AUTHOR=Zhao Ning , Guo Maozu , Wang Kuanquan , Zhang Chunlong , Liu Xiaoyan 

TITLE=Identification of Pan-Cancer Prognostic Biomarkers Through Integration of Multi-Omics Data

JOURNAL=Frontiers in Bioengineering and Biotechnology

VOLUME=8

YEAR=2020

URL=https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2020.00268

DOI=10.3389/fbioe.2020.00268

ISSN=2296-4185

ABSTRACT=<p>Prognostic biomarkers dedicating to treat cancer are very difficult to identify. Although high-throughput sequencing technology allows us to mine prognostic biomarkers much deeper by analyzing omics data, there is lack of effective methods to comprehensively utilize multi-omics data. In this work, we integrated multi-omics data [DNA methylation (DM), gene expression (GE), somatic copy number alternation, and microRNA expression (ME)] and proposed a method to rank genes by desiring a “Score.” Applying the method, cancer-specific prognostic biomarkers for 13 cancers were obtained. The prognostic powers of the biomarkers were further assessed by C-indexes (ranged from 0.76 to 0.96). Moreover, by comparing the 13 survival-related gene lists, seven genes (<italic>SLK</italic>, <italic>API5</italic>, <italic>BTBD2</italic>, <italic>PTAR1</italic>, <italic>VPS37A</italic>, <italic>EIF2B1</italic>, and <italic>ZRANB1</italic>) were found to be associated with prognosis in a variety of cancers. In particular, <italic>SLK</italic> was more likely to be cancer-related due to its high missense mutation rate and associated with cell adhesion. Furthermore, after network analysis, <italic>EPRS</italic>, <italic>HNRNPA2B1</italic>, <italic>BPTF</italic>, <italic>LRRK1</italic>, and <italic>PUM1</italic> were demonstrated to have a broad correlation with cancers. In summary, our method has a better integration of multi-omics data that can be extended to the researches of other diseases. And the prognostic biomarkers had a better prognostic power than previous methods. Our results could provide a reference for translational medicine researchers and clinicians.</p>