近年来,单细胞RNA测序技术(scRNA-seq)已经被广泛使用。使用scRNA-seq技术获取的单细胞RNA数据集日益增多,数据集中的细胞数目和基因数目也不断提高。随着数据集维度的提升,支撑聚类分析所需的数据量和计算量呈指数形式剧增,传统的单细...近年来,单细胞RNA测序技术(scRNA-seq)已经被广泛使用。使用scRNA-seq技术获取的单细胞RNA数据集日益增多,数据集中的细胞数目和基因数目也不断提高。随着数据集维度的提升,支撑聚类分析所需的数据量和计算量呈指数形式剧增,传统的单细胞聚类分析方法难以应对高维度、高噪声的scRNA-seq数据。基于对抗约束自编码器的scRNA-seq数据聚类模型(Adversarially Constrained ScRNA-seq data Clustering,ACSC)通过引入自编码器的方法,对原始的高维度稀疏数据集进行降维,能够在公开单细胞数据集上具有更好的聚类准确率。展开更多
Although changes in mitochondrial morphology consistently associated with the aging of hematopoietic stem cells(HSCs),the specific molecular and cellular mechanisms involved are partially unclear.Live-cell super-resol...Although changes in mitochondrial morphology consistently associated with the aging of hematopoietic stem cells(HSCs),the specific molecular and cellular mechanisms involved are partially unclear.Live-cell super-resolution(SR)microscopy has been used to identify distinct HSC subsets that characterized by mitochondria unique morphologies and spatial distributions.The integration of SR microscopy with single-cell RNA sequencing enabled the classification of approximately 200 HSCs from young and aged mice into 5 discrete clusters.These clusters displayed molecular profiles that corresponded to the observed mitochondria states.An integrated approach combining RNA biomarker analysis and potential regulon assessment revealed previously unrecognized roles of GDF15 in mediating mitochondrial signals and morphologies that influence HSC fate.Thus,combining SR imaging with a bioinformatics pipeline provides an effective method for identifying key molecular players in specific phases of cellular transition,even with a relatively small dataset.展开更多
目的·探究白介素-1β(interleukin-1β,IL-1β)在预测口腔颌面间隙感染(oral and maxillofacial space infection,OMSI)严重程度的作用,并探索影响IL-1β释放的关键机制、关键细胞亚群及OMSI患者免疫细胞间通信网络。方法·选...目的·探究白介素-1β(interleukin-1β,IL-1β)在预测口腔颌面间隙感染(oral and maxillofacial space infection,OMSI)严重程度的作用,并探索影响IL-1β释放的关键机制、关键细胞亚群及OMSI患者免疫细胞间通信网络。方法·选取2023年1月至2023年11月就诊于上海交通大学医学院附属第九人民医院口腔外科的OMSI患者共62例,包括中度感染20例、重度感染21例和极重度感染21例,采用Logistic回归分析影响极重度感染的危险因素,绘制受试者操作特征曲线(receiver operating characteristic curve,ROC)评估上述指标预测极重度感染的能力。分别选取2例中度、重度和极重度患者的外周血单个核细胞(peripheral blood mononuclear cell,PBMC),结合2名健康对照(GSE224198)进行单细胞RNA测序(single-cell RNA sequencing,scRNA-seq)分析,明确促炎关键细胞亚群及关键基因随着感染程度加重的变化趋势,通过CellChat分析细胞间通信。通过实时荧光定量聚合酶链反应(quantitative real-time polymerase chain reaction,qPCR)及Westernblotting验证PBMC中炎性小体激活水平。结果·与中度和重度感染患者相比,极重度感染患者降钙素原(procalcitonin,PCT)(P<0.05)和IL-1β(P<0.05)水平显著升高。Logistic回归显示IL-1β是极重度感染的独立危险因素(OR=1.814,95%CI 1.256~2.621,P=0.002)。联合IL-1β和PCT预测极重度感染的ROC曲线下面积(area under the curve,AUC)为0.943。scRNA-seq显示,感染加重过程中单核细胞NOD样受体热蛋白结构域相关蛋白3(NOD-like receptor family pyrin domain-containing 3,NLRP3)基因、IL1B基因表达持续上调,中间型单核细胞是表达IL1B基因的主要细胞亚群。IL-1Β-IL-1R信号通信、趋化因子配体(C-C motif chemokine ligand,CCL)和细胞间黏附分子(intercellular adhesion molecule,ICAM)信号通信在单核细胞中显著增强;T细胞与单核细胞间巨噬细胞迁移抑制因子(macrophage migration inhibitory factor,MIF)信号通信亦显著增强。随着感染的加重,外周血NLRP3和IL1B的mRNA水平逐渐升高,NLRP3、caspase-1 p20、凋亡相关斑点样蛋白(apoptosis-associated speck-like protein containing a CARD,ASC)、IL-1β蛋白表达水平持续升高。结论·联合入院IL-1β和PCT水平可有效预测OMSI极重度感染。感染患者PBMC中NLRP3炎性小体激活。IL-1β的升高与中间型单核细胞密切相关,同时单核细胞介导的IL-1Β-IL-1R、CCL、ICAM信号通信及T细胞介导的MIF信号通信共同促进炎症反应。展开更多
文摘近年来,单细胞RNA测序技术(scRNA-seq)已经被广泛使用。使用scRNA-seq技术获取的单细胞RNA数据集日益增多,数据集中的细胞数目和基因数目也不断提高。随着数据集维度的提升,支撑聚类分析所需的数据量和计算量呈指数形式剧增,传统的单细胞聚类分析方法难以应对高维度、高噪声的scRNA-seq数据。基于对抗约束自编码器的scRNA-seq数据聚类模型(Adversarially Constrained ScRNA-seq data Clustering,ACSC)通过引入自编码器的方法,对原始的高维度稀疏数据集进行降维,能够在公开单细胞数据集上具有更好的聚类准确率。
文摘Although changes in mitochondrial morphology consistently associated with the aging of hematopoietic stem cells(HSCs),the specific molecular and cellular mechanisms involved are partially unclear.Live-cell super-resolution(SR)microscopy has been used to identify distinct HSC subsets that characterized by mitochondria unique morphologies and spatial distributions.The integration of SR microscopy with single-cell RNA sequencing enabled the classification of approximately 200 HSCs from young and aged mice into 5 discrete clusters.These clusters displayed molecular profiles that corresponded to the observed mitochondria states.An integrated approach combining RNA biomarker analysis and potential regulon assessment revealed previously unrecognized roles of GDF15 in mediating mitochondrial signals and morphologies that influence HSC fate.Thus,combining SR imaging with a bioinformatics pipeline provides an effective method for identifying key molecular players in specific phases of cellular transition,even with a relatively small dataset.
