Comparing progression molecular mechanisms between lung adenocarcinoma and lung squamous cell carcinoma based on genetic and epigenetic networks: big data mining and genome-wide systems identification

Abstract

Non-small-cell lung cancer (NSCLC) is the predominant type of lung cancer in the world. Lung adenocarcinoma (LADC) and lung squamous cell carcinoma (LSCC) are subtypes of NSCLC. We usually regard them as different disease due to their unique molecular characteristics, distinct cells of origin and dissimilar clinical response. However, the differences of genetic and epigenetic progression mechanism between LADC and LSCC are complicated to analyze. Therefore, we applied systems biology approaches and big databases mining to construct genetic and epigenetic networks (GENs) with next-generation sequencing data of LADC and LSCC. In order to obtain the real GENs, system identification and system order detection are conducted on gene regulatory networks (GRNs) and protein-protein interaction networks (PPINs) for each stage of LADC and LSCC. The core GENs were extracted via principal network projection (PNP). Based on the ranking of projection values, we got the core pathways in respect of KEGG pathway. Compared with the core pathways, we found significant differences between microenvironments, dysregulations of miRNAs, epigenetic modifications on certain signaling transduction proteins and target genes in each stage of LADC and LSCC. Finally, we proposed six genetic and epigenetic multiple-molecule drugs to target essential biomarkers in each progression stage of LADC and LSCC, respectively.

Keywords: NSCLC; genetic and epigenetic network; lung adenocarcinoma; lung squamous cell carcinoma; potential drug target.

Figure 1. Flowchart of the construction for genome-wide GENS, core GENs, and core signaling pathways of each progression stage of LADC and LSCC and the discovery of potential genetic and epigenetic multiple drugs.

The oval blocks represent the raw data of normal lung cells and lung cancer cells (i.e. early stage, middle stage, and advanced stage of LADC and LSCC), including genome-wide mRNA/miRNA/lncRNA NGS data and DNA methylation profiles. The blue grey blocks denote the candidate protein-protein interaction network (PPIN), which was constructed by databases (BIOGRID, IntAct, DIP, BIND, and MINT), and the candidate gene/miRNA/lncRNA regulatory network (GRN), which was constructed by databases (ITFP, HTRIdb, TRANSFAC, TargetScanHuman, CircuitDB, and StarBase2.0). The rounded rectangular blocks indicate the systems biology approach to be applied to construct genome-wide candidate GEN, real GENs of each stage (normal lung cells, early stage, middle stage, and advanced stage) of LADC and LSCC, and then to obtain core pathways of LADC and LSCC at each progression stage (normal cells to early stage, early stage to middle stage, and middle stage to advanced stage) by comparing the core GENs among the different stage. The light yellow blocks represent the identified information in our results, including real GENs at each stage and core signaling pathways of each progression stage. Besides, we selected biomarkers and drugtargets based on our results (dashed line with arrow) for designing genetic and epigenetic multiple drugs via CMap drug database mining for therapeutic treatment of early stage, middle stage, and advanced stage in LADC and LSCC, respectively.

Figure 2. Core signaling pathways extracted from comparing genetic and epigenetic networks (GENs) between normal lung cells and early stage LADC and LSCC.

The dot and dashed line represent the identified signaling pathways in former stage (normal stage) and later stage (early stage), respectively. Solid line indicates the common signaling pathways identified in both former stage and later stage. The yellow and blue regions are former stage (normal stage) and later stage (early stage), respectively. The lines without arrow denote the protein-protein interactions (PPIs). The lines with arrow represent the regulations of TFs and lncRNAs with activation and inhibition. The lines with circle are post-transcription regulations of miRNA with inhibition. Besides, the bold lines with arrow indicate the interaction or stimulation of proteins and xenobiotics. The Red font represent the node with significant differential expression change with a higher expression in later stage LADC and LSCC. While the blue font represent the node with a significant differential expression change with a lower expression in later stage LADC and LSCC. Besides, the gene with flag represents that this gene has basal level change between former and later stage LADC and LSCC, suggesting that the gene may be affected by DNA methylation.

Figure 3. Core signaling pathways extracted from comparing genetic and epigenetic networks (GENs) between early stage and middle stage LADC and LSCC.

The dot and dashed line represent the identified signaling pathways in former stage (early stage) and later stage (middle stage), respectively. Solid line indicates the common signaling pathways identified in both former stage and later stage. The yellow and blue regions are former stage (early stage) and later stage (middle stage), respectively. The lines without arrow denote the protein-protein interactions (PPIs). The lines with arrow represent the regulations of TFs and lncRNAs with activation and inhibition. The lines with circle are post-transcription regulations of miRNA with inhibition. The Red font represent the node with significant differential expression change with a higher expression in later stage LADC and LSCC. While the blue font represent the node with a significant differential expression change with a lower expression in later stage LADC and LSCC. Besides, the gene with flag represents that this gene has basal level change between former and later stage LADC and LSCC, suggesting that the gene may be affected by DNA methylation.

Figure 4. Core signaling pathways extracted from comparing genetic and epigenetic networks (GENs) between middle stage and advanced stage LADC and LSCC.

The dot and dashed line represent the identified signaling pathways in former stage (middle stage) and later stage (advanced stage), respectively. Solid line indicates the common signaling pathways identified in both former stage and later stage. The yellow and blue regions are former stage (middle stage) and later stage (advanced stage), respectively. The lines without arrow denote the protein-protein interactions (PPIs). The lines with arrow represent the regulations of TFs and lncRNAs with activation and inhibition. The lines with circle are post-transcription regulations of miRNA with inhibition. The Red font represent the node with significant differential expression change with a higher expression in later stage LADC and LSCC. While the blue font represent the node with a significant differential expression change with a lower expression in later stage LADC and LSCC. Besides, the gene with flag represents that this gene has basal level change between former and later stage LADC and LSCC, suggesting that the gene may be affected by DNA methylation.

Figure 5. Summarizing the differential genetic and epigenetic progression mechanisms from normal stage to early stage, early stage to middle stage, and middle stage to advanced stage LADC and LSCC.

The figure summarizes the differential genetic and epigenetic progression mechanisms caused by core signaling pathways within each connective stage of LADC and LSCC. The red font with dash-line rectangular blocks denote the differential function between LADC and LSCC.

Figure 6. The specific core signaling pathways extracted from Figures 2–4 for investigating the differential progression molecular mechanisms between LADC and LSCC.

(A) The genetic and epigenetic progression mechanisms from normal stage to early stage LADC could be potentially caused by inflammatory microenvironment induced by bacteria infection (LPS), dysfunctions of EGFR, and TLR4 signaling, regulation of miR-130b, miR-100HG, and miR-1292, epigenetic modifications of E2F1 and SFTPA2, DNA methylation of MYC and RB1, and aberrant cellular functions, such as cell cycle. (B) The genetic and epigenetic progression mechanisms from normal stage to early stage LSCC can be potentially caused by inflammatory microenvironment induced by exposure to xenobiotic toxicity nicotine, dysfunctions of FGFR1, DDR1, and CHRNA5 signaling, regulation of miR-24-2 and miR-1247, lncRNA TUG1, epigenetic modification of KLF12 and ERCC1, DNA methylation of SHOX2, and aberrant cellular functions, such as DNA repair. (C) The genetic and epigenetic progression mechanisms from early stage LADC to middle stage LADC can be potentially induced by hypoxic tumor microenvironment, dysfunctions of NOTCH1 and ITGA4 (CD49d) signaling, regulation of miR-30c-2 and miR-27b, epigenetic modifications of VIM, MYH9, MDM4, and ETS1, and dysregulation of cellular functions, such as angiogenesis, ECM remodeling, and EMT. (D) The genetic and epigenetic progression mechanisms from early stage LADC to middle stage LADC can be potentially induced by hypoxic tumor microenvironment exposed to nicotine, dysfunctions of IGF-1R, ITGB1 (CD29), and TNS1 signaling, regulation of miR-106b, epigenetic modifications of HIF1α, IGF-1, and ETS1, DNA methylation of ITGB1, TNS1, and miR-21, and dysregulation of cellular functions, such as lymphangiogenesis, cell migration, ECM degradation. (E) The genetic and epigenetic progression mechanisms from early stage LADC to middle stage LADC can be potentially induced by the alteration of tumor microenvironment caused by hydrogen peroxide secreted by cancer cells, dysfunctions of EGFR, EPOR, and ITGB1 (CD29) signaling, regulation of miR-143HG and miR-19a, epigenetic modifications of ZEB1 and RHOB, and DNA methylation of PCK1, and dysregulation of cellular functions, such as gluconeogenesis, extracellular proteolysis. (F) The genetic and epigenetic progression mechanisms from early stage LSCC to middle stage LSCC can be potentially induced by the alteration of tumor microenvironment caused by oxidative stress induced by the stimulation of nicotine derived nitrosaminoketone (NNK), dysfunctions of ERBB4, PDPN, and EMR2 signaling, regulation of miR-9-2, epigenetic modifications of GATA3, FOXL1, and CDH3, DNA methylation of PDPN, and dysregulation of cellular functions, such as proliferation, cell mobility, and cell adhesion.