Differential miRNA Expressions Linking Environmental Risk Factors to Triple-Negative Breast Cancer Stages at Diagnosis

Abstract

Background/Objectives: Triple negative breast cancer (TNBC) is an aggressive, molecularly heterogeneous subtype of breast cancer, accounting for approximately 10-15% of all cases. While reproductive and metabolic factors contribute to breast cancer development, growing concerns about environmental exposures, alongside biological and socio-cultural influences, underscore the need for targeted prevention strategies across diverse populations. Despite increasing evidence linking biological, socioeconomic, and environmental factors to TNBC outcomes, the molecular mechanisms underlying these relationships remain poorly understood. Micro-RNAs (miRNAs), which regulate gene expression and play critical roles in cancer development, have emerged as potential mediators between environmental exposures and TNBC progression. The goal of this research is to identify environmental risk factors that directly relate to TNBC stages and enhance understanding of the mechanisms underlying how miRNAs link environmental exposures to TNBC stages. Methods: In this study, we analyzed 434 Formalin-Fixed, Paraffin-Embedded (FFPE) tumor samples from 434 women diagnosed with TNBC between 2009 and 2019, encompassing diverse cancer stages (184 cases from early stage and 250 cases from advanced stage), racial backgrounds, and socioeconomic statuses. The sequencing data were linked with the Louisiana Tumor Registry data and the Environmental Justice index. Results: A total of 348 unique miRNAs were identified as differentially expressed across environmental risk factors statistically associated with TNBC stage, adjusting for plate effects. An UpSet plot revealed 44 miRNAs commonly differentially expressed across TNBC stages and multiple environmental exposures. At least one differentially expressed (DE) miRNA was shared between the TNBC stage and each environmental factor, with many associated with receptor-negative and aggressive breast cancer subtypes. Conclusions: These findings highlight potential biological pathways through which exposures may drive the TNBC progression and contribute to disparities in outcomes.

Keywords: TMM normalization; TNBC; TNBC stage; UpSet plot; breast cancer; environmental risk factors; functional enrichment analysis; miRNA; pathway analysis.

Figure 1

UpSet plot displaying 44 differentially expressed miRNAs shared between TNBC stage and various environmental risk factors. The horizontal bars on the bottom left indicate the total number of DE miRNAs associated with each environmental variable that are also shared with the TNBC stage. The matrix layout below the main bar plot uses dark-filled circles to represent combinations of variables that share one or more DE miRNAs. The vertical bars on the top quantify the number of DE miRNAs common to each specific combination of variables indicated by the corresponding filled circles.