.org\/10.1093\/bib\/bbad002","journal-title":"Brief Bioinform"},{"key":"1988_CR54","doi-asserted-by":"publisher","first-page":"107911","DOI":"10.1016\/j.phrs.2025.107911","volume":"220","author":"C Hua","year":"2025","unstructured":"Hua C, Zhang G, Yu W, Zhou J, Ru L, Xue G, Zheng L, Wang M, Wang Y, Yu D, Wang Q, Liu J, Wang R, Deng W, Tang R, Guo W (2025) CROT overactivation within peroxisomes confers chemoresistance to non-small cell lung cancer by targeting fatty acid oxidation-Nrf2-ferroptosis resistance axis. Pharmacol Res 220:107911. https:\/\/doi.org\/10.1016\/j.phrs.2025.107911","journal-title":"Pharmacol Res"},{"key":"1988_CR56","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.bbrc.2009.01.064","volume":"380","author":"T Hubert","year":"2009","unstructured":"Hubert T, Impe KV, Vandekerckhove J, Gettemans J (2009) The actin-capping protein CapG localizes to microtubule-dependent organelles during the cell cycle. Biochem Biophys Res Commun 380:166\u2013170. https:\/\/doi.org\/10.1016\/j.bbrc.2009.01.064","journal-title":"Biochem Biophys Res Commun"},{"key":"1988_CR10","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1126\/science.1226344","volume":"338","author":"G Iyer","year":"2012","unstructured":"Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, Scott SN, Janakiraman M, Pirun M, Sander C, Socci ND, Ostrovnaya I, Viale A, Heguy A, Peng L, Chan TA, Bochner B, Bajorin DF, Berger MF, Taylor BS, Solit DB (2012) Genome Sequencing Identifies a Basis for Everolimus Sensitivity. Science 338:221\u2013221. https:\/\/doi.org\/10.1126\/science.1226344","journal-title":"Science"},{"key":"1988_CR37","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","volume":"12","author":"S Jin","year":"2021","unstructured":"Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan C-H, Myung P, Plikus MV, Nie Q (2021) Inference and analysis of cell-cell communication using CellChat. Nat Commun 12:1088. https:\/\/doi.org\/10.1038\/s41467-021-21246-9","journal-title":"Nat Commun"},{"key":"1988_CR14","doi-asserted-by":"publisher","first-page":"e694","DOI":"10.1002\/ctm2.694","volume":"12","author":"D Jovic","year":"2022","unstructured":"Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y (2022) Single-cell RNA sequencing technologies and applications: A brief overview. Clin Transl Med 12:e694. https:\/\/doi.org\/10.1002\/ctm2.694","journal-title":"Clin Transl Med"},{"key":"1988_CR2","doi-asserted-by":"publisher","unstructured":"Kamat AM, Hahn NM, Efstathiou JA, Lerner SP, Malmstr\u00f6m PU, Choi W, Guo CC, Lotan Y, Kassouf W (2016) Bladder cancer. Lancet (London England) 388. https:\/\/doi.org\/10.1016\/S0140-6736(16)30512-8","DOI":"10.1016\/S0140-6736(16)30512-8"},{"key":"1988_CR45","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1002\/1878-0261.13684","volume":"18","author":"I Kawahara","year":"2024","unstructured":"Kawahara I, Yoshino H, Fukumoto W, Arima J, Saito S, Li G, Fukuda I, Mitsuke A, Sakaguchi T, Inoguchi S, Matsushita R, Nakagawa M, Tatarano S, Yamada Y, Enokida H (2024) Targeting metabolic reprogramming to overcome drug resistance in advanced bladder cancer: insights from gemcitabine- and cisplatin-resistant models. Mol Oncol 18:2196\u20132211. https:\/\/doi.org\/10.1002\/1878-0261.13684","journal-title":"Mol Oncol"},{"key":"1988_CR20","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1002\/mdr2.70040","volume":"1","author":"X Ke","year":"2025","unstructured":"Ke X, Li K, Jiang A, Zhang Y, Wang Q, Li Z, Zhang J, Hajd A, Shi W, Kahlert U, Lin A, Zhang P, Luo P (2025) Cloud-Based GWAS Platform: An Innovative Solution for Efficient Acquisition and Analysis of Genomic Data. Med Res 1:397\u2013411. https:\/\/doi.org\/10.1002\/mdr2.70040","journal-title":"Med Res"},{"key":"1988_CR27","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.eururo.2014.06.050","volume":"67","author":"PH Kim","year":"2015","unstructured":"Kim PH, Cha EK, Sfakianos JP, Iyer G, Zabor EC, Scott SN, Ostrovnaya I, Ramirez R, Sun A, Shah R, Yee AM, Reuter VE, Bajorin DF, Rosenberg JE, Schultz N, Berger MF, Al-Ahmadie HA, Solit DB, Bochner BH (2015) Genomic predictors of survival in patients with high-grade urothelial carcinoma of the bladder. Eur Urol 67:198\u2013201. https:\/\/doi.org\/10.1016\/j.eururo.2014.06.050","journal-title":"Eur Urol"},{"key":"1988_CR30","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, Baglaenko Y, Brenner M, Loh P-R, Raychaudhuri S (2019) Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 16:1289\u20131296. https:\/\/doi.org\/10.1038\/s41592-019-0619-0","journal-title":"Nat Methods"},{"key":"1988_CR23","doi-asserted-by":"publisher","first-page":"2099","DOI":"10.1002\/ijc.33794","volume":"149","author":"H Lai","year":"2021","unstructured":"Lai H, Cheng X, Liu Q, Luo W, Liu M, Zhang M, Miao J, Ji Z, Lin GN, Song W, Zhang L, Bo J, Yang G, Wang J, Gao W-Q (2021) Single-cell RNA sequencing reveals the epithelial cell heterogeneity and invasive subpopulation in human bladder cancer. Int J Cancer 149:2099\u20132115. https:\/\/doi.org\/10.1002\/ijc.33794","journal-title":"Int J Cancer"},{"key":"1988_CR9","doi-asserted-by":"publisher","unstructured":"Li F, Zheng Z, Chen W, Li D, Zhang H, Zhu Y, Mo Q, Zhao X, Fan Q, Deng F, Han C, Tan W (2023) Regulation of cisplatin resistance in bladder cancer by epigenetic mechanisms. Drug Resist Updat 68. https:\/\/doi.org\/10.1016\/j.drup.2023.100938","DOI":"10.1016\/j.drup.2023.100938"},{"key":"1988_CR35","doi-asserted-by":"publisher","first-page":"140793","DOI":"10.1016\/j.ijbiomac.2025.140793","volume":"300","author":"C Li","year":"2025","unstructured":"Li C, Hao R, Li C, Liu L, Ding Z (2025) Integration of single-cell and bulk RNA sequencing data using machine learning identifies oxidative stress-related genes LUM and PCOLCE2 as potential biomarkers for heart failure. Int J Biol Macromol 300:140793. https:\/\/doi.org\/10.1016\/j.ijbiomac.2025.140793","journal-title":"Int J Biol Macromol"},{"key":"1988_CR5","doi-asserted-by":"publisher","unstructured":"Lopez-Beltran A, Cookson MS, Guercio BJ, Cheng L (2024) Advances in diagnosis and treatment of bladder cancer, BMJ 384. https:\/\/doi.org\/10.1136\/bmj-2023-076743","DOI":"10.1136\/bmj-2023-076743"},{"key":"1988_CR25","doi-asserted-by":"publisher","first-page":"818147","DOI":"10.3389\/fonc.2022.818147","volume":"12","author":"Y Luo","year":"2022","unstructured":"Luo Y, Tao T, Tao R, Huang G, Wu S (2022) Single-Cell Transcriptome Comparison of Bladder Cancer Reveals Its Ecosystem. Front Oncol 12:818147. https:\/\/doi.org\/10.3389\/fonc.2022.818147","journal-title":"Front Oncol"},{"key":"1988_CR11","doi-asserted-by":"publisher","first-page":"855","DOI":"10.1016\/j.eururo.2015.08.034","volume":"69","author":"DJ McConkey","year":"2016","unstructured":"McConkey DJ, Choi W, Shen Y, Lee I-L, Porten S, Matin SF, Kamat AM, Corn P, Millikan RE, Dinney C, Czerniak B, Siefker-Radtke AO (2016) A Prognostic Gene Expression Signature in the Molecular Classification of Chemotherapy-na\u00efve Urothelial Cancer is Predictive of Clinical Outcomes from Neoadjuvant Chemotherapy: A Phase 2 Trial of Dose-dense Methotrexate, Vinblastine, Doxorubicin, and Cisplatin with Bevacizumab in Urothelial Cancer. Eur Urol 69:855\u2013862. https:\/\/doi.org\/10.1016\/j.eururo.2015.08.034","journal-title":"Eur Urol"},{"key":"1988_CR33","doi-asserted-by":"publisher","first-page":"100498","DOI":"10.1016\/j.crmeth.2023.100498","volume":"3","author":"S Morabito","year":"2023","unstructured":"Morabito S, Reese F, Rahimzadeh N, Miyoshi E, Swarup V (2023) hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data. Cell Rep Methods 3:100498. https:\/\/doi.org\/10.1016\/j.crmeth.2023.100498","journal-title":"Cell Rep Methods"},{"key":"1988_CR13","doi-asserted-by":"publisher","first-page":"5554","DOI":"10.1038\/s41598-017-05623-3","volume":"7","author":"KM Patel","year":"2017","unstructured":"Patel KM, van der Vos KE, Smith CG, Mouliere F, Tsui D, Morris J, Chandrananda D, Marass F, van den Broek D, Neal DE, Gnanapragasam VJ, Forshew T, van Rhijn BW, Massie CE, Rosenfeld N (2017) der Heijden, Association Of Plasma And Urinary Mutant DNA With Clinical Outcomes In Muscle Invasive Bladder Cancer. Sci Rep 7:5554. https:\/\/doi.org\/10.1038\/s41598-017-05623-3. van","journal-title":"Sci Rep"},{"key":"1988_CR1","doi-asserted-by":"publisher","first-page":"404","DOI":"10.3322\/caac.21631","volume":"70","author":"VG Patel","year":"2020","unstructured":"Patel VG, Oh WK, Galsky MD (2020) Treatment of muscle-invasive and advanced bladder cancer in 2020. CA Cancer J Clin 70:404\u2013423. https:\/\/doi.org\/10.3322\/caac.21631","journal-title":"CA Cancer J Clin"},{"key":"1988_CR47","doi-asserted-by":"publisher","first-page":"1824","DOI":"10.2353\/ajpath.2009.090155","volume":"175","author":"C Pollard","year":"2009","unstructured":"Pollard C, Nitz M, Baras A, Williams P, Moskaluk C, Theodorescu D (2009) Genoproteomic Mining of Urothelial Cancer Suggests \u03b3-Glutamyl Hydrolase and Diazepam-Binding Inhibitor as Putative Urinary Markers of Outcome after Chemotherapy. Am J Pathol 175:1824\u20131830. https:\/\/doi.org\/10.2353\/ajpath.2009.090155","journal-title":"Am J Pathol"},{"key":"1988_CR16","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/s41586-021-03634-9","volume":"596","author":"A Rao","year":"2021","unstructured":"Rao A, Barkley D, Fran\u00e7a GS, Yanai I (2021) Exploring tissue architecture using spatial transcriptomics. Nature 596:211\u2013220. https:\/\/doi.org\/10.1038\/s41586-021-03634-9","journal-title":"Nature"},{"key":"1988_CR8","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1016\/j.eururo.2011.12.010","volume":"61","author":"R Rosenblatt","year":"2012","unstructured":"Rosenblatt R, Sherif A, Rintala E, Wahlqvist R, Ull\u00e9n A, Nilsson S, Malmstr\u00f6m P-U (2012) Pathologic Downstaging Is a Surrogate Marker for Efficacy and Increased Survival Following Neoadjuvant Chemotherapy and Radical Cystectomy for Muscle-Invasive Urothelial Bladder Cancer. Eur Urol 61:1229\u20131238. https:\/\/doi.org\/10.1016\/j.eururo.2011.12.010","journal-title":"Eur Urol"},{"key":"1988_CR57","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1038\/s41588-021-00873-4","volume":"53","author":"A Sarkar","year":"2021","unstructured":"Sarkar A, Stephens M (2021) Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis. Nat Genet 53:770\u2013777. https:\/\/doi.org\/10.1038\/s41588-021-00873-4","journal-title":"Nat Genet"},{"key":"1988_CR24","doi-asserted-by":"publisher","first-page":"2540","DOI":"10.1038\/s41467-020-16162-3","volume":"11","author":"JP Sfakianos","year":"2020","unstructured":"Sfakianos JP, Daza J, Hu Y, Anastos H, Bryant G, Bareja R, Badani KK, Galsky MD, Elemento O, Faltas BM, Mulholland DJ (2020) Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers. Nat Commun 11:2540. https:\/\/doi.org\/10.1038\/s41467-020-16162-3","journal-title":"Nat Commun"},{"key":"1988_CR41","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1007\/s11906-022-01212-6","volume":"24","author":"GFS Silva","year":"2022","unstructured":"Silva GFS, Fagundes TP, Teixeira BC, Chiavegatto Filho ADP (2022) Machine Learning for Hypertension Prediction: a Systematic Review. Curr Hypertens Rep 24:523\u2013533. https:\/\/doi.org\/10.1007\/s11906-022-01212-6","journal-title":"Curr Hypertens Rep"},{"key":"1988_CR21","doi-asserted-by":"publisher","first-page":"e32143","DOI":"10.7554\/eLife.32143","volume":"7","author":"SU Springer","year":"2018","unstructured":"Springer SU, Chen C-H, Rodriguez Pena MDC, Li L, Douville C, Wang Y, Cohen JD, Taheri D, Silliman N, Schaefer J, Ptak J, Dobbyn L, Papoli M, Kinde I, Afsari B, Tregnago AC, Bezerra SM, VandenBussche C, Fujita K, Ertoy D, Cunha IW, Yu L, Bivalacqua TJ, Grollman AP, Diaz LA, Karchin R, Danilova L, Huang C-Y, Shun C-T, Turesky RJ, Yun BH, Rosenquist TA, Pu Y-S, Hruban RH, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Dickman KG, Netto GJ (2018) Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy. Elife 7:e32143. https:\/\/doi.org\/10.7554\/eLife.32143","journal-title":"Elife"},{"key":"1988_CR3","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1200\/JCO.2001.19.3.666","volume":"19","author":"JP Stein","year":"2001","unstructured":"Stein JP, Lieskovsky G, Cote R, Groshen S, Feng AC, Boyd S, Skinner E, Bochner B, Thangathurai D, Mikhail M, Raghavan D, Skinner DG (2001) Radical cystectomy in the treatment of invasive bladder cancer: long-term results in 1,054 patients. J Clin Oncol 19:666\u2013675. https:\/\/doi.org\/10.1200\/JCO.2001.19.3.666","journal-title":"J Clin Oncol"},{"key":"1988_CR48","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1007\/s13402-018-0399-z","volume":"41","author":"X Sun","year":"2018","unstructured":"Sun X, Martin RCG, Zheng Q, Farmer R, Pandit H, Li X, Jacob K, Suo J, Li Y (2018) Drug-induced expression of EpCAM contributes to therapy resistance in esophageal adenocarcinoma. Cell Oncol (Dordr) 41:651\u2013662. https:\/\/doi.org\/10.1007\/s13402-018-0399-z","journal-title":"Cell Oncol (Dordr)"},{"key":"1988_CR34","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1186\/s12967-024-05138-2","volume":"22","author":"X Sun","year":"2024","unstructured":"Sun X, Nong M, Meng F, Sun X, Jiang L, Li Z, Zhang P (2024) Architecting the metabolic reprogramming survival risk framework in LUAD through single-cell landscape analysis: three-stage ensemble learning with genetic algorithm optimization. J Transl Med 22:353. https:\/\/doi.org\/10.1186\/s12967-024-05138-2","journal-title":"J Transl Med"},{"key":"1988_CR32","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1186\/s12967-024-05421-2","volume":"22","author":"Y Sun","year":"2024","unstructured":"Sun Y, Wu J, Zhang Q, Wang P, Zhang J, Yuan Y (2024) Single-cell hdWGCNA reveals metastatic protective macrophages and development of deep learning model in uveal melanoma. J Transl Med 22:695. https:\/\/doi.org\/10.1186\/s12967-024-05421-2","journal-title":"J Transl Med"},{"key":"1988_CR46","doi-asserted-by":"publisher","first-page":"4554","DOI":"10.1038\/s41467-022-32101-w","volume":"13","author":"Y Tan","year":"2022","unstructured":"Tan Y, Li J, Zhao G, Huang K-C, Cardenas H, Wang Y, Matei D, Cheng J-X (2022) Metabolic reprogramming from glycolysis to fatty acid uptake and beta-oxidation in platinum-resistant cancer cells. Nat Commun 13:4554. https:\/\/doi.org\/10.1038\/s41467-022-32101-w","journal-title":"Nat Commun"},{"key":"1988_CR31","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1126\/science.aad0501","volume":"352","author":"I Tirosh","year":"2016","unstructured":"Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin J-R, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CGK, Kazer SW, Gaillard A, Kolb KE, Villani A-C, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jan\u00e9-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA (2016) Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352:189\u2013196. https:\/\/doi.org\/10.1126\/science.aad0501","journal-title":"Science"},{"key":"1988_CR52","doi-asserted-by":"publisher","first-page":"183","DOI":"10.4252\/wjsc.v10.i12.183","volume":"10","author":"ME Toledo-Guzm\u00e1n","year":"2018","unstructured":"Toledo-Guzm\u00e1n ME, Bigoni-Ord\u00f3\u00f1ez GD, Ib\u00e1\u00f1ez Hern\u00e1ndez M, Ortiz-S\u00e1nchez E (2018) Cancer stem cell impact on clinical oncology. World J Stem Cells 10:183\u2013195. https:\/\/doi.org\/10.4252\/wjsc.v10.i12.183","journal-title":"World J Stem Cells"},{"key":"1988_CR26","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1016\/j.ccell.2022.08.010","volume":"40","author":"M Wang","year":"2022","unstructured":"Wang M, Chen X, Tan P, Wang Y, Pan X, Lin T, Jiang Y, Wang B, Xu H, Wang Y, Yang Y, Wang J, Zhao L, Zhang J, Zhong A, Peng Y, Du J, Zhang Q, Zheng J, Chen J, Dai S, Na F, Lu Z, Liu J, Zheng X, Yang L, Zhang P, Han P, Gong Q, Zhong Q, Xiao K, Yang H, Deng H, Zhao Y, Shi H, Man J, Gou M, Zhao C, Dai L, Xue Z, Chen L, Wang Y, Zeng M, Huang C, Wei Q, Wei Y, Liu Y, Chen C (2022) Acquired semi-squamatization during chemotherapy suggests differentiation as a therapeutic strategy for bladder cancer. Cancer Cell 40:1044\u20131059e8. https:\/\/doi.org\/10.1016\/j.ccell.2022.08.010","journal-title":"Cancer Cell"},{"key":"1988_CR17","doi-asserted-by":"publisher","first-page":"110671","DOI":"10.1016\/j.ygeno.2023.110671","volume":"115","author":"Y Wang","year":"2023","unstructured":"Wang Y, Liu B, Zhao G, Lee Y, Buzdin A, Mu X, Zhao J, Chen H, Li X (2023) Spatial transcriptomics: Technologies, applications and experimental considerations. Genomics 115:110671. https:\/\/doi.org\/10.1016\/j.ygeno.2023.110671","journal-title":"Genomics"},{"key":"1988_CR22","doi-asserted-by":"publisher","first-page":"109928","DOI":"10.1016\/j.isci.2024.109928","volume":"27","author":"L Wang","year":"2024","unstructured":"Wang L, Izadmehr S, Sfakianos JP, Tran M, Beaumont KG, Brody R, Cordon-Cardo C, Horowitz A, Sebra R, Oh WK, Bhardwaj N, Galsky MD, Zhu J (2024) Single-cell transcriptomic-informed deconvolution of bulk data identifies immune checkpoint blockade resistance in urothelial cancer. iScience 27:109928. https:\/\/doi.org\/10.1016\/j.isci.2024.109928","journal-title":"iScience"},{"key":"1988_CR55","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1083\/jcb.200101113","volume":"154","author":"W Witke","year":"2001","unstructured":"Witke W, Li W, Kwiatkowski DJ, Southwick FS (2001) Comparisons of CapG and gelsolin-null macrophages: demonstration of a unique role for CapG in receptor-mediated ruffling, phagocytosis, and vesicle rocketing. J Cell Biol 154:775\u2013784. https:\/\/doi.org\/10.1083\/jcb.200101113","journal-title":"J Cell Biol"},{"key":"1988_CR44","doi-asserted-by":"publisher","first-page":"1666","DOI":"10.1158\/0008-5472.CAN-22-2233","volume":"83","author":"R Xie","year":"2023","unstructured":"Xie R, Cheng L, Huang M, Huang L, Chen Z, Zhang Q, Li H, Lu J, Wang H, Zhou Q, Huang J, Chen X, Lin T (2023) NAT10 Drives Cisplatin Chemoresistance by Enhancing ac4C-Associated DNA Repair in Bladder Cancer. Cancer Res 83:1666\u20131683. https:\/\/doi.org\/10.1158\/0008-5472.CAN-22-2233","journal-title":"Cancer Res"},{"key":"1988_CR4","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1111\/j.1464-410X.2010.09912.x","volume":"108","author":"FA Yafi","year":"2011","unstructured":"Yafi FA, Aprikian AG, Chin JL, Fradet Y, Izawa J, Estey E, Fairey A, Rendon R, Cagiannos I, Lacombe L, Lattouf J-B, Bell D, Drachenberg D, Kassouf W (2011) Contemporary outcomes of 2287 patients with bladder cancer who were treated with radical cystectomy: a Canadian multicentre experience. BJU Int 108:539\u2013545. https:\/\/doi.org\/10.1111\/j.1464-410X.2010.09912.x","journal-title":"BJU Int"},{"key":"1988_CR15","doi-asserted-by":"publisher","unstructured":"Zhang Y, Wang D, Peng N, Tang L, Ouyang J, Xiong F, Guo C, Tang Y, Zhou Y, Liao Q, Wu X, Wang H, Yu J, Li Y, Li X, Li G, Zeng Z, Tan X, Xiong W (2021) Single-cell RNA sequencing in cancer research. J Exp Clin Cancer Res 40. https:\/\/doi.org\/10.1186\/s13046-021-01874-1","DOI":"10.1186\/s13046-021-01874-1"},{"key":"1988_CR19","doi-asserted-by":"publisher","first-page":"e18516","DOI":"10.1111\/jcmm.18516","volume":"28","author":"P Zhang","year":"2024","unstructured":"Zhang P, Feng J, Rui M, Xie J, Zhang L, Zhang Z (2024b) Integrating machine learning and single-cell analysis to uncover lung adenocarcinoma progression and prognostic biomarkers. J Cell Mol Med 28:e18516. https:\/\/doi.org\/10.1111\/jcmm.18516","journal-title":"J Cell Mol Med"},{"key":"1988_CR18","doi-asserted-by":"publisher","first-page":"4479","DOI":"10.1002\/tox.24230","volume":"39","author":"P Zhang","year":"2024","unstructured":"Zhang P, Wu X, Wang D, Zhang M, Zhang B, Zhang Z (2024a) Unraveling the role of low-density lipoprotein-related genes in lung adenocarcinoma: Insights into tumor microenvironment and clinical prognosis. Environ Toxicol 39:4479\u20134495. https:\/\/doi.org\/10.1002\/tox.24230","journal-title":"Environ Toxicol"},{"key":"1988_CR39","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1016\/j.jad.2025.02.063","volume":"377","author":"X Zhao","year":"2025","unstructured":"Zhao X, Wang Y, Li J, Liu W, Yang Y, Qiao Y, Liao J, Chen M, Li D, Wu B, Huang D, Wu D (2025) A machine-learning-derived online prediction model for depression risk in COPD patients: A retrospective cohort study from CHARLS. J Affect Disord 377:284\u2013293. https:\/\/doi.org\/10.1016\/j.jad.2025.02.063","journal-title":"J Affect Disord"}],"container-title":["Functional & Integrative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-01988-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10142-026-01988-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-026-01988-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T04:26:17Z","timestamp":1784607977000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10142-026-01988-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,21]]},"references-count":54,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["1988"],"URL":"https:\/\/doi.org\/10.1007\/s10142-026-01988-9","relation":{},"ISSN":["1438-793X","1438-7948"],"issn-type":[{"value":"1438-793X","type":"print"},{"value":"1438-7948","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,21]]},"assertion":[{"value":"5 March 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 July 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 July 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 July 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"This study was conducted in accordance with all relevant institutional and international ethical guidelines. Formal ethical approval for all experiments was obtained prior to the commencement of patient enrollment and animal studies from the Second Hospital of Lanzhou University. All research involving human participants was reviewed and approved by the Institutional Review Board (IRB) \/ Ethics Committee of the Second Hospital of Lanzhou University (Approval No. 2025\u00a0A-321). All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of the Second Hospital of Lanzhou University (Approval No. D2025-644). Animal studies were conducted in compliance with the ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines and institutional regulations for laboratory animal welfare. No patient recruitment or sample collection was performed before ethical approval was granted. The clinical trial number was not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"197"}}