ACS Publications最新文献_第3页

Analysis of Stratifin Expression and Proteome Variation in a Rat Model of Acute Lung Injury.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-02-28 DOI: 10.1021/acs.jproteome.4c00980

Ayaka Yoshida, Yuya Hashimoto, Hirotoshi Akane, Shinichiro Matsuyama, Takeshi Toyoda, Kumiko Ogawa, Yoshiro Saito, Ruri Kikura-Hanajiri, Noriaki Arakawa

{"title":"Analysis of Stratifin Expression and Proteome Variation in a Rat Model of Acute Lung Injury.","authors":"Ayaka Yoshida, Yuya Hashimoto, Hirotoshi Akane, Shinichiro Matsuyama, Takeshi Toyoda, Kumiko Ogawa, Yoshiro Saito, Ruri Kikura-Hanajiri, Noriaki Arakawa","doi":"10.1021/acs.jproteome.4c00980","DOIUrl":"10.1021/acs.jproteome.4c00980","url":null,"abstract":"Diffuse alveolar damage (DAD) is a pathological hallmark of severe interstitial lung diseases, such as acute respiratory distress syndrome (ARDS), and is linked to poor prognosis. Previously, we identified 14-3-3σ/stratifin (SFN) as a serum biomarker candidate for diagnosing DAD. To clarify the time-dependent relationship between SFN expression and DAD, we here investigated pathological and molecular changes in serum, bronchoalveolar lavage fluid (BALF), and lung tissue in an oleic acid (OA)-induced ARDS rat model. Acute alveolar edema was observed after OA administration, followed by alveolar epithelial cell proliferation and increased BALF and serum SFN levels. Proteomic analysis of lung tissue extracts revealed that proteins related to \"inflammatory response\" and \"HIF-1 signaling,\" including plasminogen activator inhibitor-1, were markedly increased 3 h after acute lung injury, followed by a gradual decrease. Conversely, proteins associated with \"cell cycle\" and \"p53 pathway,\" including SFN, showed a persistent increase starting at 3 h and peaking at 48 h. Western blotting and immunohistochemistry confirmed that SFN was expressed in a part of proliferated alveolar type-II cells, accompanied by p53 activation, an important event for differentiation into type-I cells. SFN may be a biomarker closely related to alveolar remodeling during the repair process after lung injury.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1941-1955"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530888","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

Cell Storage Conditions Impact Single-Cell Proteomic Landscapes.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-01-24 DOI: 10.1021/acs.jproteome.4c00632

Bora Onat, Amanda Momenzadeh, Ali Haghani, Yuming Jiang, Yang Song, Sarah J Parker, Jesse G Meyer

{"title":"Cell Storage Conditions Impact Single-Cell Proteomic Landscapes.","authors":"Bora Onat, Amanda Momenzadeh, Ali Haghani, Yuming Jiang, Yang Song, Sarah J Parker, Jesse G Meyer","doi":"10.1021/acs.jproteome.4c00632","DOIUrl":"10.1021/acs.jproteome.4c00632","url":null,"abstract":"Single cell transcriptomics (SCT) has revolutionized our understanding of cellular heterogeneity, yet the emergence of single cell proteomics (SCP) promises a more functional view of cellular dynamics. A challenge is that not all mass spectrometry facilities can perform SCP, and not all laboratories have access to cell sorting equipment required for SCP, which together motivate an interest in sending bulk cell samples through the mail for sorting and SCP analysis. Shipping requires cell storage, which has an unknown effect on SCP results. This study investigates the impact of cell storage conditions on the proteomic landscape at the single cell level, utilizing Data-Independent Acquisition (DIA) coupled with Parallel Accumulation Serial Fragmentation (diaPASEF). Three storage conditions were compared in 293T cells: (1) 37 °C (control), (2) 4 °C overnight, and (3) -196 °C storage followed by liquid nitrogen preservation. Both cold and frozen storage induced significant alterations in the cell diameter, elongation, and proteome composition. By elucidating how cell storage conditions alter cellular morphology and proteome profiles, this study contributes foundational technical information about SCP sample preparation and data quality.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1586-1595"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143035360","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

Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-10 DOI: 10.1021/acs.jproteome.4c00943

Taojunfeng Su, Ryan T Fellers, Joseph B Greer, Richard D LeDuc, Paul M Thomas, Neil L Kelleher

{"title":"Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics.","authors":"Taojunfeng Su, Ryan T Fellers, Joseph B Greer, Richard D LeDuc, Paul M Thomas, Neil L Kelleher","doi":"10.1021/acs.jproteome.4c00943","DOIUrl":"10.1021/acs.jproteome.4c00943","url":null,"abstract":"Proteoforms are distinct molecular forms of proteins that act as building blocks of organisms, with post-translational modifications (PTMs) being one of the key changes that generate these variations. Mass spectrometry (MS)-based top-down proteomics (TDP) is the leading technology for proteoform identification due to its preservation of intact proteoforms for analysis, making it well-suited for comprehensive PTM characterization. A crucial step in TDP is searching MS data against a database of candidate proteoforms. To extend the reach of TDP to organisms with limited PTM annotations, we developed Proteoform-predictor, an open-source tool that integrates homology-based PTM site prediction into proteoform database creation. The new tool creates databases of proteoform candidates after registration of homologous sequences, transferring PTM sites from well-characterized species to those with less comprehensive proteomic data. Our tool features a user-friendly interface and intuitive workflow, making it accessible to a wide range of researchers. We demonstrate that Proteoform-predictor expands proteoform databases with tens of thousands of proteoforms for three bacterial strains by comparing them to the reference proteome of Escherichia coli (E. coli) K12. Subsequent TDP analysis for Serratia marcescens (S. marcescens) and Salmonella typhimurium (S. typhimurium) demonstrated significant improvement in protein and proteoform identification, even for proteins with variant sequences. As TDP technology advances, Proteoform-predictor will become an important tool for expanding the applicability of proteoform identification and PTM biology to more diverse species across the phylogenetic tree of life.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1861-1870"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143583948","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

Normalized and Directional Interplay Scoring for the Interrogation of Proteoform Data.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-02-28 DOI: 10.1021/acs.jproteome.4c00877

Karl F Poncha, Alyssa T Paparella, Nicolas L Young

{"title":"Normalized and Directional Interplay Scoring for the Interrogation of Proteoform Data.","authors":"Karl F Poncha, Alyssa T Paparella, Nicolas L Young","doi":"10.1021/acs.jproteome.4c00877","DOIUrl":"10.1021/acs.jproteome.4c00877","url":null,"abstract":"Histone proteoforms, often presenting multiple co-occurring post-translational modifications (PTMs), are central to chromatin regulation and gene expression. A proteoform is a specific form of a protein that includes variations arising from genetic changes, alternative RNA splicing, proteolytic processing, and PTMs. Genome-indexed histone proteoforms define the histone code, influencing cellular phenotype by dictating DNA interacting partners. Understanding the dynamics of histone proteoforms is essential for elucidating chromatin-based regulatory mechanisms. Advances in middle-down and top-down proteomics enable accurate identification and quantitation of thousands of proteoforms in a single run. However, the resulting data complexity presents significant challenges for analysis and visualization. Here, we introduce two new computational methods to analyze the dynamics of histone PTMs and demonstrate their use in mouse organs during aging. The score that we term \"normalized interplay\" addresses limitations of the original crosstalk score \"interplay\" providing a more complete and accurate measure of PTM crosstalk. The second score, ΔI or \"directional interplay\" is an asymmetric measure quantifying the magnitude and directionality of crosstalk between PTMs. Applying our two-stage scoring approach to data from CrosstalkDB reveals the dynamics of histone H3 modifications during aging.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1765-1777"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143527836","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

Tumor Antigen-Coated Two-Dimensional Black Phosphorus as a Nanovaccine for Synergistic Cancer Photothermal Therapy and Immunotherapy.

IF 4.6

ACS Applied Bio Materials Pub Date : 2025-04-04 DOI: 10.1021/acsabm.5c00229

Xuanying Liang, Genquan Wu, Ruixuan Chen, Xintong Lin, Jiansheng Xu, Wenjie Sun, Benqing Zhou

{"title":"Tumor Antigen-Coated Two-Dimensional Black Phosphorus as a Nanovaccine for Synergistic Cancer Photothermal Therapy and Immunotherapy.","authors":"Xuanying Liang, Genquan Wu, Ruixuan Chen, Xintong Lin, Jiansheng Xu, Wenjie Sun, Benqing Zhou","doi":"10.1021/acsabm.5c00229","DOIUrl":"https://doi.org/10.1021/acsabm.5c00229","url":null,"abstract":"Vaccine immunotherapy is paving the way for an effective long-term immune response and targeted destruction of tumor cells and shows promise as a leading strategy in tumor treatment. Nanoparticles are crucial in combining vaccine immunotherapy and photothermal therapy (PTT), generating local tumor thermal ablation, and triggering a powerful antitumor immune response that inhibits tumor recurrence. In this study, we designed a nanovaccine that combined PTT and immunotherapy for tumors using two-dimensional black phosphorus (BP) as a nanoplatform that was modified with maleimide poly(ethylene glycol) (PEG-MAL) and coated with tumor antigen proteins (BP-PEG-MAL@antigen). The BP-PEG-MAL@antigen nanovaccines displayed outstanding stability and biocompatibility due to the comodification of PEG and antigen proteins. The nanovaccines induced strong immune responses in vitro and in vivo that effectively inhibited orthotopic and bilateral tumor growth, prolonged survival time, and improved the survival rate of mice. In addition, the nanovaccines generated a long-term immune response and effectively inhibited tumor recurrence.","PeriodicalId":2,"journal":{"name":"ACS Applied Bio Materials","volume":" ","pages":""},"PeriodicalIF":4.6,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Palladium-Catalyzed Transfer Iodination from Aryl Iodides to Nonactivated C(sp³)-H Bonds.

IF 14.4 1区化学

Journal of the American Chemical Society Pub Date : 2025-04-04 DOI: 10.1021/jacs.5c02553

Emilien Le Saux, Bill Morandi

引用次数: 0

Sex-Specific Markers of Neuroinflammation and Neurodegeneration in the Spinal Cord Proteome of the SOD1^G93A Mouse Model of Amyotrophic Lateral Sclerosis.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-21 DOI: 10.1021/acs.jproteome.4c00990

Liam M Koehn, Joel R Steele, Ralf B Schittenhelm, Joseph A Nicolazzo

{"title":"Sex-Specific Markers of Neuroinflammation and Neurodegeneration in the Spinal Cord Proteome of the SOD1G93A Mouse Model of Amyotrophic Lateral Sclerosis.","authors":"Liam M Koehn, Joel R Steele, Ralf B Schittenhelm, Joseph A Nicolazzo","doi":"10.1021/acs.jproteome.4c00990","DOIUrl":"10.1021/acs.jproteome.4c00990","url":null,"abstract":"Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder that has no cure. The underlying mechanistic details of sex differences in the ALS spinal cord, the site of disease onset, are not understood to an extent that could guide novel drug development. To address this, the spinal cords of 120-day-old wild-type (WT) and SOD1G93A (familial mouse model of ALS with mutant superoxide dismutase 1) mice were subjected to untargeted, quantitative proteomics using tandem mass tag acquisition on high-resolution mass spectrometric instrumentation. Compared to WT, both male and female SOD1G93A spinal cords exhibited an upregulation of neuroinflammatory cascades of both peripheral and central origins, as well as a downregulation of proteins reflective of death and dysfunction of cells within the spinal cord. However, female and male SOD1G93A mouse spinal cords exhibited sex-specific differences in proteins compared to respective WT that related to immune response, as well as cellular structure, function, and homeostasis. The proteomic datasets presented provide entire cohort and sex-specific spinal cord drug targets and disease biomarkers in the SOD1G93A mouse model of ALS that may guide future drug development and sex selection in preclinical study designs utilizing the SOD1G93A model.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1956-1970"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672928","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

ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-22 DOI: 10.1021/acs.jproteome.4c00967

Firas Hamood, Wassim Gabriel, Pia Pfeiffer, Bernhard Kuster, Mathias Wilhelm, Matthew The

引用次数: 0

Candida albicans: A Comprehensive View of the Proteome.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-14 DOI: 10.1021/acs.jproteome.4c01020

Leticia Gomez-Artiguez, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, Lucía Monteoliva, Robert L Moritz, Eric W Deutsch, Concha Gil

{"title":"Candida albicans: A Comprehensive View of the Proteome.","authors":"Leticia Gomez-Artiguez, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, Lucía Monteoliva, Robert L Moritz, Eric W Deutsch, Concha Gil","doi":"10.1021/acs.jproteome.4c01020","DOIUrl":"10.1021/acs.jproteome.4c01020","url":null,"abstract":"We describe a new release of the Candida albicans PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively. We provide a tutorial on how to use the PeptideAtlas and associated tools to access this information. The C. albicans PeptideAtlas summary web page provides \"Build overview\", \"PTM coverage\", \"Experiment contribution\", and \"Data set contribution\" information. The protein and peptide information can also be accessed via the Candida Genome Database via hyperlinks on each protein page. This allows users to peruse identified peptides, protein coverage, post-translational modifications (PTMs), and experiments that identify each protein. Given the value of understanding the PTM landscape in the sequence of each protein, a more detailed explanation of how to interpret and analyze PTM results is provided in the PeptideAtlas of this important pathogen. Candida albicans PeptideAtlas web page: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1636-1648"},"PeriodicalIF":3.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622880","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

HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX-MS Data.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-04-04 Epub Date: 2025-03-19 DOI: 10.1021/acs.jproteome.4c00700

Weronika Puchała, Michał Kistowski, Liliya Zhukova, Michał Burdukiewicz, Michał Dadlez

引用次数: 0