Expert Review of Proteomics最新文献

Oncoproteins E6/E7 of the human papillomavirus types 16 & 18 synergize in modulating oncogenes and tumor suppressor proteins in colorectal cancer. 人乳头瘤病毒16型和18型的癌蛋白E6/E7协同调节结直肠癌的癌基因和肿瘤抑制蛋白。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-02-03 DOI: 10.1080/14789450.2025.2455104

Queenie Fernandes, Lubna Therachiyil, Shahd M Younis, Said Dermime, Ala-Eddin Al Moustafa

{"title":"Oncoproteins E6/E7 of the human papillomavirus types 16 & 18 synergize in modulating oncogenes and tumor suppressor proteins in colorectal cancer.","authors":"Queenie Fernandes, Lubna Therachiyil, Shahd M Younis, Said Dermime, Ala-Eddin Al Moustafa","doi":"10.1080/14789450.2025.2455104","DOIUrl":"10.1080/14789450.2025.2455104","url":null,"abstract":"Objective: Our study presents a novel analysis of the oncogenes and tumor suppressor proteins directly modulated by E6/E7 of high-risk HPV types 16 and 18, in colorectal cancer (CRC).Methods: HCT 116 (KRAS mutant) & HT-29 (TP53 mutant) cell models of CRC were transduced with E6/E7 of HPV16 and HPV18, individually and in combination. Further, we utilized a liquid chromatography mass spectrometry (LC-MS/MS) approach to analyze and compare the proteomes of both CRC cell models.Results: We generated six stably transduced cell lines. Our data revealed a significantly higher, HPV-induced modulation of oncogenes and tumor suppressor proteins in the TP53 mutant model, as compared to the KRAS mutant model (p ≤ 0.01). Less than 1% of the genes were commonly modulated by HPV, between both models. We also report that HT-29 cells, expressing E6/E7 of both HPV types, significantly reduced the suppression of oncogenes as compared to cells expressing E6/E7 of either HPV types individually (p-value ≤0.00001).Conclusion: Our data imply that HPV coinfections leads to the sustenance of a pro-oncogenic environment in CRC. HPV modulates different oncogenes/tumor suppressor proteins in CRC of varying mutational backgrounds, thus highlighting the importance of personalized therapies for such diseases with mutational heterogeneity.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"1-14"},"PeriodicalIF":3.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015490","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}

引用次数: 0

AlphaFold and what is next: bridging functional, systems and structural biology. AlphaFold和下一步是什么：连接功能，系统和结构生物学。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-01-17 DOI: 10.1080/14789450.2025.2456046

Kacper Szczepski, Lukasz Jaremko

{"title":"AlphaFold and what is next: bridging functional, systems and structural biology.","authors":"Kacper Szczepski, Lukasz Jaremko","doi":"10.1080/14789450.2025.2456046","DOIUrl":"https://doi.org/10.1080/14789450.2025.2456046","url":null,"abstract":"Introduction: The DeepMind's AlphaFold (AF) has revolutionized biomedical research by providing both experts and non-experts with an invaluable tool for predicting protein structures. However, while AF is highly effective for predicting structures of rigid and globular proteins, it is not able to fully capture the dynamics, conformational variability, and interactions of proteins with ligands and other biomacromolecules.Areas covered: In this review, we present a comprehensive overview of the latest advancements in 3D model predictions for biomacromolecules using AF. We also provide a detailed analysis its of strengths and limitations, and explore more recent iterations, modifications, and practical applications of this strategy. Moreover, we map the path forward for expanding the landscape of AF toward predicting structures of every protein and peptide in the proteome in the most physiologically relevant form. This discussion is based on an extensive literature search performed using PubMed and Google Scholar.Expert opinion: While significant progress has been made to enhance AF's modeling capabilities, we argue that a combined approach integrating both various in silico and in vitro methods will be most beneficial for the future of structural biology, bridging the gaps between static and dynamic features of proteins and their functions.","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015483","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}

引用次数: 0

Blood plasma proteomic markers of Alzheimer's disease, current status and application prospects.

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-01-01 Epub Date: 2025-01-29 DOI: 10.1080/14789450.2025.2450804

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":"Introduction: 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.Areas covered: 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.Expert opinion: 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.","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}

引用次数: 0

T cell population size control by coronin 1 uncovered: from a spot identified by two-dimensional gel electrophoresis to quantitative proteomics.

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-01-01 Epub Date: 2025-01-26 DOI: 10.1080/14789450.2025.2450812

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":"Introduction: 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 Mycobacterium tuberculosis. 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.Areas covered: 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.Expert opinion: 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.","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}

引用次数: 0

Two decades of advances in sequence-based prediction of MoRFs, disorder-to-order transitioning binding regions. 二十年来基于序列预测morf的进展，无序到有序过渡结合区。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-01-01 Epub Date: 2025-01-19 DOI: 10.1080/14789450.2025.2451715

Jiangning Song, Lukasz Kurgan

{"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":"Introduction: 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.Areas covered: 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.Expert opinion: 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.","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}

引用次数: 0

Interaction and regulation of the mitochondrial proteome - in health and disease. 线粒体蛋白质组在健康和疾病中的相互作用和调节。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2025-01-01 Epub Date: 2025-01-15 DOI: 10.1080/14789450.2025.2451704

Johan Palmfeldt

{"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":"Introduction: 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.Areas covered: 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.Expert opinion: 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.","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}

引用次数: 0

Spatial Proteomics towards cellular Resolution. 面向细胞分辨率的空间蛋白质组学。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-25 DOI: 10.1080/14789450.2024.2445809

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":"Introduction: 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.Areas covered: 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.Expert opinion: 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.","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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Can we use proteomics to predict cardiovascular events? 我们能用蛋白质组学预测心血管事件吗？

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-22 DOI: 10.1080/14789450.2024.2445248

Zachery R Gregorich

引用次数: 0

Patient-responsive protein biomarkers for cartilage degeneration and repair identified in the infrapatellar fat pad. 髌下脂肪垫中软骨退变和修复的患者反应性蛋白生物标志物。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-12 DOI: 10.1080/14789450.2024.2438774

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":"Objectives: 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.Methods: 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.Results: 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.Conclusion: Proteins in the IPFP that have a function in extracellular matrix, inflammation and immunomodulation were identified as potentially relevant markers for cartilage repair monitoring.","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}

引用次数: 0

The path to anti-vector vaccines: current advances and limitations in proteomics and bioinformatics. 抗载体疫苗之路：蛋白质组学和生物信息学的当前进展和限制。

IF 3.8 3区生物学

Expert Review of Proteomics Pub Date : 2024-12-09 DOI: 10.1080/14789450.2024.2438792

Isidro Sobrino, Margarita Villar, José de la Fuente

引用次数: 0