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ObjectiveTo investigate the effect of Tangzhi pills on the improvement of insulin resistance （IR） in the liver with type 2 diabetes （T2DM） by regulating phosphatidylinositol 3-kinase （PI3K）/protein kinase B （Akt） signaling pathway based on differential genes and its possible molecular mechanism. MethodT2DM rat models were prepared by high fat （HFD） diet combined with streptozotocin （STZ） intraperitoneal injection. The experiment was divided into blank group， model group， metformin hydrochloride group （0.18 g·kg-1）， Tangzhi pills high （1.08 g·kg-1）， medium （0.54 g·kg-1） and low （0.27 g·kg-1） dose groups. Rat serum， liver， and pancreatic tissue were collected， and the pathological tissue of the liver and pancreas was observed using hematoxylin-eosin （HE） staining. The fasting blood glucose level （FBG） was detected， and oral glucose tolerance （OGTT） tests were conducted. Enzyme-linked immunosorbent assay （ELISA） was used to detect fasting serum insulin （FINS） and glycated hemoglobin （GHb） levels in rats. IR homeostasis model index （HOMA-IR）， β cellular homeostasis index （HOMA-β）， and insulin sensitivity index （ISI） were calculated. Biochemical methods were used to determine the levels of triglyceride （TG）， total cholesterol （TC）， low-density lipoprotein （LDL-C）， and high-density lipoprotein （HDL-C） in rat serum. Transcriptomics obtained differentially expressed mRNA from liver tissue and enriched differentially expressed pathways. Real-time reverse transcriptase polymerase chain reaction （Real-time PCR） was used to detect the mRNA expression of cyclic adenylate responsive element binding protein 3-like protein 2 antibody （CREB3l2）， B-lymphocyte tumor 2 （Bcl-2）， Toll-like receptor 2 （TLR2）， cyclin-dependent kinase inhibitor 1A （CDNK1A）， and DNA damage induced transcription factor 4-like protein （DDIT4） in liver tissue. Western blot was used to detect the protein expression of phosphorylated phosphatidylinositol 3-kinase （p-PI3K）， phosphorylated protein kinase B （p-Akt）， glucose transporter 4 （GLUT4）， insulin receptor （INSR）， and insulin receptor substrate 2 （IRS2）. ResultThe pharmacodynamic experiment results showed that compared with model group， Tangzhi pills groups repaired liver and pancreatic tissue to varying degrees， reduced blood sugar （P<0.01）， and promoted a decrease in serum FINS， GHb， and HOMA-IR （P<0.05， P<0.01）. In addition， HOMA-β and ISI increased （P<0.05， P<0.01）. The levels of TC， TG， and LDL-C decreased （P<0.05， P<0.01）， while the levels of HDL-C increased （P<0.05， P<0.01）. The transcriptomics experimental results confirmed that the PI3K/Akt signaling pathway was significantly expressed in both the blank group and model group， as well as in the high-dose Tangzhi pills group and model group. CDNK1A， DDIT4， CREB3l2， Bcl-2， and TLR2 were significantly differentially expressed mRNA during TG intervention in T2DM. Compared with the model group， the protein expression of p-PI3K， p-Akt， GLUT4， INSR， and IRS2 increased in all Tangzhi pills groups （P<0.01）. The mRNA expression of CREB3l2， Bcl-2， and TLR2 increased （P<0.01）， while that of CDNK1A and DDIT4 decreased （P<0.01）. ConclusionTangzhi pills may regulate the PI3K/Akt signaling pathway based on the differential mRNA expression of CREB3l2， Bcl-2， TLR2， CDNK1A， and DDIT4， thereby improving IR in the liver with T2DM.
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OBJECTIVES@#The common differentially expressed mRNAs in brain, heart and liver tissues of deceased sudden infant death syndrome (SIDS) and infectious sudden death in infancy (ISDI) confirmed by autopsy was screened by bioinformatics to explore the common molecular markers and pathogenesis of SIDS and ISDI.@*METHODS@#The datasets of GSE70422 and GSE136992 were downloaded, the limma of R software was used to screen differentially expressed mRNA in different tissue samples of SIDS and ISDI decedents for overlapping analysis. The clusterProfiler of R software was used to conduct gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The protein-protein interaction (PPI) network was constructed by STRING database, while the hub gene was screened by cytoHubba plug-in.@*RESULTS@#Compared with the control group, there were 19 significant differentially expressed genes in the tissue samples of SIDS and ISDI decedents, among which 16 in the heart tissue and 3 in the liver tissue, and the astrotactin 1 (ASTN1) gene expression difference in the heart tissue was most significant. The PPI network identified Ras homolog family member A (RHOA), integrin subunit alpha 1 (ITGA1), and H2B clustered histone 5 (H2BC5) were hub genes. The analysis of GO and KEGG showed that differentially expressed genes were enriched in the molecular pathways of actin cytoskeleton regulation, focal adhesion and response to mycophenolic acid.@*CONCLUSIONS@#ASTN1, RHOA and ITGA1 may participate in the development of SIDS and ISDI. The enrichment of differentially expressed genes in immune and inflammatory pathways suggests a common molecular regulatory mechanism between SIDS and ISDI. These findings are expected to provide new biomarkers for molecular anatomy and forensic identification of SIDS and ISDI.
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Humanos , Lactente , Perfilação da Expressão Gênica , Morte Súbita do Lactente/genética , Redes Reguladoras de Genes , Mapas de Interação de Proteínas/genética , Biologia ComputacionalRESUMO
AIM: To explore the key genes related to immunity and immune cell infiltration levels in diabetes retinopathy(DR)using bioinformatics.METHODS: Differential expression genes(DEGs)were obtained by “limma” R from Gene Expression Omnibus(GEO)data from September to October 2022, Gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)were analyzed, and the infiltration of immune cell types in each sample was calculated based on CIBERSORT algorithm. Weighted gene co-expression network analysis(WGCNA)was used to screen for DEGs in immune-related gene modules. The protein-protein interaction(PPI)network was established by STRING online database and Cytoscape, and the hub genes were screened by MCODE and cytoHubba plug-ins.RESULTS: The results showed that 1 426 up-regulated and 206 down-regulated differential genes were screened, where 7 immune cell types, including B cell naive, Plasma cells, CD4+T cells, T cells regulatory(Tregs), Macrophages M0, Macrophages M1 and Neutrophils were significantly overexpressed(P<0.05), while others were low expressed(P<0.05). After WGCNA, a total of 820 DEGs were found in the modules most related to immunity. After constructing the PPI network, 10 key genes were screened using plug-ins, and two key genes were further screened using the expression amount of each differential gene in PPI: DLGAP5 and AURKB.CONCLUSION: This study used bioinformatics to screen the infiltration of immune cells and key genes related to immunity in patients with DR. These findings may provide evidences for future research, diagnosis, and treatment of DR.
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【Objective】 To study the level of occult hepatitis B virus methylation and replication related genes, and to explore the effect of the former on the latter. 【Methods】 The cases in control group (healthy control, n=3), occult hepatitis B group (occult HBV group, n=3) and hepatitis B group (HBV group, n=3) were detected by Illumina methylation 850k chip. The difference analysis, GO analysis and KEGG analysis were carried out. The methylation and virus replication related genes DNMT1, DNMT2, Dnmt3a and ZHX2 were screened for RT-PCR. 【Results】 The methylation level of occult HBV group and HBV group was significantly higher than that of the control group. Difference analysis showed that there were 1 050 differential methylation sites in occult HBV group with the methylation level greater than non-methylation level, and 1 340 differential methylation sites as the opposite compared with the control group. In HBV group, there were 1 008 differential methylation sites with methylation level greater than non-methylation level, and 1 242 differential methylation sites as the opposite. Go analysis showed that compared with the control group, the differential gene expression in occult HBV group and HBV group was significantly related to many anabolic processes in biological process (BP), cell composition (CC) and molecular function (MF). The enrichment analysis of KEGG pathway between the control group and the occult HBV group showed that the differential genes were mainly involved in adhesion junction, basal cell carcinoma, endometrial carcinoma, EB virus infection, hepatocellular carcinoma and other signal pathways. The enrichment analysis of KEGG pathway in occult HBV group and HBV group showed that the differential genes were mainly involved in AMPK signal pathway, cell cycle, endometrial cancer, hepatitis C, hepatocellular carcinoma and other signal pathways. DNMT1 and DNMT3a in occult HBV group and HBV group were significantly higher while ZHX2 was significantly lower than those in control group. 【Conclusion】 The methylation level of occult HBV group and HBV group increased significantly while ZHX2 decreased significantly. Hypermethylation inhibited the expression of ZHX2 and changed the replication of hepatitis B virus. Hepatitis B virus DNA methylation provides a theoretical basis for the replication mechanism of hepatitis B virus and a new method for the treatment of hepatitis B virus.
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Objective:To establish a mouse model of intra-jugular arteriovenous fistula (AVF) to screen differentially expressed genes in the process of intimal stenosis of AVF for investigating the abnormal expression signaling pathways and the mechanisms.Methods:Forty-six male C57BL/6 mice were randomly divided into AVF group ( n=23) and sham-operated group ( n=23). The AVF group underwent internal jugular arteriovenous fistuloplasty, and the sham-operated group separated the right external jugular vein and common carotid artery and then sutured the incision. The whole-genome sequences of mice with AVF stenosis were determined by transcriptomic reversible chain terminator and synthetic sequencing. The microarray data set was established, and the Benjamini & Hochberg method of gene microarray data analysis was applied to screen the differentially expressed genes. The differentially expressed genes were screened by R-language enrichment analysis. Then, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) were performed. The subcellular localization of the differentially expressed genes was performed by BUSCA software. The protein network interaction of differentially expressed genes was analyzed by using STRING database and Cytoscape software. Results:In the AVF group, 21 mice were successfully modeled and 2 mice failed. Therefore, there were 21 mice in the AVF group and only 21 mice in the sham-operated group. This mouse internal jugular AVF model was innovated using the continuous-interrupted suture method, which improved the success rate of modeling this model. The differential gene sequencing analysis showed that there were 2 514 differentially expressed genes in the AVF process, including 1 323 up-regulated genes and 1 191 down-regulated genes. GO functional enrichment analysis showed that the differential genes were mainly enriched in metabolic process, activation, redox, mitochondria and so on. KEGG pathway enrichment analysis showed that the differential genes were enriched in metabolism, energy substance synthesis, diabetes, oxidative stress and so on. Statistical analysis of subcellular localization showed that the differences were mainly in mitochondrial proteins (24.24%), cytoplasmic proteins (17.51%), nuclear proteins (13.13%), cell membrane proteins (11.45%), and extracellular proteins (10.77%).Conclusions:Mitochondrial oxidative stress injury may be involved in the pathological damage process of endothelial proliferation stenosis in the AVF.
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Objective:To analyze the differentially expressed genes related to gastric cancer and analyze their related signaling pathways.Methods:The gastric cancer-related gene expression chips GSE63121 (miRNA) and GSE2685 (mRNA) were selected from the GEO database. After setting the screening criteria, the differentially expressed genes were obtained, and then the miRDB database was used to predict the common genes related to gastric cancer. GO and KEGG enrichment analyses were performed on consensus genes in the DAVID database. Genes with interactions were visualized using the STRING database to construct a PPI of differentially expressed genes. The relationship between differentially expressed genes and the survival rate of gastric cancer patients were predicted by the GEPIA database, and the meaningful differentially expressed genes were screened according to prognosis. Finally, the TIMER2.0 database was used to analyze the correlation between the finally screened genes and immune cell infiltration.Results:A total of 734 differentially expressed genes were obtained, of which 261 and 473 genes were up-regulated and down-regulated, respectively, and a total of 20 differentially expressed miRNA genes were obtained, of which 1 and 19 genes were up-regulated and down-regulated, respectively. Among these genes, a total of 103 genes were mapped, which were mainly involved in the regulation of immune system and metabolic process in gastric cancer. The screened significantly differentially expressed genes were CREB1 and ESR1, and gastric cancer patients had better prognosis with low expression of CREB1 and ESR1. The expressions of CREB1 and ESR1 were both positively correlated in gastric cancer tissue with the infiltration level of regulatory T cells (Tregs) in the tumor microenvironment (all P<0.05). Conclusions:CREB1 and ESR1 affect immune infiltration during the occurrence and development of gastric cancer. The high expression of CREB1 and ESR1 is associated with poor prognosis. The possible reason is that there are more Tregs cells in the tumor microenvironment. CREB1 and ESR1 are expected to become important targets for studying the pathogenesis and molecular mechanism of gastric cancer and its clinical application.
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Introdução: a Síndrome do X Frágil (FXS) é a forma mais prevalente de deficiência intelectual herdável, e é a principal causa monogênica para o desenvolvimento de Transtorno de Espectro do Autismo (TEA). Objetivo: o objetivo do presente estudo é identificar RNAm associados à possíveis vias neurocomportamentais na SFX como no TEA, através de ferramentas de bioinformática. Metodologia: para identificação de possíveis vias alteradas entre a SFX e pacientes com TEA, utilizamos os bancos de dados GSE65106 e GSE21348 para anotação, visualização e descoberta integrada (DAVID 6.8). O valor de p <0,05 e fold change maior que 2 vezes (FC > 2) definidos como os limiares para a identificação de genes diferencialmente expressos (DE-RNAm). Resultados: foi possível identificar cerca de 32 DE-RNAm com funções em vias de spliceossomo, apoptose, transcrição, e em vias neurológicas comportamentais expressos exclusivamente na SFX. Os genes CAPNS1, HNRNPK, HNRPM, foram identificados como hipoexpressos em indivíduos com síndrome do X Frágil. Estes genes tem importante função moduladora nas respostas do potencial de longo prazo (LTP), plasticidade neural, e em transportadores de serotonina (SERT) alterando respostas que englobam humor, cognição e comportamentos, além de interferirem no receptor de dopamina (D2R) alterando as funções motoras e circuitos de recompensa. Conclusão: os genes CAPNS1, HNRNPK, HNRNPM foram identificados como marcadores genéticos eurocomportamentais importantes para a síndrome do X-frágil com expressão diminuída na doença, indicando uma possível modulação desses genes em aspectos fenotípicos marcantes da doença.
Introduction: fragile X Syndrome (FXS) is the most prevalent form of inheritable intellectual disability, and is the leading monogenic cause for the development of Autism Spectrum Disorder (ASD). Objective: the aim of this study is to identify mRNA associated with possible neurobehavioral pathways in SFX as in ASD, using bioinformatics tools. Methodology: to identify possible altered pathways between SFX and ASD patients, we used the GSE65106 and GSE21348 databases for annotation, visualization and integrated discovery (DAVID 6.8). The p value <0.05 and fold change greater than 2 times (HR> 2) are defined as the thresholds for the identification of differentially expressed genes (DE-mRNA). Results: it was possible to identify about 32 DE-mRNA with functions in spliceosome, apoptosis, transcription, and behavioral neurological pathways expressed exclusively in SFX. CAPNS1, HNRNPK, HNRPM genes were identified as hypoexpressed in individuals with fragile X syndrome. These genes play an important modulating role in long-term potential (LTP), neural plasticity, and serotonin transporters (SERT) responses by altering mood, cognition, and behavioral responses, and by interfering with dopamine receptor (D2R) by motor functions and reward circuits. Conclusion: the CAPNS1, HNRNPK, HNRNPM genes have been identified as important neurobehavioral genetic markers for impaired X-syndrome, indicating a possible modulation of these genes into marked phenotypic aspects of the disease.
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Humanos , Expressão Gênica , Transtorno do Espectro Autista , Síndrome do Cromossomo X Frágil , Genes , Base de DadosRESUMO
Objective:To detect the changes of functional expression profile of energy metabolism related differential genes in sleep deprived rats before and after intervention by Tianwang Buxindan by microarray sequencing technology， so as to provide possible ideas and theoretical basis for the prevention and treatment of sleep deprivation. Method:The rats were randomLy divided into two groups： the Tianwang Buxindan group and the model group. The Tianwang Buxindan group was given the decoction of Tianwang Buxindan at the dose of 20 g·kg-1， and the model group was given the pure water of equal volume for 14 days. Taking liver， heart and hypothalamus as samples， high-throughput sequencing was used to obtain differential genes. Gene Ontology（Go）classification and kyoto Encyclopedia of Genes and Genomes （KEGG）pathway enrichment analysis were used to construct a co expression network with lncrna. Real-time fluorescence quantitative polymerase chain reaction（Real-time PCR）was used to detect the mRNA expression levels of neuropeptide Y（NPY）， bispecific phosphatase 1/mitogen-activated protein kinase phosphatase-1（DUSP1/MKP-1）and alpha-L-iduronidase（IDUA）， three key genes with significant differences in energy metabolism. Result:The 321 differentially expressed genes were obtained， 231 of which were up-regulated and 90 down regulated， which mainly promoted the process of lipid metabolism， glucose metabolism and protein metabolism， participated in the synthesis and expression of fibrinogen， vitamin B6 and mesencephalic astrocyte-derived neurotrophic factor（MANF）， and involved mitogen activated protein kinases（MAPK）， p53 gene（p53）， cyclic adenosine monophosphate（cAMP） and other signal pathways. Compared with the model group， the expression of IDUA significantly increased in the Tianwang Buxindan group （P<0.05）， but decreased significantly in NPY and DUSP1（P<0.01）. Conclusion:Tianwang Buxindan can interfere with the energy metabolism mechanism of sleep deprived rats in many ways. By down regulating the mRNA expression level of NPY and DUSP1 genes， it may activate the p38 MAPK signal pathway and affect the lipid metabolism.
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Objective To compare and analyze the differences in the transcriptomics between mycelium and early yeast phases of Sporothrix schenckii (S.schenckii),and to realize the changes in transcriptome expression profiles during mycelium-to-yeast transformation.Methods A standard strain of S.schenckii (ATCC 10268) was subjected to 96-hour culture with Sabouraud medium at 25 ℃ or 36-hour culture with brain-heart infusion medium at 37 ℃ to obtain the mycelium and yeast form of S.schenckii,and then,their transcriptomes were sequenced.Functional annotation was performed for screened unigenes by comparison using several databases (such as NR,Swiss-Prot,KEGG,COG,KOG,GO and Pfam),coding sequence prediction,and gene expression analysis in each sample.Finally,the differentially expressed genes were subjected to pattern clustering,functional annotation and enrichment analysis.Results A total of 14.76 Gb valid data (clean data) were obtained,and functional annotation results were acquired in 28 094 of 43 863 assembled unigene clusters.Compared with S.schenckii in mycelium phase,there were 10 969 up-regulated genes and 199 down-regulated genes in S.schenckii in yeast phase.These differentially expressed genes were involved in protein phosphorylation,intracellular protein transport,cellular protein modification,small guanosine triphosphate-mediated signal transduction,vesicle-mediated transport,translation,intracellular signal transduction,microtubule formation,adenosine triphosphate synthesis,coupled proton transport and so on.Sixteen genes in the mitogen-activated protein kinase (MAPK) pathway and two-component signaling pathway,which were two important signal transduction pathways involved in fungal morphogenesis,and 16 genes involved in chitin synthesis and metabolism were all confirmed to be up-regulated in S.schenckii in yeast phase.Conclusions Compared with S.schenckii in mycelium phase,great changes in gene expression profiles were observed in S.schenckii in yeast phase.These differentially expressed genes are involved in many functions,suggesting that the dimorphic transition of S.schenckii is regulated by a multi-gene network system.
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Objective To establish tree shrew model of type 2 diabetes mellitus (T2DM) combined with cerebral ischemia (IS),and to explore the regulatory mechanism of ischemic postconditioning (PC) on gene differential expression in cerebral cortex under metabolic abnormalities and cerebral ischemia condition.Methods Seventy tree shrews were divided into control,T2DM,IS,T2DM+IS and T2DM +IS +PC groups (n =14 each group).The experimental diabetes model was established by the combined use of high fat diet breeding with streptozocin injection in tree shrew.The local cerebral thrombosis was induced by photochemical reaction in tree shrews,and ischemic PC was established at 4h after cerebral ischemia followed by clipped ipsilateral common carotid artery three times (5 min/time).The metabolic status of tree shrews was measured by serum biochemical markers.TTC staining,HE staining,and electron microscopy were used to observe the changes of the body's metabolic status at 24h after IS.RNA-seq was used to analyze differentially expressed genes.Results The ultrastructure of brain cells was abnormal and the cerebral infarction area was the largest in T2DM+IS tree shrews (P＜0.01).Compared with control group,body weight of tree shrews in T2DM + IS group was significantly reduced (P＜ 0.01) while blood glucose,total cholesterol,low density lipoprotein-cholesterol,triglyceride,and C-reactive protein (CRP) levels were markedly increased(all P＜0.01).The RNA-seq analysis showed that there were 1 629 differentially expressed genes (1 109 up-regulated genes and 520 down-regulated genes) in T2DM + IS group vs control group.However,ischemic PC deceased the cortical infarction area (P＜0.01)and reduced blood glucose,lipid and CRP levels (P＜0.05),with 520 differential expression genes (203 up-regulated genes and 317 down-regulated genes).Conclusion Ischemic PC improves the metabolic disturbance-aggravated ischemic brain injury in T2DM tree shrews,which may be related to its regulation on gene expression in cerebral cortex.
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@#【Objective】 The two databases，GEO（gene expression omnibus，GEO）and TCGA（the cancer genome alas ，TCGA），were analyzed using bioinformatics methods to screen differentially expressed genes associated and their related regulatory networks in prostate carcinoma. 【Methods】 The prostate carcinoma gene expression chip data （GSE46602 ，GSE55945） downloaded from the GEO database were integrated into the RNA- seq data of the TCGA database. And the differentially expressed genes analysis was performed using GEO2R and the edgeR package of R software to extract common significant differentially expressed genes. The clusterProfiler package of R software was used to enrich the GO（gene ontology ，GO）function enrichment analysis and KEGG（kyoto encyclopedia of genes and genomes， KEGG）pathway analysis. Differentially expressed genes were further constructed into a protein-protein interaction（PPI） network to screen out key genes for regulatory protein expression in prostate carcinoma. Gene analysis results were combined with TCGA clinical follow-up data to analyze the clinical prognostic value of key node genes. 【Results】A total of 278 significant differentially expressed genes were extracted，of which 178 genes were down- regulated and 100 genes were up-regulated. These genes were closely associated with the function and pathway enrichment such as the regulation of proliferation of epithelial cells，metabolism of benzene- containing compounds，the glutathione metabolism，and focal adhesion. The protein-protein interaction network analysis revealed three key protein expression modules and 12 key node genes. Among these key genes，EDN3（endothelin-3），EDNRB（endothelin receptor B）and AMACR（alpha-methylacyl- coa racemase）were closely related to the survival rate of prostate cancer patients. 【Conclusion】Through bioinformatics analysis of gene chip and RNA-seq data in prostate carcinoma，we found that EDN3，EDNRB and AMACR may play an important role in the occurrence and development of prostate carcinoma.
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Para acortar la brecha entre lo molecular y la clínica, el personal de atención médica debe tener un conocimiento básico de los mecanismos moleculares que gobiernan la identidad celular, mediante la activación selectiva de genes. La expresión diferencial de genes permite a las células sintetizar las proteínas requeridas para cumplir con sus funciones biológicas, y ello posibilita a las células responder a estímulos internos y externos. Para esto se debe tener primero acceso a los genes que codifican las proteínas, determinando el fenotipo celular. Modificaciones en la estructura de la cromatina permiten a la maquinaria transcripcional tener acceso a secuencias de ADN. El ADN es transcripto en ARNm, que sufre diversas modificaciones antes de salir del núcleo para ser traducido en una proteína en el citoplasma. Cualquier desregulación en alguno de los procesos asociados se presenta como una patología. A inicios del siglo XXI se reportó la secuenciación del genoma humano, y sorprendentemente uno de los principales hallazgos fue que solo un 2% de la secuencia codifica para proteínas, lo cual dejó un interrogante sobre cómo funcionan y se regulan los procesos genéticos que llevan a la identidad celular. Desde entonces las investigaciones han permitido utilizar los principios que rigen estos procesos para ampliar el conocimiento de los mecanismos asociados a enfermedades. Gracias a estos avances, se ha buscado determinar aplicaciones clínicas dirigidas a los procesos involucrados en la expresión génica diferencial, lograr una mejor comprensión sobre los procesos patológicos de la enfermedad y desarrollar herramientas diagnósticas.
To narrow the gap between the bench and the clinic, healthcare personnel should have a basic understanding of molecular mechanisms ruling cell identity, since it establishes the key differences between health and disease states. Differential gene expression allows for protein synthesis required for the cell's biological function. In this process genes are selected from the entire genome to meet the cell's biological functioning and respond to internal and external stimuli. To this end, first the chromatin must be remodeled for the transcriptional machinery to gain access to DNA sequences coding for particular genes. DNA can then be transcribed into mRNA, followed by different processes leading to mature mRNA leaving the nucleus for protein synthesis in the cytoplasm. Any dysregulation in these processes results in disease. In the beginning of this millennium the human genome project sequenced the whole genome. Surprisingly, one of the main findings was only 2% of the genome represented protein coding sequences, which raised the question about the remainder of the genome and cell identity. Based on principles derived from the human genome project many investigations have shed light on mechanisms associated with disease. Thanks to advancements in differential gene expression, researchers are seeking for a better understanding in pathological processes associated with disease and the development of diagnostic tools.
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Humanos , Epigenômica , Acetilação , MetilaçãoRESUMO
Objective To analyze differences in gene expression profile of pituitary tissue in cervical spondylosis of vertebral artery type(CSA)model rats and explore the mechanism of adrenal gland's regulation of CSA.Methods Ten SPF male Wistar rats were randomly divided into model group and blank group.The CSA model was established by compound modeling method.The total RNA was extracted from the pituitary;the gene expression profile was detected by whole gene chip,ontology(GO),and signal pathway analysis.Results Compared with the normal group,the differential genes'expression profile analysis showed that the total number of the differential genes was 321(fold change︱ ＞ 2,P＜0.05),with 203 up-regulated genes and 118 down-regulated genes.A total of 1 294 genes rich in GO function were involved in the regulation of intercellular signal activity and nerve cell function;the stress response to external stimuli;and the regulation of coagulation function,angiogenesis, endometrial system,and cell cycle;There were 145 signal transducers,including adipocytokine signaling pathway, TGF-β signal transduction,AMPK signaling pathway,PPAR signal pathway,Wnt signaling pathway,and MAPK signal transduction pathway.Conclusion The pituitary regulates CSA mainly through the inflammatory stimulation,immune regulation,regulation of vertebral artery function,and endometrial system.
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Objective@#To investigate the functional classification of differentially expressed genes in manganese-poisoned rats and related metabolic pathways, and to provide a reference for the study of the mechanism of manganese poisoning and gene regulation in the prevention and treatment of manganese poisoning.@*Methods@#Six healthy specific pathogen-free male Sprague-Dawley rats were randomly divided into control group and experimental group according to body weight, with 3 rats in each group. Rats in the experimental group were injected intraperitoneally with MnCl2·4H2O (25 mg/kg) at 0.2 ml/100 g once every 48 h, and the control group was injected with phosphate-buffered saline at the same dose. After one month of exposure, the rats were anesthetized and then sacrificed by cardiac puncture blood collection. The striatum was isolated on ice, and RNA was extracted to establish a DNA data library. Whole genome sequencing was used to identify the differentially expressed genes in the rats with manganese poisoning. Gene Ontology functional enrichment analysis and pathway enrichment analysis were performed to investigate the possible metabolic pathways in which the differentially expressed genes may participate.@*Results@#A total of 18439 genes were detected in the striatum of rats, and 17 differentially expressed genes were screened out. Among them, 10 genes were up-regulated, and 7 genes were down-regulated. According to gene function analysis, 164 functional branches and 26 metabolic pathways with high gene enrichment were screened out. The genes were enriched in synaptic signaling, signal transduction, etc., especially behavioral function. The metabolic pathways with high gene enrichment were endocytosis pathway, PI3K-Akt pathway, and neuroactive ligand-receptor interaction pathway, in which the PI3K-Akt pathway had enrichment of the same differentially expressed gene (29 517) as the FoxO signaling pathway and mTOR signaling pathway, and the neuroactive ligand-receptor interaction pathway had enrichment of the same differentially expressed gene (24 415) as the glutamatergic synaptic pathway.@*Conclusion@#The differentially expressed genes in manganese-poisoned rats may influence the susceptibility to manganese poisoning through the PI3K-Akt pathway, mTOR metabolic pathway, or FoxO metabolic pathway, and may be involved in behavioral changes.
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Abstract Dikarya is a subkingdom of fungi that includes Ascomycota and Basidiomycota. The gene expression patterns of dikaryon are poorly understood. In this study, we bred a dikaryon DK13 × 3 by mating monokaryons MK13 and MK3, which were from the basidiospores of Pleurotus ostreatus TD300. Using RNA-Seq, we obtained the transcriptomes of the three strains. We found that the total transcript numbers in the transcriptomes of the three strains were all more than ten thousand, and the expression profile in DK13 × 3 was more similar to MK13 than MK3. However, the genes involved in macromolecule utilization, cellular material synthesis, stress-resistance and signal transduction were much more up-regulated in the dikaryon than its constituent monokaryons. All possible modes of differential gene expression, when compared to constituent monokaryons, including the presence/absence variation, and additivity/nonadditivity gene expression in the dikaryon may contribute to heterosis. By sequencing the urease gene poure sequences and mRNA sequences, we identified the monoallelic expression of the poure gene in the dikaryon, and its transcript was from the parental monokaryon MK13. Furthermore, we discovered RNA editing in the poure gene mRNA of the three strains. These results suggest that the gene expression patterns in dikaryons should be similar to that of diploids during vegetative growth.
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Pleurotus/genética , Perfilação da Expressão Gênica , Alelos , Genes FúngicosRESUMO
AIM:To study the protective effect of heat shock factor1(HSF1) on the mice with lipopolysaccha-ride (LPS)-induced acute lung injury(ALI),and to screen the relevant differentially-expressed genes. METHODS:ALI mouse model was established by LPS intracheal instillation. The macroscopic and pathological changes of the lung tissue were observed,and the concentrations of total protein,TNF-α, IL-β, IL-6 and VEGF in the bronchoalveolar lavage fluid (BALF) were analyzed. Differentially-expressed genes in the lung tissues of HSF1 +/ +mice and HSF1 -/- mice with ALI induced by LPS were screened by gene chips. The key gene was verified by real-time qPCR. RESULTS:The macroscopic and pathological changes of the lung injury in HSF1 -/- +LPS mice were more serious than those in HSF1 +/ ++LPS mice.The concentrations of total protein,VEGF,TNF-α,IL-1β and IL-6 in the BALF of HSF1 -/- +LPS mice were significantly higher than those of HSF1 +/ ++LPS mice(P<0.05). Compared with the HSF1 +/ +mice,a total of 918 differentially-ex-pressed genes were indentified in the HSF1 -/- mice, among which the expression levels of 65 genes had obvious diffe-rence,with 28 genes up-regulated,including Atg7,ccr1,cxcr2,Tbl1xr1,Mmp9,Pparg,Plcb2,Arrb2,Cntn1,Col4a6, etc, and 37 genes down-regulated,including Fgfr1,Fgfr2,Map4k4,Ddx58,Tfg,Stat3,Smad4,Lamc1,Sdc3,etc. The results of real-time qPCR showed that the mRNA level of CXCR2 in HSF1 -/- + LPS mice was significantly higher than that in HSF1 +/ ++ LPS mice,which was consistent with the results of gene chips. CONCLUSION:HSF1 has protective effect on the mice with LPS-induced ALI. CXCR2 may be involved in the protective effect of HSF1 on this process.
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Objective To investigate the expression of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in endometriosis (EMS) and its diagnostic value.Methods The information of EMS gene expression was collected from Gene-Cloud of Biotechnology Information (GCBI) and analyzed,in which MALAT1 gene was screened out accordingly.The total RNAs were extracted from tissues and serum samples of the patients with ovarian endometriosis and non-endometriosis and the expression of MALAT1 was detected by real-time quantitative PCR.The correlation between MALAT1 expression level and menstrual cycle was analyzed.The differential diagnostic efficacy of serum MALAT1 levels was analyzed by receiver operating characteristic (ROC) curve.Results Compared with the non-EMS group the expression of MAL4T1 gene was down-regulated by 1.35-fold (t =-3.27,P ＜ 0.01) in EMS group according to gene information analysis of GCBI.The relative expression levels of MALAT1 in ectopic and eutopic endometrium of patients with ovary endometriosis (0.41 ±0.18 and 0.61 ± 0.12) were significantly lower than those in non-endometriosis patients (1.05 ±-0.34,t =5.87 and 4.48,P ＜ 0.01).However,the expression level of MALAT1 was not related with menstrual cycle of the patients with ovarian endometriosis and non-endometriosis (t =1.54 and 1.52,P ＞ 0.05).The expression of MALAT1 in ectopic ovarian cysts was significantly lower than that in eutopic endometrium of ovary endometriosis (t =3.77,P ＜ 0.01).The relative expression of serum MALAT1 in ovary endometriosis (0.60 ±0.18) was significantly lower than that in non-endometriosis (1.05 ± 0.32,t =5.18,P ＜ 0.01).The area under the curve (AUCsOc) was 0.88.When the cut-off value of serum MALAT1 level was set as 0.74,the sensitivity and specificity of expression level of MALAT1 were 82.4％ and 92％ respectively,and Youden's index was 74.4％.Conclusion Low expression of MALAT1 in endometriosis may be related with occurrence and development of endometriosis.Serum MALAT1 level may have certain differential diagnostic value for EMS.
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To screen the differentially-expressed microRNAs (miRNAs) in mouse models with renal ischemia-reperfusion injury (IRI),aiming to offer foundation for unraveling the molecular mechanism of the incidence and progression of IRI.Methods The mouse models with acute IRI were established by renal artery clamping.Fifteen mice were divided into the IRI group and sham surgery group (E group).The animals in the IRI group were subdivided into the A group (45 min ischemia followed by 24 h reperfusion),B group (25 min ischemia followed by 24 h reperfusion),C group (45 min ischemia followed by 4 h reperfusion) and D group (25 min ischemia followed by 4 h reperfusion) (n=3 for each group).The severity ofIRI was evaluated by histological changes and renal function.The differentially-expressed miRNAs in the IRI mouse models at different ischemia time (25 and 45 min) and reperfusion time (4 and 24 h) were screened by using cluster analysis of miRNAs microarray data.The differential expression of miR-695 and miR-145 was validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR).Results Both histological changes and renal function confirmed that the IRI mouse models were successfully established.Compared with the sham surgery group,71 differentially-expressed miRNAs were detected in the IRI group including 30 down-regulated miRNAs and 40 up-regulated miRNAs.The results of qRT-PCR demonstrated that if the standardized expression level of miRNAs in the E group was 1,the relative expression levels of miR-695 and miR-145 were 11.82 and 0.31 in the IRI group (both P＜0.05),which were consistent with the chip results.Conclusions After renal IRI,different changes occur in the gene expression profile of miRNAs.These differentially-expressed miRNAs act as molecular biomarkers for renal IRI with potential clinical and scientific research values.
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Objective To analyze gene expression profiles of biopsy specimens from breast cancer patients who were treated with neoadjuvant chemotherapy(NAC) after biopsies, and to identify the genes which are closely associated with the efficacy of neoadjuvant chemotherapy with T/FAC [docetaxel(Taxotere), 5-fluorouracil, doxorubicin and cyclophosphamide] or T/FEC (Taxotere, 5-fluorouracil, epirubicin and cyclophosphamide) regimen.Methods We retrieved and collected gene expression profiles from publicly available databases.Four datasets, a total of 844 samples, were finally retained because all the patients had received a uniform neoadjuvant chemotherapy regimen.Response to neoadjuvant chemotherapy was categorized as a pathological complete response (pCR) or residual invasive cancer (RD).The differentially expressed genes (adjusted P-value<0.05) and therapeutic efficacy were analyzed and explored.Results After differential analysis, genes whose expressions were higher or lower in pCR group than in RD group were identified in each of the four datasets, respectively.There were 34 and 42 genes which were simultaneously more highly expressed or more lowly expressed in pCR group than in RD group in the four datasets.The unsupervised clustering, based on the 76 intersection genes, showed that the pCR specimens tended to form one cluster and the RD tended to form the other.Conclusion The seventy-six differentially expressed genes are associated with the efficacy of neoadjuvant chemotherapy and are likely to be novel predictive biomarkers for the efficacy of neoadjuvant chemotherapy.
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Objective To screen the tumor metastasis related differentially expressed genes in hepatocelluar carcinoma (HCC)cells 7402 after stable transfection with FATE/BJ‐HCC‐2 gene .Methods Total RNA was extracted from FATE/BJ–HCC‐2‐transfected HCC(5B4)cells and empty vector control (Mock)cells respectively .Differentially expressed genes were obtained using cDNA microarray .Results Compared with Mock cells ,a total of 1 694 differentially expressed genes were screened out in 5B4 cells ,the 11 gene expressions had obvious differences ,among which the expression amounts in 7 genes were significantly in‐creased ,including MMP‐1 ,PTGS2 ,FN ,CA9 ,IL‐8 ,ILK and Areg .The fold changes were 81 .80 ,49 .86 ,11 .30 ,16 .26 ,3 .48 ,2 .79 and 2 .20 ,respectively .The expression amounts in 4 genes were significantly decreased ,including E‐cadherin ,E‐cadherin , RHOBTB3 ,ALPP and HLA‐DRB4 .The fold changes were -5 .42 ,-2 .23 ,-5 .93 and -8 .03 ,respectively .Conclusion Adopting gene microarray technology can carefully screen the differentially expressed genes of FATE/BJ‐HCC‐2 involved HCC metastasis ,its final goal is to lay a solid theoretical foundation for studying the HCC metastasis mechanism .