Proteomic and transcriptomic analysis of clinical and in vitro flow-exposed breast cancer samples reveals pathways and markers relevant to postpartum breast cancer.
Date
2024-01-13
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Abstract
Mechanical forces are an important, yet poorly understood, influence on the metastatic capability of breast cancer cells. They exist in a dynamic interplay with the structural and immune aspects of the cancer microenvironment. Mammary gland involution is a remodeling process that occurs post-lactation and is believed to be responsible for poor outcomes observed in postpartum breast cancer. Fluid shear stress is well-linked to tissue remodeling and is likely increased during this stage of the postpartum period. In this thesis, a bioreactor system was combined with hormonal treatment to expose breast cancer cells to some of the conditions relevant to postpartum involution. We initially validated the model by studying the morphology and viability of cells upon exposure to fluid shear stress and involution and confirming the presence of relevant protein markers. Using machine learning-based analysis of publicly available RNA-seq datasets, we identified numerous genes and pathways upregulated in both postpartum and flow-exposed conditions. We further validated these findings using proteomic analysis of flow-exposed MDA-MB-231 breast cancer cells, which identified similar proteins and pathways to the initial transcriptomic analysis. These included pathways linked to inflammation, wound healing, cell migration, and extracellular matrix organization, which are all pathways critically involved in the action of mammary gland involution. Further investigation revealed that matrix metalloproteinases, a key promoter of the remodeling activities and tumorigenic effect of involution, are significantly upregulated upon exposure to fluid flow. Proteomic analysis of MCF-7 cells treated with hormones associated with lactation revealed markers and pathways related to immune-mediated progression of breast cancer. Finally, we established the utility of our model by validating that the protein expression of chemokine C-X-C motif ligand 13 (CXCL13), which was upregulated in our transcriptomics analysis and is a well-established marker of breast cancer metastasis in young patients, is upregulated in response to flow-exposure. This suggests that our model serves as an efficient method to identify relevant breast cancer biomarkers related to the mechanism of mammary gland involution. To our knowledge, these studies are the first to integrate hormonal and fluid shear stress influences in the context of breast cancer, and to suggest a link between fluid shear stress and mammary gland involution. They serve as an initial proof of concept, indicating that fluid shear stress could serve as a powerful tool in furthering our understanding of postpartum breast cancer and identification of relevant biomarkers for this unique cohort.
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Keywords
Breast cancer, Postpartum health, Proteomics, Transcriptomics, Fluid shear stress, Bioreactor
Citation
Stibbards-Lyle, M. (2024). Proteomic and transcriptomic analysis of clinical and in vitro flow-exposed breast cancer samples reveals pathways and markers relevant to postpartum breast cancer (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.