{"title":"Predicting distant metastatic sites of cancer using perturbed correlations of miRNAs with competing endogenous RNAs","authors":"Myeonghoon Cho , Byungkyu Park , Kyungsook Han","doi":"10.1016/j.compbiolchem.2025.108353","DOIUrl":null,"url":null,"abstract":"<div><div>Cancer metastasis is the dissemination of tumor cells from the primary tumor site to other parts of the body via the lymph system or bloodstream. Metastasis is the leading cause of cancer associated death. Despite the significant advances in cancer research and treatment over the past decades, metastasis is not fully understood and difficult to predict in advance. In particular, distant metastasis is more difficult to predict than lymph node metastasis, which is the spread of cancer cells to nearby lymph nodes. Distant metastatic sites is even more difficult to predict than the occurrence of distant metastasis because the problem of predicting distant metastatic sites is a multi-class and multi-label classification problem; there are more than two classes for distant metastatic sites (bone, liver, lung, and other organs), and a single sample can have multiple labels for multiple metastatic sites. This paper presents a new method for predicting distant metastatic sites based on correlation changes of miRNAs with competing endogenous RNAs (ceRNAs) in individual cancer patients. Testing the method on independent datasets of several cancer types demonstrated a high prediction performance. In comparison of our method with other state of the art methods, our method showed a much better and more stable performance than the others. Our method can be used as useful aids in determining treatment options by predicting if and where metastasis will occur in cancer patients at early stages.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"115 ","pages":"Article 108353"},"PeriodicalIF":2.6000,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Biology and Chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1476927125000131","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Cancer metastasis is the dissemination of tumor cells from the primary tumor site to other parts of the body via the lymph system or bloodstream. Metastasis is the leading cause of cancer associated death. Despite the significant advances in cancer research and treatment over the past decades, metastasis is not fully understood and difficult to predict in advance. In particular, distant metastasis is more difficult to predict than lymph node metastasis, which is the spread of cancer cells to nearby lymph nodes. Distant metastatic sites is even more difficult to predict than the occurrence of distant metastasis because the problem of predicting distant metastatic sites is a multi-class and multi-label classification problem; there are more than two classes for distant metastatic sites (bone, liver, lung, and other organs), and a single sample can have multiple labels for multiple metastatic sites. This paper presents a new method for predicting distant metastatic sites based on correlation changes of miRNAs with competing endogenous RNAs (ceRNAs) in individual cancer patients. Testing the method on independent datasets of several cancer types demonstrated a high prediction performance. In comparison of our method with other state of the art methods, our method showed a much better and more stable performance than the others. Our method can be used as useful aids in determining treatment options by predicting if and where metastasis will occur in cancer patients at early stages.
期刊介绍:
Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered.
Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered.
Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.