| Title: |
Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer ; PeerJ |
| Authors: |
Chang, Yu-Chun; Ding, Yan; Dong, Lingsheng; Zhu, Lang-Jing; Jensen, Roderick V.; Hsiao, Li-Li |
| Contributors: |
Biological Sciences |
| Publisher Information: |
PeerJ |
| Publication Year: |
2018 |
| Collection: |
VTechWorks (VirginiaTech) |
| Subject Terms: |
Housekeeping genes; Expression patterns; Lung adenocarcinoma; Small cell carcinoma; Squamous cell carcinoma; Non-small cell carcinoma; Diagnosis and prognosis |
| Description: |
Background. 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. ... |
| Document Type: |
article in journal/newspaper; still image |
| File Description: |
application/pdf |
| Language: |
English |
| Relation: |
e4719; http://hdl.handle.net/10919/91977; https://doi.org/10.7717/peerj.4719 |
| DOI: |
10.7717/peerj.4719 |
| Availability: |
http://hdl.handle.net/10919/91977; https://doi.org/10.7717/peerj.4719 |
| Rights: |
Creative Commons Attribution 4.0 International ; http://creativecommons.org/licenses/by/4.0/ |
| Accession Number: |
edsbas.FADAC48B |
| Database: |
BASE |