Expression profiling of MDA-MB-231 and MDA-MB-468 after ALDH1A3 manipulation, all-trans retinoic acid treatment, decitabine treatment. Homo sapiens

Retinoids, derivatives of vitamin A, are key physiological molecules with regulatory effects on cell differentiation, proliferation and apoptosis. As a result, they are of interest for cancer therapy. Specifically, models of breast cancer have varied responses to manipulations of the retinoid signaling cascade. This study characterizes the transcriptional response of MDA-MB-231 and MDA-MB-468 breast cancer cells to retinaldehyde dehydrogenase 1A3 (ALDH1A3) and to all-trans retinoic acid (atRA). We demonstrate limited overlap between ALDH1A3-induced gene expression and atRA-induced gene expression in both cell lines, suggesting that the function of ALDH1A3 in breast cancer progression extends beyond its role as a retinaldehyde dehydrogenase. Our data reveals divergent transcriptional responses to atRA, which are largely independent of genomic retinoic acid response elements (RAREs) and consistent with the opposing responses of MDA-MB-231 and MDA-MB-468 to in vivo atRA treatment. We identify transcription factors associated with each gene set. Manipulation of one of the transcription factors (i.e. interferon regulatory factor 1; IRF1) demonstrates that it is the level of atRA-inducible and epigenetically regulated transcription factors that determine expression of target genes (e.g. CTSS, cathepsin S). This study provides a paradigm for complex, combinatorial responses of breast cancer models to atRA treatment, and illustrates the need to characterize RARE-independent responses to atRA in a variety of models. Overall design: Samples run in triplicate: MDA-MB-231 and MDA-MB-468 with or without ALDH1A3 expression; with or without atRA treatment; with or without decitabine treatment.

类视黄醇（Retinoids）即维生素A衍生物，是一类关键的生理活性分子，对细胞分化、增殖与凋亡具有调控作用，因此在癌症治疗领域受到广泛关注。具体而言，不同乳腺癌模型对视黄醇信号通路的调控干预呈现出各异的应答反应。本研究针对MDA-MB-231与MDA-MB-468两种乳腺癌细胞，解析其对视黄醛脱氢酶1A3（retinaldehyde dehydrogenase 1A3, ALDH1A3）以及全反式维甲酸（all-trans retinoic acid, atRA）的转录应答特征。研究发现，两种细胞系中ALDH1A3诱导的基因表达谱与atRA诱导的基因表达谱仅有极少重叠，这提示ALDH1A3在乳腺癌进展中的功能并非仅局限于其作为视黄醛脱氢酶的作用。本研究数据显示，两种细胞对atRA的转录应答存在显著差异，且该差异主要不依赖于基因组维甲酸应答元件（retinoic acid response elements, RAREs），这与MDA-MB-231与MDA-MB-468在体内接受atRA处理时呈现的相反应答结果一致。本研究还分别鉴定了与两组基因表达谱相关的转录因子。通过对其中一种转录因子——干扰素调节因子1（interferon regulatory factor 1, IRF1）进行干预实验，证实靶基因（如组织蛋白酶S（cathepsin S, CTSS））的表达水平由atRA诱导且经表观遗传调控的转录因子的表达量所决定。本研究为解析乳腺癌模型对atRA处理的复杂组合应答提供了研究范式，同时也凸显了在多种模型中表征不依赖RARE的atRA应答机制的必要性。实验设计概述：所有样本均设置三次生物学重复，实验分组涵盖：MDA-MB-231与MDA-MB-468细胞分别存在或缺失ALDH1A3表达；分别接受或不接受atRA处理；分别接受或不接受地西他滨（decitabine）处理的各组样本。