mRNA and microRNA analysis reveals modulation of biochemical pathways related to addiction in the ventral tegmental area of methamphetamine self-administering rats

Background Methamphetamine is a highly addictive central nervous system stimulant with increasing levels of abuse worldwide. Alterations to mRNA and miRNA expression within the mesolimbic system can affect addiction-like behaviors and thus play a role in the development of drug addiction. While many studies have investigated the effects of high-dose methamphetamine, and identified neurotoxic effects, few have looked at the role that persistent changes in gene regulation play following methamphetamine self-administration. Therefore, the aim of this study was to identify RNA changes in the ventral tegmental area following methamphetamine self-administration. We performed microarray analyses on RNA extracted from the ventral tegmental area of Sprague–Dawley rats following methamphetamine self-administration training (2 h/day) and 14 days of abstinence. Results We identified 78 miRNA and 150 mRNA transcripts that were differentially expressed (fdr adjusted p < 0.05, absolute log2 fold change >0.5); these included genes not previously associated with addiction (miR-125a-5p, miR-145 and Foxa1), loci encoding receptors related to drug addiction behaviors and genes with previously recognized roles in addiction such as miR-124, miR-181a, DAT and Ret. Conclusion This study provides insight into the effects of methamphetamine on RNA expression in a key brain region associated with addiction, highlighting the possibility that persistent changes in the expression of genes with both known and previously unknown roles in addiction occur.

树突状细胞体外分化成熟的时程、mi/mRNA 表达谱分析和共生菌影响的研究

树突状细胞（dendritic cells, DC）作为机体天然免疫和获得性免疫反应的桥梁和枢纽，发挥着重要的启动和调控作用。随着体外诱导方法的建立和生物学技术的进步，有关DC 的基础生物学研究得到了快速的发展，在诱导方法、个体发生及基因表达和调控等方面，涌现出很多新的、未解的关键问题。同时，随着对粘膜免疫机理研究的深入，DC 在粘膜生态环境中的功能和影响，渐已成为免疫学研究前沿领域中的热点和要点。在本研究中，为了确定DC 体外分化成熟的最短时程，同时为了研究DC 分化成熟相关的基因表达调控，我们建立了快速的DC 体外诱导方法，分析了体外快速诱导 DC 的mi/mRNA 表达谱。此外，在原始分离的女性生殖道共生乳酸杆菌的基础上，以THP-1作为DC 前体细胞的细胞系模型，开展了女性生殖道共生乳酸杆菌刺激活化 THP-1 的研究，希望能够为乳酸杆菌作为生殖道粘膜免疫疫苗的应用提供理论基础。首先，采用外周血单个核细胞（peripheral blood mononuclear cells, PBMC）来源的CD14+细胞为DC 前体，经过GM-CSF 和IL-4 的刺激，1-6 天后得到未成熟DC （immature dendritic cells, iDC），并经成熟因子（TNF-α, IL-1β, IL-6 与PGE2）诱导 1-2 天后，获得成熟DC（mature dendritic cells, mDC）。经过比较和分析，明确了完全分化和成熟各2 天，即“2+2”，为DC 诱导分化的最佳和最短时程，从而证实和建立了DC 体外快速诱导的体系和方法。该方法获得的iDC 与mDC，具有与传统的“6+2” 方法获得的DC 相同的形态与表型，而且，利用该方法获得的DC 总数高于“1+1”， “1+2”与“6+2”的方法，为DC 的生物学研究提供了基础数据。我们进而采用芯片技术，对体外快速分化成熟的DC 进行了mi/mRNA 表达谱分析，确定了DC 不同分化发育阶段特征性的mi/mRNA 表达差异。结果发现，与CD14+ 单核细胞即DC 前体相比，iDC 与mDC 之间具有更加相近的mi/mRNA 表达方式。 miRNA 表达谱分析则表明，不同的miRNA 表达与DC 的不同分化和发育阶段相关。而且，位于同一基因簇内的miRNA，呈现协同表达的情况。特别值得注意的是，本研究发现了在DC 的某些发育阶段特异表达的miRNA，它们在DC 发育过程中的功能，还未得到诠释，它们在DC 某些分化阶段的特异表达，提示了DC 各分化阶段的相关性与特异性。结合mRNA 表达谱分析，我们发现miRNA 的表达与其目的基因的表达在mRNA 水平呈现负相关的特性。同时，免疫相关mRNA 与miRNA 在DC 体外不同发育阶段的表达亦呈现差异，其中，miRNA（如hsa-miR-181a, hsa-miR-223, hsa-miR-155, hsa-miR-146, hsa-miR-106a 与hsa-miR-20a 等）与mRNA（如ALM1 等）参与了特定的与免疫相关的GO（Gene Ontology）与通路（Pathway），提示这些miRNA 与mRNA 可能通过不同的方式调节控制着DC 的体外诱导过程。在有关粘膜生态环境中DC 的分化、成熟及其功能影响的研究中，我们首先通过各种乳酸杆菌鉴定方法的综合应用，确定了6 种原始分离的女性生殖道主要共生乳酸杆菌：发酵乳酸杆菌（L.Fermentum）、约氏乳酸杆菌（L.Johnsonni）、卷曲乳酸杆菌（L.Crispatus）、革氏乳酸杆菌（L.Gasseri）、詹氏乳酸杆菌（L.Jensenii）与德氏乳酸杆菌（L.Delbrueckii ）。其中，德氏乳酸杆菌（L.Delbrueckii）和发酵乳酸杆菌（L.Fermentum）具有较高的产H2O2 的能力。在此基础上，我们在与THP-1 的共同培养体系中，将乳酸杆菌对DC 前体的作用和影响进行了比较和研究。结果发现，L.Crispatus 在分离的各原始菌株中，具有最强的刺激THP-1 活化的能力，而且，在相同刺激比例下，L.Crispatus 活菌具有比死菌更强的免疫刺激能力，表现为明显上调THP-1 细胞表面标志CD40、CD80、CD86、 CD1a、CCR6 与CD324 的表达水平，同时可诱导活化THP-1 上调表达Th1 型细胞因子。通过FITC-Dextran 吞噬实验，我们发现，经过L.Crispatus 刺激的THP-1 细胞，其吞噬外来抗原的能力明显下降，但尚未检测到经过活化的THP-1 细胞刺激T 细胞增殖的能力。通过流式细胞术分析的方法，我们检测了TLR1、TLR2、TLR4 与TLR6 在不同的刺激分化阶段的表达水平，结果表明，THP-1 主要通过TLR2 与TLR6 识别女性生殖道L.Crispatus。综上所述，本研究首先通过对DC 体外分化成熟的最短时程的分析，确立了快速诱导DC 的最佳方法，进而利用芯片技术，研究了快速诱导DC 的mi/mRNA 表达谱，揭示了DC 体外分化发育过程中可能的调控途径，为进一步研究DC 的基础生物学提供了恰当的模型和具有指向性的线索。同时，通过与DC 前体THP-1 的共同培养体系，证实了生殖道共生乳酸杆菌的免疫调节作用，为以乳酸杆菌为载体的生殖道粘膜免疫疫苗的研究和应用提供了实验依据

Investigating the thymopoiesis stimulating property of interleukin-21 in aging mice

La vaccination est largement utilisée pour la génération de lymphocytes T spécifiques contre les tumeurs. Malheureusement, cette stratégie n'est pas adaptée aux personnes âgées car leur thymus régresse avec l'âge conduisant ainsi à une baisse dans la production de cellules T et à l'accumulation de cellules immunitaires âgées ayant des défauts liés à leurs stimulations. Comme il a été démontré auparavant que L’IL-21 est capable d’induire des fonctions thymiques, nous avons émis l’hypothèse que l’injection d’IL-21 à des souris âgées stimulera la thymopoïèse. Nos résultats montrent que l’administration de l’IL-21 augmente le nombre absolu de thymocytes chez les souris âgées et augmente la migration de ces cellules vers la périphérie ou ils contribuent à la diversité du TCR. De plus les cellules T en périphérie expriment un niveau plus élevé de miR181-a, et par conséquent moins de phosphatase comme SHP2, DUSP5/6 qui inhibent le TCR. En vaccinant des souris âgées avec le peptide Trp2, les souris traitées avec l’IL-21 montrent un retard dans la croissance des cellules B16 tumorales. Cette étude montre que l’IL-21 pourrait être utilisé comme stratégie pour le rétablissement du systeme immunitaire chez les personnes âgées.

Análise da expressão de miRNAs em carcinoma hepatocelular

O carcinoma hepatocelular corresponde à neoplasia maligna primária mais comum do fígado e ao quinto tumor sólido mais frequente no mundo. Altamente letal, permanece como um grave problema de saúde pública em virtude das dificuldades no diagnóstico precoce e na elaboração de medidas terapêuticas efetivas. Estudos recentes no ramo da biologia molecular sugerem que o perfil de miRNAs no carcinoma hepatocelular pode influir consideravelmente na identificação de fatores de riscos associados a oncogenes ou genes supressores. Objetivou-se avaliar a expressão de miRNA 135b, miRNA 181a-5p e miRNA 181a-3p em amostras de Carcinoma Hepatocelular e de Hepatite C Crônica e correlacioná-las de maneira a buscar prováveis biomarcadores relacionados ao mecanismo de carcinogenese. A investigação foi feita em seis pacientes com carcinoma hepatocelular e vinte e quatro casos de Hepatite C Crônica, procedentes do Pará, Norte do Brasil. Todas as amostras de Carcinoma Hepatocelular foram submetidas à microdissecção, para posterior extração do RNA. Para a extração do RNA total e do microRNA foi utilizado o kit AllPrep DNA/RNA FFPE Kit (Qiagen), quantificados pelo equipamento Qubit® 2.0 Fluorometer (Invitrogen) para concentração padrão final de 5ng/μL. Em seguida cDNA foi obtido, utilizando-se TaqMan® MicroRNA Reverse Transcription(AppliedBiosystems). As análises estatísticas foram realizadas nos softwares SPSS 17.0, usando o teste de Mann-Whitney, considerando como significantes valores de p<0,05. Os resultados demonstraram diferenças significativas dos níveis de expressão do miR181a-3p e do miR181a-5p no carcinoma hepatocelular (médias 3,94 e 17,9, respectivamente) em relação à hepatite C crônica (médias de 1,18 e 1,8, respectivamente) com P valor de 0,005 e 0,003. Nesse estudo, observou-se que os miRNAs 181a-3p e 181a-5p, especialmente o 181a-5p, foram significativamente mais expressos nas amostras de carcinoma hepatocelular, quando comparados ao tecido hepático não tumoral com hepatite C crônica. Portanto, os microRNAs possuem características interessantes que os favorecem como possíveis marcadores biológicos no rastreamento de tumores para diagnóstico precoce e terapias alvo selecionadas.

Identifying common and specific microRNAs expressed in peripheral blood mononuclear cell of type 1, type 2, and gestational diabetes mellitus patients

Abstract Background Regardless the regulatory function of microRNAs (miRNA), their differential expression pattern has been used to define miRNA signatures and to disclose disease biomarkers. To address the question of whether patients presenting the different types of diabetes mellitus could be distinguished on the basis of their miRNA and mRNA expression profiling, we obtained peripheral blood mononuclear cell (PBMC) RNAs from 7 type 1 (T1D), 7 type 2 (T2D), and 6 gestational diabetes (GDM) patients, which were hybridized to Agilent miRNA and mRNA microarrays. Data quantification and quality control were obtained using the Feature Extraction software, and data distribution was normalized using quantile function implemented in the Aroma light package. Differentially expressed miRNAs/mRNAs were identified using Rank products, comparing T1DxGDM, T2DxGDM and T1DxT2D. Hierarchical clustering was performed using the average linkage criterion with Pearson uncentered distance as metrics. Results The use of the same microarrays platform permitted the identification of sets of shared or specific miRNAs/mRNA interaction for each type of diabetes. Nine miRNAs (hsa-miR-126, hsa-miR-1307, hsa-miR-142-3p, hsa-miR-142-5p, hsa-miR-144, hsa-miR-199a-5p, hsa-miR-27a, hsa-miR-29b, and hsa-miR-342-3p) were shared among T1D, T2D and GDM, and additional specific miRNAs were identified for T1D (20 miRNAs), T2D (14) and GDM (19) patients. ROC curves allowed the identification of specific and relevant (greater AUC values) miRNAs for each type of diabetes, including: i) hsa-miR-1274a, hsa-miR-1274b and hsa-let-7f for T1D; ii) hsa-miR-222, hsa-miR-30e and hsa-miR-140-3p for T2D, and iii) hsa-miR-181a and hsa-miR-1268 for GDM. Many of these miRNAs targeted mRNAs associated with diabetes pathogenesis. Conclusions These results indicate that PBMC can be used as reporter cells to characterize the miRNA expression profiling disclosed by the different diabetes mellitus manifestations. Shared miRNAs may characterize diabetes as a metabolic and inflammatory disorder, whereas specific miRNAs may represent biological markers for each type of diabetes, deserving further attention.

Comprehensive MicroRNA expression profiling identifies novel markers in follicular variant of papillary thyroid carcinoma

BACKGROUND Follicular variant of papillary thyroid carcinoma (FVPTC) shares features of papillary (PTC) and follicular (FTC) thyroid carcinomas on a clinical, morphological, and genetic level. MicroRNA (miRNA) deregulation was extensively studied in PTCs and FTCs. However, very limited information is available for FVPTC. The aim of this study was to assess miRNA expression in FVPTC with the most comprehensive miRNA array panel and to correlate it with the clinicopathological data. METHODS Forty-four papillary thyroid carcinomas (17 FVPTC, 27 classic PTC) and eight normal thyroid tissue samples were analyzed for expression of 748 miRNAs using Human Microarray Assays on the ABI 7900 platform (Life Technologies, Carlsbad, CA). In addition, an independent set of 61 tumor and normal samples was studied for expression of novel miRNA markers detected in this study. RESULTS Overall, the miRNA expression profile demonstrated similar trends between FVPTC and classic PTC. Fourteen miRNAs were deregulated in FVPTC with a fold change of more than five (up/down), including miRNAs known to be upregulated in PTC (miR-146b-3p, -146-5p, -221, -222 and miR-222-5p) and novel miRNAs (miR-375, -551b, 181-2-3p, 99b-3p). However, the levels of miRNA expression were different between these tumor types and some miRNAs were uniquely dysregulated in FVPTC allowing separation of these tumors on the unsupervised hierarchical clustering analysis. Upregulation of novel miR-375 was confirmed in a large independent set of follicular cell derived neoplasms and benign nodules and demonstrated specific upregulation for PTC. Two miRNAs (miR-181a-2-3p, miR-99b-3p) were associated with an adverse outcome in FVPTC patients by a Kaplan-Meier (p < 0.05) and multivariate Cox regression analysis (p < 0.05). CONCLUSIONS Despite high similarity in miRNA expression between FVPTC and classic PTC, several miRNAs were uniquely expressed in each tumor type, supporting their histopathologic differences. Highly upregulated miRNA identified in this study (miR-375) can serve as a novel marker of papillary thyroid carcinoma, and miR-181a-2-3p and miR-99b-3p can predict relapse-free survival in patients with FVPTC thus potentially providing important diagnostic and predictive value.

Investigating the thymopoiesis stimulating property of interleukin-21 in aging mice

La vaccination est largement utilisée pour la génération de lymphocytes T spécifiques contre les tumeurs. Malheureusement, cette stratégie n'est pas adaptée aux personnes âgées car leur thymus régresse avec l'âge conduisant ainsi à une baisse dans la production de cellules T et à l'accumulation de cellules immunitaires âgées ayant des défauts liés à leurs stimulations. Comme il a été démontré auparavant que L’IL-21 est capable d’induire des fonctions thymiques, nous avons émis l’hypothèse que l’injection d’IL-21 à des souris âgées stimulera la thymopoïèse. Nos résultats montrent que l’administration de l’IL-21 augmente le nombre absolu de thymocytes chez les souris âgées et augmente la migration de ces cellules vers la périphérie ou ils contribuent à la diversité du TCR. De plus les cellules T en périphérie expriment un niveau plus élevé de miR181-a, et par conséquent moins de phosphatase comme SHP2, DUSP5/6 qui inhibent le TCR. En vaccinant des souris âgées avec le peptide Trp2, les souris traitées avec l’IL-21 montrent un retard dans la croissance des cellules B16 tumorales. Cette étude montre que l’IL-21 pourrait être utilisé comme stratégie pour le rétablissement du systeme immunitaire chez les personnes âgées.

Melanoma cell invasiveness is regulated by miR-211 suppression of the BRN2 transcription factor

To identify microRNAs potentially involved in melanomagenesis, we compared microRNA expression profiles between melanoma cell lines and cultured melanocytes. The most differentially expressed microRNA between the normal and tumor cell lines was miR-211. We focused on this pigment-cell-enriched miRNA as it is derived from the microphthalmia-associated transcription factor (MITF)-regulated gene, TRPM1 (melastatin). We find that miR-211 expression is greatly decreased in melanoma cells and melanoblasts compared to melanocytes. Bioinformatic analysis identified a large number of potential targets of miR-211, including POU3F2 (BRN2). Inhibition of miR-211 in normal melanocytes resulted in increased BRN2 protein, indicating that endogenous miR-211 represses BRN2 in differentiated cells. Over-expression of miR-211 in melanoma cell lines changed the invasive potential of the cells in vitro through directly targeting BRN2 translation. We propose a model for the apparent non-overlapping expression levels of BRN2 and MITF in melanoma, mediated by miR-211 expression.

Single nucleotide polymorphism in hsa-mir-196a-2 and breast cancer risk : a case control study

microRNAs are small, non-coding RNAs that influence gene expression on a post-transcriptional level. They participate in diverse biological pathways and may act as either tumor suppressor genes or oncogenes. As they may have an effect on thousands of target mRNAs, single-nucleotide polymorphisms in microRNA genes might have major functional consequences, because the microRNA's properties and/or maturation may change. miR-196a has been reported to be aberrantly expressed in breast cancer tissue. Additionally, the SNP rs11614913 in hsa-mir-196a-2 has been found to be associated with breast cancer risk in some studies although not in others. This study evaluated the association between rs11614913 and breast cancer risk in a Caucasian case-control cohort in Queensland, Australia. Results do not support an association of the tested hsa-mir-196a-2 polymorphism with breast cancer susceptibility in this cohort. As there is a discrepancy between our results and previous findings, it is important to assess the role of rs11614913 in breast cancer by further larger studies investigating different ethnic groups.

A genetic variant located in miR-423 is associated with reduced breast cancer risk

Background/Aim: Since microRNAs (miRNAs) act as translational regulators of multiple genes, single nucleotide polymorphisms (SNP) in them can have potentially wide-ranging effects. Using an association approach, this research examined the effects of the rs6505162 SNP, an A>C polymorphism located in the premiRNA region of miR-423, on breast cancer development. Materials and Methods: Caucasian Australian women with breast cancer and controls matched for age and ethnicity were genotyped for rs6505162 and their genotypic and allelic frequencies analysed for significant differences. Results: Analysis indicated that there were significant differences between the case and control populations (χ 2=6.70, p=0.035), with the CC genotype conferring reduced risk of breast cancer development (odds ratio=0.50 95% confidence interval=0.27-0.92, p=0.03). Conclusion: Further functional research is required to determine the mechanism of action of this SNP on miRNA function.

miR-451 regulates zebrafish erythroid maturation in vivo via its target gata2

We demonstrate that in zebrafish, the microRNA miR-451 plays a crucial role in promoting erythroid maturation, in part via its target transcript gata2. Zebrafish miR-144 and miR-451 are processed from a single precursor transcript selectively expressed in erythrocytes. In contrast to other hematopoietic mutants, the ze-brafish mutant meunier (mnr) showed intact erythroid specification but diminished miR-144/451 expression. Although erythropoiesis initiated normally in mnr, erythrocyte maturation was morphologically retarded. Morpholino knockdown of miR-451 increased erythrocyte immaturity in wild-type embryos, and miR-451 RNA duplexes partially rescued erythroid maturation in mnr, demonstrating a requirement and role for miR-451 in erythro-cyte maturation. mnr provided a selectively miR-144/451-deficient background, facilitating studies to discern miRNA function and validate candidate targets. Among computer-predicted miR-451 targets potentially mediating these biologic effects, the pro-stem cell transcription factor gata2 was an attractive candidate. In vivo reporter assays validated the predicted miR-451/gata2-3'UTR interaction, gata2 down-regulation was delayed in miR-451-knockdown and mnr embryos, and gata2 knockdown partially restored erythroid maturation in mnr, collectively confirming gata2down-regulation as pivotal for miR-451-driven erythroid maturation. These studies define a new genetic pathway promoting erythroid maturation (mnr/miR-451/gata2) and provide a rare example of partial rescue of a mutant phenotype solely by miRNA overexpression. © 2009 by The American Society of Hematology.

miR-126 in human cancers : clinical roles and current perspectives

miR-126 has been implicated in the processes of inflammation and angiogenesis. Through these processes, miR-126 is implicated in cancer biology, but its role there has not been well reviewed. The aim of this review is to examine the molecular mechanisms and clinicopathological significance of miR-126 in human cancers. miR-126 was shown to have roles in cancers of the gastrointestinal tract, genital tracts, breast, thyroid, lung and some other cancers. Its expression was suppressed in most of the cancers studied. The molecular mechanisms that are known to cause aberrant expression of miR-126 include alterations in gene sequence, epigenetic modification and alteration of dicer abundance. miR-126 can inhibit progression of some cancers via negative control of proliferation, migration, invasion, and cell survival. In some instances, however, miR-126 supports cancer progression via promotion of blood vessel formation. Downregulation of miR-126 induces cancer cell proliferation, migration, and invasion via targeting specific oncogenes. Also, reduced levels of miR-126 are a significant predictor of poor survival of patients in many cancers. In addition, miR-126 can alter a multitude of cellular mechanisms in cancer pathogenesis via suppressing gene translation of numerous validated targets such as PI3K, KRAS, EGFL7, CRK, ADAM9, HOXA9, IRS-1, SOX-2, SLC7A5 and VEGF. To conclude, miR-126 is commonly down-regulated in cancer, most likely due to its ability to inhibit cancer cell growth, adhesion, migration, and invasion through suppressing a range of important gene targets. Understanding these mechanisms by which miR-126 is involved with cancer pathogenesis will be useful in the development of therapeutic targets for the management of patients with cancer.

The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory

MicroRNAs are small non-coding RNAs that mediate post-transcriptional gene silencing. Fear-extinction learning in C57/Bl6J mice led to increased expression of the brain-specific microRNA miR-128b, which disrupted stability of several plasticity-related target genes and regulated formation of fear-extinction memory. Increased miR-128b activity may therefore facilitate the transition from retrieval of the original fear memory toward the formation of a new fear-extinction memory.

Combined NIR/MIR analysis: A novel method for the classification of complex substances such as Illicium verum Hook. F. and its adulterants

A novel combined near- and mid-infrared (NIR and MIR) spectroscopic method has been researched and developed for the analysis of complex substances such as the Traditional Chinese Medicine (TCM), Illicium verum Hook. F. (IVHF), and its noxious adulterant, Iuicium lanceolatum A.C. Smith (ILACS). Three types of spectral matrix were submitted for classification with the use of the linear discriminant analysis (LDA) method. The data were pretreated with either the successive projections algorithm (SPA) or the discrete wavelet transform (DWT) method. The SPA method performed somewhat better, principally because it required less spectral features for its pretreatment model. Thus, NIR or MIR matrix as well as the combined NIR/MIR one, were pretreated by the SPA method, and then analysed by LDA. This approach enabled the prediction and classification of the IVHF, ILACS and mixed samples. The MIR spectral data produced somewhat better classification rates than the NIR data. However, the best results were obtained from the combined NIR/MIR data matrix with 95–100% correct classifications for calibration, validation and prediction. Principal component analysis (PCA) of the three types of spectral data supported the results obtained with the LDA classification method.