Identification of HCG18 and MCM3AP-AS1 That Associate With Bone Metastasis, Poor Prognosis and Increased Abundance of M2 Macrophage Infiltration in Prostate Cancer

Abstract

Background: Bone metastasis is a leading cause of the high mortality rate of prostate cancer (PCa), but curative strategies remain lacking. Recent studies suggest long non-coding RNAs (lncRNAs) may be potential targets to develop drugs. However, PCa bone metastasis-specifically-related lncRNAs were rarely reported. This study aimed to identify crucial lncRNAs and reveal their function mechanisms.

Methods: GSE32269 and GSE26964 microarray datasets, downloaded from the Gene Expression Omnibus database, were used to analyze differentially expressed genes (DEGs)/lncRNAs (DELs) and miRNAs (DEMs), respectively. Weighted gene co-expression network analysis was performed to screen PCa bone metastasis-associated modules. The co-expression and competing endogenous RNAs (ceRNAs) networks were constructed to identify hub lncRNAs. Univariate Cox regression analysis was conducted to determine their prognostic values. The correlation of lncRNAs with immune infiltrating cells was analyzed by using Tumor IMmune Estimation Resource. Therapeutic drugs were predicted by querying the Connectivity Map (CMap) and the Comparative Toxicogenomics Database (CTD).

Results: A total of 18 DELs, 2,614 DEGs and 86 DEMs were screened between bone metastatic and primary PCa samples. Four modules enriched by DEGs were shown to be bone metastasis-associated. LncRNA HCG18 and MCM3AP-AS1 were identified to be important because they existed in both of the co-expression and ceRNA networks (forming the relationship pairs: HCG18/MCM3AP-AS1-KNTC1, MCM3AP-AS1-hsa-miR-508-3p-DTL and HCG18/MCM3AP-AS1-hsa-miR-127-3p-CDKN3). All the genes in these interaction pairs were significantly associated with overall survival of PCa patients. Also, HCG18, MCM3AP-AS1 and their target mRNAs were positively correlated with various tumor-infiltrated immune cells, especially increased M2 macrophages. Valproic acid and trichostatin A may be effective to treat PCa bone metastasis by targeting HCG18 and MCM3AP-AS1.

Conclusion: HCG18 and MCM3AP-AS1 that regulate M2 macrophage infiltration may be important targets to treat PCa bone metastasis and improve prognosis.

Keywords: bone metastasis; lncRNA; prognosis; prostate cancer; tumor-infiltrating.

Figure 1.

Identification of differentially expressed RNAs in bone metastatic vs primary PCa samples. A, C: volcano plot (A) and heatmap (C) of differentially expressed lncRNAs and mRNAs identified in the GSE32269 dataset; B, D: volcano plot (B) and heatmap (D) of differentially expressed miRNAs identified in the GSE26964 dataset. Red, high expression; blue, low expression. FC, fold change; FDR, false discovery rates.

Figure 2.

Weighted gene co-expression network analysis. A: selecting the soft-threshold power β (= 6) based on the scale-free topology threshold of 0.9; B: displaying the mean connectivity (= 1) when β = 6; C: showing the clustering dendrogram of genes; D, showing the correlations between gene modules and clinical traits.

Figure 3.

The co-expression relationships between differentially expressed lncRNAs and differentially expressed mRNAs identified in blue, brown, green and yellow modules.

Figure 4.

Construction of a ceRNA network using the differentially expressed lncRNAs, miRNAs and mRNAs in crucial modules.

Figure 5.

The target relationships between differentially expressed RNAs and small molecular drugs.

Figure 6.

Kaplan-Meier survival curves comparing the survival difference of the high-expression group and the low-expression group. The groups were classified according to the median expression values of each crucial lncRNA, miRNA and mRNA in prostate adenocarcinoma samples from the TCGA database. A: lncRNA HCG18; B: lncRNA MCM3AP-AS1; C: hsa-miR-508-3p; D: hsa-miR-127-3p: E: DTL; F: CDKN3; G: KNTC1. HR, hazard ratio.

Figure 7.

The correlation between the expression levels of lncRNAs/mRNAs and immune infiltration in prostate adenocarcinoma samples from the TCGA database. A: DTL; B: KNTC1; C: CDKN3; D: HCG18; E: MCM3AP-AS1.