三阴性乳腺癌相关miRNA筛选及其靶基因的生物信息学分析

应用生物信息学方法筛选并分析三阴性乳腺癌（triple-negative breast cancer,TNBC）相关miRNA及其靶基因,为TNBC的研究提供潜在的分子靶点。采用GEO2R分析TNBC相关miRNA芯片数据集,筛选差异表达倍数最大的5个上调和5个下调miRNA。miRWalk、TargetScan和miRDB预测靶基因并进行Veen分析取交集。利用DAVID对靶基因进行GO富集分析和KEGG通路分析。利用STRING数据库构建蛋白互作网络,并结合Cytoscape构建miRNA-靶基因调控网络,从而筛选出关键的miRNA及其关键靶基因。利用GEPIA2数据库对靶基因进行生存分析。GEO2R筛选出486个差异miRNA,上调和下调的miRNA分别有298个和188个。对差异倍数最大的5个上调和5个下调miRNA的靶基因进行富集分析显示,靶基因主要参与ErbB信号通路、癌症中转录调控紊乱和cGMP-PKG信号通路等。miRNA-靶基因调控网络显示,表达上调的关键miRNA为miR-611,其关键靶基因为CDC27、UBE2D2、UBR1、SPSB1、HERC2和RLIM;表达下调的关键miRNA为miR-1205,其关键靶基因为WSB1、FBXL8、UBE2W、PTPN11、ARF6、DNAJC6和COPS2。生存分析表明,UBR1（P=0.007 2）和PTPN11（P=0.029）表达上调可显著降低TNBC患者的整体生存率。经筛选获得的关键miRNA及其关键靶基因可作为潜在分子标记物用于TNBC的早期诊断、治疗靶点选择和预后判断,并为后续的研究提供参考依据。     

Identification of novel therapeutic targets for neuropathic pain based on gene expression patterns

Neuropathic pain (NP) caused by nerve injury or dysfunction is one of the most challenging neurological diseases. In-depth study of disease signatures contributes to the development of novel target treatment for NP. In this study, we analyzed expression profiles of qualified NP datasets (GSE24982 and GSE63442) deposited at Gene Expression Omnibus database by systematic bioinformatics approaches. We analyzed the differentially expressed genes of high and low pain compared with normal control group, and between spinal nerve ligation (SNL) injury model and sham-operation group. A total of 1,243 upregulated and 1,533 downregulated genes were identified in GSE24982, 380 upregulated and 355 downregulated genes were identified in GSE63442. By comparing low-pain samples with the corresponding sham-operation group, we identified 457 upregulated and 409 downregulated genes. Overlapping genes were screened out and signaling pathway and expression regulation model analyses were performed. SCN10A and SST were identified as biomarkers for NP. In conclusion, our study showed the expression pattern of gene about NP. These identified biomarkers could serve as potential therapeutic targets for treating NP.     

Identification and characterization of salt-responsive microRNAs in Populus tomentosa by high-throughput sequencing

Salt is one of the main environmental factors limiting plant growth and a better understanding of mechanisms of salt stress would aid efforts to bolster plant salt tolerance. MicroRNAs are well known for their important regulatory roles in response to abiotic stress in plants. In this study, high-throughput sequencing was employed to identify miRNAs in Populus tomentosa plantlets treated or not with salt (200 mM for 10 h). We found 141 conserved miRNAs belonging to 31 families, 29 non-conserved but previously-known miRNAs belonging to 26 families, and 17 novel miRNAs. Under salt stress, 19 miRNAs belonging to seven conserved miRNA families were significantly downregulated, and two miRNAs belonging to two conserved miRNA families were upregulated. Of seven non-conserved miRNAs with significantly altered expression, five were downregulated and two were upregulated. Furthermore, eight miRNAs were validated by qRT-PCR and their dynamic differential expressions were analyzed. In addition, 269 target genes of identified miRNAs were predicted and categorized by function. These results provide new insights into salt-responsive miRNAs in Populus.     

MicroRNA regulation of molecular networks mapped by global microRNA, mRNA, and protein expression in activated T lymphocytes

MicroRNAs (miRNAs) regulate specific immune mechanisms, but their genome-wide regulation of T lymphocyte activation is largely unknown. We performed a multidimensional functional genomics analysis to integrate genome-wide differential mRNA, miRNA, and protein expression as a function of human T lymphocyte activation and time. We surveyed expression of 420 human miRNAs in parallel with genome-wide mRNA expression. We identified a unique signature of 71 differentially expressed miRNAs, 57 of which were previously not known as regulators of immune activation. The majority of miRNAs are upregulated, mRNA expression of these target genes is downregulated, and this is a function of binding multiple miRNAs (combinatorial targeting). Our data reveal that consideration of this complex signature, rather than single miRNAs, is necessary to construct a full picture of miRNA-mediated regulation. Molecular network mapping of miRNA targets revealed the regulation of activation-induced immune signaling. In contrast, pathways populated by genes that are not miRNA targets are enriched for metabolism and biosynthesis. Finally, we specifically validated miR-155 (known) and miR-221 (novel in T lymphocytes) using locked nucleic acid inhibitors. Inhibition of these two highly upregulated miRNAs in CD4(+) T cells was shown to increase proliferation by removing suppression of four target genes linked to proliferation and survival. Thus, multiple lines of evidence link top functional networks directly to T lymphocyte immunity, underlining the value of mapping global gene, protein, and miRNA expression.