miRNA生物信息学及其在医学研究中的应用
miRNA是一类重要的基因调控因子，越来越多的证据表明miRNA在许多重要的生命过程中发挥着关键作用。因此，和miRNA有关的功能异常和许多疾病有关（根据人类miRNA疾病数据库， HMDD, http://cmbi.bjmu.edu.cn/hmdd, 的统计，目前已经有近400种人类疾病被报道了和miRNA有关）。因此，miRNA正在成为理解疾病发生发展机制的明星分子，并且疾病的预防、诊断与治疗中具有巨大的潜在的应用价值。从有关miRNA研究的一开始，生物信息学在其中就发挥着重要作用。从miRNA发现到靶基因预测，从分子进化到网络调控，从疾病易感位点确定到疾病miRNA关联分析，都可以看到生物信息学的身影。在本报告中，报告人将重点介绍本人实验室在miRNA-疾病-药物之间关系的生物信息学研究，从大规模数据分析到建模和预测，同时概括miRNA生物信息学在医学研究中的应用。
全谱miRNA非标记芯片技术
芯片技术是miRNA表达谱高通量检测的主要手段之一，而常规芯片和测序技术常需要几小时的人工操作才能完成标记，导致成本过高、操作过于繁琐，重复性较差，因此，要走向临床比较困难。我们利用自主研发的技术，首次实现了高通量microRNA芯片的非标记检测，大幅度降低了检测的标记时间和检测成本。 报告首先介绍了目前主流的miRNA芯片技术，然后阐述了我们的芯片技术原理，并对性能进行了全面的评价和对比，除了无需对miRNA进行标记以外，还具有以下优点：1，高效识别小分子RNA中间和末端的单碱基缺失、冗余的差异，常规芯片技术难以实现；2，高灵敏度，检测限为20 fM，检测丰度跨4个数量级，满足绝大多数小分子RNA的检测；3，直接使用总RNA，无需预分离小分子RNA，无需样品标记，大幅度降低了检测的时间和成本；4，检测不受植物等miRNA的3'末端甲基化影响，而其他酶法标记的技术效率大幅度降低。 最后将我们的技术与测序技术进行了比较，认为我们的技术在检测成本、大量样品处理、数据分析、检测时间和重复性方面具有优势，是对比两种状态的miRNA表达谱的一个理想技术。
转录因子和miRNA在复杂疾病中的共调控网络研究
Transcription factors (TFs) are key regulators controlling the transcription of target genes by binding to specific DNA sequences on the promoter of target genes. Both the TFs and miRNAs are regulators of gene expression and they may mutual regulate each other to form feedback loops (FBL), or they regulate the same target gene to form a feed-forward loop (FFL). It has been reported that hundreds of potential miRNA-mediated feedback and feed-forward loops are available at the genome level. To predict the TF-miRNA co-regulatory FFL and FBL loops, we integrated multiple data of TF targets and miRNA targets including both experimentally validated and predicted. Thus, we developed a strategy to predict the TF-miRNA co-regulatory FFL and FBL loops. We used these methods to study the TF-miRNA co-regulation in specific diseases including schizophrenia and T-cell acute lymphoblastic leukemia (T-ALL). We identified and verified some key miRNA and genes in these diseases. In the T-ALL, we obtained 120 FFLs among T-ALL related genes, miRNAs and TFs. Afterwards, a T-ALL miRNA and TF co-regulatory network was constructed and its significance was tested by statistical methods. Four miRNAs in the miR-17~92 cluster and 4 important genes (CYLD, HOXA9, BCL2L11, and RUNX1) were found as hubs in the network. Particularly, we found that miR-19 was highly expressed in T-ALL patients and cell lines. Ectopic expression of miR-19 repress CYLD expression, while miR-19 inhibitor treatment induce CYLD protein expression and decreases NF-κB expression in the downstream signaling pathway. Thus, miR-19, CYLD and NF-κB form a regulatory feed-forward loop, which provides new clues for sustained activation of NF-κB in T-ALL. Some single nucleotide polymorphisms (SNPs) in miRNA genes or target sites (miRNA-related SNPs) have been proved to be associated with human diseases by affecting the miRNA mediated regulatory function. To systematically analyze miRNA-related SNPs and their effects, we performed a genome-wide scan for SNPs in human pre-miRNAs, miRNA flanking regions, target sites and designed a pipeline to predict the effects of them on miRNA-target interaction. As a result, we identified 48 SNPs in human miRNA seed regions and thousands of SNPs in 3'- untranslated regions with the potential to either disturb or create miRNA-target interactions. Furthermore, we experimentally confirmed 7 loss-of-function SNPs and 1 gain-of-function SNP by luciferase assay. All useful data were complied into miRNASNP, a user-friendly free online database (http://www.bioguo.org/miRNASNP/). These data will be a useful resource for studying miRNA function, identifying disease-associated miRNAs, and further personalized medicine.
全谱miRNA非标记芯片技术
芯片技术是miRNA表达谱高通量检测的主要手段之一，而常规芯片和测序技术常需要几小时的人工操作才能完成标记，导致成本过高、操作过于繁琐，重复性较差，因此，要走向临床比较困难。我们利用自主研发的技术，首次实现了高通量microRNA芯片的非标记检测，大幅度降低了检测的标记时间和检测成本。
报告首先介绍了目前主流的miRNA芯片技术，然后阐述了我们的芯片技术原理，并对性能进行了全面的评价和对比，除了无需对miRNA进行标记以外，还具有以下优点：1，高效识别小分子RNA中间和末端的单碱基缺失、冗余的差异，常规芯片技术难以实现；2，高灵敏度，检测限为20 fM，检测丰度跨4个数量级，满足绝大多数小分子RNA的检测；3，直接使用总RNA，无需预分离小分子RNA，无需样品标记，大幅度降低了检测的时间和成本；4，检测不受植物等miRNA的3'末端甲基化影响，而其他酶法标记的技术效率大幅度降低。
最后将我们的技术与测序技术进行了比较，认为我们的技术在检测成本、大量样品处理、数据分析、检测时间和重复性方面具有优势，是对比两种状态的miRNA表达谱的一个理想技术。
miRNA生物信息学及其在医学研究中的应用
miRNA是一类重要的基因调控因子，越来越多的证据表明miRNA在许多重要的生命过程中发挥着关键作用。因此，和miRNA有关的功能异常和许多疾病有关（根据人类miRNA疾病数据库， HMDD, http://cmbi.bjmu.edu.cn/hmdd, 的统计，目前已经有近400种人类疾病被报道了和miRNA有关）。因此，miRNA正在成为理解疾病发生发展机制的明星分子，并且疾病的预防、诊断与治疗中具有巨大的潜在的应用价值。从有关miRNA研究的一开始，生物信息学在其中就发挥着重要作用。从miRNA发现到靶基因预测，从分子进化到网络调控，从疾病易感位点确定到疾病miRNA关联分析，都可以看到生物信息学的身影。在本报告中，报告人将重点介绍本人实验室在miRNA-疾病-药物之间关系的生物信息学研究，从大规模数据分析到建模和预测，同时概括miRNA生物信息学在医学研究中的应用。
转录因子和miRNA在复杂疾病中的共调控网络研究
Transcription factors (TFs) are key regulators controlling the transcription of target genes by binding to specific DNA sequences on the promoter of target genes. Both the TFs and miRNAs are regulators of gene expression and they may mutual regulate each other to form feedback loops (FBL), or they regulate the same target gene to form a feed-forward loop (FFL). It has been reported that hundreds of potential miRNA-mediated feedback and feed-forward loops are available at the genome level.