| Literature DB >> 27446297 |
Xinghua Zhang1, Xiaoli Yao2, Cong Qin1, Pengcheng Luo1, Jie Zhang1.
Abstract
The present study aimed to screen potential genes associated with metastatic prostate cancer (PCa), in order to improve the understanding of the mechanisms underlying PCa metastasis. The GSE3325 microarray dataset, which was downloaded from the Gene Expression Omnibus database, consists of seven clinically localized PCa samples, six hormone-refractory metastatic PCa samples and six benign prostate tissue samples. The Linear Models for Microarray Data package was used to identify differentially-expressed genes (DEGs) and a hierarchical cluster analysis for DEGs was performed with the pheatmap package. Furthermore, potential functions for the DEGs were predicted by a functional enrichment analysis. Subsequently, microRNAs (miRNAs) potentially involved in the regulation of PCa metastasis were identified by WebGestalt software, and the miRNA-DEG regulatory network was visualized using Cytoscape. In addition, a pathway enrichment analysis for DEGs in the regulatory network was performed. A total of 306 and 2,073 genes were differentially expressed in the clinically localized PCa and the metastatic PCa groups, respectively, as compared with the benign prostate group, of which 174 were differentially expressed in both groups. A number of the DEGs, including CAMK2D and SH3BP4, were significantly enriched in the cell cycle, and others, such as MAF, were associated with the regulation of cell proliferation. Furthermore, some DEGs (CAMK2D and PCDH17) were observed to be regulated by miR-30, whereas others (ADCY2, MAF, SH3BP4 and PCDH17) were modulated by miR-182. Additionally, ADCY2 and CAMK2D were distinctly enriched in the calcium signaling pathway. The present study identified novel DEGs, including ADCY2, CAMK2D, MAF, SH3BP4 and PCDH17, that may be involved in the metastasis of PCa.Entities:
Keywords: differentially expressed genes; metastatic prostate cancer; microRNA; pathway; regulatory network
Year: 2016 PMID: 27446297 PMCID: PMC4950782 DOI: 10.3892/etm.2016.3376
Source DB: PubMed Journal: Exp Ther Med ISSN: 1792-0981 Impact factor: 2.447
Figure 1.Venn diagram for the differentially expressed genes in the clinically localized and metastatic prostate cancer groups. Gene set A represents the genes only differentially expressed in the clinically localized prostate cancer group; Gene set B represents the genes only differentially expressed in the metastatic prostate cancer group; Gene set C represents the genes differentially expressed in both groups.
Figure 2.Hierarchical cluster analysis for the genes differentially expressed between the (A) metastatic prostate cancer and the benign prostate groups, and (B) the metastatic and clinically localized prostate cancer groups. Each row represents a single gene; each column represents a tissue sample. M represents the metastatic prostate cancer group; N represents the benign prostate group; P represents the clinically localized prostate cancer group. The gradual color change from orange to blue represents the changing process from upregulation to downregulation.
Enriched terms for Gene sets A, B and C.
| Category | Term | No. of genes | FDR | Genes |
|---|---|---|---|---|
| Gene set A | GO:0009954~proximal/distal pattern formation | 5 | 3.5500 | |
| GO:0032868~response to insulin stimulus | 8 | 7.8400 | ||
| GO:0042592~homeostatic process | 24 | 9.6200 | ||
| GO:0001501~skeletal system development | 14 | 0.0011 | ||
| GO:0048878~chemical homeostasis | 18 | 0.0019 | ||
| GO:0021877~forebrain neuron fate commitment | 3 | 0.0022 | ||
| GO:0043434~response to peptide hormone stimulus | 9 | 0.0023 | ||
| GO:0010033~response to organic substance | 22 | 0.0029 | ||
| GO:0009725~response to hormone stimulus | 14 | 0.0038 | ||
| GO:0034637~cellular carbohydrate biosynthetic process | 6 | 60.0038 | ||
| Gene set B | GO:0022402~cell cycle process | 102 | 5.2300 | |
| GO:0051726~regulation of cell cycle | 68 | 1.1100 | E | |
| GO:0007049~cell cycle | 128 | 1.8200 | ||
| GO:0051301~cell division | 61 | 4.6100 | ||
| GO:0022403~cell cycle phase | 78 | 4.7700 | ||
| GO:0010035~response to inorganic substance | 47 | 6.4600 | ||
| GO:0007346~regulation of mitotic cell cycle | 38 | 0.0011 | ||
| GO:0042127~regulation of cell proliferation | 126 | 0.0012 | ||
| GO:0030030~cell projection organization | 70 | 0.0015 | ||
| GO:0000278~mitotic cell cycle | 70 | 0.0018 | ||
| Gene set C | GO:0022402~cell cycle process | 21 | 3.3000 | |
| GO:0022403~cell cycle phase | 18 | 3.5700 | ||
| GO:0000278~mitotic cell cycle | 17 | 4.0700 | ||
| GO:0000279~M phase | 15 | 2.7400 | ||
| GO:0007049~cell cycle | 22 | 1.1800 | ||
| GO:0000280~nuclear division | 11 | 4.5000 | ||
| GO:0007067~mitosis | 11 | 4.5000 | ||
| GO:0000087~M phase of mitotic cell cycle | 11 | 5.2300 | ||
| GO:0048285~organelle fission | 11 | 6.3000 | ||
| GO:0007346~regulation of mitotic cell cycle | 9 | 9.6800 |
Gene set A represents the genes only differentially expressed in the clinically localized prostate cancer group; Gene set B represents the genes only differentially expressed in the metastatic prostate cancer group; Gene set C represents the genes differentially expressed in both groups. FDR, false discovery rate.
Enriched microRNAs in Gene set B.
| microRNA | P-value | Count | Genes targeted by microRNA |
|---|---|---|---|
| hsa_TATTATA, MIR-374 | 2.1100 | 10 | |
| hsa_CACTGTG, MIR-128 | 0.0003 | 9 | |
| hsa_ATGCAGT, MIR-217 | 0.0003 | 6 | |
| hsa_TGTTTAC, MIR-30 | 0.0005 | 11 | |
| hsa_ACAACTT, MIR-382 | 0.0032 | 4 | |
| hsa_ACTGCCT, MIR-34B | 0.0032 | 6 | |
| hsa_TTGCCAA, MIR-182 | 0.0036 | 7 | |
| hsa_CTTTGTA, MIR-524 | 0.0036 | 8 | |
| hsa_ATGTTAA, MIR-302C | 0.0038 | 6 | |
| hsa_TGCACTT, MIR-519 | 0.0038 | 8 |
Count represents the number of differentially-expressed genes targeted by microRNA. Gene set B represents the genes only differentially expressed in the metastatic prostate cancer group.
Figure 3.Regulatory network containing microRNAs and their corresponding differentially expressed genes for metastatic prostate cancer. Dark grey nodes represent upregulated genes; light grey nodes represent downregulated genes; and diamonds represent microRNAs.
Enriched pathways for the differentially-expressed genes in the regulatory network.
| Term | Description | Count | P-value | Genes |
|---|---|---|---|---|
| hsa04020 | Calcium signaling pathway | 3 | 0.02231 | |
| hsa05216 | Thyroid cancer | 2 | 0.03927 |