BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alte...BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain unclear.CASE SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and V.Targeted gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder NEC.Twelve mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and pathways.The results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder carcinoma.CONCLUSION Gallbladder NEC requires standardized treatment.Comparisons with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.展开更多
Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate trau...Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.展开更多
At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software too...At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software tools were used to analyze and predict the gene family and this gene.There were 30 members of the cucumber F-box gene family.The coding region of the cucumber CsFK111 gene was full-length 1314 bp,which encoded 437 amino acids and was predicted to be located in the nucleus.The protein encoded by this gene was a non-transmembrane protein,and the prediction of the secondary structure showed thatβ-lamellar structure and irregular crimp were dominant.A comparison of the phylogenetic tree showed that it was closest to cantaloupe and belonged to the same branch.The results provided a basis for future study on the regulation mechanism of the CsFK111 gene on cucumber dwarfing and also laid a foundation for further study of FBK family proteins.展开更多
[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of m...[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of msrA,and its bioinformatics analysis was carried out.[Results]The full length of msrA gene was 639 bp,encoding 212 amino acids,and its theoretical molecular weight was about 23729.60 Da.The protein had a stable structure,and it was hydrophobic overall.The structure of signal peptides at the N terminal of the amino acid sequence was predicted,and it was found that there was no signal peptide cleavage site and no transmembrane region.The amino acid sequence of MsrA contained multiple signal binding sites.Protein subcellular localization showed that MsrA protein was most likely located in the cytoplasm.Homology analysis showed that MsrA of V.alginolyticus had high homology with other Vibrio species,and the highest homology with V.alginolyticus.In the prediction of functional domains,MsrA had the function of methionine sulfoxide reduction.In secondary structure prediction,MsrA contained random coils at a proportion of 46.70%,which was the highest.The similarity between the tertiary structure model of MsrA and template Q87SW6.1.A was 89.15%.PTM analysis showed that MsrA protein had many PTM modification sites such as phosphorylation and glycosylation sites.[Conclusions]This study provides some reference value for further study on the role of MsrA in bacterial antioxidant stress.展开更多
Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by PCR.The results indic...Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by PCR.The results indicated that the total length of the sodB gene was 585 bp and that it could encode 194 amino acids.The predicted amino acid sequence derivation indicated that the molecular weight of the protein was approximately 21.56 kDa,with an isoelectric point of 4.95.Upon prediction of the N-terminal signal peptide structure of the protein,no significant signal peptide cleavage site was observed,indicating that the protein lacked both a signal peptide and a transmembrane region.The amino acid sequence contained an N-glycosylation site,a casein kinase II phosphorylation site,a microsomal C-terminal target signal site,and a manganese and iron superoxide dismutase signal site.The probability of intracytoplasmic localization of the SodB protein was 56.5%,which was analyzed according to the subcellular localization of the protein.The amino acid sequence of the sodB gene of V.alginolyticus exhibited 98%-100%homology to other Vibrio species,clustering into the same subfamily with V.parahaem,indicating a relatively close relationship between them.In the prediction of protein structure,the proportions ofα-helix,random coil,β-sheet,and extended strand were 48.45%,30.41%,5.67%,and 15.46%,respectively.The similarity to template 1dt0.1.A reached 71.58%.A PTM site analysis revealed the presence of phosphorylation,glycosylation,ubiquitination,sumoylation,acetylation,and methylation modification sites,as well as the absence of lactylation modification sites.展开更多
[Objectives]This study was conducted to explore the biological functions of cyaA gene of Vibrio alginolyticus.[Methods]With DNA of V.alginolyticus HY 9901 as a template,primers were designed according to the sequence ...[Objectives]This study was conducted to explore the biological functions of cyaA gene of Vibrio alginolyticus.[Methods]With DNA of V.alginolyticus HY 9901 as a template,primers were designed according to the sequence of cyaA gene,and the cyaA gene was amplified by PCR.Bioinformatics analysis was performed.[Results]The cyaA gene of V.alginolyticus HY9901 was 2529 bp in size,and encoded 842 amino acids.The molecular structure of CyaA protein was C_(4358)H_(6745)N_(1171)O_(1286)S_(35).Its theoretical molecular weight was 97.24167 kDa and the theoretical pI value was 5.56.It had no signal peptide and transmembrane domain.CyaA protein had three N-terminal glycosylation sites,one cAMP and cGMP-dependent protein kinase phosphorylation site,nine protein kinase C phosphorylation sites,nine casein kinase II phosphorylation sites,one tyrosine kinase phosphorylation site,seven N-terminal myristoylation sites,one pentenyl binding site and ten microbody C-terminal localization signal sites.Subcellular localization prediction showed that CyaA protein was mainly located in the nucleus and cytoplasm.Through multi-sequence alignment and phylogenetic tree construction,it was concluded that V.alginolyticus had high CyaA homology with other Vibrio species.cyaA of V.alginolyticus was clustered with Vibrio fluminensis and Vibrio marinisedimini,and they were closely related.The secondary structure of CyaA protein consisted ofα-helixes(43.11%),random coils(38.00%)and extended strands(14.49%).In protein network interaction,it was found that the proteins adjacent to CyaA protein were Crp-2,CpdA,Crr,PtsG-2,ANP67209.1,Crp-1,PykF,Pyk,RelA and Ndk.[Conclusions]This study provides a new idea for formulating strategies for the prevention and control of vibriosis.展开更多
Objective To screen and analyze the differentially expressed genes of Ewing’s sarcoma (ES) and Tuberculosis (TB) by bioinformatics. Methods GEO gene chip public database in NCBI was used for data retrieval, and chip ...Objective To screen and analyze the differentially expressed genes of Ewing’s sarcoma (ES) and Tuberculosis (TB) by bioinformatics. Methods GEO gene chip public database in NCBI was used for data retrieval, and chip data GSE17674 and GSE57736 were selected as analysis objects. The R language limma toolkit was used to screen DEmRNAs, and the data were standardized, and the common differentially expressed genes were screened by Venn diagram. The GO function and KEGG pathway enrichment of common differentially expressed genes were analyzed by using the R cluster Profiler package. String database was selected for PPI analysis, and the results were imported into Cytoscape software to obtain PPI interaction map, core module and Hub gene. Import Hub gene into BioGPS database. Results: A total of 3 Hub genes were screened, namely CD3D, LCK, KLRB1;The genes were imported into BioGPS database to obtain the specific genes. Conclusion The selected differential genes and related signaling pathways are helpful to understand the molecular mechanism of ES and TB, and can provide the basis for early diagnosis of ES complicated with TB. It also provides new ideas for clinical treatment and diagnosis.展开更多
Purpose: This paper aims to explore the genetic correlation between osteosarcoma (OS) and Ewing’s sarcoma (EWS) by bioinformatics, and to find the common differentially expressed genes between the two in order to pro...Purpose: This paper aims to explore the genetic correlation between osteosarcoma (OS) and Ewing’s sarcoma (EWS) by bioinformatics, and to find the common differentially expressed genes between the two in order to provide reference for early clinical diagnosis. Method: The GEO gene chip public database in NCBI was used for data retrieval, and the chip data GSE17674 and GSE16088 were selected as the analysis objects. DEmRNAs were screened by R language limma kit, and the data were standardized. The common differentially expressed genes were screened by Venn diagram. The R language clusterProfiler package was used to perform GO function and KEGG pathway enrichment analysis on the common differentially expressed genes. The String database was used for PPI analysis, and the results were imported into Cytoscape software to obtain PPI interaction map, core module and Hub gene. Result: In this study, 1482 differentially expressed genes were screened from GSE17674 and 933 differentially expressed genes were screened from GSE16088. The Wayne diagram analyzed 335 common differentially expressed genes. GO/KEGG analysis suggested that the above common differentially expressed genes were mainly involved in cell cycle, ECM receptor interaction, sister chromatid separation, ossification, etc. Five core genes NCAPG, MAD2L1, CDK1, RRM2 and RFC4 were screened from the PPI network. The five genes were highly expressed in sarcoma. Conclusion: The five core common differentially expressed genes and related signaling pathways screened by bioinformatics analysis are helpful to understand the molecular mechanism of OS and ES pathogenesis, and are related to the prognosis of patients. They may become potential biomarkers for future research on OS comorbid ES, provide a basis for early diagnosis of OS combined with ES, and provide new ideas for clinical drug treatment research.展开更多
Purpose: Bioinformatics-based approach to screen and analyze differentially expressed genes associated with the biological characteristics of Ewing sarcoma. Means: The GSE17674 dataset was selected for analysis, obtai...Purpose: Bioinformatics-based approach to screen and analyze differentially expressed genes associated with the biological characteristics of Ewing sarcoma. Means: The GSE17674 dataset was selected for analysis, obtained by data retrieval based on the GEO public database. The R language limma toolkit was used to screen DEmRNAs. After the data were normalized, the Metascape online analysis software and the R language clusterProfiler package were used to analyze the GO function and KEGG pathway enrichment of DEmRNAs lines, respectively. The string database was selected for PPI analysis, and the results were imported into Cytoscape software to derive the core modules and predicted core genes. The genes selected above were analyzed for tissue localization specificity. Results: Through the analysis of GSE17674, differentially expressed genes were screened out, and GO and KEGG analyses were performed on the differentially expressed genes. The GO functional enrichment analysis was mainly enriched in the process of muscle system, muscle contraction, myocyte development, contractile fibers, myogenic fibers, myofibers, myofibrillar segments, actin binding, structural composition of muscle, and actin filament binding. KEGG pathway analysis showed that the core pathways associated with the development of ES were the core genes for myocardial contraction, congestive cardiomyopathy, and hypertrophic cardiomyopathy. Five Hub genes were obtained based on Cytoscape prediction. Tissue localization specificity analysis of Hub genes was performed, and a total of 2 Hub genes with tissue specificity were screened;MYH6 was specifically expressed in cardiac cells and MYL1 was specifically expressed in skeletal muscle cells. Conclusions: The differential genes screened will help to understand the molecular mechanisms underlying the highly invasive and metastasis-prone biological characteristics of ES, as well as provide new ideas for clinical drug-targeted treatment of ES.展开更多
Objective: To screen and analyze the differentially expressed genes between dilated cardiomyopathy (DCM) and chronic heart failure (CHF) based on bioinformatics methods. Methods: The Gene Expression Omnibus (GEO) data...Objective: To screen and analyze the differentially expressed genes between dilated cardiomyopathy (DCM) and chronic heart failure (CHF) based on bioinformatics methods. Methods: The Gene Expression Omnibus (GEO) database was used for data retrieval, and the chip data GSE3585 was downloaded, which was the original data of DCM and normal control group. At the same time, the chip data GSE76701 was downloaded, which was the original data of CHF and control group. Differentially expressed mRNAs (DEmRNAs) were screened by R language limma package, the data were standardized, and the common differentially expressed genes were screened. GO function and KEGG pathway enrichment analysis were performed on the common differentially expressed genes. String11.0 online tool was used for data analysis to obtain differentially expressed genes, and the results were imported into Cytoscape 3.9.1 software. The results were imported into Cytoscape 3.9.1 software, and the common expression gene module was obtained by MOCDE algorithm. Nine Hub genes were obtained by 10 algorithms such as MCC. Results: A total of 248 differentially expressed genes were screened. GO analysis showed that differentially expressed genes were mainly concentrated in 9 different physiological and pathological processes. KEGG analysis showed that the main signaling pathways involved in differentially expressed genes were 2, and 9 key differentially expressed genes were predicted: NPPB, NPPA, MYH6, FRZB, ASPN, SFRP4, RPS4Y1, DDX3Y. Conclusion: This study preliminarily explored the molecular mechanism of DCM and CHF, and obtained the common differentially expressed genes of the two diseases. Further experimental studies are needed to verify the correlation between gene expression and clinicopathological features. Provide new ideas for clinical drug treatment research.展开更多
Objective:Patients with colon adenocarcinoma(COAD)who undergo radiation therapy develop radiation enteritis(RE).The predictive value of RE in COAD is yet to be established.Berberine,an active compound derived from the...Objective:Patients with colon adenocarcinoma(COAD)who undergo radiation therapy develop radiation enteritis(RE).The predictive value of RE in COAD is yet to be established.Berberine,an active compound derived from the traditional Chinese medicinal plant,Coptis chinensis,has notable anti-inflammatory properties and offers protection to the intestinal mucosa.This study aimed to evaluate the possible therapeutic effect and mechanism of berberine as a treatment for COAD complicated with RE(COAD&RE).Methods:Relevant genetic features of diverse COAD&RE populations were analyzed using bioinformatics and the Cox proportional hazards regression model.The therapeutic targets of berberine were predicted using network pharmacology and molecular docking.In vivo and in vitro experiments were conducted to validate the core genes identified using molecular docking.Results:RE has a certain impact on the prognosis of COAD and berberine may play an important role in the treatment of COAD&RE.In addition,we identified five core therapeutic targets of berberine by network pharmacology and molecular docking:CCND1,MYC,AR,LEP,and CYP19A1.In vivo experiments showed that berberine increased short-term survival rate,body weight,and intestinal epithelial cell recovery in mice after radiation.In an in vitro study,berberine promoted the proliferation of human intestinal epithelial cells and enhanced the radiosensitivity of HT29 cells after radiation,and the relative mRNA expression levels of CCND1 and MYC closely correlated with these effects.Conclusions:This study predicted the potential therapeutic effects of berberine on COAD&RE and verified the relevant mechanisms,which may provide insights and suggestions for the clinical treatment of COAD&RE.展开更多
Liver hepatocellular cancer(LIHC)is positioned as the third cancer with the highest mortalities worldwide,and high mortalities are associated with late diagnosis and recurrence.This study advances bioinformatics analy...Liver hepatocellular cancer(LIHC)is positioned as the third cancer with the highest mortalities worldwide,and high mortalities are associated with late diagnosis and recurrence.This study advances bioinformatics analysis of FAM3A expression in LIHC to evaluate its potential as a prognostic,diagnostic and therapeutic biomarker.Bioinformatics tools such as UALCAN,GEPIA2,KM plotter,TIMER2 and cBioPortal are employed to conduct analysis.Initially,the expression analysis revealed up-regulation of FAM3A in LIHC based on various variables.Further,the study observed that FAM3A methylation regulates expression as variation in methylation level of FAM3A was assessed in LIHC.Moreover,this over-expression of FAM3A results in poor overall survival(OS)in LIHC patients.All of these proposed that FAM3A has a role in the progression and development of LIHC.While examined association of FAM3A expression and infiltration level of CD8+T cells in LIHC patients using TIMER2 revealed that FAM3A has a positive correlation with purity in LIHC that highlights the molecular landscape.Analysis of genetic alteration revealed minute role of FAM3A in LIHC still provides valuable insight.Overall,our findings reveal that FAM3A has potential as diagnostic,therapeutic and prognostic biomarkers in LIHC.展开更多
Objective To uncover the mechanisms underlying the development of colorectal cancer(CRC),we applied bioinformatic analyses to identify key genes and experimentally validated their possible roles in CRC onset and progr...Objective To uncover the mechanisms underlying the development of colorectal cancer(CRC),we applied bioinformatic analyses to identify key genes and experimentally validated their possible roles in CRC onset and progression.Methods We performed Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis on differentially expressed genes(DEGs),constructed a protein-protein interaction(PPI)network to find the top 10 hub genes,and analyzed their expression in colon adenocarcinoma(COAD)and rectum adenocarcinoma(READ).We also studied the correlation between these genes and immune cell infiltration and prognosis and validated the expression of SLC9A2 in CRC tissues and cell lines using qRT-PCR and Western blotting.Functional experiments were conducted in vitro to investigate the effects of SLC9A2 on tumor growth and metastasis.Results We found 130 DEGs,with 45 up-regulated and 85 down-regulated in CRC.GO analysis indicated that these DEGs were primarily enriched in functions related to the regulation of cellular pH,zymogen granules,and transmembrane transporter activity.KEGG pathway analysis revealed that the DEGs played pivotal roles in pancreatic secretion,rheumatoid arthritis,and the IL-17 signaling pathway.We identified 10 hub genes:CXCL1,SLC26A3,CXCL2,MMP7,MMP1,SLC9A2,SLC4A4,CLCA1,CLCA4,and ZG16.GO enrichment analysis showed that these hub genes were predominantly involved in the positive regulation of transcription.Gene expression analysis revealed that CXCL1,CXCL2,MMP1,and MMP7 were highly expressed in CRC,whereas CLCA1,CLCA4,SLC4A4,SLC9A2,SLC26A3,and ZG16 were expressed at lower levels.Survival analysis revealed that 5 key genes were significantly associated with the prognosis of CRC.Both mRNA and protein expression levels of SLC9A2 were markedly reduced in CRC tissues and cell lines.Importantly,SLC9A2 overexpression in SW480 cells led to a notable inhibition of cell proliferation,migration,and invasion.Western blotting analysis revealed that the expression levels of phosphorylated ERK(p-ERK)and phosphorylated JNK(p-JNK)proteins were significantly increased,whereas there were no significant changes in the expression levels of ERK and JNK following SLC9A2 overexpression.Correlation analysis indicated a potential link between SLC9A2 expression and the MAPK signaling pathway.Conclusion Our study suggests that SLC9A2 acts as a tumor suppressor through the MAPK pathway and could be a potential target for CRC diagnosis and therapy.展开更多
Objective Gastric cancer(GC)is a deadly cancer and a challenging public health problem globally.This study aimed to analyze potential genes associated with pathogenesis and prognosis of gastric cancer.Methods This wor...Objective Gastric cancer(GC)is a deadly cancer and a challenging public health problem globally.This study aimed to analyze potential genes associated with pathogenesis and prognosis of gastric cancer.Methods This work selected the overlapping differentially expressed genes(DEGs)in GC from four datasets,the GSE29272,GSE29998,GSE54129 and GSE118916 Gene Expression Omnibus databases.These DEGs were used to carry out comprehensive bioinformatic analysis to analyze the related functions and pathways enriched,the relative expression levels and immune infiltrates,the prognostic characteristics and the interaction network.Results In total,55 DEGs increased while 98 decreased in their expression levels.For those DEGs with increased expression,they were mostly concentrated on“focal adhesion”and“ECM-receptor interaction”,whereas DEGs with decreased expression were mostly associated with“gastric acid secretion”and“drug metabolism cytochrome P450”.MCODE and ClueGO results were then integrated to screen 10 hub genes,which were FN1,COL1A1,COL3A1,BGN,TIMP1,COL1A2,LUM,VCAN,COL5A2 and SPP1.Survival analysis revealed that higher expression of the ten hub genes significantly predicted lower overall survival of GC patients.TIMP1 was most significantly related to neutrophils,CD8+T cells,as well as dendritic cells,while LUM was most significantly related to macrophages.Conclusion Immunohistochemistry results and functional testing showed that the expression of COL5A2 was elevated in GC and that it might be a key gene in GC tumorigenesis.展开更多
Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a v...Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a vital role in the exploration of cancer-related genes. Therefore, the purpose of our study was to identify the progression associated candidate genes of TC by bioinformatics analysis. Five microarray datasets of TC samples were downloaded from the Gene Expression Onmibus （GEO） database and the data of 133 TC patients were screened from The Cancer Genome Atlas （TCGA） head and neck squamous cell carcinoma （HNSC） database. The integrated analysis of five microarray datasets and the RNA sequencing data of TC samples in TCGA-HNSC was performed to obtain 1023 overlapping differentially expressed genes （DEGs） in TC and adjacent normal tissue （ANT） samples. Next, Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis was conducted to enrich the significant pathways of the 1023 DEGs and PI3K- Akt signaling pathway （P=0.011） was selected to be the candidate pathway. A total of 23 DEGs with ｜log2 fold change （FC）｜ ≥1.0 in phosphatidylinositol 3-kinase-serine/threonine kinase （PI3K-Akt） signaling pathway were subjected to survival analysis of 125 eligible TC samples in TCGA database, indicating increased integrin-α3 gene （ITGA3） expression was significantly associated with poorer prognosis. Taken together, our study suggested ITGA3 may facilitate the development of TC via activating PI3K-Akt signaling pathway.展开更多
Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking a...Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking and gait. This disease can not be clearly identified through laboratory tests at present, thus application of high-throughput technique in studying the expression profiles of PD helps to find the genetic markers for its early diagnosis. Studies on expression profiles of neurodegenerative diseases have revealed the novel genes and pathways involved in the progress of illness. In this study, the expression profiles of PD in blood were compared, showing that 181 differentially expressed genes （DEG） exhibit a similar expression trend both in patients and in normal controls.展开更多
Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPor...Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPortal databases to analyze the expression and mutation of TOP2αand its co-expressed genes in HCC tissues.GO function and KEGG pathway enrichment of TOP2αand its co-expressed genes were identified.The TIMER database was used to analyze infiltration levels of immune cells in HCC.The impacts of TOP2αand its co-expression genes and the infiltrated immune cells on the survival of HCC patients were assayed by Kaplan-Meier plotter analysis.Results TOP2αand its co-expression genes were highly expressed in HCC(P<0.001)and detrimental to overall survival of HCC patients(P<0.001).TOP2αand its co-expression genes were mainly involved in cell mitosis and proliferation,and cell cycle pathway(ID:hsa04110,P=0.001945).TOP2αand its co-expression genes were mutated in HCC and the mutations were significantly detrimental to overall survival(P=0.0247)and disease-free survival(P=0.0265)of HCC patients.High TOP2αexpression was positively correlated with the infiltration of B cell(r=0.459,P<0.01),CD8^(+)T cell(r=0.312,P<0.01),CD4^(+)T cell(r=0.370,P<0.01),macrophage(r=0.459,P<0.01),neutrophil(r=0.405,P<0.01),and dendritic cell(r=0.473,P<0.01)in HCC.The CD8^(+)T cell infiltration significantly prolonged the 3-and 5-year survival of HCC patients(all P<0.05),and CD4^(+)T cell infiltration significantly shortened the 3-,5-,and 10-year survival of HCC patients(all P<0.05).Conclusion TOP2αmay be an oncogene,which was associated with poor prognosis of HCC patients and could be used as a biomarker for the prognostic prediction of HCC.展开更多
The expression of angiopoietin(ANGPT)1,ANGPT2,vascular endothelial growth factor(VEGF)A,VEGFB,VEGFC,VEGFD,and placental growth factor(PGF)is significantly higher in tumor tissues than in normal tissues in both unpaire...The expression of angiopoietin(ANGPT)1,ANGPT2,vascular endothelial growth factor(VEGF)A,VEGFB,VEGFC,VEGFD,and placental growth factor(PGF)is significantly higher in tumor tissues than in normal tissues in both unpaired and paired hepatocellular carcinoma(HCC)samples.ANGPT2,VEGFB,VEGFC,and PGF are primarily involved in regulating the activation of the epithelialmesenchymal transition pathway;ANGPT1 is primarily involved in regulating the activation of the RAS/mitogen-activated protein kinase and receptor tyrosine kinase(RTK)pathways;VEGFA is engaged in regulating the RTK activation pathway;and VEGFD is mainly involved in regulating the activation of the tuberous sclerosis protein/mammalian target of rapamycin pathway.There is a significant difference in overall survival between HCC patients with high and low expression of ANGPT2,PGF,VEGFA,and VEGFD.Disease free survival(DFS)is significantly shorter in HCC patients with high ANGPT2,PGF,and VEGFA expression than in those with low ANGPT2,PGF,and VEGFA expression.展开更多
[Objectives]The purpose was to investigate the function and mechanism of exsA gene in type III secretion system of Vibrio alginolyticus.[Methods]The full length of exsA was cloned using molecular biology techniques to...[Objectives]The purpose was to investigate the function and mechanism of exsA gene in type III secretion system of Vibrio alginolyticus.[Methods]The full length of exsA was cloned using molecular biology techniques to analyze its biological information.Fluorescence quantitative PCR technology was used to analyze the expression of exsA after different media stress.[Results]The exsA gene contains an open reading frame(ORF)of 861 bp,encoding 286 amino acids.The physico-chemical analysis shows that the molecular structural formula is C1442H2267N393O441S12,the theoretical molecular weight is 32.549 kD,the theoretical pI value is 6.0,and the protein is non-hydrophilic and unstable.The gene does not contain a transmembrane region,and there is no obvious signal peptide.The prediction result of protein subcellular localization shows that the protein is inside the cell.The deduced amino acid sequence and constructed phylogenetic tree show that V.alginolyticus has a close relationship with Vibrio antiquarius.The qPCR results show that the expression level of exsA in different media is different,highest in TSB medium containing bile salts,followed by DMEM medium,and lowest in ordinary TSB medium.[Conclusions]The gene sequence,molecular structure and isoelectric point of exsA,as well as its expression in three different media were obtained.展开更多
Mast cells are the main effector cells in IgE-associated allergic disorders,and we have reported that mucosal mast cells(MMCs)play a more important role in the development of food allergy(FA).IgE with antigen or calci...Mast cells are the main effector cells in IgE-associated allergic disorders,and we have reported that mucosal mast cells(MMCs)play a more important role in the development of food allergy(FA).IgE with antigen or calcium ionophore stimulation can lead to the activation of MMCs via a calcium-dependent pathway.The purpose of the present study was to identify gene signatures with IgE/antigen(dinitrophenyl-bovine serum albumin,DNP-BSA)or calcium ionophore(A23187)on the activation of MMCs.Differentially expressed genes between the two types of samples were identified with microarray analysis.Gene ontology functional and pathway enrichment analyses of differentially expressed genes were performed using the database for annotation,visualization,and integrated discovery software.The results showed that IgE/antigen and A23187 could induce degranulation,increase vacuoles,and elevate the cytosolic calcium concentration in MMCs.Furthermore,GeneChip analysis showed that the same 134 mRNAs were altered with IgE/DNP-BSA and A23187,suggesting that DNP-BSA/IgE and A23187 affect the same signal pathway partly in degranulation.KEGG analysis showed that the data were enriched in NF-κB,TNF,MAPK,transcription factor activity,DNA binding,and nucleic acid binding,suggesting that activation of MMCs is a complex process.The results provide new insights on MMCs activation.展开更多
基金Supported by School-Level Key Projects at Bengbu Medical College,No.2021byzd109.
文摘BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain unclear.CASE SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and V.Targeted gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder NEC.Twelve mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and pathways.The results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder carcinoma.CONCLUSION Gallbladder NEC requires standardized treatment.Comparisons with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.
基金supported by the National Natural Science Foundation of China,No.81771355the Natural Science Foundation of Chongqing Science and Technology Bureau,Nos.CSTC2015jcyjA10096,cstc2021jcyj-msxmX0262(all to ZL)。
文摘Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.
基金Supported by the National Natural Science Foundation of China(32272724)the National Science Foundation of Heilongjiang Province,China(LH2019C033)。
文摘At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software tools were used to analyze and predict the gene family and this gene.There were 30 members of the cucumber F-box gene family.The coding region of the cucumber CsFK111 gene was full-length 1314 bp,which encoded 437 amino acids and was predicted to be located in the nucleus.The protein encoded by this gene was a non-transmembrane protein,and the prediction of the secondary structure showed thatβ-lamellar structure and irregular crimp were dominant.A comparison of the phylogenetic tree showed that it was closest to cantaloupe and belonged to the same branch.The results provided a basis for future study on the regulation mechanism of the CsFK111 gene on cucumber dwarfing and also laid a foundation for further study of FBK family proteins.
基金Supported National Natural Science Foundation of China(32073015)Undergraduate Training Program for Innovation and Entrepreneurship of Guangdong Ocean University(CXXL2024007)+2 种基金Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802)Postgraduate Education Innovation Program of Guangdong Ocean University(No.202446)Postgraduate Education Innovation Program of Guangdong Province(YJYH[2022]1).
文摘[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of msrA,and its bioinformatics analysis was carried out.[Results]The full length of msrA gene was 639 bp,encoding 212 amino acids,and its theoretical molecular weight was about 23729.60 Da.The protein had a stable structure,and it was hydrophobic overall.The structure of signal peptides at the N terminal of the amino acid sequence was predicted,and it was found that there was no signal peptide cleavage site and no transmembrane region.The amino acid sequence of MsrA contained multiple signal binding sites.Protein subcellular localization showed that MsrA protein was most likely located in the cytoplasm.Homology analysis showed that MsrA of V.alginolyticus had high homology with other Vibrio species,and the highest homology with V.alginolyticus.In the prediction of functional domains,MsrA had the function of methionine sulfoxide reduction.In secondary structure prediction,MsrA contained random coils at a proportion of 46.70%,which was the highest.The similarity between the tertiary structure model of MsrA and template Q87SW6.1.A was 89.15%.PTM analysis showed that MsrA protein had many PTM modification sites such as phosphorylation and glycosylation sites.[Conclusions]This study provides some reference value for further study on the role of MsrA in bacterial antioxidant stress.
基金Supported by Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean UniversityNational Natural Science Foundation of China(32073015)+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by PCR.The results indicated that the total length of the sodB gene was 585 bp and that it could encode 194 amino acids.The predicted amino acid sequence derivation indicated that the molecular weight of the protein was approximately 21.56 kDa,with an isoelectric point of 4.95.Upon prediction of the N-terminal signal peptide structure of the protein,no significant signal peptide cleavage site was observed,indicating that the protein lacked both a signal peptide and a transmembrane region.The amino acid sequence contained an N-glycosylation site,a casein kinase II phosphorylation site,a microsomal C-terminal target signal site,and a manganese and iron superoxide dismutase signal site.The probability of intracytoplasmic localization of the SodB protein was 56.5%,which was analyzed according to the subcellular localization of the protein.The amino acid sequence of the sodB gene of V.alginolyticus exhibited 98%-100%homology to other Vibrio species,clustering into the same subfamily with V.parahaem,indicating a relatively close relationship between them.In the prediction of protein structure,the proportions ofα-helix,random coil,β-sheet,and extended strand were 48.45%,30.41%,5.67%,and 15.46%,respectively.The similarity to template 1dt0.1.A reached 71.58%.A PTM site analysis revealed the presence of phosphorylation,glycosylation,ubiquitination,sumoylation,acetylation,and methylation modification sites,as well as the absence of lactylation modification sites.
基金Supported by National Natural Science Foundation of China(32073015)Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)+2 种基金Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802)Postgraduate Education Innovation Program of Guangdong Ocean University(202433)Postgraduate Education Innovation Program of Guangdong Province(YJYH[2022]1).
文摘[Objectives]This study was conducted to explore the biological functions of cyaA gene of Vibrio alginolyticus.[Methods]With DNA of V.alginolyticus HY 9901 as a template,primers were designed according to the sequence of cyaA gene,and the cyaA gene was amplified by PCR.Bioinformatics analysis was performed.[Results]The cyaA gene of V.alginolyticus HY9901 was 2529 bp in size,and encoded 842 amino acids.The molecular structure of CyaA protein was C_(4358)H_(6745)N_(1171)O_(1286)S_(35).Its theoretical molecular weight was 97.24167 kDa and the theoretical pI value was 5.56.It had no signal peptide and transmembrane domain.CyaA protein had three N-terminal glycosylation sites,one cAMP and cGMP-dependent protein kinase phosphorylation site,nine protein kinase C phosphorylation sites,nine casein kinase II phosphorylation sites,one tyrosine kinase phosphorylation site,seven N-terminal myristoylation sites,one pentenyl binding site and ten microbody C-terminal localization signal sites.Subcellular localization prediction showed that CyaA protein was mainly located in the nucleus and cytoplasm.Through multi-sequence alignment and phylogenetic tree construction,it was concluded that V.alginolyticus had high CyaA homology with other Vibrio species.cyaA of V.alginolyticus was clustered with Vibrio fluminensis and Vibrio marinisedimini,and they were closely related.The secondary structure of CyaA protein consisted ofα-helixes(43.11%),random coils(38.00%)and extended strands(14.49%).In protein network interaction,it was found that the proteins adjacent to CyaA protein were Crp-2,CpdA,Crr,PtsG-2,ANP67209.1,Crp-1,PykF,Pyk,RelA and Ndk.[Conclusions]This study provides a new idea for formulating strategies for the prevention and control of vibriosis.
文摘Objective To screen and analyze the differentially expressed genes of Ewing’s sarcoma (ES) and Tuberculosis (TB) by bioinformatics. Methods GEO gene chip public database in NCBI was used for data retrieval, and chip data GSE17674 and GSE57736 were selected as analysis objects. The R language limma toolkit was used to screen DEmRNAs, and the data were standardized, and the common differentially expressed genes were screened by Venn diagram. The GO function and KEGG pathway enrichment of common differentially expressed genes were analyzed by using the R cluster Profiler package. String database was selected for PPI analysis, and the results were imported into Cytoscape software to obtain PPI interaction map, core module and Hub gene. Import Hub gene into BioGPS database. Results: A total of 3 Hub genes were screened, namely CD3D, LCK, KLRB1;The genes were imported into BioGPS database to obtain the specific genes. Conclusion The selected differential genes and related signaling pathways are helpful to understand the molecular mechanism of ES and TB, and can provide the basis for early diagnosis of ES complicated with TB. It also provides new ideas for clinical treatment and diagnosis.
文摘Purpose: This paper aims to explore the genetic correlation between osteosarcoma (OS) and Ewing’s sarcoma (EWS) by bioinformatics, and to find the common differentially expressed genes between the two in order to provide reference for early clinical diagnosis. Method: The GEO gene chip public database in NCBI was used for data retrieval, and the chip data GSE17674 and GSE16088 were selected as the analysis objects. DEmRNAs were screened by R language limma kit, and the data were standardized. The common differentially expressed genes were screened by Venn diagram. The R language clusterProfiler package was used to perform GO function and KEGG pathway enrichment analysis on the common differentially expressed genes. The String database was used for PPI analysis, and the results were imported into Cytoscape software to obtain PPI interaction map, core module and Hub gene. Result: In this study, 1482 differentially expressed genes were screened from GSE17674 and 933 differentially expressed genes were screened from GSE16088. The Wayne diagram analyzed 335 common differentially expressed genes. GO/KEGG analysis suggested that the above common differentially expressed genes were mainly involved in cell cycle, ECM receptor interaction, sister chromatid separation, ossification, etc. Five core genes NCAPG, MAD2L1, CDK1, RRM2 and RFC4 were screened from the PPI network. The five genes were highly expressed in sarcoma. Conclusion: The five core common differentially expressed genes and related signaling pathways screened by bioinformatics analysis are helpful to understand the molecular mechanism of OS and ES pathogenesis, and are related to the prognosis of patients. They may become potential biomarkers for future research on OS comorbid ES, provide a basis for early diagnosis of OS combined with ES, and provide new ideas for clinical drug treatment research.
文摘Purpose: Bioinformatics-based approach to screen and analyze differentially expressed genes associated with the biological characteristics of Ewing sarcoma. Means: The GSE17674 dataset was selected for analysis, obtained by data retrieval based on the GEO public database. The R language limma toolkit was used to screen DEmRNAs. After the data were normalized, the Metascape online analysis software and the R language clusterProfiler package were used to analyze the GO function and KEGG pathway enrichment of DEmRNAs lines, respectively. The string database was selected for PPI analysis, and the results were imported into Cytoscape software to derive the core modules and predicted core genes. The genes selected above were analyzed for tissue localization specificity. Results: Through the analysis of GSE17674, differentially expressed genes were screened out, and GO and KEGG analyses were performed on the differentially expressed genes. The GO functional enrichment analysis was mainly enriched in the process of muscle system, muscle contraction, myocyte development, contractile fibers, myogenic fibers, myofibers, myofibrillar segments, actin binding, structural composition of muscle, and actin filament binding. KEGG pathway analysis showed that the core pathways associated with the development of ES were the core genes for myocardial contraction, congestive cardiomyopathy, and hypertrophic cardiomyopathy. Five Hub genes were obtained based on Cytoscape prediction. Tissue localization specificity analysis of Hub genes was performed, and a total of 2 Hub genes with tissue specificity were screened;MYH6 was specifically expressed in cardiac cells and MYL1 was specifically expressed in skeletal muscle cells. Conclusions: The differential genes screened will help to understand the molecular mechanisms underlying the highly invasive and metastasis-prone biological characteristics of ES, as well as provide new ideas for clinical drug-targeted treatment of ES.
文摘Objective: To screen and analyze the differentially expressed genes between dilated cardiomyopathy (DCM) and chronic heart failure (CHF) based on bioinformatics methods. Methods: The Gene Expression Omnibus (GEO) database was used for data retrieval, and the chip data GSE3585 was downloaded, which was the original data of DCM and normal control group. At the same time, the chip data GSE76701 was downloaded, which was the original data of CHF and control group. Differentially expressed mRNAs (DEmRNAs) were screened by R language limma package, the data were standardized, and the common differentially expressed genes were screened. GO function and KEGG pathway enrichment analysis were performed on the common differentially expressed genes. String11.0 online tool was used for data analysis to obtain differentially expressed genes, and the results were imported into Cytoscape 3.9.1 software. The results were imported into Cytoscape 3.9.1 software, and the common expression gene module was obtained by MOCDE algorithm. Nine Hub genes were obtained by 10 algorithms such as MCC. Results: A total of 248 differentially expressed genes were screened. GO analysis showed that differentially expressed genes were mainly concentrated in 9 different physiological and pathological processes. KEGG analysis showed that the main signaling pathways involved in differentially expressed genes were 2, and 9 key differentially expressed genes were predicted: NPPB, NPPA, MYH6, FRZB, ASPN, SFRP4, RPS4Y1, DDX3Y. Conclusion: This study preliminarily explored the molecular mechanism of DCM and CHF, and obtained the common differentially expressed genes of the two diseases. Further experimental studies are needed to verify the correlation between gene expression and clinicopathological features. Provide new ideas for clinical drug treatment research.
文摘Objective:Patients with colon adenocarcinoma(COAD)who undergo radiation therapy develop radiation enteritis(RE).The predictive value of RE in COAD is yet to be established.Berberine,an active compound derived from the traditional Chinese medicinal plant,Coptis chinensis,has notable anti-inflammatory properties and offers protection to the intestinal mucosa.This study aimed to evaluate the possible therapeutic effect and mechanism of berberine as a treatment for COAD complicated with RE(COAD&RE).Methods:Relevant genetic features of diverse COAD&RE populations were analyzed using bioinformatics and the Cox proportional hazards regression model.The therapeutic targets of berberine were predicted using network pharmacology and molecular docking.In vivo and in vitro experiments were conducted to validate the core genes identified using molecular docking.Results:RE has a certain impact on the prognosis of COAD and berberine may play an important role in the treatment of COAD&RE.In addition,we identified five core therapeutic targets of berberine by network pharmacology and molecular docking:CCND1,MYC,AR,LEP,and CYP19A1.In vivo experiments showed that berberine increased short-term survival rate,body weight,and intestinal epithelial cell recovery in mice after radiation.In an in vitro study,berberine promoted the proliferation of human intestinal epithelial cells and enhanced the radiosensitivity of HT29 cells after radiation,and the relative mRNA expression levels of CCND1 and MYC closely correlated with these effects.Conclusions:This study predicted the potential therapeutic effects of berberine on COAD&RE and verified the relevant mechanisms,which may provide insights and suggestions for the clinical treatment of COAD&RE.
文摘Liver hepatocellular cancer(LIHC)is positioned as the third cancer with the highest mortalities worldwide,and high mortalities are associated with late diagnosis and recurrence.This study advances bioinformatics analysis of FAM3A expression in LIHC to evaluate its potential as a prognostic,diagnostic and therapeutic biomarker.Bioinformatics tools such as UALCAN,GEPIA2,KM plotter,TIMER2 and cBioPortal are employed to conduct analysis.Initially,the expression analysis revealed up-regulation of FAM3A in LIHC based on various variables.Further,the study observed that FAM3A methylation regulates expression as variation in methylation level of FAM3A was assessed in LIHC.Moreover,this over-expression of FAM3A results in poor overall survival(OS)in LIHC patients.All of these proposed that FAM3A has a role in the progression and development of LIHC.While examined association of FAM3A expression and infiltration level of CD8+T cells in LIHC patients using TIMER2 revealed that FAM3A has a positive correlation with purity in LIHC that highlights the molecular landscape.Analysis of genetic alteration revealed minute role of FAM3A in LIHC still provides valuable insight.Overall,our findings reveal that FAM3A has potential as diagnostic,therapeutic and prognostic biomarkers in LIHC.
基金supported by grants from the National Natural Science Foundation of China(No.82070302 and No.81902018)Clinical Medical Research Center of Peritoneal Cancer of Wuhan(No.2015060911020462)+4 种基金Clinical Research Projects of Wu Jie Ping Medical Foundation(No.320.6750.2023-11-9 and No.320.6750.2023-11-23)Medical Research Project of Wuhan Municipal Health Commission(No.WX19Y23)Bethune Charitable Foundation(No.BCF-LX-XH-20221014-23)Science and Technology Innovation Cultivation Fund of Zhongnan Hospital of Wuhan University(No.CXPY2022055)Medical Science and Technology Innovation Platform Support Project of Zhongnan Hospital of Wuhan University(No.PTXM2023004 and No.PTXM2023020).
文摘Objective To uncover the mechanisms underlying the development of colorectal cancer(CRC),we applied bioinformatic analyses to identify key genes and experimentally validated their possible roles in CRC onset and progression.Methods We performed Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis on differentially expressed genes(DEGs),constructed a protein-protein interaction(PPI)network to find the top 10 hub genes,and analyzed their expression in colon adenocarcinoma(COAD)and rectum adenocarcinoma(READ).We also studied the correlation between these genes and immune cell infiltration and prognosis and validated the expression of SLC9A2 in CRC tissues and cell lines using qRT-PCR and Western blotting.Functional experiments were conducted in vitro to investigate the effects of SLC9A2 on tumor growth and metastasis.Results We found 130 DEGs,with 45 up-regulated and 85 down-regulated in CRC.GO analysis indicated that these DEGs were primarily enriched in functions related to the regulation of cellular pH,zymogen granules,and transmembrane transporter activity.KEGG pathway analysis revealed that the DEGs played pivotal roles in pancreatic secretion,rheumatoid arthritis,and the IL-17 signaling pathway.We identified 10 hub genes:CXCL1,SLC26A3,CXCL2,MMP7,MMP1,SLC9A2,SLC4A4,CLCA1,CLCA4,and ZG16.GO enrichment analysis showed that these hub genes were predominantly involved in the positive regulation of transcription.Gene expression analysis revealed that CXCL1,CXCL2,MMP1,and MMP7 were highly expressed in CRC,whereas CLCA1,CLCA4,SLC4A4,SLC9A2,SLC26A3,and ZG16 were expressed at lower levels.Survival analysis revealed that 5 key genes were significantly associated with the prognosis of CRC.Both mRNA and protein expression levels of SLC9A2 were markedly reduced in CRC tissues and cell lines.Importantly,SLC9A2 overexpression in SW480 cells led to a notable inhibition of cell proliferation,migration,and invasion.Western blotting analysis revealed that the expression levels of phosphorylated ERK(p-ERK)and phosphorylated JNK(p-JNK)proteins were significantly increased,whereas there were no significant changes in the expression levels of ERK and JNK following SLC9A2 overexpression.Correlation analysis indicated a potential link between SLC9A2 expression and the MAPK signaling pathway.Conclusion Our study suggests that SLC9A2 acts as a tumor suppressor through the MAPK pathway and could be a potential target for CRC diagnosis and therapy.
基金The authors declare that there is no conflict of interest with any financial organization or corporation or individual that can inappropriately influence this work.
文摘Objective Gastric cancer(GC)is a deadly cancer and a challenging public health problem globally.This study aimed to analyze potential genes associated with pathogenesis and prognosis of gastric cancer.Methods This work selected the overlapping differentially expressed genes(DEGs)in GC from four datasets,the GSE29272,GSE29998,GSE54129 and GSE118916 Gene Expression Omnibus databases.These DEGs were used to carry out comprehensive bioinformatic analysis to analyze the related functions and pathways enriched,the relative expression levels and immune infiltrates,the prognostic characteristics and the interaction network.Results In total,55 DEGs increased while 98 decreased in their expression levels.For those DEGs with increased expression,they were mostly concentrated on“focal adhesion”and“ECM-receptor interaction”,whereas DEGs with decreased expression were mostly associated with“gastric acid secretion”and“drug metabolism cytochrome P450”.MCODE and ClueGO results were then integrated to screen 10 hub genes,which were FN1,COL1A1,COL3A1,BGN,TIMP1,COL1A2,LUM,VCAN,COL5A2 and SPP1.Survival analysis revealed that higher expression of the ten hub genes significantly predicted lower overall survival of GC patients.TIMP1 was most significantly related to neutrophils,CD8+T cells,as well as dendritic cells,while LUM was most significantly related to macrophages.Conclusion Immunohistochemistry results and functional testing showed that the expression of COL5A2 was elevated in GC and that it might be a key gene in GC tumorigenesis.
文摘Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a vital role in the exploration of cancer-related genes. Therefore, the purpose of our study was to identify the progression associated candidate genes of TC by bioinformatics analysis. Five microarray datasets of TC samples were downloaded from the Gene Expression Onmibus （GEO） database and the data of 133 TC patients were screened from The Cancer Genome Atlas （TCGA） head and neck squamous cell carcinoma （HNSC） database. The integrated analysis of five microarray datasets and the RNA sequencing data of TC samples in TCGA-HNSC was performed to obtain 1023 overlapping differentially expressed genes （DEGs） in TC and adjacent normal tissue （ANT） samples. Next, Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis was conducted to enrich the significant pathways of the 1023 DEGs and PI3K- Akt signaling pathway （P=0.011） was selected to be the candidate pathway. A total of 23 DEGs with ｜log2 fold change （FC）｜ ≥1.0 in phosphatidylinositol 3-kinase-serine/threonine kinase （PI3K-Akt） signaling pathway were subjected to survival analysis of 125 eligible TC samples in TCGA database, indicating increased integrin-α3 gene （ITGA3） expression was significantly associated with poorer prognosis. Taken together, our study suggested ITGA3 may facilitate the development of TC via activating PI3K-Akt signaling pathway.
基金supported by the National Natural Science Foundation of China(81101302,31270185)SKLID Development Grant(2014,SKLID201)
文摘Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking and gait. This disease can not be clearly identified through laboratory tests at present, thus application of high-throughput technique in studying the expression profiles of PD helps to find the genetic markers for its early diagnosis. Studies on expression profiles of neurodegenerative diseases have revealed the novel genes and pathways involved in the progress of illness. In this study, the expression profiles of PD in blood were compared, showing that 181 differentially expressed genes （DEG） exhibit a similar expression trend both in patients and in normal controls.
基金This work was partially supported by the Key Project of Natural Science Research of Education Department of Anhui Province(No.KJ2019A0338)Industry-University Cooperation Project of the Ministry of Education(No.202101160001).
文摘Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPortal databases to analyze the expression and mutation of TOP2αand its co-expressed genes in HCC tissues.GO function and KEGG pathway enrichment of TOP2αand its co-expressed genes were identified.The TIMER database was used to analyze infiltration levels of immune cells in HCC.The impacts of TOP2αand its co-expression genes and the infiltrated immune cells on the survival of HCC patients were assayed by Kaplan-Meier plotter analysis.Results TOP2αand its co-expression genes were highly expressed in HCC(P<0.001)and detrimental to overall survival of HCC patients(P<0.001).TOP2αand its co-expression genes were mainly involved in cell mitosis and proliferation,and cell cycle pathway(ID:hsa04110,P=0.001945).TOP2αand its co-expression genes were mutated in HCC and the mutations were significantly detrimental to overall survival(P=0.0247)and disease-free survival(P=0.0265)of HCC patients.High TOP2αexpression was positively correlated with the infiltration of B cell(r=0.459,P<0.01),CD8^(+)T cell(r=0.312,P<0.01),CD4^(+)T cell(r=0.370,P<0.01),macrophage(r=0.459,P<0.01),neutrophil(r=0.405,P<0.01),and dendritic cell(r=0.473,P<0.01)in HCC.The CD8^(+)T cell infiltration significantly prolonged the 3-and 5-year survival of HCC patients(all P<0.05),and CD4^(+)T cell infiltration significantly shortened the 3-,5-,and 10-year survival of HCC patients(all P<0.05).Conclusion TOP2αmay be an oncogene,which was associated with poor prognosis of HCC patients and could be used as a biomarker for the prognostic prediction of HCC.
基金Supported by the Special Plan for Condition Construction of Gansu Provincial Scientific Research Institutes,No.20JR10RA432.
文摘The expression of angiopoietin(ANGPT)1,ANGPT2,vascular endothelial growth factor(VEGF)A,VEGFB,VEGFC,VEGFD,and placental growth factor(PGF)is significantly higher in tumor tissues than in normal tissues in both unpaired and paired hepatocellular carcinoma(HCC)samples.ANGPT2,VEGFB,VEGFC,and PGF are primarily involved in regulating the activation of the epithelialmesenchymal transition pathway;ANGPT1 is primarily involved in regulating the activation of the RAS/mitogen-activated protein kinase and receptor tyrosine kinase(RTK)pathways;VEGFA is engaged in regulating the RTK activation pathway;and VEGFD is mainly involved in regulating the activation of the tuberous sclerosis protein/mammalian target of rapamycin pathway.There is a significant difference in overall survival between HCC patients with high and low expression of ANGPT2,PGF,VEGFA,and VEGFD.Disease free survival(DFS)is significantly shorter in HCC patients with high ANGPT2,PGF,and VEGFA expression than in those with low ANGPT2,PGF,and VEGFA expression.
基金National Natural Science Foundation of China(32073015).
文摘[Objectives]The purpose was to investigate the function and mechanism of exsA gene in type III secretion system of Vibrio alginolyticus.[Methods]The full length of exsA was cloned using molecular biology techniques to analyze its biological information.Fluorescence quantitative PCR technology was used to analyze the expression of exsA after different media stress.[Results]The exsA gene contains an open reading frame(ORF)of 861 bp,encoding 286 amino acids.The physico-chemical analysis shows that the molecular structural formula is C1442H2267N393O441S12,the theoretical molecular weight is 32.549 kD,the theoretical pI value is 6.0,and the protein is non-hydrophilic and unstable.The gene does not contain a transmembrane region,and there is no obvious signal peptide.The prediction result of protein subcellular localization shows that the protein is inside the cell.The deduced amino acid sequence and constructed phylogenetic tree show that V.alginolyticus has a close relationship with Vibrio antiquarius.The qPCR results show that the expression level of exsA in different media is different,highest in TSB medium containing bile salts,followed by DMEM medium,and lowest in ordinary TSB medium.[Conclusions]The gene sequence,molecular structure and isoelectric point of exsA,as well as its expression in three different media were obtained.
基金This work was supported by the“Xinlin Young Talent Program”(A1-U1820502040237)from Shanghai University of Traditional Chinese Medicine“Sasakawa Scientific Research Grant”(23-401)from the Japan Science Society.
文摘Mast cells are the main effector cells in IgE-associated allergic disorders,and we have reported that mucosal mast cells(MMCs)play a more important role in the development of food allergy(FA).IgE with antigen or calcium ionophore stimulation can lead to the activation of MMCs via a calcium-dependent pathway.The purpose of the present study was to identify gene signatures with IgE/antigen(dinitrophenyl-bovine serum albumin,DNP-BSA)or calcium ionophore(A23187)on the activation of MMCs.Differentially expressed genes between the two types of samples were identified with microarray analysis.Gene ontology functional and pathway enrichment analyses of differentially expressed genes were performed using the database for annotation,visualization,and integrated discovery software.The results showed that IgE/antigen and A23187 could induce degranulation,increase vacuoles,and elevate the cytosolic calcium concentration in MMCs.Furthermore,GeneChip analysis showed that the same 134 mRNAs were altered with IgE/DNP-BSA and A23187,suggesting that DNP-BSA/IgE and A23187 affect the same signal pathway partly in degranulation.KEGG analysis showed that the data were enriched in NF-κB,TNF,MAPK,transcription factor activity,DNA binding,and nucleic acid binding,suggesting that activation of MMCs is a complex process.The results provide new insights on MMCs activation.
