Abstract The use of a new bioinformatics pipeline allowed the identification of deregulated transcription factors (TFs) coexpressed in lung cancer that could become biomarkers of tumor establishment and progression. A gene regulatory network (GRN) of lung cancer was created with the normalized gene expression levels of differentially expressed genes (DEGs) from the microarray dataset GSE19804. Moreover, coregulatory and transcriptional regulatory network (TRN) analyses were performed for the main regulators identified in the GRN analysis. The gene targets and binding motifs of all potentially implicated regulators were identified in the TRN and with multiple alignments of the TFs’ target gene sequences. Six transcription factors (E2F3, FHL2, ETS1, KAT6B, TWIST1, and RUNX2) were identified in the GRN as essential regulators of gene expression in non-small-cell lung cancer (NSCLC) and related to the lung tumoral process. Our findings indicate that RUNX2 could be an important regulator of the lung cancer GRN through the formation of coregulatory complexes with other TFs related to the establishment and progression of lung cancer. Therefore, RUNX2 could become an essential biomarker for developing diagnostic tools and specific treatments against tumoral diseases in the lung after the experimental validation of its regulatory function.

Conclusions In this study, we addressed the complexity of the regulatory mechanisms at the transcriptional level, which are involved in the tumor process in the lung, identifying a network of transcription factors (TFs) that are associated with the acquisition of the hallmarks of lung cancer. The regulatory network analysis identified six transcriptional (E2F3, FHL2, ETS1, KAT6B, TWIST1, and RUNX2) regulators in an NSCLC lung cancer population of female non-smokers, among which RUNX2 seems to be a very important regulator due to its ability to act as a coregulator of important TFs (E2F3, FHL2, TWIST1, BRCA1, FOXM1, and RUNX1) identified in our NSCLC-GRN and previous coexpression networks made with unique deregulated and coexpressed genes in lung cancer, as well as common connectivity patterns between lung cancer, other lung diseases, and other types of cancer, which assess the heterogeneity of lung cancer as a general disease. RUNX2, with its potential target genes, participates as a terminal regulator of lung cancer in the most important signaling pathways (PI3K-AKT, WNT, PLK1, cGMP-PKG, and P53) associated with lung cancer. This result supports previous evidence and helps to further elucidate the role played by this transcriptional regulator in lung cancer as an important coregulator in the tumorigenic process. The analysis of the expression levels of the direct targets of RUNX2 identified ETS1, a transcriptional regulator of lung cancer that appears in the NSCLC regulatory network and is a coregulator of a significant number of TFs identified in the coexpression networks, which are associated with lung cancer. The in-silico analysis identifying RUNX2 as an important deregulated gene in NSCLC suggests the possibility of further research aimed at experimental biological validation. The performance of functional assays of loss and gain of function of RUNX2 in NSCLC cells is essential to confirm the conclusions presented in this manuscript.

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