Proteomics最新文献_第3页

Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-21 DOI: 10.1002/pmic.202400455

Sneha Parmar, Nathan R. Zuniga, Valentina Rossio, Xinyue Liu, Joao A. Paulo

{"title":"Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae","authors":"Sneha Parmar, Nathan R. Zuniga, Valentina Rossio, Xinyue Liu, Joao A. Paulo","doi":"10.1002/pmic.202400455","DOIUrl":"https://doi.org/10.1002/pmic.202400455","url":null,"abstract":"<div>\u0000 \u0000 The regulation of cell cycle progression in response to environmental cues is essential for cellular adaptation. In Saccharomyces cerevisiae, the BAR1 gene modulates sensitivity to the mating pheromone α-factor, which induces cell cycle arrest in G1. Here, we investigated the dynamic proteomic response in the bar1 deletion strain using a 27-plex experimental design with TMTproD isobaric labeling. Asynchronous bar1Δ cells were treated with α-factor and then released from the pheromone-induced cell cycle arrest in G1. Using higher-order TMTpro sample multiplexing, we generated global temporal profiles of protein abundance associated with recovery from this arrest, with triplicate samples collected at eight time points from 0 to 165 min after washing out the pheromone. We identify specific proteins involved in cell cycle re-entry and in the attenuation of the pheromone signal, providing insights into the regulatory mechanisms of mating response in yeast. This study also contributes significantly to dynamic proteomic analysis of cell cycle progression. We present a versatile approach for investigating complex cellular processes and showcase cell cycle progression following release from pheromone-induced arrest in yeast.\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 9-10","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945041","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

Cross-Species Molecular Similarities Based on Omics Approaches in CKD: Toward Improved Translation From Pre-Clinical Models to Humans. 基于组学方法的CKD跨物种分子相似性：从临床前模型到人类的改进翻译。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-21 DOI: 10.1002/pmic.202400136

Raquel María García-Sáez, Mariano Rodríguez

{"title":"Cross-Species Molecular Similarities Based on Omics Approaches in CKD: Toward Improved Translation From Pre-Clinical Models to Humans.","authors":"Raquel María García-Sáez, Mariano Rodríguez","doi":"10.1002/pmic.202400136","DOIUrl":"https://doi.org/10.1002/pmic.202400136","url":null,"abstract":"The prevalence of chronic kidney disease (CKD) is very high, and it is increasing. Obviously, the care is costly. The identification of biomarkers able to predict disease progression is key for optimal patient care. Tissue, blood, and urine omics are being used to discover new biomarkers. It is challenging to compare omics in animal models with that of CKD patients. The main obstacle is the enormous genetic difference between humans and rodents. Although animal models do not fully resemble CKD, there are possibilities to combine pathologies in an attempt to be closer to the human clinical picture. This manuscript describes Zucker rat model that has been modified to better resemble diabetic CKD: obesity, diabetes, cardiovascular disease, and renal function deterioration. This model has been used to evaluate treatments such as the administration of iSGLT2, VitE antioxidant therapy, or Mg supplementation. Plasma proteomics was performed in Nx-Zucker rats, and it was found change in families of proteins similar to those in CKD patients. Unfortunately, urine omics were not performed. It would be a good strategy to gather different research groups with similar aims to develop common strategies to share not only results but also samples obtained in patients and animals to optimize efforts.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400136"},"PeriodicalIF":3.4,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954592","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

Quantitative Top-Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells. 定量自顶向下的蛋白质组学揭示了转移性和非转移性结直肠癌细胞中组蛋白蛋白形态的显著差异。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-17 DOI: 10.1002/pmic.202400336

Fei Fang, Brian Fries, Zhige Wang, Xiaowen Liu, Amanda B Hummon, Liangliang Sun

{"title":"Quantitative Top-Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells.","authors":"Fei Fang, Brian Fries, Zhige Wang, Xiaowen Liu, Amanda B Hummon, Liangliang Sun","doi":"10.1002/pmic.202400336","DOIUrl":"https://doi.org/10.1002/pmic.202400336","url":null,"abstract":"Colorectal cancer (CRC) development is closely associated with the accumulation of both genetic and epigenetic alterations. Many efforts have been made to investigate the role of epigenetic modifications in CRC metastasis. In this work, we present the quantitative top-down proteomics study focusing on histone proteoforms between metastatic (SW620) and nonmetastatic (SW480) CRC cells to reveal potentially critical histone proteoforms in CRC metastasis. We isolated histone proteins from CRC cells, fractionated them by sodium dodecyl-sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE), and analyzed them by capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS). A total of 230 histone proteoforms were quantified in SW480 and SW620 cell lines, among which 34 proteoforms were significantly altered in abundance in the metastatic cells, indicating a significant transformation of histone proteoforms during metastasis. We observed a significant increase in abundance of all nine differentially expressed histone H4 proteoforms in metastatic SW620 cells compared to SW480 cells, while differentially expressed proteoforms of other histone proteins display diversified expression patterns. Additionally, two histone H2A proteoforms with a combination of N-terminal acetylation and phosphorylation were upregulated in the metastatic CRC cells. These differentially expressed histone proteoforms could be novel proteoform biomarkers of CRC metastasis.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400336"},"PeriodicalIF":3.4,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959768","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

Plasticity of Gene Expression in Spaceflight and Postflight in Relation to Cardiovascular Disease: Mechanisms and Candidate Repurposed Drugs. 与心血管疾病相关的航天飞行和飞行后基因表达的可塑性：机制和候选再用途药物。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-14 DOI: 10.1002/pmic.202400241

Marilena M Bourdakou, Eleni M Loizidou, George M Spyrou

{"title":"Plasticity of Gene Expression in Spaceflight and Postflight in Relation to Cardiovascular Disease: Mechanisms and Candidate Repurposed Drugs.","authors":"Marilena M Bourdakou, Eleni M Loizidou, George M Spyrou","doi":"10.1002/pmic.202400241","DOIUrl":"https://doi.org/10.1002/pmic.202400241","url":null,"abstract":"Spaceflight poses unique challenges to human health due to exposure to increased levels of cosmic radiation, microgravity, and associated oxidative stress. These environmental factors can lead to cellular damage, inflammation, and a range of health complications, including cardiovascular problems, immune system impairment, and an increased risk of cancer. Nuclear factor erythroid 2-related factor 2 (NRF2) is a critical transcription factor that regulates the body's defense mechanisms against oxidative stress by promoting the expression of antioxidant enzymes. Recent research has shed more light on the critical role of NRF2 in addressing space-related health challenges. In this study, we developed a computational methodology to explore the plasticity of the gene expression profile in flight and postflight conditions, highlighting the genes and corresponding mechanisms that do not return to ground levels and correlate with gene signatures associated with cardiovascular disease (CVD). RNA sequencing (RNA-seq) data from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have been used to investigate the cellular effects of microgravity on cardiac function. Gene expression monotonicity studies were performed and linked to genome-wide association studies (GWAS) to highlight the monotonically expressed genes associated with CVD. The selected monotonically expressed genes were also mapped onto the NRF2 network to investigate the impact of spaceflight on human cardiomyocyte function in the context of redox signaling pathways. Based on this knowledge, we used computational drug repurposing methods to suggest a short list of repurposed drug candidates that can be further tested in astronauts for the prevention of CVD. This study provides insights into the molecular and redox signaling alterations in cardiomyocytes induced by spaceflight, laying the foundation for future research aimed at mitigating cardiovascular risks in astronauts and advancing clinical applications on Earth.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400241"},"PeriodicalIF":3.4,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954689","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

Peptide Property Prediction for Mass Spectrometry Using AI: An Introduction to State of the Art Models

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-10 DOI: 10.1002/pmic.202400398

Jesse Angelis, Eva Ayla Schröder, Zixuan Xiao, Wassim Gabriel, Mathias Wilhelm

引用次数: 0

Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients. 尿III型胶原降解产物与慢性肾病患者肾功能和纤维化的关系

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-10 DOI: 10.1002/pmic.202400354

Emily M Martin, Federica Genovese, Harald Mischak, Justyna Siwy, Harald Rupprecht, Lorenzo Catanese, Agnieszka Latosinska

{"title":"Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients.","authors":"Emily M Martin, Federica Genovese, Harald Mischak, Justyna Siwy, Harald Rupprecht, Lorenzo Catanese, Agnieszka Latosinska","doi":"10.1002/pmic.202400354","DOIUrl":"https://doi.org/10.1002/pmic.202400354","url":null,"abstract":"A common hallmark of chronic kidney disease (CKD) is kidney fibrosis, which manifests as an increased deposition and turnover of collagens in the kidneys. Current clinical methods of monitoring disease progression in CKD patients do not truly reflect alterations at the tissue level without the use of invasive biopsies. Naturally occurring urinary peptides associated with kidney function and fibrosis have been previously identified using CE-MS as a non-invasive alternative. Moreover, a specific peptide from collagen type III, a highly abundant interstitial collagen, is the target for the C3M enzyme-linked immunosorbent assay (ELISA)-based assay and has been recorded in the CKD273 urinary biomarker panel measured by CE-MS. We aimed to investigate the intensities of the peptides incorporating the C3M sequence captured by CE-MS in urine of patients with CKD and analyze their association with estimated glomerular filtration rate (eGFR) and kidney interstitial fibrosis and tubular atrophy (IFTA). The investigated collagen type III peptides were reduced in abundance in urine of patients with CKD compared to healthy controls and the peptide intensities were independently correlated to eGFR and inversely correlated with IFTA score. Collectively, this analysis supports that peptides containing the C3M sequence are significantly associated with kidney function decline and tissue fibrosis.","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e202400354"},"PeriodicalIF":3.4,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959765","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

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-10 DOI: 10.1002/pmic.202400187

Andrew T. Rajczewski, J. Alfredo Blakeley-Ruiz, Annaliese Meyer, Simina Vintila, Matthew R. McIlvin, Tim Van Den Bossche, Brian C. Searle, Timothy J. Griffin, Mak A. Saito, Manuel Kleiner, Pratik D. Jagtap

{"title":"Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome","authors":"Andrew T. Rajczewski, J. Alfredo Blakeley-Ruiz, Annaliese Meyer, Simina Vintila, Matthew R. McIlvin, Tim Van Den Bossche, Brian C. Searle, Timothy J. Griffin, Mak A. Saito, Manuel Kleiner, Pratik D. Jagtap","doi":"10.1002/pmic.202400187","DOIUrl":"https://doi.org/10.1002/pmic.202400187","url":null,"abstract":"<div>\u0000 \u0000 Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being data-dependent acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-independent acquisition mass spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins. We sought to evaluate the reproducibility and accuracy of DIA-MS metaproteomic measurements relative to DDA-MS using a mock community of known taxonomic composition. Artificial microbial communities of known composition were analyzed independently in three laboratories using DDA- and DIA-MS acquisition methods. In this study, DIA-MS yielded more protein and peptide identifications than DDA-MS in each laboratory for the particular instruments and software parameters chosen. In addition, the protein and peptide identifications were more reproducible in all laboratories and provided an accurate quantification of proteins and taxonomic groups in the samples. We also identified some limitations of current DIA tools when applied to metaproteomic data, highlighting specific needs to improve DIA tools enabling analysis of metaproteomic datasets from complex microbiomes. Ultimately, DIA-MS represents a promising strategy for MS-based metaproteomics due to its large number of detected proteins and peptides, reproducibility, deep sequencing capabilities, and accurate quantitation.\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 9-10","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143944552","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

Proteome Analysis of Corynebacterium diphtheriae-Macrophage Interaction. 白喉棒状杆菌-巨噬细胞相互作用的蛋白质组学分析。

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-10 DOI: 10.1002/pmic.202400317

Luca Musella, Jens Möller, Christopher Lischer, Julio Vera-Gonzalez, Jörg Hofmann, Lisa Ott, Andreas Burkovski

引用次数: 0

Editorial Board: Proteomics 7'25 编辑委员会：蛋白质组学7'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-02 DOI: 10.1002/pmic.202570024

引用次数: 0

Contents: Proteomics 7'25 内容：蛋白质组学7'25

IF 3.4 4区生物学

Proteomics Pub Date : 2025-04-02 DOI: 10.1002/pmic.202570025

引用次数: 0