Analysis and Comparison of the Transcriptome of COPD Patients with and without Lung Cancer
Introduction: COPD is related to increased risk for the development of lung cancer, which is an important cause of death in these patients.
Objectives: The primary objective was to identify transcripts associated to the pathogenesis of lung cancer in COPD patients.
Methods: We recruited 20 COPD patients undergoing bronchoscopy, 10 with and 10 withouth lung cancer. In patients with COPD and lung cancer the transcriptomic profile was obtained both from tumoral and non tumoral adjancent tissue. The whole transcriptomic profile was determined by next generation sequencing and analized using standard bioconductor pipelines. We considered differentially expressed genes (DEGs) with FDR and p â‰¤0.05, and absolute fold change â‰¥2. The significantly enriched gene ontology (GO) and Kyoto Encyclopedia Genes and Genomes (KEGG) pathway were determined for DEGs using clusterProfiler.
Results: In the paried comparison between tumor tissue versus non-tumor tissue of the same patients 246 DEGs were identified, 356 DEGs were observed between the tissue of COPD patients withouth and with tumor tissue, and 115 genes were commom between those comparisons. The comparison between non-tumor tissue of both groups did not identify DEGs. The panel of 115 genes was considered as a â€œtumorâ€ signature, and in them we assessed the biological pathway enrichement, and the most enriched was the KEGG â€œprotein processing in endoplasmic reticulum (FDR=2.8E-08)â€.
Conclusion: The present study revealed that the differences between non-tumor tissue and that of COPD patients without tumor are minial. Beside, we identified a panel of tumor specific genes that may be helpful in order to understand the mechanisms of carcinogenisis in COPD.
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