Detection of Circulating Serum microRNA/Protein Complexes in ASD Using Functionalized Chips for an Atomic Force Microscope

MicroRNAs, which circulate in blood, are characterized by high diagnostic value; in biomedical research, they can be considered as candidate markers of various diseases. Mature microRNAs of glial cells and neurons can cross the blood–brain barrier and can be detected in the serum of patients with autism spectrum disorders (ASD) as components of macrovesicles, macromolecular protein and low-density lipoprotein particles. In our present study, we have proposed an approach, in which microRNAs in protein complexes can be concentrated on the surface of AFM chips with oligonucleotide molecular probes, specific against the target microRNAs. MicroRNAs, associated with the development of ASD in children, were selected as targets. The chips with immobilized molecular probes were incubated in serum samples of ASD patients and healthy volunteers. By atomic force microscopy (AFM), objects on the AFM chip surface have been revealed after incubation in the serum samples. The height of these objects amounted to 10 nm and 6 nm in the case of samples of ASD patients and healthy volunteers, respectively. MALDI-TOF-MS analysis of protein components on the chip surface allowed us to identify several cell proteins. These proteins are involved in the binding of nucleic acids (GBG10, RT24, RALYL), in the organization of proteasomes and nucleosomes (PSA4, NP1L4), and participate in the functioning of the channel of active potassium transport (KCNE5, KCNV2).     

基于混合核和加权SVM的microRNA前体识别算法

MicroRNA是一种单链RNA小分子,是由具有发夹结构的、更长的单链RNA前体经加工后生成.相比microRNA序列本身而言,其前体序列和二级结构隐含了更多的可识别特征与信息.因此可利用加权Levenshtein距离,结合其前体序列和二级结构构造一个指数核函数.结合SVM构造识别模型,鉴别真假前体.在用5折叠法得到最佳识别模型后,对人类数据进行测试.实验结果显示,新方法表现出了较好的识别精度,和较高的敏感性与特异性.     

MicroRNA与慢性肾脏病并发动脉粥样硬化相关性与中医药干预研究进展

动脉粥样硬化(As)引起的心血管疾病是慢性肾脏病(CKD)患者主要并发症和主要死亡原因之一。microRNA是一类小的非编码RNA,是参与基因调控网络的重要因子。国内外大量研究表明部分microRNA的异常表达可通过多种机制介导CKD及其心血管并发症如As的病理进程,被确定为CKD As的病理相关因子,应用microRNA作为疾病生物标志物的独特优势和CKD As潜在治疗靶点的作用是现代研究热点。中医认为CKD As病机正虚与邪实夹杂,具有本虚标实的特点,中医药通过调控microRNA干预CKD As符合传统“扶正祛邪”治疗原则与现代中医微观辨证理念,以microRNA为切入点研究中医药防治CKD As的具体机制具有重要意义。本文就国内外microRNA与CKD As病理机制的相关性以及中药复方、中药活性成分调控CKD异常microRNA防治As的作用机制研究进展进行了综述,以期为未来相关研究提供理论参考,以便开发更有效的治疗策略,为临床中医药治疗CKD As提供新的可能途径与干预靶点。     

靶标介导DNA自组装及催化电流放大的microRNA电化学检测研究

该研究报道了一种靶标介导的DNA自组装及催化信号放大免标记电化学传感器定量检测microRNA-21的分析方法。根据靶标序列,设计一条末端标记巯基且具有茎环结构的捕获探针以及两条与捕获探针和靶标部分互补的DNA单链,通过金-硫键作用将捕获探针固定在金电极表面。当靶标(microRNA-21)存在时,自组装形成一种H结构的DNA复合结构;利用核酸链中磷酸骨架静电吸附电解液中的钌氨离子([Ru(NH₃)₆]³⁺,RuHex)以及DNA电子传递作用产生电化学信号;当无靶标时,不能形成DNA复合结构,电化学信号较弱。进一步利用铁氰根离子([Fe(CN)₆]^3-)能够氧化电化学还原产物([Ru(NH₃)₆]²⁺),产生电化学-化学偶联,从而实现催化电流信号放大。采用电化学阻抗谱确证DNA复合结构的形成,采用计时电量法考察捕获探针密度对电化学信号的影响,并优化探针浓度、比例以及自组装时间,采用差示脉冲伏安法进行定量分析。结果...     

Predicting microRNA biological functions based on genes discriminant analysis

Although thousands of microRNAs (miRNAs) have been identified in recent experimental efforts, it remains a challenge to explore their specific biological functions through molecular biological experiments. Since those members from same family share same or similar biological functions, classifying new miRNAs into their corresponding families will be helpful for their further functional analysis. In this study, we initially built a vector space by characterizing the features from miRNA sequences and structures according to their miRBase family organizations. Then we further assigned miRNAs into its specific miRNA families by developing a novel genes discriminant analysis (GDA) approach in this study. As can be seen from the results of new families from GDA, in each of these new families, there was a high degree of similarity among all members of nucleotide sequences. At the same time, we employed 10-fold cross-validation machine learning to achieve the accuracy rates of 68.68%, 80.74%, and 83.65% respectively for the original miRNA families with no less than two, three, and four members. The encouraging results suggested that the proposed GDA could not only provide a support in identifying new miRNAs’ families, but also contributing to predicting their biological functions.     

Nanoliter droplet array for microRNA detection based on enzymatic stem-loop probes ligation and SYBR Green real-time PCR

In this paper, a nanoliter droplet array based on enzymatic stem-loop probes ligation and SYBR Green real-time PCR for quantification of microRNA was developed. By employing T4 RNA ligase 2 instead of T4 DNA ligase, we designed simplified stem-loop probes to perform microRNA-templated DNA ligation and reduced the non-specific ligation of T4 DNA ligase. SYBR green I dye was employed instead of TaqMan probes in present miniaturized real-time PCR systems. Specifically, we optimized the dosage of SYBR Green I dye in nanoliter droplet and verified the performance of this system by detecting synthetic mir-122 with a 6 logs dynamic range (from 1.5 × 10⁵ to 1.5 × 10¹⁰ copies). Linear relationship of the standard curve (R² = 0.9997) and high PCR amplification efficiency (96.83%) were obtained under the optimized conditions. We detected the expression of mir-122 across five mouse tissues and the result was consistent with that TaqMan microRNA assay. We think this miniaturized real-time PCR platform reduced the detection cost considerably, thus showing the great potential to quantitative biology.     

Discovery of a Prenylated Flavonol Derivative as a Pin1 Inhibitor to Suppress Hepatocellular Carcinoma by Modulating MicroRNA Biogenesis

Peptidyl‐prolyl cis‐trans isomerase Pin1 plays a crucial role in the development of human cancers. Recently, we have disclosed that Pin1 regulates the biogenesis of miRNA, which is aberrantly expressed in HCC and promotes HCC progression, indicating the therapeutic role of Pin1 in HCC therapy. Here, 7‐(benzyloxy)‐3,5‐dihydroxy‐2‐(4‐methoxyphenyl)‐8‐(3‐methylbut‐2‐en‐1‐yl)‐4H‐chromen‐4‐one ( AF‐39 ) was identified as a novel Pin1 inhibitor. Biochemical tests indicate that AF‐39 potently inhibits Pin1 activity with an IC₅₀ values of 1.008 μm , and also displays high selectivity for Pin1 among peptidyl prolyl isomerases. Furthermore, AF‐39 significantly suppresses cell proliferation of HCC cells in a dose‐ and time‐dependent manner. Mechanistically, AF‐39 regulates the subcellular distribution of XPO5 and increases miRNAs biogenesis in HCC cells. This work provides a promising lead compound for HCC treatment, highlighting the therapeutic potential of miRNA‐based therapy against human cancer.     

Electrochemical analysis of nucleic acids as potential cancer biomarkers

In recent years, a huge progress has been made regarding the development of electrochemical (EC) assays for detection of nucleic acids — DNA or RNA — as potential cancer biomarkers. Various ingenious strategies for determination of DNA methylation of gene promoters, circulating tumor DNAs, viral nucleic acids, or short noncoding microRNAs were presented, many of them showing remarkable sensitivities. However, a majority of these assays were not applied into clinical samples from patients, which is crucial should the electrochemistry compete with conventional, routinely used techniques. In this review, we critically evaluate strengths and weaknesses of EC assays that recognized this necessity and successfully determined endogenous DNA or RNA in patient samples with various forms of tumors.     

circRNA研究进展

环形RNA（circular RNAs,circRNAs）是一类通过反向剪接所形成的闭合环状RNA分子,广泛存在于各种生物细胞中,并且具有结构稳定、表达量丰富以及在不同组织及其不同发育阶段具有表达特异性等特征。circRNAs可以作为miRNA海绵调控m iRNA的表达,通过cis或trans调控其母基因的表达,并参与蛋白的翻译。此外,circRNA在神经发育及相关疾病的发生和发展过程中起着重要的调控作用,有望成为疾病诊断的分子标志物。本文就circRNA的分子特征、形成机制、功能、常用的数据库及其与神经系统疾病的关系做一综述。