Analysis Of microRNA Expression Profiles Research Articles

Integrated analysis of microRNA and mRNA expression profiles in the rat spinal cord under inflammatory pain conditions.

Recent studies using microarray-based approaches have demonstrated that microRNAs (miRNAs) are involved in pain processing pathways. However, a significant proportion of computational predictions of miRNA targets are false-positive interactions. To increase the chance of identifying biologically relevant targets, we performed an integrated analysis of both miRNA and mRNA expression profiles in the rat spinal cord during complete Freund's adjuvant (CFA)-induced inflammatory pain. We generated miRNA and mRNA arrays from the same corresponding samples on days 5 and 14 after CFA injection. Five miRNAs and 1096 mRNAs in the CFA 5d group and 16 miRNAs and 647 mRNAs in the CFA 14d group were differentially expressed based on a filter of at least a 1.5-fold change in either direction. An integrated analysis revealed 54 mRNA targets with an inverse correlation to the expression patterns of three miRNAs in the CFA 5d group. Seventy-five targets were inversely correlated to six miRNAs in the CFA 14d group. The miRNA-mRNA interaction networks revealed significant changes in miR-124, miR-149, miR-3584 and their target genes, IL-6R, ADAM19, LAMC1 and CERS2, in the CFA 5d group. In the CFA 14d group, significant changes were noted in miR-124, miR-29, miR-34, miR-30, miR-338 and their target genes, TIMP2, CREB5 and EFNB1. We also investigated an interaction pair, miR-124-3p and IL-6R, and the results showed that miR-124-3p could attenuate inflammatory pain and decrease IL-6R expression in the spinal cord. These specific miRNAs and their target genes provide possible avenues for the diagnosis and treatment of inflammatory pain.

Preliminary identification of key miRNAs, signaling pathways, and genes associated with Hirschsprung's disease by analysis of tissue microRNA expression profiles.

Hirschsprung's disease (HSCR) is a congenital gut motility disorder of infants, and if left untreated, it is fatal to the affected infants. This study aimed to identify key microRNAs (miRNAs), signaling pathways and genes involved in the pathogenesis of HSCR. The miRNA microarray dataset GSE77296 was downloaded. Nine colon tissue samples were available: six from HSCR patients and three matched control samples. Differentially expressed miRNAs (DEMs) were identified after data preprocessing. Target genes of the selected upregulated and downregulated DEMs were predicted. In addition, functional enrichment analyses for the selected DEMs and target genes were conducted. Finally, interaction networks between the DEMs and target genes were constructed. A total of 162 DEMs (73 upregulated and 89 downregulated) were obtained. A total of 2511 DEM-target gene pairs for the 40 selected DEMs were identified, including 1645 pairs for the upregulated DEMs and 866 pairs for the downregulated DEMs. The upregulated DEM miR-141-3p and down-regulated DEM miR-30a-3p were identified as key miRNAs by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and network analyses. Besides, KEGG pathway enrichment analysis revealed that pathways in cancer and the mitogen-activated protein kinase (MAPK) signaling pathway were key pathways. The key genes frizzled class receptor 3 (FZD3) and docking protein 6 (DOK6) were obtained through the DEM-target gene interaction networks. Two key miRNAs (miR-141-3p and miR-30a-3p), the MAPK signaling pathway and two key genes (FZD3 and DOK6) were implicated in the pathogenesis of HSCR.

Integrated analysis of microRNA and mRNA expression profiles during the sex-differentiation sensitive period in oriental river prawn, Macrobrachium nipponense

Male oriental river prawns (Macrobrachium nipponense) grow faster than females, and therefore, reach larger sizes by harvest time. Histological observations have indicated that the sex-differentiation sensitive period (which includes the formation of the androgenic gland, the testis, and the ovary) is from post-larvae (PL) developmental stage for M. nipponense. In this study, we prepared four microRNA (miRNA) and mRNA libraries using samples collected from sex-differentiation sensitive period (PL7 to PL16) to perform RNA-sequencing for identifying sex-related candidate miRNAs, genes, and metabolic pathways. A total of nine intersection miRNAs were identified, of which three were highly expressed in the androgenic gland, and their expression was verified by quantitative Real-Time PCR (qPCR). These three miRNAs and their 11 predicted target genes may be strong candidates for sex-related miRNAs and sex-related genes in M. nipponense. Five vital sex-related metabolic pathways were also identified that may regulate other sex-differentiation and sex-determination mechanisms. Finding of the study provide important insights to enhance our understanding on sex-differentiation and sex-determination mechanisms for M. nipponense.

Analysis of microRNA (miRNA) expression profiles reveals 11 key biomarkers associated with non-small cell lung cancer

BackgroundNon-small cell lung cancer (NSCLC) accounts for more than 85% of lung cancer cases which cause most of cancer-related deaths globally. However, the results vary largely in different studies due to different platforms and sample sizes. Here, we aim to identify the key miRNAs in the carcinogenesis of NSCLC that might be potential biomarkers for this cancer.MethodsMeta-analysis was performed on miRNA profile using seven datasets of NSCLC studies. Furthermore, we predicted and investigated the functions of genes regulated by key miRNAs.ResultsEleven key miRNAs were identified, including 2 significantly upregulated ones (hsa-miR-21-5p and hsa-miR-233-3p) and 9 downregulated ones (hsa-miR-126-3p, hsa-miR-133a-3p, hsa-miR-140-5p, hsa-miR-143-5p, hsa-miR-145-5p, hsa-miR-30a-5p, hsa-miR-30d-3p, hsa-miR-328-3pn, and hsa-miR-451). The functional enrichment analysis revealed that both up- and downregulated miRNAs were proportionally associated with regulation of transcription from RNA polymerase II promoter. According to transcription factor analysis, there were 65 (43.9%) transcription factors influenced by both up- and downregulated miRNAs.ConclusionsIn this study, 11 meta-signature miRNAs, as well as their target genes and transcription factors, were found to play significant role in carcinogenesis of NSCLC. These target genes identified in our study may be profitable to diagnosis and prognostic prediction of NSCLC as biomarkers.

Integrated analysis of microRNA and gene expression profiles reveals a functional regulatory module associated with liver fibrosis

BackgroundLiver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation has important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. MethodsThe publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis. Differentially expressed miRNAs (DEMs) and genes (DEGs) were identified using GEO2R web tool. Putative target gene prediction of DEMs was carried out using the intersection of five major algorithms: DIANA-microT, TargetScan, miRanda, PICTAR5 and miRWalk. Functional miRNA-gene regulatory network (FMGRN) was constructed based on the computational target predictions at the sequence level and the inverse expression relationships between DEMs and DEGs. DAVID web server was selected to perform KEGG pathway enrichment analysis. Functional miRNA-gene regulatory module was generated based on the biological interpretation. Internal connections among genes in liver fibrosis-related module were determined using String database. MiRNA-gene regulatory modules related to liver fibrosis were experimentally verified in recombinant human TGFβ1 stimulated and specific miRNA inhibitor treated LX-2 cells. ResultsWe totally identified 85 and 923 dysregulated miRNAs and genes in liver cirrhosis biopsy samples compared to their normal controls. All evident miRNA–gene pairs were identified and assembled into FMGRN which consisted of 990 regulations between 51 miRNAs and 275 genes, forming two big sub-networks that were defined as down-network and up-network, respectively. KEGG pathway enrichment analysis revealed that up-network was prominently involved in several KEGG pathways, in which “Focal adhesion”, “PI3K-Akt signaling pathway” and “ECM-receptor interaction” were remarked significant (adjusted p<0.001). Genes enriched in these pathways coupled with their regulatory miRNAs formed a functional miRNA-gene regulatory module that contains 7 miRNAs, 22 genes and 42 miRNA-gene connections. Gene interaction analysis based on String database revealed that 8 out of 22 genes were highly clustered. Finally, we experimentally confirmed a functional regulatory module containing 5 miRNAs (miR-130b-3p, miR-148a-3p, miR-345-5p, miR-378a-3p, and miR-422a) and 6 genes (COL6A1, COL6A2, COL6A3, PIK3R3, COL1A1, CCND2) associated with liver fibrosis. ConclusionsOur integrated analysis of miRNA and gene expression profiles highlighted a functional miRNA-gene regulatory module associated with liver fibrosis, which, to some extent, may provide important clues to better understand the underlying pathogenesis of liver fibrosis.

Abstract P279: Mapping of Chromosome 2 Differentially Expressed Aortic Genes Linked to Vascular Inflammation Using Congenic Rats Fed a High-salt Diet

Background: Three congenic rat strains (SB2a, SB2b and SB2e) were created by chromosome (Chr) 2 fragment introgression from normotensive Brown Norway (BN) rats into hypertensive Dahl salt sensitive (SS) background. SB2a and SB2b rats fed a normal-salt diet presented reduced blood pressure (BP) and inflammation when compared to SS rats. We hypothesized that BN-Chr2 contains antihypertensive and anti-inflammatory genes that could prevent high-salt diet (HSD)-induced BP elevation and vascular injury in SB2a and SB2b rats. These genes will be identified using microRNA (miRNA) and total RNA expression profiling analysis in aorta of congenic rats fed a HSD. Methods and Results: Four-to-6 week-old male SS, SS, SB2a and SB2b rats were fed a HSD (4% NaCl) for 8 weeks or until they developed a stroke as manifested by seizures. Systolic blood pressure (SBP) was measured by telemetry. Systolic BP was higher in SB2b but not SB2a when compared to SS (185±8, 167±7 vs 168±5 mm Hg). Total RNA was extracted from aorta and used to construct libraries for small and total RNA sequencing using Illumina HiSeq-2500. The bioinformatics pipeline included: FastQC for quality control, STAR for genome (Rattus norvegicus, release-86) alignment, mirdeep2 for miRNA annotation and counting, Htseq-count for mRNA and long non-coding RNA annotation and counting; R for differential expression analysis. Differentially expressed miRNAs and genes (mRNAs and non-coding RNAs) were identified in SB2a vs SS (miRNAs: 11 up and 10 down; genes: 92 up and 91 down) and in SB2b vs SS (miRNAs: 3 up and 2 down; genes: 10 up and 13 down) with FDR&lt;0.05. Differentially expressed genes encoded within different BN-Chr2 congenic portions were identified in SB2a vs SS (genes: 7 up and 2 down) and SB2b vs SS (genes: 6 up and 4 down). Conclusions and Perspectives: Differentially expressed BN-Chr2 encoded genes were identified in aorta of congenic SB2a and SB2b rats fed HSD. Whether these genes play a role in HSD-induced BP elevation and vascular inflammation remains to be determined.

MicroRNA expression profiling and bioinformatics analysis of dysregulated microRNAs in obstructive sleep apnea patients.

Obstructive sleep apnea (OSA) is a common chronic obstructive sleep disease in clinic. The purpose of our study was to use bioinformatics analysis to identify microRNAs (miRNAs) that are differentially expressed between OSA patients and healthy controls.Serum samples were collected from OSA patients and healthy controls. To better reveal the sample specificity of differentially expressed microRNAs, supervised hierarchical clustering was conducted. We used the microT-CDS and TargetScan databases to predict target genes of the differentially expressed microRNAs and selected the common genes. The Search Tool for the Retrieval of Interacting Genes (STRING) was used to evaluate many coexpression relationships. Moreover, we used these potential microRNA-target pairs and coexpression relationships to construct a regulatory coexpression network using Cytoscape software. Functional analysis of microRNA target genes was conducted with FunRich.A total of 104 microRNAs that were differentially expressed between OSA patients and healthy controls were identified. Supervised hierarchical clustering was conducted based on the expression of the 104 microRNAs in the OSA patients and healthy controls. Overall, 6621 potential target genes were predicted, and 119 target genes were screened based on coexpression coefficients in the STRING database. A regulatory coexpression network was constructed that included 23 differentially expressed microRNAs and 18 of the most related potential target genes. Metabolic signaling pathways were the most highly enriched category. Differentially expressed microRNAs, such as hsa-miR-485-5p, hsa-miR-107, hsa-miR-574-5p, and hsa-miR-199-3p, might participate in OSA. The target gene CAD might also be closely related to OSA.Our results may provide a basis for the pathogenesis of OSA and the study of disease diagnosis, prevention, and treatment. However, more experiments are needed to verify these predictions.

Analysis of salivary microRNA expression profiles and identification of novel biomarkers in esophageal cancer.

MicroRNAs (miRNAs/miRs) regulate the expression of target genes and are considered to be associated with human cancer. The aim of the present study was to screen novel miRNA biomarkers in esophageal cancer (EC). The miRNA expression profile GSE41268 was extracted from Gene Expression Omnibus database, and differentially expressed miRNAs between whole saliva samples from patients with EC and healthy controls were identified using the Linear Models for Microarray Data package. Then, the targets of these miRNAs were screened using the miRecords database and used to construct the regulatory network. Gene ontology and pathway enrichment analyses were performed for the target genes of differentially expressed miRNAs to predict their potential functions. A total of 18 differentially expressed miRNAs were identified in saliva samples from patients with EC, and 43 validated target genes corresponding to 7 upregulated miRNAs were identified. Then, 6 miRNAs (miR-144, miR-451, miR-98, miR-10b, miR-486-5p and miR-363) and their target genes were used to construct a regulatory network. Within the network, miR-144 may target Notch homolog 1, fibrinogen α chain and fibrinogen β chain; miR-451 may regulate murine thymoma viral oncogene homolog 1, matrix metalloproteinase (MMP)9 and MMP2; miR-98 may directly target E2F transcription factor (E2F) 1, E2F2 and v-myc avian myelocytomatosis viral oncogene homolog (MYC); miR-10b may modulate peroxisome proliferator-activated receptor α and Kruppel-like factor 4; miR-485-5p and miR-363 may regulate TNF receptor superfamily member 5 and cyclin-dependent kinase inhibitor 1A. In addition, E2F1, E2F2 and MYC were associated with the cell cycle, which was the most significantly enriched function and pathway in EC. The results of the present study suggested that miR-144, miR-451, miR-98, miR-10b and miR-363 may be involved in EC by regulating their target genes, and may be used as biomarkers for EC.

MicroRNA Signatures and Molecular Subtypes of Glioblastoma: The Role of Extracellular Transfer.

SummaryDespite the importance of molecular subtype classification of glioblastoma (GBM), the extent of extracellular vesicle (EV)-driven molecular and phenotypic reprogramming remains poorly understood. To reveal complex subpopulation dynamics within the heterogeneous intratumoral ecosystem, we characterized microRNA expression and secretion in phenotypically diverse subpopulations of patient-derived GBM stem-like cells (GSCs). As EVs and microRNAs convey information that rearranges the molecular landscape in a cell type-specific manner, we argue that intratumoral exchange of microRNA augments the heterogeneity of GSC that is reflected in highly heterogeneous profile of microRNA expression in GBM subtypes.

Computational identification of mutually exclusive transcriptional drivers dysregulating metastatic microRNAs in prostate cancer

Androgen-ablation therapies, which are the standard treatment for metastatic prostate cancer, invariably lead to acquired resistance. Hence, a systematic identification of additional drivers may provide useful insights into the development of effective therapies. Numerous microRNAs that are critical for metastasis are dysregulated in metastatic prostate cancer, but the underlying molecular mechanism is poorly understood. We perform an integrative analysis of transcription factor (TF) and microRNA expression profiles and computationally identify three master TFs, AR, HOXC6 and NKX2-2, which induce the aberrant metastatic microRNA expression in a mutually exclusive fashion. Experimental validations confirm that the three TFs co-dysregulate a large number of metastasis-associated microRNAs. Moreover, their overexpression substantially enhances cell motility and is consistently associated with a poor clinical outcome. Finally, the mutually exclusive overexpression between AR, HOXC6 and NKX2-2 is preserved across various tissues and cancers, suggesting that mutual exclusivity may represent an intrinsic characteristic of driver TFs during tumorigenesis.

883 - Integrated analysis of microRNA and mRNA expression profiles in tuberous sclerosis complex angiomyolipoma

883 - Integrated analysis of microRNA and mRNA expression profiles in tuberous sclerosis complex angiomyolipoma

Comparative analysis of microRNA and mRNA expression profiles in cells and exosomes under toluene exposure

Recent studies have illustrated the growing importance of exosomes (small extracellular vesicles) and their constituent microRNAs (miRNAs) in the fields of toxicology and pathology. The mechanism of toxicity of toluene, a highly-prevalent and volatile organic compound, is largely unknown. To examine the role of miRNAs in toluene-induced toxicity, we investigated miRNAs and toluene-induced gene expression in HL-60 human promyelocytic leukemia cells and exosomes using microarrays.A total of 54 miRNAs were differentially expressed in HL-60 cell lines exposed to toluene and exosomes from the cells. Four out of the 54 miRNAs (hsa-miR-1290, hsa-miR-718, hsa-miR-3663-3p, and hsa-miR-320c) were subsequently validated by qRT-PCR. Integrated analysis of miRNA and mRNA expression profiles identified 8 miRNA-mRNA correlations. By performing Comparative Toxicogenomics Database analysis, we found that the eight putative target genes of the differentially expressed miRNAs under toluene exposure (EXOSC6, RHOH, GFER, HERC2, GOLGA4, SLC7A11, GCLM, and BACH1) are related to diverse disease categories such as nervous system disease, cancer, cardiovascular disease, and respiratory tract disease.In conclusion, our data demonstrated that miRNA-mRNA networks provide a better understanding of toxicological mechanism caused by environmental pollutants in vitro using HL-60 cells and exosomes.

MiR-494-3p overexpression promotes megakaryocytopoiesis in primary myelofibrosis hematopoietic stem/progenitor cells by targeting SOCS6.

Primary myelofibrosis (PMF) is a chronic Philadelphia-negative myeloproliferative neoplasm characterized by hematopoietic stem cell-derived clonal myeloproliferation, involving especially the megakaryocyte lineage. To better characterize how the altered expression of microRNAs might contribute to PMF pathogenesis, we have previously performed the integrative analysis of gene and microRNA expression profiles of PMF hematopoietic stem/progenitor cells (HSPCs), which allowed us to identify miR-494-3p as the upregulated microRNA predicted to target the highest number of downregulated mRNAs.To elucidate the role of miR-494-3p in hematopoietic differentiation, in the present study we demonstrated that miR-494-3p enforced expression in normal HSPCs promotes megakaryocytopoiesis. Gene expression profiling upon miR-494-3p overexpression allowed the identification of genes commonly downregulated both after microRNA overexpression and in PMF CD34+ cells. Among them, suppressor of cytokine signaling 6 (SOCS6) was confirmed to be a miR-494-3p target by luciferase assay. Western blot analysis showed reduced level of SOCS6 protein as well as STAT3 activation in miR-494-3p overexpressing cells. Furthermore, transient inhibition of SOCS6 expression in HSPCs demonstrated that SOCS6 silencing stimulates megakaryocytopoiesis, mimicking the phenotypic effects observed upon miR-494-3p overexpression. Finally, to disclose the contribution of miR-494-3p upregulation to PMF pathogenesis, we performed inhibition experiments in PMF HSPCs, which showed that miR-494-3p silencing led to SOCS6 upregulation and impaired megakaryocyte differentiation.Taken together, our results describe for the first time the role of miR-494-3p during normal HSPC differentiation and suggest that its increased expression, and the subsequent downregulation of its target SOCS6, might contribute to the megakaryocyte hyperplasia commonly observed in PMF patients.

Comparative analysis of microRNA expression profiles between A549, A549/DDP and their respective exosomes.

Exosomes were reported to transport bioactive molecules and influence the biology behavior of recipient cells. In order to study the role of exosomal microRNAs in the mechanism of cisplatin resistance to lung cancer cells, we analyzed the expression profiles of microRNAs in A549, A549/DDP cells and their exosomes by microarray. The results showed that a certain proportion of microRNAs were co-expressed in the cells and exosomes. Linear regression analysis showed that the expression of microRNAs in A549 and A549/DDP cells were strongly correlated with those in their respective exosomes. The expression level of 5 microRNAs (miR-197-5p, miR-4443, miR-642a-3p, miR-27b-3p and miR-100-5p) with the most differential expression were verified by qRT-PCR. The results were consistent with those of the microarray. Target gene prediction and pathway analysis discovered that the microRNAs in the intersections may participate in drug resistance. And the prediction of their association with diseases found that most of these microRNAs was associated with lung cancer. We could draw a preliminary conclusion that microRNAs in exosomes may be involved in the drug resistance of lung cancer cells to cisplatin.

Roles of microRNAs in immunopathogenesis of non-alcoholic fatty liver disease revealed by integrated analysis of microRNA and mRNA expression profiles

The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoholic fatty liver disease (NAFLD). We analyzed differentially expressed microRNA and mRNA expression profiles of CD4+ T lymphocytes from the liver and mesenteric lymph nodes (MLNs) of mice with NAFLD using microarrays and RNA sequencing. Normal mice were used as controls. The target genes of microRNAs were predicted by TargetScan. Integrative analysis showed that the mRNAs were overlapped with microRNAs. Furthermore, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the key genes and pathways. Then, 16 microRNAs and 10 mRNAs were validated by qRT-PCR. Microarray analysis suggested that 170 microRNAs were significantly de-regulated in CD4+ T lymphocytes from the liver between the two groups. Eighty mRNAs corresponded with microRNA targeted genes. KEGG analysis indicated that the MAPK pathway was consistently augmented in the liver of NAFLD mice. miR-23b, let-7e, miR-128 and miR-130b possibly played significant parts in the MAPK pathways. Furthermore, between the two groups, 237 microRNAs were significantly de-regulated in CD4+ T lymphocytes from MLNs. 38 mRNAs coincided with microRNA target genes. The metabolic pathway was consistently enriched in the MLNs of NAFLD mice. miR-206-3p, miR-181a-5p, miR-29c-3p and miR-30d-5p likely play important roles in the regulation of metabolic pathways. The results of this study presented a new perspective on the application of integrative analysis to identify complex regulation means involved in the immunological pathogenesis of NAFLD.

Analysis of microRNA expression profile in serum of patients with electrical burn or thermal burn

Objective: To explore the differential expression of microRNAs in the serum among patients with electrical burn or thermal burn and healthy persons and to explore the significance. Methods: In this study we included three patients with electrical burn and three patients with thermal burn, conforming to the inclusion criteria and hospitalized in our burn ward from June to August 2015, and three healthy adult volunteers. Their serum samples were separated from whole blood and divided into electrical burn group, thermal burn group, and normal control group. Total RNA was extracted from their serum samples using Trizol method. The differentially expressed microRNAs (with differential ratio larger than or equal to 2.000, less than or equal to 0.500) among the three groups were screened by microRNA chip technique. Then cluster and Venn diagram analysis of the differentially expressed microRNAs were performed. Enrichment analysis of Kyoto encyclopedia of genes and genomes (KEGG) signaling pathway was performed on the distinctly changed microRNAs (with differential ratio larger than or equal to 5.000, less than or equal to 0.500). Results: There were 220 differentially expressed microRNAs among serum of the three groups. MicroRNA expression profiles in serum of electrical burn and thermal burn groups were different from that in serum of normal control group. Compared with those in serum of normal control group, the expressions of 59 microRNAs changed more than 2.000 times in serum of electrical burn group, with 50 up-regulated microRNAs and 9 down-regulated microRNAs; the expressions of 40 microRNAs changed more than 2.000 times in serum of thermal burn group, with 21 up-regulated microRNAs and 19 down-regulated microRNAs. Compared with those in serum of thermal burn group, the expressions of 167 microRNAs changed more than 2.000 times in serum of electrical burn group. There were 17 exclusively expressed microRNAs in serum of thermal burn group and 26 exclusively expressed microRNAs in serum of electrical burn group, compared with those in serum of normal control group. Enrichment analysis of KEGG signaling pathway showed that compared with those in serum of normal control group, microRNAs which changed distinctly in serum of electrical burn group took part in the insulin secretion signaling pathway, arrhythmogenic right ventricular cardiomyopathy signaling pathway, hypertrophic cardiomyopathy signaling pathway, glutamatergic synapse signaling pathway, calcium signaling pathway, cyclic adenosine monophosphate signaling pathway, glycerophospholipid metabolism, pyrimidine metabolism, serotonergic synapse signaling pathway, etc, while microRNAs which changed distinctly in serum of thermal burn group took part in the tumor transcription misregulation signaling pathway, proteoglycans in tumor signaling pathway, microRNAs in tumor signaling pathway, long-term potentiation signaling pathway, citrate cycle signaling pathway, tumor necrosis factor signaling pathway, focal adhesion signaling pathway, endocytosis signaling pathway, insulin secretion signaling pathway, p53 signaling pathway, and estrogen signaling pathway, etc. Conclusions: MicroRNA expression profiles in serum of electrical and thermal burn are different from that in serum of healthy adult. The signaling pathways enriched with target genes which are regulated by the differentially expressed microRNAs are related to the pathological changes and clinical manifestations after electrical or thermal burn.

Analysis of MicroRNA Expression Profiling Involved in MC-LR-Induced Cytotoxicity by High-Throughput Sequencing.

In recent years, microRNAs (miRNAs) in toxicology have attracted great attention. However, the underlying mechanism of miRNAs in the cytotoxicity of microcystin-LR (MC-LR) is lacking. The objective of this study is to analyze miRNA profiling in HepG2 cells after 24 h of MC-LR-exposure to affirm whether and how miRNAs were involved in the cytotoxicity of MC-LR. The results showed that totally 21 and 37 miRNAs were found to be significantly altered in the MC-LR treated cells at concentrations of 10 and 50 μM, respectively, when compared to the control cells. In these two groups, 37,566 and 39,174 target genes were predicted, respectively. The further analysis showed that MC-LR-exposure promoted the expressions of has-miR-149-3p, has-miR-449c-5p, and has-miR-454-3p while suppressed the expressions of has-miR-4286, has-miR-500a-3p, has-miR-500a-5p, and has-miR-500b-5p in MC-LR-treated groups when compared to the control group. Moreover, the result of qPCR confirmed the above result, suggesting that these miRNAs may be involved in MC-LR-hepatotoxicity and they may play an important role in the hepatitis and liver cancer caused by MC-LR. The target genes for differentially expressed miRNAs in MC-LR treatment groups were significantly enriched to totally 23 classes of GO, in which three were significantly enriched in both 10 and 50 μM MC-LR groups. Moreover, the results of KEGG pathway analysis showed that MC-LR-exposure altered some important signaling pathways such as MAPK, biosynthesis of secondary metabolites, and pyrimidine and purine metabolism, which were possibly negatively regulated by the corresponding miRNAs and might play important role in MC-LR-mediated cytotoxicity in HepG2 cells.

Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged cDNA Libraries and a Multiplex Sequencing Strategy.

Small and long noncoding RNAs (ncRNAs) are key regulators of gene expression. Variations in ncRNA expression patterns can consequently affect the control of many cellular processes. Not just since 2006, when Andrew Z Fire and Craig C Mello were jointly awarded The Nobel Prize in Physiology or Medicine for their discovery of RNA interference, great efforts were undertaken to unleash the biomedical applicability of small noncoding RNAs, in particular microRNAs. With the technological evolution of massive parallel sequencing technologies over the last years, which now are available for an increasing number of scientists, there is a demand for comprehensible and efficient workflows reliable even for unique and valuable clinical specimens. Here we describe a highly reproducible low-cost protocol for analyses of miRNA expression patterns using tagged cDNA libraries and a multiplex sequencing strategy following an Illumina-like protocol. This protocol easily allows the identification of expression differences from samples of tissues of 1-2mm3 and fluids of 50-200μL. We further provide entry points into useful computational biology applications, whose target groups explicitly involve non-bioinformaticians.

Integrated analysis of microRNA and mRNA expression profiles in HBx-expressing hepatic cells.

AIMTo identify the miRNA-mRNA regulatory network in hepatitis B virus X (HBx)-expressing hepatic cells.METHODSA stable HBx-expressing human liver cell line L02 was established. The mRNA and miRNA expression profiles of L02/HBx and L02/pcDNA liver cells were identified by RNA-sequencing analysis. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed to investigate the function of candidate biomarkers, and the relationship between miRNA and mRNA was studied by network analysis.RESULTSCompared with L02/pcDNA cells, 742 unregulated genes and 501 downregulated genes were determined as differentially expressed in L02/HBx cells. Gene ontology analysis suggested that the differentially expressed genes were relevant to different biological processes. Concurrently, 22 differential miRNAs were also determined in L02/HBx cells. Furthermore, integrated analysis of miRNA and mRNA expression profiles identified a core miRNA-mRNA regulatory network that is correlated with the carcinogenic role of HBx.CONCLUSIONCollectively, the miRNA-mRNA network-based analysis could be useful to elucidate the potential role of HBx in liver cell malignant transformation and shed light on the underlying molecular mechanism and novel therapy targets for hepatocellular carcinoma.

MicroRNA expression profiles of human iPSCs differentiation into insulin-producing cells.

MicroRNAs are a class of small noncoding RNAs, which control gene expression by inhibition of mRNA translation. MicroRNAs are involved in the control of biological processes including cell differentiation. Here, we aim at characterizing microRNA expression profiles during differentiation of human induced pluripotent stem cells (hiPSCs) into insulin-producing cells. We differentiated hiPSCs toward endocrine pancreatic lineage following a 18-day protocol. We analyzed genes and microRNA expression levels using RT real-time PCR and TaqMan microRNA arrays followed by bioinformatic functional analysis. MicroRNA expression profiles analysis of undifferentiated hiPSCs during pancreatic differentiation revealed that 347/768 microRNAs were expressed at least in one time point of all samples. We observed 18 microRNAs differentially expressed: 11 were upregulated (miR-9-5p, miR-9-3p, miR-10a, miR-99a-3p, miR-124a, miR-135a, miR-138, miR-149, miR-211, miR-342-3p and miR-375) and 7 downregulated (miR-31, miR-127, miR-143, miR-302c-3p, miR-373, miR-518b and miR-520c-3p) during differentiation into insulin-producing cells. Selected microRNAs were further evaluated during differentiation of Sendai-virus-reprogrammed hiPSCs using an improved endocrine pancreatic beta cell derivation protocol and, moreover, in differentiated NKX6.1+ sorted cells. Following Targetscan7.0 analysis of target genes of differentially expressed microRNAs and gene ontology classification, we found that such target genes belong to categories of major significance in pancreas organogenesis and development or exocytosis. We detected a specific hiPSCs microRNAs signature during differentiation into insulin-producing cells and demonstrated that differentially expressed microRNAs target several genes involved in pancreas organogenesis.