Molecular & Cellular Proteomics最新文献_第9页

Native Top-Down Analysis of Membrane Protein Complexes Directly From In Vitro and Native Membranes. 直接来自体外和天然膜的膜蛋白复合物的自顶向下分析。

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-05-14 DOI: 10.1016/j.mcpro.2025.100993

Wonhyeuk Jung, Aniruddha Panda, Jaywon Lee, Snehasish Ghosh, Jared B Shaw, Kallol Gupta

{"title":"Native Top-Down Analysis of Membrane Protein Complexes Directly From In Vitro and Native Membranes.","authors":"Wonhyeuk Jung, Aniruddha Panda, Jaywon Lee, Snehasish Ghosh, Jared B Shaw, Kallol Gupta","doi":"10.1016/j.mcpro.2025.100993","DOIUrl":"10.1016/j.mcpro.2025.100993","url":null,"abstract":"Macromolecular organization of proteins and lipids in cellular membranes is fundamental to cell functionality. Recent advances in native mass spectrometry (nMS) have established it as a key analytical tool for capturing these associations. This typically necessitates the extraction of target membrane proteins (MPs) from their physiological environments into detergent-like surroundings. In our recent studies using in vitro synthetic liposomes, we discovered that gas phase supercharging can selectively destabilize lipid bilayers and enable MS1 detection of embedded and associated protein-lipid complexes. Here, we further extend and apply this methodology to native cell-derived membrane vesicles. We demonstrate our ability to detect and ID protein complexes and their proteoforms directly from native membranes using supercharger-assisted prequadrupole activation followed by downstream native top-down tandem mass spectrometry, which combines both collision-based and electron capture-based fragmentation approaches. We first demonstrated this approach through native top-down identification of several integral MPs from in vitro membranes. Subsequently, we developed a protocol to produce nMS-ready native membrane vesicles. Applying to Escherichia coli total membranes, we generated nMS-ready vesicles and identified both integral and membrane-associated protein complexes of homomeric and heteromeric nature using our supercharging-enabled native top-down platform. For the heteropentameric β-barrel-assembly machinery (BAM) complex, which includes the integral MP BAM-A, we detected several lipidated proteoforms. For peripheral homodimeric dihydrolipoyl dehydrogenase, we identified bound endogenous metabolite cofactors. Furthermore, using BAM complex, a crucial antibiotic target, we show how this platform could be utilized to study drug binding to MPs directly from their native membranes.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100993"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12305242/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DHODH Blockade Induces Ferroptosis in Neuroblastoma by Modulating the Mevalonate Pathway. DHODH阻断通过调节甲羟戊酸途径诱导成神经细胞瘤铁下垂。

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-06-11 DOI: 10.1016/j.mcpro.2025.101014

Jui-Chia Shir, Pin-Yu Chen, Chuan-Hao Kuo, Chiao-Hui Hsieh, Hsin-Yi Chang, Hong-Chih Lee, Chen-Hao Huang, Chun-Hua Hsu, Wen-Ming Hsu, Hsuan-Cheng Huang, Hsueh-Fen Juan

{"title":"DHODH Blockade Induces Ferroptosis in Neuroblastoma by Modulating the Mevalonate Pathway.","authors":"Jui-Chia Shir, Pin-Yu Chen, Chuan-Hao Kuo, Chiao-Hui Hsieh, Hsin-Yi Chang, Hong-Chih Lee, Chen-Hao Huang, Chun-Hua Hsu, Wen-Ming Hsu, Hsuan-Cheng Huang, Hsueh-Fen Juan","doi":"10.1016/j.mcpro.2025.101014","DOIUrl":"10.1016/j.mcpro.2025.101014","url":null,"abstract":"Neuroblastoma is the most common heterogeneous solid tumor in children, and current treatment options remain limited, especially for high-risk patients. Previous studies have identified dihydroorotate dehydrogenase (DHODH), a key enzyme in pyrimidine synthesis, as a potential therapeutic target in cancer. However, none of the existing FDA-approved DHODH inhibitors have shown effective inhibition of neuroblastoma cell growth. To address this challenge, we employed virtual screening to discover potential DHODH-targeting drugs, identifying Regorafenib as a promising candidate. Regorafenib significantly inhibited neuroblastoma growth in both neuroblastoma cells and patient-derived organoids. To unravel the underlying molecular mechanisms, we conducted Tandem Mass Tag (TMT)-based quantitative proteomics using LC-MS/MS. Our proteomic profiling revealed substantial regulation of lipid metabolism proteins, specifically those in the mevalonate pathway, correlating with ferroptosis induction. Further analysis showed that DHODH inhibition led to a reduction in total cholesterol, cholesterol esters, disrupted lipid droplet formation, and significantly decreased the expression of Squalene Epoxidase (SQLE), a key enzyme in lipid metabolism. Notably, we also observed an increase in nuclear SQLE expression following DHODH inhibition. In summary, our study highlights DHODH blockade as a novel approach to induce ferroptosis through lipid metabolism reprogramming, underscoring DHODH as a viable therapeutic target for neuroblastoma treatment. These insights open new avenues for metabolism-based interventions in aggressive pediatric cancers.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101014"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12275935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144294107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Utilizing a Negative Enrichment Strategy to Profile Protein Methylation, Leveraging the Orthogonality of LysargiNase and Trypsin. 利用负富集策略分析蛋白质甲基化，利用LysargiNase和Trypsin的正交性。

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-04-11 DOI: 10.1016/j.mcpro.2025.100970

Mingwei Sun, Shuxian Wei, Yang Li, Zichun Qiao, Zhen Liang, Yichu Shan, Yukui Zhang, Jiang Bo, Lihua Zhang

{"title":"Utilizing a Negative Enrichment Strategy to Profile Protein Methylation, Leveraging the Orthogonality of LysargiNase and Trypsin.","authors":"Mingwei Sun, Shuxian Wei, Yang Li, Zichun Qiao, Zhen Liang, Yichu Shan, Yukui Zhang, Jiang Bo, Lihua Zhang","doi":"10.1016/j.mcpro.2025.100970","DOIUrl":"10.1016/j.mcpro.2025.100970","url":null,"abstract":"Protein methylation, a prevalent post-translational modification, plays crucial roles in chromatin remodeling and gene transcription. A deeper understanding of protein methylation in these biological processes requires comprehensive characterization of the methylation sites. However, methylation induces minimal changes in the size and electrostatic status of lysine/arginine residues, especially in the case of mono-methylation and dimethylation. This significantly increases the difficulty in distinguishing methylation sites from non-methylation sites. In this study, we developed a strategy to enrich protein methylation, termed the Negative Enrichment Strategy for Profiling Protein Methylation, to comprehensively analyze lysine/arginine methylation. Initially, proteins were digested using LysargNase to generate peptides containing methylated or non-methylated lysine/arginine at the N-terminus. Subsequently, the N-terminal free α-amines of the LysargiNase-generated peptides were selectively blocked using formaldehyde in an acidic solution. Since trypsin cleaves after non-methylated lysine/arginine residues, only non-methylated peptides were digested by trypsin, exposing neo-N-terminal free amines. Finally, the non-methylated peptides with neo-N-terminal free amines were selectively removed by reacting with hyperbranched polyglycerol-aldehyde polymers, resulting in the negative enrichment of methylated peptides. Through our approach, we identified 2419 methylation forms in 2384 sites from 1440 proteins. This method provided a powerful approach for the comprehensive profiling of protein lysine and arginine methylations simultaneously, enabling a deeper understanding of protein methylation in diverse cellular conditions and human diseases.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100970"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144017787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Employing Expression-Matched Controls Enables High-Confidence Proximity-Based Interactome Classification. 使用表达式匹配控制实现高置信度基于接近的交互组分类。

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-05-27 DOI: 10.1016/j.mcpro.2025.101001

Fulin Jiang, Xuezhen Ge, Eric J Bennett

{"title":"Employing Expression-Matched Controls Enables High-Confidence Proximity-Based Interactome Classification.","authors":"Fulin Jiang, Xuezhen Ge, Eric J Bennett","doi":"10.1016/j.mcpro.2025.101001","DOIUrl":"10.1016/j.mcpro.2025.101001","url":null,"abstract":"Proximity labeling approaches have been widely utilized to define protein interactomes. Due to the inherent promiscuity of proximity labeling using TurboID-based approaches, identification and adoption of appropriate labeling controls is a pivotal step to mitigate background interference and enhance interactome assignment accuracy. Here, we evaluate the effectiveness of both expression controls and data normalization strategies in generating high-confidence interactome maps. We demonstrate that the extent of control of TurboID protein expression is strongly correlated with overall signal intensity and the number of identified proteins from streptavidin-enrichments. Discordant expression levels between the bait and control samples result in high-frequency false-negative and false-positive identifications. Data normalization strategies help correct these expression differences but also introduce data distortion for proteins with high or low endogenous expression. Using the ubiquitin ligases RNF10 and HUWE1 as bait proteins, we demonstrate that matching TurboID expression between control and bait proteins allows for similar sampling of non-specific interactions. Using a matched expression strategy results in significantly reduced background interference and increases the accuracy of interactome assignments. These results document the need to alter proximity-labeling experimental workflows to include the generation of matched expression controls to enhance proximity labeling proteomics interactome mapping robustness and reproducibility.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101001"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12226361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Multi-Omics Framework for Decoding Disease Mechanisms: Insights From Methylmalonic Aciduria. 解码疾病机制的多组学框架：来自甲基丙二酸尿症的见解

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-05-26 DOI: 10.1016/j.mcpro.2025.100998

Jianbo Fu, Vito R T Zanotelli, Cedric Howald, Nylsa Chammartin, Ilya Kolpakov, Ioannis Xenarios, D Sean Froese, Bernd Wollscheid, Patrick G A Pedrioli, Sandra Goetze

{"title":"A Multi-Omics Framework for Decoding Disease Mechanisms: Insights From Methylmalonic Aciduria.","authors":"Jianbo Fu, Vito R T Zanotelli, Cedric Howald, Nylsa Chammartin, Ilya Kolpakov, Ioannis Xenarios, D Sean Froese, Bernd Wollscheid, Patrick G A Pedrioli, Sandra Goetze","doi":"10.1016/j.mcpro.2025.100998","DOIUrl":"10.1016/j.mcpro.2025.100998","url":null,"abstract":"The diverse perspectives offered by multi-omics data analysis can aid in identifying the most relevant molecular pathways involved in disease processes, and findings in one layer can substantiate findings in other layers of information. Integrating data from multiple omics sources is becoming increasingly important to improve disease diagnosis and treatment, especially for conditions with complex and poorly understood underlying pathomechanisms. Methylmalonic aciduria (MMA), an inherited metabolic disorder, serves as an illustrative example of such a disease with poorly understood pathogenesis for which published multi-omics data are readily available. Reusing these FAIR data, obtained from the multi-omics digitization of 230 individuals (210 patients with MMA and 20 controls), we pursued advanced data integration and analysis strategies to integrate different levels of biological information, combining genomic, transcriptomic, proteomic, and metabolomic profiling with biochemical and clinical data, with the aim of elucidating molecular perturbations in individuals affected by MMA. The analysis of protein-quantitative trait loci highlighted the importance of glutathione metabolism in the pathogenesis of MMA. This finding was supported by correlation network analyses that integrated proteomics and metabolomics data, alongside gene set enrichment and transcription factor analyses based on disease severity from transcriptomic data. The correlation network analysis also revealed that lysosomal function is compromised in patients with MMA, which is critical for maintaining metabolic balance. Our research introduces a comprehensive data analysis framework that effectively addresses the challenge of prioritizing disruptions in molecular pathways by accumulating evidence from multiple omics levels.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100998"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12226375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomic Profiling Uncovers Sexual Dimorphism in the Muscle Response to Wheel Running Exercise in the FLExDUX4 Murine Model of Facioscapulohumeral Muscular Dystrophy. 蛋白质组学分析揭示了FLExDUX4小鼠面部肩胛骨-肱骨肌营养不良模型中轮式跑步运动肌肉反应的性别二态性。

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-06-09 DOI: 10.1016/j.mcpro.2025.101013

Yusuke Nishimura, Adam Bittel, Abhishek Jagan, Yi-Wen Chen, Jatin Burniston

{"title":"Proteomic Profiling Uncovers Sexual Dimorphism in the Muscle Response to Wheel Running Exercise in the FLExDUX4 Murine Model of Facioscapulohumeral Muscular Dystrophy.","authors":"Yusuke Nishimura, Adam Bittel, Abhishek Jagan, Yi-Wen Chen, Jatin Burniston","doi":"10.1016/j.mcpro.2025.101013","DOIUrl":"10.1016/j.mcpro.2025.101013","url":null,"abstract":"FLExDUX4 is a murine experimental model of facioscapulohumeral muscular dystrophy (FSHD) characterized by chronic, low levels of leaky expression of the human full-length double homeobox 4 gene (DUX4-fl). FLExDUX4 mice exhibit mild pathologies and functional deficits similar to people affected by FSHD. Proteomic studies in FSHD could offer new insights into disease mechanisms underpinned by posttranscriptional processes. We used mass spectrometry-based proteomics to quantify the abundance of 1322 proteins in triceps brachii muscle, encompassing both male and female mice in control and free voluntary wheel running in wildtype (n = 3) and FLExDUX4 (n = 3) genotypes. We report the triceps brachii proteome of FLExDUX4 mice recapitulates key skeletal muscle clinical characteristics of human FSHD, including alterations to mitochondria, RNA metabolism, oxidative stress, and apoptosis. RNA-binding proteins exhibit a sex-specific difference in FLExDUX4 mice. Sexual dimorphism of mitochondrial protein adaptation to exercise was uncovered specifically in FLExDUX4 mice, where females increased, but males decreased mitochondrial proteins after 6-weeks of voluntary wheel running. Our results highlight the importance of identifying sex-specific diagnostic biomarkers to enable more reliable monitoring of FSHD therapeutic targets. Our data provide a resource for the FSHD research community to explore the burgeoning aspect of sexual dimorphism in FSHD.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101013"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12270670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Soluble VCAM-1 May Serve as a Pharmacodynamic CSF Marker to Monitor BACE2 Activity in Non-Human Primates. 可溶性VCAM-1可作为非人类灵长类动物脑脊液药效学标志物监测BACE2活性。

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-06-04 DOI: 10.1016/j.mcpro.2025.101012

Sarah K Tschirner, Y Joy Yu Zuchero, Jennifer A Getz, Stephan A Müller, Karsten Nalbach, Matthew E Kennedy, Joseph W Lewcock, Stefan F Lichtenthaler

{"title":"Soluble VCAM-1 May Serve as a Pharmacodynamic CSF Marker to Monitor BACE2 Activity in Non-Human Primates.","authors":"Sarah K Tschirner, Y Joy Yu Zuchero, Jennifer A Getz, Stephan A Müller, Karsten Nalbach, Matthew E Kennedy, Joseph W Lewcock, Stefan F Lichtenthaler","doi":"10.1016/j.mcpro.2025.101012","DOIUrl":"10.1016/j.mcpro.2025.101012","url":null,"abstract":"The β-secretase β-site APP cleaving enzyme 1 (BACE1) is a major drug target for Alzheimer's disease (AD). Clinically tested BACE1 inhibitors induced unexpected cognitive side effects that may stem from their cross-inhibition of the homologous protease BACE2. Yet, little is known about BACE2 functions and substrates in vivo, and no biomarker is available to monitor the extent of BACE2 inhibition in vivo, particularly in cerebrospinal fluid (CSF). To identify a potential CSF biomarker for monitoring BACE2 activity, we analyzed the CSF proteome changes in non-human primates after treatment with a BACE1-selective inhibitor (a brain-targeted monoclonal antibody) in comparison to verubecestat, a clinically tested small-molecule drug inhibiting both BACE1 and BACE2. Acute treatment with either the antibody or verubecestat similarly reduced CSF abundance of the cleavage products of several known BACE1 substrates, including SEZ6, gp130, and CACHD1, demonstrating similar target engagement in vivo. One CSF protein, vascular cell adhesion protein 1 (VCAM-1), was only reduced upon inhibition with verubecestat, but not upon BACE1-selective inhibition with the antibody. We conclude that VCAM-1 is a promising biomarker candidate for monitoring BACE2 inhibition in CSF, which is instrumental for the development of BACE1-selective inhibitors for the prevention of AD.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101012"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12280488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of Small Open Reading Frame-Encoded Peptides in Glioma by an Optimized Proteomics Strategy. 利用优化的蛋白质组学策略鉴定胶质瘤中开放阅读框编码的小肽。

IF 5.5 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-07-01 Epub Date: 2025-06-11 DOI: 10.1016/j.mcpro.2025.101016

Tingting Zhang, Jian Cheng, Jiao Li, Zixia Ye, Na Li, Jifeng Wang, Xiaojuan Yang, Yong Peng

{"title":"Identification of Small Open Reading Frame-Encoded Peptides in Glioma by an Optimized Proteomics Strategy.","authors":"Tingting Zhang, Jian Cheng, Jiao Li, Zixia Ye, Na Li, Jifeng Wang, Xiaojuan Yang, Yong Peng","doi":"10.1016/j.mcpro.2025.101016","DOIUrl":"10.1016/j.mcpro.2025.101016","url":null,"abstract":"Small open reading frame-encoded peptides (SEPs), translated from previously unannotated genomic regions, have emerged as important regulators in diverse physiological and pathological processes. While ribosome profiling and bioinformatics analysis can predict putative SEPs, mass spectrometry (MS) is the only method for their definitive identification. However, MS-based SEP detection faces significant challenges due to SEP's short length and low abundance. To address these limitations, we developed an ammonium formate-mediated C8 solid-phase enrichment (AmF-C8-SPE) strategy that significantly outperforms classic C8-SPE, yielding superior SEP identification with enhanced unique peptide ratios and sequence coverage. By coupling AmF-C8-SPE with fractionation and LC-MS/MS analysis of glioma samples from 18 patients, we identified 549 novel SEPs, 113 of which exhibited differential expression between tumors and adjacent normal tissues. Importantly, randomly selected SEPs were validated by MS spectral matching with synthetic peptides and by confirming recombinant fusion protein expression in cells. Furthermore, Mfuzz clustering and ROC curve analyses revealed SEPs associated with glioma progression. DeepLoc-based prediction followed by confocal microscopy imaging confirmed nuclear localization of two candidate SEPs (IP_613981 and SPROHSA206836). Therefore, this study establishes an optimized SEP identification approach and the first comprehensive SEP profiling in glioma, providing a valuable resource to discover novel glioma biomarker and therapeutic target.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101016"},"PeriodicalIF":5.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12275937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144294108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CellEKT: A Robust Chemical Proteomics Workflow to Profile Cellular Target Engagement of Kinase Inhibitors. celllekt：一个强大的化学蛋白质组学工作流程，以分析激酶抑制剂的细胞靶标参与。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-06-01 Epub Date: 2025-04-03 DOI: 10.1016/j.mcpro.2025.100961

Joel Rüegger, Berend Gagestein, Antonius P A Janssen, Alexandra Valeanu, Alger Lazo Mori, Marielle van der Peet, Michael S Boutkan, Bogdan I Florea, Alex A Henneman, Remo Hochstrasser, Haiyan Wang, Paul Westwood, Andreas Topp, Patricia M Gomez Barila, Jan Paul Medema, Connie R Jimenez, Bigna Woersdoerfer, Stephan Kirchner, Jitao David Zhang, Uwe Grether, Arne C Rufer, Mario van der Stelt

{"title":"CellEKT: A Robust Chemical Proteomics Workflow to Profile Cellular Target Engagement of Kinase Inhibitors.","authors":"Joel Rüegger, Berend Gagestein, Antonius P A Janssen, Alexandra Valeanu, Alger Lazo Mori, Marielle van der Peet, Michael S Boutkan, Bogdan I Florea, Alex A Henneman, Remo Hochstrasser, Haiyan Wang, Paul Westwood, Andreas Topp, Patricia M Gomez Barila, Jan Paul Medema, Connie R Jimenez, Bigna Woersdoerfer, Stephan Kirchner, Jitao David Zhang, Uwe Grether, Arne C Rufer, Mario van der Stelt","doi":"10.1016/j.mcpro.2025.100961","DOIUrl":"10.1016/j.mcpro.2025.100961","url":null,"abstract":"The human genome encodes 518 protein kinases that are pivotal for drug discovery in various therapeutic areas, such as cancer and autoimmune disorders. The majority of kinase inhibitors target the conserved ATP-binding pocket, making it difficult to develop selective inhibitors. To characterize and prioritize kinase-inhibiting drug candidates, efficient methods are desired to determine target engagement (TE) across the cellular kinome. In this study, we present CellEKT (Cellular Endogenous Kinase Targeting), an optimized and robust chemical proteomics platform for investigating cellular TE of endogenously expressed kinases using the sulfonyl fluoride-based probe XO44 and two new probes ALX005 and ALX011. The optimized workflow enabled the determination of the kinome interaction landscape of covalent and noncovalent drugs across over 300 kinases, expressed as IC50, which were validated using distinct platforms like phosphoproteomics and NanoBRET. With CellEKT, TE profiles were linked to their substrate space. CellEKT has the ability to decrypt drug actions and to guide the discovery and development of drugs.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100961"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades. 无水缓步动物中罕见的n -聚糖结构。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-06-01 Epub Date: 2025-04-28 DOI: 10.1016/j.mcpro.2025.100979

Hirokazu Yagi, Taiki Saito, Shih-Yun Guu, Nao Yamakawa, Shigeru Shimamura, Sachiko Kondo, Maho Yagi-Utsumi, Ken Takai, Jun-Ichi Furukawa, Yann Guérardel, Kay-Hooi Khoo, Kazuharu Arakawa, Koichi Kato

{"title":"Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades.","authors":"Hirokazu Yagi, Taiki Saito, Shih-Yun Guu, Nao Yamakawa, Shigeru Shimamura, Sachiko Kondo, Maho Yagi-Utsumi, Ken Takai, Jun-Ichi Furukawa, Yann Guérardel, Kay-Hooi Khoo, Kazuharu Arakawa, Koichi Kato","doi":"10.1016/j.mcpro.2025.100979","DOIUrl":"10.1016/j.mcpro.2025.100979","url":null,"abstract":"We characterized the N-glycosylation profiles of anhydrobiotic tardigrades, Ramazzottius varieornatus and Hypsibius exemplaris, identifying high-mannose, paucimannose, and complex-type oligosaccharides, while hybrid-type glycans were undetectable. Notably, paucimannose-type oligosaccharides accounted for 39% of the N-glycans in R. varieornatus and 17% in H. exemplaris, with a substantial proportion of them exhibiting fucosylation of the innermost GlcNAc via an α1,6-linkage. This core fucosylation pattern, common to all animals, was observed alongside a distinctive glycosylation signature prominently observed in tardigrades: complex-type glycans lacking galactosylation but containing α1,3-fucosylated GlcNAc at non-reducing termini. This structure was more prevalent in H. exemplaris, with 22 out of 87 identified glycoproteins expressing the Fucα1,3-GlcNAc motif, including eight induced during anhydrobiosis. Key glycoproteins such as Cu/Zn-superoxide dismutase and papilin, implicated in oxidative stress protection and extracellular matrix remodeling, were among those modified. Comparative analyses reveal that non-reducing terminal α1,3-fucosylation in tardigrades is distinct from the mammalian Lewis X antigen and similar structures found in invertebrates, suggesting a unique substrate specificity of fucosyltransferases in these species. Genomic analysis identified homologs of FUT9 and FucTC, indicating potential candidates responsible for this glycosylation pattern. Our findings provide new insights into the molecular mechanisms of glycosylation in tardigrades and their relevance to their extreme stress tolerance.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100979"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12167791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033567","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}

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