BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short du...BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation.展开更多
AIM:To analyze abnormal gene expressions of mice eyes exposed to blue light using RNA-seq and analyze the related signaling pathways.METHODS:Kunming mice were divided into an experimental group that was exposed to blu...AIM:To analyze abnormal gene expressions of mice eyes exposed to blue light using RNA-seq and analyze the related signaling pathways.METHODS:Kunming mice were divided into an experimental group that was exposed to blue light and a control group that was exposed to natural light.After 14 d,the mice were euthanized and their eyeballs were collected.Whole transcriptome analysis was attempted to analyze the gene expression of the eyeballs using RNA-seq to reconstruct genetic networks.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis were used to reveal the related signaling pathways.RESULTS:The 737 differentially expressed genes were identified,including 430 up and 307 down regulated genes,by calculating the gene FPKM in each sample and conducting differential gene analysis.GO and KEGG pathway enrichment analysis showed that blue light damage may associated with the visual perception,sensory perception of light stimulus,phototransduction,and JAKSTAT signaling pathways.Differential lnc RNA,circ RNA and mi RNA analysis showed that blue light exposure affected pathways for retinal cone cell development and phototransduction,among others.CONCLUSION:Exposure to blue light can cause a certain degree of abnormal gene expression and modulate signaling pathways in the eye.展开更多
Subacute ruminal acidosis(SARA)is a common metabolic disease in the dairy farming industry which is usually caused by an excessive amount of high concentrate diet.SARA not only threatens animal welfare but also leads ...Subacute ruminal acidosis(SARA)is a common metabolic disease in the dairy farming industry which is usually caused by an excessive amount of high concentrate diet.SARA not only threatens animal welfare but also leads to economic losses in the farming industry.The liver plays an important role in the distribution of nutritional substances and metabolism;however,a high concentrate diet can cause hepatic metabolic disorders and liver injury.Recently,noncoding RNA has been considered as a critical regulator of hepatic disease,however,its role in the bovine liver is limited.In this study,12 mid-lactating dairy cows were randomly assigned to a control(CON)group(40% concentrate of dry matter,n=6)and a SARA group(60% concentrate of dry matter,n=6).After 21 d of treatment,all cows were sacrificed,and liver tissue samples were collected.Three dairy cows were randomly selected from the CON and SARA groups respectively to perform whole transcriptome analysis.More than 20,000 messenger RNA(mRNA),10,000 long noncoding RNA(lncRNA),3,500 circular RNA(circRNA)and 1,000 micro RNA(miRNA)were identified.Furthermore,43 mRNA,121 lncRNA and 3 miRNA were differentially expressed,whereas no obvious differentially expressed circRNA were detected between the 2 groups.Gene Ontology(GO)annotation revealed that the differentially expressed genes were mainly enriched in oxidoreductase activity,stress,metabolism,the immune response,cell apoptosis,and cell proliferation.Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis showed that the deferentially expressed genes were highly enriched in the phosphatidylinositol 3 kinase(PI3) K-serine/threonine kinase(AKT)signaling pathway(P<0.05).According to KEGG pathway analysis,the differentially expressed lncRNA(DElncRNA)target genes were mainly related to proteasomes,peroxisomes,and the hypoxia-inducible factor-1 signaling pathway(P<0.005).Further bioinformatics and integrative analyses revealed that the lncRNA were strongly correlated with mRNA;therefore,it is reasonable to speculate that lncRNA potentially play important roles in the liver dysfunction induced by SARA.Our study provides a valuable resource for future investigations on the mechanisms of SARA to facilitate an understanding of the importance of lncRNA,and offer functional RNA information.展开更多
基金Supported by the National Natural Science Foundation,China,No.82272568,81902247,and 32201013Natural Science Foundation of Shandong Province,China,No.ZR2021QH275+1 种基金Natural Science Foundation of Jinan City,China,No.202225070Guangdong Basic and Applied Basic Research Foundation,China,No.2022A1515220056.
文摘BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation.
基金Supported by the National Natural Science Foundation of China(No.11802209)the Natural Science Foundation of Shandong Province China(No.ZR2019MA018,No.ZR2019BC095)Shandong Project for Talents Introduction and Development on Youth Innovation Team of Higher Education。
文摘AIM:To analyze abnormal gene expressions of mice eyes exposed to blue light using RNA-seq and analyze the related signaling pathways.METHODS:Kunming mice were divided into an experimental group that was exposed to blue light and a control group that was exposed to natural light.After 14 d,the mice were euthanized and their eyeballs were collected.Whole transcriptome analysis was attempted to analyze the gene expression of the eyeballs using RNA-seq to reconstruct genetic networks.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis were used to reveal the related signaling pathways.RESULTS:The 737 differentially expressed genes were identified,including 430 up and 307 down regulated genes,by calculating the gene FPKM in each sample and conducting differential gene analysis.GO and KEGG pathway enrichment analysis showed that blue light damage may associated with the visual perception,sensory perception of light stimulus,phototransduction,and JAKSTAT signaling pathways.Differential lnc RNA,circ RNA and mi RNA analysis showed that blue light exposure affected pathways for retinal cone cell development and phototransduction,among others.CONCLUSION:Exposure to blue light can cause a certain degree of abnormal gene expression and modulate signaling pathways in the eye.
基金the financial contributions of the Fundamental Research Funds for the Central Universities(JCQY201905)National Key Research and Development Project(2016YFD0501203)。
文摘Subacute ruminal acidosis(SARA)is a common metabolic disease in the dairy farming industry which is usually caused by an excessive amount of high concentrate diet.SARA not only threatens animal welfare but also leads to economic losses in the farming industry.The liver plays an important role in the distribution of nutritional substances and metabolism;however,a high concentrate diet can cause hepatic metabolic disorders and liver injury.Recently,noncoding RNA has been considered as a critical regulator of hepatic disease,however,its role in the bovine liver is limited.In this study,12 mid-lactating dairy cows were randomly assigned to a control(CON)group(40% concentrate of dry matter,n=6)and a SARA group(60% concentrate of dry matter,n=6).After 21 d of treatment,all cows were sacrificed,and liver tissue samples were collected.Three dairy cows were randomly selected from the CON and SARA groups respectively to perform whole transcriptome analysis.More than 20,000 messenger RNA(mRNA),10,000 long noncoding RNA(lncRNA),3,500 circular RNA(circRNA)and 1,000 micro RNA(miRNA)were identified.Furthermore,43 mRNA,121 lncRNA and 3 miRNA were differentially expressed,whereas no obvious differentially expressed circRNA were detected between the 2 groups.Gene Ontology(GO)annotation revealed that the differentially expressed genes were mainly enriched in oxidoreductase activity,stress,metabolism,the immune response,cell apoptosis,and cell proliferation.Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis showed that the deferentially expressed genes were highly enriched in the phosphatidylinositol 3 kinase(PI3) K-serine/threonine kinase(AKT)signaling pathway(P<0.05).According to KEGG pathway analysis,the differentially expressed lncRNA(DElncRNA)target genes were mainly related to proteasomes,peroxisomes,and the hypoxia-inducible factor-1 signaling pathway(P<0.005).Further bioinformatics and integrative analyses revealed that the lncRNA were strongly correlated with mRNA;therefore,it is reasonable to speculate that lncRNA potentially play important roles in the liver dysfunction induced by SARA.Our study provides a valuable resource for future investigations on the mechanisms of SARA to facilitate an understanding of the importance of lncRNA,and offer functional RNA information.
