目的探讨m^(7)G-lncRNAs能否作为结肠癌患者预后及肿瘤微环境的生物标志物。方法TCGA数据库筛选m^(7)G-lncRNAs(|Pearson R|>0.4,P<0.001),多因素Cox分析构建m^(7)G-lncRNAs风险模型。使用ROC和C-index曲线对风险模型进行验证。...目的探讨m^(7)G-lncRNAs能否作为结肠癌患者预后及肿瘤微环境的生物标志物。方法TCGA数据库筛选m^(7)G-lncRNAs(|Pearson R|>0.4,P<0.001),多因素Cox分析构建m^(7)G-lncRNAs风险模型。使用ROC和C-index曲线对风险模型进行验证。构建诺莫图和诺莫图的校准曲线用于预测结肠癌患者的预后。点柱图和K-M生存曲线评估风险打分对患者临床分期和预后的影响。CIBERSORT和ESTIMATE探究高低风险组患者肿瘤微环境和免疫细胞浸润程度的联系,同时分析风险打分对结肠癌患者微卫星不稳定性,干细胞指数和免疫检查点表达的影响。使用相互作用基因搜索工具(STRING)构建蛋白质-蛋白质相互作用网络,挖掘m^(7)G-lncRNAs调控的关键靶点。最后,使用蛋白印迹实验在4对结肠癌组织与癌旁正常组织中验证这些关键靶点的表达。结果从TCGA数据库鉴别出1722个m^(7)G-lncRNAs。多因素Cox分析筛选出12个lncRNAs用于构建风险模型,其中AC003101.2、AC005014.2、AC008760.1、AC092944.1、AL1161729.4、AL301422.4、AP001619.1、AP003355.1和ZEB1-AS1为高风险lncRNAs,AC025171.4、AC073957.3及TNFRSF10A-AS1为低风险lncRNAs。ROC曲线显示风险模型对患者1年、3年、5年生存预测的AUC值分别为0.727、0.747、0.794。诺莫图预测患者预后的AUC值为0.794,校准曲线显示诺莫图对患者生存的预测与患者实际的生存基本一致。高风险组患者的T分期(T1~T2 vs T3~T4:P=0.034)、N分期(N0 vs N2:P=7.8e-08;N1 vs N2:P=0.00081)以及M分期(M0 vs M1:P=0.007)均高于低风险组患者。低风险组患者常伴随高微卫星不稳定状态(MSS vs MSI-H:P=0.034)。肿瘤干性指数与风险得分呈负相关(r=-0.19;P=7.3e-05)。高风险组患者基质细胞打分(P=0.0028)以及总打分(P=0.007)明显高于低风险组患者较高,激活的肥大细胞(r=-0.11;P=0.045)和静息CD4^(+)T细胞(r=-0.14;P=0.01)的表达也较低。多数免疫检查点在高风险患者中高表达(P<0.05)。蛋白印迹实验表明m^(7)G-lncRNAs调控的关键靶点ATXN2(P=0.006)and G3BP1(P=0.007)在4对结肠癌组织中表达均高于配对的癌旁正常组织。结论12个m^(7)G-lncRNAs构建的风险模型对结肠癌具有重要的预后价值,同时也能反映结肠癌患者肿瘤微环境及免疫治疗的疗效。展开更多
Soybean mutants withα-nullβ-conglycinin are associated with high nutritional value and low allergenic risk.Although long noncoding RNAs(lncRNAs)are increasingly recognized as functional regulatory components affecti...Soybean mutants withα-nullβ-conglycinin are associated with high nutritional value and low allergenic risk.Although long noncoding RNAs(lncRNAs)are increasingly recognized as functional regulatory components affecting eukaryotic gene expression,little is known about lnc RNA profiles inα-null-type hypoallergenic soybeans.In this study,a genome-wide integrative analysis of lncRNAs,m RNAs and epigenomic data in the soybean cgy-2(confirmedα-null)near-isogenic line(NIL)and its recurrent parent Dongnong47(DN47)was conducted.Nineteen novel lncRNAs that were differentially expressed(DE)only in the NIL at 18 days after flowering(i.e.,α-null-associated DE lncRNAs)were delected.Sixteen putative soybean stress-responsive lncRNAs were identified,and observed to regulate 257 stress-related genes DE in the NIL.This result indicated that theα-null allele might represent an intrinsic defect stress that altered the expression of various stress-related genes inα-null-type hypoallergenic soybean.Additionally,25 epigenetic-related lncRNAs regulated 831 DE epigenetic-related genes and simultaneously initiated multiple epigenetic activities,including ubiquitination,methylation and acetylation.Kyoto encyclopedia of genes and genomes(KEGG)analysis indicated that the biosynthesis of amino acids pathway was enriched with 83 DE genes regulated by nine DE lncRNAs.Changes in the expression of these lncRNAs and genes might be the reason for the altered amino acid composition in the NIL.Among all detected DE lncRNAs,MSTRG.12518 was the most conspicuousα-null-specific cis/trans-lnc RNA that played an efficient,versatile and vital role in the NIL.The data indicated that the lnc RNA profile differed between the NIL and DN47.Variations in lncRNAs,gene expression levels and DNA methylation states likely contributed to the intrinsic defect stress response mechanism inα-null-type hypoallergenic soybeans.展开更多
文摘目的探讨m^(7)G-lncRNAs能否作为结肠癌患者预后及肿瘤微环境的生物标志物。方法TCGA数据库筛选m^(7)G-lncRNAs(|Pearson R|>0.4,P<0.001),多因素Cox分析构建m^(7)G-lncRNAs风险模型。使用ROC和C-index曲线对风险模型进行验证。构建诺莫图和诺莫图的校准曲线用于预测结肠癌患者的预后。点柱图和K-M生存曲线评估风险打分对患者临床分期和预后的影响。CIBERSORT和ESTIMATE探究高低风险组患者肿瘤微环境和免疫细胞浸润程度的联系,同时分析风险打分对结肠癌患者微卫星不稳定性,干细胞指数和免疫检查点表达的影响。使用相互作用基因搜索工具(STRING)构建蛋白质-蛋白质相互作用网络,挖掘m^(7)G-lncRNAs调控的关键靶点。最后,使用蛋白印迹实验在4对结肠癌组织与癌旁正常组织中验证这些关键靶点的表达。结果从TCGA数据库鉴别出1722个m^(7)G-lncRNAs。多因素Cox分析筛选出12个lncRNAs用于构建风险模型,其中AC003101.2、AC005014.2、AC008760.1、AC092944.1、AL1161729.4、AL301422.4、AP001619.1、AP003355.1和ZEB1-AS1为高风险lncRNAs,AC025171.4、AC073957.3及TNFRSF10A-AS1为低风险lncRNAs。ROC曲线显示风险模型对患者1年、3年、5年生存预测的AUC值分别为0.727、0.747、0.794。诺莫图预测患者预后的AUC值为0.794,校准曲线显示诺莫图对患者生存的预测与患者实际的生存基本一致。高风险组患者的T分期(T1~T2 vs T3~T4:P=0.034)、N分期(N0 vs N2:P=7.8e-08;N1 vs N2:P=0.00081)以及M分期(M0 vs M1:P=0.007)均高于低风险组患者。低风险组患者常伴随高微卫星不稳定状态(MSS vs MSI-H:P=0.034)。肿瘤干性指数与风险得分呈负相关(r=-0.19;P=7.3e-05)。高风险组患者基质细胞打分(P=0.0028)以及总打分(P=0.007)明显高于低风险组患者较高,激活的肥大细胞(r=-0.11;P=0.045)和静息CD4^(+)T细胞(r=-0.14;P=0.01)的表达也较低。多数免疫检查点在高风险患者中高表达(P<0.05)。蛋白印迹实验表明m^(7)G-lncRNAs调控的关键靶点ATXN2(P=0.006)and G3BP1(P=0.007)在4对结肠癌组织中表达均高于配对的癌旁正常组织。结论12个m^(7)G-lncRNAs构建的风险模型对结肠癌具有重要的预后价值,同时也能反映结肠癌患者肿瘤微环境及免疫治疗的疗效。
基金Supported by the National Natural Science Foundation of China(31801386,31371650)the Ministry of Science and Technology of China(2016YFD0100500)+2 种基金Funding from Harbin Science and Technology Bureau(2016RQYXJ018,2017RAQXJ104)Heilongjiang Natural Science Foundation(LC2018008)the Key Laboratory of Soybean Biology in the Chinese Ministry of Education,Northeast Agricultural University(SB17A01)。
文摘Soybean mutants withα-nullβ-conglycinin are associated with high nutritional value and low allergenic risk.Although long noncoding RNAs(lncRNAs)are increasingly recognized as functional regulatory components affecting eukaryotic gene expression,little is known about lnc RNA profiles inα-null-type hypoallergenic soybeans.In this study,a genome-wide integrative analysis of lncRNAs,m RNAs and epigenomic data in the soybean cgy-2(confirmedα-null)near-isogenic line(NIL)and its recurrent parent Dongnong47(DN47)was conducted.Nineteen novel lncRNAs that were differentially expressed(DE)only in the NIL at 18 days after flowering(i.e.,α-null-associated DE lncRNAs)were delected.Sixteen putative soybean stress-responsive lncRNAs were identified,and observed to regulate 257 stress-related genes DE in the NIL.This result indicated that theα-null allele might represent an intrinsic defect stress that altered the expression of various stress-related genes inα-null-type hypoallergenic soybean.Additionally,25 epigenetic-related lncRNAs regulated 831 DE epigenetic-related genes and simultaneously initiated multiple epigenetic activities,including ubiquitination,methylation and acetylation.Kyoto encyclopedia of genes and genomes(KEGG)analysis indicated that the biosynthesis of amino acids pathway was enriched with 83 DE genes regulated by nine DE lncRNAs.Changes in the expression of these lncRNAs and genes might be the reason for the altered amino acid composition in the NIL.Among all detected DE lncRNAs,MSTRG.12518 was the most conspicuousα-null-specific cis/trans-lnc RNA that played an efficient,versatile and vital role in the NIL.The data indicated that the lnc RNA profile differed between the NIL and DN47.Variations in lncRNAs,gene expression levels and DNA methylation states likely contributed to the intrinsic defect stress response mechanism inα-null-type hypoallergenic soybeans.
