Gastélum-López, M.Á.; Aguilar-Medina, M.; García Mata, C.; López-Gutiérrez, J.; Romero-Quintana, G.; Bermúdez, M.; Avendaño-Felix, M.; López-Camarillo, C.; Pérez-Plascencia, C.; Beltrán, A.S.; Ramos-Payán, R. Organotypic 3D Cell-Architecture Impacts the Expression Pattern of miRNAs–mRNAs Network in Breast Cancer SKBR3 Cells. Non-Coding RNA2023, 9, 66.
Gastélum-López, M.Á.; Aguilar-Medina, M.; García Mata, C.; López-Gutiérrez, J.; Romero-Quintana, G.; Bermúdez, M.; Avendaño-Felix, M.; López-Camarillo, C.; Pérez-Plascencia, C.; Beltrán, A.S.; Ramos-Payán, R. Organotypic 3D Cell-Architecture Impacts the Expression Pattern of miRNAs–mRNAs Network in Breast Cancer SKBR3 Cells. Non-Coding RNA 2023, 9, 66.
Gastélum-López, M.Á.; Aguilar-Medina, M.; García Mata, C.; López-Gutiérrez, J.; Romero-Quintana, G.; Bermúdez, M.; Avendaño-Felix, M.; López-Camarillo, C.; Pérez-Plascencia, C.; Beltrán, A.S.; Ramos-Payán, R. Organotypic 3D Cell-Architecture Impacts the Expression Pattern of miRNAs–mRNAs Network in Breast Cancer SKBR3 Cells. Non-Coding RNA2023, 9, 66.
Gastélum-López, M.Á.; Aguilar-Medina, M.; García Mata, C.; López-Gutiérrez, J.; Romero-Quintana, G.; Bermúdez, M.; Avendaño-Felix, M.; López-Camarillo, C.; Pérez-Plascencia, C.; Beltrán, A.S.; Ramos-Payán, R. Organotypic 3D Cell-Architecture Impacts the Expression Pattern of miRNAs–mRNAs Network in Breast Cancer SKBR3 Cells. Non-Coding RNA 2023, 9, 66.
Abstract
Background. Currently, most of the research in breast cancer has been carried out in conventional two-dimensional (2D) cell culture due to its practical benefits, however, the three-dimensional (3D) cell culture is becoming the model of choice in cancer research because it allows cell-cell and cell-extracellular matrix (ECM) interactions, mimicking the native microenvironment of tumors in vivo. Methods. in this work, we evaluated the effect of 3D cell organization on the expression pattern of miRNAs (by Small-RNAseq) and mRNAs (by microarrays) in the breast cancer SKBR3 cell line and analyzed the biological processes and signaling pathways regulated by the differ-entially expressed protein-coding genes (DE-mRNAs) and miRNAs (DE-microRNAs) found in the organoids. Results. We obtained well-defined cell-aggregated organoids with a grape cluster-like morphology with a size up to 9.2×105 μm3. The transcriptomic assays showed that cell growth in organoids significantly affected (all p < 0.01) the gene expression patterns of both, miRNAs and mRNAs, finding 20 upregulated and 19 downregulated DE-microRNAs, as well as 49 upregulated and 123 downregulated DE-mRNAs. In silico analysis showed that a subset of 11 upregulated DE-microRNAs target 70 downregulated DE-mRNAs. These genes are involved in 150 gene on-tology (GO) biological processes such as regulation of cell morphogenesis, regulation of cell shape, regulation of canonical Wnt signaling pathway, morphogenesis of epithelium, regulation of cy-toskeleton organization, as well as in the MAPK and AGE-RAGE signaling KEGG-pathways. In-terestingly, hsa-mir-122-5p (Fold Change (FC)=15.4), hsa-mir-369-3p (FC=11.4), and hsa-mir-10b-5p (FC=20.1) regulated up to the 81 % of the 70 downregulated DE-mRNAs. Conclu-sion, the organotypic 3D cell-organization architecture of breast cancer SKBR3 cells impacts the expression pattern of miRNAs-mRNAs network mainly through overexpression of hsa-mir-122-5p, hsa-mir-369-3p, and hsa-mir-10b-5p. All these findings suggest that the interaction between cell-cell and cell-ECM as well as the change in the culture architecture impacts gene ex-pression, and therefore, support the pertinence of migrating breast cancer research from conven-tional cultures to 3D models.
Keywords
breast cancer; microRNAs; 2D cell culture; 3D cell culture; organotypic 3D cell culture
Subject
Medicine and Pharmacology, Oncology and Oncogenics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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