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1.
Article in Chinese | WPRIM | ID: wpr-880825

ABSTRACT

OBJECTIVE@#To study the changes in mRNA and long non-coding RNA (lncRNA) expression profiles in a mouse model of bleomycin-induced lung fibrosis and identify lung fibrosis-related mRNA for coding-noncoding coexpression (CNC) bioinformatics analysis of the differential lncRNAs.@*METHODS@#Lung fibrosis was induced by intratracheal injection of bleomycin in 10 C57BL/6 mice and another 10 mice with intratracheal injection of saline served as the control group. Lung tissues were harvested from the mice at 14 days after the injections and lung fibrosis was assessed using Masson and HE staining. LncRNA chip technology was used to screen the differentially expressed mRNAs and lncRNAs in mice with lung fibrosis, and GO and KEGG pathway analyses of the differential mRNAs were performed using NCBI database and UCSC database to identify possible fibrosis-related mRNAs, which were validated by qRT-PCR to construct a coding and non-coding co- expression network with the differential lncRNAs.@*RESULTS@#Compared with the control mice, the mice with intratracheal injection of bleomycin showed obvious lung fibrosis. The results of gene chip analysis showed that 127 mRNAs were upregulated and 184 mRNAs were down-regulated in the model group as compared with the control group. GO and pathway analysis suggested that the differentially expressed genes participated mainly in immune response, cell differentiation, and cytoskeletons; the involved signal pathways were associated mainly with cytokine and cytokine receptor interaction and chemokine signal transduction. Bioinformatics analysis identified a significant coexpression network between the fibrosisrelated mRNA and the differentially expressed lncRNA.@*CONCLUSIONS@#In mice with lung fibrosis, the differential expressions of fibrosis-related mRNAs in the lung tissues are closely correlated with the co- expressions of a large number of differential lncRNAs, which points to a new direction for investigation of the pathogenesis of pulmonary fibrosis.


Subject(s)
Animals , Bleomycin/toxicity , Gene Expression Profiling , Gene Regulatory Networks , Mice , Mice, Inbred C57BL , Pulmonary Fibrosis/genetics , RNA, Long Noncoding/genetics , RNA, Messenger/genetics
2.
Article in English | WPRIM | ID: wpr-880615

ABSTRACT

OBJECTIVES@#To study the gene expression of adipose tissue CD14@*METHODS@#The data of GSE54350 were obtained from the public database of gene expression profiling. The data were pre-processed by Network Analyst, String 11.0, Cytoscape 3.7.1, and other analytical software. The differentially expressed genes were analyzed by gene ontology biological function and kyoto encycopedia of genes and genomes (KEGG) signaling pathway to establish differential gene protein interaction network, transcription factor-gene regulatory network, microRNA-gene regulatory network, environmental factors-gene regulatory network, and other interaction systems.@*RESULTS@#The gene expression pattern of CD14@*CONCLUSIONS@#The gene expression of adipose tissue CD14


Subject(s)
Adipose Tissue , Computational Biology , DNA-Binding Proteins , Diabetes Mellitus, Type 2/genetics , Gene Expression , Gene Expression Profiling , Gene Regulatory Networks , Humans , MicroRNAs/genetics , Muscle Proteins
3.
Annals of Dermatology ; : 130-140, 2020.
Article in English | WPRIM | ID: wpr-811085

ABSTRACT

BACKGROUND: Atopic dermatitis (AD) is recognized as a common inflammatory skin disease and frequently occurred in Asian and Black individuals.OBJECTIVE: Since the limitation of dataset associated with human severe AD, this study aimed to screen potential novel biomarkers involved in mild AD.METHODS: Expression profile data (GSE75890) were obtained from the database of Gene Expression Omnibus. Using limma package, the differentially expressed genes (DEGs) between samples from AD and healthy control were selected. Furthermore, function analysis was conducted. Meanwhile, the protein-protein interaction (PPI) network and transcription factor (TF)-miRNA-target regulatory network were constructed. And quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the expressions patterns of key genes.RESULTS: In total, 285 DEGs including 214 upregulated and 71 downregulated genes were identified between samples from two groups. The upregulated DEGs were mainly involved in nine pathways, such as hematopoietic cell lineage, pertussis, p53 signaling pathway, staphylococcus aureus infection, and cell cycle, while tight junction was the only pathway enriched by the downregulated DEGs. Cyclin B (CCNB)1, CCNB2, cyclin A (CCNA)2, C-X-C motif chemokine ligand (CXCL)10, and CXCL9 were key nodes in PPI network. The TF-miRNA-target gene regulatory network focused on miRNAs such as miR-106b, miR-106a, and miR-17, TFs such as nuclear factor kappa B subunit 1, RELA proto-oncogene, Sp1 transcription factor, and genes such as matrix metallopeptidase 9, peroxisome proliferator activated receptor gamma , and serpin family E member 1. Moreover, the upregulation of these genes, including CCNB1, CCNB2, CCNA2, CXCL10, and CXCL9 were confirmed by qRT-PCR.CONCLUSION: CCNB1, CCNB2, CCNA2, and CXCL9 might be novel markers of mild AD. miR-106b and miR-17 may involve in regulation of immune response in AD patients.


Subject(s)
Asian Continental Ancestry Group , Biomarkers , Cell Cycle , Cell Lineage , Computational Biology , Cyclin A , Cyclin B , Dataset , Dermatitis , Dermatitis, Atopic , Gene Expression , Gene Regulatory Networks , Humans , MicroRNAs , NF-kappa B , PPAR gamma , Proto-Oncogenes , Real-Time Polymerase Chain Reaction , Skin Diseases , Sp1 Transcription Factor , Staphylococcus aureus , Tight Junctions , Transcription Factors , Up-Regulation , Whooping Cough
4.
Braz. j. med. biol. res ; 53(9): 0-0, 2020. tab, graf
Article in English | LILACS, ColecionaSUS | ID: biblio-1132553

ABSTRACT

Myocardial ischemia/reperfusion (MI/R) injury is a complex phenomenon that causes severe damage to the myocardium. However, the potential molecular mechanisms of MI/R injury have not been fully clarified. We identified potential molecular mechanisms and therapeutic targets in MI/R injury through analysis of Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were found between MI/R injury and normal samples, and overlapping DEGs were found between GSE61592 and GSE67308. Gene Ontology (GO) and pathway analysis were performed for overlapping DEGs by Database for Annotation, Visualization and Integration Discovery (DAVID). Then, a network of protein-protein interaction (PPI) was constructed through the Search Tool for the Retrieval of Interacting Genes (STRING) database. Potential microRNAs (miRNAs) and therapeutic small molecules were screened out using microRNA.org database and the Comparative Toxicogenomics database (CTD), respectively. Finally, we identified 21 overlapping DEGs related to MI/R injury. These DEGs were significantly enriched in IL-17 signaling pathway, cytosolic DNA-sensing pathway, chemokine signaling, and cytokine-cytokine receptor interaction pathway. According to the degree in the PPI network, CCL2, LCN2, HP, CCL7, HMOX1, CCL4, and S100A8 were found to be hub genes. Furthermore, we identified potential miRNAs (miR-24-3p, miR-26b-5p, miR-2861, miR-217, miR-4251, and miR-124-3p) and therapeutic small molecules like ozone, troglitazone, rosiglitazone, and n-3 polyunsaturated fatty acids for MI/R injury. These results identified hub genes and potential small molecule drugs, which could contribute to the understanding of molecular mechanisms and treatment for MI/R injury.


Subject(s)
Myocardial Reperfusion Injury , MicroRNAs , Computational Biology , Gene Expression Profiling , Gene Regulatory Networks , Protein Interaction Maps , Gene Ontology
5.
Braz. J. Psychiatry (São Paulo, 1999, Impr.) ; 41(6): 485-493, Nov.-Dec. 2019. tab, graf
Article in English | LILACS | ID: biblio-1055347

ABSTRACT

Objective: Cocaine use disorders (CUDs) represent a major public health problem in many countries. To better understand the interaction between the environmental modulations and phenotype, the aim of the present study was to investigate the DNA methylation pattern of CUD patients, who had concomitant cocaine and crack dependence, and healthy controls. Methods: We studied DNA methylation profiles in the peripheral blood of 23 CUD patients and 24 healthy control subjects using the Illumina Infinium HumanMethylation450 BeadChip arrays. Results: Comparison between CUD patients and controls revealed 186 differentially methylated positions (DMPs; adjusted p-value [adjP] < 10-5) related to 152 genes, with a subset of CpGs confirmed by pyrosequencing. DNA methylation patterns discriminated CUD patients and control groups. A gene network approach showed that the EHMT1, EHMT2, MAPK1, MAPK3, MAP2K1, and HDAC5 genes, which are involved in transcription and chromatin regulation cellular signaling pathways, were also associated with cocaine dependence. Conclusion: The investigation of DNA methylation patterns may contribute to a better understanding of the biological mechanisms involved in CUD.


Subject(s)
Humans , Male , Adult , Young Adult , Crack Cocaine , DNA Methylation , Cocaine-Related Disorders/genetics , Cocaine-Related Disorders/blood , Genome-Wide Association Study/methods , Case-Control Studies , Linear Models , Histone-Lysine N-Methyltransferase/genetics , Statistics, Nonparametric , Mitogen-Activated Protein Kinase 1/genetics , MAP Kinase Kinase 1/genetics , Mitogen-Activated Protein Kinase 3/genetics , Gene Regulatory Networks , High-Throughput Nucleotide Sequencing , Histocompatibility Antigens/genetics , Histone Deacetylases/genetics
6.
Electron. j. biotechnol ; 41: 37-47, sept. 2019. tab, graf, ilus
Article in English | LILACS | ID: biblio-1087161

ABSTRACT

Background: Circular RNAs, a novel class in the eukaryotic transcriptome, are characterized by the 3' and 5' ends that are covalently joined in a covalently closed loop without free ends. Circular RNAs are considerably stable molecules and act as microRNA sponges with regulatory potential to the protein-coding genes. Results: Eight circular RNAs were found to be significantly upregulated at anagen skin tissue of cashmere goat compared with their counterparts at telogen. Rich and complex regulatory patterns were revealed among the eight upregulated circular RNAs at anagen and related miRNAs with their potential regulatory genes. The potential regulatory genes of eight upregulated circular RNAs at anagen were involved in several pathways related to the main physiological process of hair follicle, such as histone acetylation and axon. For chi_circ_1926, chi_circ_3541, chi_circ_0483, chi_circ_3196, and chi_circ_2092, overall, the relative expression in secondary hair follicle exhibited highly similar trends with their corresponding host genes during the different stages of the hair follicle cycle. However, the expression trends of chi_circ_0100, chi_circ_2829, and chi_circ_1967 were found to diverge from their corresponding host genes during the different stages of the hair follicle cycle. Conclusions: A total of eighteen circular RNAs were identified and characterized from skin tissue of cashmere goat. The eight upregulated circular RNAs at anagen might have significant roles in the secondary hair follicle of cashmere goat. Our results would provide a novel regulatory layer to elucidate the molecular mechanisms underlying the development of secondary hair follicle and the growth of cashmere fiber in cashmere goat.


Subject(s)
Animals , Goats/genetics , Hair Follicle/growth & development , RNA, Circular/genetics , Skin , Gene Expression , Computational Biology , MicroRNAs , Eukaryotic Cells , Gene Regulatory Networks , Transcriptome , RNA, Circular/metabolism
7.
Article in English | WPRIM | ID: wpr-761916

ABSTRACT

BACKGROUND: Osteoarthritis (OA) is a highly prevalent degenerative joint disease involving joint cartilage and its surrounding tissues. OA is the leading cause of pain and disability worldwide. At present, there are no disease-modifying OA drugs, and the primary therapies include exercise and nonsteroidal anti-inflammatory drugs until total joint replacement at the end-stage of the disease. METHODS: In this review, we summarized the current state of knowledge in genetic and epigenetic associations and risk factors for OA and their potential diagnostic and therapeutic applications. RESULTS: Genome-wide association studies and analysis of epigenetic modifications (such as miRNA expression, DNA methylation and histone modifications) conducted across various populations support the notion that there is a genetic basis for certain subsets of OA pathogenesis. CONCLUSION: With recent advances in the development of genome editing technologies such as the CRISPR-Cas9 system, these genetic and epigenetic alternations in OA can be used as platforms from which potential biomarkers for the diagnosis, prognosis, drug response, and development of potential personalized therapeutic targets for OA can be approached. Furthermore, genome editing has allowed the development of “designer” cells, whereby the receptors, gene regulatory networks, or transgenes can be modified as a basis for new cell-based therapies.


Subject(s)
Biomarkers , Cartilage , Diagnosis , DNA Methylation , Epigenomics , Gene Regulatory Networks , Genetics , Genome , Genome-Wide Association Study , Histones , Humans , Joint Diseases , Joints , MicroRNAs , Osteoarthritis , Precision Medicine , Prognosis , Risk Factors , Transgenes
8.
Chinese Journal of Biotechnology ; (12): 1925-1941, 2019.
Article in Chinese | WPRIM | ID: wpr-771742

ABSTRACT

Harnessing industrial microorganisms to utilize renewable feedstocks and meanwhile produce biofuels, bulk chemicals, food ingredients, nutraceuticals, pharmaceuticals, industrial enzymes, etc. is the basis for successful biological industries. Robust traits of industrial microorganisms including high yield and productivity as well as stress tolerance are controlled by sophisticated genetic regulatory networks. Engineering robustness of industrial microorganisms requires systematic and global perturbations at the genome-wide scale to accelerate the accumulation of diversified genotypic mutations, thus generating desirable phenotypes. We review heve the mechanisms of genetic regulation and stress response in robust industrial organisms, the global perturbations and multiplex accelerated evolution at the genome-wide scale, as well as the global perturbation of cellular redox balance. In the future, based on system biology and synthetic biology, more efforts should be further devoted to understanding the mechanisms behind robust traits in industrial microorganisms under industrial niches for modeling and prediction as well as systematic engineering.


Subject(s)
Environment , Gene Expression Regulation, Bacterial , Gene Regulatory Networks , Genetics , Industrial Microbiology , Metabolic Engineering , Synthetic Biology
9.
Article in Chinese | WPRIM | ID: wpr-773697

ABSTRACT

The aim of this paper was to study the influence of triptolide in the immune response pathways of acquired immune deficiency syndrome( AIDS). Target proteins of triptolide and related genes of AIDS were searched in PubChem and Gene databases on line. Molecular networks and canonical pathways comparison analyses were performed by bioinformatics software( IPA). There were 15 targets proteins of triptolide and 258 related genes of AIDS. Close biological relationships of molecules of triptolide and AIDS were established by networks analysis. There were 21 common immune response pathways of triptolide and AIDS,including neuroinflammation signaling pathway,Th1 and Th2 activation pathway and role of pattern recognition receptors in recognition of bacteria and viruses. Triptolide stimulated immune response pathways by the main molecules of IFNγ,JAK2,NOD1,PTGS2,RORC. IFNγ is the focus nodes of triptolide and AIDS,and regulates genes of AIDS directly or indirectly. Triptolide may against AIDS by regulating molecules IFNγ in immune response pathways.


Subject(s)
Acquired Immunodeficiency Syndrome , Drug Therapy , Allergy and Immunology , Computational Biology , Diterpenes , Pharmacology , Epoxy Compounds , Pharmacology , Gene Regulatory Networks , Humans , Interferon-gamma , Genetics , Phenanthrenes , Pharmacology , Receptors, Pattern Recognition , Allergy and Immunology , Signal Transduction , T-Lymphocytes , Allergy and Immunology
10.
Article in English | WPRIM | ID: wpr-772941

ABSTRACT

Chimeric antigen receptor (CAR) T cell therapy has exhibited dramatic anti-tumor efficacy in clinical trials. In this study, we reported the transcriptome profiles of bone marrow cells in four B cell acute lymphoblastic leukemia (B-ALL) patients before and after CD19-specific CAR-T therapy. CD19-CAR-T therapy remarkably reduced the number of leukemia cells, and three patients achieved bone marrow remission (minimal residual disease negative). The efficacy of CD19-CAR-T therapy on B-ALL was positively correlated with the abundance of CAR and immune cell subpopulations, e.g., CD8 T cells and natural killer (NK) cells, in the bone marrow. Additionally, CD19-CAR-T therapy mainly influenced the expression of genes linked to cell cycle and immune response pathways, including the NK cell mediated cytotoxicity and NOD-like receptor signaling pathways. The regulatory network analyses revealed that microRNAs (e.g., miR-148a-3p and miR-375), acting as oncogenes or tumor suppressors, could regulate the crosstalk between the genes encoding transcription factors (TFs; e.g., JUN and FOS) and histones (e.g., HIST1H4A and HIST2H4A) involved in CD19-CAR-T therapy. Furthermore, many long non-coding RNAs showed a high degree of co-expression with TFs or histones (e.g., FOS and HIST1H4B) and were associated with immune processes. These transcriptome analyses provided important clues for further understanding the gene expression and related mechanisms underlying the efficacy of CAR-T immunotherapy.


Subject(s)
Adult , Antigens, CD19 , Metabolism , Bone Marrow , Metabolism , CD8-Positive T-Lymphocytes , Allergy and Immunology , Female , Gene Expression Regulation, Leukemic , Gene Regulatory Networks , Humans , Immunotherapy, Adoptive , Male , MicroRNAs , Genetics , Metabolism , Middle Aged , Precursor Cell Lymphoblastic Leukemia-Lymphoma , Genetics , Allergy and Immunology , Therapeutics , RNA, Long Noncoding , Genetics , Metabolism , Receptors, Antigen, T-Cell , Transcription Factors , Metabolism , Transcriptome , Genetics
11.
Biol. Res ; 52: 4, 2019. tab, graf
Article in English | LILACS | ID: biblio-1011407

ABSTRACT

BACKGROUND: Hematoporphyrin derivative (HPD) has a sensibilization effect in lung adenocarcinoma. This study was conducted to identify the target genes of HPD in lung adenocarcinoma. METHODS: RNA sequencing was performed using the lung adenocarcinoma cell line A549 after no treatment or treatment with X-ray or X-ray + HPD. The differentially expressed genes (DEGs) were screened using Mfuzz package by noise-robust soft clustering analysis. Enrichment analysis was carried out using "BioCloud" online tool. Protein-protein interaction (PPI) network and module analyses were performed using Cytoscape software. Using WebGestalt tool and integrated transcription factor platform (ITFP), microRNA target and transcription factor (TF) target pairs were separately predicted. An integrated regulatory network was visualized with Cytoscape software. RESULTS: A total of 815 DEGs in the gene set G1 (continuously dysregulated genes along with changes in processing conditions [untreated-treated with X-ray-X-ray + treated with HPD]) and 464 DEGs in the gene set G2 (significantly dysregulated between X-ray + HPD-treated group and untreated/X-ray-treated group) were screened. The significant module identified from the PPI network for gene set G1 showed that ribosomal protein L3 (RPL3) gene could interact with heat shock protein 90 kDa alpha, class A member 1 (HSP90AA1). TFs AAA domain containing 2 (ATAD2) and protein inhibitor of activated STAT 1 (PIAS1) were separately predicted for the genes in gene set G1 and G2, respectively. In the integrated network for gene set G2, ubiquitin-specific peptidase 25 (USP25) was targeted by miR-200b, miR-200c, and miR-429. CONCLUSION: RPL3, HSP90AA1, ATAD2, and PIAS1 as well as USP25, which is targeted by miR-200b, miR-200c, and miR-429, may be the potential targets of HPD in lung adenocarcinoma.


Subject(s)
Humans , Hematoporphyrin Derivative/pharmacology , Gene Regulatory Networks/genetics , Adenocarcinoma of Lung/genetics , Lung Neoplasms/genetics , Ribosomal Proteins/drug effects , Ribosomal Proteins/genetics , Transcription Factors , Cluster Analysis , Gene Expression Regulation, Neoplastic , Sequence Analysis, RNA , HSP90 Heat-Shock Proteins/drug effects , HSP90 Heat-Shock Proteins/genetics , Small Ubiquitin-Related Modifier Proteins/drug effects , Small Ubiquitin-Related Modifier Proteins/genetics , MicroRNAs/metabolism , Cell Line, Tumor , DNA-Binding Proteins/drug effects , DNA-Binding Proteins/genetics , Protein Inhibitors of Activated STAT/drug effects , Protein Inhibitors of Activated STAT/genetics , Flow Cytometry , ATPases Associated with Diverse Cellular Activities/drug effects , ATPases Associated with Diverse Cellular Activities/genetics , Adenocarcinoma of Lung/drug therapy , Adenocarcinoma of Lung/radiotherapy , Lung Neoplasms/drug therapy , Lung Neoplasms/radiotherapy
12.
São Paulo; s.n; s.n; 2019. 110 p. graf, tab.
Thesis in English | LILACS | ID: biblio-1023378

ABSTRACT

Metabolic Syndrome (MetS) is a combination of diseases interrelated and associated with increased mortality and risk of cardiovascular events. Among the elucidated molecular mechanisms of MetS, there are several genes regulated by miRNAs - small non-coding RNAs. A large number of transcriptomic studies in public databases integrated with new analysis methods can generate new insights. Therefore, this study aimed to identify circulating miRNAs and their target genes in MetS using a Systems Biology approach. For this, we used GEO-NCBI to download and analyse 26 microarray transcriptome studies of MetS and obesity. After preprocessing, the data underwent differential expression (LIMMA method), gene co-expression (CEMiTool), and enrichment (GSEA, Reactome) analyses. We retrieved a gene expression signature for subcutaneous adipose tissue (SAT) for obese individuals that included 291 consistent differentially expressed genes (DEG). This signature had a positive normalized enrichment score (NES) for adaptive immune system activation responses, and negative NES for metabolic pathways. The consensus co-expression network of SAT revealed 3 communities (CM) of densely interconnected genes. These CMs had a high number of up regulated genes and a consistent positive NES among the studies. The co-expressed genes of these 3 CMs were related to neutrophil degranulation, infiltration of immune system cells, and inflammatory processes. Also, a small brazillian cohort (6 individuals with MetS and 6 controls) underwent a seric miRNA profiling using PCR array. From the 222 miRNAs detected in serum, the differential expression analysis identified 4 upregulated miRNAs (miR-30c-5p, miR-421, miR-542-5p and miR-574) in MetS patients (p<0.01). The integrative miRNAs-mRNAs analysis revealed that the circulating upregulated miRNAs had 12 targets in the SAT, 3 targets in the liver; and no targets in the muscle and blood. Many of these target genes are known modulators of proinflammatory pathways. In conclusion, the use of Systems Biology in the analysis of gene networks and circulating miRNAs identified some potential molecular and pathophysiological mechanisms of the Metabolic Syndrome. The circulating miRNAs identified in this study are potential biomarkers and/or therapeutic targets. However, further studies are needed to validate these miRNAs and their target mRNA


A Síndrome Metabólica (MetS) é um conjunto de doenças inter-relacionadas e associadas ao aumento de mortalidade e risco de eventos cardiovasculares. Entre os mecanismos moleculares elucidados da MetS, existem muitos genes regulados por miRNAs - RNAs pequenos não codificadores. O grande número de estudos transcriptômicos em banco dados públicos integrado a novos métodos de análise podem gerar novas descobertas. Deste modo, o objetivo deste estudo foi identificar miRNAs circulantes e genes alvos na MetS usando a abordagem de Biologia de Sistemas. Para isso, GEO-NCBI foi usado para obter e analisar 26 estudos de transcriptoma por microarray de MetS e obesidade. Após o pré-processamento, realizamos análises de expressão diferencial (método LIMMA), co-expressão gênica (CEMiTool), e enriquecimento (GSEA, Reactome). Identificamos uma assinatura de expressão gênica do tecido adiposo subcutâneo (SAT) de indivíduos obesos, composta por 291 genes consistentemente diferencialmente expressos (DEG). Essa assinatura teve um escore de enriquecimento normalizado (NES) positivo para ativação de respostas do sistema imune adaptativo, e NES negativo para vias de metabolismo. A rede consenso de co-expressão do SAT revelou 3 comunidades (CM) de genes densamente interconectadas. Essas CMs continham muitos genes regulados positivamente e com consistência de NES positivo entre os estudos. Os genes co-expressos dessas 3 comunidades pertenciam a vias de a degranulação de neutrófilos, infiltração de células do sistema imune e processos inflamatórios. Além disso, uma pequena coorte brasileira (6 indivíduos com MetS e 6 controles) foi submetida à dosagem sérica de miRNAs por PCR array. Dos 222 miRNAs detectados no soro, a análise de expressão diferencial identificou 4 miRNAs regulados positivamente (miR-30c-5p, miR-421, miR-542-5p e miR-574) nos pacientes com MetS (p<0.01). A análise integrativa miRNAs-mRNAs revelou que osmiRNAs circulantes superexpressos tinham 12 alvos no SAT, 3 alvos no fígado; e nenhum alvo no músculo e no sangue. Muitos desses alvos são moduladores de vias ró-inflamatórias. Em conclusão, a utilização da Biologia de Sistemas na análise de redes gênicas e miRNAs circulantes identificou alguns potenciais mecanismos moleculares e fisiopatológicos da Síndrome Metabólica. Os miRNAs circulantes identificados neste trabalho são potenciais biomarcadores e/ou alvos terapêuticos. Entretanto, mais estudos são necessários para validar esses miRNAs e seus mRNAs alvos


Subject(s)
Metabolic Syndrome/diagnosis , MicroRNAs/analysis , Systems Biology/instrumentation , RNA, Messenger/analysis , Gene Regulatory Networks , Obesity/classification
13.
Acta cir. bras ; 34(4): e201900403, 2019. tab, graf
Article in English | LILACS | ID: biblio-1001087

ABSTRACT

Abstract Purpose: To investigate the long non-coding RNAs (lncRNAs) profile on renal ischemia reperfusion in a mouse model. Methods: Microarray analysis was used to study the expression of misregulated lncRNA in a mouse model of renal ischemia reperfusion(I/R) with long ischemia time. Quantitative real-time PCR (qPCR) was used to verify the expression of selected lncRNAs and mRNAs.The potential functions of the lncRNA was analyzed by bioinformatics tools and databases. Results: Kidney function was impaired in I/R group compared to the normal group. Analysis showed that a total of 2267 lncRNAs and 2341 messenger RNAs (mRNAs) were significantly expressed in I/R group (≥2.0-fold, p < 0.05).The qPCR result showed that lncRNAs and mRNAs expression were consistent with the microarray analysis. The co-expression network profile analysis based on five validated lncRNAs and 203 interacted mRNAs showed it existed a total of 208 nodes and 333 connections. The GO and KEEG pathway analysis results showed that multiple lncRNAs are involved the mechanism of I/R. Conclusion: Multiple lncRNAs are involved in the mechanism of I/R.These analysis results will help us to further understand the mechanism of I/R and promote the new methods targeted at lncRNA to improve I/R injury.


Subject(s)
Animals , Rats , RNA, Messenger/analysis , Reperfusion Injury/genetics , RNA, Long Noncoding/analysis , Kidney/blood supply , Reference Values , Down-Regulation , Gene Expression , Up-Regulation , Gene Expression Profiling , Tissue Array Analysis/methods , Gene Regulatory Networks , Real-Time Polymerase Chain Reaction , Mice, Inbred C57BL
14.
Chinese Journal of Lung Cancer ; (12): 280-288, 2019.
Article in Chinese | WPRIM | ID: wpr-775631

ABSTRACT

BACKGROUND@#Lung cancer is a malignant tumor disease with high morbidity and high mortality. The non-small cell lung cancer (NSCLC) is the most common type, among them, lung squamous cell carcinoma own special pathological type and specific treatment, is a subtype of non-small cell lung cancer and can be divided into peripheral type and central type according to clinical phenotype. This study explores the differences in gene levels and their potential values based on clinical differences between central and peripheral in lung squamous cell carcinoma.@*METHODS@#The lung squamous cell carcinoma dataset was collected from The Cancer Genome Atlas (TCGA) database, clinical information and the corresponding gene expression profiles were downloaded. Then we further sort and analyze all these data.@*RESULTS@#In clinical characteristics analysis, result showed that central lung squamous cell carcinoma was more likely to metastasis with lymph node than peripheral lung squamous cell carcinoma (46.2%, 67/145 vs 28.9%, 26/90; P=0.019), while there were no significant differences in gender, age, tumor size, distant metastasis, tumor node metastasis (TNM) stage, and EGFR mutation. Gene expression analysis showed 1,031 differentially expressed genes between central and peripheral lung squamous cell carcinoma, of which 629 genes were up-regulated and 402 genes were down-regulated (peripheral vs central). Further enrichment analysis showed differentially expressed genes were mainly riched in 6 signaling pathways. Among them, the neuroactive ligand-receptor interaction pathway was the main enrichment pathway of differentially expressed genes, and other differential expressed genes were mainly involved in lipid metabolism and glucose metabolism. The analysis of interaction network showed that hepatocyte nuclear factor 1 homeobox A (HNF1A) and cytochrome p450 family, Cytochrome P450 3A4 (CYP3A4) own widely effect in up-regulated genes, while ALB and APOA1 at the key positions of the network in down-regulated genes were CONCLUSIONS: Central and peripheral lung squamous cell carcinoma showed clinical phenotype difference not only reflected in the incidence of lymph node metastasis, but also in gene expression profiles. Among them, HNF1A, CYP3A4, ALB, APOA1 at the key position of the differential gene interaction network and maybe as regulatory factors in the phenotypic difference.


Subject(s)
Aged , Carcinoma, Squamous Cell , Genetics , Databases, Genetic , Female , Gene Expression Profiling , Gene Regulatory Networks , Humans , Kaplan-Meier Estimate , Lung Neoplasms , Genetics , Male , Middle Aged , Smoking , Genetics
15.
Article in Chinese | WPRIM | ID: wpr-775241

ABSTRACT

OBJECTIVE@#To identify the differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMC) of patients with hepatocellular carcinoma (HCC) and to analyze their regulatory network.@*METHODS@#The DEGs in PBMCs of HCC patients were screened based on GEO database. The functional enrichment analysis and interaction analysis were carried out for DEGs. MCODE algorithm was used to screen core genes of DEGs, and the mirDIP and starBase online tools were used to predict upstream miRNAs and lncRNAs of the core genes.@*RESULTS@#A total of 265 DEGs with a high credibility were identified, which were mainly enriched in the biological activity, such as regulation of cell proliferation, metabolic regulation, cell communication and signaling, and inflammatory diseases according to Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and the two analyses were correlated. Four diagnostic candidate genes were identified, including FUS RNA binding protein, C-X-C motif chemokine ligand 8, cullin 1 and RNA polymerase Ⅱ subunit H. Subsequently, 10 miRNAs, 1 lncRNAs and 38 circRNAs were predicted, and finally a lncRNA/circRNA-miRNA-mRNA-pathway regulatory networks was constructed.@*CONCLUSIONS@#The diagnostic candidate genes and its regulatory network in HCC PBMC have been identified based on data mining, which could provide potential tumor biomarkers for early diagnosis and treatment of HCC.


Subject(s)
Carcinoma, Hepatocellular , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Humans , Leukocytes, Mononuclear , Metabolism , Liver Neoplasms
16.
Neuroscience Bulletin ; (6): 200-207, 2018.
Article in English | WPRIM | ID: wpr-777071

ABSTRACT

Different physical and chemical stimuli are detected by the peripheral sensory receptors of dorsal root ganglion (DRG) neurons, and the generated inputs are transmitted via afferent fibers into the central nervous system. The gene expression profiles of DRG neurons contribute to the generation, transmission, and regulation of various somatosensory signals. Recently, the single-cell transcriptomes, cell types, and functional annotations of somatosensory neurons have been studied. In this review, we introduce our classification of DRG neurons based on single-cell RNA-sequencing and functional analyses, and discuss the technical approaches. Moreover, studies on the molecular and cellular mechanisms underlying somatic sensations are discussed.


Subject(s)
Animals , Ganglia, Spinal , Cell Biology , Gene Regulatory Networks , Humans , Pain , Genetics , Metabolism , Pathology , Sensory Receptor Cells , Metabolism , Sequence Analysis, RNA , Transcriptome
17.
Frontiers of Medicine ; (4): 412-425, 2018.
Article in English | WPRIM | ID: wpr-771297

ABSTRACT

Transcription factor networks have evolved in order to control, coordinate, and separate, the functions of distinct network modules spatially and temporally. In this review we focus on the MYC network (also known as the MAX-MLX Network), a highly conserved super-family of related basic-helix-loop-helix-zipper (bHLHZ) proteins that functions to integrate extracellular and intracellular signals and modulate global gene expression. Importantly the MYC network has been shown to be deeply involved in a broad spectrum of human and other animal cancers. Here we summarize molecular and biological properties of the network modules with emphasis on functional interactions among network members. We suggest that these network interactions serve to modulate growth and metabolism at the transcriptional level in order to balance nutrient demand with supply, to maintain growth homeostasis, and to influence cell fate. Moreover, oncogenic activation of MYC and/or loss of a MYC antagonist, results in an imbalance in the activity of the network as a whole, leading to tumor initiation, progression and maintenance.


Subject(s)
Animals , Carcinogenesis , Metabolism , Disease Progression , Gene Expression Regulation , Gene Regulatory Networks , Physiology , Humans , Protein Interaction Domains and Motifs , Physiology , Proto-Oncogene Proteins c-myc , Metabolism
18.
Article in English | WPRIM | ID: wpr-773597

ABSTRACT

Saposhnikovia divaricata is a valuable Chinese medicinal herb; the transformation from vegetative growth to reproductive growth may lead to the decrease of its pharmacological activities. Therefore, the study of bolting and flowering for Saposhnikovia divaricata is warranted. The present study aimed to reveal differentially expressed genes (DEGs) and regularity of expression during the bolting and flowering process, and the results of this study might provide a theoretical foundation for the suppression of early bolting for future research and practical application. Three sample groups, early flowering, flower bud differentiation, and late flowering (groups A, B, and C, respectively) were selected. Transcriptomic analysis identified 67, 010 annotated unigenes, among which 50, 165 were differentially expressed including 16, 108 in A vs B, and 17, 459 in B vs C, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional classification analysis were performed on these differentially expressed genes, and five important pathways were significantly impacted (P ≤ 0.01): plant circadian rhythm, other glycan degradation, oxidative phosphorylation, plant hormone signal transduction, and starch and sucrose metabolism. Plant hormone signal transduction might play an important role in the bolting and flowering process. The differentially expressed indole-3-acetic acid (IAA) gene showed significant down-regulation during bolting and flowering, while the transport inhibitor response 1 (TIR1) gene showed no significant change during the bolting process. The expression of flowering related genes FLC, LYF, and AP1 also showed a greater difference at different development stages. In conclusion, we speculate that the decrease in auxin concentration is not caused by the degrading effect of TIR1 but by an alternative mechanism.


Subject(s)
Apiaceae , Genetics , Flowers , Genetics , Gene Expression Profiling , Gene Expression Regulation, Plant , Gene Regulatory Networks , Genes, Plant , RNA, Plant , Genetics , Reproducibility of Results
19.
Article in English | WPRIM | ID: wpr-772996

ABSTRACT

The mA modification has been implicated as an important epitranscriptomic marker, which plays extensive roles in the regulation of transcript stability, splicing, translation, and localization. Nevertheless, only some genes are repeatedly modified across various conditions and the principle of mA regulation remains elusive. In this study, we performed a systems-level analysis of human genes frequently regulated by mA modification (mAfreq genes) and those occasionally regulated by mA modification (mAocca genes). Compared to the mAocca genes, the mAfreq genes exhibit gene importance-related features, such as lower dN/dS ratio, higher protein-protein interaction network degree, and reduced tissue expression specificity. Signaling network analysis indicates that the mAfreq genes are associated with downstream components of signaling cascades, high-linked signaling adaptors, and specific network motifs like incoherent feed forward loops. Moreover, functional enrichment analysis indicates significant overlaps between the mAfreq genes and genes involved in various layers of gene expression, such as being the microRNA targets and the regulators of RNA processing. Therefore, our findings suggest the potential interplay between mA epitranscriptomic regulation and other gene expression regulatory machineries.


Subject(s)
Adenosine , Metabolism , Gene Expression Regulation , Gene Regulatory Networks , Humans , MicroRNAs , Metabolism , Organ Specificity , Signal Transduction
20.
Article in English | WPRIM | ID: wpr-772982

ABSTRACT

Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM-disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of disease-associated PTM events. By reconstructing a disease-gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://ptmd.biocuckoo.org.


Subject(s)
Databases, Protein , Disease , Genetics , Gene Regulatory Networks , Humans , Phosphorylation , Protein Processing, Post-Translational , Proteins , Metabolism , Search Engine
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