Journal of Proteome Research最新文献

Multicompartment Quantitative Proteomics Revealing Potential Mechanisms Underlying the Treatment Effects of Mesenchymal-Derived Extracellular Vesicles in a Monkey Model of Cortical Injury. 多室定量蛋白质组学揭示了猴皮质损伤模型中间充质来源的细胞外囊泡治疗作用的潜在机制。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-10-01 DOI: 10.1021/acs.jproteome.5c00521

Shuo Qian, Ryan P McCann, Shichen Shen, Xiaoyu Zhu, Christina M Tsillas, Hongqi Xin, Mingjin Wang, Yi Zhang, Zheng Gang Zhang, Michael Chopp, Maria Medalla, Tara L Moore, Jun Qu

{"title":"Multicompartment Quantitative Proteomics Revealing Potential Mechanisms Underlying the Treatment Effects of Mesenchymal-Derived Extracellular Vesicles in a Monkey Model of Cortical Injury.","authors":"Shuo Qian, Ryan P McCann, Shichen Shen, Xiaoyu Zhu, Christina M Tsillas, Hongqi Xin, Mingjin Wang, Yi Zhang, Zheng Gang Zhang, Michael Chopp, Maria Medalla, Tara L Moore, Jun Qu","doi":"10.1021/acs.jproteome.5c00521","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00521","url":null,"abstract":"Previous studies have demonstrated that mesenchymal stromal cell-derived extracellular vesicles (MSC-EVs) enhance functional recovery after cortical injury in rhesus monkeys by reducing chronic microglial inflammation, neuronal damage, and myelination deficits. However, the signaling pathways underlying these therapeutic effects remain largely unexplored. In this study, employing a reliable quantitative proteomics platform UHR-IonStar, we identified the protein cargo of MSC-EVs infused intravenously to rhesus monkeys 24 h and 2 weeks post-injury to the motor cortex. We then analyzed global protein expression changes across cerebrospinal fluid (CSF), plasma, and brain tissue of MSC-EV-treated versus vehicle-treated female, aged rhesus monkeys. A total of 1241/431/4124 monkey proteins were reliably quantified in CSF/plasma/tissue samples, respectively. Longitudinal analysis of CSF and plasma samples highlighted a shift from MSC-EV modulation of inflammatory and metabolic proteins in plasma at early recovery (2 weeks), toward modulation of plasticity-related proteins in CSF and brain tissue at later stages (4 weeks). Further protein-protein interaction analysis identified potential MSC-EV targets related to complementary signaling, proteolysis, and aminoglycan stability, which aligned with our previous findings. This comprehensive, multicompartment monkey proteomics study advances understanding of MSC-EV contents and treatment effects, paving the way for novel treatment of cortical injury.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205006","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

A Lipidomic Exploration of the Effects of High-Intensity Interval Exercise in Healthy Men after Metformin Intake. 二甲双胍摄入后健康男性高强度间歇运动影响的脂质组学研究

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-30 DOI: 10.1021/acs.jproteome.5c00480

René Neuhaus, Thomas Meikopoulos, Ana Gradillas, Carolina Gonzalez-Riaño, Georgios Theodoridis, Stefanos Nikolaidis, Vassilis Mougios, Coral Barbas, Helen Gika, Alma Villaseñor

{"title":"A Lipidomic Exploration of the Effects of High-Intensity Interval Exercise in Healthy Men after Metformin Intake.","authors":"René Neuhaus, Thomas Meikopoulos, Ana Gradillas, Carolina Gonzalez-Riaño, Georgios Theodoridis, Stefanos Nikolaidis, Vassilis Mougios, Coral Barbas, Helen Gika, Alma Villaseñor","doi":"10.1021/acs.jproteome.5c00480","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00480","url":null,"abstract":"We have previously found that high-intensity interval exercise (HIIE) affected metformin pharmacokinetics compared with rest. In this scenario, changes in individual lipids could play an important role. The prolonged responses of the lipidome to HIIE have not been explored. This study aimed to explore differences in the plasma lipidomic profiles between HIIE and rest, both under metformin treatment. Nine healthy males participated in two sessions where they received 1,000 mg of metformin. In session A, they performed HIIE at an average intensity of 67% of the maximum heart rate for a total duration of 76 min, whereas in session B, they rested. Plasma was collected before taking metformin and during each session (in total, 14 time points spanning 12 h). Samples were analyzed through lipidomics using mass spectrometry. We found several variations in the lipid profiles due to HIIE, which persisted until 4 h post-exercise. Main discriminant lipid classes were fatty acids, acyl carnitines, glycerophosphocholines, sphingomyelins, and triacylglycerols. These changes were followed in time up to 12 h, showing the effect of the meals taken during the session. We hypothesize the changes are a synergic effect of HIIE and metformin in the lipidome, with the effect of HIIE being the predominant.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197545","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

TMTCrunch: A Proteomic Atlas of Alternative Splicing for Predicting Splicing-Induced Implications in Aging and Alzheimer's Disease. TMTCrunch：预测剪接诱导的衰老和阿尔茨海默病的选择性剪接蛋白质组学图谱。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-30 DOI: 10.1021/acs.jproteome.5c00426

Max Brazhnikov, Tomiris Kusainova, Anna S Kopeykina, Irina A Tarasova

{"title":"TMTCrunch: A Proteomic Atlas of Alternative Splicing for Predicting Splicing-Induced Implications in Aging and Alzheimer's Disease.","authors":"Max Brazhnikov, Tomiris Kusainova, Anna S Kopeykina, Irina A Tarasova","doi":"10.1021/acs.jproteome.5c00426","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00426","url":null,"abstract":"Alzheimer's disease (AD) is the most prevalent form of dementia with incompletely understood pathogenesis. A major gap arises from the lack of proteomics tools capable of characterizing alternative splicing (AS)-derived proteoforms and their contributions to neurodegeneration. We developed a novel bioinformatics pipeline, TMTCrunch, tailored for rigorous quantitative meta-analysis of big proteomics data at the splice-proteoform level. TMTCrunch characterizes each proteoform by unique peptides, assessing similarity to canonical peptides and unique peptide coverage, employing SMD-based quantitation, and predicting proteoform-specific alterations of protein-protein interactions (PPIs) and novel post-translational modifications (PTMs) on spliced peptides. Applying TMTCrunch to 420 brain samples, we constructed the first atlas of splicing translatomes in AD, reproducibly identifying 870 noncanonical proteoforms. Differential analysis suggests splicing affecting proteoforms implicated in cytoskeletal regulation (e.g., MAPT, CLU, DPYSL3, ACTN2, SORBS1, FHL1), glutamatergic transmission (GRIA3), pre-mRNA splicing regulation (ARL6IP4), potassium channel modulation (DPP6), and cAMP signaling (PDE4D). Our analysis predicts disruption of PPIs within the Rho GTPase and EGFR signaling pathways and PTMs (deamidation, oxidation, phosphorylation) within AS regions, regardless of disease state. This approach implicates specific proteoforms in neurodegeneration: DPP6 (P42658-2), GRIA3 (P42263-2), the three-repeat isoforms of tau (3R-MAPT), and ASPH (Q12797-7). This study provides new insights into linking splicing to neurodegeneration.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190456","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

BrainProt v3.0: An Integrative and Simplified Omics-Based Knowledge-Base About the Human Brain and Its Associated Diseases. BrainProt v3.0：一个关于人脑及其相关疾病的集成和简化的基于组学的知识库。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-26 DOI: 10.1021/acs.jproteome.4c00982

Deeptarup Biswas, Sanjyot Vinayak Shenoy, Aparna Chauhan, Ankit Halder, Advait Padhye, Sampurna Dutta, Shreeman Auromahima, Hiren Bavaskar, Deeksha Yadav, Biplab Ghosh, Souvik Sasmal, Neha Kumari, Tunuguntla Rishi Kumar, Ayan Prasad Mukherjee, Sanjeeva Srivastava

{"title":"BrainProt v3.0: An Integrative and Simplified Omics-Based Knowledge-Base About the Human Brain and Its Associated Diseases.","authors":"Deeptarup Biswas, Sanjyot Vinayak Shenoy, Aparna Chauhan, Ankit Halder, Advait Padhye, Sampurna Dutta, Shreeman Auromahima, Hiren Bavaskar, Deeksha Yadav, Biplab Ghosh, Souvik Sasmal, Neha Kumari, Tunuguntla Rishi Kumar, Ayan Prasad Mukherjee, Sanjeeva Srivastava","doi":"10.1021/acs.jproteome.4c00982","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00982","url":null,"abstract":"The advancements in neuroscience research and omics technologies generate extensive data for brain-related diseases and disorders that are scattered across various manuscript repositories and databases, potentially hindering global initiatives to advance neuroscience research. This study introduces BrainProt v3.0 (https://www.brainprot.org/), an omics-driven knowledge-base of human brain and associated diseases. BrainProt version 3.0 navigates the Human Brain Disease Atlas (HBDA) and integrates the Brain Disease Marker Curator (BDMC) and Brain Disease Drug Finder (BDDF). It features 20,202 disease-associated genes, 136,557 chemical target interactions, and 2,145 clinical trial details. Additionally, the Brain Disease Transcriptome Map (BDTM) and Brain Disease Proteome Map (BDPM) collate multiomics data from the most significant brain diseases, displaying an expression profile across 52 datasets and 1,868 samples. This platform also facilitates the exploration of biological cross-talk and correlations between transcriptomics and proteomics data to identify critical disease-associated markers. In conclusion, BrainProt is designed to advance the Human Brain Proteome Project (HBPP) by expanding the integration of diseases and datasets, thereby elucidating the complexities of brain diseases and enhancing the research on the interplay between brain tumors and neurodegenerative disorders.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147192","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

Integrative Omics and AI-Driven Systems Biology: Multilayer Networks Decoding Apis mellifera Health and Resilience. 整合组学和人工智能驱动的系统生物学：多层网络解码蜜蜂的健康和恢复能力。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-25 DOI: 10.1021/acs.jproteome.5c00294

Huan Zhong, Shuxin Chi, Armando Alcazar Magaña, Osei B Fordwour, Leonard J Foster

{"title":"Integrative Omics and AI-Driven Systems Biology: Multilayer Networks Decoding Apis mellifera Health and Resilience.","authors":"Huan Zhong, Shuxin Chi, Armando Alcazar Magaña, Osei B Fordwour, Leonard J Foster","doi":"10.1021/acs.jproteome.5c00294","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00294","url":null,"abstract":"Honey bees (Apis mellifera) are vital pollinators essential for maintaining ecosystem stability and global food production, but they face escalating threats from pathogens, agrochemicals, and climate change. Although proteomics has advanced our understanding of bee physiology, single-omics approaches are insufficient to capture the complexity of colony health. This review highlights the rise of integrative multiomics frameworks─combining proteomics, metabolomics, and lipidomics─with artificial intelligence (AI)-based strategies to decode molecular resilience in bees. We summarize recent advances in omics technologies, including spatial and single-cell platforms, mass spectrometry innovations, and customized computational pipelines. Furthermore, we highlight how AI-enhanced multiomics integration facilitates biomarker discovery, elucidates regulatory networks, especially in nonmodel organisms like honey bees. Emerging computational methods such as deep learning, graph neural networks, and multilayer network models offer predictive, scalable, and interpretable insights. Despite challenges like limited sample input and cross-omics heterogeneity, the convergence of omics and machine learning represents a transformative paradigm for decoding complex biological systems. These integrative approaches offer not only a deeper molecular understanding of bee biology but also generalizable frameworks for systems biology in other ecologically relevant species.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147171","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 and Metabolomics Profiles of Unvaccinated Nonagenarian Patients with Severe SARS-CoV-2 Infection. 未接种疫苗的老年严重SARS-CoV-2感染患者的蛋白质组学和代谢组学特征

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-25 DOI: 10.1021/acs.jproteome.5c00251

Mauricio Quiñones-Vega, Patricia Sosa-Acosta, Jéssica de Siqueira Guedes, Natália Pinto de Almeida, Mateus V de Castro, Moníze V R Silva, Luiz P Dell'Aquila, Álvaro Razuk-Filho, Pedro B Batista-Júnior, Mayana Zatz, Fábio César Sousa Nogueira, Gilberto Barbosa Domont

{"title":"Proteomics and Metabolomics Profiles of Unvaccinated Nonagenarian Patients with Severe SARS-CoV-2 Infection.","authors":"Mauricio Quiñones-Vega, Patricia Sosa-Acosta, Jéssica de Siqueira Guedes, Natália Pinto de Almeida, Mateus V de Castro, Moníze V R Silva, Luiz P Dell'Aquila, Álvaro Razuk-Filho, Pedro B Batista-Júnior, Mayana Zatz, Fábio César Sousa Nogueira, Gilberto Barbosa Domont","doi":"10.1021/acs.jproteome.5c00251","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00251","url":null,"abstract":"The mortality rate of COVID-19 increases significantly in patients over the age of 90, although some elderly people in this category have experienced mild disease or have been asymptomatic. In this context, we aim to analyze the plasma proteomic and metabolomic profiles of unvaccinated nonagenarian patients who had severe manifestations of COVID-19 and either recovered or died and compare them with noninfected control subjects. Compared with healthy individuals, nonsurviving patients showed a reduced abundance of specific lipid-related proteins and metabolites, including APOH, APOC1, LCAT, 7-α-25-dihydroxycholesterol, 7-dehydrocholesterol, and phosphatidylethanolamine, which may serve as indicative markers of severity. Acute phase response, complement activation, and sphingolipids and phospholipids remain altered in recovered patients, indicating possible persistent effects of COVID-19. This study employs a multiomics approach to unveil key immune alterations in unvaccinated nonagenarians, shedding light on molecular signatures that may serve as predictive markers for disease severity and recovery in the elderly population.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147181","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

Immunoproteomic Identification of Scedosporium boydii Antigens with Potential Diagnostic Interest in Cystic Fibrosis Patients. 对囊性纤维化患者有潜在诊断价值的波氏梭菌抗原的免疫蛋白质组学鉴定。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-25 DOI: 10.1021/acs.jproteome.5c00260

Leire Martin-Souto, Lucia Abio-Dorronsoro, Maialen Areitio, Leire Aparicio-Fernandez, Oier Rodriguez-Erenaga, Maria Teresa Martin-Gomez, Aitziber Antoran, Aitor Rementeria, Idoia Buldain, Andoni Ramirez-Garcia

{"title":"Immunoproteomic Identification of Scedosporium boydii Antigens with Potential Diagnostic Interest in Cystic Fibrosis Patients.","authors":"Leire Martin-Souto, Lucia Abio-Dorronsoro, Maialen Areitio, Leire Aparicio-Fernandez, Oier Rodriguez-Erenaga, Maria Teresa Martin-Gomez, Aitziber Antoran, Aitor Rementeria, Idoia Buldain, Andoni Ramirez-Garcia","doi":"10.1021/acs.jproteome.5c00260","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00260","url":null,"abstract":"Fungal infections caused by Scedosporium/Lomentospora species are a significant threat to patients with cystic fibrosis (pwCF), ranking as the second most common filamentous fungi in their airways after Aspergillus. Current serodiagnostic methods, such as counterimmunoelectrophoresis and ELISA using crude extracts, lack standardization and commercial availability and often show cross-reactivity with other fungi. This study aimed to identify specific Scedosporium boydii antigens with potential for serodiagnosis in pwCF. An immunoproteomic approach combining two-dimensional polyacrylamide gel electrophoresis, Western blot, and mass spectrometry was used to analyze the antigenic profile of S. boydii against sera from pwCF with positive cultures for Scedosporium/Lomentospora (Scedo+) and mice intravenously infected with these fungi. We identified 22 proteins specifically recognized by sera from pwCF Scedo+ and mice infected with S. boydii, but not by sera from pwCF or mice infected with Aspergillus spp. or uninfected controls. These proteins are primarily involved in metabolism and exhibit catalytic activity. The most prevalent antigens were the heat shock protein 70, 6-phosphogluconate dehydrogenase, 3-ketoacyl-CoA thiolase, and phosphoenolpyruvate carboxykinase, recognized by 67-81% of pwCF Scedo + sera with minimal cross-reactivity to negative samples. This work identifies promising candidates for the specific serodiagnosis of Scedosporium/Lomentospora infections in pwCF. Data are available via ProteomeXchange (PXD053392).","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147199","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

Analysis of the Porcine Reproductive and Respiratory Syndrome Virus Nucleocapsid Interactome. 猪繁殖与呼吸综合征病毒核衣壳相互作用组分析。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-25 DOI: 10.1021/acs.jproteome.5c00121

Duangnapa Kovanich, Kunjimas Ketsuwan, Kowit Hengphasatporn, Chutima Thepparit, Potchaman Sittipaisankul, Piriya Wongkongkathep, Chaitawat Sirisereewan, Navapon Techakriengkrai, Teerawut Nedumpun, Yasuteru Shigeta, Trairak Pisitkun, Sanipa Suradhat

{"title":"Analysis of the Porcine Reproductive and Respiratory Syndrome Virus Nucleocapsid Interactome.","authors":"Duangnapa Kovanich, Kunjimas Ketsuwan, Kowit Hengphasatporn, Chutima Thepparit, Potchaman Sittipaisankul, Piriya Wongkongkathep, Chaitawat Sirisereewan, Navapon Techakriengkrai, Teerawut Nedumpun, Yasuteru Shigeta, Trairak Pisitkun, Sanipa Suradhat","doi":"10.1021/acs.jproteome.5c00121","DOIUrl":"10.1021/acs.jproteome.5c00121","url":null,"abstract":"Porcine reproductive and respiratory syndrome virus (PRRSV) is a major swine pathogen that causes significant economic losses worldwide. The nucleocapsid (N) protein, the most abundant viral protein in infected cells, plays roles beyond its structural function, influencing various host cellular processes. Here, we report the identification of 301 cellular protein candidates interacting with PRRSV N using EGFP immunoprecipitation combined with label-free quantitative mass spectrometry. The analysis underscores the versatile nature of the N protein in targeting a wide range of cellular proteins and processes across multiple subcellular compartments. We observed strong enrichment of ribosomal proteins, nucleolar proteins involved in ribosome biogenesis, splicing factors, RNA helicases, and DNA-binding proteins involved in chromatin remodeling and DNA damage response. Additionally, we identified proteins involved in viral RNA sensing and intrinsic antiviral mechanisms that may contribute to the immunosuppressive properties of the viral protein. Several interactions were validated and further characterized for RNA dependence, including MYBBP1A, NCL, IGF2BP1, UPF3B, G3BP1, EIF2S1, RFC4, ABCF1, PPM1G, NSUN2, and NOP2. Notably, RTCB and MYBBP1A were identified as host dependency factors for PRRSV infection. Our findings expand the current understanding of PRRSV-host interactions and reveal novel N-interacting proteins that may contribute to viral pathogenesis and immune evasion.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135995","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

Tissue-, Blood-, and Urine-Based Proteomics Changes of Different Endometrial Receptivity Status in Patients after Fertility-Sparing Treatment of Atypical Endometrial Hyperplasia or Endometrial Cancer. 保留生育能力的非典型子宫内膜增生或子宫内膜癌患者不同子宫内膜容受状态的组织、血液和尿液蛋白质组学变化

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-25 DOI: 10.1021/acs.jproteome.5c00315

Tao Tao, Xiaoping Xiao, Yuanzheng Zhou, Haidan Sun, Xiaoyan Liu, Wei Sun, Zhengguang Guo, Chengyan Deng

{"title":"Tissue-, Blood-, and Urine-Based Proteomics Changes of Different Endometrial Receptivity Status in Patients after Fertility-Sparing Treatment of Atypical Endometrial Hyperplasia or Endometrial Cancer.","authors":"Tao Tao, Xiaoping Xiao, Yuanzheng Zhou, Haidan Sun, Xiaoyan Liu, Wei Sun, Zhengguang Guo, Chengyan Deng","doi":"10.1021/acs.jproteome.5c00315","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00315","url":null,"abstract":"Liquid biopsy noninvasively characterizes diseases by analyzing biomarker proteins in biofluids, which provide valuable insights into physiological and pathological processes. In this study, we conducted an analysis of the differences between atypical endometrial hyperplasia or endometrial cancer (AH/EC) patients after fertility-sparing treatment with different RNA-Seq-based endometrial receptivity test (rsERT) results (\"receptive\" versus \"pre-receptive\"), to investigate the proteomic connections among tissue, serum, and urine samples. Samples of endometrial tissue, serum, and urine from 40 rsERT \"pre-receptive\" and 10 rsERT \"receptive\" patients were analyzed for proteomic profiling. We integrated differentially expressed proteins from three sample types to investigate endometrial receptor (ER)-related molecular changes. Our findings indicated that both serum and urine proteomes can serve as indicators of functional changes in endometrial tissue. In serum, proteins associated with cholesterol metabolism, immune response, and coagulation exhibited a differential expression. In urine, proteins related to immune function and metabolic processes demonstrated varying levels of expression. The differentially expressed proteins in both serum and urine were associated with the immune response and metabolism. In conclusion, biofluids serve as a reflection of functional changes in endometrial tissue, which will facilitate a deeper understanding of endometrial receptivity and the discovery of potential clinical biomarkers.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147195","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

Linker H1 Histone Direct Top-Down Proteoform Analysis 连接子H1组蛋白直接自顶向下的蛋白质形态分析。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-09-23 DOI: 10.1021/acs.jproteome.5c00618

Md Shofiul Alam, , , Cassandra N. Fuller, , , Kevin Jeanne Dit Fouque, , , Lilian Valadares Tose, , , Marissa A. Carter, , , Richard M. Searfoss, , , Francisca N. de Luna Vitorino, , , Mariangela Kosmopoulou, , , Detlev Suckau, , , Mark E. Ridgeway, , , Steven L. Van Orden, , , Benjamin A. Garcia, , and , Francisco Fernandez-Lima*,

{"title":"Linker H1 Histone Direct Top-Down Proteoform Analysis","authors":"Md Shofiul Alam, , , Cassandra N. Fuller, , , Kevin Jeanne Dit Fouque, , , Lilian Valadares Tose, , , Marissa A. Carter, , , Richard M. Searfoss, , , Francisca N. de Luna Vitorino, , , Mariangela Kosmopoulou, , , Detlev Suckau, , , Mark E. Ridgeway, , , Steven L. Van Orden, , , Benjamin A. Garcia, , and , Francisco Fernandez-Lima*, ","doi":"10.1021/acs.jproteome.5c00618","DOIUrl":"10.1021/acs.jproteome.5c00618","url":null,"abstract":"Linker H1 histones are highly susceptible to a variety of post-translational modifications (PTMs) that play a critical role in chromatin dynamics and gene expression. In the present work, trapped ion mobility spectrometry in tandem with ultraviolet photodissociation followed by ultrahigh resolution mass measurements, provided by a Fourier transform ion cyclotron mass spectrometer (TIMS-q-UVPD-FT-ICR MS/MS), enabled direct characterization of the linker H1 histone proteoforms. The proposed method takes advantage of the mobility and mass preseparation of core and linker histones proteoforms prior to UVPD fragmentation and consequent high mass accuracy detection in the FT-ICR MS of the fragment ions for efficient PTM assignment. The application to a bovine histone extraction resulted in the annotation of four H1 variants (H1.2, H1.3, H1.5, and H1.4V), together with their PTM distribution with high sequence coverages (up to 60%); in particular, the H1.4V variant sequence was identified via de novo sequencing. All reported H1 proteoforms and their PTMs (e.g., mono/dimethylation, acetylation, and phosphorylation) were confirmed with complementary top-down liquid chromatography coupled to tandem MS/MS using electron-activated dissociation (LC-q-EAD-ToF MS/MS) and bottom-up analysis. This direct approach shows great promise for global H1 proteoform analysis due minimal sample preparation and large number of proteoform PTM observed.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5216–5225"},"PeriodicalIF":3.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129591","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}

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