Mucin genes are the main component of mucus. The sea anemone species, Aulactinia veratra (Phylum Cnidaria) contains different types of mucin genes. In the intertidal zone, A. veratra is found to be exposed to air duri...Mucin genes are the main component of mucus. The sea anemone species, Aulactinia veratra (Phylum Cnidaria) contains different types of mucin genes. In the intertidal zone, A. veratra is found to be exposed to air during the low tide and produces large quantities of mucus as an external covering. The relation between low tide and mucus secretion is still unclear, and what is the role of mucin during arial exposure is not yet investigated. This study hypothesised that the mucin genes in A. veratra would have significantly high expression in response to aerial exposure. Therefore, the aim of current study was to examine and analyses the response of A. veratra mucins in response to an experiment involving three hours of aerial exposure. To achieve this, aim the RNA-sequencing and bioinformatics analyses were used to examine the expression profile of A. veratra mucin genes in response to aerial exposure. The generated results have shown that, Mucin4-like and mucin5B-like were up-regulated in response to the three hours of aerial exposure in A. veratra. This finding shows a significant role of mucin5B-like and mucin4-like genes in response to air stress at low tide. The data generated from this study could be used in conjunction with future mucin gene studies of sea anemones and other cnidarians to compare A. veratra mucin gene expression results across time, and to extend our understanding of mucin stress response in this phylum.展开更多
Objective： To study the genes expression profile differences in the peripheral blood between esophageal carcinoma patients and normal subjects using the gene chip technique and screen out the esophageal early concera...Objective： To study the genes expression profile differences in the peripheral blood between esophageal carcinoma patients and normal subjects using the gene chip technique and screen out the esophageal early conceration associated genes. Methods： The total RNA was extracted and purified in the peripheral blood obtained from the patients with esophageal carcinoma and normal subjects. The first strand of cDNA was synthesized through retro-transcription and labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with a piece of 4096 double dot human whole gene chip. The acquired image was analyzed by microarrav suite software using a digital computer, and the intensity of ttuorescence signal and its ratio were calculated. Results： A total of 92 genes were screened out and its expression difference was more than 2 times in the peripheral blood between the patients with esophageal carcinoma and normal subjects. Among these, the expression difference of 36 genes was more than 3 times. Two human urokinase plasminogen activator surface receptor （UPAR） genes, 80K-L protein gene, human protein tyrosine-phosphatase gent arid proto-oncogene protein mRNA were significantly up-regulated, while the collagen V type （α-2 gene was markedly down-regulated. Conclusion： 80K-L protein gene, tyrosinephophatase gene, proto-oncogene protein arid the collagen V type α-2 gene might be associated with the ontogenesis, development and its metastasis in the esophageal carcinoma. The UPAR gene may play important roles in the diagnosing the micrometastasis in the peripheral blood of esophageal carcinoma.展开更多
Objective: To explore the molecular mechanism of gemcitabine-resistance, the relative mRNA expression of five genes related to gemcitabine-resistance was detected in six lung cancer cell lines. Methods: The total RNA ...Objective: To explore the molecular mechanism of gemcitabine-resistance, the relative mRNA expression of five genes related to gemcitabine-resistance was detected in six lung cancer cell lines. Methods: The total RNA was extracted from six lung cancer cell lines GLC-82, NCI-H460, A549, 95-C, 95-D and QG56. Then the cDNA was amplified by real-time quantitative PCR method to quantify the gene expression of RRM1, PTEN, ERCC1, dCK and CDA. The cytotoxicity of gem- citabine to cell lines was tested by MTT method. Results: Among the detected six lung cancer cell lines, the mRNA level of RRM1, PTEN and ERCC1 in lung squamous cell line QG56 was highest, and the IC50 of gemcitabine to QG56 cell line was also highest. Conclusion: The mRNA expression of RRM1, PTEN and ERCC1 was correlated, and the high expression of RRM1 was related to gemcitabine resistance of lung cancer.展开更多
This study investigated the effects of dietary Pediocuccus pentosaceus(PP)and/or ferulic acid(FA)on the performance,digestive enzymes,and growth-related genes expression in rainbow trout(Oncorhynchus mykiss).Fish(94.3...This study investigated the effects of dietary Pediocuccus pentosaceus(PP)and/or ferulic acid(FA)on the performance,digestive enzymes,and growth-related genes expression in rainbow trout(Oncorhynchus mykiss).Fish(94.30±1.77 g)were fed on the control diet(T0),108 CFU/g of PP probiotic(T1),100 mg/kg of FA(T2),and a combination of PP and FA(T3)for 8 weeks.The present results indicated that rainbow trout fed with PP and/or FA showed better final weight,weight gain,and feed conversion ratio than the control group(P<0.05).The activities of trypsin and chymotrypsin were higher in T2 and T3 than in the control group(P<0.05).Meanwhile activities protease and alpha-amylase were highest in T2,lipase activity was highest in T3.Compared to the control group,total protein,total antioxidant activity,and cholesterol levels were significantly(P<0.05)higher in T2 and T3 with no significant(P>0.05)differences between them.Supplemented diets with FA and/or PP decreased markedly(P<0.05)triglycerides levels and its lowest levels were obtained in T2 and T3 with no significant(P>0.05)differences between them.The relative expression levels of GHRL and GHr genes were significantly higher in the treatments fed with FA and/or PP(T1–T3)than those in the control group(P<0.05).Highest upregulation of IGF-1,and IGF-II gens were detected in T2 and T3 with no significant(P>0.05)differences between them.In conclusion,it was shown that both dietary supplements have the potential role to enhance the performance,digestive enzymes,and growth related-genes expression in rainbow trout.Feeding fish on FA-enriched diets showed superior enhancements than that fed on the PP diet only.展开更多
BACKGROUND The ubiquitin-proteasome pathway(UPP)has been proven to play important roles in cancer.AIM To investigate the prognostic significance of genes involved in the UPP and develop a predictive model for liver ca...BACKGROUND The ubiquitin-proteasome pathway(UPP)has been proven to play important roles in cancer.AIM To investigate the prognostic significance of genes involved in the UPP and develop a predictive model for liver cancer based on the expression of these genes.METHODS In this study,UPP-related E1,E2,E3,deubiquitylating enzyme,and proteasome gene sets were obtained from the Kyoto Encyclopedia of Genes and Genomes(KEGG)database,aiming to screen the prognostic genes using univariate and multivariate regression analysis and develop a prognosis predictive model based RESULTS Five genes(including autophagy related 10,proteasome 20S subunit alpha 8,proteasome 20S subunit beta 2,ubiquitin specific peptidase 17 like family member 2,and ubiquitin specific peptidase 8)were proven significantly correlated with prognosis and used to develop a prognosis predictive model for liver cancer.Among training,validation,and Gene Expression Omnibus sets,the overall survival differed significantly between the high-risk and low-risk groups.The expression of the five genes was significantly associated with immunocyte infiltration,tumor stage,and postoperative recurrence.A total of 111 differentially expressed genes(DEGs)were identified between the high-risk and low-risk groups and they were enriched in 20 and 5 gene ontology and KEGG pathways.Cell division cycle 20,Kelch repeat and BTB domain containing 11,and DDB1 and CUL4 associated factor 4 like 2 were the DEGs in the E3 gene set that correlated with survival.CONCLUSION We have constructed a prognosis predictive model in patients with liver cancer,which contains five genes that associate with immunocyte infiltration,tumor stage,and postoperative recurrence.展开更多
Background:How AMP activated protein kinase(AMPK)signaling regulates mito-chondrial functions and mitophagy in human trophoblast cells remains unclear.This study was designed to investigate potential players mediating...Background:How AMP activated protein kinase(AMPK)signaling regulates mito-chondrial functions and mitophagy in human trophoblast cells remains unclear.This study was designed to investigate potential players mediating the regulation of AMPK on mitochondrial functions and mitophagy by next generation RNA-seq.Methods:We compared ATP production in protein kinase AMP-activated catalytic subunit alpha 1/2(PRKAA1/2)knockdown(AKD)and control BeWo cells using the Seahorse real-time ATP rate test,then analyzed gene expression profiling by RNA-seq.Differentially expressed genes(DEG)were examined by Gene Ontology(GO)analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment.Then protein-protein interactions(PPI)among mitochondria related genes were fur-ther analyzed using Metascape and Ingenuity Pathway Analysis(IPA)software.Results:Both mitochondrial and glycolytic ATP production in AKD cells were lower than in the control BeWo cells(CT),with a greater reduction of mitochondrial ATP production.A total of 1092 DEGs were identified,with 405 upregulated and 687 downregulated.GO analysis identified 60 genes associated with the term‘mitochon-drion’in the cellular component domain.PPI analysis identified three clusters of mito-chondria related genes,including aldo-keto reductase family 1 member B10 and B15(AKR1B10,AKR1B15),alanyl-tRNA synthetase 1(AARS1),mitochondrial ribosomal protein S6(MRPS6),mitochondrial calcium uniporter dominant negative subunit beta(MCUB)and dihydrolipoamide branched chain transacylase E2(DBT).Conclusions:In summary,this study identified multiple mitochondria related genes regulated by AMPK in BeWo cells,and among them,three clusters of genes may po-tentially contribute to altered mitochondrial functions in response to reduced AMPK signaling.展开更多
BACKGROUND Pancreatic ductal adenocarcinoma(PDAC)is an aggressive lethal malignancy with limited options for treatment and a 5-year survival rate of 11%in the United States.As for other types of tumors,such as colorec...BACKGROUND Pancreatic ductal adenocarcinoma(PDAC)is an aggressive lethal malignancy with limited options for treatment and a 5-year survival rate of 11%in the United States.As for other types of tumors,such as colorectal cancer,aberrant de novo lipid synthesis and reprogrammed lipid metabolism have been suggested to be associated with PDAC development and progression.AIM To identify the possible involvement of lipid metabolism in PDAC by analyzing in tumoral and non-tumoral tissues the expression level of the most relevant genes involved in the long-chain fatty acid(FA)import into cell.METHODS A gene expression analysis of FASN,CD36,SLC27A1,SLC27A2,SLC27A3,SLC27A4,SLC27A5,ACSL1,and ACSL3 was performed by qRT-PCR in 24 tumoral PDAC tissues and 11 samples from non-tumoral pancreatic tissues obtained via fine needle aspiration or via surgical resection.The genes were considered significantly dysregulated between the groups when the p value was<0.05 and the fold change(FC)was≤0.5 and≥2.RESULTS We found that three FA transporters and two long-chain acyl-CoA synthetases genes were significantly upregulated in the PDAC tissue compared to the non-tumoral tissue:SLC27A2(FC=5.66;P=0.033),SLC27A3(FC=2.68;P=0.040),SLC27A4(FC=3.13;P=0.033),ACSL1(FC=4.10;P<0.001),and ACSL3(FC=2.67;P=0.012).We further investigated any possible association between the levels of the analyzed mRNAs and the specific characteristics of the tumors,including the anatomic location,the lymph node involvement,and the presence of metastasis.A significant difference in the expression of SLC27A3(FC=3.28;P=0.040)was found comparing patients with and without lymph nodes involvement with an overexpression of this transcript in 17 patients presenting tumoral cells in the lymph nodes.CONCLUSION Despite the low number of patients analyzed,these preliminary results seem to be promising.Addressing lipid metabolism through a broad strategy could be a beneficial way to treat this malignancy.Future in vitro and in vivo studies on these genes may offer important insights into the mechanisms linking PDAC with the long-chain FA import pathway.展开更多
Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreati...Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.展开更多
Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive...Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.展开更多
Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression...Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.展开更多
Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The...Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.展开更多
As a member of the Cancer-Testis Antigens,the Melanoma-associated antigen(MAGE)family is typically expressed in normal tissues such as the testis.However,in various types of tumor cells,their expression is abnormally ...As a member of the Cancer-Testis Antigens,the Melanoma-associated antigen(MAGE)family is typically expressed in normal tissues such as the testis.However,in various types of tumor cells,their expression is abnormally activated,which is associated with multiple critical processes of tumor cells,including proliferation,apoptosis,immune evasion,DNA damage repair,and metastasis.The abnormal expression of MAGE family genes in multiple cancers and their multifaceted roles in tumor biology have made them an important target in cancer research and treatment.This review comprehensively explores various aspects of the relationship between the MAGE family and cancer,including the molecular characteristics of its members,transcriptional regulation mechanisms,expression patterns in different cancers,phenotypes and oncogenic mechanisms,poor clinical prognosis and potential as targets for immunotherapy.The expression patterns of these genes are closely linked to the clinical features of tumors,providing molecular markers and potential therapeutic targets for the early diagnosis,treatment,and prognostic assessment of cancer.展开更多
BACKGROUND ANAPC1,a key regulator of the ubiquitination in tumour development,has not been thoroughly studied in hepatocellular carcinoma(HCC).AIM To elucidate the expression of ANAPC1 in HCC and its potential regulat...BACKGROUND ANAPC1,a key regulator of the ubiquitination in tumour development,has not been thoroughly studied in hepatocellular carcinoma(HCC).AIM To elucidate the expression of ANAPC1 in HCC and its potential regulatory mechanism related to ubiquitination.METHODS Bulk RNA(RNA sequencing and microarrays),immunohistochemistry(IHC)tissues,and single-cell RNA sequencing(scRNA-seq)data were integrated to comprehensively investigate ANAPC1 expression in HCC.Clustered regularly interspaced short palindromic repeats analysis was performed to assess growth in HCC cell lines following ANAPC1 knockout.Enrichment analyses were conducted to explore the functions of ANAPC1.ScRNA-seq data was used to examine the cell cycle and metabolic levels.CellChat analysis was applied to investigate the interactions between ANAPC1 and different cell types.The relationship between ANAPC1 expression and drug concentration was analyzed.RESULTS ANAPC1 messenger RNA was found to be upregulated in bulk RNA,IHC tissues samples and malignant hepatocytes.The proliferation of JHH2 cell lines was most significantly inhibited after ANAPC1 knockdown.In biological pathways,the development of HCC was found to be linked to the regulation of ubiquitin-mediated proteolysis.Additionally,scRNA-seq results indicated that highly expressed ANAPC1 was in the G2/M phase,with increased glycolysis/gluconeogenesis activity.A CellChat analysis showed that ANAPC1 was associated with the regulation of the migration inhibitory factor-(cluster of differentiation 74+C-X-C chemokine receptor type 4)pathway.Higher ANAPC1 expression correlated with stronger effects of sorafenib,dasatinib,ibrutinib,lapatinib,nilotinib and afatinib.CONCLUSION The high expression level of ANAPC1 may regulate the cell cycle and metabolic levels of HCC through the ubiquitination-related pathway,thereby promoting disease progression.展开更多
N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenyla...N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenylation,and the initiation of translation.With the improving understanding of RNA methylation,m^(6)A modification is known to play vital roles in plant development and growth.The multi-petalization of flowering plants has high ornamental and research value in horticultural landscapes.However,the mechanism of RNA methylation in flower formation in Magnolia wufengensis,a classical multi-petalizational plant,remains unclear.This study compared and analyzed RNA m^(6)A methylation and the transcriptome in floral buds of two varieties with large differences in tepal number at the early stage of development.It was found that the degree of RNA m^(6)A methylation and relative expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9 in‘Jiaodan’with 36 tepals were significantly higher than those in‘Jiaohong’with 9 tepals during the development of floral organ primordia.Combined with quantitative real-time PCR,the expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9were positively correlated with the number of tepals.Transgenic experiments showed that MawuAGL6-1/2,and MawuPI-4 can increase the number of petals in Arabidopsis.Moreover,MawuAGL6-2 and MawuPI-4 can restore the missing petal phenotype of mutant Arabidopsis.Yeast two hybrid and yeast three hybrid indicated that MawuAGL6-2,MawuAP3-1/2,and MawuPI-4 could interact with each other under the mediation of the class E protein MawuAGL9.Based on these results,it is hypothesized that m^(6)A methylation influences the multi-petalization of Magnolia wufengensis by affecting the expression levels of MawuAGL6-2,MawuAP3-1/2,MawuPI-4,and MawuAGL9.These findings provide a better understanding of the molecular mechanisms of epigenetic modifications in flower developmental diversity.展开更多
Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid...Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.展开更多
Intraspecific conflict induced by the innate aggressiveness is one of the main reasons for the extremely low survival rate in mud crab Scylla paramamosain aquaculture,which have impeded the sustainable culture of the ...Intraspecific conflict induced by the innate aggressiveness is one of the main reasons for the extremely low survival rate in mud crab Scylla paramamosain aquaculture,which have impeded the sustainable culture of the species.In this study,we first classified and quantified the aggressive behavior,and established a crab aggressive behavior model,laying the foundation for subsequent research on evaluating combat intensity.The contents of 5-hydroxytryptamine(5-HT),dopamine(DA),and cAMP in the hemolymph of the mud crabs before and after fighting were measured by high-performance liquid chromatography-mass spectrometry(HPLC-MS),and the mud crabs exhibited a significant increase of 5-HT(P<0.05),while the DA and cAMP decreased significantly(P<0.05).In addition,we applied EthoVision to examine the changes of the crab behavior after DA administration.After 0.5 h of injection,the movement speed,distance,duration of aggressive behavior,and intensity of aggression in the high concentration DA group were significantly higher than those in the saline injection group and the untreated control group(P<0.05).The results of real-time quantitative polymerase chain reaction(qRT PCR)analysis showed that the expression of DA 1 in the thoracic ganglia of the mud crabs was significantly down-regulated in the DA injection group,and the aggressive behavior was weakened.Conversely,DA1 expression was up-regulated when aggressive behavior was strengthened.Besides,there were significant differences in the expression levels of receptor expression genes including 5-HT1,5-HT2,and crustacean hyperglycemic hormone(CHH)in different tissues,indicating that the alteration of aggressive behavior of the mud crab after injection with different concentrations of DA could be regulated by changes in the expression levels of corresponding receptor genes.Our results contribute to a deeper analysis of the aggressive behavior mechanism of the mud crabs and provide a theoretical basis for reducing fighting-related mortalities in aquaculture.展开更多
BACKGROUND The prognosis for acute myeloid leukemia(AML)remains poor,underscoring the need for a deeper understanding of its underlying molecular mechanisms.AIM To assess the significance of SOX11 gene expression in t...BACKGROUND The prognosis for acute myeloid leukemia(AML)remains poor,underscoring the need for a deeper understanding of its underlying molecular mechanisms.AIM To assess the significance of SOX11 gene expression in the clinical features,response to treatment,and survival outcomes of adult patients with AML.METHODS This retrospective study enrolled 102 adults with AML.SOX11 gene expression in bone marrow samples was measured using real-time PCR.Data were correlated to the patients’clinical features,response to treatment,and survival rates.RESULTS Increased SOX11 expression was significantly associated with the presence of the FLT3-ITD mutation(P<0.001),the FAB-M2 subtype(P=0.008),and cytogenetic abnormalities(P=0.011).However,no significant association was found between SOX11 expression and other clinical laboratory parameters,complete remission,disease-free survival,or overall survival.CONCLUSION SOX11 expression may serve as a marker to identify specific subsets of AML patients who could benefit from intensive targeted chemotherapy.展开更多
DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expres...DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.展开更多
Background PANoptosis has the features of pyroptosis,apoptosis,and necroptosis.Numerous studies have confirmed the diverse roles of various types of cell death in acute liver failure(ALF),but limited attention has bee...Background PANoptosis has the features of pyroptosis,apoptosis,and necroptosis.Numerous studies have confirmed the diverse roles of various types of cell death in acute liver failure(ALF),but limited attention has been given to the crosstalk among them.In this study,we aimed to explore the role of PANoptosis in ALF and uncover new targets for its prevention or treatment.Methods Three ALF-related datasets(GSE14668,GSE62029,and GSE74000)were downloaded from the Gene Expression Omnibus(GEO)database to identify differentially expressed genes(DEGs).Hub genes were identified through intersecting DEGs,genes obtained from weighted gene co-expression network analysis(WGCNA),and genes related to PANoptosis.Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG),protein–protein interaction(PPI)analyses and gene set enrichment analysis(GSEA)were performed to determine functional roles.Verification was performed using an ALF mouse model.Results Our results showed that expression of seven hub genes(B-cell lymphoma-2-modifying factor(BMF),B-cell lymphoma-2-interacting protein 3-like(BNIP3L),Caspase-1(CASP1),receptor-interacting protein kinase 3(RIPK3),uveal autoantigen with coiled-coil domains and ankyrin repeats protein(UACA),uncoordinated-5 homolog B receptor(UNC5B),and Z-DNA-binding protein 1(ZBP1))was up-regulated in liver samples of patients.However,in the ALF mouse model,the expression of BNIP3L,RIPK3,phosphorylated RIPK3(P-RIPK3),UACA,and cleaved caspase-1 was up-regulated,while the expression of CASP1 and UNC5B was down-regulated.The expression of ZBP1 and BMF increased only during the development of ALF,and there was no significant change in the end stage.Immunofluorescence of mouse liver tissue showed that macrophages expressed all seven markers.Western blot results showed that pyroptosis,apoptosis,and necroptosis were always involved in lipopolysaccharide(LPS)/D-galactosamine(D-gal)-induced ALF mice.The ALF cell model showed that bone marrow-derived macrophages(BMDMs)form PANoptosomes after LPS stimulation.Conclusions Our results suggest that PANoptosis of macrophages promotes the development of ALF.The seven new ALF biomarkers identified and validated in this study may contribute to further investigation of diagnostic markers or novel therapeutic targets of ALF.展开更多
Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyz...Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.展开更多
文摘Mucin genes are the main component of mucus. The sea anemone species, Aulactinia veratra (Phylum Cnidaria) contains different types of mucin genes. In the intertidal zone, A. veratra is found to be exposed to air during the low tide and produces large quantities of mucus as an external covering. The relation between low tide and mucus secretion is still unclear, and what is the role of mucin during arial exposure is not yet investigated. This study hypothesised that the mucin genes in A. veratra would have significantly high expression in response to aerial exposure. Therefore, the aim of current study was to examine and analyses the response of A. veratra mucins in response to an experiment involving three hours of aerial exposure. To achieve this, aim the RNA-sequencing and bioinformatics analyses were used to examine the expression profile of A. veratra mucin genes in response to aerial exposure. The generated results have shown that, Mucin4-like and mucin5B-like were up-regulated in response to the three hours of aerial exposure in A. veratra. This finding shows a significant role of mucin5B-like and mucin4-like genes in response to air stress at low tide. The data generated from this study could be used in conjunction with future mucin gene studies of sea anemones and other cnidarians to compare A. veratra mucin gene expression results across time, and to extend our understanding of mucin stress response in this phylum.
基金This project was supported by a grant from the Zhejiang Medical and Health Science Foundation (No. 2002A023).
文摘Objective： To study the genes expression profile differences in the peripheral blood between esophageal carcinoma patients and normal subjects using the gene chip technique and screen out the esophageal early conceration associated genes. Methods： The total RNA was extracted and purified in the peripheral blood obtained from the patients with esophageal carcinoma and normal subjects. The first strand of cDNA was synthesized through retro-transcription and labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with a piece of 4096 double dot human whole gene chip. The acquired image was analyzed by microarrav suite software using a digital computer, and the intensity of ttuorescence signal and its ratio were calculated. Results： A total of 92 genes were screened out and its expression difference was more than 2 times in the peripheral blood between the patients with esophageal carcinoma and normal subjects. Among these, the expression difference of 36 genes was more than 3 times. Two human urokinase plasminogen activator surface receptor （UPAR） genes, 80K-L protein gene, human protein tyrosine-phosphatase gent arid proto-oncogene protein mRNA were significantly up-regulated, while the collagen V type （α-2 gene was markedly down-regulated. Conclusion： 80K-L protein gene, tyrosinephophatase gene, proto-oncogene protein arid the collagen V type α-2 gene might be associated with the ontogenesis, development and its metastasis in the esophageal carcinoma. The UPAR gene may play important roles in the diagnosing the micrometastasis in the peripheral blood of esophageal carcinoma.
基金Supported by a grant from the Capital Medical Developing Foundation of China (No. 03028)
文摘Objective: To explore the molecular mechanism of gemcitabine-resistance, the relative mRNA expression of five genes related to gemcitabine-resistance was detected in six lung cancer cell lines. Methods: The total RNA was extracted from six lung cancer cell lines GLC-82, NCI-H460, A549, 95-C, 95-D and QG56. Then the cDNA was amplified by real-time quantitative PCR method to quantify the gene expression of RRM1, PTEN, ERCC1, dCK and CDA. The cytotoxicity of gem- citabine to cell lines was tested by MTT method. Results: Among the detected six lung cancer cell lines, the mRNA level of RRM1, PTEN and ERCC1 in lung squamous cell line QG56 was highest, and the IC50 of gemcitabine to QG56 cell line was also highest. Conclusion: The mRNA expression of RRM1, PTEN and ERCC1 was correlated, and the high expression of RRM1 was related to gemcitabine resistance of lung cancer.
文摘This study investigated the effects of dietary Pediocuccus pentosaceus(PP)and/or ferulic acid(FA)on the performance,digestive enzymes,and growth-related genes expression in rainbow trout(Oncorhynchus mykiss).Fish(94.30±1.77 g)were fed on the control diet(T0),108 CFU/g of PP probiotic(T1),100 mg/kg of FA(T2),and a combination of PP and FA(T3)for 8 weeks.The present results indicated that rainbow trout fed with PP and/or FA showed better final weight,weight gain,and feed conversion ratio than the control group(P<0.05).The activities of trypsin and chymotrypsin were higher in T2 and T3 than in the control group(P<0.05).Meanwhile activities protease and alpha-amylase were highest in T2,lipase activity was highest in T3.Compared to the control group,total protein,total antioxidant activity,and cholesterol levels were significantly(P<0.05)higher in T2 and T3 with no significant(P>0.05)differences between them.Supplemented diets with FA and/or PP decreased markedly(P<0.05)triglycerides levels and its lowest levels were obtained in T2 and T3 with no significant(P>0.05)differences between them.The relative expression levels of GHRL and GHr genes were significantly higher in the treatments fed with FA and/or PP(T1–T3)than those in the control group(P<0.05).Highest upregulation of IGF-1,and IGF-II gens were detected in T2 and T3 with no significant(P>0.05)differences between them.In conclusion,it was shown that both dietary supplements have the potential role to enhance the performance,digestive enzymes,and growth related-genes expression in rainbow trout.Feeding fish on FA-enriched diets showed superior enhancements than that fed on the PP diet only.
基金the Tianjin Municipal Natural Science Foundation,No.21JCYBJC01110。
文摘BACKGROUND The ubiquitin-proteasome pathway(UPP)has been proven to play important roles in cancer.AIM To investigate the prognostic significance of genes involved in the UPP and develop a predictive model for liver cancer based on the expression of these genes.METHODS In this study,UPP-related E1,E2,E3,deubiquitylating enzyme,and proteasome gene sets were obtained from the Kyoto Encyclopedia of Genes and Genomes(KEGG)database,aiming to screen the prognostic genes using univariate and multivariate regression analysis and develop a prognosis predictive model based RESULTS Five genes(including autophagy related 10,proteasome 20S subunit alpha 8,proteasome 20S subunit beta 2,ubiquitin specific peptidase 17 like family member 2,and ubiquitin specific peptidase 8)were proven significantly correlated with prognosis and used to develop a prognosis predictive model for liver cancer.Among training,validation,and Gene Expression Omnibus sets,the overall survival differed significantly between the high-risk and low-risk groups.The expression of the five genes was significantly associated with immunocyte infiltration,tumor stage,and postoperative recurrence.A total of 111 differentially expressed genes(DEGs)were identified between the high-risk and low-risk groups and they were enriched in 20 and 5 gene ontology and KEGG pathways.Cell division cycle 20,Kelch repeat and BTB domain containing 11,and DDB1 and CUL4 associated factor 4 like 2 were the DEGs in the E3 gene set that correlated with survival.CONCLUSION We have constructed a prognosis predictive model in patients with liver cancer,which contains five genes that associate with immunocyte infiltration,tumor stage,and postoperative recurrence.
基金Dean's Office Howard University College of Medicine,Grant/Award Number:Bridge Fund/Pilot Study AwardNational Center on Minority Health and Health Disparities,Grant/Award Number:RCMI/IDC Award U54MD007597National Institute of Child Health and Human Development,Grant/Award Number:R03HD095417 and R16HD116702。
文摘Background:How AMP activated protein kinase(AMPK)signaling regulates mito-chondrial functions and mitophagy in human trophoblast cells remains unclear.This study was designed to investigate potential players mediating the regulation of AMPK on mitochondrial functions and mitophagy by next generation RNA-seq.Methods:We compared ATP production in protein kinase AMP-activated catalytic subunit alpha 1/2(PRKAA1/2)knockdown(AKD)and control BeWo cells using the Seahorse real-time ATP rate test,then analyzed gene expression profiling by RNA-seq.Differentially expressed genes(DEG)were examined by Gene Ontology(GO)analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment.Then protein-protein interactions(PPI)among mitochondria related genes were fur-ther analyzed using Metascape and Ingenuity Pathway Analysis(IPA)software.Results:Both mitochondrial and glycolytic ATP production in AKD cells were lower than in the control BeWo cells(CT),with a greater reduction of mitochondrial ATP production.A total of 1092 DEGs were identified,with 405 upregulated and 687 downregulated.GO analysis identified 60 genes associated with the term‘mitochon-drion’in the cellular component domain.PPI analysis identified three clusters of mito-chondria related genes,including aldo-keto reductase family 1 member B10 and B15(AKR1B10,AKR1B15),alanyl-tRNA synthetase 1(AARS1),mitochondrial ribosomal protein S6(MRPS6),mitochondrial calcium uniporter dominant negative subunit beta(MCUB)and dihydrolipoamide branched chain transacylase E2(DBT).Conclusions:In summary,this study identified multiple mitochondria related genes regulated by AMPK in BeWo cells,and among them,three clusters of genes may po-tentially contribute to altered mitochondrial functions in response to reduced AMPK signaling.
基金Supported by Romanian Ministry of Research,Innovation and Digitization,No.PN23.16.02.04 and No.31PFE/30.12.2021.
文摘BACKGROUND Pancreatic ductal adenocarcinoma(PDAC)is an aggressive lethal malignancy with limited options for treatment and a 5-year survival rate of 11%in the United States.As for other types of tumors,such as colorectal cancer,aberrant de novo lipid synthesis and reprogrammed lipid metabolism have been suggested to be associated with PDAC development and progression.AIM To identify the possible involvement of lipid metabolism in PDAC by analyzing in tumoral and non-tumoral tissues the expression level of the most relevant genes involved in the long-chain fatty acid(FA)import into cell.METHODS A gene expression analysis of FASN,CD36,SLC27A1,SLC27A2,SLC27A3,SLC27A4,SLC27A5,ACSL1,and ACSL3 was performed by qRT-PCR in 24 tumoral PDAC tissues and 11 samples from non-tumoral pancreatic tissues obtained via fine needle aspiration or via surgical resection.The genes were considered significantly dysregulated between the groups when the p value was<0.05 and the fold change(FC)was≤0.5 and≥2.RESULTS We found that three FA transporters and two long-chain acyl-CoA synthetases genes were significantly upregulated in the PDAC tissue compared to the non-tumoral tissue:SLC27A2(FC=5.66;P=0.033),SLC27A3(FC=2.68;P=0.040),SLC27A4(FC=3.13;P=0.033),ACSL1(FC=4.10;P<0.001),and ACSL3(FC=2.67;P=0.012).We further investigated any possible association between the levels of the analyzed mRNAs and the specific characteristics of the tumors,including the anatomic location,the lymph node involvement,and the presence of metastasis.A significant difference in the expression of SLC27A3(FC=3.28;P=0.040)was found comparing patients with and without lymph nodes involvement with an overexpression of this transcript in 17 patients presenting tumoral cells in the lymph nodes.CONCLUSION Despite the low number of patients analyzed,these preliminary results seem to be promising.Addressing lipid metabolism through a broad strategy could be a beneficial way to treat this malignancy.Future in vitro and in vivo studies on these genes may offer important insights into the mechanisms linking PDAC with the long-chain FA import pathway.
基金supported by the Russian Science Foundation(No.22-16-00128),“Investigation of the Toxic Effect of Glyphosates on the Functional State of the Bird Intestinal Microbial Community,Their Growth and Development,and the Development of a Biological Product Based on the Glyphosate Degrading Strain”.
文摘Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.
文摘Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.
基金supported by the National Natural Science Foundation of China(32172010)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006).
文摘Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
基金financially supported by the Guangdong Major Project of Basic and Applied Basic Research,China(2021B0301030004)the National Natural Science Foundation of China(32360757,U2202206 and 32361143517)the Yunnan Fundamental Research Projects,China(202201AT070037,202501AS070012)。
文摘Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.
基金supported by Startup Fund for Young Faculty at SJTU(SFYF at SJTU)(No.24X010500176).
文摘As a member of the Cancer-Testis Antigens,the Melanoma-associated antigen(MAGE)family is typically expressed in normal tissues such as the testis.However,in various types of tumor cells,their expression is abnormally activated,which is associated with multiple critical processes of tumor cells,including proliferation,apoptosis,immune evasion,DNA damage repair,and metastasis.The abnormal expression of MAGE family genes in multiple cancers and their multifaceted roles in tumor biology have made them an important target in cancer research and treatment.This review comprehensively explores various aspects of the relationship between the MAGE family and cancer,including the molecular characteristics of its members,transcriptional regulation mechanisms,expression patterns in different cancers,phenotypes and oncogenic mechanisms,poor clinical prognosis and potential as targets for immunotherapy.The expression patterns of these genes are closely linked to the clinical features of tumors,providing molecular markers and potential therapeutic targets for the early diagnosis,treatment,and prognostic assessment of cancer.
基金Co-first authors:Yu-Xing Tang 0000-0003-4382-4942Co-first authors:Wei-Zi Wu+8 种基金Corresponding author:Gang Chen,MD,Professor,Department of Pathology,The First Affiliated Hospital of Guangxi Medical University,No.6 Shuangyong Road,Nanning 530021,Guangxi Zhuang Autonomous Region,China.chengang@gxmu.edu.cn,0000-0003-2402-2987Co-corresponding authors:Yan-Ting ZhanSheng-Sheng Zhou,0000-0003-2414-460XDa-Tong Zeng,0000-0002-3338-4122Guang-Cai Zheng,0009-0001-5921-6688Rong-Quan He,0000-0002-7752-2080Di-Yuan Qin,0009-0003-3214-4762Wan-Ying Huang,0000-0002-8314-5963Yu-Lu Tang,0009-0004-0462-618X。
文摘BACKGROUND ANAPC1,a key regulator of the ubiquitination in tumour development,has not been thoroughly studied in hepatocellular carcinoma(HCC).AIM To elucidate the expression of ANAPC1 in HCC and its potential regulatory mechanism related to ubiquitination.METHODS Bulk RNA(RNA sequencing and microarrays),immunohistochemistry(IHC)tissues,and single-cell RNA sequencing(scRNA-seq)data were integrated to comprehensively investigate ANAPC1 expression in HCC.Clustered regularly interspaced short palindromic repeats analysis was performed to assess growth in HCC cell lines following ANAPC1 knockout.Enrichment analyses were conducted to explore the functions of ANAPC1.ScRNA-seq data was used to examine the cell cycle and metabolic levels.CellChat analysis was applied to investigate the interactions between ANAPC1 and different cell types.The relationship between ANAPC1 expression and drug concentration was analyzed.RESULTS ANAPC1 messenger RNA was found to be upregulated in bulk RNA,IHC tissues samples and malignant hepatocytes.The proliferation of JHH2 cell lines was most significantly inhibited after ANAPC1 knockdown.In biological pathways,the development of HCC was found to be linked to the regulation of ubiquitin-mediated proteolysis.Additionally,scRNA-seq results indicated that highly expressed ANAPC1 was in the G2/M phase,with increased glycolysis/gluconeogenesis activity.A CellChat analysis showed that ANAPC1 was associated with the regulation of the migration inhibitory factor-(cluster of differentiation 74+C-X-C chemokine receptor type 4)pathway.Higher ANAPC1 expression correlated with stronger effects of sorafenib,dasatinib,ibrutinib,lapatinib,nilotinib and afatinib.CONCLUSION The high expression level of ANAPC1 may regulate the cell cycle and metabolic levels of HCC through the ubiquitination-related pathway,thereby promoting disease progression.
基金supported by the National Natural Science Foundation of China(Grant No.31570651)。
文摘N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenylation,and the initiation of translation.With the improving understanding of RNA methylation,m^(6)A modification is known to play vital roles in plant development and growth.The multi-petalization of flowering plants has high ornamental and research value in horticultural landscapes.However,the mechanism of RNA methylation in flower formation in Magnolia wufengensis,a classical multi-petalizational plant,remains unclear.This study compared and analyzed RNA m^(6)A methylation and the transcriptome in floral buds of two varieties with large differences in tepal number at the early stage of development.It was found that the degree of RNA m^(6)A methylation and relative expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9 in‘Jiaodan’with 36 tepals were significantly higher than those in‘Jiaohong’with 9 tepals during the development of floral organ primordia.Combined with quantitative real-time PCR,the expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9were positively correlated with the number of tepals.Transgenic experiments showed that MawuAGL6-1/2,and MawuPI-4 can increase the number of petals in Arabidopsis.Moreover,MawuAGL6-2 and MawuPI-4 can restore the missing petal phenotype of mutant Arabidopsis.Yeast two hybrid and yeast three hybrid indicated that MawuAGL6-2,MawuAP3-1/2,and MawuPI-4 could interact with each other under the mediation of the class E protein MawuAGL9.Based on these results,it is hypothesized that m^(6)A methylation influences the multi-petalization of Magnolia wufengensis by affecting the expression levels of MawuAGL6-2,MawuAP3-1/2,MawuPI-4,and MawuAGL9.These findings provide a better understanding of the molecular mechanisms of epigenetic modifications in flower developmental diversity.
基金supported by the National Natural Science Foundation of China(No.32072947)the China Agriculture Research System(No.CARS-47)。
文摘Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.
基金Supported by the National Key R&D Program of China(No.2023YFD2401005)the Key R&D Program of Ningbo(No.2022Z059)the K.C.Wong Magna Fund of Ningbo University。
文摘Intraspecific conflict induced by the innate aggressiveness is one of the main reasons for the extremely low survival rate in mud crab Scylla paramamosain aquaculture,which have impeded the sustainable culture of the species.In this study,we first classified and quantified the aggressive behavior,and established a crab aggressive behavior model,laying the foundation for subsequent research on evaluating combat intensity.The contents of 5-hydroxytryptamine(5-HT),dopamine(DA),and cAMP in the hemolymph of the mud crabs before and after fighting were measured by high-performance liquid chromatography-mass spectrometry(HPLC-MS),and the mud crabs exhibited a significant increase of 5-HT(P<0.05),while the DA and cAMP decreased significantly(P<0.05).In addition,we applied EthoVision to examine the changes of the crab behavior after DA administration.After 0.5 h of injection,the movement speed,distance,duration of aggressive behavior,and intensity of aggression in the high concentration DA group were significantly higher than those in the saline injection group and the untreated control group(P<0.05).The results of real-time quantitative polymerase chain reaction(qRT PCR)analysis showed that the expression of DA 1 in the thoracic ganglia of the mud crabs was significantly down-regulated in the DA injection group,and the aggressive behavior was weakened.Conversely,DA1 expression was up-regulated when aggressive behavior was strengthened.Besides,there were significant differences in the expression levels of receptor expression genes including 5-HT1,5-HT2,and crustacean hyperglycemic hormone(CHH)in different tissues,indicating that the alteration of aggressive behavior of the mud crab after injection with different concentrations of DA could be regulated by changes in the expression levels of corresponding receptor genes.Our results contribute to a deeper analysis of the aggressive behavior mechanism of the mud crabs and provide a theoretical basis for reducing fighting-related mortalities in aquaculture.
文摘BACKGROUND The prognosis for acute myeloid leukemia(AML)remains poor,underscoring the need for a deeper understanding of its underlying molecular mechanisms.AIM To assess the significance of SOX11 gene expression in the clinical features,response to treatment,and survival outcomes of adult patients with AML.METHODS This retrospective study enrolled 102 adults with AML.SOX11 gene expression in bone marrow samples was measured using real-time PCR.Data were correlated to the patients’clinical features,response to treatment,and survival rates.RESULTS Increased SOX11 expression was significantly associated with the presence of the FLT3-ITD mutation(P<0.001),the FAB-M2 subtype(P=0.008),and cytogenetic abnormalities(P=0.011).However,no significant association was found between SOX11 expression and other clinical laboratory parameters,complete remission,disease-free survival,or overall survival.CONCLUSION SOX11 expression may serve as a marker to identify specific subsets of AML patients who could benefit from intensive targeted chemotherapy.
文摘DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.
基金supported by the National Science and Technology Major Project of China(No.2018ZX10302206).
文摘Background PANoptosis has the features of pyroptosis,apoptosis,and necroptosis.Numerous studies have confirmed the diverse roles of various types of cell death in acute liver failure(ALF),but limited attention has been given to the crosstalk among them.In this study,we aimed to explore the role of PANoptosis in ALF and uncover new targets for its prevention or treatment.Methods Three ALF-related datasets(GSE14668,GSE62029,and GSE74000)were downloaded from the Gene Expression Omnibus(GEO)database to identify differentially expressed genes(DEGs).Hub genes were identified through intersecting DEGs,genes obtained from weighted gene co-expression network analysis(WGCNA),and genes related to PANoptosis.Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG),protein–protein interaction(PPI)analyses and gene set enrichment analysis(GSEA)were performed to determine functional roles.Verification was performed using an ALF mouse model.Results Our results showed that expression of seven hub genes(B-cell lymphoma-2-modifying factor(BMF),B-cell lymphoma-2-interacting protein 3-like(BNIP3L),Caspase-1(CASP1),receptor-interacting protein kinase 3(RIPK3),uveal autoantigen with coiled-coil domains and ankyrin repeats protein(UACA),uncoordinated-5 homolog B receptor(UNC5B),and Z-DNA-binding protein 1(ZBP1))was up-regulated in liver samples of patients.However,in the ALF mouse model,the expression of BNIP3L,RIPK3,phosphorylated RIPK3(P-RIPK3),UACA,and cleaved caspase-1 was up-regulated,while the expression of CASP1 and UNC5B was down-regulated.The expression of ZBP1 and BMF increased only during the development of ALF,and there was no significant change in the end stage.Immunofluorescence of mouse liver tissue showed that macrophages expressed all seven markers.Western blot results showed that pyroptosis,apoptosis,and necroptosis were always involved in lipopolysaccharide(LPS)/D-galactosamine(D-gal)-induced ALF mice.The ALF cell model showed that bone marrow-derived macrophages(BMDMs)form PANoptosomes after LPS stimulation.Conclusions Our results suggest that PANoptosis of macrophages promotes the development of ALF.The seven new ALF biomarkers identified and validated in this study may contribute to further investigation of diagnostic markers or novel therapeutic targets of ALF.
基金supported through National Research Foundation(NRF)of Korea grants funded by the Korean Government(No.NRF-2022R1F1A1064405)the research fund of Catholic Kwandong University and Catholic Kwandong University International St.Mary’s Hospital for S.-W Kim.
文摘Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.
