PROTEOMICS – Clinical Applications最新文献_第3页

Integration of the cancer cell secretome and transcriptome reveals potential noninvasive diagnostic markers for bladder cancer. 癌细胞分泌组和转录组的整合揭示了膀胱癌的潜在非侵入性诊断标记。

IF 2.1 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-07-01 Epub Date: 2024-01-09 DOI: 10.1002/prca.202300033

Yi-Ting Chen, Wei-Ju Tu, Zong-Han Ye, Chih-Ching Wu, Shir-Hwa Ueng, Kai-Jie Yu, Chien-Lun Chen, Pei-Hua Peng, Jau-Song Yu, Ying-Hsu Chang

{"title":"Integration of the cancer cell secretome and transcriptome reveals potential noninvasive diagnostic markers for bladder cancer.","authors":"Yi-Ting Chen, Wei-Ju Tu, Zong-Han Ye, Chih-Ching Wu, Shir-Hwa Ueng, Kai-Jie Yu, Chien-Lun Chen, Pei-Hua Peng, Jau-Song Yu, Ying-Hsu Chang","doi":"10.1002/prca.202300033","DOIUrl":"10.1002/prca.202300033","url":null,"abstract":"Purpose: Bladder cancer (BLCA) is a major cancer of the genitourinary system. Although cystoscopy is the standard protocol for diagnosing BLCA clinically, this procedure is invasive and expensive. Several urine-based markers for BLCA have been identified and investigated, but none has shown sufficient sensitivity and specificity. These observations underscore the importance of discovering novel BLCA biomarkers and developing a noninvasive method for detection of BLCA. Exploring the cancer secretome is a good starting point for the development of noninvasive biomarkers for cancer diagnosis.Experimental design: In this study, we established a comprehensive secretome dataset of five representative BLCA cell lines, BFTC905, TSGH8301, 5637, MGH-U1, and MGH-U4, by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Expression of BLCA-specific secreted proteins at the transcription level was evaluated using the Oncomine cancer microarray database.Results: The expressions of four candidates-COMT, EWSR1, FUSIP1, and TNPO2-were further validated in clinical human specimens. Immunohistochemical analyses confirmed that transportin-2 was highly expressed in tumor cells relative to adjacent noncancerous cells in clinical tissue specimens from BLCA patients, and was significantly elevated in BLCA urine compared with that in urine samples from aged-matched hernia patients (controls).Conclusions: Collectively, our findings suggest TNPO2 as a potential noninvasive tumor-stage or grade discriminator for BLCA management.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139404070","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}

引用次数: 0

Integrated plasma proteomics and N-glycoproteomics reveals alterations in the N-glycosylation in Chinese hepatocellular carcinoma patients. 综合血浆蛋白质组学和N-糖蛋白组学揭示中国肝细胞癌患者N-糖基化的改变

IF 2.1 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-07-01 Epub Date: 2024-02-12 DOI: 10.1002/prca.202300029

Jiaming Zeng, Weiqi Rong, Bo Meng, Linlin Zheng, Tao Peng, Rui Zhai, You Jiang, Ting Xiao, Xiang Fang, Yong Zhang, Yang Zhao, Xinhua Dai

{"title":"Integrated plasma proteomics and N-glycoproteomics reveals alterations in the N-glycosylation in Chinese hepatocellular carcinoma patients.","authors":"Jiaming Zeng, Weiqi Rong, Bo Meng, Linlin Zheng, Tao Peng, Rui Zhai, You Jiang, Ting Xiao, Xiang Fang, Yong Zhang, Yang Zhao, Xinhua Dai","doi":"10.1002/prca.202300029","DOIUrl":"10.1002/prca.202300029","url":null,"abstract":"Hepatocellular carcinoma (HCC) is a life-threatening disease that presents diagnostic challenges due to the absence of reliable biomarkers. Recently, plasma proteomics and glycoproteomics have emerged as powerful tools for identifying potential diagnostic biomarkers for various diseases. In this study, we conducted a comprehensive proteomic and glycoproteomic analysis of plasma samples from 11 HCC patients and 11 healthy control (HC) individuals. We identified 20 differentially expressed (DE) proteins and 32 DE intact glycosylated peptides (IGPs) that can effectively differentiate between HCC patients and HC samples. Our findings demonstrate that IGP profiles had better predictive power than protein profiles for screening HCC. Pathways associated with DE proteins and IGPs were identified. It was reported that the protein expression level of galectin 3 binding protein (LGALS3BP) and its N-linked glycosylation at the N398 and N551 sites might serve as valuable candidates for HCC diagnosis. These results highlight the importance of N-glycoproteomics in advancing our understanding of HCC and suggest possible candidates for the future diagnosis of this disease.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139723800","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}

引用次数: 0

Proteomic analysis of extracellular vesicle cargoes mirror the cardioprotective effects of rivaroxaban in patients with venous thromboembolism. 细胞外囊泡货物的蛋白质组学分析反映了利伐沙班对静脉血栓栓塞患者心脏的保护作用。

IF 2.1 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-07-01 Epub Date: 2024-01-09 DOI: 10.1002/prca.202300014

Luisa Weiss, Wido Uhrig, Sarah Kelliher, Paulina B Szklanna, Tadhg Prendiville, Shane P Comer, Osasere Edebiri, Karl Egan, Áine Lennon, Barry Kevane, Sean Murphy, Fionnuala Ní Áinle, Patricia B Maguire

{"title":"Proteomic analysis of extracellular vesicle cargoes mirror the cardioprotective effects of rivaroxaban in patients with venous thromboembolism.","authors":"Luisa Weiss, Wido Uhrig, Sarah Kelliher, Paulina B Szklanna, Tadhg Prendiville, Shane P Comer, Osasere Edebiri, Karl Egan, Áine Lennon, Barry Kevane, Sean Murphy, Fionnuala Ní Áinle, Patricia B Maguire","doi":"10.1002/prca.202300014","DOIUrl":"10.1002/prca.202300014","url":null,"abstract":"Background: Venous thromboembolism (VTE) remains a significant cause of morbidity and mortality worldwide. Rivaroxaban, a direct oral factor Xa inhibitor, mediates anti-inflammatory and cardiovascular-protective effects besides its well-established anticoagulant properties; yet, these remain poorly characterized. Extracellular vesicles (EVs) are considered proinflammatory messengers regulating a myriad of (patho)physiological processes and may be highly relevant to the pathophysiology of VTE. The effects of Rivaroxaban on circulating EVs in VTE patients remain unknown. We have established that differential EV biosignatures are found in patients with non-valvular atrial fibrillation anticoagulated with Rivaroxaban versus warfarin. Here, we investigated whether differential proteomic profiles of circulating EVs could also be found in patients with VTE.Methods and results: We performed comparative label-free quantitative proteomic profiling of enriched plasma EVs from VTE patients anticoagulated with either Rivaroxaban or warfarin using a tandem mass spectrometry approach. Of the 182 quantified proteins, six were found to be either exclusive to, or enriched in, Rivaroxaban-treated patients. Intriguingly, these proteins are involved in negative feedback regulation of inflammatory and coagulation pathways, suggesting that EV proteomic signatures may reflect both Rivaroxaban's anti-coagulatory and anti-inflammatory potential.Conclusions: These differences suggest Rivaroxaban may have pleiotropic effects, supporting the reports of its emerging anti-inflammatory and cardiovascular-protective characteristics relative to warfarin.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139404071","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}

引用次数: 0

Plasma proteome analysis and validation of patients with community-acquired pneumonia: A cohort study. 社区获得性肺炎患者血浆蛋白质组分析与验证：一项队列研究。

IF 2.1 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-07-01 Epub Date: 2024-02-08 DOI: 10.1002/prca.202300069

Lili Zhao, Wenjie Bian, Ying Shang, Hui Zhi, Xinqian Ma, Yukun He, Wenyi Yu, Chunyu Liu, Yu Xu, Pihua Gong, Zhancheng Gao

{"title":"Plasma proteome analysis and validation of patients with community-acquired pneumonia: A cohort study.","authors":"Lili Zhao, Wenjie Bian, Ying Shang, Hui Zhi, Xinqian Ma, Yukun He, Wenyi Yu, Chunyu Liu, Yu Xu, Pihua Gong, Zhancheng Gao","doi":"10.1002/prca.202300069","DOIUrl":"10.1002/prca.202300069","url":null,"abstract":"Purpose: This study aimed to investigate the diagnostic potential of plasma biomarkers of community-acquired pneumonia (CAP) and their severity grading.Experimental design: Plasma proteomes from cohort I (n = 32) with CAP were analyzed by data-independent acquisition mass spectrometry (MS). MetaboAnalyst 5.0 was used to statistically evaluate significant differences in proteins from different samples, and demographic and clinical data were recorded for all enrolled patients. Cohort II (n = 80) was used to validate candidate biomarkers. Plasma protein levels were determined using quantitative enzyme-linked immunosorbent assay (ELISA). Correlations were assessed using Pearson's correlation coefficient. A receiver operating characteristic curve was used to verify the association between the variables, CAP diagnosis, and prognosis.Results: 121 differentially expressed proteins (DEPs) were obtained between CAP and controls. These DEPs were mainly aggregated in pathways of phagosome(hsa04145) and complement and coagulation cascades (hsa04610). No significant differential proteins were detected in bacterial, viral, and mixed infection groups. The plasma levels of fetuin-A, alpha-1-antichymotrypsin (AACT), α1-acid glycoprotein (A1AG), and S100A8/S100A9 heterodimers detected by ELISA were consistent with those of MS. AACT, A1AG, S100A8/S100A9 heterodimer, and fetuin-A can potentially be used as diagnostic predictors, and fetuin-A and AACT are potential predictors of SCAP.Conclusions and clinical relevance: Plasma protein profiling can successfully identify potential biomarkers for CAP diagnosis and disease severity assessment. These biomarkers should be further studied for their clinical application.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139707680","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}

引用次数: 0

Methods and clinical biomarker discovery for targeted proteomics using Olink technology. 利用 Olink 技术发现靶向蛋白质组学的方法和临床生物标记物。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-05-10 DOI: 10.1002/prca.202300233

Han Wang, Tian Zhao, Jingjing Zeng, Ruijie Zhang, Liyuan Pu, Suying Qian, Shan Xu, Yannan Jiang, Lifang Pan, Xiaoyu Dai, Xu Guo, Liyuan Han

引用次数: 0

Mass spectrometry-based proteomic applications in dental implants research. 基于质谱的蛋白质组学在牙科植入物研究中的应用。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-05-01 Epub Date: 2024-02-11 DOI: 10.1002/prca.202300019

Tim Halstenbach, Annika Topitsch, Oliver Schilling, Gerhard Iglhaut, Katja Nelson, Tobias Fretwurst

引用次数: 0

Editorial Board: Proteomics 3'24 编辑委员会：蛋白质组学 3'24

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-05-01 DOI: 10.1002/prca.202470032

引用次数: 0

Subcellular proteomics insights into Alzheimer's disease development. 亚细胞蛋白质组学对阿尔茨海默病发展的启示。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-05-01 Epub Date: 2023-08-31 DOI: 10.1002/prca.202200112

Zhiyuan Liang, Hongbin Zhuang, Xueshan Cao, Guanwei Ma, Liming Shen

{"title":"Subcellular proteomics insights into Alzheimer's disease development.","authors":"Zhiyuan Liang, Hongbin Zhuang, Xueshan Cao, Guanwei Ma, Liming Shen","doi":"10.1002/prca.202200112","DOIUrl":"10.1002/prca.202200112","url":null,"abstract":"Alzheimer's disease (AD), one of the most common dementias, is a neurodegenerative disease characterized by cognitive impairment and decreased judgment function. The expected number of AD patient is increasing in the context of the world's advancing medical care and increasing human life expectancy. Since current molecular mechanism studies on AD pathogenesis are incomplete, there is no specific and effective therapeutic agent. Mass spectrometry (MS)-based unbiased proteomics studies provide an effective and comprehensive approach. Many advances have been made in the study of the mechanism, diagnostic markers, and drug targets of AD using proteomics. This paper focus on subcellular level studies, reviews studies using proteomics to study AD-associated mitochondrial dysfunction, synaptic, and myelin damage, the protein composition of amyloid plaques (APs) and neurofibrillary tangles (NFTs), changes in tissue extracellular vehicles (EVs) and exosome proteome, and the protein changes in ribosomes and lysosomes. The methods of sample separation and preparation and proteomic analysis as well as the main findings of these studies are involved. The results of these proteomics studies provide insights into the pathogenesis of AD and provide theoretical resource and direction for future research in AD, helping to identify new biomarkers and drugs targets for AD.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10121341","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}

引用次数: 0

Masthead: Proteomics 3'24 刊头：蛋白质组学 3'24

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-05-01 DOI: 10.1002/prca.202470033

引用次数: 0

Integrative analysis of transcriptome and proteome profiles in primary and recurrent glioblastoma. 原发性和复发性胶质母细胞瘤转录组和蛋白质组的综合分析。

IF 2 4区生物学

PROTEOMICS – Clinical Applications Pub Date : 2024-05-01 Epub Date: 2023-12-01 DOI: 10.1002/prca.202200085

Jiajie Zhang, Guowei Wang, Bo Yan, Ge Yang, Qianqian Yang, Yaqin Hu, Jiuru Guo, Ningning Zhao, Liang Wang, Huijuan Wang

{"title":"Integrative analysis of transcriptome and proteome profiles in primary and recurrent glioblastoma.","authors":"Jiajie Zhang, Guowei Wang, Bo Yan, Ge Yang, Qianqian Yang, Yaqin Hu, Jiuru Guo, Ningning Zhao, Liang Wang, Huijuan Wang","doi":"10.1002/prca.202200085","DOIUrl":"10.1002/prca.202200085","url":null,"abstract":"Purpose: Glioblastoma (GBM) is the most common and aggressive primary brain tumor characterized by poor prognosis and high recurrence. The underlying molecular mechanism that drives tumor progression and recurrence is unclear. This study is intended to look for molecular and biological changes that play a key role in GBM recurrence.Experimental design: An integrative transcriptomic and proteomic analysis was performed on three primary GBM and three recurrent GBM tissues. Omics analyses were conducted using label-free quantitative proteomics and whole transcriptome sequencing.Results: A significant difference was found between primary GBM and recurrent GBM at the transcriptional level. Similar to other omics studies of cancer, a weak overlap was observed between transcriptome and proteome, and Procollagen C-Endopeptidase Enhancer 2 (PCOLCE2) was observed to be upregulated at mRNA and protein levels. Analysis of public cancer database revealed that high expression of PCOLCE2 is associated with poor prognosis of patients with GBM and that it may be a potential prognostic indicator. Functional and environmental enrichment analyses revealed significantly altered signaling pathways related to energy metabolism, including mitochondrial ATP synthesis-coupled electron transport and oxidative phosphorylation.Conclusions and clinical relevance: This study provides new insights into the recurrence process of GBM through combined transcriptomic and proteomic analyses, complementing the existing GBM transcriptomic and proteomic data and suggesting that integrated multi-omics analyses may reveal new disease features of GBM.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138462203","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}

引用次数: 0