Molecular & Cellular Proteomics最新文献_第4页

Thermal Proteome Profiling Reveals Meltome Upon NLRP3 Inflammasome Activation. 热蛋白质组分析揭示了NLRP3炎性体激活的meltome。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-16 DOI: 10.1016/j.mcpro.2025.100972

Chen Yang, Ling Wang, Yuchen Liu, Yuehui Zhang, Chaozhi Jin, Jiale Cheng, Limin Shang, Longlong Fang, Shanshan Wu, Chuan Chen, Jian Wang

{"title":"Thermal Proteome Profiling Reveals Meltome Upon NLRP3 Inflammasome Activation.","authors":"Chen Yang, Ling Wang, Yuchen Liu, Yuehui Zhang, Chaozhi Jin, Jiale Cheng, Limin Shang, Longlong Fang, Shanshan Wu, Chuan Chen, Jian Wang","doi":"10.1016/j.mcpro.2025.100972","DOIUrl":"10.1016/j.mcpro.2025.100972","url":null,"abstract":"NOD-like receptor (NLR) family pyrin domain containing 3 (NLRP3) involves in inflammasome complex assembly and innate immunity. Activation of the NLRP3 inflammasome induces conformational alterations in protein complexes, influencing their interactions with other molecules, which in turn affects protein thermal stability. To investigate the proteome-wide thermal stability alterations induced by NLRP3 inflammasome activation, we conducted a comprehensive analysis of meltome dynamics using thermal proteome profiling. Our analysis identified 337 proteins exhibiting alterations in thermal stability upon NLRP3 inflammasome activation. Subsequently, we validated three proteins by the cellular thermal shift assay. Notably, our findings reveal that the majority of these proteins tend to cluster into distinct macromolecular complexes. Furthermore, we identified FAM120A as a novel NLRP3 binding partner, with its suppression enhancing caspase-1 activation and IL-1β release in response to NLRP3 agonist. Collectively, these data provide a comprehensive framework for understanding the mechanisms of NLRP3 inflammasome activation and underscore the utility of thermal proteome profiling in exploring proteome-wide thermal stability changes during signaling transduction.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100972"},"PeriodicalIF":6.1,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of post-translationally modified MHC class I-associated peptides as potential cancer immunotherapeutic targets. 鉴定翻译后修饰的MHC i类相关肽作为潜在的癌症免疫治疗靶点。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-14 DOI: 10.1016/j.mcpro.2025.100971

Keira E Mahoney, Larry Reser, Maria Virginia Ruiz Cuevas, Jennifer G Abelin, Jeffrey Shabanowitz, Donald F Hunt, Stacy A Malaker

{"title":"Identification of post-translationally modified MHC class I-associated peptides as potential cancer immunotherapeutic targets.","authors":"Keira E Mahoney, Larry Reser, Maria Virginia Ruiz Cuevas, Jennifer G Abelin, Jeffrey Shabanowitz, Donald F Hunt, Stacy A Malaker","doi":"10.1016/j.mcpro.2025.100971","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100971","url":null,"abstract":"Over the past three decades, the Hunt laboratory has developed advancements in mass spectrometry-based technologies to enable the identification of peptides bound to major histocompatibility complex (MHC) molecules. The MHC class I processing pathway is responsible for presenting these peptides to circulating cytotoxic T cells, allowing them to recognize and eliminate malignant cells, many of which have aberrant signaling. Professor Hunt hypothesized that due to the dysregulation in phosphorylation in cancer, that abnormal phosphopeptides are likely presented by this pathway, and went on to discover the first phosphopeptide presented by the MHC processing pathway. Thereafter, the laboratory continued to sequence MHC-associated phosphopeptides and contributed several improved methods for their enrichment, detection, and sequencing. This manuscript summarizes the most recent advancements in identification of modified MHC-associated peptides and includes the cumulative list of phosphopeptides sequenced by the Hunt lab. Further, many other post-translational modifications (PTMs) were found to modify MHC peptides, including O-GlcNAcylation, methylation, and kynurenine; in total, we present here a list of 2,450 MHC-associated PTM peptides. Many of these were disease specific and found across several patients, thus highlighting their potential as cancer immunotherapy targets. We are sharing this list with the field in hopes that it might be used in investigating this potential. Overall, the Hunt lab's contributions have significantly advanced our understanding of antigen presentation and dysregulation of PTMs, supporting modern immunotherapy and vaccine development efforts.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100971"},"PeriodicalIF":6.1,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-10 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":"https://doi.org/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 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 of 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 cleaved 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 protein. 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":6.1,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteome-wide Investigation of Proline Hydroxylation in Pancreatic Ductal Adenocarcinoma Using DiLeu Isobaric Labeling Strategy. 应用DiLeu等压标记策略研究胰导管腺癌中脯氨酸羟基化的蛋白质组研究。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-09 DOI: 10.1016/j.mcpro.2025.100969

Feixuan Wu, Dylan Nicholas Tabang, Danqing Wang, Jon S Odorico, Lingjun Li

{"title":"Proteome-wide Investigation of Proline Hydroxylation in Pancreatic Ductal Adenocarcinoma Using DiLeu Isobaric Labeling Strategy.","authors":"Feixuan Wu, Dylan Nicholas Tabang, Danqing Wang, Jon S Odorico, Lingjun Li","doi":"10.1016/j.mcpro.2025.100969","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100969","url":null,"abstract":"Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by a dense fibrotic stroma intertwined with a collagen-rich extracellular matrix (ECM), which significantly contributes to tumor progression. In this study, we developed a high-throughput quantitative method that integrates enhanced hydrophilic interaction liquid chromatography (HILIC) with modified elution conditions and 12-plex N,N-dimethyl leucine (DiLeu) isobaric tags, facilitating efficient multiplexed quantitative analysis of hydroxyproline. This approach was applied to human pancreatic samples and resulted in the identification of 194 hydroxyproline peptides from 157 hydroxyproline sites and 59 proline-hydroxylated proteins, representing the first and the largest hydroxyproline proteomics dataset reported for the pancreas to date. This dataset lays a molecular foundation for understanding the structure-function relationships of hydroxyproline-containing proteins and their roles in pancreatic physiology and pathology. We then apply this strategy to investigating proline hydroxylation alterations in benign pancreatic tumors, PDAC and their normal adjacent tissues (NAT). Our findings suggest significant biological functions related to proline hydroxylation, including altered patterns of key proteins such as collagen alpha-1(I) chain and collagen alpha-1(XII) chain. These proteins emerge as potential targets for further studies on proline hydroxylation in PDAC, potentially elucidating its role in modifying protein structures and influencing cancer progression.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100969"},"PeriodicalIF":6.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Serum Disease-Specific IgG Fc Glycosylation as Potential Biomarkers for Nonproliferative and Proliferative Diabetic Retinopathy Using Mass Spectrometry. 血清疾病特异性IgG Fc糖基化作为非增殖性和增殖性糖尿病视网膜病变的潜在生物标志物

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-09 DOI: 10.1016/j.mcpro.2025.100967

Yishuang Mao, Jiyun Zhang, Yixin Zhang, Bojie Hu, Yuhua Hao, Zhonghao Yuan, Xufeng Zhao, Yusong Wang, Zhangwanyu Wei, Weihong Yu, Zhili Li

{"title":"Serum Disease-Specific IgG Fc Glycosylation as Potential Biomarkers for Nonproliferative and Proliferative Diabetic Retinopathy Using Mass Spectrometry.","authors":"Yishuang Mao, Jiyun Zhang, Yixin Zhang, Bojie Hu, Yuhua Hao, Zhonghao Yuan, Xufeng Zhao, Yusong Wang, Zhangwanyu Wei, Weihong Yu, Zhili Li","doi":"10.1016/j.mcpro.2025.100967","DOIUrl":"10.1016/j.mcpro.2025.100967","url":null,"abstract":"This study investigated the potential of serum disease-specific immunoglobulin G (DSIgG) crystallizable fragment (Fc) N-glycosylation as a diagnostic biomarker for the identification of nonproliferative and proliferative diabetic retinopathy (DR). A total of 160 patients were enrolled and categorized into three groups according to clinical diagnosis: non-diabetic retinopathy (NDR, n = 47); nonproliferative diabetic retinopathy (NPDR, n = 51); and proliferative diabetic retinopathy (PDR, n = 62). Gel electrophoresis was performed to separate IgG from morning fasting blood samples and polyaniline magnetic nanomaterials (Fe3O4@PANI) were used to enrich IgG N-glycopeptides from tryptic digestion. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI ToF MS) was used to detect the IgG N-glycopeptides. Nine DSIgG N-glycopeptide ratios were significantly different among NDR, NPDR, and PDR groups. There are six glycopeptide ratios available to classify mild, moderate, and severe NPDR. Moreover, four glycopeptide ratios could identify patients with or without diabetic macular edema (DME). The prediction model exhibited good discriminatory performance in distinguishing patients with DR or NDR (AUC = 0.8347), NPDR or PDR (AUC = 0.7002), mild/moderate or severe NPDR (AUC = 0.8059), and with or without DME (AUC = 0.7846). DSIgG Fc N-glycosylation ratios were closely associated with different stages of DR and may be used as potential biomarkers for the early diagnosis of NDR, NPDR, and PDR.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100967"},"PeriodicalIF":6.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TMT-Based Multiplexed (Chemo)Proteomics on the Orbitrap Astral Mass Spectrometer. 基于轨道rap星质谱计的多路（化学）蛋白质组学研究。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-08 DOI: 10.1016/j.mcpro.2025.100968

Yuchen He, Ka Yang, Shaoxian Li, Martin Zeller, Graeme C McAlister, Hamish I Stewart, Christian Hock, Eugen Damoc, Vlad Zabrouskov, Steven P Gygi, Joao A Paulo, Qing Yu

{"title":"TMT-Based Multiplexed (Chemo)Proteomics on the Orbitrap Astral Mass Spectrometer.","authors":"Yuchen He, Ka Yang, Shaoxian Li, Martin Zeller, Graeme C McAlister, Hamish I Stewart, Christian Hock, Eugen Damoc, Vlad Zabrouskov, Steven P Gygi, Joao A Paulo, Qing Yu","doi":"10.1016/j.mcpro.2025.100968","DOIUrl":"10.1016/j.mcpro.2025.100968","url":null,"abstract":"Ongoing advancements in instrumentation has established mass spectrometry (MS) as an essential tool in proteomics research and drug discovery. The newly released Asymmetric Track Lossless (Astral) analyzer represents a major step forward in MS instrumentation. Here, we evaluate the Orbitrap Astral mass spectrometer in the context of tandem mass tag (TMT)-based multiplexed proteomics and activity-based proteome profiling, highlighting its sensitivity boost relative to the Orbitrap Tribrid platform-50% at the peptide and 20% at the protein level. We compare TMT data-dependent acquisition and label-free data-independent acquisition on the same instrument, both of which quantify over 10,000 human proteins per sample within 1 h. TMT offers higher quantitative precision and data completeness, while data-independent acquisition is free of ratio compression and is thereby more accurate. Our results suggest that ratio compression is prevalent with the high-resolution MS2-based quantification on the Astral, while real-time search-based MS3 quantification on the Orbitrap Tribrid platform effectively restores accuracy. Additionally, we benchmark TMT-based activity-based proteome profiling by interrogating cysteine ligandability. The Astral measures over 30,000 cysteines in a single-shot experiment, a 54% increase relative to the Orbitrap Eclipse. We further leverage this remarkable sensitivity to profile the target engagement landscape of FDA-approved covalent drugs, including sotorasib and adagrasib. We herein provide a reference for the optimal use of the advanced MS platform.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":"24 5","pages":"100968"},"PeriodicalIF":6.1,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12127577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002168","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

Omics Analyses Uncover Host Networks Defining Virus-Permissive and -Hostile Cellular States. 组学分析揭示宿主网络定义病毒允许和非敌对细胞状态。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-07 DOI: 10.1016/j.mcpro.2025.100966

Honglin Chen, Philip D Charles, Quan Gu, Sabrina Liberatori, David L Robertson, Massimo Palmarini, Sam J Wilson, Shabaz Mohammed, Alfredo Castello

{"title":"Omics Analyses Uncover Host Networks Defining Virus-Permissive and -Hostile Cellular States.","authors":"Honglin Chen, Philip D Charles, Quan Gu, Sabrina Liberatori, David L Robertson, Massimo Palmarini, Sam J Wilson, Shabaz Mohammed, Alfredo Castello","doi":"10.1016/j.mcpro.2025.100966","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100966","url":null,"abstract":"The capacity of host cells to sustain or restrict virus infection is influenced by their proteome. Understanding the compendium of proteins defining cellular permissiveness is key to many questions in fundamental virology. Here, we apply a multi-omic approach to determine the proteins that are associated with highly permissive, intermediate, and hostile cellular states. We observed two groups of differentially regulated genes: (i) with robust changes in mRNA and protein levels and (ii) with protein/RNA discordances. While many of the latter are classified as interferon-stimulated genes (ISGs), most exhibit no antiviral effects in overexpression screens. This suggests that IFN-dependent protein changes can be better indicators of antiviral function than mRNA levels. Phosphoproteomics revealed an additional regulatory layer involving non-signaling proteins with altered phosphorylation. Indeed, we confirmed that several permissiveness-associated proteins with changes in abundance or phosphorylation regulate infection fitness. Altogether, our study provides a comprehensive and systematic map of the cellular alterations driving virus susceptibility.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":"24 5","pages":"100966"},"PeriodicalIF":6.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative Proteomics and Phosphoproteomics Analysis of Patient-Derived Ovarian Cancer Stem Cells. 患者来源卵巢癌干细胞的定量蛋白质组学和磷酸化蛋白质组学分析。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-07 DOI: 10.1016/j.mcpro.2025.100965

Giulia Franciosa, Valentina Nieddu, Chiara Battistini, Miriam Caffarini, Michela Lupia, Nicoletta Colombo, Nicola Fusco, Jesper V Olsen, Ugo Cavallaro

{"title":"Quantitative Proteomics and Phosphoproteomics Analysis of Patient-Derived Ovarian Cancer Stem Cells.","authors":"Giulia Franciosa, Valentina Nieddu, Chiara Battistini, Miriam Caffarini, Michela Lupia, Nicoletta Colombo, Nicola Fusco, Jesper V Olsen, Ugo Cavallaro","doi":"10.1016/j.mcpro.2025.100965","DOIUrl":"10.1016/j.mcpro.2025.100965","url":null,"abstract":"High-grade serous ovarian carcinoma (HGSOC) is the deadliest gynecologic cancer. Key to the progression and ultimate lethality of this subtype is the intra-tumoral heterogeneity, which is defined as the coexistence of different cell types and populations within a single tumor. Among those, ovarian cancer stem cells (OCSCs) are a distinct subpopulation of tumor cells endowed with stem-like properties, which can survive current standard therapies, resulting in tumor recurrence. Here, we generated ex vivo primary OCSC-enriched three-dimensional (3D) spheres from 10 distinct treatment naive patient-derived adherent (2D) cultures. We used state-of-the-art quantitative mass spectrometry to characterize the molecular events associated with OCSCs by analyzing their proteome and phosphoproteome. Our data revealed a stemness-related protein signature, shared within a heterogeneous patient cohort, which correlates with chemo-refractoriness in a clinical proteomics dataset. Moreover, we identified targetable deregulated kinases and aberrant PDGF receptor activation in OCSCs. Pharmacological inhibition of PDGFR in adherent OC cells reduced the stemness potential, measured by sphere formation assay. Overall, we provide a valuable resource to identify new OCSC markers and putative targets for OCSC-directed therapies.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100965"},"PeriodicalIF":6.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ERAP1 Activity Modulates the Immunopeptidome but Also Affects the Proteome, Metabolism, and Stress Responses in Cancer Cells. ERAP1活性调节免疫肽球，但也影响肿瘤细胞的蛋白质组、代谢和应激反应。

IF 6.1 2区生物学

Molecular & Cellular Proteomics Pub Date : 2025-04-04 DOI: 10.1016/j.mcpro.2025.100964

Martha Nikopaschou, Martina Samiotaki, Elli-Anna Stylianaki, Kamila Król, Paula Gragera, Aroosha Raja, Vassilis Aidinis, Angeliki Chroni, Doriana Fruci, George Panayotou, Efstratios Stratikos

{"title":"ERAP1 Activity Modulates the Immunopeptidome but Also Affects the Proteome, Metabolism, and Stress Responses in Cancer Cells.","authors":"Martha Nikopaschou, Martina Samiotaki, Elli-Anna Stylianaki, Kamila Król, Paula Gragera, Aroosha Raja, Vassilis Aidinis, Angeliki Chroni, Doriana Fruci, George Panayotou, Efstratios Stratikos","doi":"10.1016/j.mcpro.2025.100964","DOIUrl":"10.1016/j.mcpro.2025.100964","url":null,"abstract":"Endoplasmic reticulum (ER) aminopeptidase 1 (ERAP1) metabolizes peptides inside the ER and shapes the peptide repertoire available for binding to major histocompatibility complex class I molecules (MHC-I). However, it may have additional effects on cellular homeostasis, which have not been explored. To address these questions, we used both genetic silencing of ERAP1 expression as well as treatment with a selective allosteric ERAP1 inhibitor to probe changes in the immunopeptidome and proteome of the A375 melanoma cancer cell line. We observed significant immunopeptidome shifts with both methods of functional ERAP1 disruption, which were distinct for each method. Both methods of inhibition led to an enhancement, albeit slight, in tumor cell killing by stimulated human peripheral blood mononuclear cells and in significant proteomic alterations in pathways related to metabolism and cellular stress. Similar proteomic changes were also observed in the leukemia cell line THP-1. Biochemical analyses suggested that ERAP1 inhibition affected sensitivity to ER stress, reactive oxygen species production, and mitochondrial metabolism. Although the proteomics shifts were significant, their potential in shaping immunopeptidome shifts was limited since only 9.6% of differentially presented peptides belonged to proteins with altered expression and only 4.0% of proteins with altered expression were represented in the immunopeptidome shifts. Taken together, our findings suggest that modulation of ERAP1 activity can generate unique immunopeptidomes, mainly due to altered peptide processing in the ER, but also induce changes in the cellular proteome and metabolic state which may have further effects on tumor cells.","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100964"},"PeriodicalIF":6.1,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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 : 2025-04-03 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":"https://doi.org/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 across the cellular kinome. In this study, we present CellEKT (Cellular Endogenous Kinase Targeting), an optimized and robust chemical proteomics platform for investigating cellular target engagement 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 non-covalent drugs across over 300 kinases, expressed as half maximum inhibitory concentration (IC50), which were validated using distinct platforms like phosphoproteomics and NanoBRET. With CellEKT, target engagement 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":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0