Landscape of cancer diagnostic biomarkers from specifically expressed genes

Abstract Although there has been great progress in cancer treatment, cancer remains a serious health threat to humans because of the lack of biomarkers for diagnosis, especially for early-stage diagnosis. In this study, we comprehensively surveyed the specifically expressed genes (SEGs) using the SE...

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Bibliographic Details
Published in:Briefings in bioinformatics 2020-12, Vol.21 (6), p.2175-2184
Main Authors: Lv, Yao, Lin, Sheng-Yan, Hu, Fei-Fei, Ye, Zheng, Zhang, Qiong, Wang, Yan, Guo, An-Yuan
Format: Article
Language:English
Subjects:
Biomarkers
Cancer
Cancer research
Diagnosis
Diagnostic systems
Drugs
Gene expression
Genes
Genomes
Genotypes
Health risks
Kidney cancer
Sensitivity
Solid tumors
Transcription factors
Tumors
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Summary:Abstract Although there has been great progress in cancer treatment, cancer remains a serious health threat to humans because of the lack of biomarkers for diagnosis, especially for early-stage diagnosis. In this study, we comprehensively surveyed the specifically expressed genes (SEGs) using the SEGtool based on the big data of gene expression from the The Cancer Genome Atlas (TCGA) and the Genotype–Tissue Expression (GTEx) projects. In 15 solid tumors, we identified 233 cancer-specific SEGs (cSEGs), which were specifically expressed in only one cancer and showed great potential to be diagnostic biomarkers. Among them, three cSEGs (OGDH, MUDENG and ACO2) had a sample frequency >80% in kidney cancer, suggesting their high sensitivity. Furthermore, we identified 254 cSEGs as early-stage diagnostic biomarkers across 17 cancers. A two-gene combination strategy was applied to improve the sensitivity of diagnostic biomarkers, and hundreds of two-gene combinations were identified with high frequency. We also observed that 13 SEGs were targets of various drugs and nearly half of these drugs may be repurposed to treat cancers with SEGs as their targets. Several SEGs were regulated by specific transcription factors in the corresponding cancer, and 39 cSEGs were prognosis-related genes in 7 cancers. This work provides a survey of cancer biomarkers for diagnosis and early diagnosis and new insights to drug repurposing. These biomarkers may have great potential in cancer research and application.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbz131