Gene expression and DNA methylation analyses suggest that immune process-related ADCY6 is a prognostic factor of luminal-like breast cancer

Breast cancer is a malignant tumor that seriously threatens women's health, and luminal-like cancer subtypes account for the majority of the cases. The purpose of this study was to investigate the relationships among DNA methylation, gene expression profile, and the tumor-immune microenvironment of luminal-like breast cancer, and to identify the potential key genes that regulate immune cell infiltration in luminal-like breast cancer. The ESTIMATE algorithm was applied to calculate immune scores and stromal scores of patients with breast cancer. Kaplan-Meier curves were generated for survival analysis. The clusterProfile package was used for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Correlations between ADCY6 expression and immune cell infiltration-related pathways were analyzed by gene set variation analysis. R software was used for the statistical analysis and figure generation. Disease-free survival was higher in the immune score-high group than it was in the immune score-low group, while the stromal score had no correlation with prognosis. There were 515 genes that differed in both gene expression and DNA methylation levels, and these genes were mainly enriched in immune process-related pathways. ADCY6 was enriched in module A of the PPI network. Patients with downregulation and hypermethylation of ADCY6 associated with a better prognosis. ADCY6 expression was negatively correlated with the activation of immune process-related signaling pathways, immune checkpoint receptors, and ligands, except for CLEC4G. DNA methylation was found to be involved in the regulation of the key cellular pathways of luminal-like breast cancer immune cell infiltration. Additionally, ADCY6 was identified as a prognostic factor involved in the DNA methylation-regulated immune processes in luminal-like breast cancer.     

乳腺癌发生的特征基因筛选及模式识别

本文选取癌症基因组图谱数据库的乳腺癌样本作为数据集,在全基因组的水平上研究乳腺癌病人从正常到发病Ⅰ期基因表达的变化,寻找与乳腺癌发病密切相关的特征基因,建立乳腺癌发生的模式识别分类方法,为乳腺癌预防及早期诊断提供理论支持.研究中,综合利用相关性、t检验、置信区间等统计学方法,建立乳腺癌发生特征基因筛选方法,获得与乳腺癌发生具有显著性差异的特征基因336个.通过机器学习方法建模,得到的分类准确率能达到98%以上,与之前乳腺癌相关的研究相比,准确率更高.同时采用KEGG(kyoto encyclopedia of genes and genomes)通路分析得到与基因显著相关(P0.05)的通路有8个,GO(gene ontology)基因功能富集分析显示与基因显著相关(P0.05)的功能有18个.最后对映射在8个通路中的一部分基因进行简要功能分析,说明了其在调控水平上的密切关系,表明识别的特征基因在乳腺癌的发生过程中有重要的作用,这对了解乳腺癌发病机理以及乳腺癌的早期诊断非常重要.     

Effects of Luteolin on Human Breast Cancer Using Gene Expression Array: Inferring Novel Genes

Taraxacum officinale (dandelion) is often used in traditional Chinese medicine for the treatment of cancer; however, the downstream regulatory genes and signaling pathways mediating its effects on breast cancer remain unclear. The present study aimed to explore the effects of luteolin, the main biologically active compound of T. officinale, on gene expression profiles in MDA-MB-231 and MCF-7 breast cancer cells. The results revealed that luteolin effectively inhibited the proliferation and motility of the MDA-MB-231 and MCF-7 cells. The mRNA expression profiles were determined using gene expression array analysis and analyzed using a bioinformatics approach. A total of 41 differentially expressed genes (DEGs) were found in the luteolin-treated MDA-MB-231 and MCF-7 cells. A Gene Ontology analysis revealed that the DEGs, including AP2B1, APP, GPNMB and DLST, mainly functioned as oncogenes. The human protein atlas database also found that AP2B1, APP, GPNMB and DLST were highly expressed in breast cancer and that AP2B1 (cut-off value, 75%) was significantly associated with survival rate (p = 0.044). In addition, a Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the DEGs were involved in T-cell leukemia virus 1 infection and differentiation. On the whole, the findings of the present study provide a scientific basis that may be used to evaluate the potential benefits of luteolin in human breast cancer. Further studies are required, however, to fully elucidate the role of the related molecular pathways.     

MICB基因多态性与乳腺癌的易感关联性研究

目的:研究海南汉族人群MICB等位基因的多态性与乳腺癌易感性之间的关联性。方法:采用PCRSSP(PCR sequence-specific primers)和PCR-SBT(PCR sequence-based typing)方法对样本MICB等位基因的多态性进行检测。结果:乳腺癌患者中检出14种MICB等位基因;和对照组相比较,MICB*002和MICB*014等位基因在乳腺癌患者组分布频率较少,MICB*002和MICB*014等位基因可能对乳腺癌不易感(MICB*002:OR=0.31,95%CI:0.19-0.51,Pc0.05;MICB*014:OR=0.32,95%CI:0.17-0.60,Pc0.05)。MICB*016和MICB*003等位基因在乳腺癌患者组分布较多;MICB*016和MICB*003等位基因可能对乳腺癌易感(MICB*016:OR=10.68,95%CI:2.52-45.28,Pc0.05;MICB*003:OR=3.57,95%CI:1.34-9.49,Pc0.05);MICB*002/002和MICB*014/014基因型可能对乳腺癌不易感(MICB*002/002:OR=0.12,95%CI:0.04-0.36,Pc0.05;MICB*014/014:OR=0.30,95%CI:0.10-0.89,Pc0.05)。结论:MICB等位基因的多态性与乳腺癌的易感性之间存在关联性。     

circRNA-associated ceRNA network construction reveals the circRNAs involved in the progression and prognosis of breast cancer

Recently, increasing evidences show that circular RNAs (circRNAs) are important regulators of various diseases, especially cancer. However, the regulatory role and the potential mechanism of action of circRNAs in breast cancer remain largely unknown. In this study, weighted gene co-expression network analysis was conducted with the differentially expressed miRNAs and mRNAs in breast cancer from The Cancer Genome Atlas database to identify the key modules associated with the carcinogenesis of breast cancer. In the significant turquoise and brown modules, 22 miRNAs and 1877 mRNAs were identified, respectively. Then, We compared and predicted the target genes and performed survival analysis to identify the miRNAs and mRNAs related to the prognosis of breast cancer. A circRNA-related competitive endogenous RNA network was identified by database co-screening, and deleted in liver cancer 1 (DLC1) was identified as a key gene. Finally, to assess how genes in key modules and key genes contribute to the development of breast cancer, relevant pathway information was obtained through DAVID and Gene Set Enrichment Analysis. These data demonstrated that three circRNAs (hsa-circ-0083373, hsa-circ-0083374, and hsa-circ-0083375) that regulate DLC1 expression via hsa-mir-511 and are involved in the pathogenesis and development of breast cancer.     

乳腺癌基因芯片实验数据分析与挖掘

目的 对公共数据库上下载得到的乳腺癌基因芯片试验结果进行数据分析,找出在正常组织与癌组织中呈现差异表达的基因,并寻找差异表达基因的相关基因.方法 综合运用显著性分析（SAM）、顶级评分基因对（TSP）、关联规则挖掘等方法,对数据进行处理.结果 筛选出若干呈现差异表达的基因,并且寻找了其中一部分基因的可能高度相关的基因.结论 筛选出的基因及其相关基因可用于为进一步的研究提供候选基因.     

基于多目标评价方法的乳腺癌易感基因排序及其网络表达研究

目的利用已有的研究结果和数据,采用多目标评价方法建立乳腺癌易感基因评价模型,对与已知乳腺癌基因关系密切的其它基因进行分析和排序,并给出结果的网络表达模式。方法通过分析已有的文献,并利用有关的基因数据库和已有文献中的数据,提炼出乳腺癌易感基因的多目标评价体系,构建基于加权和法的乳腺癌易感基因评价模型,并利用Cytoscape软件进行评价结果计算和评价结果的网络模式表达。结果利用多目标模型所得到的评价结果,与已有的研究结果一致。其中,乳腺癌易感基因TopBP1排名第二,已知乳腺癌候选易感基因HMMR排名第六。结论文章提出的多目标评价模型能够准确评价被选基因与乳腺癌易感性之间的关系,所提出的评价方法与相关软件结合使用,将成为癌症易感基因研究方面有效的分析方法和途径。     

Relation of glutathione S-transferase T1, M1 and P1 genotypes and breast cancer risk

The aim of this study was to investigate associations between genetic variability in specific Glutathione S-transferases (GST) genes (GSTM1, GSTT1 and GSTP1) and susceptibility to breast cancer. Genotypes of blood specimen DNA were determined for 65 women with incident cases of breast cancer and 108 control subjects. Associations between specific genotypes and the development of breast cancer were examined by the use of logistic regression to calculate odds ratios (ORs) and 95% confidence intervals (CIs). Neither GSTT1 nor GSTM1 homozygous null genotype was associated with a significant increased risk of developing breast cancer. The presence of valine alleles compared to isoleucine alleles in codon 105 in GSTP1 did not increase the risk of breast cancer development. The risk of breast cancer associated with a combined GSTT1 and GSTM1 null genotype was 3.37 (95% CI = 0.76-2.95, p = 0.115). The only significant association between increased risk of breast cancer development and GSTs polymorphisms was found when GSTT1 null, GSTM1 null and the presence of valine in GSTP1 in codon 105 were combined (p < 0.048, OR = 3.75, 95% CI = 1.01-13.90). Our findings suggest that combined genetic variability in members of the GST gene family may be associated with an increased susceptibility to breast cancer.     

MicroRNA-21 as a predictor and prognostic factor for trastuzumab therapy in human epidermal growth factor receptor 2-positive metastatic breast cancer

Breast cancer is the second most common cancer diagnosed worldwide. Human epidermal growth factor receptor 2 (HER2)-positive breast cancer represents about 20% to 30% of all breast cancers. Trastuzumab is used in the treatment of HER2-positive breast cancer. MicroRNA-21 (miR-21) is an oncomiR that acts by inhibiting many tumor-suppressor genes. We analyzed the relative expression levels of serum miR-21 in 20 HER2-positive metastatic breast cancer patients before and after 3 months of treatment with trastuzumab. miR-21 levels decreased with a high significant difference after trastuzumab therapy (P = 0.001). Although miR-21 expression levels were lower in responders than in nonresponders, the difference was not statistically significant ( P = 0.6). Our results demonstrated a significant negative correlation between its basal expression, expression levels after treatment, and time to progression ( P = 0.03 and 0.01, respectively). These results make miR-21 a potential prognostic factor for HER2-positive metastatic breast cancer patients. Additionally, it can be an interesting potential target in therapy using antisense oligonucleotides for miR-21.     

乳腺癌转移相关基因表达调控网络的线性微分方程模型的初步研究

初步构建乳腺癌转移相关基因表达调控网络的线性微分方程模型,并分析模型的可靠性和生物学意义. 采用基因芯片技术,分别对30例伴有淋巴结转移的乳腺癌组织及其相应淋巴结转移癌组织进行基因表达谱的比较,选择差异基因通过线性微分数学方法构建表达调控网络模型. 差异表达基因共27个,其中Ratio > 3的明显上调基因14个,而Ratio < 0.33的明显下调基因13个. 比较伴有淋巴结转移的乳腺癌组织和其相应淋巴结转移癌组织,分析筛选了27个表达差异基因,应用数学线性微分方程方法初步构建乳腺癌转移相关基因表达调控网络的线性微分方程模型,通过分析模型中重要节点、通路的生物学意义,判定网络的数学特性,初步表明,调控网络的可靠性和乳腺癌转移的形成是与多基因、多通路异常引起的细胞恶性转化相关.     

Identification of a novel germline BRCA2 variant in a Chinese breast cancer family

Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer‐related deaths in women worldwide. In this study, a large Chinese pedigree with breast cancer including a proband and two female patients was recruited and a familial history of breast cancer was collected by questionnaire. Clinicopathological assessments and neoadjuvant therapy‐related information were obtained for the proband. Blood samples were taken, and gDNA was extracted. The BRCA1/2 and PALB2 genes were screened using next‐generation sequencing by a targeted gene panel. We have successfully identified a novel, germline heterozygous, missense mutation of the gene BRCA2: c.7007G>T, p.R2336L, which is likely to be pathogenic in the proband and her elder sister who both had breast cancer. Furthermore, the risk factors for developing breast cancer in this family are discussed. Thus, genetic counselling and long‐term follow‐up should be provided for this family of breast cancer patients as well as carriers carrying a germline variant of BRCA2: c.7007G>T (p.R2336L).     

Expression profiling after induction of demethylation in MCF-7 breast cancer cells identifies involvement of TNF-α mediated cancer pathways

Epigenetic methylation change is a major process that occurs during cancer development. Even though many tumor-related genes have been identified based on their relationship between methylation and expression, few studies have been conducted to investigate the relevant biological pathways involved in these changes. To identify essential pathways likely to be affected by methylation in breast cancer, we examined a pool of genes in which expression was upregulated after induction of demethylation by 5-Aza-2′-deoxycytidine (Aza) in the MCF-7 breast cancer cell line. Genome-wide demethylation was confirmed by monitoring the demethylation of a previously known gene, SULT1A1. Overall, 210 and 213 genes were found to be upregulated and downregulated (fold change ≥ 2), respectively, in common in cells treated with 5 and 10 μM of Aza. Network analysis of these 423 genes with altered expression patterns identified the involvement of a cancer related network of genes that were heavily regulated by TNF-α in breast tumorigenesis. Our results suggest that epigenetic dysregulation of cellular processes relevant to TNF-α-dependent apoptosis may be intimately involved in tumorigenesis in MCF-7 cells.     

miR-139-5p is a regulator of metastatic pathways in breast cancer

Metastasis is a complex, multistep process involved in the progression of cancer from a localized primary tissue to distant sites, often characteristic of the more aggressive forms of this disease. Despite being studied in great detail in recent years, the mechanisms that govern this process remain poorly understood. In this study, we identify a novel role for miR-139-5p in the inhibition of breast cancer progression. We highlight its clinical relevance by reviewing miR-139-5p expression across a wide variety of breast cancer subtypes using in-house generated and online data sets to show that it is most frequently lost in invasive tumors. A biotin pull-down approach was then used to identify the mRNA targets of miR-139-5p in the breast cancer cell line MCF7. Functional enrichment analysis of the pulled-down targets showed significant enrichment of genes in pathways previously implicated in breast cancer metastasis (P < 0.05). Further bioinformatic analysis revealed a predicted disruption to the TGFβ, Wnt, Rho, and MAPK/PI3K signaling cascades, implying a potential role for miR-139-5p in regulating the ability of cells to invade and migrate. To corroborate this finding, using the MDA-MB-231 breast cancer cell line, we show that overexpression of miR-139-5p results in suppression of these cellular phenotypes. Furthermore, we validate the interaction between miR-139-5p and predicted targets involved in these pathways. Collectively, these results suggest a significant functional role for miR-139-5p in breast cancer cell motility and invasion and its potential to be used as a prognostic marker for the aggressive forms of breast cancer.