Diverse extracellular vesicles (EVs) are present in all body fluids; however, knowledge of large EVs (lEVs) remains limited. Molecular EV profiles vary depending on EV size and the physiological circulatory system, even within the same patient. In this study, we aimed to characterize the proteomic profile of IEVs in ovarian cancer patients and identify lEV-protein biomarkers. We collected tissue, serum, and ascites from patients with high-grade serous ovarian cancer and concurrently separated small EVs (sEVs) and lEVs through sequential multistep centrifugation. Proteomic analysis of tissues and EVs revealed distinct EV profiles in serum and ascites, identifying 11 lEV-specific proteins in serum and 14 in ascites that were absent in sEV. Of these, seven serum-specific and 10 ascites-specific proteins were further analyzed using transcriptomic databases, revealing candidate diagnostic and prognostic lEV-protein biomarkers. Our findings underscore the importance of size-based EV separation, as particle size influences biosynthetic mechanisms, in identifying lEV-specific proteins with potential diagnostic and prognostic values. SUMMARY: This study underscores the importance of distinguishing extracellular vesicle (EV) subtypes and considering body fluid specificity in biomarker discovery. By isolating EVs based on size and stepwise separation and analyzing their proteomic profiles in ovarian cancer, we identified potential large EV (lEV)-specific biomarkers that reflect disease pathology. These findings provide a foundation for lEV-protein-based liquid biopsy approaches that could enhance the accuracy of early detection and patient stratification. Further validation in clinical settings may pave the way for more precise and personalized ovarian cancer diagnostics.
{"title":"Differential Proteomics of Large Extracellular Vesicles in Ovarian Cancer.","authors":"Kazuhiro Suzuki, Yusuke Yamamoto, Masami Kitagawa, Eri Asano-Inami, Kosuke Yoshida, Hiroaki Kajiyama, Akira Yokoi","doi":"10.1002/pmic.70054","DOIUrl":"https://doi.org/10.1002/pmic.70054","url":null,"abstract":"<p><p>Diverse extracellular vesicles (EVs) are present in all body fluids; however, knowledge of large EVs (lEVs) remains limited. Molecular EV profiles vary depending on EV size and the physiological circulatory system, even within the same patient. In this study, we aimed to characterize the proteomic profile of IEVs in ovarian cancer patients and identify lEV-protein biomarkers. We collected tissue, serum, and ascites from patients with high-grade serous ovarian cancer and concurrently separated small EVs (sEVs) and lEVs through sequential multistep centrifugation. Proteomic analysis of tissues and EVs revealed distinct EV profiles in serum and ascites, identifying 11 lEV-specific proteins in serum and 14 in ascites that were absent in sEV. Of these, seven serum-specific and 10 ascites-specific proteins were further analyzed using transcriptomic databases, revealing candidate diagnostic and prognostic lEV-protein biomarkers. Our findings underscore the importance of size-based EV separation, as particle size influences biosynthetic mechanisms, in identifying lEV-specific proteins with potential diagnostic and prognostic values. SUMMARY: This study underscores the importance of distinguishing extracellular vesicle (EV) subtypes and considering body fluid specificity in biomarker discovery. By isolating EVs based on size and stepwise separation and analyzing their proteomic profiles in ovarian cancer, we identified potential large EV (lEV)-specific biomarkers that reflect disease pathology. These findings provide a foundation for lEV-protein-based liquid biopsy approaches that could enhance the accuracy of early detection and patient stratification. Further validation in clinical settings may pave the way for more precise and personalized ovarian cancer diagnostics.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70054"},"PeriodicalIF":3.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adnan Shafiq, Alin Rai, Rong Xu, Maoshan Chen, Wittaya Suwakulsiri, David W Greening, Richard J Simpson
<p><p>Epithelial-mesenchymal transition (EMT) is a fundamental, dynamic cellular process involved in embryonic development, metastasis, organ fibrosis, and tissue regeneration. To define the molecular landscape of secreted midbody remnants (MBRs) to the EMT process, a proteome analysis of MBRs released from Madin-Darby canine kidney (MDCK) cells and following oncogenic H-Ras transformation (21D1 cells) was performed. MBRs, a new class of membranous extracellular vesicle (EV) molecularly distinct from exosomes/small EVs, were purified using sequential centrifugation/buoyant density gradient centrifugation. Proteomic profiling revealed MDCK cell-MBRs reflect their epithelial origin (e.g., enriched CDH1, DSP, THBS1, OLCN, EPCAM proteins) and 21D1 cell-MBRs their oncogenic and mesenchymal phenotype (e.g., HRAS, VIM, MMP14, CDH2, WNT5A, and enriched invasive and cell motility protein networks). Validation of proteome cargo revealed key protein networks associated with the EMT process in MBRs, and conserved MBR proteome across different cell types. Prominent findings were the unique expression of the immune checkpoint protein NT5E/CD73 (ecto-5'-nucleotidase) and ser/thr kinases LIMK1/K2 in MBRs from mesenchymal cells following their oncogenic transformation, and enrichment in Wnt signaling network proteins. These data identify the core proteome of MBRs regulated during the dynamic process of EMT and cell transformation over other EV types in context of the EMT process. SUMMARY: Epithelial-to-mesenchymal transition (EMT) is a critical cell biological process that occurs during embryonic development and cancer progression. Our study describes sequential purification of secreted midbody remnants (MBRs) and exosomes/sEVs from the in vitro cell line EMT model Madin-Darby canine kidney (MDCK) cells and MDCK cells transformed with oncogenic H-Ras (21D1 cells): Proteomics identified the repertoire of enriched MDCK-MBR proteins following EMT. MBRs display a proteome profile distinct from sEVs that is enriched with factors of the centralspindlin complex (KIF23.1, KIF4A, INCENP, CEP55, PLK1) and further includes components of the mitochondrial network, cytokinesis, microtubule movement, and intercellular connection. In the context of EMT, our data reveal enriched EMT pathways in MBRs including signaling receptor binding, regulation of cell differentiation, and Wnt, VEGF, and PDGF signaling. We have validated these findings in the context of Wnt signaling in other EV types. We identify several mesenchymal-enriched networks in MBRs associated with focal adhesion, cell matrix, kinase activity, and cell shape/organization, while epithelial-derived MBRs show enriched networks predominantly associated with mitochondrial (processing/transport), midbody, and plasma membrane annotation. Our study sheds light on the proteome architecture of MBRs following oncogenic H-Ras-induced EMT in cell transformation: collectively, our data informs ongoing efforts to delineate oncogen
{"title":"Oncogenic H-Ras Reprograms Madin-Darby Canine Kidney (MDCK) Cell-Derived Midbody Remnant Proteome Following Epithelial-Mesenchymal Transition.","authors":"Adnan Shafiq, Alin Rai, Rong Xu, Maoshan Chen, Wittaya Suwakulsiri, David W Greening, Richard J Simpson","doi":"10.1002/pmic.70051","DOIUrl":"https://doi.org/10.1002/pmic.70051","url":null,"abstract":"<p><p>Epithelial-mesenchymal transition (EMT) is a fundamental, dynamic cellular process involved in embryonic development, metastasis, organ fibrosis, and tissue regeneration. To define the molecular landscape of secreted midbody remnants (MBRs) to the EMT process, a proteome analysis of MBRs released from Madin-Darby canine kidney (MDCK) cells and following oncogenic H-Ras transformation (21D1 cells) was performed. MBRs, a new class of membranous extracellular vesicle (EV) molecularly distinct from exosomes/small EVs, were purified using sequential centrifugation/buoyant density gradient centrifugation. Proteomic profiling revealed MDCK cell-MBRs reflect their epithelial origin (e.g., enriched CDH1, DSP, THBS1, OLCN, EPCAM proteins) and 21D1 cell-MBRs their oncogenic and mesenchymal phenotype (e.g., HRAS, VIM, MMP14, CDH2, WNT5A, and enriched invasive and cell motility protein networks). Validation of proteome cargo revealed key protein networks associated with the EMT process in MBRs, and conserved MBR proteome across different cell types. Prominent findings were the unique expression of the immune checkpoint protein NT5E/CD73 (ecto-5'-nucleotidase) and ser/thr kinases LIMK1/K2 in MBRs from mesenchymal cells following their oncogenic transformation, and enrichment in Wnt signaling network proteins. These data identify the core proteome of MBRs regulated during the dynamic process of EMT and cell transformation over other EV types in context of the EMT process. SUMMARY: Epithelial-to-mesenchymal transition (EMT) is a critical cell biological process that occurs during embryonic development and cancer progression. Our study describes sequential purification of secreted midbody remnants (MBRs) and exosomes/sEVs from the in vitro cell line EMT model Madin-Darby canine kidney (MDCK) cells and MDCK cells transformed with oncogenic H-Ras (21D1 cells): Proteomics identified the repertoire of enriched MDCK-MBR proteins following EMT. MBRs display a proteome profile distinct from sEVs that is enriched with factors of the centralspindlin complex (KIF23.1, KIF4A, INCENP, CEP55, PLK1) and further includes components of the mitochondrial network, cytokinesis, microtubule movement, and intercellular connection. In the context of EMT, our data reveal enriched EMT pathways in MBRs including signaling receptor binding, regulation of cell differentiation, and Wnt, VEGF, and PDGF signaling. We have validated these findings in the context of Wnt signaling in other EV types. We identify several mesenchymal-enriched networks in MBRs associated with focal adhesion, cell matrix, kinase activity, and cell shape/organization, while epithelial-derived MBRs show enriched networks predominantly associated with mitochondrial (processing/transport), midbody, and plasma membrane annotation. Our study sheds light on the proteome architecture of MBRs following oncogenic H-Ras-induced EMT in cell transformation: collectively, our data informs ongoing efforts to delineate oncogen","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70051"},"PeriodicalIF":3.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rayan Murtada, Chiho Kim, Xu-dong Wang, Youkai Yang, Yonghao Yu
Although oxidative stress is a well-established driver of neurodegeneration, it remains poorly understood as to how the global cysteine (Cys) proteome is remodeled under oxidative stress conditions. Proteins with aberrantly modified cysteines in response to oxidative stress can induce and exacerbate neurodegeneration, contributing to disorders like Alzheimer's, Parkinson's, frontotemporal dementia, and amyotrophic lateral sclerosis. In this study, we induced oxidative stress in SH-SY5Y neuronal cells by subjecting them to the neurotoxin 6-hydroxydopamine (6-OHDA). To identify proteins with altered cysteine oxidation or PTM status, we used a desthiobiotin iodoacetamide (DBIA) probe, which selectively labels cysteines with unmodified and preserved thiols. Using these unbiased chemoproteomic strategies, we identified proteins with reduced Cys reactivity to DBIA in response to 6-OHDA-induced oxidative stress. Many of these proteins are critically involved in biological processes linked to cell stress responses (e.g., mitochondrial oxidative stress and apoptosis). Furthermore, we found that two key Cys on UCHL1 (a deubiquitinase critically involved in neurodegeneration) exhibited enhanced reactivity under oxidative stress conditions. Our study defines the remodeling of the Cys proteome under 6-OHDA-induced oxidative stress conditions. Furthermore, these findings suggest potential cysteine-mediated regulatory mechanisms in response to oxidative stress, providing a valuable resource for further exploration of cysteine modifications in the context of neurodegenerative signaling.
{"title":"Chemoproteomic Profiling of Reactive Cysteines in Response to Oxidative Stress Induced by 6-Hydroxydopamine","authors":"Rayan Murtada, Chiho Kim, Xu-dong Wang, Youkai Yang, Yonghao Yu","doi":"10.1002/pmic.70050","DOIUrl":"10.1002/pmic.70050","url":null,"abstract":"<p>Although oxidative stress is a well-established driver of neurodegeneration, it remains poorly understood as to how the global cysteine (Cys) proteome is remodeled under oxidative stress conditions. Proteins with aberrantly modified cysteines in response to oxidative stress can induce and exacerbate neurodegeneration, contributing to disorders like Alzheimer's, Parkinson's, frontotemporal dementia, and amyotrophic lateral sclerosis. In this study, we induced oxidative stress in SH-SY5Y neuronal cells by subjecting them to the neurotoxin 6-hydroxydopamine (6-OHDA). To identify proteins with altered cysteine oxidation or PTM status, we used a desthiobiotin iodoacetamide (DBIA) probe, which selectively labels cysteines with unmodified and preserved thiols. Using these unbiased chemoproteomic strategies, we identified proteins with reduced Cys reactivity to DBIA in response to 6-OHDA-induced oxidative stress. Many of these proteins are critically involved in biological processes linked to cell stress responses (e.g., mitochondrial oxidative stress and apoptosis). Furthermore, we found that two key Cys on UCHL1 (a deubiquitinase critically involved in neurodegeneration) exhibited enhanced reactivity under oxidative stress conditions. Our study defines the remodeling of the Cys proteome under 6-OHDA-induced oxidative stress conditions. Furthermore, these findings suggest potential cysteine-mediated regulatory mechanisms in response to oxidative stress, providing a valuable resource for further exploration of cysteine modifications in the context of neurodegenerative signaling.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 20","pages":"47-55"},"PeriodicalIF":3.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12522117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The following article for this Special Issue was published in an earlier Issue.
G. H. Bø, R. S. Härmä, C. Klingenberg, V. Kuchařová Pettersen, (2025). Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment. Proteomics. 25, e202400150, https://doi.org/10.1002/pmic.202400150. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400150
本特刊的以下文章发表在以前的一期上。G. H. boø， R. S. Härmä， C. Klingenberg， V. Kuchařová Pettersen,（2025）。肠道微生物组调节干预对婴儿粪便代谢组的影响：系统评价和质量评估。蛋白质组学，25,e202400150, https://doi.org/10.1002/pmic.202400150。https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400150
{"title":"Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment","authors":"Gaute Hovde Bø, Rolf Simon Härmä, Claus Klingenberg, Veronika Kuchařová Pettersen","doi":"10.1002/pmic.70047","DOIUrl":"10.1002/pmic.70047","url":null,"abstract":"<div>\u0000 \u0000 <p><b>The following article for this Special Issue was published in an earlier Issue</b>.</p>\u0000 <p>G. H. Bø, R. S. Härmä, C. Klingenberg, V. Kuchařová Pettersen, (2025). Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment. <i>Proteomics</i>. 25, e202400150, https://doi.org/10.1002/pmic.202400150. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400150</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 17-18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Berdien van Olst, Simon A. Eerden, Nella A. Eštok, Samarpita Roy, Ben Abbas, Yuemei Lin, Mark C. M. van Loosdrecht, Martin Pabst
The following article for this Special Issue was published in an earlier Issue.
B. van Olst, S. A. Eerden, N. A. Eštok et al.“ Metaproteomic Profiling of the Secretome of a Granule-forming Ca. Accumulibacter Enrichment”. Proteomic. 25 e202400189, https://doi.org/10.1002/pmic.202400189. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400189
本特刊的以下文章发表在以前的一期上。B. van Olst， S. a. Eerden， N. a. Eštok等人，“一种颗粒形成的Ca. Accumulibacter富集的分泌组的元蛋白质组学分析”。蛋白质组学，25 e202400189, https://doi.org/10.1002/pmic.202400189。https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400189
{"title":"Metaproteomic Profiling of the Secretome of a Granule-forming Ca. Accumulibacter Enrichment","authors":"Berdien van Olst, Simon A. Eerden, Nella A. Eštok, Samarpita Roy, Ben Abbas, Yuemei Lin, Mark C. M. van Loosdrecht, Martin Pabst","doi":"10.1002/pmic.70046","DOIUrl":"10.1002/pmic.70046","url":null,"abstract":"<div>\u0000 \u0000 <p><b>The following article for this Special Issue was published in an earlier Issue</b>.</p>\u0000 <p>B. van Olst, S. A. Eerden, N. A. Eštok et al.“ Metaproteomic Profiling of the Secretome of a Granule-forming Ca. Accumulibacter Enrichment”. <i>Proteomic</i>. 25 e202400189, https://doi.org/10.1002/pmic.202400189. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400189</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 17-18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Charlotte E. Lee, Lauren F. Messer, Ruddy Wattiez, Sabine Matallana-Surget
The following article for this Special Issue was published in an earlier Issue.
C. E. Lee, L. F. Messer, R. Wattiez, S. Matallana-Surget, (2025). Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms. Proteomics. 25, e202400208, https://doi.org/10.1002/pmic.202400208. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400208
本特刊的以下文章发表在以前的一期上。C. E. Lee, l.f. Messer， R. Wattiez， S. Matallana-Surget,（2025）。解码微生物塑料定植：多组学洞察早期生物膜的快速发展动态。蛋白质组学。25,e202400208, https://doi.org/10.1002/pmic.202400208。https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400208
{"title":"Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms","authors":"Charlotte E. Lee, Lauren F. Messer, Ruddy Wattiez, Sabine Matallana-Surget","doi":"10.1002/pmic.70048","DOIUrl":"10.1002/pmic.70048","url":null,"abstract":"<div>\u0000 \u0000 <p><b>The following article for this Special Issue was published in an earlier Issue</b>.</p>\u0000 <p>C. E. Lee, L. F. Messer, R. Wattiez, S. Matallana-Surget, (2025). Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms. <i>Proteomics</i>. 25, e202400208, https://doi.org/10.1002/pmic.202400208. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400208</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 17-18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The following article for this Special Issue was published in an earlier Issue.
A. T. Rajczewski, J. Alfredo Blakeley-Ruiz, A. Meyer et al. “Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.” Proteomics, 25, e70049, https://doi.org/10.1002/pmic.202400187. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400187
本特刊的以下文章发表在以前的一期上。a . T. Rajczewski， J. Alfredo blakley - ruiz, a . Meyer等人，“作为宏蛋白质组学工具的数据独立采集质谱：使用模型微生物组的实验室间比较。”蛋白质组学，25,e70049, https://doi.org/10.1002/pmic.202400187。https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400187
{"title":"Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome","authors":"","doi":"10.1002/pmic.70049","DOIUrl":"10.1002/pmic.70049","url":null,"abstract":"<div>\u0000 \u0000 <p><b>The following article for this Special Issue was published in an earlier Issue</b>.</p>\u0000 <p>A. T. Rajczewski, J. Alfredo Blakeley-Ruiz, A. Meyer et al. “Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.” <i>Proteomics</i>, 25, e70049, https://doi.org/10.1002/pmic.202400187. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400187</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 17-18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ashley N. Ives, Tyler J. Sagendorf, Lorenz Nierves, Tai-Tu Lin, Ercument Dirice, Rohit N. Kulkarni, Ljiljana Paša-Tolić, Wei-Jun Qian, James M. Fulcher
<div> <section> <p>Type 1 diabetes (T1D) results from autoimmune-mediated destruction of insulin-producing β cells in the pancreatic islet. This process is modulated by pro-inflammatory cytokine signaling, which has been previously shown to alter protein expression in ex vivo islets. Herein, we applied top-down proteomics to globally evaluate proteoforms from human islets treated with proinflammatory cytokines (interferon-γ and interleukin-1β). We measured 1636 unique proteoforms across six donors and two time points (control and 24 h post-treatment) and observed consistent changes in abundance across the glicentin-related pancreatic polypeptide (GRPP) and major proglucagon fragment regions of glucagon, as well as the LF-19/catestatin and vasostatin-1/2 region of chromogranin-A. We also observe several proteoforms that increase after cytokine-treatment or are exclusively observed after cytokine-treatment, including forms of beta-2 microglobulin (B2M), high-mobility group N2 protein (HMGN2), and chemokine (C-X-C motif) ligands (CXCL). Together, our quantitative results provide a baseline proteoform profile for human islets and identify several proteoforms that may serve as interesting candidate markers for T1D progression or therapeutic intervention.</p> </section> <section> <h3> Summary</h3> <div> <ul> <li> <p>This work applies a top-down proteomics workflow for the characterization and label-free quantification of proteoforms from human islets in the context of inflammation.</p> </li> <li> <p>The workflow is optimized for challenges unique to the islet proteome including high disulfide-linkage content and frequent truncation events, resulting in many proteoforms < 5kDa.</p> </li> <li> <p>There are limited examples of top-down proteomics characterization of human islets, thus this study provides a baseline characterization of the proteoforms of major hormones including chromogranin-A (CHGA), chromogranin-B/ secretogranin-1 (CHGB/SCG1), chromogranin-C/ secretogranin-2 (CHGC/SCG2), islet amyloid polypeptide (amylin/IAPP), insulin (INS), glucagon (GCG), pancreatic polypeptide prohormone (PPY), somatostatin (SST), and neurosecretory protein VGF (VGF).</p> </li> <li> <p>The quantitative results of proteoform abundances before and after cytokine treatment, which mimics the proinflammatory environment during T1D progression, provides interesting insights on how prohormone processing is altered under a proinflammatory environment.</p>
{"title":"Characterization of Cytokine Treatment on Human Pancreatic Islets by Top-Down Proteomics","authors":"Ashley N. Ives, Tyler J. Sagendorf, Lorenz Nierves, Tai-Tu Lin, Ercument Dirice, Rohit N. Kulkarni, Ljiljana Paša-Tolić, Wei-Jun Qian, James M. Fulcher","doi":"10.1002/pmic.70044","DOIUrl":"10.1002/pmic.70044","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>Type 1 diabetes (T1D) results from autoimmune-mediated destruction of insulin-producing β cells in the pancreatic islet. This process is modulated by pro-inflammatory cytokine signaling, which has been previously shown to alter protein expression in ex vivo islets. Herein, we applied top-down proteomics to globally evaluate proteoforms from human islets treated with proinflammatory cytokines (interferon-γ and interleukin-1β). We measured 1636 unique proteoforms across six donors and two time points (control and 24 h post-treatment) and observed consistent changes in abundance across the glicentin-related pancreatic polypeptide (GRPP) and major proglucagon fragment regions of glucagon, as well as the LF-19/catestatin and vasostatin-1/2 region of chromogranin-A. We also observe several proteoforms that increase after cytokine-treatment or are exclusively observed after cytokine-treatment, including forms of beta-2 microglobulin (B2M), high-mobility group N2 protein (HMGN2), and chemokine (C-X-C motif) ligands (CXCL). Together, our quantitative results provide a baseline proteoform profile for human islets and identify several proteoforms that may serve as interesting candidate markers for T1D progression or therapeutic intervention.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Summary</h3>\u0000 \u0000 <div>\u0000 <ul>\u0000 \u0000 <li>\u0000 <p>This work applies a top-down proteomics workflow for the characterization and label-free quantification of proteoforms from human islets in the context of inflammation.</p>\u0000 </li>\u0000 \u0000 <li>\u0000 <p>The workflow is optimized for challenges unique to the islet proteome including high disulfide-linkage content and frequent truncation events, resulting in many proteoforms < 5kDa.</p>\u0000 </li>\u0000 \u0000 <li>\u0000 <p>There are limited examples of top-down proteomics characterization of human islets, thus this study provides a baseline characterization of the proteoforms of major hormones including chromogranin-A (CHGA), chromogranin-B/ secretogranin-1 (CHGB/SCG1), chromogranin-C/ secretogranin-2 (CHGC/SCG2), islet amyloid polypeptide (amylin/IAPP), insulin (INS), glucagon (GCG), pancreatic polypeptide prohormone (PPY), somatostatin (SST), and neurosecretory protein VGF (VGF).</p>\u0000 </li>\u0000 \u0000 <li>\u0000 <p>The quantitative results of proteoform abundances before and after cytokine treatment, which mimics the proinflammatory environment during T1D progression, provides interesting insights on how prohormone processing is altered under a proinflammatory environment.</p>\u0000 ","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 24","pages":"55-66"},"PeriodicalIF":3.9,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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