Molecular & Cellular Proteomics最新文献

{"title":"Comparative Lactylomic Profiling Unveils Dynamic Reprogramming of Post-translational Lactylation Landscapes During Human Sperm Capacitation.","authors":"Guohui Zhang, Yuhong Zhao, Yu Lei, Weiwei Zhi, Wenming Xu, Jiuzhi Zeng, Li Wang, Fangyi Long, Juncen Guo, Weixin Liu","doi":"10.1016/j.mcpro.2026.101657","DOIUrl":"10.1016/j.mcpro.2026.101657","url":null,"abstract":"<p><p>Lactylation, a novel post-translational modification involving lactate conjugation to lysine residues, bridges metabolic flux and epigenetic regulation and has emerged as a conserved regulatory mechanism across eukaryotes and prokaryotes, governing cell proliferation, immune responses, and metabolic reprogramming via a \"Writer-Eraser\" system. Despite the established roles of lactylation in energy metabolism, its function in male reproduction remains unexplored. This study investigates the lactylation modification dynamics during human sperm capacitation, a process requiring metabolic reprogramming for hyperactivated motility. Through 4D FastDIA-based quantitative dynamic profiling, we first conducted the comprehensive characterization of lysine lactylation modifications during sperm capacitation, systematically mapping differential lactylation patterns at the pathway, proteomic, and site-specific levels. We identified 2030 quantifiable lactylated proteins, revealing significant capacitation-dependent modulation: 115 proteins with 133 sites demonstrated upregulated lactylation, while 287 proteins containing 471 sites showed downregulation (p < 0.05, Fold Change >1.5). Notably, 30 proteins exhibited bidirectional regulatory patterns with coexisting upregulated and downregulated sites, and a predominant proportion of modified proteins (263 of 372) displayed single-site differential lactylation. A marked reduction in lactylation levels of mitochondrial respiratory chain proteins was observed after sperm capacitation, indicating heightened ATP requirements. Moreover, proteins with differential lactylation were enriched in biological processes including fertilization, sperm capacitation, β-oxidation, and microtubule dynamics. Strikingly, the presence of known lactylation regulatory enzymes including Alanine-tRNA ligase 1 (AARS1), Sirtuin (SIRT) 2/3, and Histone deacetylase (HDAC) 1/2/6 were detected in the sperm proteome, revealing a 1.6-fold upregulation of SIRT3, implicating its role in delactylation regulation during capacitation. Collectively, these findings delineate a lactylation-coordinated mechanism governing mitochondrial oxidative phosphorylation optimization and cytoskeletal architecture remodeling. This work substantiates a trinity regulatory mechanism integrating \"metabolism-epigenetics-function\" axes through lactylation circuitry, which may have implications for understanding male infertility.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101657"},"PeriodicalIF":6.3,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912866","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":"Galectin-1 Modulates Cell Adhesions, Cavin-1 Phosphorylation, and Vascular Permeability in Kidney Endothelial Cells-Insights From Proteomics, Phosphoproteomics, and Functional Studies.","authors":"Alex Boshart, Sofia Farkona, Shravanthi Rajasekar, Chiara Pastrello, Maya Allen, Stefan Petrovic, Kieran Manion, Slaghaniya Neupane, Sergi Clotet-Freixas, Hong Sang Choi, Anne-Marie Bulboaca, Rohan John, Allen Duong, Stephen Juvet, Milica Radisic, Juan Manuel Pérez Sáez, Gabriel A Rabinovich, Sara Deir, Boyang Zhang, Igor Jurisica, Ana Konvalinka","doi":"10.1016/j.mcpro.2026.101655","DOIUrl":"10.1016/j.mcpro.2026.101655","url":null,"abstract":"<p><p>Microvascular inflammation and endothelial injury, triggered by interferon-gamma (IFNγ), are hallmarks of antibody-mediated rejection (ABMR), the leading cause of premature kidney allograft loss. Glomerular extracellular matrix (ECM) remodeling and endothelial caveolae formation are important aspects of chronic ABMR. We found galectin-1, an immunomodulatory protein that interacts with the ECM, to be increased in the glomeruli of patients with ABMR, while its gene (LGALS1) expression was decreased by IFNγ stimulation in glomerular endothelial cells. Mechanisms underlying endothelial dysfunction in ABMR, its links to ECM remodeling, and the role of immunomodulatory proteins such as galectin-1 remain incompletely understood. We studied the effects of galectin-1 modulation in glomerular microvascular endothelial cells (GMECs) in vitro. We demonstrated that galectin-1 was mainly expressed by glomerular endothelial cells in ABMR kidneys. To model aspects of endothelial injury in ABMR, we knocked down LGALS1 in GMECs, followed by stimulation with IFNγ and label-free quantitative proteomic and phosphoproteomic profiling of GMECs. Proteomic analysis identified 5446 proteins (FDR < 0.01), of which 236, 827, and 267 were differentially expressed in response to LGALS1 knockdown, IFNγ treatment, and their interaction, respectively (FDR < 0.05). Both LGALS1 knockdown and the interaction between treatments significantly altered expression of adhesion proteins (FDR < 0.01), particularly integrin subunit β5, which was validated. Phosphoproteomic profiling identified 2727 phosphopeptides (FDR < 0.01), with 28 differentially phosphorylated across LGALS1 knockdown, IFNγ treatment, and their interaction (p < 0.01). Phosphorylation of caveolae-associated protein 1 and colocalization with its partner CAV1, critical for caveolar formation, were decreased in GMECs upon LGALS1 knockdown, IFNγ stimulation, or both. In a microfluidic model of the glomerular microvasculature, the addition of recombinant galectin-1 increased endothelial permeability and secretion of proinflammatory cytokines in LGALS1-silenced GMECs. Thus, endothelial signaling pathways regulated by inflammatory cues and galectin-1 contribute to endothelial injury and may affect caveolae formation, highlighting a potential link between galectin-1 and ABMR.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101655"},"PeriodicalIF":6.3,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888125","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":"H-NOX and NosP Regulate Flagellar Protein and Virulence Factor Production in Vibrio Cholerae.","authors":"Thathmi Wathsara Herath Pathiranage, Md Shariful Islam, Cedar Stellon, Michelle D Cherne, Daniel Valencia, Diane Bimczok, Erik T Yukl","doi":"10.1016/j.mcpro.2026.101654","DOIUrl":"10.1016/j.mcpro.2026.101654","url":null,"abstract":"<p><p>The ability of Vibrio cholerae to transition between motile and sessile forms in the environment and in the host is critical to its survival and virulence. The molecular cues, sensor proteins, and signaling pathways mediating these transitions are highly complex and often overlapping. Nevertheless, a detailed understanding of them is critical for understanding the persistence and pathogenesis of this deadly pathogen. Nitric oxide functions as an important signaling molecule in many bacteria, affecting biofilm formation, motility, and virulence, often through interaction with heme protein sensors. The genome of V. cholerae encodes two such sensors called H-NOX and NosP. Here we constructed a Δhnox/nosP mutant and employed a multiomics methodology that combines tandem mass tag-based quantitative proteomics, phosphoproteomics, and targeted metabolomics to investigate the function of these sensors. A set of 258 proteins was differentially expressed in the mutant that included many proteins involved in flagellar biosynthesis and motility as well as critical virulence factors, iron acquisition systems, and metabolic enzymes. Many of the identified genes are also part of the ferric uptake regulator regulon and iron-dependent transcriptional repression of several ferric uptake regulator targets was disrupted. Phosphoproteomics analysis also revealed proteins involved in motility and virulence as differentially phosphorylated in the mutant strain. In most cases, these phosphoproteins have not been previously observed and provide a wealth of new targets for investigating mechanisms of V. cholerae signaling. Taken together, this work illustrates a role for H-NOX and NosP in promoting factors important for infection while suppressing those important for environmental survival, suggesting a function in priming the organism for infection and/or maintaining the infectious phenotype.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101654"},"PeriodicalIF":6.3,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13654575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888099","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":"Fusion Entrapment Enables Unbiased Assessment of False Discovery Rate Control in Cascaded Database Searches.","authors":"Xinpei Yi, Yan Fu","doi":"10.1016/j.mcpro.2026.101636","DOIUrl":"10.1016/j.mcpro.2026.101636","url":null,"abstract":"<p><p>Cascaded database searches boost identification sensitivity in vast proteomic search spaces but challenge false discovery rate (FDR) control. The standard target-decoy approach to FDR control relies on decoy matches providing an exchangeable and properly scaled representation of incorrect target matches. This assumption can be disrupted when protein-level filtering is used to define a reduced search space, because target and decoy entries may no longer undergo symmetric retention during database reduction. Although entrapment provides an external benchmark for assessing FDR control, conventional separate-entrapment implementations can become invalid in cascaded searches because entrapment sequences may be disproportionately discarded during protein-level filtering. Here we introduce Fusion Entrapment, a strategy that computationally fuses entrapment sequences with target proteins to preserve identical selection pressure during database reduction. Simulations show that this strategy provides accurate entrapment-based false discovery proportion (FDP) estimation in cascaded searches involving protein-level filtering. Applying Fusion Entrapment to human gut metaproteomic datasets, we further observed that conventional separate target-decoy database reduction led to substantial inflation of the entrapment-estimated FDP relative to the reported FDR threshold. In contrast, fusion target-decoy reduction maintained empirical FDR control under Fusion Entrapment assessment while retaining substantial sensitivity gains over single-step analysis.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101636"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13563576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148707065","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":"MSstatsResponse: Semiparametric Statistical Model Enhances Detection of Drug-Protein Interactions in Chemoproteomics Experiments.","authors":"Sarah Szvetecz, Devon Kohler, Joel D Federspiel, S Denise Field, Pierre Jean-Beltran, Robert J Seward, Hyunsuk Suh, Liang Xue, Olga Vitek","doi":"10.1016/j.mcpro.2026.101637","DOIUrl":"10.1016/j.mcpro.2026.101637","url":null,"abstract":"<p><p>Chemoproteomics is a popular approach for the identification of small molecule-protein interactions in biological systems. Several chemoproteomics workflows leverage functionalized chemical probes and mass spectrometry to measure protein engagement through direct protein enrichment or competition using a range of small molecule concentrations. Statistical methods for analysis of such dose-response chemoproteomics data sets are limited. For example, existing methods rely on fixed curve shapes and are sensitive to experimental variation, particularly when the number of doses or replicates is limited. Here, we present MSstatsResponse, a semiparametric statistical framework for analyzing chemoproteomic dose-response experiments that uses isotonic regression that does not require a fixed curve shape. This approach improves the accuracy and robustness of curve fitting, target identification, and half-response estimation across diverse experimental designs. We evaluate MSstatsResponse by generating a benchmark chemoproteomic data set that profiled the competition between the kinase-binding probe XO44 and the drug Dasatinib using three mass spectrometry acquisition strategies: data-independent acquisition, tandem mass tag-based data-dependent acquisition, and selected reaction monitoring. We further evaluate the method on simulated data sets that vary the number of doses, number of replicates, and levels of noise, and demonstrate that MSstatsResponse consistently improves sensitivity, specificity, and reproducibility compared to existing methods, particularly in low-replicate and low-dose settings. MSstatsResponse is implemented as an open-source R/Bioconductor package that integrates with the MSstats ecosystem for quantitative proteomics. It provides a unified workflow for preprocessing, curve fitting, target identification, and experimental design, enabling researchers to select the number of doses and replicates appropriate to their experimental goals. The software and documentation are freely available at https://bioconductor.org/packages/MSstatsResponse.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101637"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148723608","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":"Top-Down Sequencing of Intact Proteoforms Using the timsOmni Mass Spectrometer: Accurate Determination of Co-Occurring Histone Modifications.","authors":"Francis Berthias, Nurgül Bilgin, Athanasios Smyrnakis, Elisa Le Boiteux, Mariangela Kosmopoulou, Christian Albers, Detlev Suckau, Jasmin Mecinović, Dimitris Papanastasiou, Ole N Jensen","doi":"10.1016/j.mcpro.2026.101640","DOIUrl":"10.1016/j.mcpro.2026.101640","url":null,"abstract":"<p><p>Deep characterization of intact proteoforms remains an analytical challenge in functional proteomics, particularly for heterogeneous multi-site post-translational modifications at distinct amino acid residues. Histones are among the most dynamically and diversely post-translationally modified proteins in eukaryotic cells, carrying multiple, co-occurring, and reversible modifications that can give rise to isomeric proteoform species. Tandem mass spectrometry with multimodal fragmentation capabilities is a promising approach for deep characterization of intact proteoforms, such as modified histones. We applied the novel timsOmni mass spectrometer, which incorporates the Omnitrap platform enabling multimodal MSⁿ workflows using controlled in vitro acetylation of recombinant histones H3.1 and H4 by GCN5, PCAF and p300, followed by analysis of endogenous H4 proteoforms. Complementary MS² electron- and collision-based dissociation (ECD, EID, _RCID and ECciD), together with MS³ strategies, produced complete or near-complete backbone fragmentation of intact protein ions (>92% amino acid sequence coverage). For monoacetylated species generated by the more site-selective lysine acetyltransferases, the dominant proteoform matched the known catalytic preferences of the enzymes (H3.1K14ac for GCN5 and PCAF, and H4K8ac for PCAF), while minor positional isomers were also identified and their relative abundance estimated. In contrast, the broader substrate specificity of p300 produced a wide distribution of H4 proteoforms bearing up to seven acetylated lysine residues. Species carrying six and seven acetylations were characterized by multimodal MS²/MS³ experiments, enabling localization of individual acetylation sites and discrimination of positional isomers. Finally, top-down sequencing of endogenous intact H4 proteoforms from human liver extracts yielded amino acid sequence coverages of 92 to 93% for the most abundant species and confident localization of multiple, distant PTMs (acetylation and methylation). These results demonstrate that multimodal MSⁿ fragmentation of intact proteins supports residue-level assignment of combinatorial histone marks and coexisting positional isomers in controlled and endogenous proteoform mixtures.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101640"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13595144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795487","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":"Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome.","authors":"Jules Nde, Kartik Majila, Rosalyn C Zimmermann, Cassandra Kempf, Ying Zhang, Joseph Cesare, Janet L Thornton, Jerry L Workman, Laurence Florens, Shruthi Viswanath, Michael P Washburn","doi":"10.1016/j.mcpro.2026.101651","DOIUrl":"10.1016/j.mcpro.2026.101651","url":null,"abstract":"<p><p>Histone Deacetylase (HDAC) 1 and 2 are key enzymatic components in multiple large chromatin remodeling complexes including NuRD, SIN3, and CoREST. In addition, both HDAC 1 and 2 contain a large intrinsically disordered region (IDR) within their C-terminal domain (CTD). How HDAC1/2 assemble into these complexes and the structure of the CTD IDR remains poorly understood. Here, we used HDAC1/2 to isolate their protein interaction networks from cells and used crosslinking mass spectrometry coupled with the Integrative Modeling Platform to build structural models of the NuRD, SIN3A, and CoREST complexes. Next, we implemented an AlphaFold-enabled crosslinking mass spectrometry constrained modeling approach to investigate how HDAC1 could assemble into these complexes. We show that the CTD IDR of HDAC1 folds into alpha helices in these complexes. Finally, we built a complete integrative structural model of a NuRD subcomplex including the abundant HDAC1:MBD3:MTA1:GATAD2B:RBBP4 subunits, which included 6 IDRs. The approaches used herein are broadly applicable for the study of protein complexes and protein interaction networks that can provide important insights into IDRs.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101651"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13676700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148874763","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":"Urinary Proteomics Enables Noninvasive and Longitudinal Monitoring of Tumor Burden Dynamics and Early Recurrence in Hepatocellular Carcinoma.","authors":"Xiaohua Xing, En Hu, Lei Song, Zhao Zheng, Linsheng Cai, Jiahe Ouyang, Jie Li, Xinting Pan, Mingxin Liu, Yingchao Wang, Xiaolong Liu","doi":"10.1016/j.mcpro.2026.101635","DOIUrl":"10.1016/j.mcpro.2026.101635","url":null,"abstract":"<p><p>To develop a noninvasive, urine-based approach for dynamic monitoring of tumor burden and early detection of recurrence in hepatocellular carcinoma (HCC), addressing the limited sensitivity of conventional serum biomarkers such as AFP and DCP, particularly for minimal residual disease (MRD) assessment. We established a prospective, multi-cohort urinary proteomics framework encompassing four longitudinal clinical cohorts (378 patients, 972 urine samples). In the discovery cohort, 26 patients contributed 130 longitudinal urine samples from those undergoing primary and secondary resections, which were analyzed by mass spectrometry at five standardized follow-up time points to identify proteins associated with tumor burden dynamics. The validation cohort (n = 46) used parallel reaction monitoring (PRM) to confirm candidate biomarkers and construct a composite urine-based tumor burden monitoring model integrating HPGD, AFP, DCP, and GGT. The model was then applied to an early recurrence cohort (306 patients, 612 urine samples) to detect MRD and predict recurrence prior to radiological confirmation. Among 8563 quantified urinary proteins, 217 significantly correlated with tumor burden, with HPGD closely mirroring dynamic changes. The integrated model achieved a pre-recurrence AUC of 0.86, sensitivity of 73%, and specificity of 87%, outperforming AFP (0.73, 39%, 96%) and DCP (0.64, 59%, 88%). It predicted recurrence a median 4.1 months earlier than imaging and served as an independent prognostic factor for recurrence-free (RFS) and overall survival (OS, p < 0.001). This urine-based model enables dynamic assessment of tumor burden and early recurrence detection, surpassing conventional serum biomarkers and providing a clinically actionable tool for personalized surveillance and therapeutic decision-making in HCC.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101635"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13644515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148707073","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":"A Temporal Phospho-acetylome Atlas of Human Myogenesis Identifies coordinated Post-Translational Regulation.","authors":"Lauren E Smith, Christina E Hagensen, Vasileios Tsiamis, Ashley J van Waardenberg, Kamel Mamchaoui, Ole N Jensen, Veit Schwämmle, Adelina Rogowska-Wrzesinska","doi":"10.1016/j.mcpro.2026.101619","DOIUrl":"10.1016/j.mcpro.2026.101619","url":null,"abstract":"<p><p>Skeletal muscle differentiation depends on precise temporal regulation of protein modifications. To define how phosphorylation and lysine acetylation change during this process, we applied tandem mass tag (TMT)-based quantitative proteomics to human myoblasts sampled at six stages spanning proliferation, induction of differentiation, and early myotube formation. Using sequential enrichment of phosphorylated and acetylated peptides, high-pH fractionation, and high-resolution mass spectrometry, we identified more than 22,000 modified peptides and quantified their temporal behavior after correction for protein abundance. Phosphorylation exhibited extensive site-specific remodeling throughout the time course, whereas acetylation showed a pronounced relative increase during late differentiation. Integration of corrected modification levels with protein abundances and temporal clustering revealed stage-specific regulation of processes linked to cell-cycle withdrawal, metabolic transitions, cytoskeletal reorganization, and chromatin-associated functions. Predicted temporal activity profiles of kinases, acetyltransferases, and deacetylases uncovered coordinated regulatory patterns, including activity relationships involving CSNK2A1-HDAC1/2, PRKAA1-HAT1, and CDK1/2-KAT7. Dual-modified proteins such as lamin A/C and glycolytic enzymes display densely regulated clusters of phosphorylation and acetylation sites that may contribute to nuclear remodeling and metabolic adaptation during myogenesis. Together, this work provides a high-resolution temporal phospho-acetylome atlas of human muscle cell differentiation, identifies candidate phosphorylation-acetylation coordination patterns, and establishes a systems-level resource for future mechanistic studies of post-translational regulation in skeletal muscle development.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101619"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13545378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148376367","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":"Clone-By-Clone Therapy Guidance in Luminal Breast Cancer Via Spatial Proteomics and Patient-Derived Tumoroid.","authors":"Laurine Lagache, Antonella Raffo-Romero, Marie Duhamel, Yanis Zirem, Maire Vanseymortier, Isabelle Fournier, Nawale Hajjaji, Michel Salzet","doi":"10.1016/j.mcpro.2026.101639","DOIUrl":"10.1016/j.mcpro.2026.101639","url":null,"abstract":"<p><p>Breast cancer (BC) remains the leading cause of cancer-related death among women worldwide, with 2.26 million new cases and ∼685,000 deaths reported in 2020 (Globocan 2020). A major challenge in treating BC, particularly luminal subtypes, is the pronounced molecular heterogeneity both between patients and within individual tumors. This intratumoral diversity underlies many cases of therapy resistance and relapse. Here, we present a theranostic approach that integrates spatial proteomics and patient-derived tumoroids (PDTs) to guide personalized treatment in luminal BC. Formalin-fixed, paraffin-embedded tumor tissues from three patients were analyzed by MALDI mass spectrometry imaging and spatially resolved microproteomics, mapping distinct clonal subpopulations and their protein expression profiles. Proteomic pathway analysis revealed subclone-specific vulnerabilities that are not apparent from standard histopathology. We exploited these insights to design alternative combination therapies tailored to each tumor's molecular makeup. The efficacy of proteomics-guided regimens was then evaluated in vitro using PDTs established from the same patients, in direct comparison to conventional chemotherapy. Proteomic-informed treatments demonstrated significantly enhanced antitumor activity in the PDT models, yielding lower IC₅₀ values and greater cell death than standard treatments. In several cases, PDTs exhibited resistance to conventional therapy, which was explained by the presence of proteomic resistance markers (such as EDIL3, CA12, PGK1, and CapG) in the corresponding tumor clones. These results underscore the potential of spatial proteomic profiling to expose actionable intratumoral heterogeneity and to inform more effective, clone-specific therapies. Our study highlights an innovative pipeline for luminal BC therapy guidance, combining MALDI mass spectrometry imaging and PDT drug testing, and advocates for the integration of spatial proteomics into precision oncology to improve treatment outcomes.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101639"},"PeriodicalIF":6.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13579033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148725140","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}