Molecular & Cellular Proteomics最新文献

{"title":"Spinal cord phosphoproteome of SCA2 mouse model reveals alteration of ATXN2-N-term PRM-SH3-actin interactome and of autophagy.","authors":"Luis-Enrique Almaguer-Mederos, Arvind Reddy Kandi, Nesli-Ece Sen, Júlia Canet-Pons, Luca-Malena Berger, Matthew P Stokes, Kathryn Abell, Jana Key, Suzana Gispert, Georg Auburger","doi":"10.1016/j.mcpro.2025.101072","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.101072","url":null,"abstract":"<p><p>Toxic polyglutamine (polyQ) expansions in ATXN2 trigger neurodegenerative processes, causing Spinocerebellar Ataxia type 2 (SCA2), and enhancing TDP-43-dependent pathology in Amyotrophic Lateral Sclerosis (ALS) / Fronto-Temporal Dementia (FTD). Primary disease events can be compensated transiently, delaying disease manifestation. To define potential therapy targets, here we studied how cells modify phosphoprotein signals, using preferentially affected nervous tissue from end-stage Atxn2-CAG100-KnockIn mice. The spinal cord phosphoproteome revealed massive hyperphosphorylations flanking the polyQ expansion in ATXN2 and for SQSTM1, and moderate hyperphosphorylations also for ALS proteins OPTN, UBQLN2, TNIP1 and TBK1-targeted TAX1BP1. Conversely, strong hypophosphorylations of WNK1, SPARCL1 and PSMD9 were found. Significant enrichments of SH3-containing proteins, autophagy / endocytosis factors, and actin modulators could be explained by N-terminal, polyQ-adjacent, proline-rich motifs (PRM) in ATXN2, suggesting that SCA2 pathogenesis is highly similar to Huntington's disease where neurotoxicity is mediated by abnormal polyQ-PRM-SH3 interactions. Validation of protein and mRNA levels were done in mouse spinal cord, and embryonic fibroblasts or patient fibroblasts after bafilomycin or arsenite treatment, observing polyQ-dependent OPTN deficiency and SQSTM1 induction impairment. Overall, this phosphoproteome profile identified and quantified the main cellular efforts in adapting autophagy pathways to the aggregation propensity of the ATXN2-N-term.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101072"},"PeriodicalIF":5.5,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137556","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}

{"title":"Proteomic and Phosphoproteomic Characteristics of the Retina, Choroid, and Sclera in Guinea Pigs with Form-Deprivation Myopia.","authors":"Yifan Song, Zhe Xu, Hong-Tao Li, Yunxiao Xie, Lianghui Zhao, Jiaojiao Feng, Anfeng Luo, Jiajing Dai, Jing Li, Xinran Guo, Jike Song, Hongsheng Bi","doi":"10.1016/j.mcpro.2025.101069","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.101069","url":null,"abstract":"<p><p>Myopia is a growing global public health concern. Recent studies have revealed that the regulation of eye growth occurs via a complex signaling cascade, which originates in the retina and across the choroid to the sclera. Identifying key proteins and specific biological processes in the retina, choroid, and sclera is crucial for understanding the molecular mechanisms underlying myopia development. We conducted comprehensive proteomic and phosphoproteomic analyses of the retina, choroid, and sclera from form-deprivation myopia (FDM) guinea pigs using liquid chromatography-tandem mass spectrometry. Differentially expressed proteins and phosphosites were identified, followed by functional annotation and signaling pathway enrichment analyses. The expression of key proteins was assessed using Western blotting and enzyme-linked immunosorbent assay (ELISA). Distinct proteomic and phosphoproteomic profiles were observed across the three tissues, with 6,470, 6,708, and 3,236 proteins and 9,613, 9,416, and 3,685 phosphosites in the retina, choroid, and sclera, respectively. Proteomic analysis showed that neural signal transduction was enriched in the retina, with down-regulation of NTRK2, suggesting impaired neurotrophic signaling. The up-regulation of SYK and BTK, along with increased NF-κB, p65, and IL-1β levels in the choroid, indicated enhanced inflammatory responses. TNNT3, TPM2, and ACTN3 were up-regulated in the sclera, reflecting cytoskeletal remodeling associated with scleral expansion. Phosphoproteomic analysis indicated key roles of phosphoproteins in biological processes, particularly the spliceosome signaling pathway, which was broadly involved across all three tissues. Kinase network analysis revealed PRPF4B as a key kinase for SF3B1, suggesting the potential regulation roles of RNA splicing in myopia progression. The present study systematically elucidates the proteomic and phosphoproteomic characteristics of the retina, choroid, and sclera of FDM in guinea pigs, highlighting significant tissue-specific biological processes to myopia. The findings provide a theoretical foundation for understanding that different tissues exhibit distinct biological reactions to myopia, each through specific signaling pathways and regulatory mechanisms.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101069"},"PeriodicalIF":5.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113513","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}

{"title":"A simplified perchloric acid workflow with neutralization (PCA N) for democratizing deep plasma proteomics at population scale.","authors":"Vincent Albrecht, Johannes B Müller-Reif, Vincenth Brennsteiner, Matthias Mann","doi":"10.1016/j.mcpro.2025.101071","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.101071","url":null,"abstract":"<p><p>Large scale plasma proteomics studies offer tremendous potential for biomarker discovery but face significant challenges in balancing analytical depth, throughput and cost-effectiveness. We present an optimized perchloric acid-based workflow with neutralization - PCA-N - that addresses these limitations. By introducing a neutralization step following protein precipitation, PCA-N enables direct enzymatic digestion without additional purification steps, reducing sample volume requirements to only 5 μL of plasma while maintaining deep plasma proteome coverage. The streamlined protocol allows preparation of over 10,000 samples per day using 384-well formats at costs comparable to undepleted plasma analysis (NEAT). Rigorous validation according to the recently introduced CLSI C64 guideline demonstrated that despite somewhat higher technical variability compared to NEAT, PCA-N maintained excellent biological resolution and reproducibility. We confirmed the workflow's exceptional stability through analysis of over 1,700 quality control samples systematically interspersed among more than 40,000 plasma samples measured continuously over 353 days. Technical performance remained consistent across multiple instruments, sample preparation batches and nearly a year of measurements. Compared to NEAT plasma proteomics, PCA-N doubled the proteomic depth while maintaining comparable reagent costs and throughput. The minimal sample requirements, operational simplicity while using only common laboratory chemicals and exceptional scalability positions PCA-N as an attractive approach for population-level plasma proteomics, democratizing access to deep plasma proteomics analysis.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101071"},"PeriodicalIF":5.5,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113790","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}

{"title":"Multi-omics blood atlas reveals host immune response features of immunocompromised populations following SARS-CoV-2 infection.","authors":"Xiaodi Yang, Ye Shen, Bo Tang, Jialin Zhu, Bingjie Wang, Qingyun Wang, Wenmin Tian, Stefan Wuchty, Ziding Zhang, Zeyin Liang, Yujun Dong","doi":"10.1016/j.mcpro.2025.101068","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.101068","url":null,"abstract":"<p><p>The dysregulation of human genes and proteins following SARS-CoV-2 infection significantly impacts the clinical symptoms and prognosis of COVID-19, particularly in immunocompromised individuals such as hematological tumor patients. Despite this, a comprehensive multi-omics understanding of human host immune responses remains incomplete. Here, we conducted a multi-omics analysis of 89 peripheral blood samples (RNA sequencing) and 98 serum samples (proteome mass spectrometry) from 52 COVID-19 patients, including hematological tumor patients and non-tumor individuals. By integrating transcriptomic, proteomic, and interactome data, we compared differentially expressed genes (DEGs) and proteins (DEPs) across infection stages and clinical outcomes to gain insights into the mechanisms of SARS-CoV-2 infection. Our analysis revealed distinct and overlapping transcriptomic and proteomic responses to SARS-CoV-2 infection. DEGs were predominantly associated with innate immune responses and viral processes, while DEPs were linked to actin cytoskeleton organization and protein kinase regulation. Notably, DEGs and DEPs often exhibited opposing regulatory patterns, suggesting post-transcriptional and post-translational mechanisms. Tumor patients showed more severe proteomic perturbations, with a higher proportion of DEPs functioning as key hub proteins in cellular networks. Network-based drug repositioning identified potential therapeutic targets, including HSPA8, SRC, STAT1, APOE, and APP. Clinical analysis indicated that long COVID patients experienced more severe coagulation abnormalities, immunosuppression, and myocardial injury, while acutely deceased patients exhibited abnormally activated immune responses. Our study provides a comprehensive resource for understanding the molecular mechanisms of SARS-CoV-2 infection in hematological tumor patients. By integrating multi-omics data, we highlight the importance of proteomic changes in disease progression and identify potential therapeutic targets for COVID-19 and long COVID.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101068"},"PeriodicalIF":5.5,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145054165","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}

{"title":"Mycobacterial Tyrosine Phosphatase PtpB Affects Host Cytokine Expression by Dephosphorylating ERK1/2 and STAT3.","authors":"Tianxian Liu, Yameng Fan, Yijia Chen, Shuyu Xie, Jun-Yu Xu, Minjia Tan, Bang-Ce Ye","doi":"10.1016/j.mcpro.2025.101067","DOIUrl":"10.1016/j.mcpro.2025.101067","url":null,"abstract":"<p><p>Mycobacterium tuberculosis (Mtb) tyrosine phosphatases PtpA and PtpB have been widely reported to affect host immunity response and bacterial intercellular survival. However, a comprehensive investigation into the impact of PtpA and PtpB on host phosphorylation, specifically in their roles as tyrosine phosphatases, has not yet been reported. In this study, we first conducted the potential dephosphorylation substrates map of PtpA and PtpB within the host. Our findings demonstrated that PtpB significantly decreased the phosphorylation levels of ERK1/2 and STAT3. Subsequent analysis indicated that PtpB modulated the production of cytokine TNF and IL-1β by dephosphorylating ERK1/2 and preventing its nuclear translocation. PtpB also reduced IL-6 and IL-1β expression by dephosphorylating STAT3. The in vivo experiment demonstrated increased bacterial survival and reduced cytokine expression in the PtpB-overexpression strain. Consequently, our findings demonstrate that Mtb tyrosine phosphatases PtpA and PtpB play critical roles in the global tyrosine phosphorylation landscape within the host. Specifically, PtpB modulates cytokine expression through the dephosphorylation of ERK1/2 and STAT3.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101067"},"PeriodicalIF":5.5,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040810","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}

{"title":"Proline-Adjacent Phosphosites on Saccharomyces cerevisiae Histone Demethylase Rph1p are Salt Stress Responsive and Important for Cell Growth Under Salt Stress.","authors":"Nicola M Karakatsanis, Joshua J Hamey, Marc R Wilkins","doi":"10.1016/j.mcpro.2025.101066","DOIUrl":"10.1016/j.mcpro.2025.101066","url":null,"abstract":"<p><p>Phosphorylation of histone lysine demethylases is an important mechanism by which the cell modulates chromatin dynamics to regulate its response to stress. There is evidence that the Saccharomyces cerevisiae H3K36me2/3 demethylase, Rph1p, is an integrator of many signaling events. However, the regulatory function of most Rph1p phosphosites in stress response pathways remains unknown. Here, we investigated the role of Rph1p phosphorylation in the salt stress response. We showed that Rph1p is phosphorylated at seven sites in response to acute high salt stress, most of which are proline-adjacent. Genomic phosphonull mutations identified four salt-stress responsive phosphosites-S410, T411, S412, and S689-to be important for yeast cell growth in this condition. Phosphonull mutations at S412 or S689 were not associated with changes in the proteome in the chronic salt stress response. However, the Rph1p-S689A mutant downregulated a subset of 18 snoRNA genes in chronic salt stress compared to the wildtype, an effect absent in the Rph1p-S412A mutant. The downregulation of several snoRNA may cause changes to ribosomal RNA modifications and affect ribosome function. Consistent with these targeted transcriptional changes, neither mutant was associated with gross changes in H3K36 methylation in chronic salt stress. These findings suggest that S689 phosphorylation directs Rph1p to specific regions of the chromatin in the chronic salt stress response. Overall, our findings identify S689 as a key phosphorylation site linking Rph1p to salt stress-responsive gene regulation, offering new insights into stress-responsive mechanisms in eukaryotes.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101066"},"PeriodicalIF":5.5,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145033752","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}

{"title":"State-of-the-Art and Future Directions in Structural Proteomics.","authors":"Lotta J Happonen, Markku Varjosalo","doi":"10.1016/j.mcpro.2025.101065","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.101065","url":null,"abstract":"<p><p>Structural proteomics has undergone a profound transformation, driven by the convergence of advanced experimental methodologies and computational innovations. Cutting-edge mass spectrometry (MS)-based approaches, including cross-linking MS (XL-MS), hydrogen-deuterium exchange MS (HDX-MS), and limited proteolysis MS (LiP-MS), now enable unprecedented insights into protein topology, conformational dynamics, and protein-protein interactions. These methods, complemented by affinity purification (AP), co-immunoprecipitation (co-IP), proximity labeling (PL), and spatial proteomics techniques, have expanded our ability to characterize the structural proteome at a systems-wide scale. Integration with electron cryo-microscopy (cryo-EM), cryo-electron tomography (cryo-ET), nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, and small-angle X-ray/neutron scattering (SAXS/SANS) methods has further driven the field of integrative structural biology. These methods, in conjunction with AI-driven predictive models such as AlphaFold and RoseTTAFold, enable the high-resolution modeling of protein complexes and dynamic assemblies, bridging the gap between static structures and real-time conformational changes. This review explores the current state-of-the-art in structural proteomics, with a focus on methodological advances and the integration of XL-MS, HDX-MS, and LiP-MS with methods in structural biology. We further discuss application of structural proteomics in deciphering disease mechanisms, identifying therapeutic targets, and guiding drug discovery, with these techniques poised to revolutionize precision medicine. Future directions emphasize fully integrative, multimodal approaches that unify experimental and computational paradigms, fostering a holistic understanding of the human proteome.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101065"},"PeriodicalIF":5.5,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006393","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}

{"title":"Spatial Proteomics Reveals Distinct Protein Patterns in Cortical Migration Disorders Caused by LIN28A Overexpression and WNT Activation.","authors":"Jelena Navolić, Sara Hawass, Manuela Moritz, Jan Hahn, Maximilian Middelkamp, Antonia Gocke, Matthias Dottermusch, Yannis Schumann, Lisa Ruck, Christoph Krisp, Shweta Godbole, Piotr Sumislawski, Nele Köppen, Elisabetta Gargioni, Hartmut Schlüter, Julia E Neumann","doi":"10.1016/j.mcpro.2025.101037","DOIUrl":"10.1016/j.mcpro.2025.101037","url":null,"abstract":"<p><p>Developmental signaling pathways act in stage and tissue dependent relation and misactivation can drive tumor formation. The RNA-binding protein LIN28A binds to mRNA and miRNA and thereby affects the protein turnover and maintains stemness. LIN28A is overexpressed in embryonal brain tumors which show low correlation between transcriptome and proteome signatures. Additionally, stabilizing CTNNB1 mutations activating the WNT pathway have been reported in brain tumors with LIN28A overexpression. The aim of this study was to coactivate these oncogenic proteins during embryonal brain development and investigate the histomorphology of the cerebral cortex in relation to proteome levels with spatial resolution using the nanosecond infrared laser system for nano-volume sampling. The combination of both oncogenic factors in vivo did not lead to brain tumour formation during embryonal development but resulted in disturbed lamination and impaired cell migration in the murine cerebral cortex. Spatially resolved proteome analysis of the cortices revealed unique layer signatures across ablated layers. Moreover, the extracellular matrix receptors RPSA and ITGB1 were spatially disturbed comparing the mouse models and accompanied by a porous pial border and overmigration of neural cells. Cajal-Retzius cells were misplaced in deeper cortex regions without affecting general REELIN levels. Additionally, the glycosylated levels of α-dystroglycan were reduced. Taken together, the interplay of LIN28A and CTNNB1 resulted in a cortical migration disorder showing histomorphological and molecular similarities to human cobblestone lissencephaly (type 2) disorder. This highlights novel implications of the oncogene LIN28A in extracellular matrix integrity.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101037"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12419088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Characterization of the Alzheimer's Disease Risk Factor BIN1 Interactome.","authors":"Joseph D McMillan, Shuai Wang, Jessica Wohlfahrt, Jennifer Guergues, Stanley M Stevens, Gopal Thinakaran","doi":"10.1016/j.mcpro.2025.101055","DOIUrl":"10.1016/j.mcpro.2025.101055","url":null,"abstract":"<p><p>The gene BIN1 is the second-largest genetic risk factor for late-onset Alzheimer's disease (LOAD). It is expressed in neurons and glia in the brain as cell-type-specific and ubiquitous isoforms. BIN1 is an adaptor protein that regulates membrane dynamics in many cell types. Previously, we reported that BIN1 predominantly localizes to presynaptic terminals in neurons and regulates presynaptic vesicular release. However, the function of neuronal BIN1 in relation to LOAD is not yet fully understood. A significant gap in the field is the unbiased characterization of neuronal BIN1-interacting proteins and proximal neighbors. To address this gap and help define the functions of neuronal BIN1 in the brain, we employed TurboID-based proximity labeling to identify proteins biotinylated by the neuronal BIN1 isoform 1-TurboID fusion protein (BIN1iso1-TID) in cultured mouse neuroblastoma (N2a) cells in vitro and in adult mouse brain neurons in vivo. Label-free quantification-based proteomic analysis of the BIN1iso1-TID biotinylated proteins led to the discovery of 360 proteins in N2a cells and 897 proteins in mouse brain neurons, identified as BIN1iso1-associated (proximal) or interacting proteins. A total of 92 proteins were common in both datasets, indicating that these are high-confidence BIN1-interacting or proximity proteins. SynapticGO analysis of the mouse brain dataset revealed that BIN1iso1-TurboID labeled 159 synaptic proteins, with 60 corresponding to the synaptic vesicle cycle. Based on phosphorylation site analysis of the neuronal BIN1iso1-TID interactome and related kinase prediction, we selected and validated AAK1, CDK16, SYNJ1, PP2BA, and RANG through immunostaining and proximity ligation assays as members of the BIN1 interactome in the mouse brain. This study establishes a foundation for further investigations into the function of neuronal BIN1 by identifying several previously unknown proximal and potential interacting proteins of BIN1.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101055"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12475854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Analysis of Hsp90β-Selective Inhibitors Against Triple-Negative Breast Cancer to Gain a Mechanistic Insight.","authors":"Tyelor S Reynolds, Daniel D Hu, Simon D Weaver, Emma C Ronck, Sanket J Mishra, Matthew M Champion, Brian S J Blagg","doi":"10.1016/j.mcpro.2025.101043","DOIUrl":"10.1016/j.mcpro.2025.101043","url":null,"abstract":"<p><p>Hsp90 (90 kDa heat shock protein) is a central molecular chaperone responsible for the folding and activation of >400 client proteins, causing it to be a highly sought after drug target for the treatment of cancer. Hsp90 pan-inhibitors have been evaluated in the clinic, but on- and off-target toxicities have limited their development. The emergence of Hsp90β-selective inhibitors has been proposed as a safer therapeutic alternative. However, since they in theory only target a portion of the Hsp90-regulated proteome, a deeper understanding of their mechanism of action and whether they exhibit selectivity for cancer over normal cells has remained uninvestigated. Herein, we show that Hsp90β-selective inhibitors, NDNB1 and NDNB1182, exhibit a moderate selectivity for triple-negative breast cancer (TNBC) over normalized MCF-10A cells in contrast to pan-inhibitors, which do not exhibit a selectivity. This article contains the first proteomic analysis of Hsp90β-selective inhibitors. We have employed a traditional bottom-up LC-MS/MS proteomics approach to explore the potential mechanisms of action underlying the anticancer effects of NDNB1 and NDNB1182 against TNBC. Primarily, inhibition of kinases and associated cell signaling pathways, cell cycle proteins, and DNA repair were notable processes affected by Hsp90β inhibition, to name a few. Further investigation of the impact on Hsp90β interactors allowed a fuller understanding of Hsp90β-dependent processes. We also identified RAD9A, cyclin-dependent kinase 1 (CDK1), and ribosomal protein S9 (RPS9) as potential Hsp90β client substrates. The three example proteins selected exemplify a mechanistic explanation for inhibition of DNA repair (RAD9A), cell cycle (CDK1), and translation (RPS9), shedding some light on some of the implications of Hsp90β inhibition as it pertains to TNBC. Therefore, previously unknown clients, Hsp90β interactors, or Hsp90β-regulated proteins could be determined using the results from this study.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101043"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12446539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718189","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}