Molecular & Cellular Proteomics最新文献

{"title":"Proteomics and Phosphoproteomics Revealed Dysregulated Kinases and Potential Therapy for Liver Fibrosis.","authors":"Xinyu Cheng, Li Kang, Jinfang Liu, Qingye Wang, Zhenpeng Zhang, Li Zhang, Yuping Xie, Lei Chang, Daobing Zeng, Lantian Tian, Lingqiang Zhang, Ping Xu, Yanchang Li","doi":"10.1016/j.mcpro.2025.100991","DOIUrl":"10.1016/j.mcpro.2025.100991","url":null,"abstract":"<p><p>Liver fibrosis is the initial stage of most liver diseases, and it is also a pathological process involving the liver in the late stages of many metabolic diseases. Therefore, it is important to systematically understand the pathological mechanism of liver fibrosis and seek therapeutic approaches for intervention and treatment of liver fibrosis. Disordered proteins and their post-translational modifications, such as phosphorylation, play vital roles in the occurrence and development of liver fibrosis. However, the regulatory mechanisms that govern this process remain poorly understood. In this study, we analyzed and quantified the liver proteome and phosphoproteome of carbon tetrachloride-induced early liver fibrosis model in mice. Proteomic analysis revealed that the pathways involved in extracellular matrix recombination, collagen formation, metabolism and other related disorders, and protein phosphorylation modification pathways were also significantly enriched. In addition, Western blotting and phosphoproteomics demonstrated that phosphorylation levels were elevated in the context of liver fibrosis. A total of 13,152 phosphosites were identified, with 952 sites increased, whereas only 156 sites decreased. Furthermore, the upregulated phosphorylation sites, which exhibited no change at the proteome level, mainly shared a common [xxxSPxxx] motif. Consequently, the kinase-substrate analysis ascertained the overactive kinases of these upregulated substrates, which ultimately led to the identification of 13 significantly altered kinases within this dataset. These kinases were mainly cataloged into the STE, CMGC, and CAMK kinase families. Among them, STK4 (serine/threonine-protein kinase 4), GSK3α (glycogen synthase kinase 3α), and CDK11B (cyclin-dependent kinase 11B) were subsequently validated though cellular and animal experiments, and the results demonstrated that their inhibitors could effectively reduce the activation of hepatic stellate cells and extracellular matrix production. These kinases may represent potential therapeutic targets for liver fibrosis, and their inhibitors may serve as promising antihepatic fibrosis drugs.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100991"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078703","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}

{"title":"NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing.","authors":"Ngoc Hieu Tran, Rui Qiao, Zeping Mao, Shengying Pan, Qing Zhang, Wenting Li, Lei Xin, Ming Li, Baozhen Shan","doi":"10.1016/j.mcpro.2025.100939","DOIUrl":"10.1016/j.mcpro.2025.100939","url":null,"abstract":"","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":"24 6","pages":"100939"},"PeriodicalIF":5.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12289525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564949","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}

{"title":"Landscape of Steroid Dynamics in Pregnancy: Insights From the Maternal-Placental-Fetal Unit and Placental Models.","authors":"Rona Karahoda, Therina Du Toit, Barbara Fuenzalida, Sampada Kallol, Michael Groessl, Pascale Anderle, Edgar Ontsouka, Frantisek Staud, Christa E Flueck, Christiane Albrecht","doi":"10.1016/j.mcpro.2025.100976","DOIUrl":"10.1016/j.mcpro.2025.100976","url":null,"abstract":"<p><p>Recent advances in analytical methods have revolutionized our understanding of steroid biochemistry. The emergence of novel steroids such as 11-oxy androgens and 11-oxy progesterones has necessitated a reevaluation of steroid biosynthesis and metabolism within the maternal-placental-fetal unit. In this study, we employed a validated liquid chromatography high-resolution mass spectrometry method to quantify 51 steroids in paired maternal serum, neonatal serum, and placenta samples from 37 healthy pregnancies. Additionally, we characterized steroid release in various placental models, including human placenta perfusion, explants, and primary trophoblast cells isolated from human term placenta. Our findings emphasize the predominance of keto derivatives of androgens in the placenta compared to hydroxylated forms, which are dominant in maternal serum and neonatal serum. We also observed high levels of classic and novel progesterones in the placenta and across all models, with significant release on the maternal side. These results suggest that the placenta possesses an active enzymatic machinery capable of producing and metabolizing novel progesterones. Furthermore, we demonstrated that the catalytic activity of 11β-hydroxysteroid dehydrogenase type 2 extends beyond cortisol regulation to hydroxylated androgens, highlighting its significance in the broader context of steroid metabolism within the maternal-placental-fetal unit. These findings contribute to our understanding of placental physiology and impact on fetal development.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100976"},"PeriodicalIF":5.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12289528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033660","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}

{"title":"Proteomic Analysis and 2-Hydroxyisobutyrylation Profiling in Metabolic Syndrome Induced Restenosis.","authors":"Xiangyu Liu, Liping Zhou, Wenjing Huang, Yanyan Yang, Yijun Yang, Tianwei Liu, Mingjin Guo, Tao Yu, Yongxin Li","doi":"10.1016/j.mcpro.2025.100978","DOIUrl":"10.1016/j.mcpro.2025.100978","url":null,"abstract":"<p><p>Restenosis is the primary complication following stenting for coronary and peripheral arterial disease, posing an ongoing clinical challenge. Metabolic syndrome (MetS), characterized by metabolic disturbances, has been identified as an independent predictor for postoperative restenosis in coronary and carotid arteries, potentially due to endothelial dysfunction and augmented oxidative stress in cells, while its specific regulatory mechanism is still largely unknown. Lysine 2-hydroxyisobutyrylation (Khib), a recently identified posttranslational modification, plays a crucial role in transcriptional regulation and cellular metabolism. However, there is a lack of comprehensive analysis of the proteome and Khib modifications within restenotic vessels in the context of MetS, as well as in the understanding of the associated pathophysiology. In this study, we observed a significant upregulation of Khib in restenotic arteries induced by MetS, confirmed by animal and cellular experiments. Further, using high-throughput liquid chromatography-mass spectrometry, we catalogued 15,558 Khib sites across 2568 proteins, implicating a multitude of biological functions. Analysis revealed 2007 Khib sites on 1002 proteins with considerable differential modifications which are present within the cytoplasm and nucleus. Interestingly, proteins located in the mitochondria, endoplasmic reticulum, and cell membrane also exhibit distinct expression and modification profiles to varying extents that related to vascular smooth muscle contraction, platelet activation, and the PI3K-Akt signaling pathway. Notably, the level of COL1A1 protein detected in the protein-protein interaction pathway network and the level of Khib modification are diametrically opposed, suggesting a significant role in the disease's pathogenesis. This study provides the first comprehensive proteomic and Khib modification overview of MetS-related in-stent restenosis vasculature, offering key insights to inform novel therapeutic approaches for restenosis mitigation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100978"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033552","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}

{"title":"Discovery of Proteoforms Associated With Alzheimer's Disease Through Quantitative Top-Down Proteomics.","authors":"James M Fulcher, Ashley N Ives, Shinya Tasaki, Shane S Kelly, Sarah M Williams, Thomas L Fillmore, Mowei Zhou, Ronald J Moore, Wei-Jun Qian, Ljiljana Paša-Tolić, Lei Yu, Shahram Oveisgharan, David A Bennett, Philip L De Jager, Vladislav A Petyuk","doi":"10.1016/j.mcpro.2025.100983","DOIUrl":"10.1016/j.mcpro.2025.100983","url":null,"abstract":"<p><p>The complex nature of Alzheimer's disease (AD) and its heterogenous clinical presentation has prompted numerous large-scale -omic analyses aimed at providing a global understanding of the pathophysiological processes involved. AD involves isoforms, proteolytic products, and posttranslationally modified proteins such as amyloid beta (Aβ) and microtubule-associated protein tau. Top-down proteomics directly measures these species and thus, offers a comprehensive view of pathologically relevant proteoforms that are difficult to analyze using traditional proteomic techniques. Here, we broadly explored associations between proteoforms and clinicopathological traits of AD by deploying a quantitative top-down proteomics approach across frontal cortex of 103 subjects selected from the ROS and MAP cohorts. The approach identified 1213 proteins and 11,782 proteoforms, of which 154 proteoforms had at least one significant association with a clinicopathological phenotype. One important finding included identifying Aβ C-terminal truncation state as the key property for differential association between amyloid plaques and cerebral amyloid angiopathy. Furthermore, various N-terminally truncated forms of Aβ had noticeably stronger association with amyloid plaques and global cognitive function. Additionally, we discovered six VGF neuropeptides that were positively associated with cognitive function independent of pathological burden. The database of brain cortex proteoforms provides a valuable context for functional characterization of the proteins involved in AD and other late-onset brain pathologies.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100983"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12173667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027207","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}

{"title":"Glycoproteomic and Single-Protein Glycomic Analyses Reveal Zwitterionic N-Glycans on Natural and Recombinant Proteins Derived From Insect Cells.","authors":"Shi Yan, Jorick Vanbeselaere, Callum Ives, David Stenitzer, Lena Nuschy, Florian Wöls, Katharina Paschinger, Elisa Fadda, Johannes Stadlmann, Iain B H Wilson","doi":"10.1016/j.mcpro.2025.100981","DOIUrl":"10.1016/j.mcpro.2025.100981","url":null,"abstract":"<p><p>Insect cells are a convenient cell factory to produce recombinant glycoproteins. Their glycosylation potential is believed to be simple, needing primarily addition of glycosyltransferases to humanize the recombinant products. In this study, the native glycoproteome of Spodoptera frugiperda Sf9 and Trichoplusia ni High Five cells, examined using an LC-MS/MS approach, revealed not only which proteins are N-glycosylated but also indicated that the N-glycomes contain novel glucuronylated and phosphorylcholine-modified glycans, in addition to typical oligomannosidic and fucosylated structures. These data were corroborated by a parallel MALDI-TOF MS/MS analysis of N-glycosidase-released oligosaccharides. Molecular modeling analysis of one endogenous Sf9 glycoprotein correlated the occurrence of complex and oligomannosidic N-glycans with the accessibility of the occupied N-glycosylation sites. Further, we showed that the N-glycans of influenza hemagglutinins and SARS-CoV-2 spike glycoprotein produced in Spodoptera cells possess a number of glycan structures modified with phosphorylcholine, but core difucosylation was minimal; in contrast, the Trichoplusia-produced hemagglutinin had only traces of the former type, while the latter was dominant. Detection of phosphorylcholine on these glycoproteins correlated with binding to human C-reactive protein. In conclusion, not just oligomannosidic or truncated paucimannosidic N-glycans, but structures with immunogenic features occur on both natural and recombinant glycoproteins derived from insect cell lines.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100981"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023710","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}

{"title":"Generation of a Deep Mouse Brain Spectral Library for Transmembrane Proteome Profiling in Mental Disease Models.","authors":"Shanshan Li, Huoqing Luo, Pan Tang, Cuiping Tian, Ji Hu, Haojie Lu, Wenqing Shui","doi":"10.1016/j.mcpro.2025.100941","DOIUrl":"10.1016/j.mcpro.2025.100941","url":null,"abstract":"","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":"24 6","pages":"100941"},"PeriodicalIF":5.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12289524/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564890","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}

{"title":"Theileria annulata Hijacks Host Signaling: Integrated Phosphoproteomics and Transcriptomics Unveils ERK1/2 as a Central Regulator of Host Transcription Factors.","authors":"Debabrata Dandasena, Vengatachala Moorthy A, Akash Suresh, Vasundhra Bhandari, Sonti Roy, Paresh Sharma","doi":"10.1016/j.mcpro.2025.100992","DOIUrl":"10.1016/j.mcpro.2025.100992","url":null,"abstract":"<p><p>Theileria-transformed bovine leukocytes exhibit cancer-like characteristics, but the molecular mechanisms driving these transformations remain unclear. This study provides the first comprehensive phosphoproteomic analysis of both host and parasite in Theileria annulata-infected leukocyte cell lines. We show that T. annulata significantly induces changes in the host protein phosphorylation, impacting key cancer-related processes such as apoptosis suppression, CAMK signaling, and telomere maintenance. A pivotal finding is the parasite's manipulation of the MAPK pathway via sustained ERK1/2 activation, which regulates the phosphorylation of critical transcription factors like RUNX3, FOSL2, BCL6, c-JUN, JUNB, and c-MYC. Transcriptomic analysis of genes controlled by these transcription factors confirmed their role in T. annulata replication. ERK inhibition disrupts phosphorylation, deactivates these transcription factors, and induces apoptosis in infected cells. This underscores the ERK-AP-1 axis as a central mechanism of Theileria pathogenesis and a promising therapeutic target. Additionally, parasite-specific phosphoproteins and kinases were identified, offering new insights into therapeutic strategies to combat infection.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100992"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12205586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078705","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}

{"title":"Chronic Alcohol Consumption Reprograms Hepatic Metabolism Through Organelle-Specific Acetylation in Mice.","authors":"Mirjavid Aghayev, Megan R McMullen, Serguei Ilchenko, Andrea Arias-Alvarado, Victor Lufi, Jack Mathis, Hannah Marchuk, Tsung-Heng Tsai, Guo-Fang Zhang, Laura E Nagy, Takhar Kasumov","doi":"10.1016/j.mcpro.2025.100990","DOIUrl":"10.1016/j.mcpro.2025.100990","url":null,"abstract":"<p><p>Posttranslational acetylation of proteins by acetyl-CoA is a crucial regulator of proteostasis and substrate metabolism. Ethanol metabolism in the liver induces protein accumulation, acetylation, and metabolic disruption. Although acetylation impacts enzyme activity and stability, its role in ethanol-related protein accumulation and metabolic dysfunction remains unclear. Using stable isotope-based proteomics, acetylomics, and metabolic profiling in a mouse model of chronic ethanol-induced liver injury, we demonstrate that ethanol induces hepatic steatosis, inflammation, oxidative stress, and proteinopathy linked to altered protein turnover. Ethanol increased the cytosolic protein turnover related to oxidative stress and detoxification, while reducing turnover of mitochondrial metabolic enzymes. It also elevated the acetylation of mitochondrial enzymes and nuclear histones with minimal cytosolic changes, impairing mitochondrial protein degradation. These changes were associated with altered levels of acyl-CoAs and acyl-carnitines, amino acids, and tricarboxylic acid cycle intermediates, reflecting impaired fatty acid oxidation, nitrogen disposal and tricarboxylic acid cycle activities. These results suggest that ethanol-induced acetylation contributes to liver injury and that targeting acetylation may offer treatment for alcohol-induced liver diseases.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100990"},"PeriodicalIF":5.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12289531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078222","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}

{"title":"Temporal Wheat Proteome Remodeling by Deoxynivalenol Reveals Novel Detoxification Signatures and Strategies Across Cultivars.","authors":"Reid Buchanan, Kholoud Shaban, Boyan Liu, Norris Chan, Mitra Serajazari, Jennifer Geddes-McAlister","doi":"10.1016/j.mcpro.2025.100988","DOIUrl":"10.1016/j.mcpro.2025.100988","url":null,"abstract":"<p><p>Fusarium head blight (FHB) is a globally devastating fungal disease resulting in reduced grain yield and quality, along with contamination of grains with dangerous mycotoxins. Consumption of such mycotoxins through processed food or livestock feed has downstream implications for human and animal health. This interconnectivity across the environment, animal, and human health defines the One Health problem of threatened food safety and security. In this study, we explore remodeling of the wheat proteome upon exposure to a common mycotoxin, deoxynivalenol (DON). We investigate cultivar-specific responses to DON exposure in FHB-susceptible (Norwell) and -resistant (Sumai#3) cultivars across a continuum of exposure (i.e., 24 and 120 h post inoculation) and upon low (i.e., 0.1 mg/ml) and high (1.0 mg/ml) levels of the mycotoxin. This complex experimental design enables us to tease apart the dynamic relationship between each cultivar and DON tolerance. Specifically, we define precise proteins and broad categories of remodeling that are common (i.e., reduction in photosynthesis) and exclusive (i.e., glycosyltransferase) to the cultivars and align with anticipated protective mechanisms. Moreover, we adapted an in vitro DON tolerance expression system and determined that induction of an ubiquinol oxidase (UniProt ID: A0A3B6B5K8) provides heightened protection for yeast growth relative to the negative control as well as increased protection compared to a well-defined DON detoxifying protein. Our study suggests a new avenue for the identification and characterization of novel DON detoxifying proteins as putative biomarkers for selected breeding strategies. Such strategies support the production of wheat varieties with increased tolerance to DON for improved global food safety and security.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100988"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12221369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007943","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}