Polina A Strelnikova, Natalia V Zakharova, Alexey S Kononikhin, Anna E Bugrova, Maria I Indeykina, Vladimir A Mitkevich, Alexander A Makarov, Evgeny N Nikolaev
{"title":"Blood plasma proteomic markers of Alzheimer's disease, current status and application prospects.","authors":"Polina A Strelnikova, Natalia V Zakharova, Alexey S Kononikhin, Anna E Bugrova, Maria I Indeykina, Vladimir A Mitkevich, Alexander A Makarov, Evgeny N Nikolaev","doi":"10.1080/14789450.2025.2450804","DOIUrl":"10.1080/14789450.2025.2450804","url":null,"abstract":"<p><strong>Introduction: </strong>Identifying early risks of developing Alzheimer's disease (AD) is a major challenge as the number of patients with AD steadily increases and requires innovative solutions. Current molecular diagnostic modalities, such as cerebrospinal fluid (CSF) testing and positron emission tomography (PET) imaging, exhibit limitations in their applicability for large-scale screening. In recent years, there has been a marked shift toward the development of blood plasma-based diagnostic tests, which offer a more accessible and clinically viable alternative for widespread use. Furthermore, advances in large-scale proteomics technologies have boosted an interest in identifying novel biomarkers and developing panels of AD-associated proteins.</p><p><strong>Areas covered: </strong>This review mainly examines the results of recent searches for proteomic markers of AD in blood plasma (from 2022-2024 PubMed), focuses on some aspects for special attention in further studies, and discusses the prospects for their further application.</p><p><strong>Expert opinion: </strong>Recent advances in AD plasma/serum proteomic studies are largely driven using novel Olink/PEA and SomaScan/aptamer technologies, which complement the 'gold standard' of MS-based quantitative proteomics (MRM/SRM), and particularly expand the capabilities for studying low-abundant proteins.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"11-18"},"PeriodicalIF":3.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tohnyui Ndinyanka Fabrice, Katarzyna Buczak, Alexander Schmidt, Jean Pieters
{"title":"T cell population size control by coronin 1 uncovered: from a spot identified by two-dimensional gel electrophoresis to quantitative proteomics.","authors":"Tohnyui Ndinyanka Fabrice, Katarzyna Buczak, Alexander Schmidt, Jean Pieters","doi":"10.1080/14789450.2025.2450812","DOIUrl":"10.1080/14789450.2025.2450812","url":null,"abstract":"<p><strong>Introduction: </strong>Recent work identified members of the evolutionarily conserved coronin protein family as key regulators of cell population size. This work originated ~25 years ago through the identification, by two-dimensional gel electrophoresis, of coronin 1 as a host protein involved in the virulence of <i>Mycobacterium tuberculosis</i>. We here describe the journey from a spot on a 2D gel to the recent realization that coronin proteins represent key controllers of eukaryotic cell population sizes, using ever more sophisticated proteomic techniques.</p><p><strong>Areas covered: </strong>We discuss the value of 'old school' proteomics using relatively simple and cost-effective technologies that allowed to gain insights into subcellular proteomes and describe how label-free quantitative (phospho)proteomics using mass spectrometry allowed to disentangle the role for coronin 1 in eukaryotic cell population size control. Finally, we mention potential implications of coronin-mediated cell population size control for health and disease.</p><p><strong>Expert opinion: </strong>Proteome analysis has been revolutionized by the advent of modern-day mass spectrometers and is indispensable for a better understanding of biology. Here, we discuss how careful dissection of physio-pathological processes by a combination of proteomics, genomics, biochemistry and cell biology may allow to zoom in on the unexplored, thereby possibly tackling hitherto unasked questions and defining novel mechanisms.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"35-44"},"PeriodicalIF":3.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Two decades of advances in sequence-based prediction of MoRFs, disorder-to-order transitioning binding regions.","authors":"Jiangning Song, Lukasz Kurgan","doi":"10.1080/14789450.2025.2451715","DOIUrl":"10.1080/14789450.2025.2451715","url":null,"abstract":"<p><strong>Introduction: </strong>Molecular recognition features (MoRFs) are regions in protein sequences that undergo induced folding upon binding partner molecules. MoRFs are common in nature and can be predicted from sequences based on their distinctive sequence signatures.</p><p><strong>Areas covered: </strong>We overview 20 years of progress in the sequence-based prediction of MoRFs which resulted in the development of 25 predictors of MoRFs that interact with proteins, peptides, and lipids. These methods range from simple discriminant analysis to sophisticated deep transformer networks that use protein language models. They generate relatively accurate predictions as evidenced by the results of a recently published community-driven assessment.</p><p><strong>Expert opinion: </strong>MoRFs prediction is a mature field of research that is poised to continue at a steady pace in the foreseeable future. We anticipate further expansion of the scope of MoRF predictions to additional partner molecules, such as nucleic acids, and continued use of recent machine learning advances. Other future efforts should concentrate on improving availability of MoRF predictions by releasing, maintaining, and popularizing web servers and by depositing MoRF predictions to large databases of protein structure and function predictions. Furthermore, accurate MoRF predictions should be coupled with the equally accurate prediction and modeling of the resulting structures of complexes.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-9"},"PeriodicalIF":3.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Interaction and regulation of the mitochondrial proteome - in health and disease.","authors":"Johan Palmfeldt","doi":"10.1080/14789450.2025.2451704","DOIUrl":"10.1080/14789450.2025.2451704","url":null,"abstract":"<p><strong>Introduction: </strong>Mitochondria contain multiple pathways including energy metabolism and several signaling and synthetic pathways. Mitochondrial proteomics is highly valuable for studying diseases including inherited metabolic disorders, complex and common disorders like neurodegeneration, diabetes, and cancer, since they all to some degree have mitochondrial underpinnings.</p><p><strong>Areas covered: </strong>The main mitochondrial functions and pathways are outlined, and systematic protein lists are presented. The main energy metabolic pathways are as follows: iron-sulfur cluster synthesis, one carbon metabolism, catabolism of hydrogen sulfide, kynurenines and reactive oxygen species (ROS), and others, described with the aim of laying a foundation for systematic mitochondrial pathway analysis based on proteomics data. The links of the proteins and pathways to functional effects and diseases are discussed. The disease examples are focussed on inherited metabolic disorders, cancer, neurological, and cardiovascular disorders.</p><p><strong>Expert opinion: </strong>To elucidate the role of mitochondria in health and disease, there is a need for comprehensive proteomics analyses with stringent, systematic data treatment for proper interpretation of mitochondrial pathway data. In that way, comprehensive hypothesis-based research can be performed based on proteomics data.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"19-33"},"PeriodicalIF":3.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yumi Kwon, James M Fulcher, Ljiljana Paša-Tolić, Wei-Jun Qian
{"title":"Spatial Proteomics towards cellular Resolution.","authors":"Yumi Kwon, James M Fulcher, Ljiljana Paša-Tolić, Wei-Jun Qian","doi":"10.1080/14789450.2024.2445809","DOIUrl":"10.1080/14789450.2024.2445809","url":null,"abstract":"<p><strong>Introduction: </strong>Spatial biology is an emerging interdisciplinary field facilitating biological discoveries through the use of spatial omics technologies. Recent advancements in spatial transcriptomics, spatial genomics (e.g. genetic mutations and epigenetic marks), multiplexed immunofluorescence, and spatial metabolomics/lipidomics have enabled high-resolution spatial profiling of gene expression, genetic variation, protein expression, and metabolites/lipids profiles in tissue. These developments contribute to a deeper understanding of the spatial organization within tissue microenvironments at the molecular level.</p><p><strong>Areas covered: </strong>This report provides an overview of the untargeted, bottom-up mass spectrometry (MS)-based spatial proteomics workflow. It highlights recent progress in tissue dissection, sample processing, bioinformatics, and liquid chromatography (LC)-MS technologies that are advancing spatial proteomics toward cellular resolution.</p><p><strong>Expert opinion: </strong>The field of untargeted MS-based spatial proteomics is rapidly evolving and holds great promise. To fully realize the potential of spatial proteomics, it is critical to advance data analysis and develop automated and intelligent tissue dissection at the cellular or subcellular level, along with high-throughput LC-MS analyses of thousands of samples. Achieving these goals will necessitate significant advancements in tissue dissection technologies, LC-MS instrumentation, and computational tools.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-10"},"PeriodicalIF":3.8,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12187944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Can we use proteomics to predict cardiovascular events?","authors":"Zachery R Gregorich","doi":"10.1080/14789450.2024.2445248","DOIUrl":"10.1080/14789450.2024.2445248","url":null,"abstract":"","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-4"},"PeriodicalIF":3.8,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kaj S Emanuel, Luojiao Huang, Mirella J J Haartmans, Javier Sanmartin Martinez, Frank Zijta, Ron M A Heeren, Gino M M J Kerkhoffs, Pieter J Emans, Berta Cillero-Pastor
{"title":"Patient-responsive protein biomarkers for cartilage degeneration and repair identified in the infrapatellar fat pad.","authors":"Kaj S Emanuel, Luojiao Huang, Mirella J J Haartmans, Javier Sanmartin Martinez, Frank Zijta, Ron M A Heeren, Gino M M J Kerkhoffs, Pieter J Emans, Berta Cillero-Pastor","doi":"10.1080/14789450.2024.2438774","DOIUrl":"10.1080/14789450.2024.2438774","url":null,"abstract":"<p><strong>Objectives: </strong>Cartilage defects (CDs) are regarded as early manifestation of osteoarthritis (OA). The infrapatellar fat pad (IPFP) is an important mediator in maintaining joint homeostasis, disease progression and tissue repair, with a crucial role of its secreted proteins. Here, we investigate the proteome of the IPFP in relation to clinical status and response to surgical treatment of CDs.</p><p><strong>Methods: </strong>In order to characterize the proteome of the IPFP, samples from a cohort of 53 patients who received surgical treatment for knee CDs were analyzed with label-free proteomics. Patients were divided based on validated outcome scores for pain and knee function, preoperatively and at 1-year postoperatively, and on MRI assessment of the defect severity, fibrosis and synovitis.</p><p><strong>Results: </strong>Specific proteins were differentially abundant in patients with MRI features and better clinical outcome after CD surgery, including a downregulation of cartilage intermediate layer protein 2 (CILP-2) and microsomal glutathione s-transferase 1 (MGST1), and an upregulation of aggrecan (ACAN), and proteoglycan 4 (PRG4). Pathways related to cell interaction, oxidation and matrix remodeling were altered.</p><p><strong>Conclusion: </strong>Proteins in the IPFP that have a function in extracellular matrix, inflammation and immunomodulation were identified as potentially relevant markers for cartilage repair monitoring.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-11"},"PeriodicalIF":3.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isidro Sobrino, Margarita Villar, José de la Fuente
{"title":"The path to anti-vector vaccines: current advances and limitations in proteomics and bioinformatics.","authors":"Isidro Sobrino, Margarita Villar, José de la Fuente","doi":"10.1080/14789450.2024.2438792","DOIUrl":"10.1080/14789450.2024.2438792","url":null,"abstract":"","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-4"},"PeriodicalIF":3.8,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Urine proteomics in cardiovascular disease: advances in biomarker discovery and clinical applications.","authors":"Xiaohong Song, Zhaoran Chen, Yuehong Zheng, Jianqiang Wu","doi":"10.1080/14789450.2024.2436401","DOIUrl":"10.1080/14789450.2024.2436401","url":null,"abstract":"<p><strong>Introduction: </strong>Cardiovascular diseases (CVDs) are the leading causes of mortality and morbidity worldwide, making early diagnosis and effective treatment essential. As a promising and noninvasive research method, urine proteomics shows excellent potential to identify reliable urinary biomarkers that could enhance prediction, prevention, and prognosis in patients with CVD.</p><p><strong>Areas covered: </strong>This review summarizes recent advancements in urinary protein biomarker profiling using urine proteomic techniques to identify potential CVD biomarkers. Additionally, it highlights potential disease biomarkers for the early detection, risk stratification, and monitoring of CVD, including hypertension, atherosclerosis, coronary artery disease, angina, myocardial infarction, heart failure, preeclampsia, and vasculitis. A literature search was conducted through Pubmed, Scopus, Google Scholar, and Web of Science. The period is January 2009 to February 2024.</p><p><strong>Expert opinion: </strong>Over the past decade, urinary proteomics has been employed in CVD research, with the potential to facilitate the discovery of novel disease biomarkers and the exploration of prospective therapeutic targets. Proteomics-based multicenter cohort studies should be conducted in the future to gain deeper insights into the pathophysiological mechanisms of CVD, accelerate the identification of potential biomarkers for disease prediction, diagnosis, and treatment, and facilitate their clinical translation.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-15"},"PeriodicalIF":3.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142751605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Identifying therapeutic strategies for triple-negative breast cancer via phosphoproteomics.","authors":"Yuhan Sheng, Gordon Mills, Xuejiao Zhao","doi":"10.1080/14789450.2024.2432477","DOIUrl":"https://doi.org/10.1080/14789450.2024.2432477","url":null,"abstract":"<p><strong>Introduction: </strong>Given the poor prognosis of patients with TNBC, it is urgent to identify new biomarkers and therapeutic targets to enable personalized treatment strategies and improve patient survival. Comprehensive insights beyond genomic and transcriptomic analysis are crucial to improved outcomes for patients. As proteins are the workhorses of cellular function with their activity primarily regulated by phosphorylation, advanced phosphoproteomics techniques, such as mass spectrometry and antibody arrays, are essential for elucidating kinase signaling pathways that drive TNBC progression and contribute to therapy resistance.</p><p><strong>Area covered: </strong>This review discusses the critical need to integrate phosphoproteomics into TNBC research, evaluates commonly used technologies and their applications, and explores their advantages and limitations. We highlight significant findings from phosphoproteomic analyses in TNBC and address the challenges of implementing these technologies into clinical practice.</p><p><strong>Expert opinion: </strong>Rapid advances in phosphoproteomics analysis facilitate subtype stratification, adaptive response monitoring, and identification of biomarkers and therapeutic targets in TNBC. However, challenges in analyzing protein phosphorylation, especially in deep spatially resolved analysis of malignant cells and the tumor ecosystem, hinder the translation of phosphoproteomics to the CLIA setting. Nonetheless, phosphoproteomics offers a powerful tool that, when integrated into routine clinical practice, has the potential to revolutionize patient care.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-17"},"PeriodicalIF":3.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}