Molecular & Cellular Proteomics最新文献

{"title":"Benchmarking sample preservation strategies for clinical single-cell proteomics.","authors":"Heloísa Monteiro do Amaral-Prado, Jackson Gabriel Miyamoto, Daniella de Figueiredo, Elaine Cristina Cardoso, Fábio Malta de Sá Patroni, Romênia Ramos Domingues, Bianca Alves Pauletti, Adriana Franco Paes Leme","doi":"10.1016/j.mcpro.2026.101676","DOIUrl":"https://doi.org/10.1016/j.mcpro.2026.101676","url":null,"abstract":"<p><p>Single-cell proteomics (SCP) enables direct characterization of cellular states at proteome resolution but remains limited in clinical studies due to challenges in sample collection, storage, and transportation. Here, we systematically evaluated preservation strategies for SCP by comparing fresh, cryopreserved, and paraformaldehyde-fixed cells using HeLa cells as a benchmark model (n = 159 cells). Both strategies maintained comparable proteome coverage, but fixation altered protein abundance, whereas cryopreservation largely preserved the proteomic profile. To assess the translational applicability of this workflow, we analyzed single peripheral blood mononuclear cells (PBMCs) from one healthy donor, comparing freshly isolated cells (n = 77) with cells subjected to cryopreservation followed by extended-term storage (n = 75). In PBMCs, cryopreservation did not significantly affect protein group identifications, cellular morphology, proteome coverage, or global proteomic landscape. Together, these results demonstrate that cryopreservation provides a feasible strategy for preserving primary immune cells for downstream SCP under the conditions evaluated here, while comparative preservation strategies using single HeLa cells highlight the advantages and challenges of fixation and cryopreservation for future clinical applications.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101676"},"PeriodicalIF":6.3,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112107","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":"Comparative proteomics and immunoreactivity of Lonomia venomous caterpillars identify hemolins as predominant toxins.","authors":"Lina V Lozano-Morales, Francisco A Bohórquez, Juana M Díaz, Marta Gómez, Yerson Malaver, Stefan Weidt, Richard Burchmore, María Adelaida Gómez, Camila González","doi":"10.1016/j.mcpro.2026.101675","DOIUrl":"https://doi.org/10.1016/j.mcpro.2026.101675","url":null,"abstract":"<p><p>The hemotoxic venom from Lonomia caterpillars is known to cause severe human envenomation in Latin America. The cases have mainly been associated with Lonomia obliqua and Lonomia achelous, which produce venoms with opposing activity on the coagulation pathway. However, other species have recently been reported to cause human envenoming. Our research sought to characterize the bristle extract proteomes of two Lonomia species related to accidents in Colombia, L. casanarensis and L. orientoandensis, and to determine the immunoreactivity of an anti-L. casanarensis serum against these two species. Bristle extracts were digested and prepared for shot-gun proteomics. Clustering and principal component analysis (PCA) based on protein relative abundance were performed, and toxin abundance was compared between species. The immunoreactivity of an anti-L. casanarensis serum was evaluated by immunoprecipitation and western blotting. Although predicted non-toxic proteins were abundant in the proteomes of Lonomia extracts, possible toxins represented a significant proportion of the extract: 38.36% in L. casanarensis and 33.11% in L. orientoandensis. Both venoms contained toxin groups previously reported in other venomous animals, including proteins similar to L. obliqua procoagulant factors Losac and Lopap. Significant differences in the relative abundance of proteins were detected in the bristle extracts of L. casanarensis and L. orientoandensis for lipocalins, serine peptidases, and phospholipases A₂. The anti-L. casanarensis serum showed cross-reactivity with the L. orientoandensis extract. Our data suggests that polyclonal antibodies mainly recognize proteins similar to the hemolin Losac and those belonging to the hexamerin family. This study is the first to characterize the proteome and immunoreactivity of bristle extracts from two medically important Lonomia species, L. casanarensis and L. orientoandensis. Our results reveal variation in bristle extract composition within the genus, which has possible implications for the efficacy of available antivenoms and the development of alternative interventions.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101675"},"PeriodicalIF":6.3,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112054","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":"SLC35A3 remodels site-specific N-glycosylation and defines a druggable glycosylation target in hepatocellular carcinoma.","authors":"Qin Ouyang, Ke Gao, Xinwen Zhou, Jieyi Shi, Long Liao, Cun Wang, Shu Zhang","doi":"10.1016/j.mcpro.2026.101672","DOIUrl":"https://doi.org/10.1016/j.mcpro.2026.101672","url":null,"abstract":"<p><p>Aberrant N-glycosylation contributes to hepatocellular carcinoma (HCC) progression, yet the upstream regulators that coordinate nucleotide-sugar transport and site-specific N-glycosylation remain poorly characterized. Here, we identified SLC35A3, a Golgi-resident UDP-GlcNAc transporter, as a glycosylation-related tumor suppressor in HCC. SLC35A3 was downregulated in HCC tissues, and its restoration suppressed cell proliferation and tumorigenicity. Mechanistically, SLC35A3 overexpression increased Golgi-resident UDP-GlcNAc levels, indicating enhanced substrate availability for glycosyltransferases. Intact N-glycopeptide profiling demonstrated that SLC35A3 overexpression reprogrammed site-specific N-glycan processing, characterized by a predominant reduction in high-mannose (HM) glycoforms and selective remodeling of fucosylated-sialylated (FS) glycoforms. Molecular docking identified poliumoside as a putative SLC35A3 binder with anti-tumor effect in HCC models. Together, our findings establish SLC35A3 as a critical node in Golgi-dependent N-glycan remodeling and highlight its potential as a target for pharmacological activation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101672"},"PeriodicalIF":6.3,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112162","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":"Serum Protein Panel Facilitates Surgical Decision-Making for Barcelona Stage B Hepatocellular Carcinoma.","authors":"Jin-Hua Wang, Liang-Liang Ren, Wan-Jun Zhang, Xiao-Hua Xing, Jun-Qing Li, Chao-Ying Li, Wei-Jie Qin, Xiao-Long Liu, Ying Jiang","doi":"10.1016/j.mcpro.2026.101674","DOIUrl":"https://doi.org/10.1016/j.mcpro.2026.101674","url":null,"abstract":"<p><strong>Purpose: </strong>To develop a serum proteomic-based prognostic model for predicting surgical outcomes in BCLC stage B hepatocellular carcinoma (HCC) patients, addressing the clinical heterogeneity that limits uniform treatment recommendations.</p><p><strong>Methods: </strong>Preoperative serum samples from HCC patients undergoing curative resection were retrospectively collected and subjected to proteomic profiling using nanoparticle-enhanced data-independent acquisition mass spectrometry (DIA-MS). A prognostic risk model was developed in a training cohort (N = 52, BCLC stage B) using 5-fold cross-validated Lasso-Cox machine learning, with overall survival (OS) as the primary endpoint. The model was validated in an independent BCLC stage B cohort (N = 22), extended to a single huge HCC cohort (N = 26, BCLC stage A HCC with a solitary tumor measuring at least 10 cm), and benchmarked against a comparison cohort (N = 190, BCLC 0/A without huge HCC). Orthogonal validation was performed by parallel reaction monitoring (PRM) in an exploration cohort (N = 51, BCLC stage B HCC).</p><p><strong>Results: </strong>Among 2,381 identified proteins, a three-protein panel (LCP1, DOK3, CNN2) was selected to construct the model. The model demonstrated strong predictive accuracy for 3-year OS in the training cohort (AUC = 0.936, sensitivity = 0.988, specificity = 0.834), outperforming the clinical Kinki criteria, in the validation cohort (AUC = 0.812, sensitivity = 0.875, specificity = 0.786) and in the extended cohort of huge HCC patients (AUC = 0.758, sensitivity = 0.709, specificity = 0.852). Notably, low-risk BCLC stage B patients showed comparable prognosis to the comparison cohort of BCLC 0/A patients, suggesting potential surgical benefit. The PRM validation in an independent exploration cohort confirmed the model's prognostic value (AUC = 0.800, sensitivity = 0.870, specificity = 0.700).</p><p><strong>Conclusions: </strong>This serum proteomic-based prognostic model accurately predicts surgical outcomes for BCLC stage B HCC patients and outperforms clinical stratification. By identifying low-risk patients who may benefit from surgery, this tool facilitates personalized treatment planning and has the potential to improve survival and quality of life.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101674"},"PeriodicalIF":6.3,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112188","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":"Identification of Endonuclease G binding protein using a method which specifically isolates binding partners within subcellular compartments.","authors":"Hyeog Kang, Eun Bae Kim, Alexandra L Brown, Heeeun Yoon, Geunhye Hong, Jeonghan Kim","doi":"10.1016/j.mcpro.2026.101671","DOIUrl":"https://doi.org/10.1016/j.mcpro.2026.101671","url":null,"abstract":"<p><p>The elucidation of protein-protein interaction networks is crucial for understanding the regulatory mechanisms and functional roles of proteins. A commonly used technique is to express an epitope-tagged protein (bait) and perform co-immunoprecipitation with the tag antibody to identify proteins bound to the tagged protein. However, when bait proteins that are normally targeted to specific cellular organelles such as mitochondria or the endoplasmic reticulum, are exogenously expressed, a portion of these proteins may fail to localize correctly and instead accumulate in the cytosol or other non-targeted regions. This mis-localization leads to contamination during immunoprecipitation, as cytosolic proteins that bind to the bait are co-precipitated. Therefore, there is a pressing need for a method that can pinpoint organelle-specific binding partners. Proteins entering organelles such as the mitochondria or the endoplasmic reticulum usually possess an N-terminal organelle-targeting sequence that is cleaved off upon entry. In this study, we describe the internal FLAG-M1 antibody (IFM1) technique, a novel method for identifying binding partners by means of the anti-FLAG M1 antibody, which specifically recognizes an internal FLAG tag exposed after the cleavage of the targeting sequence within the organelle. Using the internal FLAG-M1 antibody (IFM1) technique, we identified binding partners of Endonuclease G and TRX2 within mitochondria and discovered novel interactions with Peroxiredoxin 3 and ATP synthase subunits α and β. In conclusion, IFM1 is a reliable method for identifying mitochondria-specific binding partners and has proven to be a straightforward and effective proteomics tool.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101671"},"PeriodicalIF":6.3,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112174","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 Profiling of Post-COVID -19 Sequelae.","authors":"Sepehr Golriz Khatami, Rieke Baumkötter, Thomas Köck, Ayesha Syed Mamoor Alam, Julian Chalabi, Steffen Rapp, Federico Marini, Markus Schepers, Tobias Bopp, Stefan Bittner, Alexander K Schuster, Manfred E Beutel, Thomas Münzel, Karl J Lackner, Vincent Ten Cate, Philipp S Wild","doi":"10.1016/j.mcpro.2026.101670","DOIUrl":"https://doi.org/10.1016/j.mcpro.2026.101670","url":null,"abstract":"<p><p>The emergence of Post-COVID sequelae (PCS) represents a global challenge. However, understanding of biological mechanisms and the definition of quantifiable risk factors remains limited. This study employed machine learning-based classification to explore the potential of proteomics in identifying associations with individual Post-COVID symptoms and their collective manifestation as PCS. The analysis utilized a panel of approximately 2900 proteins measured in 495 COVID-19 patients. The study identified 235 unique proteins associated with 15 of the 21 evaluated Post-COVID symptoms. Symptoms more closely linked by similar protein profiles tended to co-occur more frequently in patients. Six symptom clusters with characteristic molecular pathway associations were identified, with metabolic and inflammatory pathways prominently involved across several clusters. The relevance of the specific protein profiles for Post-COVID symptoms further explored by objective, quantifiable clinical tests, including cognitive and somatic assessments, providing supportive evidence for their biological relevance. Data from various modalities, including pre-existing conditions, disease risk factors and genetic susceptibility, revealed relevant relations that may contribute to PCS heterogeneity. This work illustrates the complex and multifaceted nature of Post-COVID symptoms. It emphasizes the need for systematic and more specific approaches to facilitate the identification of potential pathways for future therapeutic investigation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101670"},"PeriodicalIF":6.3,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149075316","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":"Optimized Detection of Acidic ADP-Ribosylation by PARP14 in Vitro Using Multi-Modal Mass Spectrometry Reveals Putative Autoregulatory Patches.","authors":"Steph Nivaggioli, Hannah H Nguyen, Kiana K Harker, Christian M Mohr, Jake Wood, Mikayla Dupen, Zeeshan Javed, Natalia Karjalainen, Violetta Yousefpor, Ashok Reddy, Ian Carter-O'Connell","doi":"10.1016/j.mcpro.2026.101666","DOIUrl":"10.1016/j.mcpro.2026.101666","url":null,"abstract":"<p><p>ADP-ribosylation is a highly dynamic process that is increasingly linked to a diverse set of cellular functions and pathophysiological outcomes. The modification of target substrates (e.g., proteins, DNA, RNA) involves ligation to an array of different chemical moieties. Recent work has shown that the ester bonds formed between ribose and aspartate (Asp)/glutamate (Glu) residues are particularly labile. A common strategy to overcome this lability is the replacement of the ADP-ribose (ADPr) by hydroxylamine. Attachment of hydroxamic acid (HA) permanently shifts the mass of labeled Asp/Glu residues by +15 Da. However, this method suffers from two notable limitations: HA treatment for long periods of time will label Asp/Glu sites that are solvent exposed, but not modified by ADPr; and the competing hydrolysis reaction still occurs in the conditions routinely used for HA labeling. Herein, we optimize a MS workflow that overcomes these drawbacks. As a proof-of-principle, a truncated form of PARP14 was assessed for its ability to ADP-ribosylate peptides and itself. Conditions that prioritize HA attack over the background rate of hydrolysis were determined using an ultrathin matrix-assisted laser-desorption/ionization time-of-flight method with ADPr-peptides. These efforts doubled HA labeling efficiency and completely removed ADPr within an hour. Next, a series of MS experiments identified the sites of PARP14 automodification using both standard HA labeling conditions (overnight, pH 7.0, 25 °C) and the optimized conditions. Of the identified 9 ADPr sites on PARP14, five are unique to the optimized conditions and six are newly identified. Mutagenesis revealed a set of sites that down-regulated PARP14 and another set that appears to activate PARP14. Taken together, these efforts have improved the true positive site identification rate using HA and have revealed a novel role for several automodification sites in PARP14 regulation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101666"},"PeriodicalIF":6.3,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149017712","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":"Top-Down Proteomics in the Assessment of Kidney Donor Quality: A Proof of Concept for Increased Organ Utilization.","authors":"Claudia Ctortecka, Dinesh Jaishankar, Pei Su, Che-Fan Huang, Indira Pla, Nathaniel Henning, Michael A R Hollas, Michelle A Callegari, Meredith E Taylor, Yu Min Lee, Amna Daud, David F Pinelli, Vinayak Rohan, Michael A Caldwell, Eleonora Forte, Aniel Sanchez, Neil L Kelleher, Satish N Nadig","doi":"10.1016/j.mcpro.2026.101664","DOIUrl":"10.1016/j.mcpro.2026.101664","url":null,"abstract":"<p><p>A persistent barrier to optimizing the utilization of deceased donor kidneys, nearly 30% of which are discarded, is the absence of objective, molecularly resolved metrics of organ quality. To address this gap, we integrated high-resolution proteoform imaging mass spectrometry (PiMS) of donor kidney biopsies with deep LC-MS-based intact proteoform profiling of recipient peripheral blood mononuclear cells (PBMCs) and standard clinical assays. This approach enables direct delineation of proteoform landscapes and reveals immunological and cell stress signatures. Across donor types, living donor (LD) kidneys were enriched for proteoforms associated with oxidative metabolism and cellular homeostasis, whereas kidneys from donation after brain death (DBD), donation after circulatory death (DCD), and discarded organs exhibited elevated abundance of stress-responsive proteoforms, including acetylated CRYAB, PARK7, S100A4, and ACTG1. Despite more pronounced early allograft dysfunction in DCD recipients, DCD tissue proteoform landscapes were globally more similar to LD than to DBD kidneys, indicating distinct injury biology not captured by clinical metrics or peptide-centric proteomics. To extend these findings beyond the graft, we performed the first paired tissue and PBMC proteoform profiling across donor types. Baseline PBMC proteoform differences were minimal; however, by day 7 post-transplant, recipients of deceased donor kidneys exhibited platelet activation, cytoskeletal stress, and inflammatory signaling. Several PBMC-derived proteoforms correlated with serum creatinine, highlighting their potential as early, objective indicators of graft adaptation. Collectively, this proof-of-concept study defines conserved injury-associated proteoforms across tissue and immune compartments and supports the idea that proteoform-resolved analysis may provide a mechanistically grounded, objective framework for assessing donor kidney quality and early graft function.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101664"},"PeriodicalIF":6.3,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149001591","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":"Autoantibody Reactome Profiling Reveals Distinct Humoral Immune Signatures Induced by Simulated Microgravity, Radiation, and Combined Exposure in Mice.","authors":"Lining Wu, Kaipeng Zheng, Bomiao Yu, Bingxin Gao, Pancheng Xiao, Saiya Wang, Yanjun Li, Ruimin Liu, Xiaomei Zhang, Mansheng Li, Chun-Ping Cui, Weiming Tian, Xiaobo Yu","doi":"10.1016/j.mcpro.2026.101665","DOIUrl":"10.1016/j.mcpro.2026.101665","url":null,"abstract":"<p><p>Microgravity (μG) and space radiation are major environmental stressors leading to immune dysfunction in astronauts, but the mechanisms governing humoral immunity and effective interventions remain unclear. In this study, we used a high-throughput autoantigen microarray derived from the AAgAtlas 1.0 database to profile humoral immune responses in mice exposed to μG and proton irradiation. We generated 70,490 autoantibody reactivity measurements and observed combined effects of radiation and μG on humoral immunity. Specifically, 38 IgM and 57 IgG autoantibody candidates showed dose-associated changes across 0, 1 and 5 Gy proton irradiation. We further established a global autoantibody landscape for mice under μG, 1 Gy, 5 Gy and μG & 1 Gy. Autoantibody targets altered under μG were enriched for cardiovascular-associated proteins, whereas proton irradiation-associated targets were enriched for DNA repair-related proteins and co-exposure-associated targets were enriched for inflammation-related proteins, revealing distinct humoral immune recognition signatures across exposure conditions. Additionally, a glutamine-free diet (GFD) was associated with changes in autoantibody profiles and shifts in selected bone and hematological parameters toward control levels under μG and μG & 1 Gy conditions. This work provides a resource for investigating humoral immunity under space-related stress and identifies candidate autoantibody signatures and a potential role of dietary modulation that warrant further validation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101665"},"PeriodicalIF":6.3,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149002145","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":"PRC2 loss in MPNST is accompanied by SWI/SNF complex rewiring and sensitization to SMARCA2/4 and BET inhibition in vivo.","authors":"Kirill Miachin, Marc Alard Morgan, Guangfeng Wang, Jacquelyn A Myers, John J Navarro, Joanna Lempiäinen, Xingyu Liu, Mingzhou Zhou, Kuangying Yang, Diana Akinyi Odhiambo, David W W Hill, Charles W M Roberts, Angela C Hirbe, Benjamin A Garcia","doi":"10.1016/j.mcpro.2026.101662","DOIUrl":"https://doi.org/10.1016/j.mcpro.2026.101662","url":null,"abstract":"<p><p>Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are aggressive sarcomas of peripheral nerve sheath that frequently arise in patients with neurofibromatosis type 1 (NF1) and currently have no approved targeted treatment. Loss of Polycomb Repressive Complex 2 (PRC2) activity, through inactivating mutations in SUZ12 or EED, occurs in 50 to 80% of NF1-associated MPNSTs, leads to depletion of H3K27me3 in cells, global epigenetic dysregulation, and serves as an indicator of poor clinical outcomes. SWI/SNF (BAF) complexes are ATPase-driven chromatin remodelers essential for orderly transcriptional activity in cells. Because PRC2 and SWI/SNF enforce functionally antagonistic effects on chromatin, we hypothesized that PRC2-deficient MPNSTs undergo alterations in the SWI/SNF complex that create a therapeutic vulnerability to SWI/SNF inhibition. We performed integrated proteogenomic profiling of patient-derived MPNST cell lines stratified by PRC2 status: Loss of Function (LoF) or Wild Type (WT). We found that PRC2 loss in MPNST was associated with broad reduction in global SWI/SNF protein abundance, recurrent enrichment of SMARCD3 in SMARCA4-containing complexes, and context-dependent enrichment of DPF3 and PBAF-specific subunits. ChIP-seq analyses showed redistribution of cBAF and PBAF chromatin occupancy in PRC2 LoF models followed by concordant increases in H3K27ac signal and gene expression. Cell fitness assays revealed that the SWI/SNF ATPase inhibitor, FHD-286, reduced cell viability in PRC2 LoF MPNST lines at low nanomolar concentrations and disrupted the colony forming ability, while PRC2 WT cell lines were less sensitive to treatment. Finally, evaluating the efficacy of FHD-286 alone, and in combination with I-BET-762, in an isogenic PRC2 loss murine allograft MPNST model, we observed enhanced efficacy of the combination regimen compared to either single agent in the Suz12 KO arm, while in the Suz12 WT arm, the combo was outperformed by I-BET-762 alone. Together, our findings indicate that PRC2 loss in MPNST is accompanied by selective subunit remodeling and genomic redistribution of SWI/SNF complexes and support SWI/SNF ATPase inhibition, alone and in combination with BET inhibition, as an attractive therapeutic strategy for PRC2-deficient MPNSTs.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101662"},"PeriodicalIF":6.3,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149002197","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}