A Systematic Analysis Identifies Key Regulators Involved in Cell Proliferation and Potential Drugs for the Treatment of Human Lung Adenocarcinoma

Abstract

Lung adenocarcinoma (LUAD) is one of the most common and malignant cancer types. Abnormal cell proliferation, exemplified by cell cycle and cell division dysregulation, is one of the most prominent hallmarks of cancer and is responsible for recurrence, metastasis, and resistance to cancer therapy. However, LUAD-specific gene regulation and clinical significance remain obscure. Here, by using both tissues and cells from LUAD and normal lung samples, 434 increased and 828 decreased genes of biological significance were detected, including 127 cell cycle-associated genes (95 increased and 32 decreased), 66 cell division-associated genes (56 increased and 10 decreased), and 81 cell proliferation-associated genes (34 increased and 47 decreased). Among them, 12 increased genes (TPX2, CENPF, BUB1, PLK1, KIF2C, AURKB, CDKN3, BUB1B, HMGA2, CDK1, ASPM, and CKS1B) and 2 decreased genes (TACC1 and MYH10) were associated with all the three above processes. Importantly, 2 (CDKN3 and CKS1B) out of the 11 increased genes (except HMGA2) are previously uncharacterized ones in LUAD and can potentially be prognostic markers. Moreover, PLK1 could be a promising therapeutic target for LUAD. Besides, protein-protein interaction network analysis showed that CDK1 and CDC20 were the hub genes, which might play crucial roles in cell proliferation of LUAD. Furthermore, transcriptional regulatory network analysis suggested that the transcription factor E2F1 could be a key regulator in controlling cell proliferation of LUAD via expression modulation of most cell cycle-, cell division-, and cell proliferation-related DEGs. Finally, trichostatin A, hycanthone, vorinostat, and mebeverine were identified as four potential therapeutic agents for LUAD. This work revealed key regulators contributing to cell proliferation in human LUAD and identified four potential therapeutic agents for treatment strategy.

Keywords: cell proliferation; lung adenocarcinoma; prognosis; protein–protein interaction; transcriptional regulation.

Figure 1

The global expression profiles of human lung cancer cells/tissues and adjacent lung normal cells/tissues. (A) The first two principal components plot of LUAD tissues via PCA. (B) Volcano plot of genes between human lung cancer tissues and adjacent lung normal tissues. The absolute FC of ≥2.0 and p-value of ≤0.05 were used. (C) Venn diagram plot of DEGs based on tissues and cells with the absolute FC of ≥ 2.0 and p-value of ≤ 0.05. (D) Bubble diagram plot of the top 15 enriched biological processes for the upregulated (left) and downregulated (right) DEGs. (E) Bubble diagram plot of the top 15 enriched KEGG pathways for the upregulated (left) and downregulated (right) DEGs.

Figure 2

The up- and downregulated genes that are involved in cell cycle, cell division, and cell proliferation. (A) Venn diagram plot of the up- and downregulated genes that are involved in cell cycle, cell division, and cell proliferation. (B) Heatmap of the 12 upregulated and 2 downregulated genes involved in all the above three processes. (C) Expression validation of the 12 upregulated DEGs by GEPIA2. Reads box is the expression of LUAD samples; gray box is the expression of normal samples. (D) Expression validation of the two downregulated DEGs by GEPIA2. Reads box is the expression of LUAD samples; gray box is the expression of normal samples. *p.adj ≤ 0.05.

Figure 3

DEGs validated by qRT-PCR experiment. Four biological repetitions were applied to patient tissues; two biological repetitions and two technical repetitions were applied to cell lines. Human tumor-adjacent tissues and lung fibroblast cells (MRC-5) were used for control, respectively.

Figure 4

Overall survival (OS) analysis of 12 increased DEGs involved in cell cycle, cell division, and cell proliferation. The high-expression group was represented by red colors, and the low-expression group was represented by blue colors. Both high and low cutoffs were set to 25%, n (high) = 359, n (low) = 120. HR, hazard ratio.

Figure 5

The protein–protein interaction network of DEGs involved in cell cycle, cell division, and cell proliferation. (A) The protein–protein interaction network. (B) ClueGO functional annotation of 61 other genes (purple nodes in A) that interacted with the up- and downregulated DEGs in (A). A p-value of ≤0.01 was used, and experimental validated biological processes (BP), cellular components (CC), and molecular functions (MF) were plotted.

Figure 6

The transcriptional regulatory network of DEGs involved in cell cycle, cell division, and cell proliferation. (A) The TF–target interaction network. (B) Heatmap of Pearson correlation coefficient between E2F1 and its targets. The correlation coefficient was calculated by the cor function in R packages. Only the pairs with absolute values ≥ 0.5 were shown and no negative correlation was detected. (C) Expression verification of E2F1 between human lung cancer cells and adjacent lung normal tissues by GEPIA2. *p.adj ≤ 0.05.

Figure 7

Conserved expression pattern of E2F1 among various cancers. ***p.adj ≤ 0.001.

Figure 8

The 2D structures of compounds identified by cMAP analysis. (A) Trichostatin A, (B) hycanthone, (C) vorinostat, and (D) mebeverine.