Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction

AbstractmicroRNAs (miRNAs) regulate gene expression at the post-transcriptional level and they play an important role in various biological processes in the human body. Therefore, identifying their regulation mechanisms is essential for the diagnostics and therapeutics for a wide range of diseases. There have been a large number of researches which use gene expression profiles to resolve this problem. However, the current methods have their own limitations. Some of them only identify the correlation of miRNA and mRNA expression levels instead of the causal or regulatory relationships while others infer the causality but with a high computational complexity. To overcome these issues, in this study, we propose a method to identify miRNA-mRNA regulatory relationships in breast cancer using the invariant causal prediction. The key idea of invariant causal prediction is that the cause miRNAs of their target mRNAs are the ones which have persistent causal relationships with the target mRNAs across different environments. In this research, we aim to find miRNA targets which are consistent across different breast cancer subtypes. Thus, first of all, we apply the Pam50 method to categorise BRCA samples into different ‘‘environment” groups based on different cancer subtypes. Then we use the invariant causal prediction method to find miRNA-mRNA regulatory relationships across subtypes. We validate the results with the miRNA-transfected experimental data and the results show that our method outperforms the state-of-the-art methods. In addition, we also integrate this new method with the Pearson correlation analysis method and Lasso in an ensemble method to take the advantages of these methods. We then validate the results of the ensemble method with the experimentally confirmed data and the ensemble method shows the best performance, even comparing to the proposed causal method. Functional enrichment analyses show that miRNAs in the regulatory relationship predicated by the proposed causal method tend to synergistically regulate target genes, indicating the usefulness of these methods, and the identified miRNA targets could be used in the design of wet-lab experiments to discover the causes of breast cancer.Author summaryCancer is a disease of cells in human body and it causes a high rate of deaths world wide. There has been evidence that non-coding RNAs are key players in the development and progression of cancer. Among the different types of non-coding RNAs, miRNAs, which are short non-coding RNAs, regulate gene expression and play an important role in different biological processes as well as various cancer types. To design better diagnostic and therapeutic plans for cancer patients, we need to know the roles of miRNAs in cancer initialisation and development, and their regulation mechanisms in the human body. In this study, we propose algorithms to identify miRNA-mRNA regulatory relationships in breast cancer. Comparing our methods with existing methods in predicting miRNA targets, our methods show a better performance. The estimated miRNA targets from our methods could be a potential source for further wet-lab experiments to discover the causes of breast cancer.