scholarly journals Differentially Regulated miRNAs and Their Related Molecular Pathways in Lichen Sclerosus

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2291
Author(s):  
Xiaohui Tan ◽  
Shuyang Ren ◽  
Canyuan Yang ◽  
Shuchang Ren ◽  
Melinda Z. Fu ◽  
...  
Keyword(s):  
Normal Tissue ◽  
Dermal Fibroblast ◽  
Lichen Sclerosus ◽  
Differentially Expressed ◽  
Molecular Networks ◽  
Adjacent Normal Tissue ◽  
Aberrant Expression ◽  
Next Generation Sequencing Technology ◽  
Functional Studies ◽  
Differentially Expressed Mirnas

Lichen sclerosus (LS) is a chronic inflammatory skin disorder with unknown pathogenesis. The aberrant expression of microRNAs (miRNAs) is considered to exert a crucial role in LS. We used the next-generation sequencing technology (RNASeq) for miRNA profiling and Ingenuity Pathway Analysis (IPA) for molecular network analysis. We performed qRT-PCR, miRNA transfection and Matrigel assays for functional studies. We identified a total of 170 differentially expressed miRNAs between female LS and matched adjacent normal tissue using RNASeq, with 119 upregulated and 51 downregulated. Bioinformatics analysis revealed molecular networks that may shed light on the pathogenesis of LS. We verified the expression of a set of miRNAs that are related to autoimmunity, such as upregulated miR-326, miR-142-5p, miR-155 and downregulated miR-664a-3p and miR-181a-3p in LS tissue compared to the matched adjacent normal tissue. The differentially expressed miRNAs were also verified in blood samples from LS patients compared to healthy female volunteers. Functional studies demonstrated that a forced expression of miR-142-5p in human dermal fibroblast PCS-201-010 cells resulted in decreased cell proliferation and migration. These findings suggest that differentially expressed miRNAs may play an important role in LS pathogenesis; therefore, they could serve as biomarkers for LS management.

scholarly journals Role of miRNAs in Sigmoid Colon Cancer: A Search for Potential Biomarkers

Cancers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3311
Author(s):  
Diego Marques ◽  
Layse Raynara Ferreira-Costa ◽  
Lorenna Larissa Ferreira-Costa ◽  
Ana Beatriz Bezerra-Oliveira ◽  
Romualdo da Silva Correa ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Sigmoid Colon ◽  
Cancer Progression ◽  
Target Genes ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Sigmoid Colon Cancer ◽  
Colon Tissue ◽  
Aberrant Expression ◽  
Differentially Expressed Mirnas

The aberrant expression of microRNAs in known to play a crucial role in carcinogenesis. Here, we evaluated the miRNA expression profile of sigmoid colon cancer (SCC) compared to adjacent-to-tumor (ADJ) and sigmoid colon healthy (SCH) tissues obtained from colon biopsy extracted from Brazilian patients. Comparisons were performed between each group separately, considering as significant p-values < 0.05 and |Log2(Fold-Change)| > 2. We found 20 differentially expressed miRNAs (DEmiRNAs) in all comparisons, two of which were shared between SCC vs. ADJ and SCC vs. SCH. We used miRTarBase, and miRTargetLink to identify target-genes of the differentially expressed miRNAs, and DAVID and REACTOME databases for gene enrichment analysis. We also used TCGA and GTEx databases to build miRNA-gene regulatory networks and check for the reproducibility in our results. As findings, in addition to previously known miRNAs associated with colorectal cancer, we identified three potential novel biomarkers. We showed that the three types of colon tissue could be clearly distinguished using a panel composed by the 20 DEmiRNAs. Additionally, we found enriched pathways related to the carcinogenic process in which miRNA could be involved, indicating that adjacent-to-tumor tissues may be already altered and cannot be considered as healthy tissues. Overall, we expect that these findings may help in the search for biomarkers to prevent cancer progression or, at least, allow its early detection, however, more studies are needed to confirm our results.

scholarly journals Identification of key miRNAs in the progression of hepatocellular carcinoma using an integrated bioinformatics approach

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9000
Author(s):  
Qi Zheng ◽  
Xiaoyong Wei ◽  
Jun Rao ◽  
Cuncai Zhou
Keyword(s):  
Expression Profiles ◽  
Differentially Expressed ◽  
Data Set ◽  
Aberrant Expression ◽  
External Data ◽  
Genes Expression ◽  
Mirna Expression Profiles ◽  
Differentially Expressed Mirnas ◽  
Microarray Datasets ◽  
The Relationship

Backgroud It has been shown that aberrant expression of microRNAs (miRNAs) and transcriptional factors (TFs) is tightly associated with the development of HCC. Therefore, in order to further understand the pathogenesis of HCC, it is necessary to systematically study the relationship between the expression of miRNAs, TF and genes. In this study, we aim to identify the potential transcriptomic markers of HCC through analyzing common microarray datasets, and further establish the differential co-expression network of miRNAs–TF–mRNA to screen for key miRNAs as candidate diagnostic markers for HCC. Method We first downloaded the mRNA and miRNA expression profiles of liver cancer from the GEO database. After pretreatment, we used a linear model to screen for differentially expressed genes (DEGs) and miRNAs. Further, we used weighed gene co-expression network analysis (WGCNA) to construct the differential gene co-expression network for these DEGs. Next, we identified mRNA modules significantly related to tumorigenesis in this network, and evaluated the relationship between mRNAs and TFs by TFBtools. Finally, the key miRNA was screened out in the mRNA–TF–miRNA ternary network constructed based on the target TF of differentially expressed miRNAs, and was further verified with external data set. Results A total of 465 DEGs and 215 differentially expressed miRNAs were identified through differential genes expression analysis, and WGCNA was used to establish a co-expression network of DEGs. One module that closely related to tumorigenesis was obtained, including 33 genes. Next, a ternary network was constructed by selecting 256 pairs of mRNA–TF pairs and 100 pairs of miRNA–TF pairs. Network mining revealed that there were significant interactions between 18 mRNAs and 25 miRNAs. Finally, we used another independent data set to verify that miRNA hsa-mir-106b and hsa-mir-195 are good classifiers of HCC and might play key roles in the progression of HCC. Conclusion Our data indicated that two miRNAs—hsa-mir-106b and hsa-mir-195—are identified as good classifiers of HCC.

scholarly journals Evaluation of microRNA expression in a sheep model for lung fibrosis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Udari Eshani Perera ◽  
Habtamu B. Derseh ◽  
Sasika N. V. Dewage ◽  
Andrew Stent ◽  
Rukmali Wijayarathna ◽  
...  
Keyword(s):  
Pulmonary Fibrosis ◽  
Lung Fibrosis ◽  
Expression Profiles ◽  
Interstitial Lung Diseases ◽  
Differentially Expressed ◽  
Sheep Model ◽  
Aberrant Expression ◽  
Pathway Enrichment ◽  
Differentially Expressed Mirnas ◽  
Novel Therapeutic Strategies

Abstract Background Idiopathic pulmonary fibrosis (IPF) is a chronic progressive fibroproliferative disorder that has one of the poorest prognoses amongst interstitial lung diseases. Recently, the finding of aberrant expression levels of miRNAs in IPF patients has drawn significant attention to the involvement of these molecules in the pathogenesis of this disease. Clarification of the differential expression of miRNAs in health and disease may identify novel therapeutic strategies that can be employed in the future to combat IPF. This study evaluates the miRNA expression profiles in a sheep model for lung fibrosis and compares them to the miRNA profiles of both IPF patients and the mouse bleomycin model for pulmonary fibrosis. Pathway enrichment analyses were performed on differentially expressed miRNAs to illustrate which biological mechanisms were associated with lung fibrosis. Results We discovered 49 differentially expressed miRNAs in the sheep fibrosis model, in which 32 miRNAs were significantly down regulated, while 17 miRNAs were significantly upregulated due to bleomycin-induced lung injury. Moreover, the miRNA families miR-29, miR-26, miR-30, let-7, miR-21, miR-19, miR-17 and miR-199 were aberrantly expressed in both sheep and mouse models, with similar differential miRNAs expression observed in IPF cases. Importantly, 18 miRNAs were aberrantly expressed in both the sheep model and IPF patients, but not in mice. Conclusion Together with pathway enrichment analyses, these results show that the sheep model can potentially be used to characterize previously unrecognized biological pathways associated with lung fibrosis.

Reconstruction and analysis of the aberrant lncRNA–miRNA–mRNA network in systemic lupus erythematosus

Lupus ◽  
2020 ◽  
Vol 29 (4) ◽  
pp. 398-406 ◽  
Author(s):  
H Xu ◽  
W Chen ◽  
F Zheng ◽  
D Tang ◽  
D Liu ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Lupus Erythematosus ◽  
Venous Blood ◽  
Differentially Expressed ◽  
Systemic Lupus ◽  
Aberrant Expression ◽  
Differentially Expressed Mirnas ◽  
Non Coding Rnas ◽  
New Perspective ◽  
Pathway Analyses

Objective A new perspective of determining the pathophysiology of systemic lupus erythematosus (SLE) development is required. The current study explores the aberrant expression of long non-coding RNAs (lncRNA), microRNA (miRNA) and mRNA. The study further constructs and analyses the lncRNA–miRNA–mRNA network to elucidate their gene regulation roles in SLE. Method We extracted mRNA, lncRNA and miRNA from the whole venous blood of 20 SLE patients and 20 normal control (NC) healthy individuals. A lncRNA–mRNA–miRNA network in SLE was constructed using a bioinformatics approach. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed using the Cytoscape plug-in BinGo, the DAVID database and Cytoscape software to explore the function of mRNAs in this network. Result A total of 855 mRNA, 7311 lncRNA and 134 miRNA with differentially expressed profiles were identified. Meanwhile, we established a competing endogenous RNA (ceRNA) subnetwork composed of 52 differentially expressed lncRNAs (DElncRNAs), seven differentially expressed miRNAs and 10 differentially expressed mRNAs. We extracted the subnetwork from the ceRNA network and found that three novel miRNAs were key: hsa-miR-145, hsa-miR-17 and hsa-miR-143. We also deduced that the DElncRNAs MIAT and NEAT1 might play crucial roles in the pathogenesis of SLE. The results were verified by bioinformatics analysis. Conclusion Our results provide a novel perspective for studying lncRNA-related and miRNA-related ceRNA networks in SLE.

160. THE POTENTIAL ROLE OF microRNAs IN THE DEVELOPMENT OF THE HUMAN PLACENTA IN EARLY PREGNANCY

2009 ◽  
Vol 21 (9) ◽  
pp. 78
Author(s):  
W. Kong ◽  
R. Nowak ◽  
C. T. Roberts ◽  
J. A. Owens
Keyword(s):  
Gene Expression ◽  
Transcriptional Repression ◽  
Regulatory Networks ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Molecular Networks ◽  
Placental Development ◽  
Altered Expression ◽  
Differentially Expressed Mirnas ◽  
Pathways Analysis

Placental functional development is characterised by dynamic and co-ordinated changes in expression of genes that drive invasion, differentiation and growth. These changes may arise in part from altered expression of microRNAs (miRNAs) via their regulatory networks. MiRNAs are short, single-stranded, non-coding RNAs involved in the post-transcriptional repression of gene expression. MiRNAs bind to complementary sites in the 3'UTR of target mRNAs to repress or silence translation. MiRNAs have been detected in the mammalian placenta, but their patterns of expression throughout pregnancy have not been systematically characterized. Using microarrays, miRNA gene expression was compared at two stages (6–8 weeks, 10–12 weeks) in early gestation, in chorionic villi of human placentas (term ~40 weeks). Putative and validated targets of differentially expressed miRNAs were extracted from freely accessible databases, miRBase [1], PicTar [2], TargetScan [3] and miRecords [4]. 15 miRNAs were differentially expressed between these gestational ages (p<0.05). 11 of these miRNAs were upregulated in 10–12 week villi and 4 were downregulated. Many of the differentially expressed miRNAs are members of the same polycistronic clusters, suggesting that these miRNAs may be co-expressed. Shared targets of differentially expressed miRNAs from the same clusters were assessed using Ingenuity Pathways Analysis, to search for significantly represented molecular networks. All downregulated miRNAs at 10–12 weeks shared 35 putative targets and fell into 1 of 2 clusters, on chromosome 13 or X. Previously validated targets include PTEN [5], Notch1 [6], VEGFA [7], CDKN2A [8] and DHFR [9] . Six of the upregulated miRNAs at 10–12 weeks are members of 3 clusters on chromosome 19, 9 and X. Networks targeted by these cluster members include PTEN, HIF1α and IL-12 signalling. Together all of these processes are active and important in early placentation and their predicted targeting by differentially expressed miRNAs is consistent with an important role in placental development.

scholarly journals Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 956 ◽  
Author(s):  
Allison R. Kolbe ◽  
Matthew L. Bendall ◽  
Alexander T. Pearson ◽  
Doru Paul ◽  
Douglas F. Nixon ◽  
...  
Keyword(s):  
Head And Neck Cancer ◽  
Head And Neck ◽  
Neck Cancer ◽  
Normal Tissue ◽  
Endogenous Retroviruses ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Human Endogenous Retrovirus ◽  
Adjacent Normal Tissue ◽  
Herv Expression

Human endogenous retroviruses (HERVs) have been implicated in a variety of human diseases including cancers. However, technical challenges in analyzing HERV sequence data have limited locus-specific characterization of HERV expression. Here, we use the software Telescope (developed to identify expressed transposable elements from metatranscriptomic data) on 43 paired tumor and adjacent normal tissue samples from The Cancer Genome Atlas Program to produce the first locus-specific retrotranscriptome of head and neck cancer. Telescope identified over 3000 expressed HERVs in tumor and adjacent normal tissue, and 1078 HERVs were differentially expressed between the two tissue types. The majority of differentially expressed HERVs were expressed at a higher level in tumor tissue. Differentially expressed HERVs were enriched in members of the HERVH family. Hierarchical clustering based on HERV expression in tumor-adjacent normal tissue resulted in two distinct clusters with significantly different survival probability. Together, these results highlight the importance of future work on the role of HERVs across a range of cancers.

Gene expression in prostate tissue according to frequency of ejaculation.

2016 ◽  
Vol 34 (2_suppl) ◽  
pp. 25-25
Author(s):  
Jennifer R. Rider ◽  
Jennifer A Sinnott ◽  
Lorelei A. Mucci
Keyword(s):  
Gene Expression ◽  
Normal Tissue ◽  
Tumor Tissue ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Adjacent Normal Tissue ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Ejaculation Frequency

25 Background: Long-term prospective data from within the Health Professionals Follow-up Study (HPFS) suggest more frequent ejaculation throughout adult life may be protective against future development of prostate cancer (PCa). Compared to men with an average monthly ejaculation frequency (EF) of 4-7 times/month during adulthood, men who ejaculated at least 21 times per month were 30% less likely to be diagnosed with PCa after adjustment for a number of potential confounders and PCa screening. We sought to explore mechanisms through which EF may influence PCa development utilizing gene expression data assessed on tumor and adjacent normal tissue. Methods: In 1992, 31,925 HPFS participants were questioned on their average monthly EF at ages 20-29, 40-49, and in the previous year; 3,839 of these men were later diagnosed with PCa. Expression of 20,254 genes was available from archival tumor tissue from 156 cases; 84 of these cases also had data from adjacent normal tissue. We regressed each gene expression value as a continuous outcome on EF, age at diagnosis, and year at diagnosis. We calculated the p value associated with the coefficient for the EF variable as a measure of the strength of the trend test. We then used t values for the coefficients to rank the genes, and ran a gene set enrichment analysis to identify pathways with genes associated with EF. Results: We observed that while there was not much signal in the tumor tissue, there was enrichment of smaller p values in the adjacent normal tissue. EF in the time period most proximal to diagnosis is most strongly associated with gene expression in normal tissue. Focusing on the association between gene expression in normal tissue and EF in the year prior to the questionnaire (1991), the top six differentially expressed genes were OR4K1, CCDC138, SERPINA9, TRMT61B, ZNF302, and ASB4. Gene set enrichment analysis revealed a substantial number of pathways differentially expressed at the FDR <0.05 threshold. Conclusions: Identifying changes in gene expression associated with EF in normal prostate tissue provides further support for a biological role of ejaculation frequency in the etiology of PCa. Notably, pathways downregulated with increasing ejaculation frequency were primarily immune related.

Differentially expressed miRNAs in spindle cell oncocytoma of the pituitary gland

2019 ◽  
Author(s):  
Lilla Krokker ◽  
Gabor Nyirő ◽  
Lilla Reininger ◽  
Otto Darvasi ◽  
Nikolette Szucs ◽  
...  
Keyword(s):  
Pituitary Gland ◽  
Spindle Cell ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Spindle Cell Oncocytoma

Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

2021 ◽  
Vol 15 (8) ◽  
pp. 927-936 ◽  
Author(s):  
Yan Peng ◽  
Yuewu Liu ◽  
Xinbo Chen
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Hot Spot ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Promising Tool ◽  
Differentially Expressed Mirnas ◽  
Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identified. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

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