Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation

Abstract

The microRNA (miRNA) biomolecules have a significant role in the development of breast cancer, and their expression profiles are different in each subtype of breast cancer. Thus, our goal is to use the Next Generation Sequencing provided high-throughput miRNA expression and clinical data in an integrated fashion to perform survival analysis in order to identify breast cancer subtype specific miRNAs, and analyze associated genes and transcription factors. We select top 100 miRNAs for each of the four subtypes, based on the value of hazard ratio and p-value, thereafter, identify 44 miRNAs that are related to all four subtypes, which we call as four-star miRNAs. Moreover, 12, 14, 9, and 15 subtype specific, viz. one-star miRNAs, are also identified. The resulting miRNAs are validated by using machine learning methods to differentiate tumor cases from controls (for four-star miRNAs), and subtypes (for one-star miRNAs). The four-star miRNAs provide 95% average accuracy, while in case of one-star miRNAs 81% accuracy is achieved for HER2-Enriched. Differences in expression of miRNAs between cancer stages is also analyzed, and a subset of eight miRNAs is found, for which expression is increased in stage II relative to stage I, including hsa-miR-10b-5p, which contributes to breast cancer metastasis. Subsequently we prepare regulatory networks in order to identify the interactions among miRNAs, their targeted genes and transcription factors (TFs), that are targeting those miRNAs. In this way, key regulatory circuits are identified, where genes such as TP53, ESR1, BRCA1, MYC, and others, that are known to be important genetic factors for the cause of breast cancer, produce transcription factors that target the same genes as well as interact with the selected miRNAs. To provide further biological validation the Protein-Protein Interaction (PPI) networks are prepared and Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology (GO) enrichment analysis are performed. Among the enriched pathways many are breast cancer-related, such as PI3K-Akt or p53 signaling pathways, and contain proteins such as TP53, also present in the regulatory networks. Moreover, we find that the genes are enriched in GO terms associated with breast cancer. Our results provide detailed analysis of selected miRNAs and their regulatory networks.

MicroRNAs in Molecular Classification and Pathogenesis of Breast Tumors

“…Despite the fact that most circulating miRNAs in cancer patients may not originate from tumors but rather reflect the host homeostatic response, the systemic miRNAs do have the potential to be used in monitoring disease progression and predicting long-term risk. Dysregulation of microRNAs is also an early event in tumorigenesis, most significant during the transition from normal to atypical ductal hyperplasia (ADH), thereby marking them as promising cancer biomarkers, targets and effectors for the early diagnosis of cancer [ 17 , 21 , 22 ]. MicroRNA expression profiles alone or integrated with mRNA profiles are reported to improve breast cancer subtyping and are even more informative than protein-coding RNAs [ 22 ].…”

Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell Resolution

“…Previous studies have revealed several molecular subtypes of BC. For example, a study reported the genetic determinants of BC immune phenotypes based on integrative genome-scale analysis ( Hendrickx et al, 2017 ), and Denkiewicz et al (2019) identified BC subtype-specific microRNAs based on survival analysis to explore the roles of microRNAs in transcriptomic regulation. In our study, we mainly concentrated on the overall immune profiles, which may offer more detailed information about the immune landscape of ER+ BC.…”

The Possible Influence of Mediterranean Diet on Extracellular Vesicle miRNA Expression in Breast Cancer Survivors

“…“Tissue development pathway (GO:0009888)” and “multicellular organismal development pathway (GO:2000026)” were associated with genes altered in invasive breast cancer [ 54 ] and multidrug resistance in MCF-7/MDR breast cancer cells [ 55 ]. Most pathways enriched in annotations of genes targeted by downregulated miRNAs were associated with the pathogenesis and progression of breast cancer: microRNAs in cancer [hsa05206] [ 56 ], translation [GO:0006412] [ 57 ], reproductive system development [GO:0061458] [ 58 ], cell cycle [GO:0007049] [ 58 ], adherens junction [GO:0005912], and anchoring junction [GO:0070161]) [ 59 ]. Although it is impossible to understand fully all biological phenomena driving gene expression and phenotypic changes, our approach has a potential clinical applicability and paves the way for future research on breast cancer prognosis.…”