Uncovering Prognosis-Related Genes and Pathways by Multi-Omics Analysis in Lung Cancer

• Main Authors: Ken Asada, Kazuma Kobayashi, Samuel Joutard, Masashi Tubaki, Satoshi Takahashi, Ken Takasawa, Masaaki Komatsu, Syuzo Kaneko, Jun Sese, Ryuji Hamamoto
• Format: Article
• Language: English
• Published: MDPI AG 2020-03-01
• Series: Biomolecules
• Subjects: multi-omics analysis; lung cancer; survival-associated genes
• Online Access: https://www.mdpi.com/2218-273X/10/4/524

Lung cancer is one of the leading causes of death worldwide. Therefore, understanding the factors linked to patient survival is essential. Recently, multi-omics analysis has emerged, allowing for patient groups to be classified according to prognosis and at a more individual level, to support the use of precision medicine. Here, we combined RNA expression and miRNA expression with clinical information, to conduct a multi-omics analysis, using publicly available datasets (the cancer genome atlas (TCGA) focusing on lung adenocarcinoma (LUAD)). We were able to successfully subclass patients according to survival. The classifiers we developed, using inferred labels obtained from patient subtypes showed that a support vector machine (SVM), gave the best classification results, with an accuracy of 0.82 with the test dataset. Using these subtypes, we ranked genes based on RNA expression levels. The top 25 genes were investigated, to elucidate the mechanisms that underlie patient prognosis. Bioinformatics analyses showed that the expression levels of six out of 25 genes (<i>ERO1B</i>, <i>DPY19L1</i>, <i>NCAM1</i>, <i>RET</i>, <i>MARCH1</i>, and <i>SLC7A8</i>) were associated with LUAD patient survival (<i>p</i> < 0.05), and pathway analyses indicated that major cancer signaling was altered in the subtypes.