Journal of Proteome Research最新文献

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Attribute-Weighted Aggregation of Tandem Mass Reporter Ion Intensity for Protein Quantification Using Isobaric Labeling 等压标记用于蛋白质定量的串联质量报告离子强度属性加权聚集。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-23 DOI: 10.1021/acs.jproteome.4c00992
Jiahua Tan, , , Gian L. Negri, , , Gregg B. Morin*, , and , David D. Y. Chen*, 
{"title":"Attribute-Weighted Aggregation of Tandem Mass Reporter Ion Intensity for Protein Quantification Using Isobaric Labeling","authors":"Jiahua Tan,&nbsp;, ,&nbsp;Gian L. Negri,&nbsp;, ,&nbsp;Gregg B. Morin*,&nbsp;, and ,&nbsp;David D. Y. Chen*,&nbsp;","doi":"10.1021/acs.jproteome.4c00992","DOIUrl":"10.1021/acs.jproteome.4c00992","url":null,"abstract":"<p >Isobaric labeling is a commonly used technique in proteomics. In bottom-up proteomics, protein abundance estimation requires combining reporter ion intensities from the corresponding peptide-spectrum matches (PSMs), a process referred to as aggregation. It is usually assumed that PSMs in this step represent protein abundance equally, but the differences in ionizability and propensity for isolation interference result in different levels of quantitative accuracy for PSMs. This work developed an attribute-weighted aggregation (AWA) method that considers PSM attributes with reporter ion intensities to provide a more accurate estimate of protein abundance. A random forest model was trained on the characteristics of PSMs using three spike-in data sets and used to predict the quantitative inaccuracy of PSMs to be aggregated based on their attributes. These PSMs were aggregated to the protein level based on the predicted inaccuracy. AWA was evaluated using the three spike-in data sets and applied to two large cancer cohorts. The results showed that applying AWA to different data sets can lead to better recall in differential expression analyses while maintaining high precision. To facilitate the application of AWA, an R package AWAggregator was developed, which also offers functions to retrain the random forest model for additional or alternative spike-in data sets.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"4875–4887"},"PeriodicalIF":3.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129652","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 Profiling Reveals RisR as a Novel Regulatory Element in the Virulence Network of Bordetella pertussis 蛋白质组学分析揭示RisR是百日咳杆菌毒力网络中的一个新的调控元件。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-20 DOI: 10.1021/acs.jproteome.5c00675
Mariela C. Carrica*, , , Kristin Surmann, , , Juan P. Gorgojo, , , Jimena Alvarez Hayes, , , Christian Hentschker, , , Manuela Gesell Salazar, , , Yanina A. Lamberti, , , Uwe Völker, , and , Maria E. Rodriguez*, 
{"title":"Proteomic Profiling Reveals RisR as a Novel Regulatory Element in the Virulence Network of Bordetella pertussis","authors":"Mariela C. Carrica*,&nbsp;, ,&nbsp;Kristin Surmann,&nbsp;, ,&nbsp;Juan P. Gorgojo,&nbsp;, ,&nbsp;Jimena Alvarez Hayes,&nbsp;, ,&nbsp;Christian Hentschker,&nbsp;, ,&nbsp;Manuela Gesell Salazar,&nbsp;, ,&nbsp;Yanina A. Lamberti,&nbsp;, ,&nbsp;Uwe Völker,&nbsp;, and ,&nbsp;Maria E. Rodriguez*,&nbsp;","doi":"10.1021/acs.jproteome.5c00675","DOIUrl":"10.1021/acs.jproteome.5c00675","url":null,"abstract":"<p ><i>Bordetella pertussis</i>, the causative agent of whooping cough, regulates its virulence through the BvgAS two-component system, which controls the transition between virulent (Bvg<sup>+</sup>) and avirulent (Bvg<sup>–</sup>) phases. In the virulent phase, virulence-activated genes (<i>vag</i>s) are expressed, while in the avirulent phase, these are repressed. Virulence-repressed genes (<i>vrg</i>s) are induced under the control of the response regulator RisA. Phosphorylation of RisA by the nonoperonic kinase RisK is essential for <i>vrg</i>s expression. Adjacent to <i>risK</i> lies <i>risR</i>, a gene encoding a putative response regulator, whose function remained unexplored. To investigate the RisR’s role in <i>B. pertussis</i> biology, we performed comparative proteomic analyses between wild-type and an isogenic <i>risR</i>-deficient strain, grown under both virulent and avirulent conditions. Our data show that RisR modulates the abundance of proteins encoded by <i>vag</i>s and <i>vrg</i>s, suggesting a previously unrecognized interplay between RisR and the BvgAS–RisAK regulatory network. Moreover, RisR regulates the abundance of proteins important for bacterial fitness, including those involved in iron acquisition and intracellular adaptation. Functional assays further support the role of RisR in promoting intracellular survival. This study provides the first proteome-wide characterization of the RisR regulon and identifies it as a novel regulator of <i>B. pertussis</i> virulence and adaptation.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5254–5265"},"PeriodicalIF":3.6,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090847","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
Specimen Inactivation Methods for Proteomics─Comparisons of Irradiation, Chemical, and Heat Treatments on Downstream Serum Analyses 蛋白质组学的标本失活方法──辐射、化学和热处理对下游血清分析的比较。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-19 DOI: 10.1021/acs.jproteome.5c00290
Brooke N. Genovese, , , Nistara Randhawa, , , Gabriela Grigorean, , , Tracy Drazenovich, , , Brett S. Phinney, , , Koen K. A. Van Rompay, , , JoAnn Yee, , , Jonna A. K. Mazet, , and , Brian H. Bird*, 
{"title":"Specimen Inactivation Methods for Proteomics─Comparisons of Irradiation, Chemical, and Heat Treatments on Downstream Serum Analyses","authors":"Brooke N. Genovese,&nbsp;, ,&nbsp;Nistara Randhawa,&nbsp;, ,&nbsp;Gabriela Grigorean,&nbsp;, ,&nbsp;Tracy Drazenovich,&nbsp;, ,&nbsp;Brett S. Phinney,&nbsp;, ,&nbsp;Koen K. A. Van Rompay,&nbsp;, ,&nbsp;JoAnn Yee,&nbsp;, ,&nbsp;Jonna A. K. Mazet,&nbsp;, and ,&nbsp;Brian H. Bird*,&nbsp;","doi":"10.1021/acs.jproteome.5c00290","DOIUrl":"10.1021/acs.jproteome.5c00290","url":null,"abstract":"<p >Multiomic techniques, including proteomics, can provide novel insights for both pathogen detection and assessment of host responses to infection. Numerous studies have described the efficacy of heat inactivation, γ irradiation, or treatment with guanidinium-based chaotropic salts (e.g., TRIzol) for pathogen inactivation of biological samples to ensure biosafety and biosecurity. However, the effect of these methods on the greater serum proteome is less studied. Here, we sought to comprehensively measure the effects of four routinely used pathogen inactivation methods on the serum proteome of Rhesus macaques by characterizing the serum proteome pre-and-post inactivation treatment. Using the R-package MS-DAP for statistical benchmarking, our analysis revealed distinct changes in total peptide/protein detection and individual protein abundances (e.g., ALB, APOA1, and CRP) across inactivation methods and compared to their untreated controls. Specifically, we observed improved quantitative reproducibility in γ-irradiated samples across biological, technical, and experimental replicates compared to chemical inactivation and different heat combinations. These findings represent the first direct, experimental comparisons of effective pathogen inactivation methods on the serologic profiles of nonhuman primates and provide useful criteria for evaluating methods for biological specimen inactivation prior to proteomic analysis.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5282–5291"},"PeriodicalIF":3.6,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.5c00290","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084512","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
Investigate the Insoluble Fraction in Heart Tissue Preparation after Deoxycholate for Potential Loss of Proteins in Heart Proteomics 研究脱氧胆酸后心脏组织制备中的不溶性部分对心脏蛋白质组学中潜在蛋白质损失的影响。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-18 DOI: 10.1021/acs.jproteome.5c00333
Soroush Torkamannejad, , , Hoi-ying Yip, , and , Bingyun Sun*, 
{"title":"Investigate the Insoluble Fraction in Heart Tissue Preparation after Deoxycholate for Potential Loss of Proteins in Heart Proteomics","authors":"Soroush Torkamannejad,&nbsp;, ,&nbsp;Hoi-ying Yip,&nbsp;, and ,&nbsp;Bingyun Sun*,&nbsp;","doi":"10.1021/acs.jproteome.5c00333","DOIUrl":"10.1021/acs.jproteome.5c00333","url":null,"abstract":"<p >The heart proteome has been intensively characterized because of its ability to elucidate the molecular mechanisms involved in normal development and disease pathology. Human heart tissue, however, poses unique challenges for proteomic sample preparation, because of the abundance of cardiac myofibrils, which contain some of the largest proteins in the human proteome and are difficult to solubilize. We investigated the insoluble fraction after the use of a popular sodium deoxycholate (SDC) detergent to aid in the solubilization of proteins in human ventricular homogenates to prevent potential protein loss. To bring potential proteins from the insoluble fractions into solution, we investigated the effect of digestion-aided protein solubilization (DAPS). To facilitate downstream data analysis, we demonstrated the possibility of using spectral counting, a facile and flexible label-free quantitation scheme, to quantify proteins identified in a variety of tissue fractions with drastically different matrix backgrounds. Among the differentially distributed proteins and peptides, we discovered that large sarcomere proteins, represented by titin and myosin heavy chains, were enriched in the insoluble fraction of SDC, and our strategy resolved a more comprehensive sarcomere proteome. In addition, acid precipitation of SDC preferentially resulted in the loss of hydrophobic peptides, which might not be significant for identification, but is crucial for quantitation in proteomics.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5046–5055"},"PeriodicalIF":3.6,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079154","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
Identification of Potential Salivary Biomarkers and Enriched Protein Domain/Motif Families for Early Detection and Lymph Node Invasion in OSCC Patients of the Indian Population 印度人群OSCC患者早期检测和淋巴结侵袭的潜在唾液生物标志物和富集蛋白结构域/基元家族的鉴定
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-18 DOI: 10.1021/acs.jproteome.5c00587
Avinash Singh, , , Pratibha Sharma, , , Aditi Balasubramani, , , Sathwik Prakash Shetty, , , Sudesh Roy, , , Subhash Beloor Vasudeva, , , Seema Patil, , , Richa Vaish, , , Sudhir Nair, , and , Sanjeeva Srivastava*, 
{"title":"Identification of Potential Salivary Biomarkers and Enriched Protein Domain/Motif Families for Early Detection and Lymph Node Invasion in OSCC Patients of the Indian Population","authors":"Avinash Singh,&nbsp;, ,&nbsp;Pratibha Sharma,&nbsp;, ,&nbsp;Aditi Balasubramani,&nbsp;, ,&nbsp;Sathwik Prakash Shetty,&nbsp;, ,&nbsp;Sudesh Roy,&nbsp;, ,&nbsp;Subhash Beloor Vasudeva,&nbsp;, ,&nbsp;Seema Patil,&nbsp;, ,&nbsp;Richa Vaish,&nbsp;, ,&nbsp;Sudhir Nair,&nbsp;, and ,&nbsp;Sanjeeva Srivastava*,&nbsp;","doi":"10.1021/acs.jproteome.5c00587","DOIUrl":"10.1021/acs.jproteome.5c00587","url":null,"abstract":"<p >Oral squamous cell carcinoma (OSCC) is a major public health concern in India, ranking first in cancer-related mortality among men and fourth among women, causing about nine deaths per hour. Despite advances in clinical management, prognosis remains poor due to late-stage detection and a lack of reliable biomarkers for early diagnosis and disease monitoring. This study aimed to identify salivary biomarkers and enriched protein domain/motif families for early OSCC detection and progression assessment, including lymph node invasion, in the Indian population. Using diaPASEF-based comparative salivary proteomics, 45 saliva samples from healthy individuals, premalignant lesions (PM), and OSCC patients (with/without nodal invasion) were analyzed and validated through public data sets and targeted proteomics. A total of 1068 proteins were identified, with significant differential expression across disease stages. Enriched domain/motif families included ITIs, lipocalins, calcium-binding EF-hand motifs, SERine Proteinase Inhibitors (SERPINs), trypsin-like serine proteases, and annexin repeats. Functional enrichment revealed pathways related to endopeptidase regulation, wound healing, and calcium ion binding. Key multiclass biomarkers, NUCB2, ITIH4, ITIH2, RBP4, CALU, and SDF4, achieved area under the curve (AUC) &gt; 0.7 in receiver operating characteristic (ROC) models across our data, The Cancer Genome Atlas (TCGA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC), and were validated using parallel reaction monitoring (PRM). These findings highlight novel non-invasive salivary biomarkers with potential for early OSCC detection and lymph node invasion prediction.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5204–5215"},"PeriodicalIF":3.6,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079146","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
Identification of Colorectal Cancer-Associated Protein Signatures in Small Extracellular Vesicles Based on Proteomics 基于蛋白质组学的细胞外小泡结直肠癌相关蛋白特征鉴定
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-17 DOI: 10.1021/acs.jproteome.5c00509
Xiaoqing Ding*, , , Xuan Huang, , , Junfeng Jiang, , , Shuang Han, , , Yanjun Zhou, , , Zhonghu Bai*, , and , Fang Gong*, 
{"title":"Identification of Colorectal Cancer-Associated Protein Signatures in Small Extracellular Vesicles Based on Proteomics","authors":"Xiaoqing Ding*,&nbsp;, ,&nbsp;Xuan Huang,&nbsp;, ,&nbsp;Junfeng Jiang,&nbsp;, ,&nbsp;Shuang Han,&nbsp;, ,&nbsp;Yanjun Zhou,&nbsp;, ,&nbsp;Zhonghu Bai*,&nbsp;, and ,&nbsp;Fang Gong*,&nbsp;","doi":"10.1021/acs.jproteome.5c00509","DOIUrl":"10.1021/acs.jproteome.5c00509","url":null,"abstract":"<p >The clinical management of colorectal cancer (CRC) urgently requires more accurate serum protein biomarkers. While conventional proteomic approaches are hindered by the high abundance of resident blood proteins, this study utilized a highly sensitive four-dimensional label-free quantitative (4D-LFQ) proteomic strategy to analyze the protein cargo of small extracellular vesicles (sEVs). We purified sEVs via ultracentrifugation from pooled serum samples of 76 CRC patients and 40 healthy controls, alongside seven paired CRC tumors and adjacent normal tissues. A total of 1187 high-confidence proteins were identified in serum sEVs using 4D-LFQ analysis. Validation in an independent cohort using four-dimensional parallel reaction monitoring (4D-PRM) confirmed the significant elevation of six candidate proteins (ANXA11, ANXA5, CALR, KPNB1, OIT3, and OLFM4) in CRC sEVs. These candidates exhibited strong diagnostic performance (AUCs 0.769 – 0.869). Crucially, in early-stage CRC, the sEV candidate proteins were significantly elevated compared to controls (<i>p</i> &lt; 0.001), whereas conventional markers CEA and CA19-9 failed to discriminate (<i>p</i> &gt; 0.05). A logistic regression model combining the five available sEV proteins and two conventional markers demonstrated 78.26% sensitivity and 96.67% specificity for early detection (AUC = 0.961). Our findings nominate these sEV protein signatures as promising noninvasive biomarkers for CRC diagnosis.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5127–5138"},"PeriodicalIF":3.6,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074050","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
Differentiating Gastric Cancers from Acid Peptic Diseases through Integrative Targeted Proteomics and Machine Learning Approaches 通过综合靶向蛋白质组学和机器学习方法区分胃癌和酸性消化性疾病。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-17 DOI: 10.1021/acs.jproteome.5c00547
Poornima Ramesh, , , Shubham Sukerndeo Upadhyay, , , Sonet Daniel Thomas, , , Chandrashekar Jeevaraj Sorake, , , Ganesh M. K., , , Vijith Vittal Shetty, , , Prashant Kumar Modi, , , Rohan Shetty, , , Manavalan Vijayakumar, , , Jalaluddin Akbar Kandel Codi*, , and , Thottethodi Subrahmanya Keshava Prasad*, 
{"title":"Differentiating Gastric Cancers from Acid Peptic Diseases through Integrative Targeted Proteomics and Machine Learning Approaches","authors":"Poornima Ramesh,&nbsp;, ,&nbsp;Shubham Sukerndeo Upadhyay,&nbsp;, ,&nbsp;Sonet Daniel Thomas,&nbsp;, ,&nbsp;Chandrashekar Jeevaraj Sorake,&nbsp;, ,&nbsp;Ganesh M. K.,&nbsp;, ,&nbsp;Vijith Vittal Shetty,&nbsp;, ,&nbsp;Prashant Kumar Modi,&nbsp;, ,&nbsp;Rohan Shetty,&nbsp;, ,&nbsp;Manavalan Vijayakumar,&nbsp;, ,&nbsp;Jalaluddin Akbar Kandel Codi*,&nbsp;, and ,&nbsp;Thottethodi Subrahmanya Keshava Prasad*,&nbsp;","doi":"10.1021/acs.jproteome.5c00547","DOIUrl":"10.1021/acs.jproteome.5c00547","url":null,"abstract":"<p >Gastric cancers (GCs) are often diagnosed in advanced stages owing to nonspecific early symptoms resembling Acid Peptic Diseases (APDs). Despite recent efforts, a simple, liquid biopsy-based multiprotein panel prediagnostic assay capable of differentiating GCs from APDs is lacking. Mass spectrometry (MS)-based targeted proteomics methods, including Multiple Reaction Monitoring (MRM), are utilized as the method of choice to develop Laboratory Developed Tests (LDTs) that revolutionize GC early diagnosis and screening. In this study, a 22-min MS-MRM LDT was developed and tested to quantify a serum protein panel in 135 serum samples from treatment-naive cases of GCs, APDs, and healthy individuals. Notably, a novel Deep Neural Network (DNN)-based pattern recognition scoring architecture, integrated with a model explainability tool (SHAP), was developed to score and categorize GCs. The MRM-MS assay produced minimal carryover and matrix effects, with adequate limits of detection/quantification. Quantities of SAA1 and IGFBP2, as determined through ELISA, demonstrated similar sensitivity compared to the LDT. Importantly, the DNN-based scoring architecture efficiently differentiated GCs from the rest of the samples (AUROC = 0.95), with average precision marking &gt;0.90 and minimal bias in protein expression affecting model performance. This LDT can serve as a prediagnostic screening method to distinguish GCs from APDs, guiding clinicians and patients in proceeding with a confirmatory diagnosis.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5159–5176"},"PeriodicalIF":3.6,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074097","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
High-Intensity Focused Ultrasound Elevates Il-2rb on CD8+ T Cells: Enhancing JAK-STAT and IL-2 Efficacy in Triple-Negative Breast Cancer 高强度聚焦超声提高CD8+ T细胞上的Il-2rb:增强三阴性乳腺癌中JAK-STAT和IL-2的疗效
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-17 DOI: 10.1021/acs.jproteome.5c00583
Qihuan Fu, , , Hang Zhou, , , Xinzhi Xu, , , Yujie Wan, , , Ying Li, , , Kaifeng Huang, , , Jiaqi Gong, , , Jia Tang, , , Qizhi Wang, , , Yizhe Zhong, , , Na Wang, , , Jiangbei Yuan*, , and , Fang Li*, 
{"title":"High-Intensity Focused Ultrasound Elevates Il-2rb on CD8+ T Cells: Enhancing JAK-STAT and IL-2 Efficacy in Triple-Negative Breast Cancer","authors":"Qihuan Fu,&nbsp;, ,&nbsp;Hang Zhou,&nbsp;, ,&nbsp;Xinzhi Xu,&nbsp;, ,&nbsp;Yujie Wan,&nbsp;, ,&nbsp;Ying Li,&nbsp;, ,&nbsp;Kaifeng Huang,&nbsp;, ,&nbsp;Jiaqi Gong,&nbsp;, ,&nbsp;Jia Tang,&nbsp;, ,&nbsp;Qizhi Wang,&nbsp;, ,&nbsp;Yizhe Zhong,&nbsp;, ,&nbsp;Na Wang,&nbsp;, ,&nbsp;Jiangbei Yuan*,&nbsp;, and ,&nbsp;Fang Li*,&nbsp;","doi":"10.1021/acs.jproteome.5c00583","DOIUrl":"10.1021/acs.jproteome.5c00583","url":null,"abstract":"<p >Triple-negative breast cancer (TNBC) is characterized by a lack of effective targeted therapies and a challenging immunosuppressive microenvironment that limits the efficacy of immunotherapy. This study explores the potential of high-intensity focused ultrasound (HIFU) in modulating the immune response. Using the 4T1 mouse tumor model, we assessed the effects of thermal (T-HIFU) and mechanical (M-HIFU) HIFU on CD8+ T cells. Proteomic analysis revealed that T-HIFU and M-HIFU increased Il-2rb expression on CD8+ T cells, activating the JAK-STAT pathway and enhancing the efficacy of IL-2, leading to improved tumor growth inhibition and survival rates. The combination of HIFU and IL-2 demonstrated synergistic antitumor effects, indicating a new strategy for enhancing immunotherapy in TNBC. This approach uniquely boosts antitumor immunity by upregulating Il-2rb on CD8+ T cells, offering a promising avenue for overcoming the immunosuppression in TNBC.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5190–5203"},"PeriodicalIF":3.6,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145073984","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
PAMPA: A Software for Peptide Markers and Taxonomic Identification for ZooMS Samples in Archaeology and Paleontology PAMPA:一个用于考古和古生物学缩放样本的肽标记和分类鉴定的软件。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-15 DOI: 10.1021/acs.jproteome.5c00389
Fabrice Bray,  and , Hélène Touzet*, 
{"title":"PAMPA: A Software for Peptide Markers and Taxonomic Identification for ZooMS Samples in Archaeology and Paleontology","authors":"Fabrice Bray,&nbsp; and ,&nbsp;Hélène Touzet*,&nbsp;","doi":"10.1021/acs.jproteome.5c00389","DOIUrl":"10.1021/acs.jproteome.5c00389","url":null,"abstract":"<p >ZooMS (Zooarcheology by Mass Spectrometry) is a rapid and cost-effective method for species identification of animal remains through peptide mass fingerprinting. After mass spectrum generation, a common way to perform taxonomic identification is to compare the mass fingerprints to a reference database of diagnostic peptide markers to determine the species of origin. This analytical stage, however, is tedious and error-prone, often necessitating a manual examination of spectra. In this article, we present a comprehensive approach to automate and standardize the usage of peptide markers and the classification of ZooMS spectra. We have developed software called PAMPA (protein analysis by mass spectrometry for ancient species), for which we demonstrate the effectiveness using a variety of spectral data from bone samples generated by MALDI-TOF and MALDI-FTICR. PAMPA is open source and comes with a database of peptide markers and a collection of curated COL1A1 and COL1A2 sequences. We believe it will be a valuable resource for the scientific community.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"5011–5025"},"PeriodicalIF":3.6,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145062876","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
Molecular Profiling of Belumosudil-Treated IOMM-Lee Meningioma Cells Reveals Repurposing Potential via Enhanced Oxidative Phosphorylation and ROS-Mediated Cell Death belumosudil处理的IOMM-Lee脑膜瘤细胞的分子谱揭示了通过增强氧化磷酸化和ros介导的细胞死亡的再利用潜力。
IF 3.6 2区 生物学
Journal of Proteome Research Pub Date : 2025-09-13 DOI: 10.1021/acs.jproteome.5c00262
Ankit Halder, , , Archisman Maitra, , , Diksha Attrish, , , Adrita Saha, , , Deeptarup Biswas, , , Bhavuk Dhamija, , , Rahul Purwar, , and , Sanjeeva Srivastava*, 
{"title":"Molecular Profiling of Belumosudil-Treated IOMM-Lee Meningioma Cells Reveals Repurposing Potential via Enhanced Oxidative Phosphorylation and ROS-Mediated Cell Death","authors":"Ankit Halder,&nbsp;, ,&nbsp;Archisman Maitra,&nbsp;, ,&nbsp;Diksha Attrish,&nbsp;, ,&nbsp;Adrita Saha,&nbsp;, ,&nbsp;Deeptarup Biswas,&nbsp;, ,&nbsp;Bhavuk Dhamija,&nbsp;, ,&nbsp;Rahul Purwar,&nbsp;, and ,&nbsp;Sanjeeva Srivastava*,&nbsp;","doi":"10.1021/acs.jproteome.5c00262","DOIUrl":"10.1021/acs.jproteome.5c00262","url":null,"abstract":"<p >Meningioma is the most prevalent primary brain tumor. The aggressive forms of the tumor pose a major challenge to clinicians, as it becomes difficult to eradicate them surgically. This has necessitated a concerted effort to explore novel therapeutic candidates. A multiomics-based pathway analysis, followed by drug repurposing, was undertaken to identify a suitable drug candidate that could potentially be used to control proliferation. Multiomics analysis indicates that IOMM-Lee (high-grade meningioma) cells show enhanced oxidative phosphorylation and ROS-mediated cell-death upon treatment with belumosudil, an FDA-approved Rho kinase inhibitor. Dysregulation of key pathways, including Wnt, p53, and phosphoinositol signaling, was also observed. It suggests that the drug treatment induces a ROS-rich environment, primarily affecting the nucleus and mitochondria. The cellular metabolome also shows an increase in lipid peroxidation product in concordance to an increase in ROS production. The intracellular and mitochondrial ROS concentrations have also been found to be increased with FACS-based assays. The efficacy of belumosudil observed in the cell-line-based study opens up the possibility of advancing to the next stages of <i>in vivo</i> studies and clinical trials for its use in the treatment of high-grade meningioma, either as a standalone therapy or in combination with other therapeutics.</p>","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"24 10","pages":"4935–4951"},"PeriodicalIF":3.6,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145051412","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}
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