Journal of Proteome Research最新文献_第10页

Impact of Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration 静态肌母细胞负载对与小细胞迁移相关的蛋白质分泌的影响

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.5c0006810.1021/acs.jproteome.5c00068

Junhong Li*, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J. Kingham and Ludvig J. Backman,

{"title":"Impact of Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration","authors":"Junhong Li*, Xin Zhou, Jialin Chen, Shaochun Zhu, Andre Mateus, Pernilla Eliasson, Paul J. Kingham and Ludvig J. Backman, ","doi":"10.1021/acs.jproteome.5c0006810.1021/acs.jproteome.5c00068","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00068https://doi.org/10.1021/acs.jproteome.5c00068","url":null,"abstract":"Exercise has been shown to promote wound healing, including tendon repair. Myokines released from the exercised muscles are believed to play a significant role in this process. In our previous study, we used an in vitro coculture and loading model to demonstrate that 2% static loading of myoblasts increased the migration and proliferation of cocultured tenocytes─two crucial aspects of wound healing. IGF-1, released from myoblasts in response to 2% static loading, was identified as a contributor to the increased proliferation. However, the factors responsible for the enhanced migration remained unknown. In the current study, we subjected myoblasts in single culture conditions to 2, 5, and 10% static loading and performed proteomic analysis of the cell supernatants. Gene Ontology (GO) analysis revealed that 2% static loading induced the secretion of NBL1, C5, and EFEMP1, which is associated with cell migration and motility. Further investigation by adding exogenous recombinant proteins to human tenocytes showed that NBL1 increased tenocyte migration but not proliferation. This effect was not observed with treatments using C5 and EFEMP1.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2529–2541 2529–2541"},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.5c00068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894189","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}

引用次数: 0

Calf Fitness Associates with Early Embryo and Recipient Metabolomes and with Calf Epigenetic Marks 犊牛健康与早期胚胎和受体代谢组以及犊牛表观遗传标记有关

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.4c0098710.1021/acs.jproteome.4c00987

Isabel Gimeno*, María Berdasco, Miguel L. Pato, Pascal Salvetti, Susana Carrocera, Aurora García and Enrique Gómez*,

{"title":"Calf Fitness Associates with Early Embryo and Recipient Metabolomes and with Calf Epigenetic Marks","authors":"Isabel Gimeno*, María Berdasco, Miguel L. Pato, Pascal Salvetti, Susana Carrocera, Aurora García and Enrique Gómez*, ","doi":"10.1021/acs.jproteome.4c0098710.1021/acs.jproteome.4c00987","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00987https://doi.org/10.1021/acs.jproteome.4c00987","url":null,"abstract":"We used metadata to explore the metabolic interplay between culture medium from in vitro-produced bovine embryos transferred fresh or frozen, recipient blood plasma, and calf fitness, alongside gene expression and methylation in calf lymphocytes. Principal component (PC) analysis (PCA) identified covariates that were depicted in Debiased Sparse Partial Correlation networks and analyzed as enriched pathways. Four PCs explained 13.77, 9.58, 7.73 and 5.84% variability. PC1 clustered only mother weight and two embryonic metabolites. PC2, PC3 and PC4 associated 10, 17, and 5 calf features with 10, 6, and 16 embryonic and 2, 20, and 5 recipient metabolites, respectively. Subsequently, gene methylation and expression, and calf fitness were analyzed by PCA. Three PCs covered 100% variability. PC1 associated acid–base balance, protein metabolism, Cl–, and Ca2+ with IGF2 and IL1R1 expression, and IL4 and IL12B methylation. PC2 linked H19 expression and methylation with growth and biochemical traits. PC3 clustered growth, hydration, and redox balance, with IGF2, IGF2R, IL1R1 and IL3 methylation, and H19, IGF2, IGF2R and IL12B expression. Gene methylation connected with embryo metabolites through networks via K+, Cl–, HCO3– and TCO2. Calf fitness parallels the early metabolic fingerprints of the embryo and recipient, allowing embryo transfer decision-making based on calf health.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2386–2402 2386–2402"},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894192","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}

引用次数: 0

Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency 酸性铁硫杆菌适应城市生活垃圾焚烧残渣以提高生物浸出效率的蛋白质组学研究

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-09 DOI: 10.1021/acs.jproteome.4c0052710.1021/acs.jproteome.4c00527

Jiri Kucera*, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M. Guebitz and Martin Mandl,

{"title":"Proteomic Insights into the Adaptation of Acidithiobacillus ferridurans to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency","authors":"Jiri Kucera*, Klemens Kremser, Pavel Bouchal, David Potesil, Tomas Vaculovic, Dalibor Vsiansky, Georg M. Guebitz and Martin Mandl, ","doi":"10.1021/acs.jproteome.4c0052710.1021/acs.jproteome.4c00527","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00527https://doi.org/10.1021/acs.jproteome.4c00527","url":null,"abstract":"Acidithiobacillus spp. have traditionally been utilized to extract metals from mineral ores through bioleaching. This process has recently expanded to include artificial ores, such as those derived from municipal solid waste incineration (MSWI) residues. Previous studies have indicated that microbial adaptation enhances bioleaching efficiency, prompting this study to identify proteins involved in the adaptation of A. ferridurans to MSWI residues. We employed data-independent acquisition-parallel accumulation serial fragmentation to determine the proteomic response of A. ferridurans DSM 583 to three distinct materials: bottom ash (BA), kettle ash (KA), and filter ash (FA), which represent typical MSWI residues. Our findings indicate that, irrespective of the residue type, a suite of membrane transporters, porins, efflux pumps, and specific electron and cation transfer proteins was notably upregulated. The upregulation of certain proteins involved in anaerobic pathways suggested the development of a spontaneous microaerobic environment, which minimally impacted the bioleaching efficiency. Additionally, the adaptation was most efficient at half the target FA concentration, marked by a significant increase in the detoxification and efflux systems required by microorganisms to tolerate high heavy metal concentrations. Given that metal recovery peaked at lower FA concentrations for most metals of interest, further adaptation at the level of protein expression may not be warranted for improved bioleaching outcomes.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2243–2255 2243–2255"},"PeriodicalIF":3.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00527","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894190","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}

引用次数: 0

MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation MSIght：一个模块化平台，用于提高全球非靶向质谱成像注释的信心

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-08 DOI: 10.1021/acs.jproteome.4c0114010.1021/acs.jproteome.4c01140

Lauren Fields, Hannah N. Miles, Alexis E. Adrian, Elliot Patrenets, William A. Ricke and Lingjun Li*,

{"title":"MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation","authors":"Lauren Fields, Hannah N. Miles, Alexis E. Adrian, Elliot Patrenets, William A. Ricke and Lingjun Li*, ","doi":"10.1021/acs.jproteome.4c0114010.1021/acs.jproteome.4c01140","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01140https://doi.org/10.1021/acs.jproteome.4c01140","url":null,"abstract":"Mass spectrometry imaging (MSI) has gained popularity in clinical analyses due to its high sensitivity, specificity, and throughput. However, global profiling experiments are often still restricted to LC-MS/MS analyses that lack spatial localization due to low-throughput methods for on-tissue peptide identification and confirmation. Additionally, the integration of parallel LC-MS/MS peptide confirmation, as well as histological stains for accurate mapping of identifications, presents a large bottleneck for data analysis, limiting throughput for untargeted profiling experiments. Here, we present a novel platform, termed MSIght, which automates the integration of these multiple modalities into an accessible and modular platform. Histological stains of tissue sections are coregistered to their respective MSI data sets to improve spatial localization and resolution of identified peptides. MS/MS peptide identifications via untargeted LC-MS/MS are used to confirm putative MSI identifications, thus generating MS images with greater confidence in a high-throughput, global manner. This platform has the potential to enable large-scale clinical cohorts to utilize MSI in the future for global proteomic profiling that uncovers novel biomarkers in a spatially resolved manner, thus widely expanding the utility of MSI in clinical discovery.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2478–2490 2478–2490"},"PeriodicalIF":3.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894187","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}

引用次数: 0

Temporal Proteome Profiling of Anterior Cruciate Ligament Tear Remnants: Secretory Proteins in the Acute Phase Potentially Promote Tissue Repair 前交叉韧带撕裂残余的时间蛋白质组分析：急性期分泌蛋白可能促进组织修复

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-07 DOI: 10.1021/acs.jproteome.4c0079210.1021/acs.jproteome.4c00792

Yiming Liu, Bin Li, Jun Zhang, Boming Zhao, Liaobin Chen* and Biao Chen*,

{"title":"Temporal Proteome Profiling of Anterior Cruciate Ligament Tear Remnants: Secretory Proteins in the Acute Phase Potentially Promote Tissue Repair","authors":"Yiming Liu, Bin Li, Jun Zhang, Boming Zhao, Liaobin Chen* and Biao Chen*, ","doi":"10.1021/acs.jproteome.4c0079210.1021/acs.jproteome.4c00792","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00792https://doi.org/10.1021/acs.jproteome.4c00792","url":null,"abstract":"Previous studies reported that preserving the anterior cruciate ligament (ACL) remnants following ACL rupture during reconstruction surgery could promote graft healing. However, the temporal proteomic expression of ACL remnants remains unclear. Based on previous reports, we have redefined the initial 6 weeks following ACL rupture as the acute phase and the subsequent 6 weeks to 6 months as the subacute phase. High-throughput proteomic sequencing on ACL remnants from the two groups was utilized. Our study unveiled a total of 381 differential expression proteins (DEPs), with 136 upregulated and 245 downregulated proteins in the acute phase. By intersecting these findings with secretory protein databases, we identified 26 upregulated secretory proteins and 19 downregulated in the acute phase. The upregulation of MMP9 and VTN and the downregulation of COL1A1 and POSTN in the acute phase were further confirmed by immunohistochemistry. These findings suggest that the elevated expression of secretory proteins in the acute phase may play crucial roles in promoting cell proliferation, angiogenesis, and tissue repair of the graft. This study not only enhances our understanding of repair mechanisms in ACL remnant preservation but also provides a theoretical foundation for guiding rational clinical surgical timing.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2302–2313 2302–2313"},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894166","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}

引用次数: 0

Comparison of N- and O-Glycosylation on Spike Glycoprotein 1 of SARS-CoV-1 and MERS-CoV SARS-CoV-1和MERS-CoV刺突糖蛋白1 N-和o -糖基化的比较

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-07 DOI: 10.1021/acs.jproteome.4c0071610.1021/acs.jproteome.4c00716

Yuan Tian, and , John F. Cipollo*,

{"title":"Comparison of N- and O-Glycosylation on Spike Glycoprotein 1 of SARS-CoV-1 and MERS-CoV","authors":"Yuan Tian,  and , John F. Cipollo*, ","doi":"10.1021/acs.jproteome.4c0071610.1021/acs.jproteome.4c00716","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00716https://doi.org/10.1021/acs.jproteome.4c00716","url":null,"abstract":"SARS-CoV-1 and MERS-CoV were the infective agents of the 2002 and 2012 coronavirus outbreaks, respectively. Here, we report a comparative liquid chromatography/mass spectrometry (LC/MS) Orbitrap N- and O-glycosylation glycoproteomics study of the recombinant S1 spike derived from these two viruses. The former was produced in HEK293 cells and the latter in both HEK293 and insect cells. Both proteins were highly glycosylated, with SARS-CoV-1 S1 having 13 and MERS-CoV S1 having 12 N-glycosites. Nearly all were occupied at 85% or more. Between 2 and 113 unique N-glycan compositions were detected at each N-glycosite across the three proteins. Complex N-glycans dominated in HEK293 cell-derived spike S1 proteins. While glycosylation differs between HEK293 and insect cells, the extent of glycan processing at glycosites was similar for the two MERS-CoV S1 forms. The HEK293-derived SARS-CoV-1 S1 N-glycans were more highly sialylated and fucosylated compared to MERS S1, while the latter had more high-mannose glycosides, particularly in the N-terminus and near the RBD. Seven and 8 O-glycosites were identified in SARS-CoV-1 S1 and MERS-CoV S1, respectively. Mapping of predicted antigenic and glycosylation sites reveals colocalization consistent with a role for glycosylation in immune system avoidance. Glycosylation patterns of these S1 proteins differ from those of other SARS-CoV-1 and MERS-CoV spike reported forms such as recombinant trimeric and virus-propagated forms, which has implications for virus research, including vaccine development, as glycosylation plays a role in spike function and epitope structure.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2256–2265 2256–2265"},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894167","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}

引用次数: 0

NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential NA_mCNN：基于多窗口深度学习和ProtTrans的膜蛋白钠转运蛋白分类研究

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-07 DOI: 10.1021/acs.jproteome.4c0088410.1021/acs.jproteome.4c00884

Muhammad Shahid Malik, Van The Le and Yu-Yen Ou*,

{"title":"NA_mCNN: Classification of Sodium Transporters in Membrane Proteins by Integrating Multi-Window Deep Learning and ProtTrans for Their Therapeutic Potential","authors":"Muhammad Shahid Malik, Van The Le and Yu-Yen Ou*, ","doi":"10.1021/acs.jproteome.4c0088410.1021/acs.jproteome.4c00884","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00884https://doi.org/10.1021/acs.jproteome.4c00884","url":null,"abstract":"Sodium transporters maintain cellular homeostasis by transporting ions, minerals, and nutrients across the membrane, and Na+/K+ ATPases facilitate the cotransport of solutes in neurons, muscle cells, and epithelial cells. Sodium transporters are important for many physiological processes, and their dysfunction leads to diseases such as hypertension, diabetes, neurological disorders, and cancer. The NA_mCNN computational method highlights the functional diversity and significance of sodium transporters in membrane proteins using protein language model embeddings (PLMs) and multiple-window scanning deep learning models. This work investigates PLMs that include Tape, ProtTrans, ESM-1b-1280, and ESM-2-128 to achieve more accuracy in sodium transporter classification. Five-fold cross-validation and independent testing demonstrate ProtTrans embedding robustness. In cross-validation, ProtTrans achieved an AUC of 0.9939, a sensitivity of 0.9829, and a specificity of 0.9889, demonstrating its ability to distinguish positive and negative samples. In independent testing, ProtTrans maintained a sensitivity of 0.9765, a specificity of 0.9991, and an AUC of 0.9975, which indicates its high level of discrimination. This study advances the understanding of sodium transporter diversity and function, as well as their role in human pathophysiology. Our goal is to use deep learning techniques and protein language models for identifying sodium transporters to accelerate identification and develop new therapeutic interventions.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 5","pages":"2324–2335 2324–2335"},"PeriodicalIF":3.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jproteome.4c00884","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894093","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}

引用次数: 0

MGVB: a New Proteomics Toolset for Fast and Efficient Data Analysis. MGVB：一个新的蛋白质组学工具集，用于快速有效的数据分析。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-16 DOI: 10.1021/acs.jproteome.4c00994

Metodi V Metodiev

引用次数: 0

A Comparison of Derivatives of Alanine and d-Alanine Used in Gas Chromatography-Mass Spectrometry Analysis for Protein Kinetics. 丙氨酸和d-丙氨酸衍生物在蛋白质动力学气相色谱-质谱分析中的应用比较。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-16 DOI: 10.1021/acs.jproteome.4c01004

Yihong Kaufmann, Rick Williams, Matthew Cotter, Arny Ferrando, Elisabet Børsheim

{"title":"A Comparison of Derivatives of Alanine and d-Alanine Used in Gas Chromatography-Mass Spectrometry Analysis for Protein Kinetics.","authors":"Yihong Kaufmann, Rick Williams, Matthew Cotter, Arny Ferrando, Elisabet Børsheim","doi":"10.1021/acs.jproteome.4c01004","DOIUrl":"10.1021/acs.jproteome.4c01004","url":null,"abstract":"Stable isotope techniques serve as invaluable tools for kinetic measurements in metabolic research. In particular, deuterated water (D2O) administration is increasingly being applied in human health research. For use in protein kinetic studies, this includes measurements on gas chromatography-mass spectrometry (GC-MS) analysis of alanine (ALA) and deuterium-labeled alanines (d-ALAs) coming from D2O administration. However, the choice of the derivative of ALA and d-ALAs used in such analyses has not been evaluated thoroughly. Hence, we conducted a comprehensive head-to-head comparison to determine the most effective and reliable derivative. Two derivatization reagents, N,N-dimethylformamide dimethyl acetal (methyl-8 reagent) and N-methyl-N-tert-butyldimethylsilyltrifluoroacetamide (MtBSTFA), were considered as candidates. Using chemical standards and available rodent muscle tissue, both reagents underwent testing, including the standard curve linear regression fit, sensitivity, reproducibility, and, importantly, column effectiveness. Our findings indicate that both reagents were suitable for ALA/d-ALAs analyses. However, the MtBSTFA derivative exhibited a better linear regression fit, higher sensitivity, and greater reproducibility than methyl-8. More importantly, the methyl-8 derivative resulted in severe column damage. In conclusion, our study highlights the MtBSTFA derivative as a preferred choice for ALA and d-ALAs GC-MS analysis, contributing to a reliable and sensitive analytical method for D2O administration studies for measurements of in vivo metabolic rates.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1983-1991"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646538","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}

引用次数: 0

Multiomics Analysis Reveals Neuroblastoma Molecular Signature Predicting Risk Stratification and Tumor Microenvironment Differences. 多组学分析揭示神经母细胞瘤分子特征预测风险分层和肿瘤微环境差异。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-01-06 DOI: 10.1021/acs.jproteome.4c00882

Xing Zhou, Zhaokai Zhou, Xiaohan Qin, Jian Cheng, Yongcheng Fu, Yuanyuan Wang, Jingyue Wang, Pan Qin, Da Zhang

{"title":"Multiomics Analysis Reveals Neuroblastoma Molecular Signature Predicting Risk Stratification and Tumor Microenvironment Differences.","authors":"Xing Zhou, Zhaokai Zhou, Xiaohan Qin, Jian Cheng, Yongcheng Fu, Yuanyuan Wang, Jingyue Wang, Pan Qin, Da Zhang","doi":"10.1021/acs.jproteome.4c00882","DOIUrl":"10.1021/acs.jproteome.4c00882","url":null,"abstract":"Neuroblastoma (NB) remains associated with high mortality and low initial response rate, especially for high-risk patients, thus warranting exploration of molecular markers for precision risk classifiers. Through integrating multiomics profiling, we identified a range of hub genes involved in cell cycle and associated with dismal prognosis and malignant cells. Single-cell transcriptome sequencing revealed that a subset of malignant cells, subcluster 1, characterized by high proliferation and dedifferentiation, was strongly correlated with the hub gene signature and orchestrated an immunosuppressive tumor microenvironment (TME). Furthermore, we constructed a robust malignant subcluster 1 related signature (MSRS), which was an independent prognostic factor and superior to other clinical characteristics and published signatures. Besides, TME differences conferred remarkably distinct therapeutic responses between high and low MSRS groups. Notably, polo-like kinase-1 (PLK1) was one of the most crucial contributors to MSRS and remarkably correlated with malignant subcluster 1, and PLK1 inhibition was effective for NB treatment as demonstrated by in silico analysis and in vitro experiments. Overall, our study constructs a novel molecular model to further guide the clinical classification and individualized treatment of NB.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 4","pages":"1606-1623"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778610","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}

引用次数: 0