Journal of proteomics最新文献

{"title":"Differential gene expression networks and auxin responses during maize callus induction from explant tissues with contrasting embryogenic potential","authors":"Vasti T. Juárez-González ,&nbsp;Eduardo Luján-Soto ,&nbsp;Paola I. Aguirre de la Cruz ,&nbsp;Mayra Aquino-Luna ,&nbsp;Jorge Herrera-Díaz ,&nbsp;Brenda A. López-Ruiz ,&nbsp;Tzvetanka D. Dinkova","doi":"10.1016/j.jprot.2025.105457","DOIUrl":"10.1016/j.jprot.2025.105457","url":null,"abstract":"<div><div>Maize somatic embryogenesis process depends on explant characteristics and genotype. The relationship between explant developmental timing and embryogenic potential of derived tissues is still poorly understood. The present work explored the adjustments of transcriptomes and proteomes from explants with contrasting embryogenic potential – immature and mature zygotic embryos from the Tuxpeño VS-535 genotype – during callus induction. Differentially accumulated transcripts and proteins were represented by oxidation/reduction, stress response, and metabolic process adjustments during the dedifferentiation of both explants. However, the explant with high embryogenic potential and derived callus displayed more significant enrichment in cell proliferation and plant hormone signal transduction pathways. Between the differentially accumulated proteins, it is of notice a significantly higher enrichment of catabolic and anoxia processes in non-embryogenic as opposed to anabolic and oxidation-reduction processes in the embryogenic callus induction. Transcription factors such as Auxin Response Factors (ARFs), signal transduction (Homeobox; HB), and embryogenesis-related AP2-EREB mRNAs characterized the immature embryos. Activator and repressor ARFs substantially differed at the early stages of callus induction between immature and mature embryo explants. The overall analysis of these findings helps to understand the molecular basis of gene expression regulation during callus dedifferentiation and auxin responses from maize explants with contrasting embryogenic potential.</div></div><div><h3>Significance</h3><div>This work contributes with overall transcript and protein patterns during the callus induction phase of Mexican landrace Tuxpeño VS-535 maize somatic embryogenesis from immature and mature embryos. Using comparisons between explants, between each explant and the induced callus, and between callus, differential biological process enrichment at transcript and protein levels for the embryogenic callus induction indicated key roles for cell proliferation, hormone signaling and biosynthetic processes for embryogenic callus induction. Furthermore, a battery of TF family enriched in the immature embryo, including several auxin response factors support the differential gene expression reprogramming during dedifferentiation from explants with contrasting embryogenic potential in maize somatic embryogenesis.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"318 ","pages":"Article 105457"},"PeriodicalIF":2.8,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144105231","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}

{"title":"Comparative proteomics uncovers vital molecular players of central nervous system leukemia among Mexican pediatric patients","authors":"Eliel Ruiz-May ,&nbsp;Esaú Bojórquez-Velázquez ,&nbsp;Humberto Carrasco-Vargas ,&nbsp;Silverio Soto-Alvarez ,&nbsp;Laura S. Rangel-Cova ,&nbsp;Marco Antonio Vargas-Hernández ,&nbsp;José M. Elizalde-Contreras ,&nbsp;Víctor M. Torres De La Cruz ,&nbsp;Armando Vilchis-Ordoñez ,&nbsp;Miguel Ángel Palomo-Colli ,&nbsp;Tania Angeles Floriano ,&nbsp;Israel Parra Ortega ,&nbsp;Rosana Pelayo-Camacho ,&nbsp;Lidia F.E. Huerta-Nuñez","doi":"10.1016/j.jprot.2025.105458","DOIUrl":"10.1016/j.jprot.2025.105458","url":null,"abstract":"<div><div>Acute lymphoblastic leukemia (ALL) is the most common pediatric hematologic malignancy. The leukemic cells start in the bone marrow and spread to other vital organs and tissues, including the central nervous system (CNS). Hispanic males are the community with the highest incidence of ALL. Unfortunately, there is limited information on the molecular signatures of leukemic cell infiltration into the CNS, which marks the progression from ALL to central nervous system leukemia (CNSL). To address this knowledge gap, we performed a label-free shotgun proteomics between the cerebrospinal fluid (CSF) from patients with ALL compared to those with confirmed CNSL. We were able to identify 619 proteins, including 340 proteins that had not been reported prevously in the CSF of subjects with CNSL. The major features associated with CNSL included the over-accumulation of cell-adhesion proteins such as L-selectin and several cadherin proteins, along with the modulation of enzymes associated with protein glycosylation, which may provide the appropriate conditions for leukemic cell infiltration into the CNS. The over-accumulation of proteins associated with ROS scavenging processes reveals hypoxic and redox homeostasis microenvironment conditions that favors ALL progression to CNSL. The further characterization of key differential proteins will be essential for establishing reliable molecular markers for CSNL.</div></div><div><h3>Biological significance</h3><div>Central nervous system leukemia (CNSL) is a catastrophic progression of ALL defined by leukemic cells reaching the CNS. Limited comparative proteomics studies have been conducted previously between patients with ALL versus CNSL. While these studies were important pioneering steps, they were hindered by difficulties in obtaining the proper amount of protein samples related to CSF. They were based on minimal study subjects, and their proteomics pipelines did not include the depletion of high-abundance proteins. Defining the manners in which the CNSL proteome is perturbed compared to the ALL condition is paramount to understanding the molecular foundations of CNSL and identifying and characterizing protein markers for proper diagnosis. Improving the sensitivity and reliability of diagnosis using molecular markers would help clinicians to maximize patient outcomes and quality of life by implementing aggressive CNSL treatments as soon as possible in cases where infiltration has occurred, while avoiding exposure to toxic chemotherapies in patients where they are not yet necessary.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"318 ","pages":"Article 105458"},"PeriodicalIF":2.8,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102298","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}

{"title":"Protein digestion, peptide mass and peptide fragmentation with MZCal: A user-friendly phone-compatible application","authors":"Brittannie Willis ,&nbsp;Harry J. Whitwell","doi":"10.1016/j.jprot.2025.105456","DOIUrl":"10.1016/j.jprot.2025.105456","url":null,"abstract":"<div><div>MZCal is a user-friendly, mobile-compatible web application designed for assisting peptide analysis in bottom-up mass spectrometry (MS). There are many tools for basic in-silico digestion, peptide mass and peptide mz calculations, though not in a single, convenient and mobile-friendly format. Since internet availability can often be limited on mass-spectrometry linked computers, we developed MZCal for use in our laboratory, featuring tools that we commonly use in evaluating MS methods for bottom-up proteomics while working at the mass spectrometer. MZCal provides a single platform for in silico protein digestion, peptide mass and fragmentation calculations, and spectral prediction using MS2PIP. Optimised for use on both Android and iOS devices, MZCal enables convenient, real-time mass spectrum interpretation in laboratory settings and as a teaching resource. Unlike more complex web-tools, MZCal offers a streamlined interface that prioritises ease of use and accessibility. Overall, MZCal serves as a practical, portable solution for essential peptide calculations, providing an intuitive and accessible tool for both researchers and educators.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"318 ","pages":"Article 105456"},"PeriodicalIF":2.8,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089244","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}

{"title":"Fecal metaproteomics enables functional characterization of remission in patients with inflammatory bowel disease","authors":"Maximilian Wolf ,&nbsp;Julian Lange ,&nbsp;Dirk Benndorf ,&nbsp;Lina Welz ,&nbsp;Susanna Nikolaus ,&nbsp;Laura Katharina Siever ,&nbsp;Florian Tran ,&nbsp;Kay Schallert ,&nbsp;Patrick Hellwig ,&nbsp;Stefan Schreiber ,&nbsp;Matthias Gunzer ,&nbsp;Philip Rosenstiel ,&nbsp;Udo Reichl ,&nbsp;Timon Adolph ,&nbsp;Almina Jukic ,&nbsp;Konrad Aden ,&nbsp;Robert Heyer","doi":"10.1016/j.jprot.2025.105455","DOIUrl":"10.1016/j.jprot.2025.105455","url":null,"abstract":"<div><div>The gut microbiome is an important contributor to the development and the course of inflammatory bowel disease (IBD). While changes in the gut microbiome composition were observed in response to IBD therapy using biologics, studies elucidating human and microbial proteins and pathways in dependence on therapy success are sparse. Fecal samples of a cohort of IBD patients were collected before and after 14 weeks of treatment with three different biologics. Clinical disease activity scores were used to determine the clinical response and remission. Fecal metaproteomes of remitting patients (<em>n</em> = 12) and of non-remitting patients (n = 12) were compared before treatment and changes within both groups were assessed over sampling time to identify functional changes and potential human and microbial biomarkers. The abundance of proteins associated with neutrophilic granulocytes, and immunoglobulins significantly decreased in remitting patients. There were changes in pathways of microbial metabolism in samples from patients with remission after therapy, including an increased butyrate fermentation. Distinct changes of proteins related to gut inflammation and gut microbiome metabolism showed whether IBD remission was achieved or not. This suggests that metaproteomics could be a useful tool for monitoring remission in IBD therapies.</div></div><div><h3>Significance</h3><div>IBD is rising in incidence, especially in newly industrialized countries, and the microbiome is an important contributor to its pathogenesis. Despite manifold therapeutical options, achieving remission is often ineffective, and choosing new alternative drugs remains often empirical. Therefore, efficient tools for monitoring therapeutic response and assessing the effectiveness of drugs in specific patients are mandatory. In the present study, we show that the use of metaproteomics is a promising avenue to address these challenges. We observed the amelioration of inflammation and restoration of a healthy microbiome in remitting patients in contrast to non-remitting patients. Therefore, metaproteomics is a valuable tool for monitoring the therapy success in IBD.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"318 ","pages":"Article 105455"},"PeriodicalIF":2.8,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012774","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}

{"title":"Detection and identification of highly antigenic proteins from cytoskeleton of Toxoplasma gondii by immune-proteomics","authors":"Noé Lagunas-Cortés ,&nbsp;Brenda Yomara García-Sánchez ,&nbsp;Emmanuel Ríos-Castro ,&nbsp;Marco Antonio Vega-López ,&nbsp;Sirenia González-Pozos ,&nbsp;Rubén Darío Diaz-Martín ,&nbsp;Juan Manuel Carranza ,&nbsp;Carlos J. Ramírez-Flores ,&nbsp;Ricardo Mondragón-Flores","doi":"10.1016/j.jprot.2025.105454","DOIUrl":"10.1016/j.jprot.2025.105454","url":null,"abstract":"<div><div>Research on the immunogenic molecules of <em>Toxoplasma</em> is a key priority in the development of protective vaccines against the parasite. In the present study, we analyzed the profile of immunorecognized proteins from the <em>Toxoplasma</em> cytoskeleton using sera from patients with both acute and chronic toxoplasmosis. The immunorecognized spots were analyzed by mass spectrometry and characterized by bioinformatic methods, leading to the identification of a total of 313 proteins. Sixty-three antigenic proteins were recognized by IgM antibodies and 250 antigenic proteins were recognized by IgG antibodies. About 10 proteins specifically reported as cytoskeletal proteins were identified with the IgG antibodies while 9 cytoskeletal proteins were detected by IgM antibodies. Bioinformatic analyses of the identified antigenic proteins were performed to determine their immunogenic potential, including the number of epitopes recognized by B lymphocytes, cytotoxic T lymphocytes (CD8+), and helper T lymphocytes (CD4+) receptors. This analysis enabled the selection of highly immunogenic proteins, which could serve as potential candidates for the design of a future vaccine against toxoplasmosis.</div></div><div><h3>Significance</h3><div>The study of immunogenic molecules from <em>Toxoplasma gondii</em> is a key priority in the search for protective vaccines. Despite partial success in previous strategies, identifying immunogenic proteins from the <em>T. gondii</em> cytoskeleton using immune-proteomics and bioinformatic approaches is crucial for vaccine development. This study provides valuable data that could serve as the foundation for designing novel immunogenic and immunoprotective molecules against toxoplasmosis.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"317 ","pages":"Article 105454"},"PeriodicalIF":2.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143929377","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}

{"title":"Resveratrol exerts antiviral activity against pseudorabies virus through regulation of the OPN-ERK/JNK-IL-1β signaling axis","authors":"Hongliang Luan ,&nbsp;Yizhen Song ,&nbsp;Hongqiao Hu ,&nbsp;Wenrui Zhang ,&nbsp;Hui Zhang ,&nbsp;Tianli Su ,&nbsp;Juan Wang ,&nbsp;Gang Ye ,&nbsp;Zhongqiong Yin ,&nbsp;Xinhong Zhao ,&nbsp;Xun Zhou ,&nbsp;Lixia Li ,&nbsp;Yuanfeng Zou ,&nbsp;Yingying Zhang ,&nbsp;Xu Song","doi":"10.1016/j.jprot.2025.105444","DOIUrl":"10.1016/j.jprot.2025.105444","url":null,"abstract":"<div><div>Pseudorabies virus (PRV) can infect most mammals and has caused significant economic losses in global pig production. The emergence of new mutants significantly reduces the protective effect of vaccination, indicating an urgent need for the development of specific therapeutic agents against PRV infection. In this study, we analyzed the changes in the cellular proteome after PRV infection in resveratrol-treated PK-15 cells using TMT quantitative proteomics combined with LC-MS/MS. The results identified the differential proteins osteopontin (iOPN) and interleukin-1 receptor accessory protein (IL-1RAP), which have significant biological implications. The regulation of OPN-IL-1β signaling by PRV infection was further studied through the OPN-ERK/JNK-IL-1β signaling axis. The transcriptional levels of OPN, C-JUN, IL-1RAP, and IL-1β, along with the protein levels of ERK, JNK, C-Jun, and their phosphorylated forms at 8, 12, and 16 h post-infection, were determined. The results showed that PRV infection inhibited the activation of this signaling axis, which was upregulated by resveratrol treatment. Down-regulation of OPN by siRNA increased PRV proliferation and inhibited the activation of the signaling axis, which was antagonized by resveratrol treatment. In PRV-infected mice, resveratrol treatment produced the same changes observed in vitro. The present study demonstrated that resveratrol can promote innate immune responses by regulating the OPN-ERK/JNK-IL-1β signaling axis, thereby activating host antiviral defenses against PRV infection.</div></div><div><h3>Significance</h3><div>Resveratrol targets the OPN-ERK/JNK-IL-1β axis to enhance innate immunity, offering a novel antiviral strategy against PRV infection. This study identifies OPN as a key regulator of host defense, linking ERK/JNK signaling to IL-1β-mediated antiviral responses. In vivo validation demonstrates resveratrol's therapeutic potential, reducing PRV replication and mortality in mice via immune pathway activation.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"317 ","pages":"Article 105444"},"PeriodicalIF":2.8,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898563","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}

{"title":"Comparative secretome analysis of Oudemansiella raphanipes grown on different agricultural residues","authors":"Liping Zhu ,&nbsp;Shunan Ma ,&nbsp;Xia Gao ,&nbsp;Jiandong Han ,&nbsp;Weidong Lu ,&nbsp;Hao Yu ,&nbsp;Song Yang","doi":"10.1016/j.jprot.2025.105445","DOIUrl":"10.1016/j.jprot.2025.105445","url":null,"abstract":"<div><div><em>Oudemansiella raphanipes</em> can degrade lignocellulose-rich biomass, especially agricultural residues. However, its substrate utilization and degradation mechanisms remain poorly understood. To explore this, we cultured <em>O. raphanipes</em> mycelium in Kirk's liquid medium supplemented with eight distinct substrates and conducted studies on extracellular enzyme activities and secretome analysis. A total of 905 secreted proteins were identified, with the cornstalk group having the highest counts. Carbohydrate-active enzymes (CAZymes) were the predominant type (32.8–48.9 %), followed by oxidoreductases (2.8 %–13.3 %), while lipase and phosphatase were minor categories. Functional annotation of the secreted proteins comprehensively revealed their diversity in various biological processes. Among the 340 secreted proteins with Enzyme Commission codes, (Methyl)glyoxal oxidase, chitinase, and β-glucosidase were most prominent. Bran, cottonseed hulls, corncobs, and the mixture promoted mycelium growth and conserved CAZymes expression patterns. In contrast, sawdust, corn steep liquor, and cornstalk induced divergent secretome profiles. Sawdust led to a higher proportion of hemicellulose- and lignin-degrading enzymes. Corn steep liquor induced relatively high activities and abundances of laccase and MnP, while cornstalk induced a broad spectrum of oxidoreductases, lipases, and protease &amp; peptidases. In addition, redundancy analysis further indicated that the extracellular enzyme activities (notably laccase, MnP, and xylanase) induced by different substrates significantly impacted the secretome.</div></div><div><h3>Significance</h3><div><em>O. raphanipes</em> can efficiently utilize a variety of lignocellulosic materials, and genomic sequencing has confirmed the presence of abundant CAZymes in its genome. This study employed various agricultural residues as substrate inducers to elucidate the extracellular enzyme profiles of <em>O. raphanipes</em> involved in lignocellulose degradation, which indicated its metabolic plasticity in response to varying substrate composition. These findings facilitate further exploration of the biomass bioconversion mechanism of <em>O. raphanipes</em> and provide novel perspectives for the induction of combined agro-residues in its industrial cultivation.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"317 ","pages":"Article 105445"},"PeriodicalIF":2.8,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873851","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}

{"title":"Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata","authors":"Ping Zheng ,&nbsp;Enrique Audain ,&nbsp;Henry Webel ,&nbsp;Chengxin Dai ,&nbsp;Joshua Klein ,&nbsp;Marc-Phillip Hitz ,&nbsp;Timo Sachsenberg ,&nbsp;Mingze Bai ,&nbsp;Yasset Perez-Riverol","doi":"10.1016/j.jprot.2025.105440","DOIUrl":"10.1016/j.jprot.2025.105440","url":null,"abstract":"<div><div>Intensity-based absolute quantification (iBAQ) is essential in proteomics as it allows for the assessment of a protein's absolute abundance in various samples or conditions. However, the computation of these values for increasingly large-scale and high-throughput experiments, such as those using DIA, TMT, or LFQ workflows, poses significant challenges in scalability and reproducibility. Here, we present ibaqpy (<span><span>https://github.com/bigbio/ibaqpy</span><svg><path></path></svg></span>), a Python package designed to compute iBAQ values efficiently for experiments of any scale. Ibaqpy leverages the Sample and Data Relationship Format (SDRF) metadata standard to incorporate experimental metadata into the quantification workflow. This allows for automatic normalization and batch correction while accounting for key aspects of the experimental design, such as technical and biological replicates, fractionation strategies, and sample conditions. Designed for large-scale proteomics datasets, ibaqpy can also recompute iBAQ values for existing experiments when an SDRF is available. We showcased ibaqpy's capabilities by reanalyzing 17 public proteomics datasets from ProteomeXchange, covering HeLa cell lines with 4921 samples and 5766 MS runs, quantifying a total of 11,014 proteins. In our reanalysis, ibaqpy is a key component in automating reproducible quantification, reducing manual effort and making quantitative proteomics more accessible while supporting FAIR principles for data reuse.</div></div><div><h3>Significance</h3><div>Proteomics studies often rely on intensity-based absolute quantification (iBAQ) to assess protein abundance across various biological conditions. Despite its widespread use, computing iBAQ values at scale remains challenging due to the increasing complexity and volume of proteomics experiments. Existing tools frequently lack metadata integration, limiting their ability to handle experimental design intricacies such as replicates, fractions, and batch effects. Our work introduces ibaqpy, a scalable Python package that leverages the Sample and Data Relationship Format (SDRF) to compute iBAQ values efficiently while incorporating critical experimental metadata. By enabling automated normalization and batch correction, ibaqpy ensures reproducible and comparable quantification across large-scale datasets.</div><div>We validated the utility of ibaqpy through the reanalysis of 17 public HeLa datasets, comprising over 200 million peptide features and quantifying 11,000 proteins across thousands of samples. This comprehensive reanalysis highlights the robustness and scalability of ibaqpy, making it an essential tool for researchers conducting large-scale proteomics experiments. Moreover, by promoting FAIR principles for data reuse and interoperability, ibaqpy offers a transformative approach to baseline protein quantification, supporting reproducible research and data integration within the proteomics community.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"317 ","pages":"Article 105440"},"PeriodicalIF":2.8,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873947","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}

{"title":"Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center","authors":"Henriett Oskolas ,&nbsp;Fábio C.N. Nogueira ,&nbsp;Gilberto B. Domont ,&nbsp;Kun-Hsing Yu ,&nbsp;Yevgeniy R. Semenov ,&nbsp;Peter Sorger ,&nbsp;Erik Steinfelder ,&nbsp;Les Corps ,&nbsp;Lesley Schulz ,&nbsp;Elisabet Wieslander ,&nbsp;David Fenyö ,&nbsp;Sarolta Kárpáti ,&nbsp;Péter Holló ,&nbsp;Lajos V. Kemény ,&nbsp;Balazs Döme ,&nbsp;Zsolt Megyesfalvi ,&nbsp;Krzysztof Pawłowski ,&nbsp;Toshihide Nishimura ,&nbsp;HoJeong Kwon ,&nbsp;Sergio Encarnación-Guevara ,&nbsp;Jeovanis Gil","doi":"10.1016/j.jprot.2025.105442","DOIUrl":"10.1016/j.jprot.2025.105442","url":null,"abstract":"<div><div>This white paper presents a comprehensive biobanking framework developed at the European Cancer Moonshot Lund Center that merges rigorous sample handling, advanced automation, and multi-omic analyses to accelerate precision oncology.</div><div>Tumor and blood-based workflows, supported by automated fractionation systems and standardized protocols, ensure the collection of high-quality biospecimens suitable for proteomic, genomic, and metabolic studies. A robust informatics infrastructure, integrating LIMS, barcoding, and REDCap, supports end-to-end traceability and realtime data synchronization, thereby enriching each sample with critical clinical metadata. Proteogenomic integration lies at the core of this initiative, uncovering tumor- and blood-based molecular profiles that inform cancer heterogeneity, metastasis, and therapeutic resistance. Machine learning and AI-driven models further enhance these datasets by stratifying patient populations, predicting therapeutic responses, and expediting the discovery of actionable targets and companion biomarkers. This synergy between technology, automation, and high-dimensional data analytics enables individualized treatment strategies in melanoma, lung, and other cancer types. Aligned with international programs such as the Cancer Moonshot and the ICPC, the Lund Center's approach fosters open collaboration and data sharing on a global scale. This scalable, patient-centric biobanking paradigm provides an adaptable model for institutions aiming to unify clinical, molecular, and computational resources for transformative cancer research.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105442"},"PeriodicalIF":2.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143833325","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}

{"title":"Proteomics analysis of the mechanism of the treatment of corneal injury in dry-eye mice","authors":"Zhirui Zhang ,&nbsp;Changxing Liu ,&nbsp;Jiadi Wang ,&nbsp;Yue Liu ,&nbsp;Yuhang Li ,&nbsp;Jing Yao","doi":"10.1016/j.jprot.2025.105443","DOIUrl":"10.1016/j.jprot.2025.105443","url":null,"abstract":"<div><div>Dry eye disease (DED) is a common ocular surface disorder affecting millions globally. Clinical and experimental studies have shown that the traditional Chinese medicine formula Qingxuan Runmu Yin decoction (QXRMY) is effective in treating DED. This study aimed to explore the molecular mechanisms of corneal damage in DED and evaluate QXRMY's therapeutic effects. A total of 120 C57BL/6 mice were divided into control, DED model, and QXRMY treatment groups. DIA sequencing of corneal tissue identified 2411 differentially expressed proteins. Enrichment analysis revealed these proteins were involved in RNA polymerase II regulation, apoptosis, and protein phosphorylation. KEGG pathway analysis highlighted key roles of the PI3K/AKT, HIF-1 signaling pathways, and cytoskeleton regulation in QXRMY's effects. FL, BUT, Schirmer I tests, HE, and PAS staining confirmed corneal damage in DED and the repair effects of QXRMY. ELISA showed QXRMY significantly reduced IL-1β, IL-6, and TNF-α levels, suggesting anti-inflammatory properties. PCR and Western blot further confirmed QXRMY repairs corneal damage via the PI3K/AKT/HIF1α pathway. This study provides new insights into the pathogenesis of DED and supports QXRMY's therapeutic potential in treating DED by alleviating inflammation and promoting corneal repair.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"316 ","pages":"Article 105443"},"PeriodicalIF":2.8,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143838505","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}