Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer

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dc.contributor.authorChang, Yu-Chunen
dc.contributor.authorDing, Yanen
dc.contributor.authorDong, Lingshengen
dc.contributor.authorZhu, Lang-Jingen
dc.contributor.authorJensen, Roderick V.en
dc.contributor.authorHsiao, Li-Lien
dc.contributor.departmentBiological Sciencesen
dc.date.accessioned2019-07-24T17:26:15Zen
dc.date.available2019-07-24T17:26:15Zen
dc.date.issued2018-05-09en
dc.description.abstractBackground. Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these "housekeeping genes" (HKGs) could separate one normal human tissue type from another. Current focus on identifying "specific disease markers" is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers. Methods. Microarray and RNA-seq data for normal lungs, lung adenocarcinomas (AD), squamous cell carcinomas of the lung (SQCLC), and small cell carcinomas of the lung (SCLC) were collected from online databases. Using 374 of 451 HKGs, differentially expressed genes between pairs of sample types were determined via two-sided, homoscedastic t -test. Principal component analysis and hierarchical clustering classified normal lung and lung cancers subtypes according to relative gene expression variations. We used uni- and multi-variate cox-regressions to identify significant predictors of overall survival in AD patients. Classifying genes were selected using a set of training samples and then validated using an independent test set. Gene Ontology was examined by PANTHER. Results. This study showed that the differential expression patterns of 242, 245, and 99 HKGs were able to distinguish normal lung from AD, SCLC, and SQCLC, respectively. From these, 70 HKGs were common across the three lung cancer subtypes. These HKGs have low expression variation compared to current lung cancer markers (e.g., EGFR, KRAS) and were involved in the most common biological processes (e.g., metabolism, stress response). In addition, the expression pattern of 106 HKGs alone was a significant classifier of AD versus SQCLC. We further highlighted that a panel of 13 HKGs was an independent predictor of overall survival and cumulative risk in AD patients. Discussion. Here we report HKG expression patterns may be an effective tool for evaluation of lung cancer states. For example, the differential expression pattern of 70 HKGs alone can separate normal lung tissue from various lung cancers while a panel of 106 HKGs was a capable class predictor of subtypes of non-small cell carcinomas. We also reported that HKGs have significantly lower variance compared to traditional cancer markers across samples, highlighting the robustness of a panel of genes over any one specific biomarker. Using RNA-seq data, we showed that the expression pattern of 13 HKGs is a significant, independent predictor of overall survival for AD patients. This reinforces the predictive power of a HKG panel across different gene expression measurement platforms. Thus, we propose the expression patterns of HKGs alone may be sufficient for the diagnosis and prognosis of individuals with lung cancer.en
dc.description.notesThis work was supported by SDSC Global Foundation. Lang-Jing Zhu was supported by grants from the Chinese National Natural Science Research Grant (No. 81373183 and 81001334). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.description.sponsorshipSDSC Global Foundationen
dc.description.sponsorshipChinese National Natural Science Research Grant [81373183, 81001334]en
dc.identifier.doihttps://doi.org/10.7717/peerj.4719en
dc.identifier.issn2167-8359en
dc.identifier.othere4719en
dc.identifier.pmid29761043en
dc.identifier.urihttp://hdl.handle.net/10919/91977en
dc.identifier.volume6en
dc.language.isoenen
dc.publisherPeerJen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectHousekeeping genesen
dc.subjectExpression patternsen
dc.subjectLung adenocarcinomaen
dc.subjectSmall cell carcinomaen
dc.subjectSquamous cell carcinomaen
dc.subjectNon-small cell carcinomaen
dc.subjectDiagnosis and prognosisen
dc.titleDifferential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung canceren
dc.title.serialPeerJen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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