Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer
- Autores: He Y.1, Wei H.1, Liao S.1, Ou R.2, Xiong Y.1, Zuo Y.3, Yang L.1
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Afiliações:
- College of Bioinformatics Science and Technology, Harbin Medical University
- College of Basic Medicine, Harbin Medical University
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University
- Edição: Volume 19, Nº 10 (2024)
- Páginas: 963-976
- Seção: Life Sciences
- URL: https://ter-arkhiv.ru/1574-8936/article/view/643767
- DOI: https://doi.org/10.2174/0115748936288453240124082031
- ID: 643767
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Resumo
Background:Bladder cancer is a prevalent malignancy globally, characterized by rising incidence and mortality rates. Stratifying bladder cancer patients into different subtypes is crucial for the effective treatment of this form of cancer. Therefore, there is a need to develop a stratification model specific to bladder cancer.
Purpose:This study aims to establish a prognostic prediction model for bladder cancer, with the primary goal of accurately predicting prognosis and treatment outcomes.
Methods:We collected datasets from 10 bladder cancer samples sourced from the Gene Expression Omnibus (GEO), the Cancer Genome Atlas (TCGA) databases, and IMvigor210 dataset. The machine learning based algorithms were used to generate 96 models for establishing the risk score for each patient. Based on the risk score, all the patients was classified into two different risk score groups.
Results:The two groups of bladder cancer patients exhibited significant differences in prognosis, biological functions, and drug sensitivity. Nomogram model demonstrated that the risk score had a robust predictive effect with good clinical utility.
Conclusion:The risk score constructed in this study can be utilized to predict the prognosis, response to drug treatment, and immunotherapy of bladder cancer patients, providing assistance for personalized clinical treatment of bladder cancer.
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Sobre autores
Yuanyuan He
College of Bioinformatics Science and Technology, Harbin Medical University
Email: info@benthamscience.net
Haodong Wei
College of Bioinformatics Science and Technology, Harbin Medical University
Email: info@benthamscience.net
Siqing Liao
College of Bioinformatics Science and Technology, Harbin Medical University
Email: info@benthamscience.net
Ruiming Ou
College of Basic Medicine, Harbin Medical University
Email: info@benthamscience.net
Yuqiang Xiong
College of Bioinformatics Science and Technology, Harbin Medical University
Email: info@benthamscience.net
Yongchun Zuo
The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University
Autor responsável pela correspondência
Email: info@benthamscience.net
Lei Yang
College of Bioinformatics Science and Technology, Harbin Medical University
Autor responsável pela correspondência
Email: info@benthamscience.net
Bibliografia
- Sung H, Ferlay J, Siegel RL, et al. Global cancer statistics 2020: GLOBOCAN estimates of Incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2021; 71(3): 209-49. doi: 10.3322/caac.21660 PMID: 33538338
- Robertson AG, Kim J, Al-Ahmadie H, et al. Comprehensive molecular characterization of muscle-invasive bladder cancer. Cell 2017; 171(3): 540-556.e25. doi: 10.1016/j.cell.2017.09.007 PMID: 28988769
- van Kessel KEM, Zuiverloon TCM, Alberts AR, Boormans JL, Zwarthoff EC. Targeted therapies in bladder cancer: An overview of in vivo research. Nat Rev Urol 2015; 12(12): 681-94. doi: 10.1038/nrurol.2015.231 PMID: 26390971
- Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2018; 68(6): 394-424. doi: 10.3322/caac.21492 PMID: 30207593
- Kamoun A, de Reyniès A, Allory Y, et al. A consensus molecular classification of muscle-invasive bladder cancer. Eur Urol 2020; 77(4): 420-33. doi: 10.1016/j.eururo.2019.09.006 PMID: 31563503
- Jubber I, Ong S, Bukavina L, et al. Epidemiology of bladder cancer in 2023: A systematic review of risk factors. Eur Urol 2023; 84(2): 176-90. doi: 10.1016/j.eururo.2023.03.029 PMID: 37198015
- Tutsoy O, Tanrikulu MY. Priority and age specific vaccination algorithm for the pandemic diseases: A comprehensive parametric prediction model. BMC Med Inform Decis Mak 2022; 22(1): 4. doi: 10.1186/s12911-021-01720-6 PMID: 34991566
- Tutsoy O. Graph theory based large-scale machine learning with multi-dimensional constrained optimization approaches for exact epidemiological modeling of pandemic diseases. IEEE Trans Pattern Anal Mach Intell 2023; 45(8): 9836-45. doi: 10.1109/TPAMI.2023.3256421 PMID: 37028303
- Hänzelmann S, Castelo R, Guinney J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics 2013; 14(1): 7. doi: 10.1186/1471-2105-14-7 PMID: 23323831
- Su D, Wang S, Xi Q, et al. Prognostic and predictive value of a metabolic risk score model in breast cancer: An immunogenomic landscape analysis. Brief Funct Genomics 2022; 21(2): 128-41. doi: 10.1093/bfgp/elab040 PMID: 34755827
- Su D, Lu Q, Pan Y, et al. Immune-related gene-based prognostic signature for the risk stratification analysis of breast cancer. Curr Bioinform 2022; 17(2): 196-205. doi: 10.2174/1574893616666211005110732
- Wang S, Zhang Q, Yu C, Cao Y, Zuo Y, Yang L. Immune cell infiltration-based signature for prognosis and immunogenomic analysis in breast cancer. Brief Bioinform 2021; 22(2): 2020-31. doi: 10.1093/bib/bbaa026 PMID: 32141494
- Wang S, Xiong Y, Zhang Q, et al. Clinical significance and immunogenomic landscape analyses of the immune cell signature based prognostic model for patients with breast cancer. Brief Bioinform 2020. PMID: 33302293
- Miao YR, Zhang Q, Lei Q, et al. ImmuCellAI: A unique method for comprehensive T-cell subsets abundance prediction and its application in cancer immunotherapy. Adv Sci 2020; 7(7): 1902880. doi: 10.1002/advs.201902880 PMID: 32274301
- Yang L, Lv Y, Wang S, et al. Identifying FL11 subtype by characterizing tumor immune microenvironment in prostate adenocarcinoma via Chous 5-steps rule. Genomics 2020; 112(2): 1500-15. doi: 10.1016/j.ygeno.2019.08.021 PMID: 31472243
- Xiao Y, Ma D, Zhao S, et al. Multi-omics profiling reveals distinct microenvironment characterization and suggests immune escape mechanisms of triple-negative breast cancer. Clin Cancer Res 2019; 25(16): 5002-14. doi: 10.1158/1078-0432.CCR-18-3524 PMID: 30837276
- Leone RD, Powell JD. Metabolism of immune cells in cancer. Nat Rev Cancer 2020; 20(9): 516-31. doi: 10.1038/s41568-020-0273-y PMID: 32632251
- Xiao Y, Ma D, Yang YS, et al. Comprehensive metabolomics expands precision medicine for triple-negative breast cancer. Cell Res 2022; 32(5): 477-90. doi: 10.1038/s41422-022-00614-0 PMID: 35105939
- Chu G, Ji X, Wang Y, Niu H. Integrated multiomics analysis and machine learning refine molecular subtypes and prognosis for muscle-invasive urothelial cancer. Mol Ther Nucleic Acids 2023; 33: 110-26. doi: 10.1016/j.omtn.2023.06.001 PMID: 37449047
- Liu Z, Liu L, Weng S, et al. Machine learning-based integration develops an immune-derived lncRNA signature for improving outcomes in colorectal cancer. Nat Commun 2022; 13(1): 816. doi: 10.1038/s41467-022-28421-6 PMID: 35145098
- Ning J, Sun K, Fan X, et al. Use of machine learning-based integration to develop an immune-related signature for improving prognosis in patients with gastric cancer. Sci Rep 2023; 13(1): 7019. doi: 10.1038/s41598-023-34291-9 PMID: 37120631
- Liu J, Shi Y, Zhang Y. Multi-omics identification of an immunogenic cell death-related signature for clear cell renal cell carcinoma in the context of 3P medicine and based on a 101-combination machine learning computational framework. EPMA J 2023; 14(2): 275-305. doi: 10.1007/s13167-023-00327-3 PMID: 37275552
- Qin H, Abulaiti A, Maimaiti A, et al. Integrated machine learning survival framework develops a prognostic model based on inter-crosstalk definition of mitochondrial function and cell death patterns in a large multicenter cohort for lower-grade glioma. J Transl Med 2023; 21(1): 588. doi: 10.1186/s12967-023-04468-x PMID: 37660060
- Wang L, Liu Z, Liang R, et al. Comprehensive machine-learning survival framework develops a consensus model in large-scale multicenter cohorts for pancreatic cancer. eLife 2022; 11: e80150. doi: 10.7554/eLife.80150 PMID: 36282174
- Colaprico A, Silva TC, Olsen C, et al. TCGAbiolinks: An R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res 2016; 44(8): e71-1. doi: 10.1093/nar/gkv1507 PMID: 26704973
- Mariathasan S, Turley SJ, Nickles D, et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature 2018; 554(7693): 544-8. doi: 10.1038/nature25501 PMID: 29443960
- Wu Y, Yang S, Ma J, et al. Spatiotemporal immune landscape of colorectal cancer liver metastasis at single-cell level. Cancer Discov 2022; 12(1): 134-53. doi: 10.1158/2159-8290.CD-21-0316 PMID: 34417225
- Jassal B, Matthews L, Viteri G, et al. The reactome pathway knowledgebase. Nucleic Acids Res 2020; 48(D1): D498-503. PMID: 31691815
- Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 2012; 28(6): 882-3. doi: 10.1093/bioinformatics/bts034 PMID: 22257669
- Liu Z, Guo C, Dang Q, et al. Integrative analysis from multi-center studies identities a consensus machine learning-derived lncRNA signature for stage II/III colorectal cancer. EBioMedicine 2022; 75: 103750. doi: 10.1016/j.ebiom.2021.103750 PMID: 34922323
- Xu H, Liu Z, Weng S, et al. Artificial intelligence‐driven consensus gene signatures for improving bladder cancer clinical outcomes identified by multi‐center integration analysis. Mol Oncol 2022; 16(22): 4023-42. doi: 10.1002/1878-0261.13313 PMID: 36083778
- Pickett KL, Suresh K, Campbell KR, Davis S, Juarez-Colunga E. Random survival forests for dynamic predictions of a time-to-event outcome using a longitudinal biomarker. BMC Med Res Methodol 2021; 21(1): 216. doi: 10.1186/s12874-021-01375-x PMID: 34657597
- Goeman JJ. L1 penalized estimation in the Cox proportional hazards model. Biom J 2010; 52(1): 70-84. doi: 10.1002/bimj.200900028 PMID: 19937997
- Robinson MD, McCarthy DJ, Smyth GK. edgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26(1): 139-40. doi: 10.1093/bioinformatics/btp616 PMID: 19910308
- Wu T, Hu E, Xu S, et al. ClusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation 2021; 2(3): 100141. doi: 10.1016/j.xinn.2021.100141 PMID: 34557778
- Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005; 102(43): 15545-50. doi: 10.1073/pnas.0506580102 PMID: 16199517
- Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst 2015; 1(6): 417-25. doi: 10.1016/j.cels.2015.12.004 PMID: 26771021
- Bhattacharya S, Dunn P, Thomas CG, et al. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci Data 2018; 5(1): 180015. doi: 10.1038/sdata.2018.15 PMID: 29485622
- Charoentong P, Finotello F, Angelova M, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep 2017; 18(1): 248-62. doi: 10.1016/j.celrep.2016.12.019 PMID: 28052254
- Maeser D, Gruener RF, Huang RS. oncoPredict: An R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data. Brief Bioinform 2021; 22(6): bbab260. doi: 10.1093/bib/bbab260 PMID: 34260682
- Yang W, Soares J, Greninger P, et al. Genomics of drug sensitivity in cancer (GDSC): A resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res 2013; 41(Database issue): D955-61. PMID: 23180760
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