Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique DNA Methylation and Gene Expression Profiles

2020 ◽  
Vol 27 (7) ◽  
pp. 1041-1054 ◽  
Author(s):  
Weiqing Wang ◽  
Shaohua Wang ◽  
Xiao Chu ◽  
Hui Liu ◽  
Ming Xiang
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Lung Squamous Cell Carcinoma ◽  
Diagnosis And Prognosis

scholarly journals Weighted gene expression profiles identify diagnostic and prognostic genes for lung adenocarcinoma and squamous cell carcinoma

2019 ◽  
Vol 48 (3) ◽  
pp. 030006051989383 ◽  
Author(s):  
Xing Wu ◽  
Linlin Wang ◽  
Fan Feng ◽  
Suyan Tian
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Squamous Cell Carcinoma ◽  
Lung Adenocarcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Prognostic Signature ◽  
Diagnostic Signature

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.

scholarly journals Review and screening of key genes in esophageal squamous cell carcinoma

2021 ◽  
Author(s):  
Xizi Sun
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
P53 Signaling

Abstract Esophageal squamous cell carcinoma (ESCC) is the most common type of human esophageal cancer with high mortality due to late stage diagnosis. Efforts have been made to figure out the genetic events underlying its carcinogenesis and progression, but the molecular mechanisms of these processes remain elusive. To identify the candidate genes involved in ESCC, literature about significantly mutated genes (SMGs) was extensively reviewed and gene expression profiles of GSE161533, GSE20347 and GSE77861 were downloaded from the Gene Expression Omnibus (GEO) database. Following the identification of 230 differentially expressed genes (DEGs), hub gene identification was performed by the plug-in MCODE in Cytoscape software. 14 hub genes were identified which were enriched in cell cycle, DNA replication and p53 signaling pathway. In summary, genes mentioned in this study may provide potential targets for treatment and diagnosis of ESCC and help us better understand the pathogenesis and progression of ESCC from genetic perspective.

scholarly journals Analysis of Laser Therapy Effects on Squamous Cell Carcinoma Patients: A System Biology Study

2019 ◽  
Vol 10 (5) ◽  
pp. S1-S6 ◽  
Author(s):  
Vahid Mansouri ◽  
Mostafa Rezaei-Tavirani ◽  
Mohammad-Mehdi Zadeh-Esmaeel ◽  
Sina Rezaei-Tavirani ◽  
Mohammadreza Razzaghi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Laser Therapy ◽  
Squamous Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
Laser Exposure ◽  
Biological Processes

Introduction: The Mechanism of laser therapy and also its safety are 2 important features of the application of different types of lasers in medicine. This study aims to investigate the critically affected genes after the treatment of squamous cell carcinoma patients. Methods: The gene expression profiles of 4 squamous cell carcinoma patients that were treated via chemoradiotherapy (CRT) plus the laser and 3 similar patients without laser exposure from Gene Expression Omnibus (GEO) were downloaded and were screened to find critical genes via network analysis. The STRING database, Cytoscape software, and the Clue GO plug-in of Cytoscape software were used. Results: The genes HSX70 and NCC27 were determined as neighbors and HSPA1B, CLIC1, RAB13, PPIF, and LCE3D as hub genes. The over-expression of LCE3D was interpreted as the side effect of laser therapy. Apoptosis and the cell cycle were the dominant biological processes regulated by the HSP molecules in the laser-treated patients. Conclusion: The laser affected the main biological processes and simultaneously issued side effects

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