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Weighted gene expression profiles identify diagnostic and prognostic genes for lung adenocarcinoma and squamous cell carcinoma
- Source :
- The Journal of International Medical Research, Journal of International Medical Research, Vol 48 (2020)
- Publication Year :
- 2019
- Publisher :
- SAGE Publications, 2019.
-
Abstract
- Objective To construct a diagnostic signature to distinguish lung adenocarcinoma from lung squamous cell carcinoma and a prognostic signature to predict the risk of death for patients with nonsmall-cell lung cancer, with satisfactory predictive performances, good stabilities, small sizes and meaningful biological implications. Methods Pathway-based feature selection methods utilize pathway information as a priori to provide insightful clues on potential biomarkers from the biological perspective, and such incorporation may be realized by adding weights to test statistics or gene expression values. In this study, weighted gene expression profiles were generated using the GeneRank method and then the LASSO method was used to identify discriminative and prognostic genes. Results The five-gene diagnostic signature including keratin 5 ( KRT5), mucin 1 ( MUC1), triggering receptor expressed on myeloid cells 1 ( TREM1), complement C3 ( C3) and transmembrane serine protease 2 ( TMPRSS2) achieved a predictive error of 12.8% and a Generalized Brier Score of 0.108, while the five-gene prognostic signature including alcohol dehydrogenase 1C (class I), gamma polypeptide ( ADH1C), alpha-2-glycoprotein 1, zinc-binding ( AZGP1), clusterin ( CLU), cyclin dependent kinase 1 ( CDK1) and paternally expressed 10 ( PEG10) obtained a log-rank P-value of 0.03 and a C-index of 0.622 on the test set. Conclusions Besides good predictive capacity, model parsimony and stability, the identified diagnostic and prognostic genes were highly relevant to lung cancer. A large-sized prospective study to explore the utilization of these genes in a clinical setting is warranted.
- Subjects :
- 0301 basic medicine
Lung adenocarcinoma
squamous cell carcinoma
Medicine (General)
Lung Neoplasms
Adenocarcinoma of Lung
Validation Study
Biochemistry
03 medical and health sciences
R5-920
0302 clinical medicine
Gene expression
medicine
Humans
Basal cell
Prospective Studies
Gene
pathway information
Lung
Prognostic signature
business.industry
Biochemistry (medical)
Lung squamous cell carcinoma
Cell Biology
General Medicine
medicine.disease
Prognosis
GeneRank
030104 developmental biology
medicine.anatomical_structure
classification
030220 oncology & carcinogenesis
Cancer research
Carcinoma, Squamous Cell
Adenocarcinoma
Risk of death
business
Transcriptome
Subjects
Details
- Language :
- English
- ISSN :
- 14732300 and 03000605
- Volume :
- 48
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- The Journal of International Medical Research
- Accession number :
- edsair.doi.dedup.....8f82cdc64fa987a0447d03db4ccffa1b