Molecular & Cellular Proteomics最新文献

{"title":"Proximity labeling and SILAC based proteomic approach identifies proteins at the interface of homotypic and heterotypic cancer cell interactions.","authors":"Nazan Saner, Ceren Uzun, Büşra Aytül Akarlar, Sena Nur Özkan, Daniel Jon Geiszler, Ece Öztürk, Nurcan Tunçbağ, Nurhan Özlü","doi":"10.1016/j.mcpro.2025.100986","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100986","url":null,"abstract":"<p><p>Cell-cell interactions are critical for the growth of organisms and maintaining homeostasis. In the tumor microenvironment, these interactions promote cancer progression. Given their importance in healthy and diseased conditions, we have developed a method to analyze the cell-to-cell interactome. Our approach uses enzyme-catalyzed proximity labeling and SILAC-based proteomics to identify the proteins involved in cancer cell interactions. By targeting HRP to the outer leaflet of the plasma membrane in bait cells, we were able to label the neighboring prey cells and distinguish between the proteomes of bait and prey cells using SILAC labeling in a co-culture system. We mapped both the homotypic and heterotypic interactomes of epithelial and mesenchymal breast cancer cells. The enrichment of cell surface and extracellular proteins confirms the specificity of our methodology. We further verified selected hits from different cell-cell interactomes in co-cultures using microscopy. This method revealed prominent signaling pathways orchestrating homotypic and heterotypic interactions of epithelial and mesenchymal cells. It also highlights the importance of exosomes in these interactions. Our methodology can be applied to any type of cell-cell interaction in 2D co-culture or 3D tumor models.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100986"},"PeriodicalIF":6.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012873","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":"Quantitative Label-Free Single-Cell Proteomics on the Orbitrap Astral MS.","authors":"Valdemaras Petrosius, Pedro Aragon-Fernandez, Tabiwang N Arrey, Jakob Woessman, Nil Üresin, Bauke de Boer, Jinyu Su, Benjamin Furtwängler, Hamish Stewart, Eduard Denisov, Johannes Petzoldt, Amelia C Peterson, Christian Hock, Eugen Damoc, Alexander Makarov, Vlad Zabrouskov, Bo T Porse, Erwin M Schoof","doi":"10.1016/j.mcpro.2025.100982","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100982","url":null,"abstract":"<p><p>Single-cell proteomics by mass spectrometry (scp-MS) holds the potential to provide unprecedented insights into molecular features directly linked to the cellular phenotype, while deconvoluting complex organisms into their basic building blocks. Tailored sample preparation that maximizes the extracted amount of material that is introduced into the mass spectrometer has rapidly propelled the field forward. However, the measured signal is still at the lower edge of detection approaching the sensitivity boundary of current instrumentation. Here, we investigate the capacity of the enhanced sensitivity of the Orbitrap Astral mass spectrometer to facilitate deeper proteome profiles from low-input to single-cell samples. We carry out a comprehensive data acquisition method survey to pinpoint which parameters provide most sensitivity. Furthermore, we explore the quantitative accuracy of the obtained measurements to ensure that the obtained abundances are in line with expected ground truth values. We culminate our technical exploration by generating small datasets from two cultured cell lines and a primary bone marrow sample, to showcase obtainable proteome coverage differences from different source materials. Finally, as a proof of concept we explore protein covariation to showcase how information on known protein complexes is captured inherently in our scp-MS data.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100982"},"PeriodicalIF":6.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143990360","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":"Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms.","authors":"Ashley M Frankenfield, Kevin L Yang, Wan Nur Atiqah Binti Mazli, Jamison Shih, Fengchao Yu, Edwin Lo, Alexey I Nesvizhskii, Ling Hao","doi":"10.1016/j.mcpro.2025.100980","DOIUrl":"10.1016/j.mcpro.2025.100980","url":null,"abstract":"<p><p>Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful metabolic labeling technique with broad applications and various study designs. SILAC proteomics relies on the accurate identification and quantification of all isotopic versions of proteins and peptides during both data acquisition and analysis. However, a comprehensive comparison and evaluation of SILAC data analysis platforms is currently lacking. To address this critical gap and offer practical guidelines for SILAC proteomics data analysis, we designed a comprehensive benchmarking pipeline to evaluate various in vitro SILAC workflows and commonly used data analysis software. Ten different SILAC data analysis workflows using five software packages (MaxQuant, Proteome Discoverer, FragPipe, DIA-NN, and Spectronaut) were evaluated for static and dynamic SILAC labeling with both DDA and DIA methods. For benchmarking, we used both in-house generated and repository SILAC proteomics datasets from HeLa and neuron culture samples. We assessed 12 performance metrics for SILAC proteomics including identification, quantification, accuracy, precision, reproducibility, filtering criteria, missing values, false discovery rate, protein half-life measurement, data completeness, unique software features, and speed of data analysis. Each method/software has its strengths and weaknesses when evaluated for these performance metrics. Most software reaches a dynamic range limit of 100-fold for accurate quantification of light/heavy ratios. We do not recommend using Proteome Discoverer for SILAC DDA analysis despite its wide use in label-free proteomics. To achieve greater confidence in SILAC quantification, researchers could use more than one software packages to analyze the same dataset for cross-validation. In summary, this study offers the first systematic evaluation of various SILAC data analysis platforms, providing practical guidelines to support decision-making in SILAC proteomics study design and data analysis.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100980"},"PeriodicalIF":6.1,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018351","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":"Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades.","authors":"Hirokazu Yagi, Taiki Saito, Shih-Yun Guu, Nao Yamakawa, Shigeru Shimamura, Sachiko Kondo, Maho Yagi-Utsumi, Ken Takai, Jun-Ichi Furukawa, Yann Guerardel, Kay-Hooi Khoo, Kazuharu Arakawa, Koichi Kato","doi":"10.1016/j.mcpro.2025.100979","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100979","url":null,"abstract":"<p><p>We characterized the N-glycosylation profiles of anhydrobiotic tardigrades, R. varieornatus and H. exemplaris, identifying high-mannose, paucimannose, and complex-type oligosaccharides, while hybrid-type glycans were undetectable. Notably, paucimannose-type oligosaccharides accounted for 39% of the N-glycans in R. varieornatus and 17% in H. exemplaris, with a substantial proportion of them exhibiting fucosylation of the innermost GlcNAc via an α1,6-linkage. This core fucosylation pattern, common to all animals, was observed alongside a distinctive glycosylation signature prominently observed in tardigrades: complex-type glycans lacking galactosylation but containing α1,3-fucosylated GlcNAc at non-reducing termini. This structure was more prevalent in H. exemplaris, with 22 out of 87 identified glycoproteins expressing the Fucα1,3-GlcNAc motif, including eight induced during anhydrobiosis. Key glycoproteins such as Cu/Zn-superoxide dismutase and papilin, implicated in oxidative stress protection and extracellular matrix remodeling, were among those modified. Comparative analyses reveal that non-reducing terminal α1,3-fucosylation in tardigrades is distinct from the mammalian Lewis X antigen and similar structures found in invertebrates, suggesting a unique substrate specificity of fucosyltransferases in these species. Genomic analysis identified homologs of Fut9 and FucTC, indicating potential candidates responsible for this glycosylation pattern. Our findings provide new insights into the molecular mechanisms of glycosylation in tardigrades and its relevance to their extreme stress tolerance.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100979"},"PeriodicalIF":6.1,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Analysis and 2-Hydroxyisobutyrylation Profiling in Metabolic Syndrome Induced Restenosis.","authors":"Xiangyu Liu, Liping Zhou, Wenjing Huang, Yanyan Yang, Yijun Yang, Tianwei Liu, Mingjin Guo, Tao Yu, Yongxin Li","doi":"10.1016/j.mcpro.2025.100978","DOIUrl":"10.1016/j.mcpro.2025.100978","url":null,"abstract":"<p><p>Restenosis is the primary complication following stenting for coronary and peripheral arterial disease, posing an ongoing clinical challenge. Metabolic syndrome (MetS), characterized by metabolic disturbances, has been identified as an independent predictor for postoperative restenosis in coronary and carotid arteries, potentially due to endothelial dysfunction and augmented oxidative stress in cells, while its specific regulatory mechanism is still largely unknown. Lysine 2-hydroxyisobutyrylation (Khib), a recently identified posttranslational modification, plays a crucial role in transcriptional regulation and cellular metabolism. However, there is a lack of comprehensive analysis of the proteome and Khib modifications within restenotic vessels in the context of MetS, as well as in the understanding of the associated pathophysiology. In this study, we observed a significant upregulation of Khib in restenotic arteries induced by MetS, confirmed by animal and cellular experiments. Further, using high-throughput liquid chromatography-mass spectrometry, we catalogued 15,558 Khib sites across 2568 proteins, implicating a multitude of biological functions. Analysis revealed 2007 Khib sites on 1002 proteins with considerable differential modifications which are present within the cytoplasm and nucleus. Interestingly, proteins located in the mitochondria, endoplasmic reticulum, and cell membrane also exhibit distinct expression and modification profiles to varying extents that related to vascular smooth muscle contraction, platelet activation, and the PI3K-Akt signaling pathway. Notably, the level of COL1A1 protein detected in the protein-protein interaction pathway network and the level of Khib modification are diametrically opposed, suggesting a significant role in the disease's pathogenesis. This study provides the first comprehensive proteomic and Khib modification overview of MetS-related in-stent restenosis vasculature, offering key insights to inform novel therapeutic approaches for restenosis mitigation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100978"},"PeriodicalIF":6.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033552","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":"Landscape of Steroid Dynamics in Pregnancy: Insights From the Maternal-Placental-Fetal Unit and Placental Models.","authors":"Rona Karahoda, Therina Du Toit, Barbara Fuenzalida, Sampada Kallol, Michael Groessl, Pascale Anderle, Edgar Ontsouka, Frantisek Staud, Christa E Flueck, Christiane Albrecht","doi":"10.1016/j.mcpro.2025.100976","DOIUrl":"10.1016/j.mcpro.2025.100976","url":null,"abstract":"<p><p>Recent advances in analytical methods have revolutionized our understanding of steroid biochemistry. The emergence of novel steroids such as 11-oxy androgens and 11-oxy progesterones has necessitated a reevaluation of steroid biosynthesis and metabolism within the maternal-placental-fetal unit. In this study, we employed a validated liquid chromatography high-resolution mass spectrometry method to quantify 51 steroids in paired maternal serum, neonatal serum, and placenta samples from 37 healthy pregnancies. Additionally, we characterized steroid release in various placental models, including human placenta perfusion, explants, and primary trophoblast cells isolated from human term placenta. Our findings emphasize the predominance of keto derivatives of androgens in the placenta compared to hydroxylated forms, which are dominant in maternal serum and neonatal serum. We also observed high levels of classic and novel progesterones in the placenta and across all models, with significant release on the maternal side. These results suggest that the placenta possesses an active enzymatic machinery capable of producing and metabolizing novel progesterones. Furthermore, we demonstrated that the catalytic activity of 11β-hydroxysteroid dehydrogenase type 2 extends beyond cortisol regulation to hydroxylated androgens, highlighting its significance in the broader context of steroid metabolism within the maternal-placental-fetal unit. These findings contribute to our understanding of placental physiology and impact on fetal development.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100976"},"PeriodicalIF":6.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033660","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":"DExH-Box Helicase 9 Participates in De Novo Nrf2 Protein Translation Under Oxidative Stress.","authors":"Wujing Dai, Hongting Diao, Han Qu, Daniel Wurm, Yingying Lu, Qin M Chen","doi":"10.1016/j.mcpro.2025.100977","DOIUrl":"10.1016/j.mcpro.2025.100977","url":null,"abstract":"<p><p>Nrf2 transcript factor plays an important role in cellular defense against oxidative stress due to its control for expression of antioxidant and detoxification genes. We have found that Nrf2 gene undergoes de novo protein translation when mammalian cells encounter oxidative stress. Here, we report the discovery of DExH-box helicase-9 (DHX9), also known as RNA helicase A, as a binding protein for Nrf2 mRNA at 5'UTR. DHX9 binding to Nrf2 5'UTR increased with increasing doses (50-300 μM) of H₂O₂ or treatment time (10-120 min). This incease was in parallel with elevation of Nrf2 protein. Inhibiting DHX9 expression with siRNA or its activity with YK-4-279 inhibitor blocked H₂O₂ from inducing Nrf2 mRNA recruitment to the ribosomes or Nrf2 protein elevation. As a nuclear protein, DHX9 was found to increase its abundance in the cytosol with oxidative stress. An increase of DHX9 was detected in the ribosomes from cells treated with H₂O₂, most significantly with 100 μM H₂O₂, and at 60 min. Ribosomal fractionation revealed an increase of DHX9 protein at 43/48S and 80S fractions in H₂O₂-treated cells. H₂O₂ treatment caused an RNA-dependent increase of DHX9 interaction with eIF3η. The binding of DHX9 to Nrf2 5'UTR was enhanced by H₂O₂-treated cells or by deducting the length of Nrf2 5'UTR. RNase digestion enhanced DHX9 association with the ribosomes. Our data have revealed a novel mechanism of de novo Nrf2 protein translation under oxidative stress involving DHX9 binding to Nrf2 5'UTR, perhaps via removal of a negative RNA element, to recruit 43S preinitiation complex for translation initiation.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100977"},"PeriodicalIF":6.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143982357","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":"Global analysis of protein and small-molecule substrates of ubiquitin-like proteins (UBLs).","authors":"Guang-Can Shao, Zhen-Lin Chen, Shan Lu, Qing-Cui Wu, Yao Sheng, Jing Wang, Yan Ma, Jian-Hua Sui, Hao Chi, Xiang-Bing Qi, Si-Min He, Li-Lin Du, Meng-Qiu Dong","doi":"10.1016/j.mcpro.2025.100975","DOIUrl":"https://doi.org/10.1016/j.mcpro.2025.100975","url":null,"abstract":"<p><p>Ubiquitin-like proteins (UBLs) constitute a family of evolutionarily conserved proteins that share similarities with ubiquitin in 3D structures and modification mechanisms. For most UBLs including Small-Ubiquitin-like Modifiers (SUMO), their modification sites on substrate proteins cannot be identified using the mass spectrometry-based method that has been successful for identifying ubiquitination sites, unless a UBL protein is mutated accordingly. To identify UBL modification sites without having to mutate UBL, we have developed a dedicated search engine pLink-UBL on the basis of pLink, a software tool for identification of cross-linked peptide pairs. pLink-UBL exhibited superior precision, sensitivity, and speed than \"make-do\" search engines such as MaxQuant, pFind, and pLink. For example, compared to MaxQuant, pLink-UBL increased the number of identified SUMOylation sites by 50 ∼ 300% from the same datasets. Additionally, we present a method for identifying small-molecule modifications of UBLs. This method involves antibody enrichment of a UBL C-terminal peptide following enrichment of a UBL protein, followed by LC-MS/MS analysis and a pFind 3 blind search to identify unexpected modifications. Using this method, we have discovered non-protein substrates of SUMO, of which spermidine is the major one for fission yeast SUMO Pmt3. Spermidine can be conjugated to the C-terminal carboxylate group of Pmt3 through its N¹ or also likely, N⁸ amino group in the presence of SUMO E1, E2, and ATP. Pmt3-spermidine conjugation does not require E3 and can be reversed by SUMO isopeptidase Ulp1. SUMO-spermidine conjugation is present in mice and humans. Also, spermidine can be conjugated to ubiquitin in vitro by E1 and E2 in the presence of ATP. The above observations suggest that spermidine may be a common small molecule substrate of SUMO and possibly ubiquitin across eukaryotic species.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100975"},"PeriodicalIF":6.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144035372","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":"SysQuan: Repurposing SILAC Mice for the Cost-Effective Absolute Quantitation of the Human Proteome.","authors":"Yassene Mohammed, Vincent R Richard, M Immanuel Reyes Madlangsakay, Ying Lao, Victor Spicer, Robert Popp, Claudia Gaither, Laura Hennecken, Wolfgang Kleinekofort, René P Zahedi, Christoph H Borchers","doi":"10.1016/j.mcpro.2025.100974","DOIUrl":"10.1016/j.mcpro.2025.100974","url":null,"abstract":"<p><p>Relative quantitation, used by most mass spectrometry-based proteomics laboratories to determine protein fold-changes, requires samples being processed and analyzed together for best comparability through minimizing batch differences. This limits the adoption of mass spectrometry-based proteomics in population-wide studies and the detection of subtle but relevant changes in heterogeneous samples. Absolute quantitation circumvents these limitations and enables comparison of results across laboratories, studies, and over time. However, high cost of the essential stable isotope labeled (SIL) standards prevents widespread access and limits the number of quantifiable proteins. Our new approach, called \"SysQuan\", repurposes SILAC mouse tissues/biofluids as system-wide internal standards for matched human samples to enable absolute quantitation of, theoretically, two-thirds of the human proteome using 157,086 shared tryptic peptides, of which 73,901 with lysine on the c terminus. We demonstrate that SysQuan enables quantification of 70% and 31% of the liver and plasma proteomes, respectively. We demonstrate for 14 metabolic proteins that abundant SIL mouse tissues enable cost-effective reverse absolute quantitation in, theoretically, 1000s of human samples. Moreover, 10,000s of light/heavy doublets in untargeted SysQuan datasets enable unique postacquisition absolute quantitation. SysQuan empowers researchers to replace relative quantitation with affordable absolute quantitation at scale, making data comparable across laboratories, diseases and tissues, enabling completely novel study designs and increasing reusability of data in repositories.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100974"},"PeriodicalIF":6.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002024","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":"SIRT3 Functions as an Eraser of Histone H3K9 Lactylation to Modulate Transcription for Inhibiting the Progression of Esophageal Cancer.","authors":"Chen Chen, Yingao Zhang, Yong Zang, Zilong Fan, Yanpu Han, Xue Bai, Aiyuan Wang, Jianji Zhang, Ju Wang, Kai Zhang","doi":"10.1016/j.mcpro.2025.100973","DOIUrl":"10.1016/j.mcpro.2025.100973","url":null,"abstract":"<p><p>Lysine lactylation (Kla) links lactate metabolism to epigenetic regulation, playing a key role in modulation of gene expression in tumor and immune microenvironment. Our recent study shows that HBO1-mediated histone H3K9la activates the transcription of genes encoding tumorigenesis, suggesting the potential significance of intervening in this Kla site for tumor therapy. Evidence so far indicates that traditional deacetylases can catalyze the removal of Kla; however, the precise demodifying enzyme to histone H3K9la in vivo and functional consequence remain elusive. Herein, we combined an antibody-based proximity labeling approach with mass spectrometry analysis to identify SIRT3 as a major binder to histone H3K9la and showed the specific catalysis of SIRT3 for the removal of lactylation. Molecular docking further revealed the molecular mechanism of the binding of histone H3K9la to SIRT3. More importantly, SIRT3 can specifically modulate gene transcription by regulating H3K9la, inhibiting the progression of esophageal squamous cancer cells. Together, our work identifies the specific delactylase of H3K9la and reveals an H3K9la-mediated molecular mechanism catalyzed by SIRT3 for gene transcription regulation in esophageal squamous cancer cells, and our findings provide an opportunity to investigate the physiological significance of Kla controlled by SIRT3 in cancer.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100973"},"PeriodicalIF":6.1,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028359","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}