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The Regulatory Role of miR-107-Cdk6-Rb Pathway in Airway Smooth Muscle Cells in Asthma

JOURNAL OF ASTHMA AND ALLERGY 2023年 16卷 433-445页

作者： Xiong, Yi Luo, Yani Ting, Yuwen Li, Jiana Chen, Rongchang Shi, Fei Shenzhen Peoples Hosp Emergency Dept Shenzhen Guangdong Provi Peoples R China Shenzhen Peking Univ Hong Kong Univ Sci & Technol Biomed Res Inst Med Ctr Shenzhen Guangdong Provi Peoples R China Shenzhen Peoples Hosp Inst Shenzhen Resp Dis Key Lab Shenzhen Resp Dis Shenzhen Guangdong Provi Peoples R China

Purpose: Airway remodeling is a significant pathological change of asthma. This study aimed to detect differentially expressed micrornas in the serum of asthma patients and airway smooth muscle cells (ASMCs) of asthmatic mice, exploring their role in the airway remodeling of ***: The differentially expressed micrornas in the serum of mild and moderate-severe asthma patients compared to healthy subjects were revealed using the "limma" package. Gene Ontology (GO) analysis was used to annotate the functions of microrna target genes. The relative expressions of miR-107 (miR-107-3p in mice sharing the same sequence) in the primary airway smooth muscle cells (ASMCs) of the asthma mice model were tested by RT-qPCR. Cyclin-dependent kinases 6 (Cdk6), a target gene of miR-107, was predicted by algorithms and validated by dual-luciferase reporter assay and Western blot. The roles of miR-107, Cdk6, and protein Retinoblastoma (Rb) in ASMCs were examined by transwell assay and EDU KIT in ***: The expression of miR-107 was down-regulated in both mild and moderate-severe asthma patients. Intriguingly, the level of miR-107 was also decreased in ASMCs of the asthma mice model. Up-regulating miR-107 suppressed ASMCs' proliferation by targeting Cdk6 and the phosphorylation level of Rb. Increasing the expression of Cdk6 or suppressing Rb activity abrogated the proliferation inhibition effect of ASMCs induced by miR-107. In addition, miR-107 also inhibits ASMC migration by targeting ***: The expression of miR-107 is down-regulated in serums of asthma patients and ASMCs of asthmatic mice. It plays a critical role in the and of ASMCs via Cdk6.

关键词： asthma microrna microarray airway smooth muscle cells miR-107 Cdk6

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microarray-based measurement of microrna-449c-5p levels in hepatocellular carcinoma and bioinformatic analysis of potential signaling pathways

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PATHOLOGY RESEARCH AND PRACTICE 2019年第1期215卷 68-81页

作者： Jiang, Li Wu, Chang-Liang Wu, Ji-Zhou Yang, Xia Wang, Han-lin Li, Guo-Jian Guangxi Med Univ Affiliated Hosp 1 Dept Infect Dis 6 Shuangyong Rd Nanning 530021 Guangxi Zhuang Peoples R China Guangxi Med Univ Affiliated Hosp 2 Dept Gastroenterol Nanning Guangxi Zhuang Peoples R China Guangxi Med Univ Affiliated Hosp 1 Dept Pathol Nanning Guangxi Zhuang Peoples R China

The clinical role and potential molecular mechanisms of microrna-449c-5p (miR-449c-5p) in hepatocellular carcinoma (HCC) tissues remains unclear. Combining multiple bioinformatic tools, we studied the miR-449c-5p expression levels in HCC tissues and explored possible target genes and related signaling pathways. First, miR-449c-5p expression data from microarrays provided by publicly available sources were mined and analyzed using various meta-analysis methods. Next, genes that were downregulated after miR-449c-5p mimic transfection into HCC cells were identified, and in silico methods were used to predict potential target genes. Several bioinformatic assessments were also performed to evaluate the possible signaling pathways of miR-449c-5p in HCC. Five microarrays were included in the current study, including GSE98269, GSE64632, GSE74618, GSE40744 and GSE57555. The standard mean difference was 0.44 (0.07-0.80), and the area under the curve was 0.68 (0.63-0.72), as assessed by meta-analyses, which consistently indicated the upregulation of miR-449c-5p in HCC tissues. A total of 2244 genes were downregulated after miR-449c-5p mimic transfection into an HCC cell line, while 5217 target genes were predicted by in silico methods. The overlap of these two gene pools led to a final group of 428 potential target genes of miR-449c-5p. These 428 potential target genes were primarily enriched in the homologous recombination pathway, which includes DNA Polymerase Delta 3 (POLD3). Data mining with Oncomine and the Human Protein Atlas showed a decreasing trend in POLD3 mRNA and protein levels in HCC tissue samples. This evidence suggests that miR-449c-5p could play an essential role in HCC through various pathways and that POLD3 could be a potential miR-449c-5p target. However, these in silico findings should be validated with further experiments.

关键词： microrna microarray miR-449c-5p Hepatocellular carcinoma Pathways Bioinformatics

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Downregulation of hsa-microrna-204-5p and identification of its potential regulatory network in non-small cell lung cancer: RT-qPCR, bioinformatic- and meta-analyses

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RESPIRATORY RESEARCH 2020年第1期21卷 60-60页

作者： Liang, Chang-Yu Li, Zu-Yun Gan, Ting-Qing Fang, Ye-Ying Gan, Bin-Liang Chen, Wen-Jie Dang, Yi-Wu Shi, Ke Feng, Zhen-Bo Chen, Gang Guangxi Med Univ Dept Pathol Affiliated Hosp 1 Nanning 530021 Guangxi Zhuang Peoples R China Guangxi Med Univ Dept Med Oncol Affiliated Hosp 2 Nanning 530007 Guangxi Zhuang Peoples R China Guangxi Med Univ Affiliated Hosp 1 Dept Radiotherapy Nanning 530021 Guangxi Zhuang Peoples R China

Background Pulmonary malignant neoplasms have a high worldwide morbidity and mortality, so the study of these malignancies using micrornas (miRNAs) has attracted great interest and enthusiasm. The aim of this study was to determine the clinical effect of hsa-microrna-204-5p (miR-204-5p) and its underlying molecular mechanisms in non-small cell lung cancer (NSCLC). Methods Expression of miR-204-5p was investigated by real-time quantitative PCR (RT-qPCR). After data mining from public online repositories, several integrative assessment methods, including receiver operating characteristic (ROC) curves, hazard ratios (HR) with 95% confidence intervals (95% CI), and comprehensive meta-analyses, were conducted to explore the expression and clinical utility of miR-204-5p. The potential objects regulated and controlled by miR-204-5p in the course of NSCLC were identified by estimated target prediction and analysis. The regulatory network of miR-204-5p, with its target genes and transcription factors (TFs), was structured from database evidence and literature references. Results The expression of miR-204-5p was downregulated in NSCLC, and the downtrend was related to gender, histological type, vascular invasion, tumor size, clinicopathologic grade and lymph node metastasis (P<0.05). MiR-204-5p was useful in prognosis, but was deemed unsuitable at present as an auxiliary diagnostic or prognostic risk factor for NSCLC due to the lack of statistical significance in meta-analyses and absence of large-scale investigations. Gene enrichment and annotation analyses identified miR-204-5p candidate targets that took part in various genetic activities and biological functions. The predicted TFs, like MAX, MYC, and RUNX1, interfered in regulatory networks involving miR-204-5p and its predicted hub genes, though a modulatory loop or axis of the miRNA-TF-gene that was out of range with shortage in database prediction, experimental proof and literature confirmation. Conclusions The frequen

关键词： miRNA-204-5p NSCLC Real time -qPCR microrna microarray microrna-sequencing Molecular mechanisms

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Performance evaluation of transcriptomics data normalization for survival risk prediction

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BRIEFINGS IN BIOINFORMATICS 2021年第6期22卷 bbab257-bbab257页

作者： Ni, Ai Qin, Li-Xuan Ohio State Univ Columbus OH 43210 USA Mem Sloan Kettering Canc Ctr Biostat New York NY USA

One pivotal feature of transcriptomics data is the unwanted variations caused by disparate experimental handling, known as handling effects. Various data normalization methods were developed to alleviate the adverse impact of handling effects in the setting of differential expression analysis. However, little research has been done to evaluate their performance in the setting of survival outcome prediction, an important analysis goal for transcriptomics data in biomedical research. Leveraging a unique pair of datasets for the same set of tumor samples-one with handling effects and the other without, we developed a benchmarking tool for conducting such an evaluation in microrna microarrays. We applied this tool to evaluate the performance of three popular normalization methods-quantile normalization, median normalization and variance stabilizing normalization-in survival prediction using various approaches for model building and designs for sample assignment. We showed that handling effects can have a strong impact on survival prediction and that quantile normalization, a most popular method in current practice, tends to underperform median normalization and variance stabilizing normalization. We demonstrated with a small example the reason for quantile normalization's poor performance in this setting. Our finding highlights the importance of putting normalization evaluation in the context of the downstream analysis setting and the potential of improving the development of survival predictors by applying median normalization. We make available our benchmarking tool for performing such evaluation on additional normalization methods in connection with prediction modeling approaches.

关键词： penalized Cox regression survival prediction data normalization handling effects microrna microarray transcriptomics data

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microrna Profiling of Transgenic Mice with Myocardial Overexpression of Nucleolin

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Chinese Medical Journal 2018年第3期131卷 339-346页

作者： Qing-Lan Lyu Bi-Mei Jiang Bin Zhou Li Sun Zhong-Yi Tong Yuan-Bin Li Yu-Ting Tang Hui Sun Mei-Dong Liu Xian-Zhong Xiao Department of Pathophysiology Xiangya School of Basic Medical Sciences Central South University Changsha Hunan 410078 China Department of Rheumatology Xiangya Hospital Central South University Changsha Hunan 410008 China Department of Pathology The Second Xiangya Hospital Central South University Changsha Hunan 410000 China

Background：Nucleolin （NCL） is the most abundant RNA-binding protein in the cell nucleolus and plays an important role in chromatin stability,ribosome assembly,ribosomal RNA maturation,ribosomal DNA transcription,nucleocytoplasmic transport,and regulation of RNA stability and translation *** addition to its anti-apoptotic properties,the underlying mechanisms associated with NCL-related roles in different cellular processes remain *** this study,the effect of NCL on microrna （miRNA） expression was evaluated by generating transgenic mice with myocardial overexpression of NCL and by analyzing microarrays of mature and precursor miRNAs from ***：Using microinjection ofalpha-MyHc clone 26-NCL plasmids,we generated transgenic mice with myocardial overexpression of NCL firstly,and then mature and precursor miRNAs expression profiles were analyzed in NCL transgenic mice （n =3） and wild-type （WT） mice （n =3） by miRNA *** Package for the Social Sciences version 16.0 software （SPSS,Inc.,Chicago,IL,USA） was used to perform Student＇s t-test,and statistical significance was determined at P 〈 ***：Several miRNAs were found to be differentially expressed,of which 11 were upregulated and 4 were downregulated in transgenic mice with myocardial overexpression of NCL compared to those in WT *** differentially expressed miRNAs were subsequently confirmed and quantified by real-time quantitative reverse transcription-polymerase chain *** analysis was used for the prediction of miRNA ***,in vitro experiments showed that NCL regulated miR-21 expression following hydrogen peroxide ***：Myocardial-protection mechanisms exerted by NCL might be mediated by the miRNAs identified in this study.

关键词： microrna microarray Myocardium Nucleolin Transgenic mice

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Differentially Expressed micrornas as Potential Markers for Vital Reaction of Burned Skin

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Journal of Forensic Science and Medicine 2018年第3期4卷 135-141,I0016-I0023页

作者： Hao‑Pin Lyu Ming Cheng Jin‑Cen Liu Ming‑Yuan Ye Di Xu Jie‑Tao He Xiao‑Li Xie Qi Wang Department of Forensic Pathology School of Forensic MedicineSouthern Medical UniversityForensic Science Centre of Guangdong Provincial Public Security DepartmentSchool of Public Health and Tropical MedicineSouthern Medical UniversityGuangzhouChina Department of Toxicology School of Public Health and Tropical MedicineSouthern Medical UniversityGuangzhouChina

The identification of antemortem burns and postmortem burns is essential in forensic *** this study,microrna(miRNA)microarray analysis was conducted to identify differentially expressed miRNAs in the skin of an experimental burn *** analysis revealed 24 differentially expressed miRNAs in antemortem burned mice skin,with 19 miRNAs significantly upregulated and 5 *** on the intersection predicted using three databases(Targetscan,***,and PITA),293 potential miRNA targets were *** dysregulated miRNAs and their predicted targets were further analyzed using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes *** functional categories and signaling pathways were enriched,including the“fc epsilon ri signaling pathway,”“endometrial cancer,”and“mTOR signaling pathway.”Expression patterns of 10 differentially expressed miRNAs were verified by reverse transcription‑quantitative polymerase chain reaction in mice *** results agreed with the results of microarray *** findings suggest that differentially expressed miRNAs revealed by microarray are potential markers for forensic molecular diagnosis of antemortem burns.

关键词： Forensic pathology microrna microarray skin burns vital reactio

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hsa-mir-183 is frequently methylated and related to poor survival in human hepatocellular carcinoma

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World Journal of Gastroenterology 2017年第9期23卷 1568-1575页

作者： Sumadi Lukman Anwar Till Krech Britta Hasemeier Elisa Schipper Nora Schweitzer Arndt Vogel Hans Kreipe Reena Buurman Britta Skawran Ulrich Lehmann Ulrich Lehmann Institute of PathologyMedizinische Hochschule Hannover Department of Surgery Faculty of Medicine Universitas Gadjah Mada Department of Gastroenterology Hepatology and EndocrinologyMedizinische Hochschule Hannover Institute of Human Genetics Medizinische Hochschule Hannover

To screen clinically relevant micrornas (miRNAs) silenced by DNA methylation in human hepatocellular carcinoma (HCC).METHODSKnockdown of DNA methyltransferases (DNMTs) using siRNAs and miRNA profiling in HCC cell lines were performed to identify DNA hypermethylation-mediated miRNA downregulation. Confirmation using individual quantitative real-time PCR (qRT-PCR) assays was then performed followed by DNA methylation quantification at the promoter of the miRNA genes. Quantification of DNA methylation and miRNA expression was then performed in primary HCC tumor samples and related with clinicopathological *** profiling after DNMT knockdown in HCC cell lines revealed upregulation of miR-23, miR-25 and miR-183. After qRT-PCR confirmation and CpG island methylation quantification of these miRNAs in cell lines, further analysis in primary HCC specimens showed that hsa-miR-183 is hypermethylated in 30% of HCC (n = 40). Expression of mature miR-183 showed an inverse correlation with DNA methylation levels. In HCC cells, DNMT knockdown and 5-aza-2’-deoxycytidine treatment reduced methylation and stimulated expression of miR-183. In HCC patients, hypermethylation at hsa-miR-183 promoter significantly correlates with poor survival (log-rank test P = 0.03). DNA methylation analysis in healthy liver, benign liver tumors (hepatocellular adenoma and focal nodular hyperplasia) and their corresponding adjacent tissues showed absence of hypermethylation supporting the notion that aberrant methylation at hsa-miR-183 is specific for the malignant transformation of *** data indicate that hypermethylation of hsa-miR-183 is a frequent event in HCC and potentially useful as a novel surrogate diagnostic and prognostic marker.

关键词： hsa-miR-183 DNA methylation DNMT knockdown microrna microarray

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Endometrial microrna Signature during the Window of Implantation Changed in Patients with Repeated Implantation Failure

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Chinese Medical Journal 2017年第5期130卷 566-573页

作者： Cheng Shi Huan Shen Li-Juan Fan Jing Guan Xin-Bang Zheng Xi Chen Rong Liang Xiao-Wei Zhang Qing-Hua Cui Kun-Kun Sun Zhu-Ran Zhao Hong-Jing Han Reproductive Medical Center Peking University People's Hospital Beijing 100044 China Department of Urology Peking University People's Hospital Beijing 100044 China Department of Biomedical Informatics School of Basic Medical Sciences Peking University Beijing 100191 China Department of Pathology Peking University People's Hospital Beijing 100044 China Department of Paediatrics Peking University People's Hospital Beijing 100044 China

Background： At present, a diagnostic tool with high specificity for impaired endometrial receptivity, which may lead to implantation failure, remains to be developed. We aimed to assess the different endometrial microrna （miRNA） signatures for impaired endometrial receptivity by microarray analysis. Methods： A total of 12 repeated implantation failure （RIF） patients and I0 infertile patients, who conceived and delivered after one embryo transfer attempt, were recruited as RIF and control groups, respectively. Endometrial specimens from the window of implantation （WOI） were collected from these two groups. MiRNA microarray was conducted on seven and five samples from the RIF and control groups, respectively. Comparative, functional, and network analyses were performed for the microarray results. Quantitative real-time polymerase chain reaction （PCR） was performed on other samples to validate the expression of specific miRNAs. Results： Compared with those in the control group, the expression levels of 105 miRNAs in the RIF group were found to be significantly up- or down-regulated （at least 2-fold） by microarray analysis. The most relevant miRNA functional sets of these dysregulated miRNAs were miR-30 family, human embryonic stern cell regulation, epithelial-mesenchymal transition, and miRNA tumor suppressors by tool for annotations ofmicrorna analysis. Network regulatory analysis found 176 miRNA-mRNA interactions, and the top 3 core miRNAs were has-miR-4668-5p, has-miR-429, and has-miR-5088. Expression levels of the 18 selected miRNAs in new samples by real-time PCR were found to be regulated with the same trend, as the result ofmicroarray analysis. Conclusions： There is a significant different expression of certain miRNAs in the WOI endometrium for RIF patients. These miRNAs may contribute to impaired endometrial receptivity.

关键词： Embryo Implantation Endometrial Receptivity microrna microarray Repeated Implantation Failure Window of Implantation

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microrna expression profile of bone marrow mesenchymal stem cell-derived neural progenitor by microarray under the influence of EGF, bFGF and IGF-1

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GENOMICS DATA 2015年 5卷 201-205页

作者： Huat, Tee Jong Khan, Amir Ali Abdullah, Jafri Malin Idris, Fauziah Mohamad Jaafar, Hasnan Univ Sains Malaysia Sch Med Sci Dept Pathol Jalan Raja Perempuan Zainab II Kota Baharu 16150 Kelantan Malaysia Univ Sains Malaysia Sch Med Sci Dept Neurosci Kota Baharu 16150 Kelantan Malaysia Univ Sharjah Coll Sci Dept Appl Biol Emirates Sharjah U Arab Emirates Univ Sharjah Sharjah Inst Med Res Emirates Sharjah U Arab Emirates Univ Sains Malaysia Ctr Neurosci Serv & Res Kota Baharu 16150 Kelantan Malaysia Hosp Univ Sains Malaysia Jabatan Neurosains Kota Baharu 16150 Kelantan Malaysia Univ Sains Malaysia Sch Med Sci Dept Med Microbiol Kota Baharu 16150 Kelantan Malaysia

Recently there has been growing interest in the differentiation of mesenchymal stem cells (MSCs) into neural lineages. Research suggests that MSCs can be differentiated into neural progenitor-like cells (NPCs) under the specific influence of paracrine factors particularly epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF). Our recent research has found that the addition of insulin-like growth factor 1 (IGF-1) with the combination of the EGF and bFGF could significantly improve the growth and survivability of MSC-derived NPCs. To unravel the molecular mechanism of the improved differentiation we compared the microrna expression profiles of the differentiation under various combinations of growth factors. MSCs were differentiated into neural lineage in 3 groups;Group A (EGF + bFGF), Group B (EGF + bFGF + IGF-1), and Group C (without growth factor). Regulated micrornas during the early differentiation were identified by detailed microrna profiling using Affymetrix GeneChip version 2.0 at three time intervals (day 1, day 3 and day 5). The data were deposited in the Gene Expression Omnibus, series GSE60060. (C) 2015 The Authors. Published by Elsevier Inc.

关键词： microrna microarray Mesenchymal stem cell Neural differentiation IGF-1 microrna expression

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Screening and bioinformatics analysis of the specific micrornas involved in the protective effects of morphine preconditioning on cardiomyocytes in rats with heart failure

Screening and bioinformatics analysis of the specific microR...

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中国医师协会麻醉学医师分会2016年年会

作者：朱海娟安徽省妇幼保健院安徽医科大学第二附属医院

Background Heart failure is the serious phase of a variety of cardiovascular *** ischemia-reperfusion injury is more sensitive to these patients.

关键词： heart failure morphine preconditioning hypoxia-reoxygenation injury cardioprotection microrna microarray bioinformatic analysis

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