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Objective To detect and analyze the susceptibility genes of methyl acetate poisoning in patients by whole exome sequencing. Methods Two patients with occupational acute severe methyl acetate poisoning and their first-degree relatives who work in the same occupation and position with similar working hours were selected as the research subjects by judgment sampling method. Peripheral blood was collected for whole exome sequencing. The sequencing data was compared with the public genome database to screen the mutation sites and find out the gene sites related to methyl acetate poisoning. The suspected pathogenic mutation genes were annotated and interpreted. Results The results of whole exome sequencing showed that there were 40 differential genes between the patients with methyl acetate poisoning and their first-degree relatives, including 80 single nucleotide polymorphisms and eight Indel with specific marker sequence index. Among these, the genes with strong correlation were carboxyesterase 1 (CES1) and mucin (MUC) 5B. The CES1 gene loci c.248C>T (p.Ser83Leu) heterozygous mutations, MUC5B gene loci c.6635C>T (p.Thr2212Met) and c.7685C>T (p.Thr2562Met) heterozygous mutations in patients with methyl acetate poisoning were detected. They were missense mutations. By constructing a protein-protein interaction network, a total of 11 pairs of interactions with high levels of evidence were identified, involving genes such as lysine methyltransferase 2C, HECT and RLD domains containing E3 ubiquitin protein ligase 2, neutrophil cytoplasmic factor 1, nicotinamide adenine dinucleotide phosphate oxidase 3, C-terminal binding protein 2, zinc finger protein 717, FSHD region gene 2 family member C, FSHD region gene 1, MUC4, MUC6, MUC5B, and MUC12. Conclusion The polymorphism of CES1 and MUC5B genes may be related to the occurrence and development of methyl acetate poisoning in patients.
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Objective:To screening differentially expressed genes (DEGs) in proliferative diabetic retinopathy (DR) patients to provide new biological therapeutic targets for proliferative DR (PDR) therapy.Methods:A basic research. A total of 3 PDR patients (group PDR) and 3 non-diabetic patients (control group) were enrolled in the study in Tianjin Medical University Eye Hospital in October 2020. In addition, 40 cases of PDR and non-diabetic patients were selected and divided into PDR validation group and control validation group. Peripheral blood validation test was performed in PDR validation group and control validation group; RNA sequencing was performed in PDR group and control group. Transcriptomics (RNAseq) sequencing technology was used to screen DEG in PDR group and control group. The selected DEGs were analyzed by gene ontology (GO) function enrichment analysis, signal pathway enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction network (PPI). The gene expression database was used to find the high-throughput data related to PDR, and multi queue comparison analysis was carried out. The target genes of differentially expressed miRNAs were predicted through targetscan platform, so as to clearly screen the correlation between DEG and PDR. Reverse transcription polymerase chain reaction and Western blot were used to verify the expression of DEG mRNA and protein related to PDR. The relative expression of PDR related DEG mRNA and protein between PDR validation group and control validation group were compared by paired t-test. Results:A total of 1 337 DEGs were screened by RNAseq sequencing in the peripheral blood of patients with PDR, of which 419 genes were up-regulated and 918 down-regulated. Among them, direct inhibitor of apoptosis protein-binding protein with low isoelectric point ( DIABLO), zinc finger and BTB domain containing 10 ( ZBTB10), polo-like kinases 3 ( PLK3), regulatory subunit 1 ( PIK3R1) and B cell translocation gene 3 (BTG3) were differentially expressed in PDR patients. The function of GO was enriched from the analysis of molecular function, biological process and cellular composition. The results showed that DIABLO, ZBTB10, PLK3, PIK3R1, BTG3 were involved in the pathological process related to PDR. KEGG enrichment analysis showed that glucose metabolic pathways such as extracellular matrix receptors, cytokine regulatory pathway, p53 signal pathway and galactose metabolism may be involved in the process of differential genes. The analysis of PPI protein interaction network showed that the larger the DEG-associated protein node, the greater the number of associated nodes. Among them, DIABLO, ZBTB10, PLK3, PIK3R1 and BTG3 played significant roles in the formation of the action network. By comparing and analyzing the existing high-throughput data related to diabetic retinopathy in Gene Expression Omnibus database and predicting by Targetscan platform, it was found that some significant differences in miRNA reported in aqueous humor, vitreous fluid and plasma of DR patients can be regulated by the differential genes found in this study. Compared with the control verification group, the relative expressions of DIABLO, ZBTB10, PLK3, PIK3R1 mRNA and protein in peripheral blood of the PDR verification group were up-regulated, and the relative expression of BTG3 mRNA and protein was down-regulated. Conclusion:DIABLO, ZBTB10, PLK3, PIK3R1 and BTG3 are DEGs in patients with PDR, and they can participate in the disease process by regulating the biological processes of cell proliferation, fibrosis and oxidative stress.
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ObjectiveTo investigate the metabolites and gene expression characteristics in fibrous roots of Dioscorea zingiberensis in response to low phosphorus stress. MethodThe severe stress group， the moderate stress group， and the normal group were set up to stimulate the low phosphorus stress experiment. The fibrous roots of D. zingiberensis were collected during initial stress. The metabolites and transcriptomic characteristics were analyzed by gas chromatography-mass spectrometry （GC-MS） derivatization and RNA-seq techniques. Through multivariate statistical analysis of metabolites treated by different methods，functional analysis of differentially expressed genes， and data mining， the metabolism markers produced in fibrous roots of D. zingiberensis under low phosphorus stress were screened out， and the metabolic pathway characteristics of different genes were analyzed. ResultA total of 116 GC-MS metabolites were detected from the fibrous roots of D. zingiberensis. The metabolic characteristics of fibrous roots of D. zingiberensis under different low phosphorus treatments were obviously different. Orthogonal partial least squares discriminant analysis（OPLS-DA） model was used to screen six differential metabolites represented by sugars and alcohols from metabolites of fibrous roots treated with different methods，and these components were presumedly metabolism markers of fibrous roots of D. zingiberensis in response to low phosphorus stress. The differential genes screened out from the severe stress group and the normal group were mainly enriched in peroxidase pathway，phosphate and hypophosphate metabolism pathway，while the differential genes screened out from the severe stress group and the moderate stress group were mainly enriched in glutathione metabolism pathway and phosphopentose pathway. A total of 177 differential genes in response to low phosphorus stress were screened out from fibrous roots， involving many pathways such as terpenoid skeleton and inositol biosynthesis，which was consistent with the fact that the metabolic differential components in fibrous roots in response to low phosphorus stress were mainly saccharides and inositol. ConclusionThe metabolites and gene expression in fibrous roots of D. zingiberensis responded to low phosphorus stress，and the differential metabolites were closely related to differentially expressed genes. This study is expected to provide a theoretical basis for the research on the molecular mechanism of D. zingiberensis in response to low phosphorus stress.
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OBJECTIVE: To explore the related signaling pathways, biomarkers and prognostic genes of malignant pleural mesothelioma(MPM) based on the gene chip and second-generation sequencing datasets in public database by bioinformatics-related method. METHODS: MPM microarray expression datasets GSE51024 and GSE2549, with 82 and 49 MPM patients, respectively, were downloaded from the Gene Expression Omnibus database. The RNA sequencing data of 86 MPM patients were downloaded from the The Cancer Genome Atlas(TCGA). The weighted gene co-expression network analysis(WGCNA) and differentially expressed genes(DEGs) screening were used to screen and identify hub genes in the GSE51024 dataset by RStudio 4.0 software. The gene set enrichment analysis(GSEA) was used to explore relevant signaling pathways. Finally, a total of 135 MPM gene expression data from GSE2549 dataset and TCGA database were used to verify the hub genes. RESULTS: The green key gene module identified by the WGCNA was highly correlated with MPM, with a correlation coefficient of 0.83(P<0.01). A total of 3 245 DEGs were screened by DEGs analysis. Among them, 1 229 genes were up-regulated and 2 016 genes were down-regulated. GSEA results showed that the genes were significantly enriched in the areas of G2/M cell cycle checkpoint, epithelial-mesenchymal transition, E2 F target gene, and mitotic spindle pathways. Three hub genes were screened, including the proliferating cell nuclear antigen-associated factor(PCLAF), nucleolar and spindle-associated protein 1(NUSAP1) and topoisomerase Ⅱ-α(TOP2 A). Compared with para-cancerous tissues, normal pleural tissues or lung tissues, the relative expression of PCLAF, NUSAP1 and TOP2 A were increased in the MPM tissues(all P<0.05). Downregulation of these three genes was correlated with good prognosis, and upregulation of these three genes was correlated with poor prognosis in the patients. CONCLUSION: G2/M checkpoint, epithelial-mesenchymal transition, E2 F target gene and mitotic spindle pathway are the key signaling pathways in the occurrence and development of MPM. PCLAF, TOP2 A and NUSAP1 genes could be the biomarkers for the prognosis of MPM.
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Growth arrest specific protein 6 (GAS6) plays an important role in the occurrence and development of tumors, and its signal transduction is involved in cell proliferation, adhesion and migration, but its related functions and molecular mechanisms in endometriosis (EMs) are still unclear. In this study, we searched and downloaded the transcriptome datasets of EMs from GEO database and performed GEO online analysis, and then screened out the differentially expressed genes and performed cluster analysis based on GO and KEGG pathway. The mRNA levels of the differentially expressed genes shared by more than three datasets were verified by qRT-PCR in the endometrium of ten women with no endometriosis and no clear disease and the ectopic endometrium of 11 patients with ovarian chocolate cysts. Immunohistochemistry and qRT-PCR were used to verify the expression of GAS6 and epithelial mesenchymal transition (EMT) marker genes, and immunofluorescence was used to co-label GAS6 and E-cadherin in endometriosis clinical samples. In this study, a total of 47 differentially expressed genes were screened out of the four transcriptome datasets, which were mainly enriched in processes such as cell migration and related signal pathways such as MAPK, PI3K-AKT, and tight junction. The mRNA levels of the nine differentially expressed genes shared by more than three datasets in endometriosis patients were consistent with the results of bioinformatics analysis. GAS6 expression levels in ectopic endometrium of EMs patients are higher than the control group (P < 0. 05), and EMs patients have the characteristics of EMT in the ectopic endometrial tissue, that is, the expression of E-cadherin is down-regulated (P < 0. 05) and the expression of vimentin is up-regulated (P < 0. 01). The expression of E-cadherin in the ectopic endometrial glandular epithelial cells of EMs patients is low while the expression of GAS6 is up-regulated, suggesting that GAS6 may mediate the EMT process in endometriosis. In conclusion, this study reveals that GAS6 is highly expressed in endometriosis patients and may mediate the EMT process to participate in the occurrence and development of endometriosis, providing a potential target for clinical treatment of endometriosis.
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@#【Objective】To explore the function and mechanism of differentially expressed Apolipoprotein H（APOH） gene in liver failure by bioinformatics. 【Methods】Multiple chip datasets（GSE14688，GSE38941 and GSE96851） were downloaded from the Gene Expression Omnibus （CEO）database. The differentially expressed genes were screened out based on P value < 0.05 and |log2FC| > 5. Biological function enrichment and KEGG pathway analysis of APOH gene， which was among the top ten key genes screened，was analyzed by Cytoscape and R，for further validation of expression of APOH in chronic hepatitis B virus-related liver failure.【Results】A total of 2 438 differentially expressed genes were screened，among which 1 162 were significantly up-regulated and 1 276 were significantly down-regulated. According to Protein-protein Interaction Network（PPIN）analysis，the top ten key genes were KNG1，IGF1，SPARC，APOH，CLU， SERPING1，TGFB2，CDC37L1，PCYOX1L and APOOL. High expression of APOH was found in chronic hepatitis B virus- related liver failure tissues and GeneMANIA predicted that APOH was associated with inflammation. GO analysis and KEGG analysis showed that APO，which was closely related to complement/coagulation cascade pathway and carbon metabolism pathway，positively correlated with C3（complement C3）.【Conclusion】APOH is involved in the occurrence and development of liver failure by C3 regulating complement/coagulation cascade pathway and carbon metabolism pathway.
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@#Objective To explore the mechanism of DDX46 regulation of esophageal squamous cell carcinoma. Methods Picture signals of fluorescence in gene array were scanned and differential expression of gene in two groups (a DDX46-shRNA-LV group and a control-LV group) were compared by GCOSvL.4 software. These differential expressed genes were analyzed by bioinformatics methods finally, and validated by quantitative real time polymerase chain reaction (qRT-PCR) analysis. Results According to the screening criteria of fold change ≥2 and P<0.05, 1 006 genes were differentially expressed after DDX46 knockdown, including 362 up-regulated and 644 down-regulated genes. Bioinformatics analysis and gene co-expression network building identified that these differentially expressed genes were mainly involved in cell cycle, proliferation, apoptosis, adhesion, energy metabolism, immune response, etc. Phosphatidylinositol 3-kinase (PI3K) was the key molecule in the network. The results of RT-qPCR were completely consistent with the results of gene microarra. Conclusion Bioinformatics can effectively exploit the microarray data of esophageal squamous cell carcinoma after DDX46 knockdown, which provides a valuable clue for further exploration of DDX46 tumorigenesis mechanism and helps to find potential drug therapy.
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BACKGROUND: Fat infiltration is a key factor in the failure of rotator cuff repair. However, the pathological mechanism of fatty infiltration after rotator cuff injury is unclear. OBJECTIVE: To explore the differences in the expression of key genes after rotator cuff injury, to determine their functions and mechanism pathways, and to provide a theoretical basis for the pathological mechanism of fatty infiltration after rotator cuff injury. METHODS: GSE93661 was obtained through GEO database to screen differentially expressed genes. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to analyze the underlying mechanism of fatty infiltration. The protein-protein interaction network was constructed to obtain the pivot genes and analyze the potential pathogenic targets. RESULTS AND CONCLUSION: A total of 471 differentially expressed genes were identified. GO and KEGG analysis showed that neuroactive ligand-receptor interactions and cell adhesion molecular pathways were potential mechanisms of fat infiltration in rotator cuff tears. Leukotriene B4 receptor, as a pivot gene in the protein-protein interaction network, may be a key target for fat infiltration in rotator cuff tears. We have discovered potential key genes and pathways in the pathological development of fatty infiltration, providing a reference direction for future treatment.
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We used exogenous GA_3 to break the seed dormancy of Thesium chinense. We used high-throughput sequencing technology was used to sequence the transcriptome of dormant seed embryos and dormancy breaking seed embryos of Th. chinense, and the data was analyzed bioinformatically and systematically. The results showed that exogenous GA_3 could effectively break the seed dormancy of Th. chinense; 73 794 up-regulated genes and 42 776 down regulated genes were obtained by transcriptome sequencing; 116 570 diffe-rential genes were annotated by GO function to GO items such as metabolism process, cell process, cell, cell component, binding and catalytic activity. A total of 133 metabolic pathways were found by Pathway analysis of 26 508 differentially expressed genes. In the process of dormancy release, DEGs were mainly enriched in translation, carbohydrate metabolism, folding, classification, degradation and amino acid metabolism. Based on the annotation results in KEGG database, 20 metabolic pathways related to dormancy release were found. Dormancy release of Th. chinense seeds is a complex biological process, including cell morphology construction, secondary metabolite synthesis, sugar metabolism and plant signal transduction, among which plant hormone signal transduction is one of the key factors to regulate dormancy release. The results of qRT-PCR showed that the sequencing results were consistent with the actual results.
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Gene Expression Profiling , Gene Expression Regulation, Plant , Plant Dormancy , Plant Growth Regulators , Santalaceae , Seeds , TranscriptomeABSTRACT
The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood.In this study,the jaundice model was established by bile duct ligation (BDL) in mice,and differential gene expression patterns were analyzed in the lower thoracic spinal cord involved in cholestatic pruritus after BDL operation using high-throughput RNA sequencing.At 21st day after BDL,the expression levels of ENSRNOG00000060523,ENSRNOG00000058405 and ENSRNOG00000055193 mRNA were significantly up-regulated,and those of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289,Gemin8,Serpina3n and Trim63 mRNA were significantly down-regulated in BDL group.The RNAseq data of selected mRNAs were validated by RT-qPCR.The expression levels of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289 and Serpina3n mRNA were significantly down-regulated in BDL group.This study suggested that cholestatic pruritus in experimental obstructive jaundice mouse model is related with in the changes of gene expression profiles in spinal cord.
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The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood.In this study,the jaundice model was established by bile duct ligation (BDL) in mice,and differential gene expression patterns were analyzed in the lower thoracic spinal cord involved in cholestatic pruritus after BDL operation using high-throughput RNA sequencing.At 21st day after BDL,the expression levels of ENSRNOG00000060523,ENSRNOG00000058405 and ENSRNOG00000055193 mRNA were significantly up-regulated,and those of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289,Gemin8,Serpina3n and Trim63 mRNA were significantly down-regulated in BDL group.The RNAseq data of selected mRNAs were validated by RT-qPCR.The expression levels of ENSRNOG00000042197,ENSRNOG00000008478,ENSRNOG00000019607,ENSRNOG00000020647,ENSRNOG00000046289 and Serpina3n mRNA were significantly down-regulated in BDL group.This study suggested that cholestatic pruritus in experimental obstructive jaundice mouse model is related with in the changes of gene expression profiles in spinal cord.
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Background and purpose: Gene chip is a nucleic acid sequence analysis method which is based on hybridization. It is a high-through put assay which can widely detect the level of gene expression in different tissues and cell types. This study aimed to compare and bioinformatically analyze differentially expressed genes between higher malignant degree of prostate cancer tissues and prostate inflammation tissues. Methods: The total RNAs were isolated from tissues of prostate cancer and prostate inflammation by TRIzol method and then purified, reversely tran-scribed to cDNA with incorporating biotin labeling probe, hybridized with Affymetrix Human U133 Plus 2.0 (covering 47000 transcripts,representing 38500 distinct genes). Picture signals of fluorescence in gene array were scanned and differential expression of gene in two tissues were compared by Command Console Software 4.0. These differential expressed genes were analyzed by bioinformatics methods finally. Results: According to the fold change ≥2, P<0.05, 1819 differential expression genes including 1025 up-regulated genes and 794 down-regulated genes were discovered. GO enrichment analysis displayed that these differentially expressed genes were mainly involved in cell cycle, cell metabolism, etc. KEGG pathway analysis found that these genes were mainly involved in some metabolism pathways including purine nucleotide metabolism. The interactions between the proteins encoded by these genes were analyzed by STING. Twenty key nodes genes including TPX2, ANLN, NUSAP1, MELK, DLGAP5, KIF11, TOP2A, RRM2 were dis-covered. Then this study revealed CEP55 and ANLN might be related to the occurrence and metastasis of prostate cancer by looking through literature. Conclusion: During the development of prostate cancer, the activation of genes related to cell cycle and cell migration, the abnormalities of genes related to metabolism and the inhibition of genes related to cell adhesion play critical roles in the development of prostate cancer. CEP55 and ANLN were related to the occurrence and prognosis of prostate cancer by systematic analysis which provided a valuable clue for the next experiment.
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Objective To observe the effects of PM2.5 exposure on A549 cells,and explore the mechanism of toxicity. Method The concentra?tions of PM2.5 exposure were determined utilizing cell viability assay. The morphological characteristics of exposed cell were observed with trans?mission electron microscope. Using big date from RNA?Seq and qRT?PCR,the mechanism was explored. Results The final concentration of PM2.5 exposure was 50μg/cm2;morphological detection showed that chromatin condensation after exposure which was also found on the boundary of nuclear membrane. KEGG pathway analysis and interaction network were finished ,and 8 kinds of apoptosis?related genes were found to be in?volved in the process of damage. Conclusion PM2.5 induces apoptosis in A549 cells by stimulating the changes of apoptosis?related genes ex?pressions.