Proteomics最新文献

FOXA2 Loss in TGF-β1-Induced EMT Suppresses Bisecting-GlcNAc N-Glycan Synthesis in Lung Adenocarcinoma.

IF 3.4 4区生物学

Proteomics Pub Date : 2025-03-06 DOI: 10.1002/pmic.202400216

Wei Ge, Shengye Wen, Xiaoli Zhou, Yan Chen, Daxiong Zeng, Junhong Jiang, Shuang Yang

{"title":"FOXA2 Loss in TGF-β1-Induced EMT Suppresses Bisecting-GlcNAc N-Glycan Synthesis in Lung Adenocarcinoma.","authors":"Wei Ge, Shengye Wen, Xiaoli Zhou, Yan Chen, Daxiong Zeng, Junhong Jiang, Shuang Yang","doi":"10.1002/pmic.202400216","DOIUrl":"https://doi.org/10.1002/pmic.202400216","url":null,"abstract":"Glycosylation, a major posttranslational modification (PTM), is often dysregulated in cancer due to altered glycosyltransferase activity. Studies have shown specific changes in glycan structures associated with epithelial-mesenchymal transition (EMT) in cancer cells. However, the specific mechanism by which glycosyltransferases contribute to EMT remains unclear. In this study, we used bronchoalveolar lavage fluid (BALF) from lung adenocarcinoma (LUAD) patients to comparatively characterize glycopatterns and identify dysregulated glycosyltransferases in LUAD. We found a significant reduction in N-glycans containing the bisecting GlcNAc structure and confirmed by Western blot that N-acetylglucosaminyltransferase-III (MGAT3) is downregulated in LUAD. We observed a notable downregulation of both messenger RNA (mRNA) and protein expression of Forkhead box protein A2 (FOXA2) in early-stage LUAD, with FOXA2 loss emerging as an EMT promoter. Interestingly, cellular EMT models demonstrated that FOXA2 deficiency decreased MGAT3 expression during TGF-β1-driven EMT, leading to reduced levels of bisecting-GlcNAc N-glycans in LUAD cells. Our findings unveil a novel mechanism underlying the downregulation of MGAT3 and bisecting GlcNAc N-glycan expression during EMT, a process crucial for tumor metastasis.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400216"},"PeriodicalIF":3.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin-3 Treatment.

IF 3.4 4区生物学

Proteomics Pub Date : 2025-03-06 DOI: 10.1002/pmic.202400333

Luke Way, Lenka Hernychova, Jerome Vialaret, Li Ruidong, Borek Vojtesek, Ted Hupp, Atef Mahmoud Mannaa

{"title":"Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin-3 Treatment.","authors":"Luke Way, Lenka Hernychova, Jerome Vialaret, Li Ruidong, Borek Vojtesek, Ted Hupp, Atef Mahmoud Mannaa","doi":"10.1002/pmic.202400333","DOIUrl":"https://doi.org/10.1002/pmic.202400333","url":null,"abstract":"Developing methodological approaches for discovering novel pathways is a key challenge in the life science research. Biological pathways are regulated-in higher eukaryotes-by a vast diversity of linear peptide motifs that mediate combinatorial specificity in signal transduction pathways. The E3 ubiquitin ligase component (MDM2) is such a protein that interacts with target proteins containing linear motifs such as p53. Drug leads, such as Nutlin-3, that bind to the MDM2 hydrophobic pocket mimic p53 and can release p53 from MDM2 control and this can lead to cell death. However, these drug leads act allosterically, having agonist effects on MDM2's functions and there are other proteins whose steady state levels can be altered by Nutlin-3. As cell density can alter the proliferation state of cell populations, we examined the impact of Nutlin-3 on levels of newly synthesized proteins using pulse-SILAC mass spectrometry. The data demonstrate that at differing cell densities or population-wide proliferation rates, different newly synthesized proteins dominate the proteome landscape in a Nutlin-3 dependent manner. These data further confirm that the cell state in a population of cells can in turn impact on the MDM2 signalling landscape. This methodology forms a blueprint for biomarker discovery using clinical samples that can detect changes in the synthesis rate of proteins in cell populations treated with specific agents. Broader implications highlight tools that can be used to study allosteric regulation of protein-drug combinations.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400333"},"PeriodicalIF":3.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143571650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment.

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-27 DOI: 10.1002/pmic.202400150

Gaute Hovde Bø, Rolf Simon Härmä, Claus Klingenberg, Veronika Kuchařová Pettersen

{"title":"Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment.","authors":"Gaute Hovde Bø, Rolf Simon Härmä, Claus Klingenberg, Veronika Kuchařová Pettersen","doi":"10.1002/pmic.202400150","DOIUrl":"https://doi.org/10.1002/pmic.202400150","url":null,"abstract":"The development of the gut microbiome in infancy is a vulnerable process that may be perturbed by antibiotics or supported by probiotics. Although effects of these \"biotics\" have been well-studied through DNA sequencing, it remains unclear how the resulting compositional changes affect the microbiome metabolic functions. Additionally, limits in method standardization require careful quality assessment of studies reporting fecal metabolome. We conducted a systematic search in Embase and MEDLINE for studies describing fecal metabolites from term and near-term infants, together with anti-, pre-, or probiotic intervention. The search identified 680 articles, of which 60 were assessed for eligibility and 21 were included. We first developed operational checklists for transparent and reproducible reporting and evaluated the quality of metabolomic methodologies. This analysis supported our aim to summarize changes in the fecal metabolome induced by biotic interventions. Despite a varying quality of metabolomic methodology, we identified similarities in the fecal metabolome profiles in response to specific biotic interventions. Among the most frequently observed metabolites, which were consistently reported to be altered after biotic interventions, were bile acids, aromatic amino acids, and short-chain fatty acids. We conclude with a discussion on appropriate experimental design, controls, and metabolomics reporting to guide future research permitting meta-analyses.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400150"},"PeriodicalIF":3.4,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamic Proteomic and Acetylomic Profiling of Mechanically Induced Cancer Stemness in Breast Cancer Cells.

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-21 DOI: 10.1002/pmic.202400409

Rong Han, Yue Wu, Yehong Yang, Qiaochu Wang, Tao Ding, Xutong Zhang, Juntao Yang

{"title":"Dynamic Proteomic and Acetylomic Profiling of Mechanically Induced Cancer Stemness in Breast Cancer Cells.","authors":"Rong Han, Yue Wu, Yehong Yang, Qiaochu Wang, Tao Ding, Xutong Zhang, Juntao Yang","doi":"10.1002/pmic.202400409","DOIUrl":"https://doi.org/10.1002/pmic.202400409","url":null,"abstract":"Compared to regular tumor cells, cancer stem cells exhibit dangerous characteristics, including high proliferation, high metastatic potential, and significantly increased in vivo tumorigenicity. Although some studies have emphasized the impact of the microenvironment on cell stemness, they have largely overlooked the mechanical forces derived from the stiffness of the surrounding extracellular matrix. Our previous research demonstrated that a 90 Pa soft fibrin matrix in three-dimensional (3D) culture can induce cells to become cancer repopulating cells with high stemness. Acetylation modification significantly influences the metabolism, epigenetics, proliferation, migration, and immune evasion of tumor cells. In this study, we performed a comprehensive analysis of the proteome and acetyl-proteome of breast cancer cells under two-dimensional (2D) plate and 3D matrix conditions with varying stiffness. This dataset provides a valuable resource for understanding the dynamic regulation of protein acetylation in response to mechanical stiffness. The mass spectrometry-based proteomics data have been uploaded to the ProteomeXchange Consortium with the dataset identifier PXD057820.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400409"},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exoproteomic Evidence for BcTSPO-Mediated Regulation of Virulence Factors in Bacillus cereus.

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-21 DOI: 10.1002/pmic.202400293

Catherine Duport, Jean Armengaud

{"title":"Exoproteomic Evidence for BcTSPO-Mediated Regulation of Virulence Factors in Bacillus cereus.","authors":"Catherine Duport, Jean Armengaud","doi":"10.1002/pmic.202400293","DOIUrl":"https://doi.org/10.1002/pmic.202400293","url":null,"abstract":"Bacillus cereus translocator protein (BcTSPO) is a transmembrane protein that plays a regulatory role in various Bacillus cereus phenotypes, potentially including its virulence. Given that the exoproteome is a major determinant of B. cereus virulence, particularly during the late stages of active growth, its analysis is crucial for understanding the regulatory functions of BcTSPO. In this study, we conducted a comparative analysis of the exoproteomes and cellular proteomes of a Δtspo mutant and the wild-type ATCC 14579 strain during the late exponential and early stationary growth phases. Shotgun proteomics revealed that the absence of BcTSPO significantly depleted the exoproteome of secreted virulence factors, including the HBL, NHE, and CytK enterotoxins. Interestingly, the cholesterol-dependent cereolysin O (CLO) was more abundant in the Δtspo exoproteome, indicating a distinct regulatory mechanism. The cellular proteome analysis further confirmed that BcTSPO positively regulates, likely indirectly, the synthesis of enterotoxins and negatively regulates the production of CLO. Additionally, the Δtspo exoproteome was enriched in moonlighting proteins, reflecting the impact of BcTSPO absence on cellular metabolism and stress responses. Overall, these findings highlight the critical role of BcTSPO in shaping the composition of both the exoproteome and cellular proteome, with significant implications for the virulence of B. cereus.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400293"},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-21 DOI: 10.1002/pmic.202400149

Alexandria Bartlett, J Alfredo Blakeley-Ruiz, Tanner Richie, Casey M Theriot, Manuel Kleiner

{"title":"Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.","authors":"Alexandria Bartlett, J Alfredo Blakeley-Ruiz, Tanner Richie, Casey M Theriot, Manuel Kleiner","doi":"10.1002/pmic.202400149","DOIUrl":"10.1002/pmic.202400149","url":null,"abstract":"Diet has been shown to greatly impact the intestinal microbiota. To understand the role of individual dietary components, defined diets with purified components are frequently used in diet-microbiota studies. Defined diets frequently use purified casein as the protein source. Previous work indicated that casein contains microbial DNA potentially impacting results of microbiome studies. Other diet-based microbially derived molecules that may impact microbiome measurements, such as proteins detected by metaproteomics, have not been determined for casein. Additionally, other protein sources used in microbiome studies have not been characterized for their microbial content. We used metagenomics and metaproteomics to identify and quantify microbial DNA and protein in a casein-based defined diet to better understand potential impacts on metagenomic and metaproteomic microbiome studies. We further tested six additional defined diets with purified protein sources with an integrated metagenomic-metaproteomic approach and found that contaminating microbial protein is unique to casein within the tested set as microbial protein was not identified in diets with other protein sources. We also illustrate the contribution of diet-derived microbial protein in diet-microbiota studies by metaproteomic analysis of stool samples from germ-free mice (GF) and mice with a conventional microbiota (CV) following consumption of diets with casein and non-casein protein. This study highlights a potentially confounding factor in diet-microbiota studies that must be considered through evaluation of the diet itself within a given study.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400149"},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Contents: Proteomics 4'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-17 DOI: 10.1002/pmic.202570017

引用次数: 0

Editorial Board: Proteomics 4'25 编辑委员会：蛋白质组学 4'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-17 DOI: 10.1002/pmic.202570016

引用次数: 0

Standard abbreviations

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-17 DOI: 10.1002/pmic.202570018

引用次数: 0

Differences Between Unstimulated and Stimulated Human Male and Female Neutrophils in Protein and Phosphoprotein Profiles.

IF 3.4 4区生物学

Proteomics Pub Date : 2025-02-12 DOI: 10.1002/pmic.202400232

Darrell Pilling, Kristen M Consalvo, Sara A Kirolos, Richard H Gomer

{"title":"Differences Between Unstimulated and Stimulated Human Male and Female Neutrophils in Protein and Phosphoprotein Profiles.","authors":"Darrell Pilling, Kristen M Consalvo, Sara A Kirolos, Richard H Gomer","doi":"10.1002/pmic.202400232","DOIUrl":"10.1002/pmic.202400232","url":null,"abstract":"Human males and females show differences in the incidence of neutrophil-associated diseases and differences in neutrophil responses such as a faster response to the chemorepellent Ser-Leu-Ile-Gly-Lys-Val-NH2 (SLIGKV) in males. Little is known about the basis of sex-based differences in human neutrophils. We used mass spectrometry to identify proteins and phosphoproteins in unstimulated human neutrophils and in neutrophils incubated with the SLIGKV, a protease-activated receptor 2 agonist. There were 132 proteins with higher levels in unstimulated male neutrophils; these proteins tended to be associated with RNA regulation, ribosome, and phosphoinositide signaling pathways, whereas 30 proteins with higher levels in unstimulated female neutrophils were associated with metabolic processes, proteasomes, and phosphatase regulatory proteins. Unstimulated male neutrophils had increased phosphorylation of 32 proteins compared to females. After exposure to SLIGKV, male neutrophils showed a faster response in terms of protein phosphorylation compared to female neutrophils. Male neutrophils have higher levels of proteins and higher phosphorylation of proteins associated with RNA processing and signaling pathways. Female neutrophils have higher levels of proteins associated with metabolism and proteolytic pathways. This suggests that male neutrophils might be more ready to adapt to a new environment, and female neutrophils might be more effective at responding to pathogens.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400232"},"PeriodicalIF":3.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0