Deep Learning Based Identification of Tissue of Origin for Carcinomas of Unknown Primary utilizing micro-RNA expression

Carcinoma of Unknown Primary (CUP) is a subset of metastatic cancers in which the primary tissue source, or origin, remains unidentified. CUP accounts for three to five percent of all malignancies [2]. Representing an exceptionally aggressive category of metastatic cancers, the median survival of those diagnosed with CUP is approximately three to six months [1]. The tissue in which a cancer arises plays a key role in our understanding of altered gene expression, altered cellular pathways, and sensitivities to various forms of cell death in cancer cells [3]. Thus, the lack of knowledge on tissue of origin makes it difficult to devise tailored treatments for patients with CUP [4]. Developing clinically implementable methods to identify the tissue of origin of the primary site is crucial in treating CUP patients [4]. In particular, the expression profiles of non-coding RNAs can provide insight into the tissue of origin for CUP. Non-coding RNAs provide a robust route to clinical implementation due to their resistance against chemical degradation [5]. In this work, we investigate the potential of microRNAs as highly accurate biomarkers for detecting the tissue of origin for metastatic cancers. We further hypothesize that data driven approaches can identify specific microRNA biomarker targets. We used microRNA expression data from the Cancer Genome Atlas (TCGA) dataset [6] and assessed various machine learning approaches. Our results show that it is possible to design robust classifiers to detect the tissue of origin for metastatic samples on the TCGA dataset with an accuracy of up to 96%, which may be utilized in situations of CUP. As a validation of our classifiers, we evaluated the accuracy on a separate set of 194 primary tumor samples from the Sequence Read Archive (SRA) [7]. Our findings demonstrate that deep learning techniques enhance prediction accuracy. We progressed from an initial accuracy prediction of 62.5% with decision trees to 93.2% with logistic regression, finally achieving 96.1% accuracy using deep learning on metastatic samples. On the SRA validation set, a lower accuracy of 41.2% was achieved by decision tree, while deep learning achieved a higher accuracy of 81.2%. Notably, our feature importance analysis showed the top three important biomarkers for predicting tissue of origin to be mir-10b, mir-205, and mir-196b, which aligns with previous work [10]. Our findings highlight the potential of using machine learning techniques to devise tests for detecting tissue of origin for CUP. Since microRNAs are carried throughout the body via vesicles secreted from cells, they may serve as key biomarkers for liquid biopsy due to their presence in blood plasma [11]. Our work serves as a foundation towards developing blood-based cancer detection tests based on microRNA presence.