Comparative gene expression analysis in lung cancer

Introduction: Since the most common lung cancers are lung adenocarcinoma, squamous lung cancer (SLC) and the small cell lung cancer (SCLC), a comparative diferential expression between these types of lung cancer deserves investigation. Material and Methods: RNA-seq data were obtained for samples from tumoral and adjacent healthy tissue from adenocarcinoma (7 patients), SLC (8 patients) both from Hospital Regional (Malaga, Spain), and SCLC (14 patients) from EGA (European Genome Archive) with code EGAS00001000334. An automated workflow was designed for pre-processing, mapping against the human genome hg38, assessing differential expression, and sample comparison, taking into account that samples are matched by patient. Results: A total of 2853, 3686 and 4863 genes were differentially expressed in adenocarcinoma, SLC and SCLC, respectively. There are 933 genes having a similar expression in the three cancers. Among the genes with a specific expression in each cancer we have found: 5 genes in adenocarcinoma (C4BPB, IYD, MSLN, TMC5, TRDN), 4 in SLC (AZGP1, HSPB3, MSLN, TP63) and 11 in SCLC (ADCYAP1, AKR1C1, AKR1C2, AKR1C3, ALDH3A1, GPA33, LAMB3, MSLN, PRAME, TARP, TUBA1A). Also we have found a gene that is the most different among the three, MSLN, which presents a differential logFC2 of –6,42, –2,23 and 2,84 in adeno, SLC and SCLC, respectively. Conclusions: The specific differential expression of genes in three different lung cancers conform a set of putative biomarker genes with a possible use on future prognostic and diagnostic methods.