Study of miRNA expression profile in HCV infected human serum samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Genotypic technology
PROVIDER: E-GEOD-41829 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2010-04-01 | E-GEOD-21126 | biostudies-arrayexpress
Project description:To investigate whether the microRNA expression profile changes with modulation of severity, GlycophorinA positive cells were isolated by immunomagnetic procedure from peripheral blood of two Eb thalassemia patients with same b globin gene mutation but differing in transfusion requirment. MicroRNA expression profile of the two samples were monitored. Agilent one-color experiment,Organism: Human ,Agilent-019118 Human miRNA Microarray Labeling kit: Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408
2012-07-30 | E-GEOD-24428 | biostudies-arrayexpress
Project description:The main objective of the study is to identify the de-regulated miRNAs in association with HMGA2 (oncogene) in the Retinoblastoma tumorus. The present experiment was carried out using Y79 (Retinoblastoma cell line), as the invitro model of Retinoblastoma tumor. The HMGA2 transcripts were silenced using siRNA and the post-silenced RB cells (at the end of 48 hours) were subjected to miRNA profiling using agilent platform.The key miRNAs de-regulated in this experiment has been validated using qRT-PCR and further their role has been evaluated by addition of specific antagomirs in RB cell lines (Y79 and Weri Rb 1). Agilent one-color experiment,Organism: Homo sapiens ,Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408] RB cells (Y79) treated with anti-HMGA2 siRNA or with control
2013-10-26 | E-GEOD-51696 | biostudies-arrayexpress
Project description:To predict differentially expressed miRNAs between monosomy 3 and disomy 3, and to associate these miRNAs with the clinico-pathological parameters in South Asian Indian population with uveal melanoma (UM). The study consists of six uveal melanoma primary tumour tissues of South Asian-Indian population. These six tumours have been screened for chromosome 3 aberration using Chromogenic in-situ hybridisation (CISH). Thus, sample under the study includes, three each of monosomy 3 and disomy 3. The miRNA profiling was carried out from the tumor sections of formalin-fixed paraffin embedded eyeball samples. miRNA expression profile was obtained in monosomy 3 and disomy 3 samples, analysed by unsupervised analysis (Principal Component Analysis) and supervised analysis (Significance analysis of microarray). The select up-regulated and candidate miRNAs associated with monosomy 3 uveal melanoma tumors were validated further with qRT-PCR (n=86). Thus, this study indicates the role of miRNAs in UM tumor progression and their implication in predetermining the liver metastasis. The study consists of six uveal melanoma primary tumour tissues of South Asian-Indian population. These six tumours have been screened for chromosome 3 abberation using chromogenic in-situ hybridisation (CISH). Thus, samples under the study includes three each of monosomy 3 and disomy 3. The miRNA profiling were carried out from the tumor sections of formalin-fixed paraffin embedded eyeball samples. The up-regulated miRNAs associated with monosomy 3 uveal melanoma tumors were short listed and the candidate miRNAs were validated further with qRT-PCR. Agilent one-color experiment, Organism: Homo sapiens, Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408]
2015-05-14 | E-GEOD-68828 | biostudies-arrayexpress
Project description:To study the role of miRNAs in the transition from latent to active TB and to discover candidate biomarkers that may help predict TB progression, we have employed miRNA microarray expression profiling as a discovery platform to probe the transcriptome of peripheral blood mononuclear cells (PBMCs) with active TB, latent TB infection (LTBI), and healthy donors.Patients were recruited at the Shanghai Public Health Clinical Centre (Shanghai, China) from December, 2008 to May, 2009. The diagnosis of active TB was based on clinical presentation, chest radiography, and acid-fast stain of sputum smear.All the patients were HIV negative, as diagnosed by the Livzon Anti-HIV1/2 EIA Kit (Livzon Pharmaceutical Group Inc., Guangdong, China). Additional tests were also performed to detect hepatitis B virus (HBV) and hepatitis C virus (HCV) by using the Abbott AxSYM anti-HBsAg and HCV 3.0 antibody assay kit (Abbott Laboratories, Illinois) to exclude HBV- and HCV-positive patients (these 2 diseases are highly prevalent in China). Patients with a diabetes history were also excluded because diabetes could increase the risk of TB. Peripheral venous blood was drawn before treatment. Subjects with LTBI and healthy donors both without a history of clinical TB or other infectious diseases were recruited from the staff at the Shanghai Public Health Clinical Centre. TST and IGRA (T-SPOTM-BM-..TB, Oxford Immunuotec, Oxfordshire, U.K) results were used to distinguish the two groups. The LTBI group was TST-positive (TST>10 mm) and IGRA-positive while the healthy donors were TST-negative (TST<5 mm) and IGRA-negative. RNA of PBMC from 6 patients with active TB, 6 donors with Latent TB, and 3 healthy controls (total of 15 biologically independent samples) were used to perform Agilent Human miRNA (version 3) microarray , No replicates were included
2011-05-10 | E-GEOD-29190 | biostudies-arrayexpress
Project description:Pheochromocytoma (PCC) and paraganglioma (PGL) are rare neuroendocrine neoplasias of neural crest origin. They can be part of several syndromes, and their mRNA profile is dependent on genetic background, but questions related to clinical behavior or even main location remain unanswered. MicroRNAs are key modulators of target genes through translational repression, mRNA degradation, or both, and therefore they could resolve some of these issues. To determine the role microRNAs play in tumorigenesis and progression of PCC/PGL, as well as to identify microRNA biomarkers specifically related to different PCC/PGL genetic classes known so far, we characterized microRNA profiles in a large series of frozen tumors with germline mutations in SDHD, SDHB, VHL, RET, NF1, and TMEM127 genes through microarray analysis. We identified microRNA signatures specific to, as well as common among, the genetic classes of PCC/PGLs, and the best candidate microRNAs (miR-122, miR-126*, miR-129*, miR-133b, miR-137, miR-183, miR-210, miR-382, miR-488, miR-885-5p, and miR-96) were validated in an independent series of formalin-fixed paraffin-embedded PCC/PGL samples by qRT-PCR. MicroRNA-137, -96/183, and -143/145 expression in PCC/PGLs correlated inversely with the differentiation status of tumor cells. MicroRNA-210, -382, and -380 could modulate pseudohypoxic cellular response in VHL-deficient PCC/PGL. MicroRNA-193b, -365, and -424 were commonly downregulated among all genetic classes, suggesting their involvement in cell cycle control and differentiation. Herein, we demonstrate that PCC/PGLs have different microRNA profiles according to the underlying primary mutation, suggesting they could be used as specific biomarkers and add information on the etiology of these tumors. For this study, we employed the Agilent-019118 Human miRNA Microarray 2.0 G4470B (with Labeling kit: Agilent miRNA labeling reagent and Hybridization Kit, Cat # 5190-0408) to perform microRNA expression profiling on a large series of 54 fresh-frozen tissue samples, including a total of 48 genetically characterized pheochromocytomas (n=37) and paragangliomas (n=11) (8 SDHB-related tumors, 4 SDHD-related tumors, 14 Ret-related tumors, 12 VHL-related tumors, 4 NF1-related tumors, 3 TMEM127-related tumors, and 3 familial pheochromocytoma (FPCC) samples), and 6 normal adrenal medulla. Normalization of array data was performed applying the robust multiarray average (RMA) method using the AgiMicroRna package in Bioconductor. RMA normalization, by default, merges replicates of each probe and produces an Eset with a single value for each microRNA.
2013-07-02 | E-GEOD-29742 | biostudies-arrayexpress
Project description:The aim of the presented study was to define tissue and plasma miRNA signatures, which could potentially serve as diagnostic and prognostic markers in endometrioid endometrial cancer (EEC), and to investigate miRNA profiles in regard to clinicopathological characteristics of the tumors. Results: qPCR validation revealed regulation of 14 miRNAs in EEC tissues (miR-9, miR-141,miR-205,miR-203,miR-183,miR-200a*,miR-200b*,miR-200a,miR-200c,miR-429,miR-200b,miR-410,miR-92a,miR-1305) and 9 in plasma samples (miR-449a,miR-1290,miR-1228,miR-203,miR-200a,miR-141,miR-92a, miR-9, miR-301b). Expression of certain miRNAs showed association with FIGO stage, grade and relapse. Two miRNA signatures, miR-205/miR-410 and miR-410/miR-429/miR-92a, classified tumor tissues with higher accuracy in comparison to single miRNAs (AUC 0.972, 95% CI 0.919-0.995 and 0.991, 95% CI 0.948-1.000, resepctively). miRNA signature composed of miR-205 and miR-200a predicted relapse with AUC of 0.854 (95% CI 0.691-0.951). Tissue miRNA signatures were independent prognostic markers of overall (miR-1228/miR-200c/miR-429, HR 2.98) and progression-free survival (miR-1228/miR-429, HR 4.149). Plasma miRNA signatures classified EEC plasma samples with high accuracy. Conclusions: We conclude that miRNA signatures hold great promise for becoming non-invasive biomarkers for early EEC detection and prognosis. Tissue samples were collected from 122 women (77 EEC and 45 controls). Expression profiling of 866 human miRNAs and 89 human viral miRNAs was performed in 24 samples and was followed by qPCR validation in 104 patients. Of 24 samples analyzed by microarrays, 22 (18 EEC, 4 normal controls) were available for final analysis. Expression of 14 miRNAs was analysed in 48 plasma samples by qPCR.
2012-05-31 | E-GEOD-35794 | biostudies-arrayexpress
Project description:Background & aims: The role of microRNAs (miRNAs) in Alcoholic Hepatitis (AH) and their potential as therapeutic targets in liver disease has not been explored yet. This study aims at profiling miRNA in AH and identifying dysregulated miRNAs involved in AH pathophysiology. Methods: miRNA expression arrays were performed in 13 AH, 5 alcohol liver disease-induced cirrhosis (ALD-CH), 5 nonalcoholic steatohepatitis induced cirrhosis (NASH-CH), 4 HCV-induced cirrhosis (HCV-CH) and 6 non-injured liver control samples. Genome wide expression profile was retrieved for 12 paired AH and control samples. MiRNA and mRNA expression data was integrated and identified miRNAs were validated in AH samples and in animal models of liver injury. Results: The miRNA array showed 111 upregulated and 66 downregulated miRNAs in AH versus healthy subjects. The comparison of miRNA profile in liver samples from AH among ALD-CH, HCV-CH and NASH-CH identified 18 miRNAs specifically dysregulated in AH. Integrative miRNA and mRNA analysis in AH identified dysregulated miRNAs for which their target genes were also dysregulated. A functional analysis of identified miRNAs and their targets revealed their involvement in the regulation of canonical pathways related to apoptosis, fatty acid metabolism and cell cycle among others. miRNAs expression (miR-182, miR-21, miR-155, miR-214, miR-432, miR-422a) was validated in an independent cohort of AH. MiR-182 expression correlated with cholestasis, disease severity and short-term mortality. Moreover, miR-182 expression is associated to cholestasis with ductular reaction but not to fibrosis and inflammation in animal models of liver injury. Conclusions: AH is characterized by an important dysregulation of miRNA expression with a unique miRNA profile. MiRNAs specifically expressed in AH are associated to cholestasis⦠Uncovered miRNAs are involved in important pathophysiological features in AH suggesting ta regulation of he role of miRNAs in the regulation of AH, and highlight miR-182 as a potential regulator of its pathophysiology. miRNA expression arrays were performed in 13 AH(Alcoholic hepatitis), 5 alcohol liver disease-induced cirrhosis (ALD-CH), 5 nonalcoholic steatohepatitis induced cirrhosis (NASH-CH), 4 HCV-induced cirrhosis (HCV-CH) and 6 non-injured liver control samples(CTRL).
2016-08-02 | E-GEOD-59492 | biostudies-arrayexpress
Project description:To gain insight into the potential role of miRNA in major depressive disorder, in this study we assessed global expression of miRNAs in the ventrolateral prefrontal cortex (PFC) of depressed individuals in comparison to psychiatrically healthy controls. Our screening pointed to miR-1202, a miRNA specific to primates and enriched in the human brain. We validated our findings using quantitative real-time PCR and identified target genes of the differentially expressed miRNAs using bioinformatics analysis. MiR-1202 interacts with and regulates the expression of the metabotropic glutamate receptor 4 (GRM4) gene, and it responds to antidepressant treatment. These results suggest that miR-1202 is associated with the pathophysiology of depression, and is a potential target for novel antidepressant treatments. We assessed the global expression pattern of miRNAs in the ventrolateral PFC of depressed individuals (n = 14) in comparison with psychiatrically healthy controls (n = 11) using the Agilent human miRNA microarrays. Statistical analysis after multiple test correction identified miR-1202 as the most significantly dysregulated miRNA, with levels down-regulated in depressed brains. We validated the microarray miR-1202 findings by qRT-PCR using TaqMan probes, and found consistent results across the two expression analysis methods.
2014-05-30 | E-GEOD-58105 | biostudies-arrayexpress
Project description:Global microRNA expression profiling of serum were collected using Agilent miRNA microarrays (G4471A Human, Amadid 29297, Sanger 14) carrying 887 individual human miRNA probes. Two different sources of RNA were analyzed: serum from healthy controls (N=5) and patients with ovarian carcinoma (CA, n=5) Two conditions (CA, N), each condition is represented by 5 biological replicates
2014-02-05 | E-GEOD-48485 | biostudies-arrayexpress