Journal of Proteome Research最新文献

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Human Coronavirus-229E Hijacks Key Host-Cell RNA-Processing Complexes for Replication 人类冠状病毒- 229e劫持关键宿主细胞rna加工复合物进行复制
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-12 DOI: 10.1021/acs.jproteome.5c00400
Snigdha Sarkar, , , Song Feng, , , Hugh D. Mitchell, , , Madelyn R. Berger, , , Tong Zhang, , , Isaac K. Attah, , , Chelsea M. Hutchinson-Bunch, , , Victoria N. Prozapas, , , Kristin Engbrecht, , , Stephanie King, , , Amy C. Sims*, , and , John T. Melchior*, 
{"title":"Human Coronavirus-229E Hijacks Key Host-Cell RNA-Processing Complexes for Replication","authors":"Snigdha Sarkar,&nbsp;, ,&nbsp;Song Feng,&nbsp;, ,&nbsp;Hugh D. Mitchell,&nbsp;, ,&nbsp;Madelyn R. Berger,&nbsp;, ,&nbsp;Tong Zhang,&nbsp;, ,&nbsp;Isaac K. Attah,&nbsp;, ,&nbsp;Chelsea M. Hutchinson-Bunch,&nbsp;, ,&nbsp;Victoria N. Prozapas,&nbsp;, ,&nbsp;Kristin Engbrecht,&nbsp;, ,&nbsp;Stephanie King,&nbsp;, ,&nbsp;Amy C. Sims*,&nbsp;, and ,&nbsp;John T. Melchior*,&nbsp;","doi":"10.1021/acs.jproteome.5c00400","DOIUrl":"10.1021/acs.jproteome.5c00400","url":null,"abstract":"<p >The recent rise in zoonotic coronavirus outbreaks underscores the urgency to understand virus–host interactions to develop potent antiviral therapeutics. Systems biology approaches, particularly proteomics, have been invaluable in providing a global overview of such interactions. However, these conventional approaches rely on measuring protein abundance changes that do not capture all molecular changes associated with altered regulatory pathways. In this study, we employed a high-throughput structural proteomics approach called limited proteolysis-based mass spectrometry (LiP-MS) to capture protein conformational changes, which we demonstrate are better proxies for functional alterations. We applied this tool to profile the molecular landscape of different human lung cells following human coronavirus-229E (HCoV-229E) infection. We found that HCoV-229E uses a multipronged approach to hijack key RNA-processing pathways and assemblies as part of a host-shutoff strategy to achieve effective replication. We confirm our results with structural data derived from changes in the assemblies after infection. We go on to show that modulation of two of these assemblies, the Nop56-associated pre-rRNA complex and the spliceosome C-complex, can attenuate HCoV-229E replication, indicating that we have identified viable host-cell therapeutic targets with potential to provide broad efficacy against coronavirus infection.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5026–5045"},"PeriodicalIF":3.6,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.5c00400","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface 通过单一软件接口跨多个Orbitrap平台的实时仪器控制。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-12 DOI: 10.1021/acs.jproteome.5c00269
Michael R. Hoopmann*, , , Christopher D. McGann, , , Jesse D. Canterbury, , , Priska D. von Haller, , and , Devin K. Schweppe*, 
{"title":"Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface","authors":"Michael R. Hoopmann*,&nbsp;, ,&nbsp;Christopher D. McGann,&nbsp;, ,&nbsp;Jesse D. Canterbury,&nbsp;, ,&nbsp;Priska D. von Haller,&nbsp;, and ,&nbsp;Devin K. Schweppe*,&nbsp;","doi":"10.1021/acs.jproteome.5c00269","DOIUrl":"10.1021/acs.jproteome.5c00269","url":null,"abstract":"<p >Applications using real-time spectral analysis and real-time instrument control have emerged in recent years as powerful tools to improve the capabilities and sensitivity of mass spectrometers. Software resources, such as the Instrument Application Programming Interface (IAPI) provided by Thermo Fisher Scientific, enable researchers to develop customized and powerful new real-time analysis and instrument control applications. The IAPI is segregated by instrument architecture, and therefore real-time applications developed for the Exploris instrument platform will not operate on the Tribrid instrument platform. We present Helios, a unified API that wraps IAPI for the Exploris and Tribrid series of instruments into a single interface with syntax synonymous to the IAPI. Helios automatically resolves differences in metadata provided by real-time data streams from either platform, and we illustrate how to send a customized instrument control command capable of operating on both Exploris and Tribrid instrument platforms. We provide two example applications that operate the same on both Exploris and Tribrid instruments from a single code base, eliminating the need to fork source trees and develop applications separately for each platform. The Helios API simplifies the development of real-time instrument control applications, while also increasing the number of instruments supported by those applications.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5277–5281"},"PeriodicalIF":3.6,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145051384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Improving Proteomic Dynamic Range with Multiple Accumulation Precursor Mass Spectrometry 多重积累前体质谱法提高蛋白质组学动态范围。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-12 DOI: 10.1021/acs.jproteome.5c00469
Teeradon Phlairaharn, , , Ariana E. Shannon, , , Xinlei Zeng, , , Dong-Jiunn Jeffery Truong, , , Erwin M. Schoof, , , Zilu Ye, , and , Brian C. Searle*, 
{"title":"Improving Proteomic Dynamic Range with Multiple Accumulation Precursor Mass Spectrometry","authors":"Teeradon Phlairaharn,&nbsp;, ,&nbsp;Ariana E. Shannon,&nbsp;, ,&nbsp;Xinlei Zeng,&nbsp;, ,&nbsp;Dong-Jiunn Jeffery Truong,&nbsp;, ,&nbsp;Erwin M. Schoof,&nbsp;, ,&nbsp;Zilu Ye,&nbsp;, and ,&nbsp;Brian C. Searle*,&nbsp;","doi":"10.1021/acs.jproteome.5c00469","DOIUrl":"10.1021/acs.jproteome.5c00469","url":null,"abstract":"<p >Orbitrap (OT)-based mass spectrometer platforms are a gold standard in high-resolution mass spectrometry, where their primary disadvantage is slower-scanning speed in comparison to time-of-flight or linear ion trap mass analyzers. In this study, we utilize long OT transients to extend the precursor dynamic range by modifying the selected ion monitoring method to multiplex several precursor <i>m</i>/<i>z</i> ranges into a single scan, which we call “multiple accumulation precursor mass spectrometry”. Our approach requires no software or hardware modifications and hides the additional ion accumulation steps during the time it takes to make other Orbitrap measurements, producing precursor spectra with nearly 2× dynamic range and essentially no consequences. We collected data using both data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods to evaluate a range of approaches. With DDA, MAP-MS precursor quantification improves with higher quality measurements. At the same time, DIA detection is enhanced by up to 11% when combining precursor and tandem mass spectra for peptide detection.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5116–5126"},"PeriodicalIF":3.6,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145051456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Proteomics-Based Mapping of the Lymph Node Metastasis Landscape in Cervical Cancer 基于蛋白质组学的宫颈癌淋巴结转移图谱研究。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-11 DOI: 10.1021/acs.jproteome.5c00570
Yiping Hao, , , Qingqing Liu, , , Bingyu Wang, , , Wenjing Zhang, , , Xinlin Jiao, , , Teng Zhang*, , and , Baoxia Cui*, 
{"title":"Proteomics-Based Mapping of the Lymph Node Metastasis Landscape in Cervical Cancer","authors":"Yiping Hao,&nbsp;, ,&nbsp;Qingqing Liu,&nbsp;, ,&nbsp;Bingyu Wang,&nbsp;, ,&nbsp;Wenjing Zhang,&nbsp;, ,&nbsp;Xinlin Jiao,&nbsp;, ,&nbsp;Teng Zhang*,&nbsp;, and ,&nbsp;Baoxia Cui*,&nbsp;","doi":"10.1021/acs.jproteome.5c00570","DOIUrl":"10.1021/acs.jproteome.5c00570","url":null,"abstract":"<p >Lymph node metastasis (LNM) in cervical cancer is a critical determinant of the disease progression and prognosis. Elucidating its molecular mechanisms and identifying specific biomarkers are crucial for optimizing treatment. DIA-based quantitative proteomic sequencing was conducted on 49 cervical cancer patients. We screened differentially expressed proteins and performed functional enrichment, pathway scoring, time-series analysis, protein interaction studies, and integrated proteomic and TCGA transcriptomic data to identify biomarkers. 56 genes showed consistent expression trends, with 2 upregulated (SERPINB5, FABP5) and 54 downregulated (including ZNF512). Novel findings include activation of unsaturated fatty acid/steroid biosynthesis and inhibition of cell junction pathways during progression. Lymphovascular space invasion (LVSI) precedes LNM, but a subset of LNM cases lacks LVSI and exhibits a unique cholesterol metabolism activation. SERPINB5, FABP5, and ZNF512 were validated as potential prognostic and LNM-predictive biomarkers. DIA proteomics characterized cervical cancer lymph node metastasis, revealing molecular changes and potential biomarkers and offering new insights into its biological mechanisms.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5226–5241"},"PeriodicalIF":3.6,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 Proteomic High-Performance Biomarkers for Early Diagnosis of Colorectal Cancer 血浆蛋白质组学高性能生物标志物在结直肠癌早期诊断中的应用。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-10 DOI: 10.1021/acs.jproteome.5c00483
Haoran Jin, , , Kai Deng, , , Shaochong Qi, , , Zhaomin Deng, , , Lu Pu, , , Dongqin Xu, , , Weina Jing, , , Jin Wang, , , Zhiliang Zuo, , , Jinlin Yang*, , and , Hao Jiang*, 
{"title":"Plasma Proteomic High-Performance Biomarkers for Early Diagnosis of Colorectal Cancer","authors":"Haoran Jin,&nbsp;, ,&nbsp;Kai Deng,&nbsp;, ,&nbsp;Shaochong Qi,&nbsp;, ,&nbsp;Zhaomin Deng,&nbsp;, ,&nbsp;Lu Pu,&nbsp;, ,&nbsp;Dongqin Xu,&nbsp;, ,&nbsp;Weina Jing,&nbsp;, ,&nbsp;Jin Wang,&nbsp;, ,&nbsp;Zhiliang Zuo,&nbsp;, ,&nbsp;Jinlin Yang*,&nbsp;, and ,&nbsp;Hao Jiang*,&nbsp;","doi":"10.1021/acs.jproteome.5c00483","DOIUrl":"10.1021/acs.jproteome.5c00483","url":null,"abstract":"<p >Colorectal cancer (CRC) is a major global health challenge due to its high incidence, mortality, and low rate of early detection. Early diagnosis, targeting precancerous lesions (advanced adenomas) and early stage CRC (Tis and T1), is critical for improving patient survival. Given the limitations of current detection methods for advanced adenomas, developing high-performance early diagnostic strategies is essential for effective prevention. In this study, we employed the proximity extension assay using the Olink Explore 384 Cardiometabolic panel to identify 15 protein biomarkers, of which 8 proteins (MMP7, GDF15, REG1B, RNASE3, REG1A, TFF3, MFAP5, and TGM2) were incorporated into multiple machine learning models to diagnose colorectal advanced neoplasia (AN) in the discovery cohort (<i>n</i> = 80), achieving AUC values above 0.90. These models also demonstrated significant diagnostic performance, with AUCs greater than 0.88, for patients with AN or advanced adenomas in the validation cohort (<i>n</i> = 69). Furthermore, hub biomarkers (MMP7 and GDF15) were identified and subsequently validated along with an analysis of their clinical significance. Thus, our study identifies multiprotein signatures validated in two cohorts with high diagnostic performance for colorectal AN, contributing to the development of the clinical detection kit for noninvasive early diagnosis of CRC.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5177–5189"},"PeriodicalIF":3.6,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Development and Validation of a Novel LC-MS/MS-Based Proteomics Method for Quantitation of Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR) 一种新的基于LC-MS/ ms的蛋白质组学方法的建立和验证,用于定量视黄醇结合蛋白4 (RBP4)和转甲状腺素(TTR)。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-10 DOI: 10.1021/acs.jproteome.5c00679
Aprajita S. Yadav, , , Katya B. Rubinow, , , Alex Zelter, , , Aurora K. Authement, , , Bryan R. Kestenbaum, , , John K. Amory, , and , Nina Isoherranen*, 
{"title":"Development and Validation of a Novel LC-MS/MS-Based Proteomics Method for Quantitation of Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR)","authors":"Aprajita S. Yadav,&nbsp;, ,&nbsp;Katya B. Rubinow,&nbsp;, ,&nbsp;Alex Zelter,&nbsp;, ,&nbsp;Aurora K. Authement,&nbsp;, ,&nbsp;Bryan R. Kestenbaum,&nbsp;, ,&nbsp;John K. Amory,&nbsp;, and ,&nbsp;Nina Isoherranen*,&nbsp;","doi":"10.1021/acs.jproteome.5c00679","DOIUrl":"10.1021/acs.jproteome.5c00679","url":null,"abstract":"<p >Retinol binding protein 4 (RBP4), the circulating carrier of retinol, complexes with transthyretin (TTR) and is a potential biomarker of cardiometabolic disease. However, RBP4 quantitation relies on immunoassays and Western blots without retinol and TTR measurement. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous absolute quantitation of circulating RBP4 and TTR is critical to establishing their biomarker potential. Surrogate peptides with reproducible, linear LC-MS/MS response were selected. Purified proteins were used as quantitation standards and heavy-labeled peptides as internal standards. Matrix effects were evaluated. The validated method was applied to measure inter- and intraindividual variability in RBP4 and TTR concentrations in healthy individuals and patients with diabetic kidney disease. Quantitation was linear for the clinically relevant concentration ranges of RBP4 (0.5–6 μM) and TTR (5.8–69 μM). Assay interday variability was &lt;12% and precision within 5%. The interindividual variability for RBP4 and TTR concentrations was 18–26%, while intraindividual variability was similar to assay variability. RBP4 and TTR quantitation correlated with commercially available enzyme-linked immunoassays (ELISA) assays. The developed LC-MS/MS method enables simultaneous absolute quantitation of RBP4 and TTR in serum and plasma. It can be applied to clinical biomarker studies and stoichiometric measurements of circulating RBP4, TTR, and retinol.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5266–5276"},"PeriodicalIF":3.6,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Exosomal Proteome from Hepatocellular Carcinoma Patient-Derived Xenograft Mice Serves as Identity of Liver Cancer 肝癌患者来源的异种移植小鼠的外泌体蛋白质组可作为肝癌的鉴定。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-09 DOI: 10.1021/acs.jproteome.5c00307
Tao Zuo, , , Peiru Chen, , , Zhenpeng Zhang, , , Mingsong Mao, , , Yuan Li, , , Zilin Li, , , Xin Feng, , , Yihao Wang, , , Zhen Sun, , , Fenglong Jiao, , , Fangyuan Gao, , , Tao Zhang, , , Yanchang Li, , , Yao Zhang, , , Fengsong Liu, , , Yangjun Zhang, , , Yuanyuan Ruan, , , Lei Chang*, , , Lianghai Hu*, , , Yali Zhang*, , and , Ping Xu*, 
{"title":"Exosomal Proteome from Hepatocellular Carcinoma Patient-Derived Xenograft Mice Serves as Identity of Liver Cancer","authors":"Tao Zuo,&nbsp;, ,&nbsp;Peiru Chen,&nbsp;, ,&nbsp;Zhenpeng Zhang,&nbsp;, ,&nbsp;Mingsong Mao,&nbsp;, ,&nbsp;Yuan Li,&nbsp;, ,&nbsp;Zilin Li,&nbsp;, ,&nbsp;Xin Feng,&nbsp;, ,&nbsp;Yihao Wang,&nbsp;, ,&nbsp;Zhen Sun,&nbsp;, ,&nbsp;Fenglong Jiao,&nbsp;, ,&nbsp;Fangyuan Gao,&nbsp;, ,&nbsp;Tao Zhang,&nbsp;, ,&nbsp;Yanchang Li,&nbsp;, ,&nbsp;Yao Zhang,&nbsp;, ,&nbsp;Fengsong Liu,&nbsp;, ,&nbsp;Yangjun Zhang,&nbsp;, ,&nbsp;Yuanyuan Ruan,&nbsp;, ,&nbsp;Lei Chang*,&nbsp;, ,&nbsp;Lianghai Hu*,&nbsp;, ,&nbsp;Yali Zhang*,&nbsp;, and ,&nbsp;Ping Xu*,&nbsp;","doi":"10.1021/acs.jproteome.5c00307","DOIUrl":"10.1021/acs.jproteome.5c00307","url":null,"abstract":"<p >Hepatocellular carcinoma (HCC) constitutes approximately 90% of liver cancers, yet its early detection remains challenging due to the low sensitivity of current diagnostic methods and the difficulty in identifying minimal cancer cells within the body. This study employed a patient-derived xenograft (PDX) mouse model to screen for biomarkers, leveraging its advantage of low background interference compared to human serum exosome studies. Using a novel microextraction technique, exosomes were isolated from just one microliter of serum from HCC PDX mice, followed by proteomic profiling. Analysis revealed that serum exosomal proteins from PDX mice were enriched in cancer-related pathways. The exosomal proteome not only distinguished PDX mice from controls but also differentiated between individual PDX groups, supporting its use as a tumor-specific identifier (tumor ID) and a noninvasive tool for monitoring tumors. Bioinformatics identified a panel of serum exosomal protein biomarkers predictive of HCC patient outcomes, which were validated via targeted proteomics and array-based high-throughput detection. These upregulated biomarkers in HCC patients positively correlate with disease severity and poor prognosis, underscoring their clinical potential.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"4977–4987"},"PeriodicalIF":3.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Uncovering Urinary Proteome Differences in Very Preterm Infants with and without Preterm Brain Injury 发现有和没有早产儿脑损伤的极早产儿尿蛋白质组差异。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-09 DOI: 10.1021/acs.jproteome.5c00392
Magdalena Zasada*, , , Maciej Suski, , , Marta Olszewska, , , Aleksandra Kowalik, , , Natalia Łapińska, , , Weronika Pogoda, , and , Przemko Kwinta, 
{"title":"Uncovering Urinary Proteome Differences in Very Preterm Infants with and without Preterm Brain Injury","authors":"Magdalena Zasada*,&nbsp;, ,&nbsp;Maciej Suski,&nbsp;, ,&nbsp;Marta Olszewska,&nbsp;, ,&nbsp;Aleksandra Kowalik,&nbsp;, ,&nbsp;Natalia Łapińska,&nbsp;, ,&nbsp;Weronika Pogoda,&nbsp;, and ,&nbsp;Przemko Kwinta,&nbsp;","doi":"10.1021/acs.jproteome.5c00392","DOIUrl":"10.1021/acs.jproteome.5c00392","url":null,"abstract":"<p >Premature infants are at high risk for brain injuries such as intraventricular hemorrhage and periventricular white matter injury. This study applies omics technology to analyze urinary protein expression, aiming to clarify preterm brain injury mechanisms and identify therapeutic targets. Urine samples were collected from 29 very preterm infants (VPI) without brain injury and 11 with moderate/severe injury at eight time points: Days 1, 2, 3, 4, 6, 8, 28, and term-equivalent age (TEA). Brain damage was assessed using the Kidokoro scale and MRI at TEA. SWATH-MS and bioinformatics were used to identify differentially expressed urinary proteins and affected pathways. Fifty-six proteins showed significant expression differences. Notably, extracellular proteoglycans (NCAN, ACAN, BCAN), associated with neuroprotection, were markedly reduced in infants with brain injury. Conversely, fatty acid-binding proteins (FABP1, FABP3, FABP4, FABP7) decreased over time in uninjured infants but increased in those with brain injury, suggesting a role in exacerbating damage. In summary, the urinary proteome of VPI with moderate/severe brain injury differs significantly from those without injury. Reduced neuroprotective proteoglycans and elevated FABPs highlight potential molecular markers and targets for intervention in preterm brain injury.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5139–5147"},"PeriodicalIF":3.6,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.5c00392","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proteomics Uncovers Enrichment Bias of Common Extracellular Vesicle Isolation Methods in HEK293T Cells 蛋白质组学揭示了HEK293T细胞中常见的细胞外囊泡分离方法的富集偏倚。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-08 DOI: 10.1021/acs.jproteome.5c00123
Shipan Fan, , , Yuqi Lin, , , Zuoquan Chen, , and , Ansgar Poetsch*, 
{"title":"Proteomics Uncovers Enrichment Bias of Common Extracellular Vesicle Isolation Methods in HEK293T Cells","authors":"Shipan Fan,&nbsp;, ,&nbsp;Yuqi Lin,&nbsp;, ,&nbsp;Zuoquan Chen,&nbsp;, and ,&nbsp;Ansgar Poetsch*,&nbsp;","doi":"10.1021/acs.jproteome.5c00123","DOIUrl":"10.1021/acs.jproteome.5c00123","url":null,"abstract":"<p >Extracellular vesicles (EVs) are membranous structures consisting of lipid bilayers that are released by most cell types and serve as important mediators of intercellular communication. The HEK293T cell line model has gained considerable attention from the scientific community, particularly in the fields of engineering and drug delivery. Nevertheless, there is a dearth of systematic comparisons of the most prevalent EV isolation methodologies for HEK293T in terms of recovery and specificity. In this study, common EV isolation workflows using either ultracentrifugation (UC), ultrafiltration (UF), polyethylene glycol precipitation (PEG), or EXODUS were compared in HEK293T cells and profiled using proteomics, which enabled the identification of almost 4000 proteins. Moreover, the observed large discrepancy between PEG and other methods can be attributed to the cofractionation of two EV populations that differed in density and protein composition, as revealed by isopycnic ultracentrifugation. Therefore, it was assumed that the cargo inside EVs is correlated with their density, which presents intrinsic heterogeneity in HEK293T EVs. This study aimed to facilitate the selection and implementation of an EV enrichment procedure for the HEK293T cell line and to discern heterogeneity in the HEK293T EV population.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"4900–4910"},"PeriodicalIF":3.6,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Brief Evaluation of Olink Reveal Proximity Extension Assay for High-Throughput Proteomics: A Case Study Using NIST SRM 1950 and Two Spike-In Protein Standards 对高通量蛋白质组学的Olink揭示接近扩展试验的简要评价:使用NIST SRM 1950和两个峰值蛋白标准的案例研究。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-08 DOI: 10.1021/acs.jproteome.5c00571
Yuri E. M. van der Burgt, , , Emile de Meijer, , and , Magnus Palmblad*, 
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