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Aberrant LncRNA Expression Profile in a Contusion Spinal Cord Injury Mouse Model

BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 9249401-9249401页

作者： Ding, Ya Song, Zhiwen Liu, Jinbo Soochow Univ Affiliated Hosp 3 Dept Orthoped Changzhou Jiangsu Peoples R China Anhui Med Univ Fuyang Peoples Hosp Dept Orthoped Surg 63 Luci St Fuyang City 236004 Anhui Peoples R China

Long noncoding RNAs (LncRNAs) play a crucial role in cell growth, development, and various diseases related to the central nervous system. However, LncRNA differential expression profiles in spinal cord injury are yet to be reported. In this study, we profiled the expression pattern of LncRNAs using a microarray method in a contusion spinal cord injury (SCI) mouse model. Compared with a spinal cord without injury, few changes in LncRNA expression levels were noted 1 day after injury. The differential changes in LncRNA expression peaked 1 week after SCI and subsequently declined until 3 weeks after injury. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the reliability of the microarray, demonstrating that the results were reliable. Gene ontology (GO) analysis indicated that differentially expressed mRNAs were involved in transport, cell adhesion, ion transport, and metabolic processes, among others. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the neuroactive ligand-receptor interaction, the PI3K-Akt signaling pathway, and focal adhesions were potentially implicated in SCI pathology. We constructed a dynamic LncRNA-mRNA network containing 264 LncRNAs and 949 mRNAs to elucidate the interactions between the LncRNAs and mRNAs. Overall, the results from this study indicate for the first time that LncRNAs are differentially expressed in a contusion SCI mouse model.

关键词： SPINAL cord injuries ANIMAL experimentation BIOLOGICAL models CHI-squared test CLUSTER analysis (Statistics) CORRELATION (Statistics) FISHER exact test MICE POLYMERASE chain reaction PROBABILITY theory FINANCING of research RNA BRUISES microarray technology GENE expression profiling GENETIC aspects

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MicroRNA Expression Signature in Degenerative Aortic Stenosis

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BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 4682172-4682172页

作者： Shi, Jing Liu, Hui Wang, Hui Kong, Xiangqing Nanjing Med Univ Affiliated Hosp 1 Dept Cardiol Nanjing 210029 Jiangsu Peoples R China

Degenerative aortic stenosis, characterized by narrowing of the exit of the left ventricle of the heart, has become the most common valvular heart disease in the elderly. The aim of this study was to investigate the microRNA (miRNA) signature in degenerative AS. Through microarray analysis, we identified the miRNA expression signature in the tissue samples from healthy individuals (n = 4) and patients with degenerative AS (n = 4). Six miRNAs (hsa-miR-193a-3p, hsa-miR-29b-1-5p, hsa-miR-505-5p, hsa-miR-194-5p, hsa-miR-99b-3p, and hsa-miR-200b-3p) were overexpressed and 14 (hsa-miR-3663-3p, hsa-miR-513a-5p, hsa-miR-146b-5p, hsa-miR-1972, hsa-miR-718, hsa-miR-3138, hsa-miR-21-5p, hsa-miR-630, hsa-miR-575, hsa-miR-301a-3p, hsa-miR-636, hsa-miR-34a-3p, hsa-miR-21-3p, and hsa-miR-516a-5p) were downregulated in aortic tissue from AS patients. GeneSpring 13.1 was used to identify potential human miRNA target genes by comparing a 3-way comparison of predictions from TargetScan, PITA, and microRNAorg databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to identify potential pathways and functional annotations associated with AS. Twenty miRNAs were significantly differentially expressed between patients with AS samples and normal controls and identified potential miRNA targets and molecular pathways associated with this morbidity. This study describes the miRNA expression signature in degenerative AS and provides an improved understanding of the molecular pathobiology of this disease.

关键词： RNA physiology RNA analysis AORTA AORTIC stenosis CLUSTER analysis (Statistics) DATABASES RESEARCH methodology MOLECULAR pathology PROBABILITY theory FINANCING of research RNA T-test (Statistics) TISSUE culture BIOINFORMATICS DATA analysis software microarray technology DESCRIPTIVE statistics

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Integrated Analysis of DNA Methylation and mRNA Expression Profiles Data to Identify Key Genes in Lung Adenocarcinoma

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BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 4369431-4369431页

作者： Jin, Xiang Liu, Xingang Li, Xiaodan Guan, Yinghui Jilin Univ Dept Respirat Hosp 1 Changchun 130021 Peoples R China Jilin Univ ICU Dept Hosp 1 Changchun 130021 Peoples R China

Introduction. Lung adenocarcinoma (LAC) is the most frequent type of lung cancer and has a high metastatic rate at an early stage. This study is aimed at identifying LAC-associated genes. Materials and Methods. GSE62950 downloaded from Gene Expression Omnibus included a DNA methylation dataset and an mRNA expression profiles dataset, both of which included 28 LAC tissue samples and 28 adjacent normal tissue samples. The differentially expressed genes (DEGs) were screened by Limma package in R, and their functions were predicted by enrichment analysis using TargetMine online tool. Then, protein-protein interaction (PPI) network was constructed using STRING and Cytoscape. Finally, LAC-associated methylation sites were identified by CpGassoc package in R and mapped to the DEGs to obtain LAC-associated DEGs. Results. Total 913 DEGs were identified in LAC tissues. In the PPI networks, MAD2L1, AURKB, CCNB2, CDC20, and WNT3A had higher degrees, and the first four genes might be involved in LAC through interaction. Total 8856 LAC-associated methylation sites were identified and mapped to the DEGs. And there were 29 LAC-associated methylation sites located in 27 DEGs (e.g., SH3GL2, BAI3, CDH13, JAM2, MT1A, LHX6, and IGFBP3). Conclusions. These key genes might play a role in pathogenesis of LAC.

关键词： ADENOCARCINOMA METASTASIS SURVIVAL analysis (Biometry) TRANSCRIPTION factors BIOINFORMATICS microarray technology DNA methylation GENE expression profiling

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Genetic Comparison of Stemness of Human Umbilical Cord and Dental Pulp

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STEM CELLS INTERNATIONAL 2016年第1期2016卷 3453890-3453890页

作者： Kang, Chung-Min Kim, Hyunok Song, Je Seon Choi, Byung-Jai Kim, Seong-Oh Jung, Han-Sung Moon, Seok-Jun Choi, Hyung-Jun Yonsei Univ Coll Dent Dept Pediat Dent Seoul 120749 South Korea Yonsei Univ Coll Dent Div Histol Dept Oral Biol Seoul 120749 South Korea Yonsei Univ Coll Dent Div Pharmacol Dept Oral Biol Seoul 120749 South Korea

This study focuses on gene expression patterns and functions in human umbilical cord (UC) and dental pulp (DP) containing mesenchymal stem cells (MSCs). DP tissues were collected from 25 permanent premolars. UC tissue samples were obtained from three newborns. Comparative gene profiles were obtained using cDNA microarray analysis and the expression of tooth development-associated and MSC-related genes was assessed by the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Genes related to cell proliferation, angiogenesis, and immune responses were expressed at higher levels in UC, whereas genes related to growth factor and receptor activity and signal transduction were more highly expressed in DP. Although UC and DP tissues exhibited similar expression of surface markers for MSCs, UC showed higher expression of CD29, CD34, CD44, CD73, CD105, CD146, and CD166. qRT-PCR analysis showed that CD146, CD166, and MYC were expressed 18.3, 8.24, and 1.63 times more highly in UC, whereas the expression of CD34 was 2.15 times higher in DP. Immunohistochemical staining revealed significant differences in the expression of genes (DSPP, DMP1, and CALB1) related to odontogenesis and angiogenesis in DP. DP and UC tissue showed similar gene expression, with the usual MSC markers, while they clearly diverged in their differentiation capacity.

关键词： DENTAL pulp UMBILICAL cord PHYSIOLOGY GENE expression MESENCHYMAL stem cells NEWBORN infants -- Physiology microarray technology ANTISENSE DNA

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Expression of Migration-Related Genes in Human Colorectal Cancer and Activity of a Disintegrin and Metalloproteinase 17

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BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 8208904-8208904页

作者： Walkiewicz, Katarzyna Koziel, Pawel Bednarczyk, Martyna Blazelonis, Adam Mazurek, Urszula Muc-Wierzgon, Malgorzata Med Univ Silesia Fac Publ Hlth Bytom Dept Internal Med PL-40055 Katowice Poland Med Univ Silesia Fac Pharm Sosnowiec Dept Mol Biol PL-40055 Katowice Poland

Introduction. The ability to form metastases which depends on the mechanisms of cell migration is an important element of the progression of cancer. In the present study we analyzed the genes involved in the regulation of migration in colon cancer cells. Materials and Methods. A total of 20 pairs of surgically removed tumoral and healthy (marginal) tissues samples from colorectal cancer patients at clinical stages I-II and III-IV were analyzed. The isolation of RNA from CRC and normal tissues and its subsequent molecular analysis were performed according to manufacturer's instructions. microarray data analysis was performed using the GeneSpring 11.5 platform and Significance Analysis of microarrays (SAM). In SAM analysis to identify significantly differentially expressed genes score and q-value parameters were used. Results. The largest increase in expression of genes was shown by MMP9, ADAM17, EphA2, and TIMP. Conclusions. Presented genes, especially ADAM17, MMP9, EphA2, TIMP1, ICAM 11, and CD4, may be used as prognostic markers of advanced stages of colorectal cancer, contributing to the development of new lines of therapy focused on reducing metastasis of the primary tumor.

关键词： METASTASIS PROGNOSIS COLON tumors RNA analysis ANALYSIS of variance BIOCHEMICAL markers CELL motility GENE expression RESEARCH methodology PEPTIDES PROBABILITY theory PROTEOLYTIC enzymes STATISTICS TISSUE culture TUMOR necrosis factor DATA analysis DATA analysis software microarray technology DESCRIPTIVE statistics MATRIX metalloproteinases GENETIC aspects RECTUM tumors RECTUM tumors -- Treatment TREATMENT RECTUM tumors -- Genetic aspects

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TBL1XR1 Is Highly Expressed in Gastric Cancer and Predicts Poor Prognosis

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DISEASE MARKERS 2016年第1期2016卷 1-7页

作者： Liu, Fang He, Yuan Cao, Qinghua Liu, Ni Zhang, Wenhui Southern Med Univ Nanfang Hosp Dept Oncol Guangzhou 510515 Guangdong Peoples R China Sun Yat Sen Univ Ctr Canc State Key Lab Oncol South China Collaborat Innovat Ctr Canc Med Guangzhou 510060 Guangdong Peoples R China Sun Yat Sen Univ Ctr Canc Dept Mol Diagnost Guangzhou 510060 Guangdong Peoples R China Sun Yat Sen Univ Affiliated Hosp 1 Dept Pathol Guangzhou 510080 Guangdong Peoples R China

Objective. To investigate the expression of transducin- (beta-) like 1 X-linked receptor 1 (TBL1XR1) in human gastric cancer (GC) and its correlation with prognostic and biologic significance. Methods. TBL1XR1 mRNA expression was analyzed in gastric cancer using a microarray dataset (GSE2701) from the Gene Expression Omnibus (GEO). Immunohistochemistry (IHC) analysis of TBL1XR1 was performed on GC tissue microarray (TMA) to assess its prognostic and biological significance in 334 patients of GC. Results. Analysis of GSE2701 showed that the mRNA levels of TBL1XR1 were significantly elevated in primary gastric tumor and lymph node tissues than normal gastric tissues (P < 0.05). The same results of TBL1XR1 protein level were observed by IHC staining in 334 GC tissues. 204 of 334 (60.1%) primary gastric cancer tissues showed high expression of TBL1XR1 protein. TBL1XR1 overexpression was significantly correlated with lymph node metastasis (P = 0.000) and advanced TNM stage (P = 0.001). Moreover, high levels of TBL1XR1 predicted worse overall survival (P = 0.015). Multivariate Cox regression analysis indicated that high expression of TBL1XR1 was an independent prognostic factor for poor overall survival (HR, 0.525;95% confidence interval, 0.367-0.752;P = 0.005). Conclusion. This present study demonstrates that TBL1XR1 is overexpressed in gastric cancer and may be a potential predictor and therapeutic target for GC patients.

关键词： GENE expression TRANSDUCIN STOMACH cancer -- Treatment MESSENGER RNA IMMUNOHISTOCHEMISTRY microarray technology REGRESSION analysis CANCER genetics

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Transcriptome Analysis of Long Noncoding RNAs in Toll-Like Receptor 3-Activated Mesenchymal Stem Cells

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STEM CELLS INTERNATIONAL 2016年第1期2016卷 6205485-6205485页

作者： Wang, Shihua Li, Xiaoxia Zhao, Robert Chunhua Chinese Acad Med Sci Ctr Excellence Tissue Engn Inst Basic Med Sci Beijing 100005 Peoples R China Chinese Acad Med Sci Peking Union Med Coll Hosp Sch Basic Med Peking Union Med Coll Beijing 100005 Peoples R China

Mesenchymal stem cells (MSCs) possess great immunomodulatory capacity which lays the foundation for their therapeutic effects in a variety of diseases. Recently, toll-like receptors (TLR) have been shown to modulate MSC functions;however, the underlying molecular mechanisms are poorly understood. Emerging evidence suggests that long noncoding RNAs (lncRNAs) are an important class of regulators involved in a wide range of biological processes. To explore the potential involvement of lncRNAs in TLR stimulated MSCs, we performed a comprehensive lncRNA and mRNA profiling through microarray. 10.2% of lncRNAs (1733 out of 16967) and 15.1% of mRNA transcripts (1760 out of 11632) were significantly differentially expressed (absolute fold-change >= 5, P value <= 0.05) in TLR3 stimulated MSCs. Furthermore, we characterized the differentially expressed lncRNAs through their classes and length distribution and correlated them with differentially expressed mRNA. Here, we are the first to determine genome-wide lncRNAs expression patterns in TLR3 stimulated MSCs by microarray and this work could provide a comprehensive framework of the transcriptome landscapes of TLR3 stimulated MSCs.

关键词： TOLL-like receptors STEM cell treatment NON-coding RNA MESENCHYMAL stem cells GENETIC transcription IMMUNE response -- Regulation microarray technology

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A Novel Homozygous p.L539F Mutation Identified in PINK1 Gene in a Moroccan Patient with Parkinsonism

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BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 3460234-3460234页

作者： Ben El Haj, Rafiqua Regragui, Wafaa Tazi-Ahnini, Rachid Skalli, Asmae Bouslam, Naima Benomar, Ali Yahyaoui, Mohamed Bouhouche, Ahmed Mohammed V Univ Med Sch & Pharm Res Team Neurodegenerat Dis Rabat 10100 Morocco CHU Ibn Sina Specialties Hosp Dept Neurol & Neurogenet Rabat 10100 Morocco Mohammed V Univ Med Sch & Pharm Biotechnol Lab Rabat 10100 Morocco

Parkinson's disease (PD) is the secondmost common neurodegenerative disorder after Alzheimer's disease. Ten of fifteen causative genes linked to familial forms of PD have been reported to cause autosomal recessive forms. Among them, mutations in the PTEN-induced kinase 1 (PINK1) gene were shown to be responsible for a phenotype characterized by early onset, good response to levodopa, and a benign course. Using chromosomal microarray analysis and Sanger sequencing, we identified a homozygous G/C substitution in a 58-year-oldMoroccan man diagnosed with recessive inherited Parkinson's disease. This G-to-C transition occurred at position 1617 leading to an amino acid change L/F at position 539 located in highly conserved motif in the C terminal sequence of PINK1. Interestingly, the c.1617G>C substitution is absent in 192 ethnically matched control chromosomes. Our findings have shown that the p.L539F is a novel mutation located in the C terminal sequence of the PINK1 protein that could be pathogenic and responsible for a clinical phenotype resembling idiopathic Parkinson's disease with rapid progression and early cognitive impairment.

关键词： CHROMOSOME analysis DRUG therapy for Parkinson's disease PARKINSON'S disease diagnosis PARKINSON'S disease & genetics ANALYSIS of DNA DOPA AMANTADINE HETEROCYCLIC compounds HYPOKINESIA MUTATION (Biology) FINANCING of research TREMOR BIOINFORMATICS DATA analysis software microarray technology SEQUENCE analysis

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Poly-L-lysine Prevents Senescence and Augments Growth in Culturing Mesenchymal Stem Cells Ex Vivo

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BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 8196078-8196078页

作者： Heo, June Seok Kim, Hyun Ok Song, Seung Yong Lew, Dae Hyun Choi, Youjeong Kim, Sinyoung Severance Hosp Cell Therapy Ctr Seoul 03722 South Korea Yonsei Univ Coll Med Dept Lab Med Seoul 03722 South Korea Yonsei Univ Coll Med Dept Plast & Reconstruct Surg Seoul 03722 South Korea

Mesenchymal stem cells (MSCs) possess great therapeutic potential. Efficient in vitro expansion of MSCs is however necessary for their clinical application. The extracellular matrix (ECM) provides structural and biochemical support to the surrounding cells, and it has been used as a coating substrate for cell culture. In this study, we have aimed to improve the functionality and stemness of MSCs during culture using poly-L-lysine (PLL). Functionality of MSCs was analysed by cell cycle analysis, differentiation assay, beta-galactosidase staining, and RT-PCR. Furthermore, we assessed the global gene expression profile of MSCs on uncoated and PLL-coated plates. MSCs on PLL-coated plates exhibited a faster growth rate with increased S-phase and upregulated expression of the stemness markers. In addition, their osteogenic differentiation potential was increased, and genes involved in cell adhesion, FGF-2 signalling, cell cycle, stemness, cell differentiation, and cell proliferation were upregulated, compared to that of the MSCs cultured on uncoated plates. We also confirmed that MSCs on uncoated plates expressed higher beta-galactosidase than the MSCs on PLL-coated plates. We demonstrate that PLL provides favourable microenvironment for MSC culture by reversing the replicative senescence. This method will significantly contribute to effective preparation of MSCs for cellular therapy.

关键词： BIOLOGICAL assay CELL culture CELL cycle CELL differentiation CELL physiology CELLULAR aging CELLULAR signal transduction DYNAMICS FLOW cytometry GENE expression GLYCOSIDASES GROWTH factors LYSINE POLYMERASE chain reaction PROBABILITY theory FINANCING of research STAINS & staining (Microscopy) STEM cells T-test (Statistics) REVERSE transcriptase polymerase chain reaction DATA analysis software microarray technology DESCRIPTIVE statistics

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Systematic Identification and Bioinformatic Analysis of MicroRNAs in Response to Infections of Coxsackievirus A16 and Enterovirus 71

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BIOMED RESEARCH INTERNATIONAL 2016年第0期2016卷 4302470-4302470页

作者： Zhu, Zheng Qi, Yuhua Fan, Huan Cui, Lunbiao Shi, Zhiyang Jiangsu Prov Ctr Dis Prevent & Control Minist Hlth Key Lab Enter Pathogen Microbiol 172 Jiangsu Rd Nanjing 210009 Jiangsu Peoples R China

Hand, foot, and mouth disease (HFMD), mainly caused by coxsackievirus A16 (CVA16) and enterovirus 71 (EV71) infections, remains a serious public health issue with thousands of newly diagnostic cases each year since 2008 in China. The mechanisms underlying viral infection, however, are elusive to date. In the present study, we systematically investigated the host cellular microRNA (miRNA) expression patterns in response to CVA16 and EV71 infections. Through microarray examination, 27 miRNAs (15 upregulated and 12 downregulated) were found to be coassociated with the replication process of two viruses, while the expression levels of 15 and 5 miRNAs were significantly changed in CVA16- and EV71-infected cells, respectively. A great number of target genes of 27 common differentially expressed miRNAs were predicted by combined use of two computational target prediction algorithms, TargetScan and MiRanda. Comprehensive bioinformatic analysis of target genes in GO categories and KEGG pathways indicated the involvement of diverse biological functions and signaling pathways during viral infection. These results provide an overview of the roles of miRNAs in virus-host interaction, which will contribute to further understanding of HFMD pathological mechanisms.

关键词： RNA analysis ALGORITHMS BIOLOGICAL assay CELL culture CELLULAR signal transduction COXSACKIEVIRUS diseases ELECTROPHORESIS ENTEROVIRUS diseases GENES POLYMERASE chain reaction PROBABILITY theory FINANCING of research BIOINFORMATICS REVERSE transcriptase polymerase chain reaction HAND, foot & mouth disease microarray technology DESCRIPTIVE statistics

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