通过计算机和体外方法鉴定与癌症调节相关的差异表达miRNA和mRNA。

IF 2 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Cytotechnology Pub Date : 2023-10-01 Epub Date: 2023-07-03 DOI:10.1007/s10616-023-00583-1
Pelin Telkoparan-Akillilar, Dilek Cevik
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引用次数: 0

摘要

miRNA的表达在癌症(BC)的发展过程中发生改变。本研究的目的是识别新的癌症相关miRNA和途径,以了解BC亚型的机制。从基因表达综合数据库下载GSE59247数据集,并用GEO2R软件进行分析。通过miRNome PCR阵列评估BC细胞中miRNA的差异表达。Venn图用于揭示GSE59247数据集和miRNome阵列之间共差异表达的miRNA。通过Kaplan-Meier曲线评估所选miRNA的临床预后意义。进行KEGG通路富集分析以寻找miRNA靶点,并通过TNM图分析和q-RT-PCR验证结果。TargetScan数据库用于预测miRNA与靶基因3'-非翻译区的关联,并通过人类蛋白质图谱数据库对其表达进行可视化。Venn图分析显示,来自计算机和体外分析的11个miRNA重叠。KEGG分析显示“赖氨酸降解途径”是最显著富集的靶向途径。q-RT-PCR结果证实赖氨酸降解途径相关基因SETD7、SETDB2、EHHADH、SETMAR、KMT2A和SUV39H2在BC细胞中差异表达。靶点预测分析确定了SETD7的miR-1323-5p和3'-UTR、EHHADH的miR-129-5p和2'-UTR以及SETDB2 mRNA的miR-628-5p和5'-UTR之间的结合位点。值得注意的是,miR-1323-5p、miR-129-5p和miR-628-5p在BC中差异表达,它们与赖氨酸降解途径的关键基因,即SETD7、SETDB2和EHHADH的3’UTR结合。这些miRNA可能是进展的潜在诊断和预后生物标志物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Identification of differentially expressed miRNAs and mRNAs associated with the regulation of breast cancer via in silico and in vitro methods.

Identification of differentially expressed miRNAs and mRNAs associated with the regulation of breast cancer via in silico and in vitro methods.

miRNA expressions are altered during development of breast cancer (BC). The aim of this study is to identify novel cancer-related miRNAs and pathways to understand the mechanisms of BC subtypes. GSE59247 dataset was downloaded from gene expression omnibus (GEO) database and analyzed with GEO2R software. The differential miRNA expressions in BC cells were evaluated by miRNome PCR array. Venn diagram was used to reveal co-differentially expressed miRNAs between GSE59247 dataset and miRNome array. Clinical prognostic significance of selected miRNAs was evaluated via Kaplan Meier curve. KEGG pathway enrichment analysis was performed to find miRNA targets and results were validated by TNM plot analysis and q-RT-PCR. TargetScan database was used to predict the association of miRNAs and 3'-untranslated regions of target genes and their expressions were visualized by human protein atlas database. Venn diagram analysis showed overlap of 11 miRNAs from in silico and in vitro analysis. KEGG analysis revealed 'Lysine Degradation Pathway' as the most significantly enriched targeted pathway. q-RT-PCR results confirmed that Lysine degradation pathway related genes SETD7, SETDB2, EHHADH, SETMAR, KMT2A and SUV39H2 were differentially expressed in BC cells. Target prediction analysis identified binding sites between miR-1323-5p and 3'-UTR of SETD7, miR-129-5p and 3'-UTR of EHHADH and miR-628-5p and 3'-UTR of SETDB2 mRNA. Notably, miR-1323-5p, miR-129-5p, and miR-628-5p are differentially expressed in BC and they bind to 3'UTR of critical genes of Lysine degradation pathway, namely SETD7, SETDB2 and EHHADH. These miRNAs might serve as potential diagnostic and prognostic biomarkers for progression.

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来源期刊
Cytotechnology
Cytotechnology 生物-生物工程与应用微生物
CiteScore
4.10
自引率
0.00%
发文量
49
审稿时长
6-12 weeks
期刊介绍: The scope of the Journal includes: 1. The derivation, genetic modification and characterization of cell lines, genetic and phenotypic regulation, control of cellular metabolism, cell physiology and biochemistry related to cell function, performance and expression of cell products. 2. Cell culture techniques, substrates, environmental requirements and optimization, cloning, hybridization and molecular biology, including genomic and proteomic tools. 3. Cell culture systems, processes, reactors, scale-up, and industrial production. Descriptions of the design or construction of equipment, media or quality control procedures, that are ancillary to cellular research. 4. The application of animal/human cells in research in the field of stem cell research including maintenance of stemness, differentiation, genetics, and senescence, cancer research, research in immunology, as well as applications in tissue engineering and gene therapy. 5. The use of cell cultures as a substrate for bioassays, biomedical applications and in particular as a replacement for animal models.
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