Breast Cancer Cells Reprogram the Oncogenic lncRNAs/mRNAs Coexpression Networks in Three-Dimensional Microenvironment

• DOI: 10.3390/cells11213458
• Publication Date: 2022-11-02T07:36:44Z
• Authors: Stephanie I. Nuñe...; Lorena Aguilar-Arnal; Mireya Cisneros-V...; Alfredo Hidalgo-M...; Laurence A. Marchat; Yarely M. Salinas...; Rosalio Ramos-Payán; Carlos Pérez-Plas...; Ángeles Carlos-Reyes; Jonathan Puente-R...; Cesar López-Camar...
• Keywords: 0303 health sciences; QH573-671; Carcinogenesis; Chromosomal Proteins, Non-Histone; therapy response; lncRNAs; organotypic 3D cultures; Breast Neoplasms; Oncogenes; co-regulation networks; Article; 3. Good health; Gene Expression Regulation, Neoplastic; 03 medical and health sciences; breast cancer; Tumor Microenvironment; Humans; Female; RNA, Long Noncoding; RNA, Messenger; Cytology; breast cancer; organotypic 3D cultures; lncRNAs; co-regulation networks; therapy response

Organotypic three-dimensional (3D) cell cultures more accurately mimic the characteristics of solid tumors in vivo comparison with traditional two-dimensional (2D) monolayer models. Currently, studies on regulation long non-coding RNAs (lncRNAs) have not been explored breast cancer cells cultured 3D microenvironments. In present research, we studied expression and potential roles lncRNAs estrogen receptor-positive luminal B subtype BT-474 grown over extracellular matrix proteins-enriched cultures. Global profiling using DNA microarrays identifies 290 upregulated 183 downregulated relative to 2D condition. Using a co-expression analysis approach mRNAs pairs expressed same experimental conditions, identify hundreds regulatory axes modulating genes involved hallmarks, such as responses estrogens, proliferation, hypoxia, apical junctions, resistance endocrine therapy. addition, identified 102 lncRNAs/mRNA correlations cultures, which were similar those reported TCGA datasets obtained from patients. Interestingly, also found set transcripts co-expressed LINC00847 CTD-2566J3.1 lncRNAs, predictors pathologic complete response overall survival. Finally, both CTD -2566J3.1 essential for genetic dependencies, FOXA1 y GINS2. Our predictive findings show that lncRNAs/mRNAs exhibit high degree similarity patients, suggesting they could be adequate pre-clinical tools only biomarkers related therapy PCR, but understand biological behavior