Neonate lung injury is a common phenomenon after perinatal asphyxia To evaluate proteomic profiles of exosomes isolated from lung injury offspring serum after perinatal asphyxia. Serum samples were collected at 12 h, 24 h, and 72 h after birth in neonates with perinatal asphyxia-induced lung injury. Exosomes were isolated, and the concentration and size distribution were assessed. The exosome surface markers CD9, CD63, CD81, HSP70, and TSG101 were detected by Western blot. The exosome proteins were evaluated by quantitative proteomics using a tandem mass tag (TMT). All the identified proteins were submitted to the Weighted Gene Co-Expression Network Analysis (WGCNA), GO function, and KEGG pathway analysis. A protein-protein interaction network (PPI) was utilized to identify hub proteins with the Cytohubba plugin of Cytoscape. The exosomes were round or oval vesicular structures at a diameter range of 100-200 nm, and the size distribution was standard and consistent. Exosome surface markers CD9, CD63, CD81, HSP70, and TSG101 were detected. 444 out of 450 proteins were mapped with gene names. A brown module containing 71 proteins was highly linked with the 12 h phenotype and was predominantly concentrated in lipoprotein and complement activation. The top 10 proteins, APOA1, APOB, APOE, LPA, APOA2, CP, C3, FGB, FGA, and TF, were determined as hub proteins. The present study demonstrates comprehensive information for understanding molecular changes of lung injury following perinatal asphyxia, which provides a reliable basis for screening potential biomarkers and therapeutic targets in the clinic.
{"title":"Proteome Profiling of Serum Exosomes from Newborns with Lung Injury after Perinatal Asphyxia","authors":"Haiying Li, Chuangli Hao, Feifei Shen, Ying Li, W. Gu, Xingmei Yu, Youjia Wu, Gui-hai Suo, Yu-qin Zheng","doi":"10.2174/1570164620666230714115822","DOIUrl":"https://doi.org/10.2174/1570164620666230714115822","url":null,"abstract":"\u0000\u0000Neonate lung injury is a common phenomenon after perinatal asphyxia\u0000\u0000\u0000\u0000To evaluate proteomic profiles of exosomes isolated from lung injury offspring serum after perinatal asphyxia.\u0000\u0000\u0000\u0000Serum samples were collected at 12 h, 24 h, and 72 h after birth in neonates with perinatal asphyxia-induced lung injury. Exosomes were isolated, and the concentration and size distribution were assessed. The exosome surface markers CD9, CD63, CD81, HSP70, and TSG101 were detected by Western blot. The exosome proteins were evaluated by quantitative proteomics using a tandem mass tag (TMT). All the identified proteins were submitted to the Weighted Gene Co-Expression Network Analysis (WGCNA), GO function, and KEGG pathway analysis. A protein-protein interaction network (PPI) was utilized to identify hub proteins with the Cytohubba plugin of Cytoscape.\u0000\u0000\u0000\u0000The exosomes were round or oval vesicular structures at a diameter range of 100-200 nm, and the size distribution was standard and consistent. Exosome surface markers CD9, CD63, CD81, HSP70, and TSG101 were detected. 444 out of 450 proteins were mapped with gene names. A brown module containing 71 proteins was highly linked with the 12 h phenotype and was predominantly concentrated in lipoprotein and complement activation. The top 10 proteins, APOA1, APOB, APOE, LPA, APOA2, CP, C3, FGB, FGA, and TF, were determined as hub proteins.\u0000\u0000\u0000\u0000The present study demonstrates comprehensive information for understanding molecular changes of lung injury following perinatal asphyxia, which provides a reliable basis for screening potential biomarkers and therapeutic targets in the clinic.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72521095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-08DOI: 10.2174/1570164620666230508140912
Ajay Vir Singh, Shweta Kushwaha, R. Yadav, Kusuma Sai Davuluri, A. Goel, Devendra Singh Chauhan
Despite the crucial involvement of vitronectin in affecting the perseverance of certain respiratory pathogens and the progression of several lung diseases, the association of vitronectin with tuberculosis (TB) has been poorly studied. The present study aimed to determine whether vitronectin levels are altered in TB patients compared to healthy humans. Twenty-four laboratory-confirmed tuberculosis patients (pulmonary TB -8, extrapulmonary-8 and HIV-TB dual infected -8) and eight healthy individuals were included in this study. The quantitative detection of vitronectin in serum-derived exosomes of study participants was performed using a sandwich enzyme-linked immunosorbent assay. Measured concentrations of vitronectin were compared with the demographic variables of the study participants and between the study groups. The Mann–Whitney U unpaired test was used in statistical analysis, and the p-value < 0.05 was considered statistically significant. Vitronectin was detected in serum-derived exosomes of all study participants. The demographic characteristics (gender, age, smoking and alcohol consumption habit, history of cough, and weight loss) were not significantly correlated with the vitronectin concentrations of the study participants (p-value> 0.05). The level of vitronectin was higher in patients with pulmonary TB (778.54 ng/l) and extra-pulmonary-TB patients (773.04 ng/l) while lower in HIV-pulmonary TB dual-infected patients (354.86 ng/l) as compared to healthy humans (456.20ng/l). There was a significant difference between vitronectin concentrations of patients with pulmonary TB (p-value: 0.0002) and extrapulmonary TB (p-value: 0.003) compared to healthy controls. The present study reported an increased concentration of vitronectin in serum-derived exosomes of pulmonary and extra-pulmonary TB patients compared to HIV-TB dual-infected patients and healthy humans. Further studies are needed to fully elucidate the diagnostic potential and functionalities of higher concentrations of vitronectin in the pathogenic processes of human TB.
尽管玻璃体粘连蛋白在影响某些呼吸道病原体的持久性和几种肺部疾病的进展中起着至关重要的作用，但玻璃体粘连蛋白与结核病(TB)的关系研究甚少。目前的研究旨在确定结核患者的玻璃体粘连蛋白水平是否与健康人相比有所改变。本研究纳入24例实验室确诊结核病患者(肺结核-8、肺外-8和HIV-TB双重感染-8)和8例健康个体。使用三明治酶联免疫吸附法定量检测研究参与者血清衍生外泌体中的玻璃体粘连蛋白。将检测到的玻璃体粘连素浓度与研究参与者的人口学变量以及研究组之间的变量进行比较。统计学分析采用Mann-Whitney U unpaired检验，p值< 0.05认为有统计学意义。在所有研究参与者的血清衍生外泌体中检测到玻璃体连接蛋白。人口统计学特征(性别、年龄、吸烟和饮酒习惯、咳嗽史和体重减轻)与研究参与者的玻璃体粘连素浓度无显著相关性(p值> 0.05)。肺结核患者(778.54 ng/l)和肺外结核患者(773.04 ng/l)的玻璃连接蛋白水平较高，而hiv -肺结核双感染患者(354.86 ng/l)的玻璃连接蛋白水平低于健康人(456.20ng/l)。肺结核患者的玻璃体粘连蛋白浓度(p值:0.0002)和肺外结核患者的玻璃体粘连蛋白浓度(p值:0.003)与健康对照有显著差异。本研究报道，与HIV-TB双重感染患者和健康人相比，肺部和肺外结核患者血清衍生黏着体中的玻璃体粘连蛋白浓度增加。需要进一步的研究来充分阐明较高浓度的玻璃体粘连蛋白在人结核发病过程中的诊断潜力和功能。
{"title":"Higher Abundance of Vitronectin (S-protein) in Serum-derived Exosomes\u0000of Pulmonary and Extra-Pulmonary Tuberculosis Patients as Compared\u0000to HIV-Tuberculosis Dual-infected Patients and Healthy Humans","authors":"Ajay Vir Singh, Shweta Kushwaha, R. Yadav, Kusuma Sai Davuluri, A. Goel, Devendra Singh Chauhan","doi":"10.2174/1570164620666230508140912","DOIUrl":"https://doi.org/10.2174/1570164620666230508140912","url":null,"abstract":"\u0000\u0000Despite the crucial involvement of vitronectin in affecting the perseverance\u0000of certain respiratory pathogens and the progression of several lung diseases, the association of vitronectin with tuberculosis (TB) has been poorly studied. The present study aimed to determine whether\u0000vitronectin levels are altered in TB patients compared to healthy humans.\u0000\u0000\u0000\u0000Twenty-four laboratory-confirmed tuberculosis patients (pulmonary TB -8, extrapulmonary-8 and HIV-TB dual infected -8) and eight healthy individuals were included in this study.\u0000The quantitative detection of vitronectin in serum-derived exosomes of study participants was performed using a sandwich enzyme-linked immunosorbent assay. Measured concentrations of vitronectin were compared with the demographic variables of the study participants and between the study\u0000groups. The Mann–Whitney U unpaired test was used in statistical analysis, and the p-value < 0.05\u0000was considered statistically significant.\u0000\u0000\u0000\u0000Vitronectin was detected in serum-derived exosomes of all study participants. The demographic characteristics (gender, age, smoking and alcohol consumption habit, history of cough, and\u0000weight loss) were not significantly correlated with the vitronectin concentrations of the study participants (p-value> 0.05). The level of vitronectin was higher in patients with pulmonary TB (778.54 ng/l)\u0000and extra-pulmonary-TB patients (773.04 ng/l) while lower in HIV-pulmonary TB dual-infected patients (354.86 ng/l) as compared to healthy humans (456.20ng/l). There was a significant difference\u0000between vitronectin concentrations of patients with pulmonary TB (p-value: 0.0002) and extrapulmonary TB (p-value: 0.003) compared to healthy controls.\u0000\u0000\u0000\u0000The present study reported an increased concentration of vitronectin in serum-derived\u0000exosomes of pulmonary and extra-pulmonary TB patients compared to HIV-TB dual-infected patients\u0000and healthy humans. Further studies are needed to fully elucidate the diagnostic potential and functionalities of higher concentrations of vitronectin in the pathogenic processes of human TB.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90681594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-03DOI: 10.2174/1570164620666230503163349
Ping Zhang, Yali Le, Chenchen Geng, Guanghui Zhao, Xiao‐Qiang Gao, Shuzhen Zhu, Ziqiang Liu
S100 calcium-binding protein A11 (S100A11) has important roles in tumorigenesis and multiple cancer progression. In this study, we aimed to analyze the expression and prognostic value of S100A11 across cancers and further explore the relationship between S100A11 and the tumor immune microenvironment. We analyzed the differential expression of S100A11 in the TIMER, GEPIA, and BioGPS databases and searched for its prognostic impact in the GEPIA and Kaplan-Meier plotter databases. We used the SangerBox database to investigate the relationship between S100A11 expression and the tumor immune microenvironment. The TIMER database explored the relationship between S100A11 expression and tumor immune-infiltrated cells (TILs). Correlation analysis of S100A11 expression with clinical parameters in thyroid carcinoma (THCA) was performed using the UALCAN database. The co-expression network of S100A11 in THCA was explored through the LinkedOmics database. RT‒qPCR and immunohistochemical (IHC) staining were used to analyze the expression level of S100A11 in THCA. S100A11 expression was higher in many tumors than in paired normal tissues, and increased expression was associated with poor prognosis, including overall survival (OS), recurrence-free survival (RFS), and disease-free survival (DFS). S100A11 was differentially expressed in immune subtypes and molecular subtypes of some cancers. The expression of S100A11 was correlated with immune checkpoints (ICP), tumor mutational burden (TMB), microsatellite instability (MSI), neoantigens, and TILs. The methylation level of S100A11 was negatively correlated with mRNA expression. S100A11 expression had a specific correlation with the clinical parameters of THCA. In THCA, the coexpression network of S100A11 was mainly involved in regulating inflammation and immune responses. RT‒qPCR and IHC staining confirmed that S100A11 was upregulated in THCA. S100A11 may be related to the regulation of the tumor microenvironment. S100A11 may serve as a potential pan-cancer biomarker for prognosis. S100A11 could be a potential target for THCA immunotherapy.
{"title":"A pan-cancer signature for S100A11------ Prognostic and Immunotherapeutic Value","authors":"Ping Zhang, Yali Le, Chenchen Geng, Guanghui Zhao, Xiao‐Qiang Gao, Shuzhen Zhu, Ziqiang Liu","doi":"10.2174/1570164620666230503163349","DOIUrl":"https://doi.org/10.2174/1570164620666230503163349","url":null,"abstract":"\u0000\u0000S100 calcium-binding protein A11 (S100A11) has important roles in tumorigenesis and multiple cancer progression. In this study, we aimed to analyze the expression and prognostic value of S100A11 across cancers and further explore the relationship between S100A11 and the tumor immune microenvironment.\u0000\u0000\u0000\u0000We analyzed the differential expression of S100A11 in the TIMER, GEPIA, and BioGPS databases and searched for its prognostic impact in the GEPIA and Kaplan-Meier plotter databases. We used the SangerBox database to investigate the relationship between S100A11 expression and the tumor immune microenvironment. The TIMER database explored the relationship between S100A11 expression and tumor immune-infiltrated cells (TILs). Correlation analysis of S100A11 expression with clinical parameters in thyroid carcinoma (THCA) was performed using the UALCAN database. The co-expression network of S100A11 in THCA was explored through the LinkedOmics database. RT‒qPCR and immunohistochemical (IHC) staining were used to analyze the expression level of S100A11 in THCA.\u0000\u0000\u0000\u0000S100A11 expression was higher in many tumors than in paired normal tissues, and increased expression was associated with poor prognosis, including overall survival (OS), recurrence-free survival (RFS), and disease-free survival (DFS). S100A11 was differentially expressed in immune subtypes and molecular subtypes of some cancers. The expression of S100A11 was correlated with immune checkpoints (ICP), tumor mutational burden (TMB), microsatellite instability (MSI), neoantigens, and TILs. The methylation level of S100A11 was negatively correlated with mRNA expression. S100A11 expression had a specific correlation with the clinical parameters of THCA. In THCA, the coexpression network of S100A11 was mainly involved in regulating inflammation and immune responses. RT‒qPCR and IHC staining confirmed that S100A11 was upregulated in THCA.\u0000\u0000\u0000\u0000S100A11 may be related to the regulation of the tumor microenvironment. S100A11 may serve as a potential pan-cancer biomarker for prognosis. S100A11 could be a potential target for THCA immunotherapy.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86895184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-31DOI: 10.2174/1570164620666230331102317
Juan Manuel Guzman-Flores, Fernando Martínez-Esquivias, Julieta Sarai Becerra-Ruiz, Sandra Berenice Vázquez-Rodríguez
Dental caries can affect the expression of salivary proteins. Proteomics allows us to analyze and identify many proteins in a single sample and experiment; bioinformatics is essential to analyze proteomic data. Objective: This research aims to identify and integrate the main differentially expressed proteins in the saliva of children with caries, infer their Gene Ontology and interactions, and identify regulatory factors. Dental caries can affect the expression of salivary proteins. Proteomics allows us to analyze and identify many proteins in a single sample and a single experiment; bioinformatics is essential to analyze proteomic data. We extracted proteins from a bibliographic search in the Scopus and PubMed databases. We analyzed these proteins with the web application ShinyGO v0.76, ToppGene and NetworkAnalyst 3.0, and the Cytoscape platform. This research aims to identify and integrate the main differentially expressed proteins in the saliva of children with caries, infer their Gene Ontology and interactions, and identify regulatory factors. In the literature search, we extracted 26 differentially expressed proteins. These proteins show enrichment in antioxidant activity, antimicrobial response, immune response, and vitamin and mineral metabolism. We found three transcription factors that regulate most of the genes of these proteins: TFDP1, SOX13, and BCL6. We also identified three microRNAs that highly restrict the expression of these proteins: hsa-mir-124-3p, hsa-mir-27a-3p, and hsa-mir-26b-5p. On the other hand, the main drugs associated with these proteins are potassium persulfate, aluminum, and cadmium. The differentially expressed proteins in the saliva of children with dental caries are involved in metabolic pathways related to folate, selenium, and vitamin B12 metabolism. In addition, some transcription factors (TFDP1, SOX13, and BCL6) miRNAs (hsa-mir-124-3p, hsa-mir-27a-3p, and hsa-mir-26b-5p) and chemical compounds (potassium persulfate, aluminum, and cadmium) can regulate the genes, mRNAs or proteins studied. The differentially expressed proteins in the saliva of children with dental caries reflect the cariogenic state of the patients and the immune system's response to combat this condition. These proteins participate in numerous important interactions, and transcription factors, microRNAs, and drugs can regulate their expression. None
{"title":"Integration of proteomic data obtained from the saliva of children with caries through bioinformatic analysis","authors":"Juan Manuel Guzman-Flores, Fernando Martínez-Esquivias, Julieta Sarai Becerra-Ruiz, Sandra Berenice Vázquez-Rodríguez","doi":"10.2174/1570164620666230331102317","DOIUrl":"https://doi.org/10.2174/1570164620666230331102317","url":null,"abstract":"\u0000\u0000Dental caries can affect the expression of salivary proteins. Proteomics allows us to analyze and identify many proteins in a single sample and experiment; bioinformatics is essential to analyze proteomic data. Objective: This research aims to identify and integrate the main differentially expressed proteins in the saliva of children with caries, infer their Gene Ontology and interactions, and identify regulatory factors.\u0000\u0000\u0000\u0000Dental caries can affect the expression of salivary proteins. Proteomics allows us to analyze and identify many proteins in a single sample and a single experiment; bioinformatics is essential to analyze proteomic data.\u0000\u0000\u0000\u0000We extracted proteins from a bibliographic search in the Scopus and PubMed databases. We analyzed these proteins with the web application ShinyGO v0.76, ToppGene and NetworkAnalyst 3.0, and the Cytoscape platform.\u0000\u0000\u0000\u0000This research aims to identify and integrate the main differentially expressed proteins in the saliva of children with caries, infer their Gene Ontology and interactions, and identify regulatory factors.\u0000\u0000\u0000\u0000In the literature search, we extracted 26 differentially expressed proteins. These proteins show enrichment in antioxidant activity, antimicrobial response, immune response, and vitamin and mineral metabolism. We found three transcription factors that regulate most of the genes of these proteins: TFDP1, SOX13, and BCL6. We also identified three microRNAs that highly restrict the expression of these proteins: hsa-mir-124-3p, hsa-mir-27a-3p, and hsa-mir-26b-5p. On the other hand, the main drugs associated with these proteins are potassium persulfate, aluminum, and cadmium.\u0000\u0000\u0000\u0000The differentially expressed proteins in the saliva of children with dental caries are involved in metabolic pathways related to folate, selenium, and vitamin B12 metabolism. In addition, some transcription factors (TFDP1, SOX13, and BCL6) miRNAs (hsa-mir-124-3p, hsa-mir-27a-3p, and hsa-mir-26b-5p) and chemical compounds (potassium persulfate, aluminum, and cadmium) can regulate the genes, mRNAs or proteins studied.\u0000\u0000\u0000\u0000The differentially expressed proteins in the saliva of children with dental caries reflect the cariogenic state of the patients and the immune system's response to combat this condition. These proteins participate in numerous important interactions, and transcription factors, microRNAs, and drugs can regulate their expression.\u0000\u0000\u0000\u0000None\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75236233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-28DOI: 10.2174/1570164620666230328120621
Baochang Su, Sheng-Fu Yang, Xun-da Ye, Zhang-Xiong Huang, Yuwei Song, San-Huang Xu
Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer, and it is a significant global health problem causing significant morbidity and mortality. Long noncoding RNAs (lncRNAs) have been identified as a class of gene expression regulators that play a critical role in the immune system. However, the function of lncRNAs in the immune microenvironment of ccRCC remains unclear Long noncoding RNAs (lncRNAs) have been identified as a class of gene expression regulators that play a critical role in the immune system. The least absolute shrinkage and selection operator regression techniques, robust likelihoodbased survival modeling, and Cox regression analysis were used to identify potential prognostic lncRNAs. The relationship between the signature and the tumor's immune infiltration was analyzed using gene set enrichment analysis and the subset analysis of immune cells. LINC00839, LINC01671, AC093673, and AC008760 were selected to create a risk signature. For 3-, 5-, and 8-year overall survival rates, the areas under the receiver operating characteristic curves of the risk signature set were 0.689, 0.721, and 0.719 in the training set and 0.683, 0.686, and 0.665 in the validation set, respectively. A model and nomogram were constructed using the risk signature and clinical characteristics. The C-index of the model was 0.78 in the training set and 0.773 in the validation set. he relationship between the signature and the tumor's immune infiltration was analyzed using gene set enrichment analysis and the subset analysis of immune cells. A model and nomogram were constructed using the risk signature and clinical characteristics. The risk signature reflects the tumor's current immune infiltration and is associated with regulatory T cell differentiation, interleukin 17 production regulation, negative regulation of inflammatory response to an antigenic stimulus, and the IL6-JAK-STAT3 signaling pathway. This study provides prognostic information for ccRCC patients and may also serve as a useful clue for future immunotherapies. The study's first major strength was the use of stricter criteria (both sample and lncRNAs) to increase the precision of the findings and the model's efficiency. Simultaneously, a variety of calculation methods are used to ensure the validity of the results, including univariate/multivariate Cox regression, robust likelihood-based survival modeling, and LASSO regression analyses. Second, the immune-cell components of the samples were thoroughly analyzed (not just using immune scoring) in order to establish a more detailed relationship between tumor immune infiltration and risk signature. Thirdly, a visually recognizable nomogram of the model has been created for clinicians' ease of use. no avaiable
{"title":"LINC00839, LINC01671, AC093673 and AC008760 are Associated with\u0000the Prognosis and Immune Infiltration of Clear-cell Renal Cell Carcinoma","authors":"Baochang Su, Sheng-Fu Yang, Xun-da Ye, Zhang-Xiong Huang, Yuwei Song, San-Huang Xu","doi":"10.2174/1570164620666230328120621","DOIUrl":"https://doi.org/10.2174/1570164620666230328120621","url":null,"abstract":"\u0000\u0000Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney\u0000cancer, and it is a significant global health problem causing significant morbidity and mortality. Long\u0000noncoding RNAs (lncRNAs) have been identified as a class of gene expression regulators that play a\u0000critical role in the immune system. However, the function of lncRNAs in the immune microenvironment of ccRCC remains unclear\u0000\u0000\u0000\u0000Long noncoding RNAs (lncRNAs) have been identified as a class of gene expression regulators that play a critical role in the immune system.\u0000\u0000\u0000\u0000The least absolute shrinkage and selection operator regression techniques, robust likelihoodbased survival modeling, and Cox regression analysis were used to identify potential prognostic\u0000lncRNAs. The relationship between the signature and the tumor's immune infiltration was analyzed\u0000using gene set enrichment analysis and the subset analysis of immune cells.\u0000\u0000\u0000\u0000LINC00839, LINC01671, AC093673, and AC008760 were selected to create a risk signature.\u0000For 3-, 5-, and 8-year overall survival rates, the areas under the receiver operating characteristic curves of\u0000the risk signature set were 0.689, 0.721, and 0.719 in the training set and 0.683, 0.686, and 0.665 in the\u0000validation set, respectively. A model and nomogram were constructed using the risk signature and clinical characteristics. The C-index of the model was 0.78 in the training set and 0.773 in the validation set.\u0000\u0000\u0000\u0000he relationship between the signature and the tumor's immune infiltration was analyzed using gene set enrichment analysis and the subset analysis of immune cells. A model and nomogram were constructed using the risk signature and clinical characteristics.\u0000\u0000\u0000\u0000The risk signature reflects the tumor's current immune infiltration and is associated with\u0000regulatory T cell differentiation, interleukin 17 production regulation, negative regulation of inflammatory response to an antigenic stimulus, and the IL6-JAK-STAT3 signaling pathway. This study\u0000provides prognostic information for ccRCC patients and may also serve as a useful clue for future\u0000immunotherapies.\u0000\u0000\u0000\u0000The study's first major strength was the use of stricter criteria (both sample and lncRNAs) to increase the precision of the findings and the model's efficiency. Simultaneously, a variety of calculation methods are used to ensure the validity of the results, including univariate/multivariate Cox regression, robust likelihood-based survival modeling, and LASSO regression analyses. Second, the immune-cell components of the samples were thoroughly analyzed (not just using immune scoring) in order to establish a more detailed relationship between tumor immune infiltration and risk signature. Thirdly, a visually recognizable nomogram of the model has been created for clinicians' ease of use.\u0000\u0000\u0000\u0000no avaiable\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90807976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-14DOI: 10.2174/1570164620666230314102530
Wenzhong Liu, Hualan Li
Such factors as diabetes and obesity can dramatically worsen COVID-19 symptoms. In addition, macrophage accumulation in adipose tissue is related to obesity. Therefore, macrophages play a significant role in raising COVID-19 susceptibility and severity in diabetes and obese patients. Lipopolysaccharide activates the natural immune system response in obese and diabetic patients’ adipose tissue and increases the risk of susceptibility and severity of COVID-19. In this study, the functional impact of SARS-CoV-2 ORF7a on macrophages was analyzed using a domain-searching bioinformatics technique. Ca2+ binding domain, kinase and phosphatase, SMB/SRCR, LBP/BPI/CETP, ABC, TIR,PARP, Flavivirus Cap enzyme, Cyclin, and other domains have been identified in SARS-CoV-2 ORF7a. ORF7a binds to oxidized low-density lipoprotein cholesterol particles by the macrophage receptor-like domains such as SMB/SRCR and enters macrophages via macropinocytosis. Then, ORF7a prevents 18 S rRNA maturation and adds flavivirus cap 0/1/2 to mRNA to interfere with transcription and translation via PARP, Flavivirus Cap enzyme, and other associated domains. Meanwhile, ORF7a activates and promotes G2/M phase transition via cyclin-related enzymatic activity domains. The destructive activity of ORF7a hijacks the nitric oxide release pathway of macrophages and promotes macrophage death, enabling the virus to elude the innate immune system and aggravate diabetes-related problems in patients. We speculated that cells infected by the SARS-COV-2 virus often used its surface lipopolysaccharides to build expanded barriers to resist T cells, NK cells, and drugs.
{"title":"ORF7a Palsies Macrophage to Worsen Diabetes by SMB/BPI/ABC Domains and PARP/Cap/Cyclin Enzyme System","authors":"Wenzhong Liu, Hualan Li","doi":"10.2174/1570164620666230314102530","DOIUrl":"https://doi.org/10.2174/1570164620666230314102530","url":null,"abstract":"\u0000\u0000Such factors as diabetes and obesity can dramatically worsen COVID-19 symptoms. In addition, macrophage accumulation in adipose tissue is related to obesity. Therefore, macrophages play a significant role in raising COVID-19 susceptibility and severity in diabetes and obese patients.\u0000\u0000\u0000\u0000Lipopolysaccharide activates the natural immune system response in obese and diabetic patients’ adipose tissue and increases the risk of susceptibility and severity of COVID-19.\u0000\u0000\u0000\u0000In this study, the functional impact of SARS-CoV-2 ORF7a on macrophages was analyzed using a domain-searching bioinformatics technique. Ca2+ binding domain, kinase and phosphatase, SMB/SRCR, LBP/BPI/CETP, ABC, TIR,PARP, Flavivirus Cap enzyme, Cyclin, and other domains have been identified in SARS-CoV-2 ORF7a. ORF7a binds to oxidized low-density lipoprotein cholesterol particles by the macrophage receptor-like domains such as SMB/SRCR and enters macrophages via macropinocytosis. Then, ORF7a prevents 18 S rRNA maturation and adds flavivirus cap 0/1/2 to mRNA to interfere with transcription and translation via PARP, Flavivirus Cap enzyme, and other associated domains.\u0000\u0000\u0000\u0000Meanwhile, ORF7a activates and promotes G2/M phase transition via cyclin-related enzymatic activity domains.\u0000\u0000\u0000\u0000The destructive activity of ORF7a hijacks the nitric oxide release pathway of macrophages and promotes macrophage death, enabling the virus to elude the innate immune system and aggravate diabetes-related problems in patients.\u0000\u0000\u0000\u0000We speculated that cells infected by the SARS-COV-2 virus often used its surface lipopolysaccharides to build expanded barriers to resist T cells, NK cells, and drugs.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91158532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-20DOI: 10.2174/1570164620666230220112500
A. Nikolić, Kevin J. Mark, S. Dragicevic, T. Babic, K. Milosevic, B. Nestorović, V. Beškoski
Leukocytes are key cellular effectors of inflammation in asthma and understanding their function in this disease is of crucial importance. Blood leukocytes reflect the actions of their counterparts in the lungs and they can be obtained through minimal invasive procedures as part of the peripheral blood. Leukocytes are key cellular effectors of inflammation in asthma and understanding their function in this disease is of crucial importance. Blood leukocytes reflect the actions of their counterparts in the lungs and they can be obtained through minimal invasive procedure as part of the peripheral blood. The aim of the study was to identify proteins in blood leukocyte proteomes that respond to ex vivo treatment by prednisone in order to pinpoint candidates for predictive biomarkers in corticosteroid-responsive asthma. The study included five children diagnosed with asthma and five healthy children. After the ex vivo treatment of blood samples with prednisone, lysis of erythrocytes was performed and proteins were extracted from the remaining leukocytes by ultrasonic disintegration. Protein extracts were analyzed by reversed phase nano-liquidchromatography–tandem mass spectrometry (LC–MS/MS). The stimulation of asthmatics' leukocytes with prednisone has led to an increase in the levels of FYB (fold change 3.4) and LYZ (fold change 2.2) with a statistical significance of p<0.005. The two proteins with expressions significantly altered upon the prednisone treatment should be further explored as tools to evaluate the patient's response before therapy administration, especially when lung function measurements are not possible, as is the case with young pediatric patients. The approach that entails ex vivo response of blood leukocytes to therapeutics can facilitate asthma management and help overcome the need for therapeutic adjustments in a clinical setting. /
{"title":"Pilot Study of the ex vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma","authors":"A. Nikolić, Kevin J. Mark, S. Dragicevic, T. Babic, K. Milosevic, B. Nestorović, V. Beškoski","doi":"10.2174/1570164620666230220112500","DOIUrl":"https://doi.org/10.2174/1570164620666230220112500","url":null,"abstract":"\u0000\u0000Leukocytes are key cellular effectors of inflammation in asthma and understanding their function in this disease is of crucial importance. Blood leukocytes reflect the actions of their counterparts in the lungs and they can be obtained through minimal invasive procedures as part of the peripheral blood.\u0000\u0000\u0000\u0000Leukocytes are key cellular effectors of inflammation in asthma and understanding their function in this disease is of crucial importance. Blood leukocytes reflect the actions of their counterparts in the lungs and they can be obtained through minimal invasive procedure as part of the peripheral blood.\u0000\u0000\u0000\u0000The aim of the study was to identify proteins in blood leukocyte proteomes that respond to ex vivo treatment by prednisone in order to pinpoint candidates for predictive biomarkers in corticosteroid-responsive asthma.\u0000\u0000\u0000\u0000The study included five children diagnosed with asthma and five healthy children. After the ex vivo treatment of blood samples with prednisone, lysis of erythrocytes was performed and proteins were extracted from the remaining leukocytes by ultrasonic disintegration. Protein extracts were analyzed by reversed phase nano-liquidchromatography–tandem mass spectrometry (LC–MS/MS).\u0000\u0000\u0000\u0000The stimulation of asthmatics' leukocytes with prednisone has led to an increase in the levels of FYB (fold change 3.4) and LYZ (fold change 2.2) with a statistical significance of p<0.005. The two proteins with expressions significantly altered upon the prednisone treatment should be further explored as tools to evaluate the patient's response before therapy administration, especially when lung function measurements are not possible, as is the case with young pediatric patients.\u0000\u0000\u0000\u0000The approach that entails ex vivo response of blood leukocytes to therapeutics can facilitate asthma management and help overcome the need for therapeutic adjustments in a clinical setting.\u0000\u0000\u0000\u0000/\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2023-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74731257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Following the publication of the original article [1], the authors reported that the complete grant number of the funding was omitted. In this correction, the incorrect and correct grant numbers are mentioned. The original publication of this article has been corrected.
The funding acknowledgement published previously is as follows:
The study was funded by Fundamental Research Grant Scheme (FRGS) by the Ministry of Education, Malaysia, Grant number: FP067-2018A, Geran Penyelidikan Fakulti by the Faculty of Medicine, University of Malaya, Grant number: GPF001C- 2019, and UGC mid-career award, Grant number: F.19-221/2018 (BSR) dt. 28.03.2018.
We would like to request a revision to one of the funding numbers (in blue) in the funding acknowledgement below: The correct funding acknowledgement is:
The study was funded by Fundamental Research Grant Scheme (FRGS) by the Ministry of Education, Malaysia, Grant number: FRGS/1/2018/STG05/UM/02/5, Geran Penyelidikan Fakulti by the Faculty of Medicine, University of Malaya, Grant number: GPF001C-2019 and UGC mid-career award, Grant number: F.19-221/2018 (BSR) dt. 28.03.2018.
The original article can be found online at: https://www.eurekaselect.com/public/article/109117.
{"title":"Corrigendum to: Cancer Proteomics: New Horizons and Insights into Therapeutic Applications","authors":"Jaime Jacqueline Jayapalan, Perumal Subramanian, Puteri Shafinaz Abdul-Rahman","doi":"10.2174/157016462001230717161726","DOIUrl":"https://doi.org/10.2174/157016462001230717161726","url":null,"abstract":"Following the publication of the original article [1], the authors reported that the complete grant number of the funding was omitted. In this correction, the incorrect and correct grant numbers are mentioned. The original publication of this article has been corrected. <P> The funding acknowledgement published previously is as follows: <P> The study was funded by Fundamental Research Grant Scheme (FRGS) by the Ministry of Education, Malaysia, Grant number: FP067-2018A, Geran Penyelidikan Fakulti by the Faculty of Medicine, University of Malaya, Grant number: GPF001C- 2019, and UGC mid-career award, Grant number: F.19-221/2018 (BSR) dt. 28.03.2018. <P> We would like to request a revision to one of the funding numbers (in blue) in the funding acknowledgement below: The correct funding acknowledgement is: <P> The study was funded by Fundamental Research Grant Scheme (FRGS) by the Ministry of Education, Malaysia, Grant number: FRGS/1/2018/STG05/UM/02/5, Geran Penyelidikan Fakulti by the Faculty of Medicine, University of Malaya, Grant number: GPF001C-2019 and UGC mid-career award, Grant number: F.19-221/2018 (BSR) dt. 28.03.2018. <P> The original article can be found online at: https://www.eurekaselect.com/public/article/109117.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135147183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-12-09DOI: 10.2174/1570164620666221209121936
D. Ong, S. Shahrudin, M. Ismail
The advancement of proteomics studies leads to various benefits in research. However, in Malaysia, proteomics studies are still in their early stage. Four adult Pulchrana glandulosa individuals were collected from the stream of Temurun Waterfall for their proteomics information. These frogs’ skin secretions were collected, extracted, and analysed for their protein antimicrobial peptide compounds and biomedical potentials using liquid chromatography-mass spectrometry. Forty-six proteins had been identified from the skin secretion of this species. They contained unreviewed proteins, enzymes, AMPs, receptors, regulatory, transport, hormone, and developmental proteins. In addition, 11 AMP had been identified, consisting of esculentin-2, brevinin 1, and other AMPs. These proteins and AMPs have a wide range of biomedical importance, such as antimicrobials, anti-tumour, anti-cancerous, anti-viral, wound healing, anti-inflammation, anti-ageing and maintaining homeostasis.
{"title":"Proteomics of the skin secretion of Pulchrana glandulosa (Anura: Ranidae) (Boulenger, 1882), Langkawi Island, Kedah, Peninsular Malaysia","authors":"D. Ong, S. Shahrudin, M. Ismail","doi":"10.2174/1570164620666221209121936","DOIUrl":"https://doi.org/10.2174/1570164620666221209121936","url":null,"abstract":"\u0000\u0000The advancement of proteomics studies leads to various benefits in research. However, in Malaysia, proteomics studies are still in their early stage.\u0000\u0000\u0000\u0000Four adult Pulchrana glandulosa individuals were collected from the stream of Temurun Waterfall for their proteomics information.\u0000\u0000\u0000\u0000These frogs’ skin secretions were collected, extracted, and analysed for their protein antimicrobial peptide compounds and biomedical potentials using liquid chromatography-mass spectrometry.\u0000\u0000\u0000\u0000Forty-six proteins had been identified from the skin secretion of this species. They contained unreviewed proteins, enzymes, AMPs, receptors, regulatory, transport, hormone, and developmental proteins. In addition, 11 AMP had been identified, consisting of esculentin-2, brevinin 1, and other AMPs.\u0000\u0000\u0000\u0000These proteins and AMPs have a wide range of biomedical importance, such as antimicrobials, anti-tumour, anti-cancerous, anti-viral, wound healing, anti-inflammation, anti-ageing and maintaining homeostasis.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83786941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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