The mechanisms underlying cell polarization are fundamental to biology but remain incompletely understood. This is especially true for hepatocytes, which display a particularly complex polarization that enables the formation of the bile canaliculi (BC) network crucial for liver excretory functions. To identify key proteins involved in hepatocyte polarization, BC formation, structure or function, we employed a proteomic approach comparing the human hepatocyte cell line HepG2 to its sub clone HepG2/C3A known for its markedly greater efficiency in forming mature BCs. Through this analysis, we localized LimA1 and Espin to the BC for the first time, suggesting their important role in this compartment, and confirmed the presence of NHE-RF1. Using a targeted protein repression strategy, we identified E cadherin as essential for the initiation of BC formation, unlike other adherens junction components such as N cadherin or α-catenin. Our findings demonstrate, for the first time, that in the absence of E cadherin, hepatocytes lose the capacity to form BCs.
Significance
This study aims to deepen our understanding of the highly specialized polarization of hepatocytes in relation to bile canaliculus formation. The major finding is the key role of E cadherin in this process, where it appears to be essential for bile canaliculus formation in both 2D and 3D culture models. Additionally, the study led to the identification of several proteins potentially localized to the bile canaliculi, whose functions remain to be elucidated.
{"title":"E cadherin appears to be an essential on/off switch for initiating bile canaliculi formation","authors":"Mireille Chevallet , Thierry Rabilloud , Hélène Diemer , Fabrice Bertile , Alexandra Fuchs , Aurélien Deniaud","doi":"10.1016/j.jprot.2025.105508","DOIUrl":"10.1016/j.jprot.2025.105508","url":null,"abstract":"<div><div>The mechanisms underlying cell polarization are fundamental to biology but remain incompletely understood. This is especially true for hepatocytes, which display a particularly complex polarization that enables the formation of the bile canaliculi (BC) network crucial for liver excretory functions. To identify key proteins involved in hepatocyte polarization, BC formation, structure or function, we employed a proteomic approach comparing the human hepatocyte cell line HepG2 to its sub clone HepG2/C3A known for its markedly greater efficiency in forming mature BCs. Through this analysis, we localized LimA1 and Espin to the BC for the first time, suggesting their important role in this compartment, and confirmed the presence of NHE-RF1. Using a targeted protein repression strategy, we identified E cadherin as essential for the initiation of BC formation, unlike other adherens junction components such as N cadherin or α-catenin. Our findings demonstrate, for the first time, that in the absence of E cadherin, hepatocytes lose the capacity to form BCs.</div></div><div><h3>Significance</h3><div>This study aims to deepen our understanding of the highly specialized polarization of hepatocytes in relation to bile canaliculus formation. The major finding is the key role of E cadherin in this process, where it appears to be essential for bile canaliculus formation in both 2D and 3D culture models. Additionally, the study led to the identification of several proteins potentially localized to the bile canaliculi, whose functions remain to be elucidated.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105508"},"PeriodicalIF":2.8,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718127","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}
Pub Date : 2025-10-30Epub Date: 2025-07-29DOI: 10.1016/j.jprot.2025.105510
Qiaozhen Xu , Feng Tian , Xinyun Wang , Juanqi Lian , Xiaowei Zhang , Xiangmin Lin , Yanling Liu
Biofilms play a pivotal role in the survival and persistence of microorganisms, endowing them with heightened resistance to environmental stressors and antimicrobial agents. The EamB protein, which encodes an inner membrane transporter, acted as a negative regulator of biofilm formation, and the gene eamB deletion in the pathogen Aeromonas hydrophila LP-2 resulted in a significant increase in biofilm formation. Proteomic analysis revealed a total of 616 differentially abundant proteins between the ΔeamB and wild-type (WT) strains, with 308 downregulated and 308 upregulated. RT-qPCR was employed to verify the stability and accuracy of the proteomics data. Bioinformatic analysis indicated that EamB is involved in critical bacterial biological processes, including flagellar assembly, amino acid metabolism, and fatty acid degradation. Biofilm formation assays further revealed that supplementation with exogenous lysine significantly inhibited biofilm formation in the ΔeamB strain, conversely, exogenous cysteine and O-acetylserine obviously increased biofilm formation in the ΔeamB strain. These findings demonstrated that EamB may modulate bacterial biofilm formation in A. hydrophila through the regulation of amino acid metabolism. This finding provides novel insights into the regulatory mechanism underlying biofilm formation and highlights potential targets for the development of future antibacterial strategies.
Significance statement
This study elucidates the critical role of the eamB gene in Aeromonas hydrophila, a significant aquatic pathogen, by demonstrating its impact on biofilm formation and physiological traits. Through comparative proteomic analysis, we identified 616 differentially abundant proteins in the ΔeamB mutant, revealing its involvement in key metabolic pathways such as amino acid metabolism, flagellar assembly, and fatty acid degradation. Notably, eamB deletion enhanced biofilm formation, while exogenous amino acids like cysteine and O-acetylserine obviously increased biofilm formation in the ΔeamB strain. These findings highlight EamB as a regulator of biofilm formation, offering novel molecular insights into bacterial pathogenicity. This research advances our understanding of biofilm-associated antibiotic resistance and provides potential targets for developing strategies to mitigate infections caused by A. hydrophila in aquaculture and public health.
{"title":"Proteomics reveals the role of the EamB transporter from Aeromonas hydrophila LP-2 in biofilm formation","authors":"Qiaozhen Xu , Feng Tian , Xinyun Wang , Juanqi Lian , Xiaowei Zhang , Xiangmin Lin , Yanling Liu","doi":"10.1016/j.jprot.2025.105510","DOIUrl":"10.1016/j.jprot.2025.105510","url":null,"abstract":"<div><div>Biofilms play a pivotal role in the survival and persistence of microorganisms, endowing them with heightened resistance to environmental stressors and antimicrobial agents. The EamB protein, which encodes an inner membrane transporter, acted as a negative regulator of biofilm formation, and the gene <em>eamB</em> deletion in the pathogen <em>Aeromonas hydrophila</em> LP-2 resulted in a significant increase in biofilm formation. Proteomic analysis revealed a total of 616 differentially abundant proteins between the <em>ΔeamB</em> and wild-type (WT) strains, with 308 downregulated and 308 upregulated. RT-qPCR was employed to verify the stability and accuracy of the proteomics data. Bioinformatic analysis indicated that EamB is involved in critical bacterial biological processes, including flagellar assembly, amino acid metabolism, and fatty acid degradation. Biofilm formation assays further revealed that supplementation with exogenous lysine significantly inhibited biofilm formation in the <em>ΔeamB</em> strain, conversely, exogenous cysteine and <em>O</em>-acetylserine obviously increased biofilm formation in the <em>ΔeamB</em> strain. These findings demonstrated that EamB may modulate bacterial biofilm formation in <em>A. hydrophila</em> through the regulation of amino acid metabolism. This finding provides novel insights into the regulatory mechanism underlying biofilm formation and highlights potential targets for the development of future antibacterial strategies.</div></div><div><h3>Significance statement</h3><div>This study elucidates the critical role of the <em>eamB</em> gene in <em>Aeromonas hydrophila</em>, a significant aquatic pathogen, by demonstrating its impact on biofilm formation and physiological traits. Through comparative proteomic analysis, we identified 616 differentially abundant proteins in the <em>ΔeamB</em> mutant, revealing its involvement in key metabolic pathways such as amino acid metabolism, flagellar assembly, and fatty acid degradation. Notably, <em>eamB</em> deletion enhanced biofilm formation, while exogenous amino acids like cysteine and <em>O</em>-acetylserine obviously increased biofilm formation in the Δ<em>eamB</em> strain. These findings highlight EamB as a regulator of biofilm formation, offering novel molecular insights into bacterial pathogenicity. This research advances our understanding of biofilm-associated antibiotic resistance and provides potential targets for developing strategies to mitigate infections caused by <em>A. hydrophila</em> in aquaculture and public health.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105510"},"PeriodicalIF":2.8,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760414","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}
Pub Date : 2025-10-30Epub Date: 2025-07-25DOI: 10.1016/j.jprot.2025.105509
Karina Araujo-Ruiz , Daniel Ignacio López-Flores , María Karla Martínez-Muné , Brenda Yomara García-Sánchez , Carlos J. Ramírez-Flores , Francisco Ernesto Sandoval-Rodríguez , Emmanuel Ríos-Castro , Mónica Edith Mondragón-Castelán , Sirenia González-Pozos , Ricardo Mondragón-Flores
The Toxoplasma gondii cytoskeleton is a highly organized structure essential for parasite motility, replication, and host cell invasion. To identify its components, a highly enriched fraction of tachyzoite cytoskeletons was obtained and quantitatively analyzed by mass spectrometry. We identified 623 proteins classified into 18 functional groups, including 30 IMC proteins, 34 cytoskeleton proteins, and 14 uncharacterized proteins. A comprehensive bioinformatic analysis was conducted to assess protein abundance (fmol), antigenicity, accessibility, interactome, and homology, with the aim of identifying immunogenic targets. Among the top vaccine candidates were -GRA12, IMC1, ROP8, and -IMC4, with ROP8 emerging as the most promising based on epitope prediction. Data are available via ProteomeXchange with identifier PXD063409.
Significance
Toxoplasma gondii represents one of the most virulent and successful parasites in human and veterinary pathogenesis. Since T. gondii is a highly dynamic parasite that depends on its cytoskeleton to invade and disseminate through tissues, knowledge of its cytoskeleton composition is essential for understanding the biological mechanisms involved in parasite-host interactions and for the design of pharmaceutical and vaccination strategies. Quantitative proteomic analysis of the T. gondii cytoskeleton provided new and extensive information on its composition and, through bioinformatics approaches, allowed us to suggest several candidate molecules for future immunoprotective design.
{"title":"Quantitative proteomic analysis of the Toxoplasma gondii cytoskeleton and bioinformatic identification of highly antigenic proteins","authors":"Karina Araujo-Ruiz , Daniel Ignacio López-Flores , María Karla Martínez-Muné , Brenda Yomara García-Sánchez , Carlos J. Ramírez-Flores , Francisco Ernesto Sandoval-Rodríguez , Emmanuel Ríos-Castro , Mónica Edith Mondragón-Castelán , Sirenia González-Pozos , Ricardo Mondragón-Flores","doi":"10.1016/j.jprot.2025.105509","DOIUrl":"10.1016/j.jprot.2025.105509","url":null,"abstract":"<div><div>The <em>Toxoplasma gondii</em> cytoskeleton is a highly organized structure essential for parasite motility, replication, and host cell invasion. To identify its components, a highly enriched fraction of tachyzoite cytoskeletons was obtained and quantitatively analyzed by mass spectrometry. We identified 623 proteins classified into 18 functional groups, including 30 IMC proteins, 34 cytoskeleton proteins, and 14 uncharacterized proteins. A comprehensive bioinformatic analysis was conducted to assess protein abundance (fmol), antigenicity, accessibility, interactome, and homology, with the aim of identifying immunogenic targets. Among the top vaccine candidates were -GRA12, IMC1, ROP8, and -IMC4, with ROP8 emerging as the most promising based on epitope prediction. Data are available <em>via</em> ProteomeXchange with identifier <span><span>PXD063409</span><svg><path></path></svg></span>.</div></div><div><h3>Significance</h3><div><em>Toxoplasma gondii</em> represents one of the most virulent and successful parasites in human and veterinary pathogenesis. Since <em>T. gondii</em> is a highly dynamic parasite that depends on its cytoskeleton to invade and disseminate through tissues, knowledge of its cytoskeleton composition is essential for understanding the biological mechanisms involved in parasite-host interactions and for the design of pharmaceutical and vaccination strategies. Quantitative proteomic analysis of the <em>T. gondii</em> cytoskeleton provided new and extensive information on its composition and, through bioinformatics approaches, allowed us to suggest several candidate molecules for future immunoprotective design.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105509"},"PeriodicalIF":2.8,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144722115","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}
Pub Date : 2025-10-30Epub Date: 2025-08-18DOI: 10.1016/j.jprot.2025.105523
Maritza G. Verdugo-Molinares , Marco Ku-Centurion , Laura Cortes-Sanabria , Yadira O. Lugo-Melchor , Emilie Pinault , Luis Evangelista , Cesar O. Ramos-Garcia , Pierre Marquet , Zesergio Melo
Chronic kidney disease is a multifactorial entity characterized by decreased glomerular filtration rate (GFR). The last stage of the disease requires renal replacement therapy or kidney transplantation. As a disease with no treatment at earlier stages, and few biomarkers available, proteomics represent an excellent tool searching for new more efficient biomarkers. Urinary extracellular vesicles are an important source of information for kidney alterations, and their collection is not invasive. In this exploratory study, we worked on urine samples collected from patients at Centro Medico Nacional de Occidente in Guadalajara, Jalisco, and isolated urinary extracellular vesicles (uEVs) by ultracentrifugation. Our objective was to compare the Proteomic Profile of uEVs between Mexican patients with normal kidney function, end-stage renal disease, or kidney transplantation. High resolution mass spectrometry analysis reveals alterations in end-stage renal disease regarding the energy metabolism, cytoskeleton organization and cell motility. Proteomic alterations in transplant patients point towards the conservation of fibrotic process. Important proteins such as cystatins can be proposed as candidates for kidney transplant monitoring, while Gelsolin, a protein with an important role in assessing podocyte damage, stands out as a probable marker of chronic kidney disease. Data are available via ProteomeXchange with identifier PXD065380.
Significance
Chronic Kidney disease is a growing public health burden, increasing each year, and favored by major chronic diseases such as diabetes and hypertension. Although Mexico is one of the countries with the highest incidence of chronic kidney disease, proteomics studies involving Mexican patients had not yet been conducted. uEVs are features of particular interest to study the disease and discover biomarkers. We characterized the uEVs proteomic profile in Mexican patients, providing new insights into the pathogenesis of chronic kidney disease and kidney transplantation disorders. We identified promising biomarker candidates for transplant monitoring, and one as an early indicator of ESRD progression. uEVs may serve as a non-invasive platform for renal disease investigation, potentially offering non-invasive biomarkers for patient monitoring as well as mechanistic insights for future research into kidney pathophysiology.
{"title":"Potential kidney biomarkers in urinary extracellular vesicles from end stage renal disease and post-transplant patients","authors":"Maritza G. Verdugo-Molinares , Marco Ku-Centurion , Laura Cortes-Sanabria , Yadira O. Lugo-Melchor , Emilie Pinault , Luis Evangelista , Cesar O. Ramos-Garcia , Pierre Marquet , Zesergio Melo","doi":"10.1016/j.jprot.2025.105523","DOIUrl":"10.1016/j.jprot.2025.105523","url":null,"abstract":"<div><div>Chronic kidney disease is a multifactorial entity characterized by decreased glomerular filtration rate (GFR). The last stage of the disease requires renal replacement therapy or kidney transplantation. As a disease with no treatment at earlier stages, and few biomarkers available, proteomics represent an excellent tool searching for new more efficient biomarkers. Urinary extracellular vesicles are an important source of information for kidney alterations, and their collection is not invasive. In this exploratory study, we worked on urine samples collected from patients at Centro Medico Nacional de Occidente in Guadalajara, Jalisco, and isolated urinary extracellular vesicles (uEVs) by ultracentrifugation. Our objective was to compare the Proteomic Profile of uEVs between Mexican patients with normal kidney function, end-stage renal disease, or kidney transplantation. High resolution mass spectrometry analysis reveals alterations in end-stage renal disease regarding the energy metabolism, cytoskeleton organization and cell motility. Proteomic alterations in transplant patients point towards the conservation of fibrotic process. Important proteins such as cystatins can be proposed as candidates for kidney transplant monitoring, while Gelsolin, a protein with an important role in assessing podocyte damage, stands out as a probable marker of chronic kidney disease. Data are available via ProteomeXchange with identifier PXD065380.</div></div><div><h3>Significance</h3><div>Chronic Kidney disease is a growing public health burden, increasing each year, and favored by major chronic diseases such as diabetes and hypertension. Although Mexico is one of the countries with the highest incidence of chronic kidney disease, proteomics studies involving Mexican patients had not yet been conducted. uEVs are features of particular interest to study the disease and discover biomarkers. We characterized the uEVs proteomic profile in Mexican patients, providing new insights into the pathogenesis of chronic kidney disease and kidney transplantation disorders. We identified promising biomarker candidates for transplant monitoring, and one as an early indicator of ESRD progression. uEVs may serve as a non-invasive platform for renal disease investigation, potentially offering non-invasive biomarkers for patient monitoring as well as mechanistic insights for future research into kidney pathophysiology.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105523"},"PeriodicalIF":2.8,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886149","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}
Redox regulation has emerged as a key process in cellular signaling. The role of extracellular cell surface redox-sensitive proteins in redox regulation and intracellular communication has been supported by secretion of oxidoreductases that modulate thiol-disulfide switches. Despite these advances, redox-sensitive targets on the cell surface remain little explored. We established a comprehensive redox proteomic workflow using plasma membrane impermeable thiol labeling where we identified 1159 cell surface and extracellular proteins susceptible to oxidation. Treatment with diamide or urate hydroperoxide (HOOU) resulted in 377 and 12 differentially abundant redox-modulated proteins compared to control. Such proteins represent chaperones, adhesion molecules, vesicle-associated proteins, channels, receptors, cytoskeleton, and others, which may play a relevant role in several signaling pathway. Eleven oxidoreductases were redox-modulated by diamide, including members of the protein disulfide isomerase (PDI), peroxiredoxin (PRDX), and quiescin sulfhydryl oxidase (QSOX) families, with a particular focus on PDI TMX3 (TMX3), which provides the first evidence of its secretion in endothelial cells. In conclusion, our findings not only revealed potential redox-sensitive targets on the cell surface but also offer a useful tool for future investigations aiming to analyze redox regulation in the extracellular environment across diverse biological contexts.
Significance
Redox signaling at the cell surface is emerging as a crucial regulator of vascular function, emphasizing its role in cardiovascular disease. However, the extracellular redox proteome remains underexplored because of the complexity of the method. We developed a reproducible workflow combining differential thiol labeling and mass spectrometry to systematically map oxidized extracellular proteins in endothelial cells exposed to oxidants. Hundreds of proteins were identified as redox-sensitive targets. Key functional groups included molecular chaperones, adhesion molecules, vesicle-associated proteins, channels, receptors, and cytoskeleton. This work reveals novel insights into extracellular redox regulation, expands the repertoire of known redox-sensitive proteins, and establishes a versatile platform to investigate redox dynamics at cell surface both in vascular biology and other pathophysiological contexts.
{"title":"Redox proteomics workflow to unveil extracellular targets of oxidation in vascular endothelial cells","authors":"Danielle Fernandes Vileigas, Railmara Pereira da Silva, Bianca Dempsey, Mariana Pereira Massafera, Mikaela Peglow Pinz, Flavia Carla Meotti","doi":"10.1016/j.jprot.2025.105506","DOIUrl":"10.1016/j.jprot.2025.105506","url":null,"abstract":"<div><div>Redox regulation has emerged as a key process in cellular signaling. The role of extracellular cell surface redox-sensitive proteins in redox regulation and intracellular communication has been supported by secretion of oxidoreductases that modulate thiol-disulfide switches. Despite these advances, redox-sensitive targets on the cell surface remain little explored. We established a comprehensive redox proteomic workflow using plasma membrane impermeable thiol labeling where we identified 1159 cell surface and extracellular proteins susceptible to oxidation. Treatment with diamide or urate hydroperoxide (HOOU) resulted in 377 and 12 differentially abundant redox-modulated proteins compared to control. Such proteins represent chaperones, adhesion molecules, vesicle-associated proteins, channels, receptors, cytoskeleton, and others, which may play a relevant role in several signaling pathway. Eleven oxidoreductases were redox-modulated by diamide, including members of the protein disulfide isomerase (PDI), peroxiredoxin (PRDX), and quiescin sulfhydryl oxidase (QSOX) families, with a particular focus on PDI TMX3 (TMX3), which provides the first evidence of its secretion in endothelial cells. In conclusion, our findings not only revealed potential redox-sensitive targets on the cell surface but also offer a useful tool for future investigations aiming to analyze redox regulation in the extracellular environment across diverse biological contexts.</div></div><div><h3>Significance</h3><div>Redox signaling at the cell surface is emerging as a crucial regulator of vascular function, emphasizing its role in cardiovascular disease. However, the extracellular redox proteome remains underexplored because of the complexity of the method. We developed a reproducible workflow combining differential thiol labeling and mass spectrometry to systematically map oxidized extracellular proteins in endothelial cells exposed to oxidants. Hundreds of proteins were identified as redox-sensitive targets. Key functional groups included molecular chaperones, adhesion molecules, vesicle-associated proteins, channels, receptors, and cytoskeleton. This work reveals novel insights into extracellular redox regulation, expands the repertoire of known redox-sensitive proteins, and establishes a versatile platform to investigate redox dynamics at cell surface both in vascular biology and other pathophysiological contexts.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105506"},"PeriodicalIF":2.8,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718128","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}
Pub Date : 2025-09-15Epub Date: 2025-07-19DOI: 10.1016/j.jprot.2025.105503
Giulia Riccomi , Lisa Rosselli , Marinella Marchesi , Federica Guidi , Maria Taloni , Giovanni Ricci , Carmine Pellegrino , Shevan Wilkin
Periodontitis, a chronic inflammatory disease affecting the tooth-supporting structures, is a key indicator of oral health in palaeopathology. While poor oral hygiene, systemic diseases, and genetics are well-established contributors, the dietary impact has often been underestimated. Clinical studies, however, link diets high in fermentable carbohydrates and meat to inflammation. We investigated periodontal disease by analyzing interdental septa in 63 individuals from elite and non-elite groups in pre-Roman Italy (7th–4th centuries BCE), a period of social stratification, intensified agriculture, and increased cereal consumption. Macroscopic analysis was combined with proteomics of dental calculus from 33 individuals. Of the 1890 septa considered, 23 % displayed signs of periodontitis, with significantly higher rates in males. Prevalence increased with age in both sexes. Proteomic findings identified Porphyromonas gingivalis, a key periodontal pathogen, in 10 of 19 well-preserved dental calculus samples. While plaque accumulation is the main trigger for periodontitis, our findings highlight the dietary role in disease susceptibility. Carbohydrate-rich foods adhere to teeth and nourish bacteria, worsening periodontal conditions. At the same time, greater access to animal protein, particularly among emerging elites, may have contributed to inflammation. We propose that a proinflammatory diet may have been a major contributor to the proliferation of pathogenic oral microbiota.
{"title":"Palaeoproteomic characterization of archaeological dental calculus reveals precarious periodontal health in pre-Roman Italy (7th–4th century BCE)","authors":"Giulia Riccomi , Lisa Rosselli , Marinella Marchesi , Federica Guidi , Maria Taloni , Giovanni Ricci , Carmine Pellegrino , Shevan Wilkin","doi":"10.1016/j.jprot.2025.105503","DOIUrl":"10.1016/j.jprot.2025.105503","url":null,"abstract":"<div><div>Periodontitis, a chronic inflammatory disease affecting the tooth-supporting structures, is a key indicator of oral health in palaeopathology. While poor oral hygiene, systemic diseases, and genetics are well-established contributors, the dietary impact has often been underestimated. Clinical studies, however, link diets high in fermentable carbohydrates and meat to inflammation. We investigated periodontal disease by analyzing interdental septa in 63 individuals from elite and non-elite groups in pre-Roman Italy (7th–4th centuries BCE), a period of social stratification, intensified agriculture, and increased cereal consumption. Macroscopic analysis was combined with proteomics of dental calculus from 33 individuals. Of the 1890 septa considered, 23 % displayed signs of periodontitis, with significantly higher rates in males. Prevalence increased with age in both sexes. Proteomic findings identified <em>Porphyromonas gingivalis,</em> a key periodontal pathogen, in 10 of 19 well-preserved dental calculus samples. While plaque accumulation is the main trigger for periodontitis, our findings highlight the dietary role in disease susceptibility. Carbohydrate-rich foods adhere to teeth and nourish bacteria, worsening periodontal conditions. At the same time, greater access to animal protein, particularly among emerging elites, may have contributed to inflammation. We propose that a proinflammatory diet may have been a major contributor to the proliferation of pathogenic oral microbiota.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105503"},"PeriodicalIF":2.8,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682762","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}
Pub Date : 2025-09-15Epub Date: 2025-07-21DOI: 10.1016/j.jprot.2025.105505
Junmei Zhang , Shanling Cao , Zheng Tian , Zhengzhe Zhang , Yu Zhou , Yixuan Wu , Xuenong Luo , Shuai Wang , Xiaola Guo
Alveolar echinococcosis is a zoonotic disease that poses serious threats to public health. We observed subcutaneous cysts (SCs) of E. multilocularis had fewer protoscoleces (PSCs) compared to intraperitoneal cysts (ICs) at 60 days post-infection. However, the mechanisms underlying the development of E. multilocularis cysts in different tissues remain unclear. In this study, we compared the proteomic profiles of E. multilocularis cysts derived from mice intraperitoneally and subcutaneously infected with PSCs at 30 days post-infection, prior to the development of mature PSCs. Proteomic analysis identified 284 differentially expressed proteins (DEPs) in SCs compared to ICs, with 147 upregulated DEPs and 137 downregulated DEPs. Enzymatic proteins involved in carbohydrate and amino acid metabolism were predominantly upregulated in SCs compared to ICs, whereas proteins associated with protein folding, sorting, a degradation were downregulated. Western blotting analysis confirmed that phosphoenolpyruvate carboxykinase (PEPCK) and fructose-bisphosphate aldolase (FBA) were upregulated, whereas transitional endoplasmic reticulum ATPase (TER ATPase) was downregulated in SCs compared to ICs. The identified DEPs may play crucial roles in shaping the unique characteristics of E. multilocularis cysts. This study offers valuable insights into exploring the mechanisms underlying the occurrence and development of metacestodes.
{"title":"Comparative proteomic analysis of subcutaneous and intraperitoneal cysts of Echinococcus multilocularis","authors":"Junmei Zhang , Shanling Cao , Zheng Tian , Zhengzhe Zhang , Yu Zhou , Yixuan Wu , Xuenong Luo , Shuai Wang , Xiaola Guo","doi":"10.1016/j.jprot.2025.105505","DOIUrl":"10.1016/j.jprot.2025.105505","url":null,"abstract":"<div><div>Alveolar echinococcosis is a zoonotic disease that poses serious threats to public health. We observed subcutaneous cysts (SCs) of <em>E. multilocularis</em> had fewer protoscoleces (PSCs) compared to intraperitoneal cysts (ICs) at 60 days post-infection. However, the mechanisms underlying the development of <em>E. multilocularis</em> cysts in different tissues remain unclear. In this study, we compared the proteomic profiles of <em>E. multilocularis</em> cysts derived from mice intraperitoneally and subcutaneously infected with PSCs at 30 days post-infection, prior to the development of mature PSCs. Proteomic analysis identified 284 differentially expressed proteins (DEPs) in SCs compared to ICs, with 147 upregulated DEPs and 137 downregulated DEPs. Enzymatic proteins involved in carbohydrate and amino acid metabolism were predominantly upregulated in SCs compared to ICs, whereas proteins associated with protein folding, sorting, a degradation were downregulated. Western blotting analysis confirmed that phosphoenolpyruvate carboxykinase (PEPCK) and fructose-bisphosphate aldolase (FBA) were upregulated, whereas transitional endoplasmic reticulum ATPase (TER ATPase) was downregulated in SCs compared to ICs. The identified DEPs may play crucial roles in shaping the unique characteristics of <em>E. multilocularis</em> cysts. This study offers valuable insights into exploring the mechanisms underlying the occurrence and development of metacestodes.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105505"},"PeriodicalIF":2.8,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698902","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}
Seed aging in chickpeas during storage highlights significant economic and agricultural concerns. In this study, chickpea seeds were aged at 45 °C and 85 % humidity for 4 days, which affected both seeds' viability and vigor. Comparative biochemical analyses showed a higher production of ROS and membrane damage in the aged seeds. Comparative proteomics and metabolomics analyses of seeds were conducted using Easy-nLC LC-MS/MS and GC–MS techniques. This examination identified 2605 proteins, 17654 peptides, and 68 metabolites between the control and aged seeds. A total of 118 statistically significant proteins were identified, with 98 proteins exhibiting differential abundance in response to the aging treatment. The in-silico functional and subcellular analysis revealed that these proteins and metabolites are related to germination, desiccation tolerance, phytohormones, fatty acid, amino acid metabolism, carbon assimilation pathways, and exhibited several locations inside the cell.
The relative expression of 8 selected genes was verified using qRT-PCR to check the pattern with proteomics results. Temperature-induced lipocalin (CaTIL) is a protective protein that stabilizes the membrane and provides tolerance to aging, and was selected for molecular characterization. The subcellular localization of CaTIL was found to be in the plasma membrane of the onion cells.
{"title":"Integrated proteomics and metabolomics analysis of chickpea seeds under aging condition","authors":"Rinku Malviya , Shuvobrata Majumder , Punam Sharma , Dipak Gayen","doi":"10.1016/j.jprot.2025.105487","DOIUrl":"10.1016/j.jprot.2025.105487","url":null,"abstract":"<div><div>Seed aging in chickpeas during storage highlights significant economic and agricultural concerns. In this study, chickpea seeds were aged at 45 °C and 85 % humidity for 4 days, which affected both seeds' viability and vigor. Comparative biochemical analyses showed a higher production of ROS and membrane damage in the aged seeds. Comparative proteomics and metabolomics analyses of seeds were conducted using Easy-nLC LC-MS/MS and GC–MS techniques. This examination identified 2605 proteins, 17654 peptides, and 68 metabolites between the control and aged seeds. A total of 118 statistically significant proteins were identified, with 98 proteins exhibiting differential abundance in response to the aging treatment. The in-silico functional and subcellular analysis revealed that these proteins and metabolites are related to germination, desiccation tolerance, phytohormones, fatty acid, amino acid metabolism, carbon assimilation pathways, and exhibited several locations inside the cell.</div><div>The relative expression of 8 selected genes was verified using qRT-PCR to check the pattern with proteomics results. Temperature-induced lipocalin (CaTIL) is a protective protein that stabilizes the membrane and provides tolerance to aging, and was selected for molecular characterization. The subcellular localization of CaTIL was found to be in the plasma membrane of the onion cells.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105487"},"PeriodicalIF":2.8,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584255","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}
Cytokinins are well-known for their multifaceted roles in fine-tuning the plant growth and development during abiotic stresses in plants. An optimized concentration of cytokinins is essential to positively-influence a range of stress-dependent signaling pathways. Our study focuses on how the alteration in cytokinin levels, post CPPU (N-2-(chloro-4-pyridyl)-N-phenyl urea) application, influences the protein components of drought susceptible rice cultivar, PTT1 (Pathumthani1), under water deficit stress. The proteome was investigated by shotgun proteomics and liquid chromatography-tandem mass spectrometry (LC-MS) at tillering and grain-filling stages of rice. The results indicated that the application of CPPU had an antagonistic effect of on the biosynthesis and signaling of ABA. Drought-stressed rice plants without CPPU treatment revealed enhanced abundance of negative regulator proteins of cytokinin signaling (ORR12 and ORR21) and cytokinin dehydrogenases (CKX2 and CKX3) which are antagonistic to cytokinin responses. By contrast, CPPU treated rice plants had reduced abundance of proteins implicated in ABA biosynthesis and signaling (ZEP, NCED4, PYL9, OSK1/SnRK1A, OSK4/SnRK1B and ABIL5) but showed greater abundance proteins implicated in cytokinin signaling and responses. Further, CPPU treatment induced the abundance of some proteins implicated in maintaining the osmotic balance. The results unravel the antagonistic nature of interaction between two major phytohormones, ABA and cytokinin.
细胞分裂素因其在植物非生物胁迫下调控植物生长发育的多方面作用而闻名。细胞分裂素的优化浓度对一系列应激依赖性信号通路的积极影响至关重要。本研究的重点是在水分亏缺胁迫下，施用CPPU （N-2-（氯-4-吡啶基）- n -苯基尿素）后细胞分裂素水平的变化对干旱易感水稻品种PTT1 （Pathumthani1）蛋白质成分的影响。采用散弹枪蛋白质组学和液相色谱-串联质谱（LC-MS）技术对水稻分蘖期和灌浆期的蛋白质组学进行了研究。结果表明，CPPU的应用对ABA的生物合成和信号传导具有拮抗作用。干旱胁迫下未经CPPU处理的水稻细胞分裂素信号负调控蛋白（ORR12和ORR21）和细胞分裂素脱氢酶（CKX2和CKX3）的丰度增加，这些蛋白对细胞分裂素反应具有拮抗作用。相比之下，CPPU处理的水稻植株中与ABA生物合成和信号传导相关的蛋白（ZEP、NCED4、PYL9、OSK1/SnRK1A、OSK4/SnRK1B和ABIL5）丰度降低，但与细胞分裂素信号传导和反应相关的蛋白丰度更高。此外，CPPU处理诱导了一些与维持渗透平衡有关的蛋白质的丰度。结果揭示了两种主要植物激素ABA和细胞分裂素之间相互作用的拮抗性质。
{"title":"Rice proteome revealed antagonistic interactions between signaling components of cytokinin and ABA phytohormones during drought stress","authors":"Ranjit Singh Gujjar , Phapawee Worakan , Wannisa Chuekong , Darunmas Sankhuan , Siriyaporn Chanapanchai , Sittiruk Roytrakul , Kanyaratt Supaibulwatana","doi":"10.1016/j.jprot.2025.105489","DOIUrl":"10.1016/j.jprot.2025.105489","url":null,"abstract":"<div><div>Cytokinins are well-known for their multifaceted roles in fine-tuning the plant growth and development during abiotic stresses in plants. An optimized concentration of cytokinins is essential to positively-influence a range of stress-dependent signaling pathways. Our study focuses on how the alteration in cytokinin levels, post CPPU (N-2-(chloro-4-pyridyl)-<em>N</em>-phenyl urea) application, influences the protein components of drought susceptible rice cultivar, PTT1 (Pathumthani1), under water deficit stress. The proteome was investigated by shotgun proteomics and liquid chromatography-tandem mass spectrometry (LC-MS) at tillering and grain-filling stages of rice. The results indicated that the application of CPPU had an antagonistic effect of on the biosynthesis and signaling of ABA. Drought-stressed rice plants without CPPU treatment revealed enhanced abundance of negative regulator proteins of cytokinin signaling (ORR12 and ORR21) and cytokinin dehydrogenases (CKX2 and CKX3) which are antagonistic to cytokinin responses. By contrast, CPPU treated rice plants had reduced abundance of proteins implicated in ABA biosynthesis and signaling (ZEP, NCED4, PYL9, OSK1/SnRK1A, OSK4/SnRK1B and ABIL5) but showed greater abundance proteins implicated in cytokinin signaling and responses. Further, CPPU treatment induced the abundance of some proteins implicated in maintaining the osmotic balance. The results unravel the antagonistic nature of interaction between two major phytohormones, ABA and cytokinin.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105489"},"PeriodicalIF":2.8,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144605594","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}
Pub Date : 2025-09-15Epub Date: 2025-07-05DOI: 10.1016/j.jprot.2025.105490
Lihong Fu , Liwen Zhang , Guanyuan Huo , Jiahao Qiu , Fengjie Qiao , Lingying Huang , Xiaojun Zhu , Zhuo Yu , Yifei Tang , Mei Wu , Bowu Chen , Chao Zheng , Jia lv , Lei Shi , Xin Zhang , Seonghwan Hwang , Xuehua Sun , Man Li , Zhi Shang , Yueqiu Gao
Drug-induced liver injury (DILI) may occur after the combination therapy of multiple drugs, which makes it difficult to identify the causative drug for liver injury in epidemiological research and clinical practice. Scutellaria baicalensis (SB), a widely used herb in traditional Chinese medicine, has been reported to cause liver injury when combined with antibiotics. However, diagnosing SB-drug induced liver injury (SB-DILI) and its distinction from antibiotic-induced DILI (AILI) is one of the significant challenges in modern clinical practice. There are still no effective indicators to distinguish between SB-DILI and AILI. Therefore, to discover and validate highly relevant indicators, we implemented a mass spectrometry workflow using label-free quantitative proteomics and Parallel Reaction Monitoring (PRM) in serum microvesicles (MVs) from 29 patients with SB-DILI, 28 patients with AILI, and 33 healthy volunteers (HVs). The results showed that a combined analysis of lysozyme (LYZ), component 4-binding protein α (C4BPA), and complement component 1r (C1R) from serum MVs yielded an area under the curve (AUC) ≥ 0.95, indicating that the combination analysis nearly fully distinguished between SB-DILI and AILI in these cohorts. This study underscores the potential of circulating MV indicators in differentiating between SB-DILI and AILI, offering significant implications for clinical diagnosis and therapeutic approaches for DILI.
Significance
Drug-induced liver injury (DILI) poses significant diagnostic challenges in clinical practice, particularly when caused by herbal-antibiotic combination therapies, where identifying the causative agent is critical yet elusive. This study addresses this unmet need by establishing the first serum microvesicle (MV)-based biomarker panel (LYZ, C4BPA, and C1R) capable of distinguishing Scutellaria baicalensis-induced DILI (SB-DILI) from antibiotic-induced DILI (AILI) with high accuracy (AUC ≥ 0.95). Leveraging label-free quantitative proteomics and rigorous validation via parallel reaction monitoring (PRM), our work advances the field of translational proteomics by demonstrating that MV-derived proteins reflect disease-specific pathophysiological processes, such as complement dysregulation and immune activation.
Clinically, this panel addresses the rarity of SB-DILI and AILI (incidence <30/100,000) by providing an objective diagnostic tool to guide timely drug discontinuation, thereby reducing liver damage progression and optimizing therapeutic decisions. Methodologically, our workflow—combining MV isolation with targeted proteomics—sets a precedent for biomarker discovery in rare DILI subtypes. While preliminary, these findings lay the groundwork for multicenter validation studies to translate this innovation into clinical practice, ultimately improving precision medicine strategies for hepatotoxicity management.
{"title":"Potential use of serum microvesicle indicators to distinguish different types of drug-induced liver injury","authors":"Lihong Fu , Liwen Zhang , Guanyuan Huo , Jiahao Qiu , Fengjie Qiao , Lingying Huang , Xiaojun Zhu , Zhuo Yu , Yifei Tang , Mei Wu , Bowu Chen , Chao Zheng , Jia lv , Lei Shi , Xin Zhang , Seonghwan Hwang , Xuehua Sun , Man Li , Zhi Shang , Yueqiu Gao","doi":"10.1016/j.jprot.2025.105490","DOIUrl":"10.1016/j.jprot.2025.105490","url":null,"abstract":"<div><div>Drug-induced liver injury (DILI) may occur after the combination therapy of multiple drugs, which makes it difficult to identify the causative drug for liver injury in epidemiological research and clinical practice. <em>Scutellaria baicalensis</em> (SB), a widely used herb in traditional Chinese medicine, has been reported to cause liver injury when combined with antibiotics. However, diagnosing SB-drug induced liver injury (SB-DILI) and its distinction from antibiotic-induced DILI (AILI) is one of the significant challenges in modern clinical practice. There are still no effective indicators to distinguish between SB-DILI and AILI. Therefore, to discover and validate highly relevant indicators, we implemented a mass spectrometry workflow using label-free quantitative proteomics and Parallel Reaction Monitoring (PRM) in serum microvesicles (MVs) from 29 patients with SB-DILI, 28 patients with AILI, and 33 healthy volunteers (HVs). The results showed that a combined analysis of lysozyme (LYZ), component 4-binding protein α (C4BPA), and complement component 1r (C1R) from serum MVs yielded an area under the curve (AUC) ≥ 0.95, indicating that the combination analysis nearly fully distinguished between SB-DILI and AILI in these cohorts. This study underscores the potential of circulating MV indicators in differentiating between SB-DILI and AILI, offering significant implications for clinical diagnosis and therapeutic approaches for DILI.</div></div><div><h3>Significance</h3><div>Drug-induced liver injury (DILI) poses significant diagnostic challenges in clinical practice, particularly when caused by herbal-antibiotic combination therapies, where identifying the causative agent is critical yet elusive. This study addresses this unmet need by establishing the first serum microvesicle (MV)-based biomarker panel (LYZ, C4BPA, and C1R) capable of distinguishing <em>Scutellaria baicalensis</em>-induced DILI (SB-DILI) from antibiotic-induced DILI (AILI) with high accuracy (AUC ≥ 0.95). Leveraging label-free quantitative proteomics and rigorous validation via parallel reaction monitoring (PRM), our work advances the field of translational proteomics by demonstrating that MV-derived proteins reflect disease-specific pathophysiological processes, such as complement dysregulation and immune activation.</div><div>Clinically, this panel addresses the rarity of SB-DILI and AILI (incidence <30/100,000) by providing an objective diagnostic tool to guide timely drug discontinuation, thereby reducing liver damage progression and optimizing therapeutic decisions. Methodologically, our workflow—combining MV isolation with targeted proteomics—sets a precedent for biomarker discovery in rare DILI subtypes. While preliminary, these findings lay the groundwork for multicenter validation studies to translate this innovation into clinical practice, ultimately improving precision medicine strategies for hepatotoxicity management.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"320 ","pages":"Article 105490"},"PeriodicalIF":2.8,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584256","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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