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Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of FAM83A and FAM83B

1
Quantitative Biomedical Research Center, Department of Population and Data Sciences, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
2
Howard Hughes Medical Institute and Children’s Medical Center Research Institute, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
3
Hamon Center for Therapeutic Oncology Research, Department of Pharmacology, Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
*
Author to whom correspondence should be addressed.
Cancers 2019, 11(6), 886; https://doi.org/10.3390/cancers11060886
Received: 4 June 2019 / Revised: 15 June 2019 / Accepted: 16 June 2019 / Published: 25 June 2019
(This article belongs to the Special Issue Molecular Profiling of Lung Cancer)
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Abstract

Introduction: In our previous study, we constructed a Lung Cancer Explorer (LCE) database housing lung cancer-specific expression data and clinical data from over 6700 patients in 56 studies. Methods: Using this dataset of the largest collection of lung cancer gene expression along with our meta-analysis method, we systematically interrogated the association between gene expression and overall survival as well as the expression difference between tumor and normal (adjacent non-malignant tissue) samples in lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SQCC). A case study for FAM83A and FAM83B was performed as a demonstration for hypothesis testing with our database. Results: We showed that the reproducibility of results across studies varied by histological subtype and analysis type. Genes and pathways unique or common to the two histological subtypes were identified and the results were integrated into LCE to facilitate user exploration. In our case study, we verified the findings from a previous study on FAM83A and FAM83B in non-small cell lung cancer. Conclusions: This study used gene expression data from a large cohort of patients to explore the molecular differences between lung ADC and SQCC. View Full-Text
Keywords: lung cancer; gene expression difference between tumor and normal; survival association analysis; systematic analysis; meta-analysis; FAM83 lung cancer; gene expression difference between tumor and normal; survival association analysis; systematic analysis; meta-analysis; FAM83
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Cai, L.; Luo, D.; Yao, B.; Yang, D.M.; Lin, S.; Girard, L.; DeBerardinis, R.J.; Minna, J.D.; Xie, Y.; Xiao, G. Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of FAM83A and FAM83B. Cancers 2019, 11, 886.

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