Triple-negative breast cancer(TNBC)poses a significant challenge due to the lack of reliable prognostic gene signatures and an understanding of its immune behavior.Methods:We analyzed clinical information and mRNA exp...Triple-negative breast cancer(TNBC)poses a significant challenge due to the lack of reliable prognostic gene signatures and an understanding of its immune behavior.Methods:We analyzed clinical information and mRNA expression data from 162 TNBC patients in TCGA-BRCA and 320 patients in METABRIC-BRCA.Utilizing weighted gene coexpression network analysis,we pinpointed 34 TNBC immune genes linked to survival.The least absolute shrinkage and selection operator Cox regression method identified key TNBC immune candidates for prognosis prediction.We calculated chemotherapy sensitivity scores using the“pRRophetic”package in R software and assessed immunotherapy response using the Tumor Immune Dysfunction and Exclusion algorithm.Results:In this study,34 survival-related TNBC immune gene expression profiles were identified.A least absolute shrinkage and selection operator-Cox regression model was used and 15 candidates were prioritized,with a concomitant establishment of a robust risk immune classifier.The high-risk TNBC immune groups showed increased sensitivity to therapeutic agents like RO-3306,Tamoxifen,Sunitinib,JNK Inhibitor VIII,XMD11-85h,BX-912,and Tivozanib.An analysis of the Search Tool for Interaction of Chemicals database revealed the associations between the high-risk group and signaling pathways,such as those involving Rap1,Ras,and PI3K-Akt.The low-risk group showed a higher immunotherapy response rate,as observed through the tumor immune dysfunction and exclusion analysis in the TCGA-TNBC and METABRIC-TNBC cohorts.Conclusion:This study provides insights into the immune complexities of TNBC,paving the way for novel diagnostic approaches and precision treatment methods that exploit its immunological intricacies,thus offering hope for improved management and outcomes of this challenging disease.展开更多
BACKGROUND Single-cell sequencing technology provides the capability to analyze changes in specific cell types during the progression of disease.However,previous single-cell sequencing studies on gastric cancer(GC)hav...BACKGROUND Single-cell sequencing technology provides the capability to analyze changes in specific cell types during the progression of disease.However,previous single-cell sequencing studies on gastric cancer(GC)have largely focused on immune cells and stromal cells,and further elucidation is required regarding the alterations that occur in gastric epithelial cells during the development of GC.AIM To create a GC prediction model based on single-cell and bulk RNA sequencing(bulk RNA-seq)data.METHODS In this study,we conducted a comprehensive analysis by integrating three singlecell RNA sequencing(scRNA-seq)datasets and ten bulk RNA-seq datasets.Our analysis mainly focused on determining cell proportions and identifying differentially expressed genes(DEGs).Specifically,we performed differential expression analysis among epithelial cells in GC tissues and normal gastric tissues(NAGs)and utilized both single-cell and bulk RNA-seq data to establish a prediction model for GC.We further validated the accuracy of the GC prediction model in bulk RNA-seq data.We also used Kaplan–Meier plots to verify the correlation between genes in the prediction model and the prognosis of GC.RESULTS By analyzing scRNA-seq data from a total of 70707 cells from GC tissue,NAG,and chronic gastric tissue,10 cell types were identified,and DEGs in GC and normal epithelial cells were screened.After determining the DEGs in GC and normal gastric samples identified by bulk RNA-seq data,a GC predictive classifier was constructed using the Least absolute shrinkage and selection operator(LASSO)and random forest methods.The LASSO classifier showed good performance in both validation and model verification using The Cancer Genome Atlas and Genotype-Tissue Expression(GTEx)datasets[area under the curve(AUC)_min=0.988,AUC_1se=0.994],and the random forest model also achieved good results with the validation set(AUC=0.92).Genes TIMP1,PLOD3,CKS2,TYMP,TNFRSF10B,CPNE1,GDF15,BCAP31,and CLDN7 were identified to have high importance values in multiple GC predictive models,and KM-PLOTTER analysis showed their relevance to GC prognosis,suggesting their potential for use in GC diagnosis and treatment.CONCLUSION A predictive classifier was established based on the analysis of RNA-seq data,and the genes in it are expected to serve as auxiliary markers in the clinical diagnosis of GC.展开更多
功能超网络广泛地应用于脑疾病诊断和分类研究中,而现有的关于超网络创建的研究缺乏解释分组效应的能力或者仅考虑到脑区间组级的信息,这样构建的脑功能超网络会丢失一些有用的连接或包含一些虚假的信息,因此,考虑到脑区间的组结构问题...功能超网络广泛地应用于脑疾病诊断和分类研究中,而现有的关于超网络创建的研究缺乏解释分组效应的能力或者仅考虑到脑区间组级的信息,这样构建的脑功能超网络会丢失一些有用的连接或包含一些虚假的信息,因此,考虑到脑区间的组结构问题,引入sparse group Lasso(sgLasso)方法进一步改善超网络的创建。首先,利用sgLasso方法进行超网络创建;然后,引入两组超网络特有的属性指标进行特征提取以及特征选择,这些指标分别是基于单一节点的聚类系数和基于一对节点的聚类系数;最后,将特征选择后得到的两组有显著差异的特征通过多核学习进行特征融合和分类。实验结果表明,所提方法经过多特征融合取得了87.88%的分类准确率。该结果表明为了改善脑功能超网络的创建,需要考虑到组信息,但不能逼迫使用整组信息,可以适当地对组结构进行扩展。展开更多
<strong>Objective</strong>: This paper aims to explore clinical status and related influence factors of pressure injury (PI) in the elderly inpatients with kidney disease, so as to provide reference for th...<strong>Objective</strong>: This paper aims to explore clinical status and related influence factors of pressure injury (PI) in the elderly inpatients with kidney disease, so as to provide reference for the prevention and treatment of PI in the elderly inpatients with kidney disease. <strong>Methods</strong>: Retrospective collection method is adopted to collect 158 clinical cases of the elderly inpatients with kidney disease aged ≥ 60 in the Nephrology Department, the First Affiliated Hospital of Jinan University from January 2017 to December 2019, and then least absolute shrinkage and selection Operator (LASSO) regression analysis is used to analyze 17 possible influence factors;finally Logistic regression model is established to analyze and screen influence factors of risk. <strong>Results</strong>: 1) Among 158 elderly inpatients with medium and high risk of PI, the incidence of PI is 20.25%;the most common stage of injury is stage I (42.5%);sacrococcygeal (60%) is the high-risk site of pressure injury. 2) LASSO regression analysis shows that history of present respiratory infection/respiratory failure (<em>β </em>= 1.2714. <em>P</em> < 0.05) and hospitalization time (<em>β</em> = 0.4177. <em>P </em>< 0.05) are independent factors influencing PI risk in the elderly inpatients with kidney disease. <strong>Concl</strong><strong>usio</strong><strong>n</strong>: The elderly patients with kidney disease and PI risk are the high incidence population of hospital acquired PI;for the elderly inpatients with kidney disease and having respiratory infection history or respiratory failure, prolonged hospitalization will significantly increase the risk of PI. Therefore, targeted preventive and control measures should be taken to reduce the incidence of PI.展开更多
文摘Triple-negative breast cancer(TNBC)poses a significant challenge due to the lack of reliable prognostic gene signatures and an understanding of its immune behavior.Methods:We analyzed clinical information and mRNA expression data from 162 TNBC patients in TCGA-BRCA and 320 patients in METABRIC-BRCA.Utilizing weighted gene coexpression network analysis,we pinpointed 34 TNBC immune genes linked to survival.The least absolute shrinkage and selection operator Cox regression method identified key TNBC immune candidates for prognosis prediction.We calculated chemotherapy sensitivity scores using the“pRRophetic”package in R software and assessed immunotherapy response using the Tumor Immune Dysfunction and Exclusion algorithm.Results:In this study,34 survival-related TNBC immune gene expression profiles were identified.A least absolute shrinkage and selection operator-Cox regression model was used and 15 candidates were prioritized,with a concomitant establishment of a robust risk immune classifier.The high-risk TNBC immune groups showed increased sensitivity to therapeutic agents like RO-3306,Tamoxifen,Sunitinib,JNK Inhibitor VIII,XMD11-85h,BX-912,and Tivozanib.An analysis of the Search Tool for Interaction of Chemicals database revealed the associations between the high-risk group and signaling pathways,such as those involving Rap1,Ras,and PI3K-Akt.The low-risk group showed a higher immunotherapy response rate,as observed through the tumor immune dysfunction and exclusion analysis in the TCGA-TNBC and METABRIC-TNBC cohorts.Conclusion:This study provides insights into the immune complexities of TNBC,paving the way for novel diagnostic approaches and precision treatment methods that exploit its immunological intricacies,thus offering hope for improved management and outcomes of this challenging disease.
文摘BACKGROUND Single-cell sequencing technology provides the capability to analyze changes in specific cell types during the progression of disease.However,previous single-cell sequencing studies on gastric cancer(GC)have largely focused on immune cells and stromal cells,and further elucidation is required regarding the alterations that occur in gastric epithelial cells during the development of GC.AIM To create a GC prediction model based on single-cell and bulk RNA sequencing(bulk RNA-seq)data.METHODS In this study,we conducted a comprehensive analysis by integrating three singlecell RNA sequencing(scRNA-seq)datasets and ten bulk RNA-seq datasets.Our analysis mainly focused on determining cell proportions and identifying differentially expressed genes(DEGs).Specifically,we performed differential expression analysis among epithelial cells in GC tissues and normal gastric tissues(NAGs)and utilized both single-cell and bulk RNA-seq data to establish a prediction model for GC.We further validated the accuracy of the GC prediction model in bulk RNA-seq data.We also used Kaplan–Meier plots to verify the correlation between genes in the prediction model and the prognosis of GC.RESULTS By analyzing scRNA-seq data from a total of 70707 cells from GC tissue,NAG,and chronic gastric tissue,10 cell types were identified,and DEGs in GC and normal epithelial cells were screened.After determining the DEGs in GC and normal gastric samples identified by bulk RNA-seq data,a GC predictive classifier was constructed using the Least absolute shrinkage and selection operator(LASSO)and random forest methods.The LASSO classifier showed good performance in both validation and model verification using The Cancer Genome Atlas and Genotype-Tissue Expression(GTEx)datasets[area under the curve(AUC)_min=0.988,AUC_1se=0.994],and the random forest model also achieved good results with the validation set(AUC=0.92).Genes TIMP1,PLOD3,CKS2,TYMP,TNFRSF10B,CPNE1,GDF15,BCAP31,and CLDN7 were identified to have high importance values in multiple GC predictive models,and KM-PLOTTER analysis showed their relevance to GC prognosis,suggesting their potential for use in GC diagnosis and treatment.CONCLUSION A predictive classifier was established based on the analysis of RNA-seq data,and the genes in it are expected to serve as auxiliary markers in the clinical diagnosis of GC.
文摘功能超网络广泛地应用于脑疾病诊断和分类研究中,而现有的关于超网络创建的研究缺乏解释分组效应的能力或者仅考虑到脑区间组级的信息,这样构建的脑功能超网络会丢失一些有用的连接或包含一些虚假的信息,因此,考虑到脑区间的组结构问题,引入sparse group Lasso(sgLasso)方法进一步改善超网络的创建。首先,利用sgLasso方法进行超网络创建;然后,引入两组超网络特有的属性指标进行特征提取以及特征选择,这些指标分别是基于单一节点的聚类系数和基于一对节点的聚类系数;最后,将特征选择后得到的两组有显著差异的特征通过多核学习进行特征融合和分类。实验结果表明,所提方法经过多特征融合取得了87.88%的分类准确率。该结果表明为了改善脑功能超网络的创建,需要考虑到组信息,但不能逼迫使用整组信息,可以适当地对组结构进行扩展。
文摘<strong>Objective</strong>: This paper aims to explore clinical status and related influence factors of pressure injury (PI) in the elderly inpatients with kidney disease, so as to provide reference for the prevention and treatment of PI in the elderly inpatients with kidney disease. <strong>Methods</strong>: Retrospective collection method is adopted to collect 158 clinical cases of the elderly inpatients with kidney disease aged ≥ 60 in the Nephrology Department, the First Affiliated Hospital of Jinan University from January 2017 to December 2019, and then least absolute shrinkage and selection Operator (LASSO) regression analysis is used to analyze 17 possible influence factors;finally Logistic regression model is established to analyze and screen influence factors of risk. <strong>Results</strong>: 1) Among 158 elderly inpatients with medium and high risk of PI, the incidence of PI is 20.25%;the most common stage of injury is stage I (42.5%);sacrococcygeal (60%) is the high-risk site of pressure injury. 2) LASSO regression analysis shows that history of present respiratory infection/respiratory failure (<em>β </em>= 1.2714. <em>P</em> < 0.05) and hospitalization time (<em>β</em> = 0.4177. <em>P </em>< 0.05) are independent factors influencing PI risk in the elderly inpatients with kidney disease. <strong>Concl</strong><strong>usio</strong><strong>n</strong>: The elderly patients with kidney disease and PI risk are the high incidence population of hospital acquired PI;for the elderly inpatients with kidney disease and having respiratory infection history or respiratory failure, prolonged hospitalization will significantly increase the risk of PI. Therefore, targeted preventive and control measures should be taken to reduce the incidence of PI.
