目的:探讨RNA m^(6)A甲基化修饰在脂肪细胞胰岛素抵抗中的作用及机制。方法:收集2型糖尿病患者术中赘余皮下脂肪组织,以非2型糖尿病患者同样组织为对照,检测组间RNA m^(6)A水平。高脂饮食诱导C57BL/6J小鼠构建胰岛素抵抗(in⁃sulin resis...目的:探讨RNA m^(6)A甲基化修饰在脂肪细胞胰岛素抵抗中的作用及机制。方法:收集2型糖尿病患者术中赘余皮下脂肪组织,以非2型糖尿病患者同样组织为对照,检测组间RNA m^(6)A水平。高脂饮食诱导C57BL/6J小鼠构建胰岛素抵抗(in⁃sulin resistance,IR)模型(HFD组,n=5,60%高脂饲料喂养16周),对照组10%低脂饲料喂养16周(CD组,n=5)。模型构建成功后,取附睾周围脂肪组织行表观转录组学m^(6)A甲基化修饰芯片检测,并借助MeRIP-qPCR实验、RT-qPCR以及RNA结合蛋白免疫沉淀测定(RNA Binding Protein Immunoprecipitation Assay,RIP)实验验证胰岛素信号转导相关基因变化;进一步观察METTL3小分子抑制剂STM2457对高脂饮食诱导下小鼠胰岛素信号转导基因的影响。结果:2型糖尿病患者和小鼠IR模型脂肪组织中总体m^(6)A修饰水平均升高(患者200 ng RNA t=-8.375,P<0.001;患者100 ng RNA t=-3.722,P=0.006;患者50 ng RNA t=-4.937;P=0.001;小鼠100 ng RNA t=-3.590,P=0.023;小鼠50 ng RNA t=-2.760,P=0.025)。表观转录组学检测证实IR的脂肪组织中1175个基因发生高m^(6)A修饰,55个基因发生低m^(6)A修饰,同时有182个基因呈现高m^(6)A修饰且低表达,包括AKT2、INSR、PIK3R1、ACACA、SREBF1等5个胰岛素信号转导关键基因,其中AKT2、INSR、ACACA、SREBF1等4个基因被确证并证实其与METTL3存在直接结合,其m^(6)A修饰水平受METTL3正向调控。STM2457作用下,胰岛素敏感性提高,且AKT2、INSR、ACACA、SREBF1转录水平上调,提示IR表型改善明显。结论:高脂饮食通过METTL3诱导脂肪细胞胰岛素信号转导基因AKT2、INSR、ACACA、SREBF1发生m^(6)A高甲基化修饰,诱导其低表达,阻滞胰岛素信号转导,进而参与诱发IR。展开更多
Objective:Middle ear cholesteatoma is a non-tumorous condition that typically leads to hearing loss,bone destruction,and other severe complications.Despite surgery being the primary treatment,the recurrence rate remai...Objective:Middle ear cholesteatoma is a non-tumorous condition that typically leads to hearing loss,bone destruction,and other severe complications.Despite surgery being the primary treatment,the recurrence rate remains high.Therefore,exploring the molecular mechanisms underlying cholesteatoma is crucial for discovering new therapeutic approaches.This study aims to explore the involvement of N6-methyladenosine(m^(6)A)methylation in long non-coding RNAs(lncRNAs)in the biological functions and related pathways of middle ear cholesteatoma.Methods:The m^(6)A modification patterns of lncRNA in middle ear cholesteatoma tissues(n=5)and normal post-auricular skin tissues(n=5)were analyzed using an lncRNA m^(6)A transcriptome microarray.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analyses were conducted to identify potential biological functions and signaling pathways involved in the pathogenesis of middle ear cholesteatoma.Methylated RNA immunoprecipitation(MeRIP)-PCR was used to validate the m^(6)A modifications in cholesteatoma and normal skin tissues.Results:Compared with normal skin tissues,1525 lncRNAs were differentially methylated in middle ear cholesteatoma tissues,with 1048 showing hypermethylation and 477 showing hypomethylation[fold change(FC)≥3 or<1/3,P<0.05].GO enrichment analysis indicated that hypermethylated lncRNAs were involved in protein phosphatase inhibitor activity,neuron-neuron synapse,and regulation ofα-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid(AMPA)receptor activity.Hypomethylated lncRNAs were associated with mRNA methyltransferase activity,secretory granule membrane,and mRNA methylation.KEGG analysis revealed that hypermethylated lncRNAs were mainly associated with 5 pathways:the Hedgehog signaling pathway,viral protein interaction with cytokines and cytokine receptors,mitogen-activated protein kinase(MAPK)signaling pathway,cytokine-cytokine receptor interaction,and adrenergic signaling in cardiomyocytes.Hypomethylated lncRNAs were mainly involved in 4 pathways:Renal cell carcinoma,tumor necrosis factor signaling pathway,transcriptional misregulation in cancer,and cytokine-cytokine receptor interaction.Additionally,MeRIP-PCR confirmed the changes in m^(6)A methylation levels in NR_033339,NR_122111,NR_130744,and NR_026800,consistent with microarray analysis.Real-time PCR also confirmed the significant upregulation of MAPK1 and NF-κB,key genes in the MAPK signaling pathway.Conclusion:This study reveals the m^(6)A modification patterns of lncRNAs in middle ear cholesteatoma,suggests a direction for further research into the role of lncRNA m^(6)A modification in the etiology of cholesteatoma.The findings provide potential therapeutic targets for the treatment of middle ear cholesteatoma.展开更多
N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insi...N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.展开更多
文摘目的:探讨RNA m^(6)A甲基化修饰在脂肪细胞胰岛素抵抗中的作用及机制。方法:收集2型糖尿病患者术中赘余皮下脂肪组织,以非2型糖尿病患者同样组织为对照,检测组间RNA m^(6)A水平。高脂饮食诱导C57BL/6J小鼠构建胰岛素抵抗(in⁃sulin resistance,IR)模型(HFD组,n=5,60%高脂饲料喂养16周),对照组10%低脂饲料喂养16周(CD组,n=5)。模型构建成功后,取附睾周围脂肪组织行表观转录组学m^(6)A甲基化修饰芯片检测,并借助MeRIP-qPCR实验、RT-qPCR以及RNA结合蛋白免疫沉淀测定(RNA Binding Protein Immunoprecipitation Assay,RIP)实验验证胰岛素信号转导相关基因变化;进一步观察METTL3小分子抑制剂STM2457对高脂饮食诱导下小鼠胰岛素信号转导基因的影响。结果:2型糖尿病患者和小鼠IR模型脂肪组织中总体m^(6)A修饰水平均升高(患者200 ng RNA t=-8.375,P<0.001;患者100 ng RNA t=-3.722,P=0.006;患者50 ng RNA t=-4.937;P=0.001;小鼠100 ng RNA t=-3.590,P=0.023;小鼠50 ng RNA t=-2.760,P=0.025)。表观转录组学检测证实IR的脂肪组织中1175个基因发生高m^(6)A修饰,55个基因发生低m^(6)A修饰,同时有182个基因呈现高m^(6)A修饰且低表达,包括AKT2、INSR、PIK3R1、ACACA、SREBF1等5个胰岛素信号转导关键基因,其中AKT2、INSR、ACACA、SREBF1等4个基因被确证并证实其与METTL3存在直接结合,其m^(6)A修饰水平受METTL3正向调控。STM2457作用下,胰岛素敏感性提高,且AKT2、INSR、ACACA、SREBF1转录水平上调,提示IR表型改善明显。结论:高脂饮食通过METTL3诱导脂肪细胞胰岛素信号转导基因AKT2、INSR、ACACA、SREBF1发生m^(6)A高甲基化修饰,诱导其低表达,阻滞胰岛素信号转导,进而参与诱发IR。
基金supported by the National Natural Science Foundation(82071036,82000973)the Natural Science Foundation of Hunan Province(2022JJ30821,2019JJ50967)the Special Project for the Construction of Innovative Provinces in Hunan Province(2023SK4030),China。
文摘Objective:Middle ear cholesteatoma is a non-tumorous condition that typically leads to hearing loss,bone destruction,and other severe complications.Despite surgery being the primary treatment,the recurrence rate remains high.Therefore,exploring the molecular mechanisms underlying cholesteatoma is crucial for discovering new therapeutic approaches.This study aims to explore the involvement of N6-methyladenosine(m^(6)A)methylation in long non-coding RNAs(lncRNAs)in the biological functions and related pathways of middle ear cholesteatoma.Methods:The m^(6)A modification patterns of lncRNA in middle ear cholesteatoma tissues(n=5)and normal post-auricular skin tissues(n=5)were analyzed using an lncRNA m^(6)A transcriptome microarray.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analyses were conducted to identify potential biological functions and signaling pathways involved in the pathogenesis of middle ear cholesteatoma.Methylated RNA immunoprecipitation(MeRIP)-PCR was used to validate the m^(6)A modifications in cholesteatoma and normal skin tissues.Results:Compared with normal skin tissues,1525 lncRNAs were differentially methylated in middle ear cholesteatoma tissues,with 1048 showing hypermethylation and 477 showing hypomethylation[fold change(FC)≥3 or<1/3,P<0.05].GO enrichment analysis indicated that hypermethylated lncRNAs were involved in protein phosphatase inhibitor activity,neuron-neuron synapse,and regulation ofα-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid(AMPA)receptor activity.Hypomethylated lncRNAs were associated with mRNA methyltransferase activity,secretory granule membrane,and mRNA methylation.KEGG analysis revealed that hypermethylated lncRNAs were mainly associated with 5 pathways:the Hedgehog signaling pathway,viral protein interaction with cytokines and cytokine receptors,mitogen-activated protein kinase(MAPK)signaling pathway,cytokine-cytokine receptor interaction,and adrenergic signaling in cardiomyocytes.Hypomethylated lncRNAs were mainly involved in 4 pathways:Renal cell carcinoma,tumor necrosis factor signaling pathway,transcriptional misregulation in cancer,and cytokine-cytokine receptor interaction.Additionally,MeRIP-PCR confirmed the changes in m^(6)A methylation levels in NR_033339,NR_122111,NR_130744,and NR_026800,consistent with microarray analysis.Real-time PCR also confirmed the significant upregulation of MAPK1 and NF-κB,key genes in the MAPK signaling pathway.Conclusion:This study reveals the m^(6)A modification patterns of lncRNAs in middle ear cholesteatoma,suggests a direction for further research into the role of lncRNA m^(6)A modification in the etiology of cholesteatoma.The findings provide potential therapeutic targets for the treatment of middle ear cholesteatoma.
基金supported in part by the National Natural Science Foundation of China(62373348)the Natural Science Foundation of Xinjiang Uygur Autonomous Region(2021D01D05)+1 种基金the Tianshan Talent Training Program(2023TSYCLJ0021)the Pioneer Hundred Talents Program of Chinese Academy of Sciences.
文摘N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.
