MicroRNA expression profiles in peri-miniscrew implant crevicular fluid in orthodontics: a pilot study

Abstract Background This study systematically evaluated microRNA (miRNA) expression patterns in peri-miniscrew implant crevicular fluid (PMICF) in orthodontic patients. Methods Next-generation sequencing (NGS) was performed to obtain miRNA profiles in PMICF or gingival crevicular fluid (GCF) collected from 3 healthy volunteers (H), 3 peri-implantitis patients (PMSII) and 5 periodontitis patients (P). MiRNA expression patterns were compared between normal and orthodontic PMICF and GCF. Differentially expressed miRNAs were estimated by quantitative real-time PCR (qRT-PCR). Enrichment analyses of the gene targets controlled by these miRNAs were conducted by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results Compared with healthy donors, in PMSII patients, a total of 206 upregulated miRNAs and 152 downregulated miRNAs were detected in PMICF, while periodontitis patients had 333 upregulated miRNAs and 318 downregulated miRNAs. MiR-544a, miR-1245b-3p, miR-1825, miR-4291, miR-3689e, and miR-4477a were chosen randomly for further examination. qRT-PCR examination confirmed that the expression levels of miR-1245b-3p and miR-4291 were higher in PMSII than in H samples and that the expression levels of miR-1825 were higher in PMSII than in P samples. However, contrary to the NGS results, qRT-PCR analysis showed decreased expression of miR544a in PMSII. MiR3689e and miR4477a expression did not differ significantly among all samples. According to GO and KEGG pathway analyses of miR-1825, miR-4291, and miR-1245b-3p high enrichment of target genes involved in the PI3K-AKT signalling pathway was observed. Conclusions The NGS analysis of normal and orthodontic PMICF/CGF showed different miRNA profiles, which may lay the foundation for future research on the molecular mechanism of PMSII. miR-4291, miR-1245b-3p and miR-1825 may be used as diagnostic markers and potential therapeutic targets for PMSII.

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Comparison of Stemness and Gene Expression between Gingiva and Dental Follicles in Children

Stem Cells International ◽

10.1155/2016/8596520 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Chung-Min Kang ◽

Seong-Oh Kim ◽

Mijeong Jeon ◽

Hyung-Jun Choi ◽

Han-Sung Jung ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Pcr Analysis ◽

Expression Levels ◽

Qrt Pcr ◽

Stem Cell Source ◽

Regenerative Dentistry ◽

Induced Pluripotent

The aim of this study was to compare the differential gene expression and stemness in the human gingiva and dental follicles (DFs) according to their biological characteristics. Gingiva (n=9) and DFs (n=9) were collected from 18 children. Comparative gene expression profiles were collected using cDNA microarray. The expression of development, chemotaxis, mesenchymal stem cells (MSCs), and induced pluripotent stem cells (iPSs) related genes was assessed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Histological analysis was performed using hematoxylin-eosin and immunohistochemical staining. Gingiva had greater expression of genes related to keratinization, ectodermal development, and chemotaxis whereas DFs exhibited higher expression levels of genes related to tooth and embryo development. qRT-PCR analysis showed that the expression levels of iPSc factors includingSOX2,KLF4, andC-MYCwere58.5±26.3,12.4±3.5, and12.2±1.9times higher in gingiva andVCAM1(CD146) andALCAM(CD166) were33.5±6.9and4.3±0.8times higher in DFs. Genes related to MSCs markers includingCD13,CD34,CD73,CD90, andCD105were expressed at higher levels in DFs. The results of qRT-PCR and IHC staining supported the microarray analysis results. Interestingly, this study demonstrated transcription factors of iPS cells were expressed at higher levels in the gingiva. Given the minimal surgical discomfort and simple accessibility, gingiva is a good candidate stem cell source in regenerative dentistry.

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The long non-coding RNA landscape of periodontal ligament stem cells subjected to compressive force

European Journal of Orthodontics ◽

10.1093/ejo/cjy057 ◽

2018 ◽

Vol 41 (4) ◽

pp. 333-342 ◽

Cited By ~ 6

Author(s):

Yiping Huang ◽

Yingying Zhang ◽

Xiaobei Li ◽

Hao Liu ◽

Qiaolin Yang ◽

...

Keyword(s):

Stem Cells ◽

Compressive Stress ◽

Periodontal Ligament ◽

Kegg Pathway ◽

Compressive Force ◽

Differentially Expressed ◽

Periodontal Ligament Stem Cells ◽

Expression Levels ◽

Qrt Pcr ◽

Pathway Analyses

Summary Objective The role of long non-coding ribonucleic acids (lncRNAs) during orthodontic tooth movement remains unclear. We explored the lncRNA landscape of periodontal ligament stem cells (PDLSCs) subjected to compressive force. Materials and methods PDLSCs were subjected to static compressive stress (2 g/cm2) for 12 hours. Total RNA was then extracted and sequenced to measure changes in lncRNA and messenger RNA (mRNA) expression levels. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the expression levels of certain lncRNAs. Differential expression analysis as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also performed. Results In total, 90 lncRNAs and 519 mRNAs were differentially expressed in PDLSCs under compressive stress. Of the lncRNAs, 72 were upregulated and 18 downregulated. The levels of eight lncRNAs of interest (FER1L4, HIF1A-AS2, MIAT, NEAT1, ADAMTS9-AS2, LUCAT1, MIR31HG, and DHFRP1) were measured via qRT-PCR, and the results were found to be consistent with those of RNA sequencing. GO and KEGG pathway analyses showed that a wide range of biological functions were expressed during compressive loading; most differentially expressed genes were involved in extracellular matrix organization, collagen fibril organization, and the cellular response to hypoxia. Conclusions The lncRNA expression profile was significantly altered in PDLSCs subjected to compressive stress. These findings expand our understanding of molecular regulation in the mechanoresponse of PDLSCs.

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Chinese Herbal Medicine Formula Shenling Baizhu San Ameliorates High-Fat Diet-Induced NAFLD in Rats by Modulating Hepatic MicroRNA Expression Profiles

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2019/8479680 ◽

2019 ◽

Vol 2019 ◽

pp. 1-14

Author(s):

Maoxing Pan ◽

Yuanjun Deng ◽

Chuiyang Zheng ◽

Huan Nie ◽

Kairui Tang ◽

...

Keyword(s):

Mirna Expression ◽

High Fat Diet ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

High Fat ◽

Expression Levels ◽

Qrt Pcr ◽

Mirna Expression Profiles ◽

Differentially Expressed Mirnas

Objective. The purpose of present study was to investigate the potential mechanism underlying the protective effect of Shenling Baizhu San (SLBZS) on nonalcoholic fatty liver disease (NAFLD) by microRNA (miRNA) sequencing. Methods. Thirty male Wistar rats were randomly divided into a normal control (NC) group, a high-fat diet (HFD) group, and an SLBZS group. After 12 weeks, the biochemical parameters and liver histologies of the rats were assessed. The Illumina HiSeq 2500 sequencing platform was used to analyse the hepatic miRNA expression profiles. Representative differentially expressed miRNAs were further validated by qRT-PCR. The functions of the differentially expressed miRNAs were analysed by bioinformatics. Results. Our results identified 102 miRNAs that were differentially expressed in the HFD group compared with the NC group. Among those differentially expressed miRNAs, the expression levels of 28 miRNAs were reversed by SLBZS administration, suggesting the modulation effect of SLBZS on hepatic miRNA expression profiles. The qRT-PCR results confirmed that the expression levels of miR-155-5p, miR-146b-5p, miR-132-3p, and miR-34a-5p were consistent with those detected by sequencing. Bioinformatics analyses indicated that the target genes of the differentially expressed miRNAs reversed by SLBZS were mainly related to metabolic pathways. Conclusion. This study provides novel insights into the mechanism of SLBZS in protecting against NAFLD; this mechanism may be partly related to the modulation of hepatic miRNA expression and their target pathways.

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MiRNAs expression profiling of rat ovaries displaying PCOS with insulin resistance

Archives of Gynecology and Obstetrics ◽

10.1007/s00404-020-05730-z ◽

2020 ◽

Vol 302 (5) ◽

pp. 1205-1213

Author(s):

Chunren Zhang ◽

Chuyi Yu ◽

Zengxian Lin ◽

Haixia Pan ◽

Kunyin Li ◽

...

Keyword(s):

Insulin Resistance ◽

Target Genes ◽

Kegg Pathway ◽

Polycystic Ovary ◽

Expression Profiles ◽

Differentially Expressed ◽

Real Time Quantitative Pcr ◽

Qrt Pcr ◽

Differentially Expressed Mirnas ◽

Pathway Analyses

Abstract Purpose The present study established microRNA (miRNA) expression profiles for rat ovaries displaying polycystic ovary syndrome (PCOS) with insulin resistance and explored the underlying biological functions of differentially expressed miRNAs. Methods A PCOS with insulin resistance rat model was created by administering letrozole and a high-fat diet. Total RNA was extracted from the ovaries of PCOS with insulin resistance rats and normal rats. Three ovaries from each group were used to identify differentially expressed miRNAs by deep sequencing. A hierarchical clustering heatmap and volcano plot were used to display the pattern of differentially expressed miRNAs. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to explore the potential target genes of the differentially expressed miRNAs and identify their putative biological function. Nine of the differentially expressed miRNAs were selected for validation by Real-time Quantitative PCR (qRT-PCR). Results A total of 58 differentially expressed miRNAs were identified in the rat ovaries exhibiting PCOS with insulin resistance compared with control ovaries, including 23 miRNAs that were upregulated and 35 miRNAs that were downregulated. GO and KEGG pathway analyses revealed that the predicted target genes were related to metabolic processes, cellular processes, and metabolic pathways. Furthermore, qRT-PCR confirmed that miR-3585-5p and miR-30-5p were significantly upregulated and miR-146-5p was downregulated in the ovaries of PCOS with insulin resistance rats compared with the controls. Conclusion These results indicate that differentially expressed miRNAs in rat ovaries may be involved in the pathophysiology of insulin resistance in PCOS. Our study may be beneficial in establishing miRNAs as novel diagnostic and therapeutic biomarkers for insulin resistance in PCOS.

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Real-time qRT-PCR analysis of EGF receptor in cumulus-oocyte complexes recovered by laparoscopy in hormonally treated goats

Zygote ◽

10.1017/s0967199410000225 ◽

2010 ◽

Vol 19 (2) ◽

pp. 127-136 ◽

Cited By ~ 9

Author(s):

K.C. Almeida ◽

A.F. Pereira ◽

A.S. Alcântara Neto ◽

S.R.G. Avelar ◽

L.R. Bertolini ◽

...

Keyword(s):

Real Time ◽

Ovarian Stimulation ◽

Egf Receptor ◽

Expression Profiles ◽

Expression Patterns ◽

Cumulus Cells ◽

Pcr Analysis ◽

Qrt Pcr ◽

Egfr Expression ◽

Meiotic Competence

SummaryOvarian stimulation with exogenous follicle stimulating hormone (FSH) has been used to increase the number of viable oocytes for laparoscopic oocyte recovery (LOR) in goats. The aim of this study was to evaluate the effect of two FSH protocols for ovarian stimulation in goats on the expression pattern of epidermal growth factor (EGF) receptor (EGFR) in cumulus–oocyte complexes (COCs) recovered by LOR. After real-time qRT-PCR analysis, expression profiles of morphologically graded COCs were compared prior to and after in vitro maturation (IVM) on a FSH protocol basis. The use of a protocol with higher number of FSH injections at a shorter interval resulted in GI/GII COCs with a higher level of EGFR expression in cumulus cells, but not in the oocyte, which was correlated with an elevated meiotic competence following IVM. Based on the maturation profile and EGFR expression patterns observed between groups, the morphological selection of COCs prior to IVM was not a good predictor of oocyte meiotic competence. Therefore, EGFR may be a good candidate marker for indirect prediction of goat oocyte quality. The IVM process of goat COCs increased the EGFR expression in oocytes and cumulus cells, which seemed to be strongly associated with the resumption of meiosis. In summary, differential EGFR expression in goat cumulus cells was associated with the in vivo prematuration process, and in turn, the upregulation in the entire COC was associated with IVM. Cause-and-effect relationships between such increased expression levels, particularly in the oocyte, and oocyte competence itself still need to be further investigated.

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The Predominant microRNAs in β-cell Clusters for Insulin Regulation and Diabetic Control

Current Drug Targets ◽

10.2174/1389450121666191230145848 ◽

2020 ◽

Vol 21 (7) ◽

pp. 722-734

Author(s):

Adele Soltani ◽

Arefeh Jafarian ◽

Abdolamir Allameh

Keyword(s):

Mirna Expression ◽

Expression Profiles ◽

Expression Patterns ◽

Diabetic Control ◽

In Vitro Proliferation ◽

Cell Functions ◽

Mirna Expression Profiles ◽

Multiple Processes ◽

The Impact

micro (mi)-RNAs are vital regulators of multiple processes including insulin signaling pathways and glucose metabolism. Pancreatic β-cells function is dependent on some miRNAs and their target mRNA, which together form a complex regulative network. Several miRNAs are known to be directly involved in β-cells functions such as insulin expression and secretion. These small RNAs may also play significant roles in the fate of β-cells such as proliferation, differentiation, survival and apoptosis. Among the miRNAs, miR-7, miR-9, miR-375, miR-130 and miR-124 are of particular interest due to being highly expressed in these cells. Under diabetic conditions, although no specific miRNA profile has been noticed, the expression of some miRNAs and their target mRNAs are altered by posttranscriptional mechanisms, exerting diverse signs in the pathobiology of various diabetic complications. The aim of this review article is to discuss miRNAs involved in the process of stem cells differentiation into β-cells, resulting in enhanced β-cell functions with respect to diabetic disorders. This paper will also look into the impact of miRNA expression patterns on in vitro proliferation and differentiation of β-cells. The efficacy of the computational genomics and biochemical analysis to link the changes in miRNA expression profiles of stem cell-derived β-cells to therapeutically relevant outputs will be discussed as well.

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Influence of atrial fibrillation on microRNA expression profiles in left and right atria from patients with valvular heart disease

Physiological Genomics ◽

10.1152/physiolgenomics.00111.2011 ◽

2012 ◽

Vol 44 (3) ◽

pp. 211-219 ◽

Cited By ~ 61

Author(s):

Nicola Cooley ◽

Mark J. Cowley ◽

Ruby C. Y. Lin ◽

Silvana Marasco ◽

Chiew Wong ◽

...

Keyword(s):

Atrial Fibrillation ◽

Heart Disease ◽

Mirna Expression ◽

Valvular Heart Disease ◽

Left Atrial ◽

Expression Profiles ◽

Artery Bypass ◽

Expression Patterns ◽

Right Atrial ◽

Detectable Effect

Chronic atrial fibrillation (AF) is a complication associated with the dilated atria of patients with valvular heart disease and contributes to worsened pathology. We examined microRNA (miRNA) expression profiles in right and left atrial appendage tissue from valvular heart disease (VHD) patients. Right atrial (RA) appendage from patients undergoing coronary artery bypass grafting and left atrial (LA) appendage from healthy hearts, not used for transplant, were used as controls. There was no detectable effect of chronic AF on miRNA expression in LA tissue, but miRNA expression in RA was strongly influenced by AF, with 47 miRNAs (15 higher, 32 lower) showing differential expression between the AF and control sinus rhythm groups. VHD induced different changes in miRNA expression in LA compared with RA. Fifty-three (12 higher, 41 lower) miRNAs were altered by VHD in LA, compared with 5 (4 higher, 1 lower) in RA tissue. miRNA profiles also differed between VHD-LA and VHD-RA (13 higher, 26 lower). We conclude that VHD and AF influence miRNA expression patterns in LA and RA, but these are affected differently by disease progression and by the development of AF. These findings provide new insights into the progression of VHD.

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Identification of Novel Biomarkers Associated With the Prognosis and Potential Pathogenesis of Breast Cancer via Integrated Bioinformatics Analysis

Technology in Cancer Research & Treatment ◽

10.1177/1533033821992081 ◽

2021 ◽

Vol 20 ◽

pp. 153303382199208 ◽

Cited By ~ 1

Author(s):

Meng Wu ◽

Qingdai Li ◽

Hongbing Wang

Keyword(s):

Breast Cancer ◽

Survival Data ◽

Expression Profiles ◽

Cancer Prognosis ◽

Data Sets ◽

Expression Levels ◽

Human Protein Atlas ◽

Novel Biomarkers ◽

Pathway Analyses ◽

Cancer Tissues

Background: Breast cancer is the most commonly diagnosed malignancy and a major cause of cancer-related deaths in women globally. Identification of novel prognostic and pathogenesis biomarkers play a pivotal role in the management of the disease. Methods: Three data sets from the GEO database were used to identify differentially expressed genes (DEGs) in breast cancer. Gene Ontology (GO) enrichment and Kyoto Encyclopaedia of Genes and Genomes pathway analyses were performed to elucidate the functional roles of the DEGs. Besides, we investigated the translational and protein expression levels and survival data of the DEGs in patients with breast cancer from the Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine, Human Protein Atlas, and Kaplan Meier plotter tool databases. The corresponding change in the expression level of microRNAs in the DEGs was also predicted using miRWalk and TargetScan, and the expression profiles were analyzed using OncomiR. Finally, the expression of novel DEGs were validated in Chinese breast cancer tissues by RT-qPCR. Results: A total of 46 DEGs were identified, and GO analysis revealed that these genes were mainly associated with biological processes involved in fatty acid, lipid localization, and regulation of lipid metabolism. Two novel biomarkers, ADH1A and IGSF10, and 4 other genes ( APOD, KIT, RBP4, and SFRP1) that were implicated in the prognosis and pathogenesis of breast cancer, exhibited low expression levels in breast cancer tissues. Besides, 14/25 microRNAs targeting 6 genes were first predicted to be associated with breast cancer prognosis. RT-qPCR results of ADH1A and IGSF10 expression in Chinese breast cancer tissues were consistent with the database analysis and showed significant down-regulation. Conclusion: ADH1A, IGSF10, and the 14 microRNAs were found to be potential novel biomarkers for the diagnosis, treatment, and prognosis of breast cancer.

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Microarray Profiling of TGF-β1-Induced Long Non-Coding RNA Expression Patterns in Human Lung Bronchial Epithelial BEAS-2B Cells

Cellular Physiology and Biochemistry ◽

10.1159/000495052 ◽

2018 ◽

Vol 50 (6) ◽

pp. 2071-2085 ◽

Cited By ~ 4

Author(s):

Wentao Hu ◽

Weiwei Pei ◽

Lin Zhu ◽

Jing Nie ◽

Hailong Pei ◽

...

Keyword(s):

Human Lung ◽

Expression Patterns ◽

Differentially Expressed ◽

Bronchial Epithelial ◽

Qrt Pcr ◽

Microarray Profiling ◽

Underlying Mechanisms ◽

Pathway Analyses ◽

Trans Regulation ◽

Tgf Β1

Background/Aims: TGF-β1 mediated radiation-induced bystander effects (RIBE) have been linked with malignant transformation and tumorigenesis. However, the underlying mechanisms are not fully understood. Methods: To reveal new molecules of regulatory functions in this process, lncRNA microarray was performed to profile both lncRNA and mRNA expression patterns in human lung bronchial epithelial BEAS-2B cells treated with TGF-β1 at a concentration measured in the medium conditioned by directly irradiated BEAS-2B cells. The potential functions of the differentially expressed lncRNAs were predicted by GO and KEGG pathway analyses of their co-expressed mRNAs. Cis- and trans-regulation of the lncRNAs were analyzed and the interaction networks were constructed using Cytoscape. qRT-PCR was conducted to validate the results of microarray profiling. CCK-8 assay was employed for functional validation of 3 identified lncRNAs. Results: 224 lncRNAs were found to be dysregulated, among which 6 lncRNAs were chosen for expression validation by qRT-PCR assay. Pathway analyses showed that differentially expressed lncRNAs are highly correlated with cell proliferation, transformation, migration, etc. Trans-regulation analyses showed that the differentially expressed lncRNAs most likely participate in the pathways regulated by four transcriptional factors, FOS, STAT3, RAD21 and E2F1, which have been identified to be involved in the modulation of oncogenic transformation, cell cycle progression, genomic instability, etc. lnc-THEMIS-2 and lnc-ITGB6-4, predicted to be regulated by STAT3 and E2F1 respectively, were found to rescue the decrease of cell viability induced by TGF-β1 treatment. Conclusion: Our findings suggest that the differentially expressed lncRNAs induced by TGF-β1 play crucial roles in the oncogenic transformation and tumorigenesis, which provide a better understanding of the underlying mechanisms related to tumorigensis induced by LD/LDR radiations.

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Identification of Type II Interferon Receptors in Geese: Gene Structure, Phylogenetic Analysis, and Expression Patterns

BioMed Research International ◽

10.1155/2015/537637 ◽

2015 ◽

Vol 2015 ◽

pp. 1-14

Author(s):

Hao Zhou ◽

Shun Chen ◽

Yulin Qi ◽

Qin Zhou ◽

Mingshu Wang ◽

...

Keyword(s):

Expression Profiles ◽

Expression Patterns ◽

Harderian Gland ◽

Distribution Analysis ◽

Expression Levels ◽

Age Related ◽

Cecal Tonsil ◽

Immune Tissues ◽

First Time

Interferonγreceptor 1 (IFNGR1) and IFNGR2 are two cell membrane molecules belonging to class II cytokines, which play important roles in the IFN-mediated antiviral signaling pathway. Here, goose IFNGR1 and IFNGR2 were cloned and identified for the first time. Tissue distribution analysis revealed that relatively high levels of goose IFNγmRNA transcripts were detected in immune tissues, including the harderian gland, cecal tonsil, cecum, and thymus. Relatively high expression levels of both IFNGR1 and IFNGR2 were detected in the cecal tonsil, which implicated an important role of IFNγin the secondary immune system of geese. No specific correlation between IFNγ, IFNGR1, and IFNGR2 expression levels was observed in the same tissues of healthy geese. IFNγand its cognate receptors showed different expression profiles, although they appeared to maintain a relatively balanced state. Furthermore, the agonist R848 led to the upregulation of goose IFNγbut did not affect the expression of goose IFNGR1 or IFNGR2. In summary, trends in expression of goose IFNγand its cognate receptors showed tissue specificity, as well as an age-related dependency. These findings may help us to better understand the age-related susceptibility to pathogens in birds.

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