Differentially expressed miRNAs in triple negative breast cancer between African-American and non-Hispanic white women

Abstract

Triple Negative Breast Cancer (TNBC), a clinically aggressive subtype of breast cancer, disproportionately affects African American (AA) women when compared to non-Hispanic Whites (NHW). MiRNAs(miRNAs) play a critical role in these tumors, through the regulation of cancer driver genes. In this study, our goal was to characterize and compare the patterns of miRNA expression in TNBC of AA (n = 27) and NHW women (n = 30). A total of 256 miRNAs were differentially expressed between these groups, and distinct from the ones observed in their respective non-TNBC subtypes. Fifty-five of these miRNAs were mapped in cytobands carrying copy number alterations (CNAs); 26 of them presented expression levels concordant with the observed CNAs. Receiving operating characteristic (ROC) analysis showed a good power (AUC ≥ 0.80; 95% CI) for over 65% of the individual miRNAs and a high combined power with superior sensitivity and specificity (AUC = 0.88 (0.78-0.99); 95% CI) of the 26 miRNA panel in discriminating TNBC between these populations. Subsequent miRNA target analysis revealed their involvement in the interconnected PI3K/AKT, MAPK and insulin signaling pathways. Additionally, three miRNAs of this panel were associated with early age at diagnosis. Altogether, these findings indicated that there are different patterns of miRNA expression between TNBC of AA and NHW women and that their mapping in genomic regions with high levels of CNAs is not merely physical, but biologically relevant to the TNBC phenotype. Once validated in distinct cohorts of AA women, this panel can potentially represent their intrinsic TNBC genome signature.

Keywords: African American; copy number; microRNA; non-Hispanic white; triple negative breast cancer.

Figure 1. Workflow of miRNA expression and copy number profiling and downstream comprehensive computational analysis performed in the TNBC and non-TNBC cases of AA and NHW group of patients

Figure 2. Unsupervised (A) and Supervised (B) Hierarchical Clustering analysis applied to the TNBC (green bars) and non-TNBC (yellow bars) cases of the AA and NHW group of patients (left and right panel respectively)

Up-regulated miRNAs (yellow) and down-regulated miRNAs (blue). (MeV4.9; Pearson correlation, P < 0.01, FDR < 0.05).

Figure 3. Unsupervised (A) and Supervised (B) Hierarchical Clustering analysis applied to the TNBC cases of the AA (green bars) and NHW (blue bars) group of patients

Up-regulated miRNAs (yellow) and down-regulated miRNAs (blue). (MeV4.9; Pearson correlation, P < 0.01, FDR < 0.05).

Figure 4. Penetrance plot of the array-CGH profiling of the TNBC cases from the AA patients analyzed, showing the corresponding genome location (arrows) of the 26 miRNAs of the identified panel

Vertical lines represent each chromosome number. Red peaks indicate copy number gains and green peaks indicate copy number losses. MiRNAs with up- and down-regulated expression levels are annotated in red and green color boxes, respectively.

Figure 5. Expression levels of the 26 differentially expressed miRNAs observed between the AA and NHW TNBC cases

In (A) and (B): miRNAs up-and down-regulated, respectively, in the AA group of patients when compared to the NHW group.

Figure 6. Venn diagrams showing integration of genes located at the identified cytobands (A) and in the most frequent cytobands (present in greater than or equal to 50% of the cases) (B) with CNAs in the TNBC-AA cases and the corresponding miRNA target genes

Figure 7. ROC plots of the individual and combined 26 miRNAs differentially expressed between the AA and NHW-TNBC group of patients

Figure 8. Ingenuity Pathway Analysis (IPA) showing the main gene network interaction of 12 out of the 26 miRNA panel identified