基于生物信息学和实验室研究的乳腺癌样本中部分编码和非编码基因的表达水平评估

IF 0.4 Q4 ONCOLOGY
Elmira Rostamnejad, Ronak Rashidi, Zohreh Akbari, M. Maghsoudloo, Mehrdad Hashemi, Amirnader Emami Razavi, M. Entezari, Majid Sadeghizadeh
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引用次数: 0

摘要

背景:乳腺癌(BC)是全球妇女因癌症死亡的主要原因。然而,该过程的分子机制仍不清楚。在这方面,生物信息学研究在促进生物学研究的道路上起着决定性的作用,并能最终确定更好的候选分子供进一步研究。研究目的鉴于各类癌症中许多编码基因和非编码基因的异常表达及其与各种致癌机制的关系,本研究旨在根据生物信息学研究结果和实验室调查,评估参与 BC 癌症的某些编码基因和非编码基因的表达水平。研究方法基于生物信息学方法和实验室研究,进行基因表达数据集、模块提取、功能富集分析、蛋白-蛋白相互作用网络构建和 RT-qPCR。此外,通过对福尔马林固定石蜡包埋(FFPE)肿瘤组织中提取的 DNA 进行测序,研究了这些基因的启动子区域突变。结果选择了一个模块作为进一步研究的候选基因。雌激素受体 1(ESR1)和叉头盒 A1(FOXA1)在 PPI 网络中的关联度最高,分别为 9 个和 7 个。此外,与对照组相比,肿瘤组中 FOXA1 基因、线粒体 RNA 处理内切酶 RNA 成分(RMRP)和核富集丰富转录本 1(NEAT1)的表达水平显著上调(依次为 P = 0.044、P = 0.014 和 P = 0.0004)。与阴性转移样本相比,阳性转移患者肿瘤中 NEAT1 和 RMRP 的表达水平明显更高(P < 0.05)。此外,与阴性样本相比,HER2 阳性患者的 RMRP 表达水平大幅下降(P = 0.011)。最后,与正常样本相比,阳性转移样本的启动子测序未发现突变。结论所有三个受检基因的上调水平可能与 BC 的进展相关。因此,它们有可能被用作检测 BC 发展的生物标志物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Evaluation of the Expression Level of Some Coding and Non-coding Genes in Breast Cancer Samples Based on Bioinformatics and Laboratory Studies
Background: Breast cancer (BC) is the leading cause of cancer-associated mortality in women worldwide. However, the molecular mechanism underlying the process is still unclear. In this regard, bioinformatics studies play a decisive role in facilitating the path of biological investigations and can ultimately lead to the identification of better molecular candidates for further study. Objectives: Due to the abnormal expression of many coding and non-coding genes in all types of cancers and their relationship with various mechanisms of carcinogenesis, this study aimed at evaluating the expression levels of certain coding and non-coding genes involved in BC based on bioinformatics findings and laboratory investigations. Methods: Gene expression dataset, module extraction, functional enrichment analysis, protein-protein interaction network construction, and RT-qPCR were performed based on bioinformatics methods and laboratory investigations. Additionally, the promoter region mutations of these genes were investigated, using sequencing of extracted DNAs from formalin-fixed paraffin-embedded (FFPE) tumor tissues. Results: A module was selected as a candidate for further investigation. Estrogen receptor 1 (ESR1) and forkhead box A1 (FOXA1) showed the highest degrees in the PPI network with 9 and 7 links, respectively. Furthermore, the expression levels of the FOXA1 gene, RNA component of mitochondrial RNA processing endoribonuclease (RMRP), and nuclear enriched abundant transcript 1 (NEAT1) were significantly upregulated in the tumor group compared to the control group (in order, P = 0.044, P = 0.014, and P = 0.0004). The tumors of patients with positive metastasis displayed significantly higher levels of NEAT1 and RMRP expression compared to those of negative metastasis samples (P < 0.05). Moreover, the expression level of RMRP dramatically decreased in HER2-positive patients compared to negative samples (P = 0.011). Finally, no mutations were observed in the promoter sequencing of positive metastasis samples compared to normal samples. Conclusions: The upregulation levels of all three examined genes may correlate with BC progression. Therefore, they could potentially be used as biomarkers for detecting BC development.
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来源期刊
CiteScore
1.10
自引率
0.00%
发文量
67
期刊介绍: International Journal of Cancer Management (IJCM) publishes peer-reviewed original studies and reviews on cancer etiology, epidemiology and risk factors, novel approach to cancer management including prevention, diagnosis, surgery, radiotherapy, medical oncology, and issues regarding cancer survivorship and palliative care. The scope spans the spectrum of cancer research from the laboratory to the clinic, with special emphasis on translational cancer research that bridge the laboratory and clinic. We also consider original case reports that expand clinical cancer knowledge and convey important best practice messages.
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