Identification of Gene Signatures and Expression Patterns During Epithelial-to-Mesenchymal Transition From Single-Cell Expression Atlas

Abstract

Cancer, which refers to abnormal cell proliferative diseases with systematic pathogenic potential, is one of the leading threats to human health. The final causes for patients’ deaths are usually cancer recurrence, metastasis, and drug resistance against continuing therapy. Epithelial-to-mesenchymal transition (EMT), which is the transformation of tumor cells (TCs), is a prerequisite for pathogenic cancer recurrence, metastasis, and drug resistance. Conventional biomarkers can only define and recognize large tissues with obvious EMT markers but cannot accurately monitor detailed EMT processes. In this study, a systematic workflow was established integrating effective feature selection, multiple machine learning models [Random forest (RF), Support vector machine (SVM)], rule learning, and functional enrichment analyses to find new biomarkers and their functional implications for distinguishing single-cell isolated TCs with unique epithelial or mesenchymal markers using public single-cell expression profiling. Our discovered signatures may provide an effective and precise transcriptomic reference to monitor EMT progression at the single-cell level and contribute to the exploration of detailed tumorigenesis mechanisms during EMT.