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Updated: Dec 5, 2025
Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
Interactive Verification Analysis of Multiple Sequencing Data for Identifying Potential Biomarker of Lung
Hongjun Fei1, Songchang Chen1, Chenming Xu1
1Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
Background:
Lung adenocarcinoma (LUAD) comprises around 40% of all lung cancers, and in about 70% of patients, it has spread locally or systemically when first detected leading to a worse prognosis.
Methods:
We filtered out differentially expressed genes (DEGs) based on the RNA sequencing data in the Gene Expression Omnibus database and verified and deeply analyzed screened DEGs using a combined bioinformatics approach.
Results:
Expressions of 11,143 genes in 694 nontumor lung tissues and LUAD cases from 8 independent laboratories were analyzed; 188 mRNAs were identified as differentially expressed genes (DEGs). A PPI network constructed with 188 DEGs screened out 8 hub DEGs (CDH5, PECAM1, VWF, CLDN5, COL1A1, MMP9, SPP1, and IL6) which highly interconnected with other nodes. The expression levels of 8 hub genes in LUAD and control were assessed in the Oncomine database, and the results were consistent. The survival curves of 8 hub genes showed that their expressions are significantly related to the prognosis of lung cancer and LUAD patients except for IL6. Since the expression of IL6 is nonspecific and highly sensitive, we choose the other 7 hub genes we had verified to do the next analysis. Mutual exclusivity or cooccurrence analysis of 7 hub genes identified a tendency towards cooccurrence between CDH5, PECAM1, and VWF in LUAD. The coexpression profiles of CDH5 in LUAD were identified, and we found that PECAM1 and VWF coexpressed with CDH5. Immunohistochemistry and RT-PCR analysis showed that higher levels of CDH5, PECAM1, and VWF were expressed in normal lung tissues but a low or undetectable level was found in LUAD tissues.
Conclusions:
Taken together, we speculate that CDH5, PECAM1, and VWF played an important role in LUAD.
