Current Proteomics最新文献

{"title":"Effects of Chronic Cold Exposure on Proteomics of Lung Tissue in Mice","authors":"Moyou Li, Ying Liu, Xiaoye Tian, Zhuojun Wang, Feng Cheng, Xiao Han, Zheyuan Chen, Ruihang Ma, Hongxu Jin","doi":"10.2174/0115701646245422231013072302","DOIUrl":"https://doi.org/10.2174/0115701646245422231013072302","url":null,"abstract":"Background: Cold exposure can induce inflammation-related injury in lung tissue, but the exact mechanism is still unclear. Objective: The study aimed to clarify the proteomic characteristics of lung tissue under cold exposure. Methods: Forty mice were randomly equally divided into a control group and a model group. The model group was exposed to - 20 °C for two weeks (4 hours per day), while the control group was maintained at 22 ± 2 °C. H&E staining and ELISA were used to verify the injury of lung tissue. Furthermore, a quantitative analysis of the overall proteome in the lung of mice exposed to cold stress was conducted by using LC-MS/MS. 15 differentially expressed proteins were selected for PRM validation. Results: According to our results, cold exposure induced lung injury, and the expressions of 151 proteins were upregulated and those of 95 proteins were downregulated. Bioinformatics analysis showed that differentially expressed proteins were associated with tricarboxylic acid cycle, fat metabolism, glycolysis, and oxidative phosphorylation. The expression of gabra2, Klkb1, and complement-related proteins was significantly upregulated. The results of PRM validation were consistent with those of proteomics. Conclusion: We found changes in glycolysis, gabra2, Klkb1, and the complement system in the lung tissue of cold-stressed mice, which may play an important role in cold stress-induced lung injury","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"6 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134910347","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}

{"title":"LncRNA SH3BP5-AS1 Regulates the Proliferation and Cell Cycle of Non- Small Cell Lung Cancer Cells","authors":"Xiaowu Fan","doi":"10.2174/0115701646253656231013141100","DOIUrl":"https://doi.org/10.2174/0115701646253656231013141100","url":null,"abstract":" Background: Non-small cell lung cancer (NSCLC) consists of a class of heterogeneous diseases. Objective: LncRNAs are exceedingly implicated in the pathogenesis of NSCLC. Herein, the current study set out to illustrate the molecular mechanism of SH3BP5-AS1 in NSCLC cells. Methods: SH3BP5-AS1 expression in clinical NSCLC tissues and its impact on prognosis were analyzed by bioinformatics database. SH3BP5-AS1 expression patterns in NSCLC cell lines (A549/H1299/H1975/H460) and human normal lung epithelial cell lines (BEAS-2B) were examined by RT-qPCR. SH3BP5-AS1 was overexpressed in A549 or silenced in H1975 cells through transfection to assess its effect on proliferation, cell cycle distribution, and apoptosis, apoptosisrelated protein (Cleaved Caspase-3, Bax, Bcl-2) levels, invasive, migratory, and healing capacity through CCK-8, colony formation assay, flow cytometry, Western blot, Transwell, and cell scratch test. Results: SH3BP5-AS1 was under-expressed in NSCLC clinical tissues, and NSCLC patients with low SH3BP5-AS1 expression showed poor prognosis. A549/H1299/H1975/H460 cells had reduced levels of SH3BP5-AS1, with the relative level lowest/highest expression in A549/H1975 cells, respectively. SH3BP5-AS1 overexpression repressed A549 cell proliferation, slowed down cell cycle progression, enhanced apoptosis, elevated Cleared Caspase-3, Bax, suppressed Bcl-2 protein levels, and inhibited migratory, invasive, and scratch healing capacities, while SH3BP5-AS1 silencing brought about the opposite results in H1975 cells. Conclusion: SH3BP5-AS1 could suppress NSCLC cell proliferation, slow down cell cycle progression, stimulate apoptosis, and limit invasion and migration.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"67 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138816628","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}

{"title":"RNA Sequencing of A2780 Cells Treated with CCL2 Identified Genes Associated with A2780 Cell Growth","authors":"Zhenling Ma, Lei Wang, Kun Cheng, Guozhen Xing, Jiajia Zhang, Wei Liu","doi":"10.2174/0115701646256131231013111220","DOIUrl":"https://doi.org/10.2174/0115701646256131231013111220","url":null,"abstract":"abstract: Introduction: Ovarian cancer is a common gynecological malignancy. It is one of the leading causes of death among women worldwide. The incidence of ovarian cancer ranks third, and mortality is the first among gynecological malignant tumors. CCL2 (Chemokine C-C motif Ligand 2) is associated with the progression of a variety of tumors, including ovarian cancer. However, the mechanism of CCL2 in A2780 cell growth has not been clarified. Method: In this study, we found that exogenous CCL2 promoted A2780 cell activity. RNA sequencing was used to identify the transcriptomic changes in CCL2-treated A2780 cells. Based on a p-value less than 0.05 and |log2 Fold Change| greater than 1, 190 differentially expressed genes were selected. Of these genes, 82 were observed to be upregulated and 108 downregulated. Result: The GO (gene ontology) analysis of differentially expressed genes was used to identify the underlying functions and biological processes. In addition, the expression of the topmost upregulated genes was verified by qPCR. Conclusion: This work may provide new markers and reveal the underlying mechanism of exogenous CCL2 in A2780 cell proliferation. other: /","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135666282","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}

{"title":"Current understanding of dried spots platform for blood proteomics","authors":"R. Vitorino, Luís Perpétuo, H. Rocha, R. Ferreira, B. Manadas, Francisco Amado, Sofia Guedes, Atef Mahmoud Mannaa, J. Vialaret, C. Hirtz","doi":"10.2174/1570164620666230727104921","DOIUrl":"https://doi.org/10.2174/1570164620666230727104921","url":null,"abstract":"\u0000\u0000Dry blood spots (DBS) have been used in combination with liquid chromatography-mass spectrometry for targeted proteomics to identify sensitive and specific novel biomarkers. DBS presents several advantages over other traditional blood sampling methods. This re-view discusses the past, present and future of the technology, focusing on studies with clin-ical and population relevance. Arguments for and against DBS are presented by discussing technological advances, particularly those related to mass spectrometry (MS) and multiple reaction monitoring (MRM), sample preparation issues, disease biomarkers, pharmacoki-netics, and pharmacodynamics. There will be a focus on proteomic studies that rely on DBS as a sampling method. In this context, numerous studies on the diagnosis and treatment of several diseases. To date, proteomic reports of studies using DBS have shown that DBS can facilitate diagnosis and prognosis. DBS offers several advantages that make it a viable op-tion for many fields. Moreover, some of its disadvantages can be easily overcome through automation to increase reproducibility and reduce protocol variability and standardization of parameters such as the volume of sample used. Within this context, here we propose to review the advantages and disadvantages of using DBS for blood proteomics and provide an understanding of how current DBS-based protocols are being conducted for future stand-ardization and protocol optimization.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"29 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2023-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73676095","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}

{"title":"Evaluation of the interaction between ricin protein and quercetin using different analytical methods","authors":"L. Hernández-Ochoa, M. Martínez-Ceniceros, L. O. Nevarez-Prado, David Neder‐Suárez, F. Sandoval-Salas, L. Rodríguez-Valdez, L. Landeros-Martínez, Karla Bernal-Alvarado","doi":"10.2174/1570164620666230717114018","DOIUrl":"https://doi.org/10.2174/1570164620666230717114018","url":null,"abstract":"\u0000\u0000Ricin is the most toxic protein known. It is part of the ribosome-inactivating proteins, RIPs, type 2, which has generated importance in his research; it is possible to detoxify this protein with phenolic compounds; however, it is essential to understand how this detoxification occurs.\u0000To analyze using electrophoresis, UV-visible spectroscopy, and high-performance liquid chromatography (HPLC) the protein ricin with the flavonol quercetin, understanding the detoxification process.\u0000\u0000\u0000\u0000The UV-visible analysis was performed on both the supernatant and the precipitate of the samples; these results were analyzed using one-factor analysis of variance (ANOVA) and a Tukey test with a significance level of 0.05.\u0000\u0000\u0000\u000034.9 μg / mL of total protein and 4.2 μg / mL of ricin were obtained in the extraction method. Eight interactions were carried out, and all presented precipitation, observing through the electrophoresis technique a decrease in the bands corresponding to the protein; these results were analyzed with HPLC observing a decrease in the size of the area of the peaks in the chromatograms.\u0000\u0000\u0000\u0000The results obtained in this study suggest an agglomeration of the protein, generating a precipitate that could benefit the protein's inactivation as a detoxification process.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"44 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83189338","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}

{"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":"23 1","pages":""},"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}

{"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":"12 1 1","pages":""},"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}

{"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":"166 1","pages":""},"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}

{"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":"15 1","pages":""},"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}

{"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":"15 1","pages":""},"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}