Integrated multiomics analysis and machine learning refine molecular subtypes and prognosis for muscle-invasive urothelial cancer

• Published in: Molecular therapy. Nucleic acids Vol. 33; pp. 110 - 126
• Main Authors: Chu, Guangdi, Ji, Xiaoyu, Wang, Yonghua, Niu, Haitao
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 12.09.2023; American Society of Gene & Cell Therapy; Elsevier
• Subjects: immunotherapy; machine learning; MT: Bioinformatics; multiomics; muscle-invasive urothelial cancer; Original; prognosis; MT: Bioinformatics; multiomics; machine learning; prognosis; immunotherapy; muscle-invasive urothelial cancer
• ISSN: 2162-2531; 2162-2531
• DOI: 10.1016/j.omtn.2023.06.001

Muscle-invasive urothelial cancer (MUC), characterized by high aggressiveness and significant heterogeneity, is currently lacking highly precise individualized treatment options. We used a computational pipeline to synthesize multiomics data from MUC patients using 10 clustering algorithms, which were then combined with 10 machine learning algorithms to identify molecular subgroups of high resolution and develop a robust consensus machine learning-driven signature (CMLS). Through multiomics clustering, we identified three cancer subtypes (CSs) that are related to prognosis, with CS2 exhibiting the most favorable prognostic outcome. Subsequent screening enabled identification of 12 hub genes that constitute a CMLS with robust predictive power for prognosis. The low-CMLS group exhibited a more favorable prognosis and greater responsiveness to immunotherapy and was more likely to exhibit the “hot tumor” phenotype. The high-CMLS group had a poor prognosis and lower likelihood of benefitting from immunotherapy, but dasatinib and romidepsin may serve as promising treatments for them. Comprehensive analysis of multiomics data can offer important insights and further refine the molecular classification of MUC. Identification of CMLS represents a valuable tool for early prediction of patient prognosis and for screening potential candidates likely to benefit from immunotherapy, with broad implications for clinical practice. [Display omitted] Niu and colleagues first combined 5 types of multiomics data, 10 clustering algorithms, and 99 machine learning algorithm combinations to refine the molecular subtype of MUC and build a robust prognostic signature, which will improve precise treatment and treatment options for MUC.