Journal of Proteome Research最新文献_第7页

Distinct Inflammatory Profiles and Clinical Characteristics of NMOSD: A Comparative Analysis with NMOSD-like and Encephalitis-like MOG-AD NMOSD的不同炎症特征和临床特征：与NMOSD样和脑炎样MOG-AD的比较分析。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-13 DOI: 10.1021/acs.jproteome.5c00448

Quanfeng Wei, Su Meng, Chenyang Zhao, Minghe Wang, Shanshan Yang, Zhe Wu, Fang Liu, Na Liu, Lingling Cui, Yinan Zhao* and Wenyu Hu*,

{"title":"Distinct Inflammatory Profiles and Clinical Characteristics of NMOSD: A Comparative Analysis with NMOSD-like and Encephalitis-like MOG-AD","authors":"Quanfeng Wei, Su Meng, Chenyang Zhao, Minghe Wang, Shanshan Yang, Zhe Wu, Fang Liu, Na Liu, Lingling Cui, Yinan Zhao* and Wenyu Hu*, ","doi":"10.1021/acs.jproteome.5c00448","DOIUrl":"10.1021/acs.jproteome.5c00448","url":null,"abstract":"To better differentiate neuromyelitis optica spectrum disorder (NMOSD) from myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD), it is crucial to systematically explore the correlation between their clinical and immunological characteristics. Utilizing high-throughput protein detection technologies, we analyzed 92 inflammation-related proteins in plasma samples from NMOSD (n = 50), NMOSD-like MOGAD (n = 12), and encephalitis-like MOGAD (n = 8) groups. In this study, we found that seizures (2% vs 30%, p < 0.001) and acute disseminated encephalomyelitis (0% vs 30%, p < 0.001) were more common in MOGAD, while transverse myelitis (52% vs 5%, p < 0.001) was more common in NMOSD. The signs and symptoms of NMOSD-like and encephalitis-like MOGAD were largely similar. There were no significant differentially expressed proteins identified between the NMOSD group and the NMOSD-like MOGAD group, while the elevated IL-24 and TRANCE were in the encephalitis-like MOGAD group rather than in the NMOSD group. There was a positive correlation of CCL20 expression with EDSS scores in the NMOSD group, while this association was not found in the other groups. In conclusion, encephalitis-like MOGAD has distinct clinical and peripheral inflammatory protein characteristics compared to NMOSD and NMOSD-like MOGAD. Some differential IRPs are closely associated with specific clinical parameters.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 9","pages":"4744–4753"},"PeriodicalIF":3.6,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843833","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

Screening, Validation, and Machine Learning-Based Evaluation of Serum Protein Biomarkers for Esophageal Squamous Cell Carcinoma Based on Single-Cell Subtype-Specific Genes 基于单细胞亚型特异性基因的食管鳞状细胞癌血清蛋白生物标志物的筛选、验证和机器学习评估

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-12 DOI: 10.1021/acs.jproteome.5c00475

Xiuzhi Zhang, Zhefeng Xiao, Fengqi Chen, Wenke Sun, Tiandong Li, Hua Ye, Peng Wang*, Liping Dai* and Xiaoli Liu*,

{"title":"Screening, Validation, and Machine Learning-Based Evaluation of Serum Protein Biomarkers for Esophageal Squamous Cell Carcinoma Based on Single-Cell Subtype-Specific Genes","authors":"Xiuzhi Zhang, Zhefeng Xiao, Fengqi Chen, Wenke Sun, Tiandong Li, Hua Ye, Peng Wang*, Liping Dai* and Xiaoli Liu*, ","doi":"10.1021/acs.jproteome.5c00475","DOIUrl":"10.1021/acs.jproteome.5c00475","url":null,"abstract":"Cellular heterogeneity of epithelial cells and fibroblasts is critical in esophageal squamous cell carcinoma development (ESCC). Identifying dysregulated subtype-specific genes in these cells is essential for early diagnosis and treatment. In this study, our pipeline integrated scRNA-seq, proteomics, and ELISA to screen biomarkers: scRNA-seq defined epithelial and fibroblast subtypes and their markers, while proteomics and secretory profiling identified dysregulated secretory proteins. Serum levels of five selected proteins were measured in 344 ESCC patients, 46 HGIN cases, and 390 normal controls. Machine learning was employed to construct diagnostic models. An interactive web tool was implemented in R Shiny. Six epithelial and four fibroblast subtypes, proportionally distinct between ESCC and normal tissues, were identified. Four validated dysregulated proteins were used to build diagnostic models; among 12 algorithms, the Support Vector Machine (SVM) achieved the best performance with AUCs of 0.829 and 0.767 in the training and validation sets, respectively (p > 0.05). The model effectively distinguished early- and late-stage ESCC and HGIN from normal controls. The web-based diagnostic tool is publicly available at https://zhangxz.shinyapps.io/P4_Pred/. The identified serum biomarkers may enhance early ESCC detection and diagnosis. Our pipeline, leveraging heterogeneity-related genes in fibroblasts and epithelial cells, is readily adaptable to other tumors.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 9","pages":"4719–4733"},"PeriodicalIF":3.6,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833480","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

Fast and Memory-Efficient Searching of Large-Scale Mass Spectrometry Data Using Tide 基于Tide的大规模质谱数据快速高效搜索。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-12 DOI: 10.1021/acs.jproteome.5c00297

Attila Kertesz-Farkas*, Frank Lawrence Nii Adoquaye Acquaye, Vladislav Ostapenko, Rufino Haroldo Locon, Yang Lu, Charles E. Grant and William Stafford Noble*,

引用次数: 0

Serum N-Glycan Profiling Identifies Candidate Glycan Biomarkers for Early Detection and Prediction of Alzheimer’s Disease 血清n -聚糖分析鉴定早期检测和预测阿尔茨海默病的候选聚糖生物标志物。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-12 DOI: 10.1021/acs.jproteome.5c00018

Sherifdeen Onigbinde, Joy Solomon, Cristian D. Gutierrez-Reyes, Oluwatosin Daramola, Mojibola Fowowe, Moyinoluwa Adeniyi, Kelly N. DuBois, Kelly M. Bakulski, Nicholas M. Kanaan, David M. Lubman and Yehia Mechref*,

{"title":"Serum N-Glycan Profiling Identifies Candidate Glycan Biomarkers for Early Detection and Prediction of Alzheimer’s Disease","authors":"Sherifdeen Onigbinde, Joy Solomon, Cristian D. Gutierrez-Reyes, Oluwatosin Daramola, Mojibola Fowowe, Moyinoluwa Adeniyi, Kelly N. DuBois, Kelly M. Bakulski, Nicholas M. Kanaan, David M. Lubman and Yehia Mechref*, ","doi":"10.1021/acs.jproteome.5c00018","DOIUrl":"10.1021/acs.jproteome.5c00018","url":null,"abstract":"Alzheimer’s disease (AD) is a neurodegenerative disorder marked by progressive cognitive decline, affecting millions worldwide. Early diagnosis and intervention are crucial yet challenging, particularly in distinguishing between Mild Cognitive Impairment (MCI) subtypes, which often precede AD. Recent studies have highlighted the significant role of glycosylation, specifically N-glycan alterations, in the pathogenesis of AD. This study utilizes advanced LC–MS/MS techniques to profile N-glycan changes between serum samples from participants with normal cognition denoted as (CTRL), nonamnestic MCI (naMCI), amnestic MCI (aMCI), and AD. The analysis identified 99 unique N-glycans and revealed distinct glycan expression patterns among the groups. Notably, sialylation was significantly upregulated in AD, while fucosylation was downregulated, suggesting their involvement in AD pathology. Additionally, the study examined the role of isomeric N-glycans, identifying several isomers that differentiate naMCI from aMCI and those that can monitor progression from aMCI to AD dementia. These findings emphasize the potential of N-glycans as biomarkers for early detection of AD and its precursors, offering new avenues for therapeutic intervention. The differential expression of specific N-glycans and their isomers could serve as valuable biomarkers for distinguishing MCI subtypes and predicting progression to AD dementia, thereby aiding in the development of targeted therapies aimed at mitigating cognitive decline in affected individuals.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 9","pages":"4417–4436"},"PeriodicalIF":3.6,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820151","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

Systematic Comparison of Bone Proteome Extraction Methods to Allow for Integrated Proteomics–Metabolomics Correlation 骨蛋白质组提取方法的系统比较，以实现蛋白质组学与代谢组学的综合关联。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-12 DOI: 10.1021/acs.jproteome.4c01060

Vivien Wiltzsch, Johannes R. Schmidt, Klaudia Adamowicz, Theresa Lauterbach, Jörg Lehmann, Jan Baumbach, Tanja Laske and Stefan Kalkhof*,

{"title":"Systematic Comparison of Bone Proteome Extraction Methods to Allow for Integrated Proteomics–Metabolomics Correlation","authors":"Vivien Wiltzsch, Johannes R. Schmidt, Klaudia Adamowicz, Theresa Lauterbach, Jörg Lehmann, Jan Baumbach, Tanja Laske and Stefan Kalkhof*, ","doi":"10.1021/acs.jproteome.4c01060","DOIUrl":"10.1021/acs.jproteome.4c01060","url":null,"abstract":"Bone tissue poses significant challenges for proteomic analysis due to its dense, mineral-rich matrix and predominance of collagen, overshadowing low-abundance proteins critical for understanding bone physiology during LC–MS/MS-based proteomic analysis. In this study, we present a rapid sequential two-step extraction protocol designed to enhance proteome coverage, reduce collagen interference without using collagenase, and ensure robust quantification while enabling simultaneous metabolome analysis. We systematically compared it with two previously reported methods, which attempt to reduce collagen content through enzymatic collagen digestion or by employing four sequential extractions. Performance was evaluated based on reproducible protein quantification, variance, collagen content, processing, and instrument time. Our protocol reproducibly quantified 4,518 proteins across a dynamic range of 4 orders of magnitude. It demonstrated only marginally inferior quantification performance compared to the four-step protocol while reducing extraction and measurement time by half. Further, it significantly outperformed the collagenase-based method, which quantified only 2,689 proteins. Incorporating a chloroform–methanol metabolite extraction only led to a minimal reduction in quantifiable proteins, making the protocol suitable for multiomics applications. In conclusion, this protocol facilitates comprehensive coverage of proteins after metabolite extraction, enabling comprehensive multiomics analyses and aiding in the assessment of bone diseases and therapeutic developments.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 9","pages":"4362–4376"},"PeriodicalIF":3.6,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.4c01060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833481","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

Taurine as a Protective Metabolite in Radiation-Induced Liver Disease: Evidence from 1H NMR Metabolomics 牛磺酸作为辐射引起的肝脏疾病的保护性代谢物：来自1H NMR代谢组学的证据。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-11 DOI: 10.1021/acs.jproteome.5c00398

Yi-Hsiu Chung, Chi-Chang Weng, Fujie Jhang, Gigin Lin, Ching-Fang Yu* and Fang-Hsin Chen*,

{"title":"Taurine as a Protective Metabolite in Radiation-Induced Liver Disease: Evidence from 1H NMR Metabolomics","authors":"Yi-Hsiu Chung, Chi-Chang Weng, Fujie Jhang, Gigin Lin, Ching-Fang Yu* and Fang-Hsin Chen*, ","doi":"10.1021/acs.jproteome.5c00398","DOIUrl":"10.1021/acs.jproteome.5c00398","url":null,"abstract":"Radiation therapy for liver and upper abdominal malignancies is associated with a high risk of radiation-induced liver disease (RILD), often involving metabolic disturbances. This study aimed to characterize metabolomic alterations in a murine RILD model using 1H-nuclear magnetic resonance (NMR) spectroscopy. RILD was induced in mice via 15 Gy hepatic irradiation. Liver tissues were subjected to time-course metabolomic profiling using 1H NMR. Validation was performed through liver enzyme assays, histological analysis, and qPCR. Taurine was selected for therapeutic evaluation based on metabolomic findings. Significant reductions in glutathione and pyruvate levels were observed in the acute stage, whereas increases in phenylalanine and tyrosine levels were observed in the chronic stage. These metabolite alterations were correlated with reactive oxygen species (ROS) production, glycolysis modulation, and fibrosis progression in RILD. Notably, taurine levels increased during the acute stage but decreased during the chronic stage. Furthermore, in mice at 12 weeks postirradiation, taurine supplementation maintained liver enzyme activity, cytokine profiles, and taurine metabolism at levels similar to those of the control group. In conclusion, this study revealed dynamic metabolic changes associated with physiological alterations in a murine RILD model and identified, through 1H NMR metabolomics, taurine as a potential target for alleviating nonclassical RILD symptoms.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 9","pages":"4708–4718"},"PeriodicalIF":3.6,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.5c00398","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820153","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

SomaModules: A Pathway Enrichment Approach Tailored to SomaScan Data somammodules：一种针对SomaScan数据的途径富集方法。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-11 DOI: 10.1021/acs.jproteome.4c01114

Julián Candia*, Giovanna Fantoni, Francheska Delgado-Peraza, Nader Shehadeh, Toshiko Tanaka, Ruin Moaddel, Keenan A. Walker and Luigi Ferrucci,

{"title":"SomaModules: A Pathway Enrichment Approach Tailored to SomaScan Data","authors":"Julián Candia*, Giovanna Fantoni, Francheska Delgado-Peraza, Nader Shehadeh, Toshiko Tanaka, Ruin Moaddel, Keenan A. Walker and Luigi Ferrucci, ","doi":"10.1021/acs.jproteome.4c01114","DOIUrl":"10.1021/acs.jproteome.4c01114","url":null,"abstract":"Motivated by the lack of adequate tools to perform pathway enrichment analysis, this work presents an approach specifically tailored to SomaScan data. Starting from annotated gene sets, we developed a greedy, top-down procedure to iteratively identify strongly intracorrelated SOMAmer modules, termed “SomaModules”, based on 11K SomaScan data. We generated two repositories based on the latest MSigDB and MitoCarta releases, containing more than 40,000 SOMAmer-based gene sets combined. These repositories can be utilized by any unstructured pathway enrichment analysis tool. We validated our results with two case examples: (i) Alzheimer’s disease specific pathways in a 7K SomaScan case–control study, and (ii) mitochondrial pathways using 11K SomaScan data linked to physical performance outcomes. Using gene set enrichment analysis (GSEA), we found that, in both examples, SomaModules had significantly higher enrichment than the original gene set counterparts. These findings were robust and not significantly affected by the choice of enrichment metric or the Kolmogorov enrichment statistic used in the GSEA procedure. We provide users with access to all code, documentation and data needed to reproduce our current repositories, which also will enable them to leverage our framework to analyze SomaModules derived from other sources, including custom, user-generated gene sets.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 9","pages":"4391–4402"},"PeriodicalIF":3.6,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.4c01114","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820152","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

Evaluating Novel Direct Injection Liquid Chromatography-Mass Spectrometry Method and Extraction-Based Workflows for Untargeted Lipidomics of Extracellular Vesicles. 评价细胞外囊泡非靶向脂质组学的新型直接注射液相色谱-质谱法和基于提取的工作流程。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-11 DOI: 10.1021/acs.jproteome.5c00156

Michał Młynarczyk, Felicja Gajdowska, Jorge Matinha-Cardoso, Paulo Oliveira, Paula Tamagnini, Mariusz Belka, Jagoda Mantej, Danuta Gutowska-Owsiak, Weronika Hewelt-Belka

{"title":"Evaluating Novel Direct Injection Liquid Chromatography-Mass Spectrometry Method and Extraction-Based Workflows for Untargeted Lipidomics of Extracellular Vesicles.","authors":"Michał Młynarczyk, Felicja Gajdowska, Jorge Matinha-Cardoso, Paulo Oliveira, Paula Tamagnini, Mariusz Belka, Jagoda Mantej, Danuta Gutowska-Owsiak, Weronika Hewelt-Belka","doi":"10.1021/acs.jproteome.5c00156","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00156","url":null,"abstract":"Lipids of extracellular vesicles (EVs) are attracting attention due to their crucial biological functions and potential roles in processes such as carcinogenesis. This study compares three commonly used lipid extraction techniques, i.e., liquid-liquid extraction, single-phase extraction, and solid-phase extraction, with a novel direct injection liquid chromatography-mass spectrometry (DI-LC-MS) workflow tailored to EV lipidomics. In the DI-LC-MS approach, EVs are disrupted and released directly in the chromatographic system, enabling the analysis of lipids without a prior extraction step. The applicability of the DI-LC-MS workflow was demonstrated by profiling lipids in mammalian and bacterial EVs. The lipidome coverage and high precision of the DI-LC-MS method (coefficient of variation of peak area lower than 20% for all the identified lipids) enabled identification of differences in lipid profiles of EV samples. The column used in the DI-LC-MS method exhibited a sufficient lifespan and stability for comparative lipidomic studies. Lipidome coverage, lipid species distribution, and precision varied across the studied workflows; our findings highlight the strengths and limitations of these methods. The DI-LC-MS emerges as a sustainable alternative for EV lipidomic studies by eliminating the need for sample preparation and reducing analysis time, solvent use, and chemical noise while requiring less than 1 μL of sample.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820150","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

Assessing Long-Term Stored Tissues for Multi-Omics Data Quality and Proteogenomics Suitability 评估长期储存组织的多组学数据质量和蛋白质基因组学适用性。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-10 DOI: 10.1021/acs.jproteome.5c00289

Kyu Jin Song, Minsuh Kim, Yong Jin Heo, Kyung-Cho Cho, Jae-Won Oh, Dae Ho Kim, Chanwoong Hwa, Yeji Do, Seunghyuk Choi, Hee Sang Hwang, Kwoneel Kim, Kyunggon Kim, Seungjin Na, Eunok Paek, Joon-Yong An, Se Jin Jang, Min-Sik Kim* and Kwang Pyo Kim*,

{"title":"Assessing Long-Term Stored Tissues for Multi-Omics Data Quality and Proteogenomics Suitability","authors":"Kyu Jin Song, Minsuh Kim, Yong Jin Heo, Kyung-Cho Cho, Jae-Won Oh, Dae Ho Kim, Chanwoong Hwa, Yeji Do, Seunghyuk Choi, Hee Sang Hwang, Kwoneel Kim, Kyunggon Kim, Seungjin Na, Eunok Paek, Joon-Yong An, Se Jin Jang, Min-Sik Kim* and Kwang Pyo Kim*, ","doi":"10.1021/acs.jproteome.5c00289","DOIUrl":"10.1021/acs.jproteome.5c00289","url":null,"abstract":"As research into cancer biology progresses, multiomics analyses have become essential for unraveling its molecular complexities. However, sample availability remains a challenge due to factors such as collection procedures and long-term storage effects. Archived samples present an opportunity to expand multiomics studies, but concerns persist regarding storage duration’s impact on data reliability. This study examines the genomic, transcriptomic, and proteomic profiles of samples stored for over a decade. Transcriptomic analysis revealed a decline in read counts for protein-coding genes but preserved core gene expression patterns. Proteomic measurements remained stable, with minimal changes in post-translational modifications. While phosphorylation and acetylation rates were largely unaffected, a slight increase in modification frequencies was observed. Housekeeping genes and proteins exhibited consistent expression across samples, yet proteomic differences between the tumor and normal tissues were distinct. Despite technical variations in transcriptomic data, essential transcription factors and kinases retained functionality. These findings underscore the viability of archived samples for multiomics research, enabling broader investigations into cancer biology and providing insights into molecular mechanisms. By leveraging archived specimens, researchers can overcome sample limitations and advance precision oncology efforts, ultimately deepening our understanding of cancer at the systems level.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 9","pages":"4563–4574"},"PeriodicalIF":3.6,"publicationDate":"2025-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815288","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

Quantifying Hydrolytic Enzymes in the Vitreous Humor of Humans and Nonhuman Species Using Targeted Proteomics 用靶向蛋白质组学定量测定人类和非人类玻璃体中的水解酶。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-10 DOI: 10.1021/acs.jproteome.5c00208

Sarah M. Ruttenberg, , , Joshua M. Rowe, , and , Alireza Abdolvahabi*,

{"title":"Quantifying Hydrolytic Enzymes in the Vitreous Humor of Humans and Nonhuman Species Using Targeted Proteomics","authors":"Sarah M. Ruttenberg, , , Joshua M. Rowe, , and , Alireza Abdolvahabi*, ","doi":"10.1021/acs.jproteome.5c00208","DOIUrl":"10.1021/acs.jproteome.5c00208","url":null,"abstract":"The vitreous humor is a viscous ocular fluid that contains a complex proteome including hydrolytic enzymes. Differences between concentrations of these enzymes may contribute to the variable hydrolysis of some intravitreal drugs/implants. Here, we developed a targeted proteomics method to quantify six hydrolytic enzymes in the vitreous humor of eight human donors as well as in the vitreous humor of rabbits, minipigs, and monkeys. These enzymes include cathepsin D (CTSD), ectonucleotide pyrophosphatase 2 (ENPP2), B-hexosaminidase subunit alpha (HEXA), serum paraoxonase 1 (PON1), tripeptidyl peptidase 1 (TPP1), and ubiquitin carboxy-terminal hydrolase lysozyme 1 (UCHL1). The results showed that enzyme concentrations were different among human subjects and between nonhuman species. Within human samples, CTSD and ENPP2 showed the highest levels. A gender-based comparison also revealed that two enzymes, UCHL1 and TPP1, showed significantly higher levels in female subjects compared to those in male subjects. Comparisons between humans and other species revealed potentially significant inter- and intraspecies differences between the levels of hydrolytic enzymes. Although performed on a limited number of samples to draw a robust biological conclusion, these results can guide researchers in the design of in vitro models of vitreous humor for prodrug metabolism and implant polymer degradation studies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5297–5304"},"PeriodicalIF":3.6,"publicationDate":"2025-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811441","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