Detection of Microvesicle miRNA Expression in ALL Subtypes and Analysis of Their Functional Roles

Microvesicles （MVs） are the heterogeneous mixtures of vesicles. MVs released by leukemia cells constitute an important part of the leukemia microenvironment. MVs might act as important reser- voirs of microRNAs （miRNAs）. It is worth evaluating whether MVs possess some unique miRNA con- tents that are valuable in understanding the pathogenesis. In this study, we investigated the miRNA ex- pression patterns of Nalm-6-derived MVs, Jurkat-derived MVs and normal cell-derived MVs using miRNA microarrays. The potential target genes regulated by differentially expressed miRNAs were also predicted and analyzed. Results demonstrated that 182 miRNAs and 166 miRNAs were differentially expressed in Nalm-6-MVs and Jurkat-MVs, respectively. Many oncogenes, tumor suppressors and sig- nal pathway genes were targeted by these aberrantly expressed miRNAs, which might contribute to the development of B-ALL or T-ALL. Our findings expanded the potential diagnostic markers of ALL and provided useful information for ALL pathogenesis.

Relationship between Mutations in DNA Sequences Loci Coding Pre-miRNAs and Genes Related to Biogenesis of SncRNAs with MiRNA Expression in Endometrial Carcinoma Tissues

Endometrial cancer （EC） is the most common and lethal gynaecological cancer type in Europe and in North America. Frequently EC arises more in the corpus proper and manifests as round, polypoid expansile masses, but it may also originate in the lower uterine segment or spread in endometrium with necrosis and hemorrhage. The analysis was performed using a custom panel containing all DNA sequences loci coding pre-miRNAs and genes related to biogenesis and regulation of sncRNAs in normal and tumor tissues extracted from 6 unrelated patients with endometrial carcinoma. The identified variations were correlated with mature miRNAs differentially expressed in the same normal and tumor endometrial tissues. The comparison analysis confirmed the high degree of cellular and genetic intratumoral heterogeneity with a temporal and spatial miRNA expression distribution in association with genomic variants identified. The classification of specific DNA mutations, onto the loci identified, should be suitable to characterize possible instability genome regions and help classification of tumors to ameliorate the clinical management of patients affected by endometrial carcinoma.

miRNA expression profiles in cerebrospinal fluid and blood of patients with Alzheimer’s disease and other types of dementia-an exploratory study

Background:MicroRNAs(miRNAs)are small non-coding RNA molecules that function as posttranscriptional regulators of gene expression.Measurements of miRNAs in cerebrospinal fluid(CSF)and blood have just started gaining attention as a novel diagnostic tool for various neurological conditions.The purpose of this exploratory investigation was to analyze the expression of miRNAs in CSF and blood of patients with Alzheimer’s disease(AD)and other neurodegenerative disorders in order to identify potential miRNA biomarker candidates able to separate AD from other types of dementia.Methods:CSF was collected by lumbar puncture performed on 10 patients diagnosed with AD and 10 patients diagnosed with either vascular dementia,frontotemporal dementia or dementia with Lewy bodies.Blood samples were taken immediately after.Total RNA was extracted from cell free fractions of CSF and plasma,and a screening for 372 known miRNA sequences was carried out by real time quantitative polymerase chain reactions(miRCURY LNA™Universal RT miRNA PCR,Polyadenylation and cDNA synthesis kit,Exiqon).Results:Fifty-two miRNAs were detected in CSF in at least nine out of ten patients in both groups.Among these,two miRNAs(let-7i-5p and miR-15a-5p)were found significantly up-regulated and one miRNA(miR-29c-3p)was found significantly down-regulated in patients with AD compared to controls.One hundred and sixty-eight miRNAs were frequently detected in the blood,among which miR-590-5p and miR-142-5p were significantly up-regulated and miR-194-5p was significantly down-regulated in AD patients compared to controls.Conclusions:Detection of miRNA expression profiles in blood and in particular CSF of patients diagnosed with different types of dementia is feasible and it seems that several expressional differences between AD and other dementia types do exist when measured in a clinically relevant setup.In this explorative pilot study,the deregulated miRNAs in CSF of AD patients may be associated with relevant target genes related to AD pathology,including APP and BACE1,which suggests that miRNAs are interesting candidates for AD biomarkers in the future.

Herb-partitioned moxibustion regulated the miRNA expression profile in the thyroid tissues of rats with experimental autoimmune thyroiditis

OBJECTIVE:To observe the effect of herb-partitioned moxibustion(HPM)on the miRNA expression profile of thyroid tissue in experimental autoimmune thyroiditis(EAT)rats.METHODS:Rats were randomly divided into normal control(NC)group,EAT model(EAT)group,HPM group and western medicine(Med)group.EAT model rats were prepared by a combined immunization with complete and incomplete Freund’s adjuvant emulsified with porcine thyroglobulin and iodine.Rats in the HPM group were treated with HPM,while rats in the Med group were treated with levothyrocine(1μg/2 m L)by gavage.HE staining was used to observe the pathological morphological changes of thyroid tissue,ELISAs was uaed to detect the serum concentrations of TGAb,TPOAb,FT3,FT4,TSH.We then performed high-throughput mi RNA sequencing to analyse the mi RNA expression profiles in the thyroid tissues,followed by a bioinformatics analysis.RT-q PCR was used to verify the identified differentially expressed mi RNAs.RESULTS:HPM improved the thyroid tissue morphology and reduced serum TPOAb,TGAb,TSH concentration in EAT rats(P<0.05),but with no obvious effect on FT3 and FT4 concentration.While the TSH,FT3 and FT4 concentration was significantly changed in the Med group(P<0.01 or P<0.05)compared with that of EAT group.Sequencing results showed that a total of 17 mi RNAs were upregulated,and 4 were downregulated in the EAT rats,in which the expression levels of mi R-346 and mi R-331-5 p were reversed by HPM.The target genes of the mi RNAs that regulated by HPM wereassociated with a variety of immune factors and immune signals.RT-q PCR verification showed that the expression of mi RNA-346 and mi RNA-331-5 p was consistent with the sequencing results.CONCLUSIONS:HPM could regulate the the expression of mi RNA-346 and mi RNA-331-5 p,then act on their target genes to immune and inflammation-related pathways,which may be one of the mechanisms of HPM on EAT rats.

Impact of tiny miRNAs on cancers

miRNAs are a class of small, ∽22nt, non-coding RNAs that negatively regulate gene expression at the posttranscriptional level. They play profound and pervasive roles in manipulating gene expression involved in cell development, proliferation and apoptosis in various eukaryotes, which, in theory, could provide an access to many human diseases in theory. Recent evidence demonstrates that aberrant miRNA expression is a hallmark of tumor development, revealing that miRNA genes could function as potential oncogenes and repressors in the human body. miRNAs can affect tumorigenesis mainly by interrupting the cell cycle at the cellular level and by interacting with signaling, oncogenes and with the response to environmental factors at the molecular level. The established miRNA expression signature could be a potent tool to diagnose and treat human cancers in the future.

An integrated analysis of mRNA-miRNA transcriptome data revealed hub regulatory networks in three genitourinary cancers

Bladder,kidney,prostate and testicular carcinoma are the top four genitourinary cancers in China.Here we analyzed mRNA and miRNA expression profiles of carcinomas of the bladder(TCC),kidney(ccRCC)and testis(TGCT)to uncover their specific regulatory mechanisms.The gene expression profiles of GSE31617 were downloaded from GEO database,which contained 27 samples,including 10 TCC,7 TGCT and 10 ccRCC.Specific up-and downregulated differentially expressed genes(DEGs)and differentially expressed microRNAs(DEmiRNAs)of each cancer were selected and target genes of DEmiRNAs were predicted.Gene interaction network of the shared genes and target genes of DEmiRNAs of each cancer was predicted by STRING and constructed by Cytoscape.In each cancer,we build regulatory networks of hub genes selected and conducted GO analysis of enriched genes.Furthermore,we chose four hub genes(SALL4,RHEB,CDC42 and TNN)for survival analysis in OncoLnc database,and they all had effects on the survival rate of another genitourinary cancer-kidney renal clear cell carcinoma(KIRC).In conclusion,the present study indicated that the identified hub genes promote our understanding of molecular mechanisms underlying the development of three genitourinary cancers,and might be used as molecular targets and diagnostic biomarkers for the treatment of them.

MicroRNAs: a novel promising therapeutic target for cerebral ischemia/reperfusion injury?

To determine the molecular mechanism of cerebral ischemia/reperfusion injury, we examined the micro RNA（mi RNA） expression profile in rat cortex after focal cerebral ischemia/reperfusion injury using mi RNA microarrays and bioinformatic tools to systematically analyze Gene Ontology（GO） function classifications, as well as the signaling pathways of genes targeted by these differentially expressed mi RNAs. Our results show significantly changed mi RNA expression profiles in the reperfusion period after focal cerebral ischemia, with a total of 15 mi RNAs up-regulated and 44 mi RNAs down-regulated. Target genes of these differentially expressed mi RNAs were mainly involved in metabolic and cellular processes, which were identified as hub nodes of a mi RNA-GO-network. The most correlated pathways included D-glutamine and D-glutamate metabolism, the renin-angiotensin system, peroxisomes, the PPAR signaling pathway, SNARE interactions in vesicular transport, and the calcium signaling pathway. Our study suggests that mi RNAs play an important role in the pathological process of cerebral ischemia/reperfusion injury. Understanding mi RNA expression and function may shed light on the molecular mechanism of cerebral ischemia/reperfusion injury.

Interplay of SOX transcription factors and microRNAs in the brain under physiological and pathological conditions

Precise tuning of gene expression,accomplished by regulato ry networks of transcription factors,epigenetic modifiers,and microRNAs,is crucial for the proper neural development and function of the brain cells.The SOX transcription factors are involved in regulating diverse cellular processes during embryonic and adult neurogenesis,such as maintaining the cell stemness,cell prolife ration,cell fate decisions,and terminal diffe rentiation into neurons and glial cells.MicroRNAs represent a class of small non-coding RNAs that play important roles in the regulation of gene expression.Together with other gene regulatory factors,microRNAs regulate different processes during neurogenesis and orchestrate the spatial and temporal expression important for neurodevelopment.The emerging data point to a complex regulatory network between SOX transcription factors and microRNAs that govern distinct cellular activities in the developing and adult brain.Deregulated SOX/mic roRNA interplay in signaling pathways that influence the homeostasis and plasticity in the brain has been revealed in various brain pathologies,including neurodegenerative disorders,traumatic brain injury,and cancer.Therapeutic strategies that target SOX/microRNA interplay have emerged in recent years as a promising tool to target neural tissue regeneration and enhance neuro restoration.N umerous studies have confirmed complex intera ctions between microRNAs and SOX-specific mRNAs regulating key features of glioblastoma.Keeping in mind the crucial roles of SOX genes and microRNAs in neural development,we focus this review on SOX/microRNAs interplay in the brain during development and adulthood in physiological and pathological conditions.Special focus was made on their interplay in brain pathologies to summarize current knowledge and highlight potential future development of molecular therapies.

MiR-96-5p inhibition induces cell apoptosis in gastric adenocarcinoma

BACKGROUND Gastric adenocarcinoma(GAC)mortality rates have remained relatively changed over the past 30 years,and it continues to be one of the leading causes of cancerrelated death.AIM To search for novel miRNAs related to GAC prognosis and further investigate the effect of miR-96-5p on MGC-803 cells.METHODS The miRNA expression profile data of GAC based on The Cancer Genome Atlas were obtained and used to screen differently expressed miRNAs(DEMs)and DEMs related to GAC prognosis.Then,the expression of DEMs related to GAC prognosis was identified in GAC tumor samples and adjacent normal samples by qRT-PCR.The target gene,ZDHHC5,of miR-96-5p was predicted using TargetScan,miRTarBase,and miRDB databases and confirmed by luciferase reporter assay.Furthermore,MGC-803 cells were transfected with inhibitor NC,miR-96-5p inhibitor,si-ZDHHC5,or miR-96-5p inhibitor+si-ZDHHC5,and then cell apoptosis was detected by flow cytometry.The expression of ZDHHC5,Bcl-2,and COX-2 was detected using western blotting.RESULTS A total of 299 DEMs and 35 DEMs related to GAC prognosis were screened based on The Cancer Genome Atlas.Then compared with adjacent normal samples,the levels of miR-96-5p,miR-222-5p,and miR-652-5p were remarkably increased,while miR-125-5p,miR-145-3p,and miR-379-3p levels were reduced in GAC tumor samples(P<0.01),which were consistent with bioinformatics analysis.Furthermore,ZDHHC5 was defined as a direct target gene of miR-96-5p.miR-96-5p inhibition increased the number of apoptotic cells as well as promoted the expression of ZDHHC5,Bcl-2,and COX-2 in MGC-803 cells(P<0.01).After ZDHHC5 inhibition,the number of apoptotic cells and the expression of ZDHHC5,Bcl-2,and COX-2 were reduced.The addition of an miR-96-5p inhibitor partly reversed these effects(P<0.01).CONCLUSION Our findings identified six miRNAs related to GAC prognosis and suggested that downregulated miR-96-5p might induce cell apoptosis via upregulating ZDHHC5 expression in MGC-803 cells.

MicroRNAs Involved in the Pathogenesis of Phytophthora Root Rot of Soybean (Glycine max)

Phytophthora root rot is one of the most prevalent diseases in the world,which can infect the seedlings and plants,with substantial negative impact on soybean yield and quality.MicroRNAs （miRNAs） are a class of post-transcriptional regulators of gene expression during growth and development of organisms.A soybean disease-resistance variety Suinong 10 was inoculated with Phytophthora sojae race No.1,and the specific miRNA resistant expression profile was acquired by microarray for the first time.Different expressional miRNAs have been found after comparing the results of the treated sample with the control sample.Furthermore,the target genes of different expressional miRNAs were predicted.Two miRNAs,cbr-mir-241 and ath-miR854a,regulated the disease-resistance process directly through their targets,some enzymes.Another two miRNAs,gma-miR169a and ath-miR169h,participated in disease-resistance regulation as transcription factors.Similarly,one miRNA,ptc-miR164f,has been reported to regulate the plant development.All of these studies would be served as the foundation for exploring the resistance mechanism.

Cancer stem cells:therapeutic implications and perspectives in cancer therapy

The cancer stem cell(CSC)theory is gaining increasing attention from researchers and has become an important focus of cancer research.According to the theory,a minority population of cancer cells is capable of self-renewal and generation of differentiated progeny,termed cancer stem cells(CSCs).Understanding the properties and characteristics of CSCs is key to future study on cancer research,such as the isolation and identification of CSCs,the cancer diagnosis,and the cancer therapy.Standard oncology treatments,such as chemotherapy,radiotherapy and surgical resection,can only shrink the bulk tumor and the tumor tends to relapse.Thus,therapeutic strategies that focus on targeting CSCs and their microenvironmental niche address the ineffec-tiveness of traditional cancer therapies to eradicate the CSCs that otherwise result in therapy resistance.The combined use of traditional therapies with targeted CSC-specific agents may target the whole cancer and offer a promising strategy for lasting treatment and even cure.

大鼠心力衰竭细胞microRNA表达谱及生物信息学分析

目的：观察大鼠心力衰竭细胞中microRNA （ miRNA）表达变化，利用生物信息学分析技术探索差异miRNA靶基因的功能。方法18只成年雄性SD大鼠，体质量200-220g，随机数字表法随机分为两组：正常对照组（ CON组）和心力衰竭组（ HF组）。 HF组制备阿霉素致心力衰竭模型， CON组注射等量生理盐水。提取大鼠心脏， Largendorff逆行灌注法分离心室肌细胞，提取总RNA行miRNA表达谱检测，筛选两组差异表达的miRNA，荧光定量RT-PCR 技术验证结果， Targetscan、 miRanda软件预测差异表达miRNA的靶基因，并对靶基因行生物信息学分析。结果芯片检测结果显示，与CON组相比， HF组共有37个miRNA表达发生显著改变，其中22个miRNA上调，15个miRNA下调（均P＜0.01， FDR＜0.05）。荧光定量RT-PCR检测miR-133b-5p （t ＝14.56， P＜0.1）、 miR-6216（t＝9.32， P＜0.1）、 let-7e-5p （ t＝13.92， P＜0.1）表达水平，变化趋势与芯片结果一致。生物信息学分析显示，差异表达miRNA调控的靶基因显著富集于31个基因组（均P＜0.01， FDR＜0.05）和12条信号通路（均P＜0.05， FDR＜0.05），其中泛素蛋白酶体系统、 MAPK信号通路、 Toll样受体信号通路富集程度较高。结论阿霉素诱导的心力衰竭模型大鼠心肌细胞中miRNA表达谱发生显著改变，这些差异表达miRNA可能通过调控靶基因功能参与心力衰竭的病理生理过程。