Predicting Distant Metastatic Sites in Cancer Using miRNA and mRNA Expression Data

Background: Cancer patients with metastasis face a much lower survival rate and a higher risk of recurrence than those without metastasis. So far, several learning methods have been proposed to predict cancer metastasis, but most of these methods are intended to predict lymph node metastasis rather than distant metastasis. Distant metastasis is more difficult to predict than lymph node metastasis because distant metastasis is detected after a comprehensive examination of the entire body, and there are not enough publicly available tumor samples with distant metastasis that can be used for training learning methods. Predicting distant metastatic sites is even more challenging than predicting whether distant metastasis will occur or not. Methods: 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, brain, liver, lung, and other organs), and a single sample can have multiple labels for multiple metastatic sites. We transformed the multi‐label and multi‐class problem into multiple single‐label binary problems. For each metastatic site, we built a random forest model that deals with binary classification and linked the models along a chain. Results: Testing the model on miRNA and mRNA expression datasets of several cancer types showed a high performance in all performance measures. In the comparison of our model with other methods, our method outperformed the others. Conclusion: We developed a new method for predicting multiple metastatic sites using miRNA and mRNA expression data. The technique will be useful in predicting distant metastatic sites before distant metastasis occurs, which in turn will help clinicians determine treatment options for cancer patients.