Gastélum-López María de Los Ángeles, Aguilar-Medina Maribel, García Mata Cristina, López-Gutiérrez Jorge, Romero-Quintana Geovanni, Bermúdez Mercedes, Avendaño-Felix Mariana, López-Camarillo César, Pérez-Plascencia Carlos, Beltrán Adriana S, Ramos-Payán Rosalío
Faculty of Biological and Chemical Sciences, Autonomous University of Sinaloa, Josefa Ortiz de Domínguez s/n y Avenida de las Américas, Culiacan 80013, Sinaloa, Mexico.
Faculty of Dentistry, Autonomous University of Chihuahua, Av. Escorza No. 900, Centro, Chihuahua 31125, Chihuahua, Mexico.
Noncoding RNA. 2023 Oct 26;9(6):66. doi: 10.3390/ncrna9060066.
Currently, most of the research on breast cancer has been carried out in conventional two-dimensional (2D) cell cultures 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.
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 differentially expressed protein-coding genes (DE-mRNAs) and miRNAs (DE-microRNAs) found in the organoids.
We obtained well-defined cell-aggregated organoids with a grape cluster-like morphology with a size up to 9.2 × 10 μm. The transcriptomic assays showed that cell growth in organoids significantly affected (all < 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 ontology (GO) biological processes such as regulation of cell morphogenesis, regulation of cell shape, regulation of canonical Wnt signaling pathway, morphogenesis of epithelium, regulation of cytoskeleton organization, as well as in the MAPK and AGE-RAGE signaling KEGG-pathways. Interestingly, 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 81% of the 70 downregulated DE-mRNAs.
The organotypic 3D cell-organization architecture of breast cancer SKBR3 cells impacts the expression pattern of the 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 expression, and, therefore, support the pertinence of migrating breast cancer research from conventional cultures to 3D models.
目前，由于其实际优势，大多数关于乳腺癌的研究是在传统的二维（2D）细胞培养中进行的。然而，三维（3D）细胞培养正成为癌症研究中的首选模型，因为它允许细胞 - 细胞和细胞 - 细胞外基质（ECM）相互作用，模拟体内肿瘤的天然微环境。
在这项工作中，我们评估了3D细胞组织对乳腺癌SKBR3细胞系中miRNA（通过Small - RNAseq）和mRNA（通过微阵列）表达模式的影响，并分析了类器官中差异表达的蛋白质编码基因（DE - mRNAs）和miRNA（DE - 微RNA）所调控的生物学过程和信号通路。
我们获得了形态呈葡萄串状、大小可达9.2×10μm的明确的细胞聚集类器官。转录组分析表明，类器官中的细胞生长显著影响（所有P < 0.01）miRNA和mRNA的基因表达模式，发现20个上调和19个下调的DE - 微RNA，以及49个上调和123个下调的DE - mRNAs。计算机分析表明，11个上调的DE - 微RNA的一个子集靶向70个下调的DE - mRNAs。这些基因参与150个基因本体（GO）生物学过程，如细胞形态发生调控、细胞形状调控、经典Wnt信号通路调控、上皮形态发生、细胞骨架组织调控，以及MAPK和AGE - RAGE信号KEGG通路。有趣的是，hsa - mir - 122 - 5p（倍数变化（FC）= 15.4）、hsa - mir - 369 - 3p（FC = 11.4）和hsa - mir - 10b - 5p（FC = 20.1）调控了70个下调的DE - mRNAs中的多达81%。
乳腺癌SKBR3细胞的器官型3D细胞组织结构主要通过hsa - mir - 122 - 5p、hsa - mir - 369 - 3p和hsa - mir - 10b - 5p的过表达影响miRNA - mRNA网络的表达模式。所有这些发现表明，细胞 - 细胞和细胞 - ECM之间的相互作用以及培养结构的变化会影响基因表达，因此，支持将乳腺癌研究从传统培养向3D模型迁移的相关性。
