MicroRNA-based regulation of Aurora A kinase in breast cancer

Abstract

The involvement of non-coding RNAs (ncRNAs) in cellular physiology and disease pathogenesis is becoming increasingly relevant in recent years specifically in cancer research. Breast cancer (BC) has become a health concern and accounts for most of the cancer-related incidences and mortalities reported amongst females. In spite of the presence of promising tools for BC therapy, the mortality rate of metastatic BC cases is still high. Therefore, the genomic exploration of the BC subtype and the use of ncRNAs for possible regulation is pivotal. The expression and prognostic values of AURKA gene were assessed by Oncomine, GEPIA, KM-plotter, and bc-GenExMiner v4.4, respectively. Associated proteins and functional enrichment were evaluated by Cytoscape and DAVID databases. Additionally, molecular docking approach was employed to investigate the regulatory role of hsa-miR-32-3p assisted argonaute (AGO) protein of AURKA gene in BC. AURKA gene was highly expressed in patients with BC relative to normal counterpart and significantly correlated with poor survival. The docking result suggested that AURKA could be regulated by hsa-miR-32-3p as confirmed by the reported binding energy and specific interactions. The study gives some insights into role of AURKA and its regulation by microRNAs through AGO protein. It also provides exciting opportunities for cancer therapeutic intervention.

Keywords: AURKA; breast cancer therapy; gene expression; human argonaute; regulatory microRNA.

Figure 1. The transcription levels of AURKA in different types of cancers (Oncomine).

The graphic demonstrated the numbers of datasets with statistically significant mRNA over-expression (red) or down-expression (blue) of the target gene. (A) the expression of AURKA in 20 datasets (Oncomine). (B) the expression of AURKA in BC (GEPIA). The threshold was designed with following parameters: Threshold (p-value): 1.0 × 10^-6; threshold (fold change) × 2; and gene rank of top 5%; TPM: Transcript per million. Abbreviations: GEPIA, Gene Expression Profiling Interactive Analysis.

Figure 2. mRNA expression of AURKA in BC subtypes (Oncomine database).

The three datasets (A) and the BC subtypes (B). Note: Curtis Breast Statistics: 0. Breast (B); 1. Benign Breast Neoplasm (BBN); 2. Breast Carcinoma (BC); 3. Breast Phyllodes Tumor (BPT); 4. Ductal Breast Carcinoma in situ (DBCi); 5. Invasive Breast Carcinoma (IBC); 6. Invasive Ductal Breast Carcinoma (IDBC); 7. Invasive ductal and invasive lobular breast carcinoma; 8. invasive lobular Breast Carcinoma; 9. Medullary Breast Carcinoma (MBC); 10. Mucinous Breast Carcinoma (MuBC); 11. Tubular Breast Carcinoma (TCB). Zhao Breast Statistics: 0. Breast; 1. Invasive ductal BC; 2. Lobular BC. TCGA Breast Statistics: 0. Breast; 1. Apocrine Breast Carcinoma; 2. Breast Large Cell Neuroendocrine Carcinoma; 3. Ductal Breast Carcinoma; 4. Intraductal Cribriform Breast Carcinoma; 5. Invasive Breast Carcinoma; 6. Invasive Cribriform Breast Carcinoma; 7. Invasive Ductal Breast Carcinoma; 8. Invasive Ductal and Lobular Carcinoma; 9. Invasive Lobular Carcinoma; 10. Invasive Papillary Breast Carcinoma; 11. Male Breast Carcinoma; 12. Metastatic Breast Carcinoma; 13. Mixed Lobular and Ductal Breast Carcinoma; 14. Mucinous Breast Carcinoma; 15. Papilary Breast Carcinoma; 16. Pleomorphic Breast Carcinoma.

Figure 3. The prognostic value of mRNA level of AURKA in BC patients (Kaplan–Meier plotter).

Notes: The OS, PPS, DMFS, and RFS survival curve comparing the patient with high (red) and low (black) AURKA expression in BC were plotted from Kaplan–Meier plotter database as the threshold of P-value < 0.05, respectively. Endpoints Affymetrix IDs: 208079_s_at. Abbreviations: OS: overall survival; PPS: progression free survival; RFS: relapses free survival; DMFS: distance metastasis free survival.

Figure 4. Survival analysis of AURKA in BC.

The meta-analysis of the hazard ration with their p-values (A), and the four end points pictorial images from PrognoScan database. (B) The survival curves depict the high (Red) and low (blue) expressions with the datasets and endpoints. Abbreviations: OS: overall survival; DFS: disease free survival; RFS: relapses free survival; DMFS: distance metastasis free survival; HR: hazard ratio.

Figure 5. Intrinsic molecular subtype of AURKA in BC patients (bc-GenExMiner v4.4).

The box plots are based on Intrinsic molecular subtype of AURKA. Correlation between AURKA expression and genetic information in BC patients. The significant different between groups was assessed by Welch’s test to generate p value, along with Dunnett-Tukey-Kramer’s and the P-value was set at 0.05.

Figure 6. The protein interaction network of genes associated with AURKA (STRING in Cytoscape).

Figure 7. The structural models of microRNA and microRNA-AURKA duplex.

The dot-bracket notations are colored by base-pairing probability (A), the secondary structures are colored by positional entropy (B), the 3D structures were modeled and visualized by DSV v19 (C), the Ramachandra plot of the prepared hAgo2 receptor was verified by PDBSum PROCHEK. The area marked with green arrows are residues in the most favored region while the regions marked with teal arrows are residues in additional allowed region (D) and the 3D model of the prepared hAgo2 was done by Maestro v12.2 (E).

Figure 8. Molecular docking result of miR-32 and hAgo2.

The binding position of the miR-32 in the pocket of hAgo2 (A); Residual amino acids participating in their interaction (B); Amino acid residues (C).

Figure 9. The docking result of miR-32-AURKA and hAgo2.

The binding position of the complex in the pocket of hAgo2 (A); Residual amino acids participating in their interaction (B); Amino acid residues (C).