ProteomesPub Date : 2025-06-16DOI: 10.3390/proteomes13020025
Davide Perico, Pierluigi Mauri
{"title":"Deciphering Radiotherapy Resistance: A Proteomic Perspective.","authors":"Davide Perico, Pierluigi Mauri","doi":"10.3390/proteomes13020025","DOIUrl":"10.3390/proteomes13020025","url":null,"abstract":"<p><p>Radiotherapy resistance represents a critical aspect of cancer treatment, and molecular characterization is needed to explore the pathways and mechanisms involved. DNA repair, hypoxia, metabolic reprogramming, apoptosis, tumor microenvironment modulation, and activation of cancer stem cells are the primary mechanisms that regulate radioresistance, and understanding their complex interactions is essential for planning the correct therapeutic strategy. Proteomics has emerged as a key approach in precision medicine to study tumor heterogeneity and treatment response in cancer patients. The integration of mass spectrometry-based techniques with bioinformatics has enabled high-throughput, quantitative analyses to identify biomarkers, pathways, and new potential therapeutic targets. This review highlights recent advances in proteomic technologies and their application in identifying biomarkers predictive of radiosensitivity and radioresistance in different tumors, including head and neck, breast, lung, and prostate cancers. Sample variability, data interpretation, and the translation of findings into clinical practice remain challenging elements of proteomics. However, technological advancements support its application in a wide range of topics, allowing a comprehensive approach to radiobiology, which helps overcome radiation resistance. Ultimately, incorporating proteomics into the radiotherapy workflow offers significant potential for enhancing treatment efficacy, minimizing toxicity, and guiding precision oncology strategies.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-06-05DOI: 10.3390/proteomes13020024
Sunil S Adav
{"title":"Advances in the Study of Protein Deamidation: Unveiling Its Influence on Aging, Disease Progression, Forensics and Therapeutic Efficacy.","authors":"Sunil S Adav","doi":"10.3390/proteomes13020024","DOIUrl":"10.3390/proteomes13020024","url":null,"abstract":"<p><p>Protein deamidation, a nonenzymatic post-translational modification that converts asparagine and glutamine residues into their acidic forms, such as aspartic acid, iso-aspartic acid, or glutamic acid, has emerged as a pivotal process affecting protein stability and function. Once considered a minor biochemical occurrence, deamidation is now recognized for its significant role in aging, age-associated diseases, disease progression, cancer, and therapeutic efficacy. This review explores the recent advances in understanding protein deamidation, its impact on cellular homeostasis, protein misfolding, and age-related and chronic diseases including neurodegeneration and cancer. The study also highlights the challenges posed by deamidation in biopharmaceuticals, where it compromises therapeutic stability and efficacy. Advancements in state-of-the-art analytical techniques and computational approaches for identifying deamidation sites and predicting deamidation-prone regions are discussed, along with deeper insights into how deamidation affects protein structure and function. Based on the current insights, this review underscores the dual role of deamidation as both a natural regulatory process and a contributor to pathological states, providing a roadmap for future research in aging biology, disease mechanisms, and therapeutics.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-06-04DOI: 10.3390/proteomes13020023
Jordana Sheahan, Iris Wang, Peter Galettis, David I Watson, Virendra Joshi, Michelle M Hill, Richard Lipscombe, Kirsten Peters, Scott Bringans
{"title":"A Clinical Validation of a Diagnostic Test for Esophageal Adenocarcinoma Based on a Novel Serum Glycoprotein Biomarker Panel: PromarkerEso.","authors":"Jordana Sheahan, Iris Wang, Peter Galettis, David I Watson, Virendra Joshi, Michelle M Hill, Richard Lipscombe, Kirsten Peters, Scott Bringans","doi":"10.3390/proteomes13020023","DOIUrl":"10.3390/proteomes13020023","url":null,"abstract":"<p><strong>Background: </strong>Esophageal adenocarcinoma (EAC) diagnosis involves invasive and expensive endoscopy with biopsy, but rising EAC incidence has not been reduced by increased surveillance. This study aimed to develop and clinically validate a novel glycoprotein biomarker blood test for EAC, named PromarkerEso.</p><p><strong>Methods: </strong>Serum glycoprotein relative concentrations were measured using a lectin-based magnetic bead array pulldown method, with multiple reaction monitoring mass spectrometry in 259 samples across three independent cohorts. A panel of glycoproteins: alpha-1-antitrypsin, alpha-1-antichymotrypsin, complement C9 and plasma kallikrein, were combined with clinical factors (age, sex and BMI) in an algorithm to categorize the samples by the risk of EAC.</p><p><strong>Results: </strong>PromarkerEso demonstrated a strong discrimination of EAC from the controls (area under the curve (AUC) of 0.91 in the development cohort and 0.82 and 0.98 in the validation cohorts). The test exhibited a high sensitivity for EAC (98% in the development cohort, and 99.9% and 91% in the validation cohorts) and a high specificity (88% in the development cohort, and 86% and 99% in the validation cohorts). PromarkerEso identified individuals with and without EAC (96% and 95% positive and negative predictive values).</p><p><strong>Conclusions: </strong>This less invasive approach for EAC detection with the novel combination of these glycoprotein biomarkers and clinical factors coalesces in a potential step toward improved diagnosis.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-06-03DOI: 10.3390/proteomes13020022
Rui Yan, Heng-Wee Tan, Na-Li Cai, Le Yu, Yan Gao, Yan-Ming Xu, Andy T Y Lau
{"title":"Chromosome X Open Reading Frame 38 (CXorf38) Is a Tumor Suppressor and Potential Prognostic Biomarker in Lung Adenocarcinoma: The First Characterization.","authors":"Rui Yan, Heng-Wee Tan, Na-Li Cai, Le Yu, Yan Gao, Yan-Ming Xu, Andy T Y Lau","doi":"10.3390/proteomes13020022","DOIUrl":"10.3390/proteomes13020022","url":null,"abstract":"<p><p><b>Background:</b> Previously, we found that an uncharacterized protein CXorf38 is significantly downregulated in human ZIP8-knockout (KO) cells. Given that ZIP8 regulates essential micronutrients linked to diseases including cancer, this study aims to characterize CXorf38 and evaluate its role in lung adenocarcinoma. <b>Methods:</b> iTRAQ-based proteomics was previously used to identify the abundance of proteins in ZIP8-KO cells. Cell proliferation and colony formation assays were used to examine the function of CXorf38 by overexpressing the gene in lung adenocarcinoma cell lines. Kaplan-Meier survival analysis was used to assess the prognostic value of <i>CXorf38</i>, while TCGA clinical database analysis was used to evaluate its expression in lung cancer tissues, particularly in smokers. Bioinformatics analyses (GO, KEGG, PPI, and ICI) were performed on <i>CXorf38</i>-coexpressed genes derived from patients with lung cancer. <b>Results:</b> CXorf38 overexpression suppressed lung cancer cell proliferation and colony formation, suggesting a tumor-suppressive role. Higher <i>CXorf38</i> expression correlated with improved survival in patients with lung adenocarcinoma, but not in lung squamous cell carcinoma. Clinical data showed <i>CXorf38</i> downregulation with lung cancer tissues of smokers, indicating a potential role in smoking-induced cancer progression and treatment. Functional analysis using bioinformatics linked CXorf38 to immune response regulation, suggesting involvement in the tumor immune microenvironment. <b>Conclusions:</b> Our study reveals for the first time that CXorf38 is a potential tumor suppressor, prognostic biomarker, and/or tumor immune regulator in lung adenocarcinoma-further research is warranted to explore its role in tumor immunity and its therapeutic potential.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Oxidative Stress and Its Role in the Emergence and Progression of Myelodysplastic Syndromes: Insights from Proteomic Analysis and Other Methodologies.","authors":"Anastasia Boura-Theodorou, Konstantina Psatha, Stefania Maniatsi, Areti Kourti, Georgia Kaiafa, Michalis Aivaliotis, Kali Makedou","doi":"10.3390/proteomes13020021","DOIUrl":"10.3390/proteomes13020021","url":null,"abstract":"<p><p>Myelodysplastic syndromes (MDS) belong to a category of malignant stem-cell and myeloid disorders that deteriorate the function of the hematopoietic system exacerbated by the omnipresent anemia that characterizes myelodysplasia. The pathogenesis of MDS is driven by cytogenetic abnormalities along with the excessive production of pro-inflammatory cytokines and disruptions in inflammatory signaling pathway, particularly through the influence of carbonylated proteins, which are linked to MDS progression. An additional and major contributor to the pathogenesis of MDS is oxidative stress marked by uncontrolled levels of reactive oxygen species (ROS), which have been suggested as potential biomarkers for assessing disease severity and stratifying MDS cases throughout a variety of methods. Excessive and non-accumulative levels of free iron can also lead to iron overload (IOL)-related promotion of a high oxidative state, whether we refer to treatment-related IOL or natural IOL mechanisms. Proteomic analysis has emerged as a powerful tool for profiling protein samples, and, consequently, understanding the molecular changes underlying MDS. In this review, we evaluated studies and their methodologies aiming in investigating distinctive proteomics signatures associated with MDS pathogenesis, focusing on the role of oxidative stress at the protein level.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12197278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-05-29DOI: 10.3390/proteomes13020020
Mathilde Resell, Elisabeth Pimpisa Graarud, Hanne-Line Rabben, Animesh Sharma, Lars Hagen, Linh Hoang, Nan T Skogaker, Anne Aarvik, Magnus K Svensson, Manoj Amrutkar, Caroline S Verbeke, Surinder K Batra, Gunnar Qvigstad, Timothy C Wang, Anil Rustgi, Duan Chen, Chun-Mei Zhao
{"title":"Knowledge Discovery in Databases of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer.","authors":"Mathilde Resell, Elisabeth Pimpisa Graarud, Hanne-Line Rabben, Animesh Sharma, Lars Hagen, Linh Hoang, Nan T Skogaker, Anne Aarvik, Magnus K Svensson, Manoj Amrutkar, Caroline S Verbeke, Surinder K Batra, Gunnar Qvigstad, Timothy C Wang, Anil Rustgi, Duan Chen, Chun-Mei Zhao","doi":"10.3390/proteomes13020020","DOIUrl":"10.3390/proteomes13020020","url":null,"abstract":"<p><strong>Background: </strong>Knowledge discovery in databases (KDD) can contribute to translational research, also known as translational medicine, by bridging the gap between <i>in vitro</i> and <i>in vivo</i> studies, and clinical applications. Here, we propose a 'systems modeling' workflow for KDD.</p><p><strong>Methods: </strong>This framework includes the data collection of a composition model (various research models), processing model (proteomics) and analytical model (bioinformatics, artificial intelligence/machine leaning and pattern evaluation), knowledge presentation, and feedback loops for hypothesis generation and validation. We applied this workflow to study pancreatic ductal adenocarcinoma (PDAC).</p><p><strong>Results: </strong>We identified the common proteins between human PDAC and various research models <i>in vitro</i> (cells, spheroids and organoids) and <i>in vivo</i> (mouse mice). Accordingly, we hypothesized potential translational targets on hub proteins and the related signaling pathways, PDAC-specific proteins and signature pathways, and high topological proteins.</p><p><strong>Conclusions: </strong>This systems modeling workflow can be a valuable method for KDD, facilitating knowledge discovery in translational targets in general, and in particular to PADA in this case.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-05-23DOI: 10.3390/proteomes13020019
Siyu Zhu, Feng Liu, Hao Wang, Yongqian Zhang
{"title":"Unraveling the Central Role of Global Regulator PprI in <i>Deinococcus radiodurans</i> Through Label-Free Quantitative Proteomics.","authors":"Siyu Zhu, Feng Liu, Hao Wang, Yongqian Zhang","doi":"10.3390/proteomes13020019","DOIUrl":"10.3390/proteomes13020019","url":null,"abstract":"<p><strong>Background: </strong><i>Deinococcus radiodurans</i>, renowned for its exceptional resistance to radiation, provides a robust model for elucidating cellular stress responses and DNA repair mechanisms. Previous studies have established PprI as a key regulator contributing to radiation resistance through its involvement in DNA damage repair pathways, oxidative stress response, and metabolic regulation.</p><p><strong>Methods: </strong>Building upon these foundations, our study employs label-free quantitative (LFQ) proteomics coupled with high-resolution mass spectrometry to systematically map <i>pprI</i> deletion protein networks by comparing the global proteomic profiles of <i>pprI</i> knockout and wild-type <i>D. radiodurans</i> strains.</p><p><strong>Results: </strong>Under stringent screening criteria, we identified 719 significantly higher and 281 significantly lower abundant proteins in the knockout strain compared to wild-type strains. Functional analysis revealed that PprI deficiency disrupts homologous recombination (HR) repair, activates nucleotide excision repair (NER) and base excision repair (BER) as a compensatory mechanism, and impairs Mn/Fe homeostasis and carotenoid biosynthesis, leading to increased oxidative stress. Furthermore, PprI deficiency induces significant metabolic reprogramming, including impaired purine synthesis, compromised cell wall integrity, etc. Conclusions: These proteomic findings delineate the extensive regulatory network influenced by PprI, revealing coordinated perturbations across multiple stress response systems when PprI is absent.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12197293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-05-22DOI: 10.3390/proteomes13020018
Anu Jain, Rafaela Muniz de Queiroz, Jayanta K Chakrabarty, Karl A T Makepeace, Carol Prives, Lewis M Brown
{"title":"Analysis of p53-Independent Functions of the Mdm2-MdmX Complex Using Data-Independent Acquisition-Based Profiling.","authors":"Anu Jain, Rafaela Muniz de Queiroz, Jayanta K Chakrabarty, Karl A T Makepeace, Carol Prives, Lewis M Brown","doi":"10.3390/proteomes13020018","DOIUrl":"10.3390/proteomes13020018","url":null,"abstract":"<p><strong>Background: </strong>We utilized data-independent acquisition (DIA) to study the poorly understood biology of Mdm2 and MdmX in a p53-null context. Mdm2 and MdmX form an E3-ligase complex that has as its most well-studied function the negative regulation of the tumor suppressor p53; however, it is also known to interact with many other proteins in a p53-independent manner.</p><p><strong>Methods: </strong>In this work, small-molecule and siRNA-based technology were used to modify Mdm2/MdmX activity in a human non-small-cell lung carcinoma cell line lacking p53 expression. Study of the proteome of these cells helped identify biological processes where Mdm2 and MdmX may play roles in a p53-independent manner. Proteins from H1299 cells, treated with the drug MEL23 or siRNA against Mdm2 or MdmX, were analyzed.</p><p><strong>Results: </strong>Protein ontology and function were analyzed, revealing which pathways are affected by modulation of the proteins that form the complex. Insights into how those functions are dependent on the activity of the complex also gained via comparisons among the three groups of samples.</p><p><strong>Conclusions: </strong>We selected a potential target from the DIA analysis and validated it by immunoblotting and qPCR, and this allows us to demonstrate a new interaction partner of the Mdm2-MdmX complex in human cells.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-05-22DOI: 10.3390/proteomes13020017
Xue Wang, Fei Wang, Archana S Iyer, Heather Knight, Lori J Duggan, Yingli Yang, Liang Jin, Baoliang Cui, Yupeng He, Jan Schejbal, Lucy A Phillips, Bohdan P Harvey, Sílvia Sisó, Yu Tian
{"title":"Integrative Spatial Proteomics and Single-Cell RNA Sequencing Unveil Molecular Complexity in Rheumatoid Arthritis for Novel Therapeutic Targeting.","authors":"Xue Wang, Fei Wang, Archana S Iyer, Heather Knight, Lori J Duggan, Yingli Yang, Liang Jin, Baoliang Cui, Yupeng He, Jan Schejbal, Lucy A Phillips, Bohdan P Harvey, Sílvia Sisó, Yu Tian","doi":"10.3390/proteomes13020017","DOIUrl":"10.3390/proteomes13020017","url":null,"abstract":"<p><p>Understanding the heterogeneity of Rheumatoid Arthritis (RA) and identifying therapeutic targets remain challenging using traditional bulk transcriptomics alone, as it lacks the spatial and protein-level resolution needed to fully capture disease and tissue complexities. In this study, we applied Laser Capture Microdissection (LCM) coupled with mass spectrometry-based proteomics to analyze histopathological niches of the RA synovium, enabling the identification of protein expression profiles of the diseased synovial lining and sublining microenvironments compared to their healthy counterparts. In this respect, key pathogenetic RA proteins like membrane proteins (TYROBP, AOC3, SLC16A3, TCIRG1, and NCEH1), and extracellular matrix (ECM) proteins (PLOD2, OGN, and LUM) showed different expression patterns in diseased synovium compartments. To enhance our understanding of cellular dynamics within the dissected regions, we further integrated the proteomic dataset with single-cell RNA sequencing (scRNA-seq), and deduced cell type enrichment, including T cells, fibroblasts, NK cells, myeloid cells, B cells, and synovial endothelial cells. By combining high-resolution spatial proteomics and transcriptomic analyses, we provide novel insights into the molecular mechanisms driving RA, and highlight potential protein targets for therapeutic intervention. This integrative approach offers a more comprehensive view of RA synovial pathology, and mitigates the limitations of traditional bulk transcriptomics in target discovery.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12196869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ProteomesPub Date : 2025-04-28DOI: 10.3390/proteomes13020016
Shivam Shukla, Sean S Lastorka, Vladimir N Uversky
{"title":"Intrinsic Disorder and Phase Separation Coordinate Exocytosis, Motility, and Chromatin Remodeling in the Human Acrosomal Proteome.","authors":"Shivam Shukla, Sean S Lastorka, Vladimir N Uversky","doi":"10.3390/proteomes13020016","DOIUrl":"10.3390/proteomes13020016","url":null,"abstract":"<p><p>Intrinsic disorder refers to protein regions that lack a fixed three-dimensional structure under physiological conditions, enabling conformational plasticity. This flexibility allows for diverse functions, including transient interactions, signaling, and phase separation via disorder-to-order transitions upon binding. Our study focused on investigating the role of intrinsic disorder and liquid-liquid phase separation (LLPS) in the human acrosome, a sperm-specific organelle essential for fertilization. Using computational prediction models, network analysis, Structural Classification of Proteins (SCOP) functional assessments, and Gene Ontology, we analyzed 250 proteins within the acrosomal proteome. Our bioinformatic analysis yielded 97 proteins with high levels (>30%) of structural disorder. Further analysis of functional enrichment identified associations between disordered regions overlapping with SCOP domains and critical acrosomal processes, including vesicle trafficking, membrane fusion, and enzymatic activation. Examples of disordered SCOP domains include the PLC-like phosphodiesterase domain, the t-SNARE domain, and the P-domain of calnexin/calreticulin. Protein-protein interaction networks revealed acrosomal proteins as hubs in tightly interconnected systems, emphasizing their functional importance. LLPS propensity modeling determined that over 30% of these proteins are high-probability LLPS drivers (>60%), underscoring their role in dynamic compartmentalization. Proteins such as myristoylated alanine-rich C-kinase substrate and nuclear transition protein 2 exhibited both high LLPS propensities and high levels of structural disorder. A significant relationship (<i>p</i> < 0.0001, R² = 0.649) was observed between the level of intrinsic disorder and LLPS propensity, showing the role of disorder in facilitating phase separation. Overall, these findings provide insights into how intrinsic disorder and LLPS contribute to the structural adaptability and functional precision required for fertilization, with implications for understanding disorders associated with the human acrosome reaction.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"13 2","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}