Proteomes最新文献_第9页

Applications of Proteomics in Ovarian Cancer: Dawn of a New Era 蛋白质组学在卵巢癌中的应用:一个新时代的黎明

IF 3.3

Proteomes Pub Date : 2022-05-09 DOI: 10.3390/proteomes10020016

Aruni Ghose, Srikar Gullapalli, Naila Chohan, A. Bolina, M. Moschetta, E. Rassy, S. Boussios

引用次数: 51

Proteomes of Uropathogenic Escherichia coli Growing in Human Urine and in J82 Urinary Bladder Cells 尿路致病性大肠杆菌在人尿和J82膀胱细胞中的蛋白质组学研究

IF 3.3

Proteomes Pub Date : 2022-05-05 DOI: 10.3390/proteomes10020015

S. Andersen, A. Nawrocki, A. E. Johansen, Ana Herrero-Fresno, Vanesa García Menéndez, J. Møller-Jensen, J. E. Olsen

{"title":"Proteomes of Uropathogenic Escherichia coli Growing in Human Urine and in J82 Urinary Bladder Cells","authors":"S. Andersen, A. Nawrocki, A. E. Johansen, Ana Herrero-Fresno, Vanesa García Menéndez, J. Møller-Jensen, J. E. Olsen","doi":"10.3390/proteomes10020015","DOIUrl":"https://doi.org/10.3390/proteomes10020015","url":null,"abstract":"Uropathogenic Escherichia coli (UPEC) are the most common cause of urinary tract infection (UTI). UPEC normally reside in the intestine, and during establishment of UTI, they undergo metabolic adaptations, first to urine and then upon tissue invasion to the bladder cell interior. To understand these adaptations, we used quantitative proteomic profiling to characterize protein expression of the UPEC strain UTI89 growing in human urine and when inside J82 bladder cells. In order to facilitate detection of UPEC proteins over the excess amount of eukaryotic proteins in bladder cells, we developed a method where proteins from UTI89 grown in MOPS and urine was spiked-in to enhance detection of bacterial proteins. More than 2000 E. coli proteins were detected. During growth in urine, proteins associated with iron acquisition and several amino acid uptake and biosynthesis systems, most prominently arginine metabolism, were significantly upregulated. During growth in J82 cells, proteins related to iron uptake and arginine metabolisms were likewise upregulated together with proteins involved in sulfur compound turnover. Ribosomal proteins were downregulated relative to growth in MOPS in this environment. There was no direct correlation between upregulated proteins and proteins reported to be essential for infections, showing that upregulation during growth does not signify that the proteins are essential for growth under a condition.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46687601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Transcriptional and Epigenetic Factors Associated with Early Thrombosis of Femoral Artery Involved in Arteriovenous Fistula 动静脉瘘早期股动脉血栓形成的转录和表观遗传学因素

IF 3.3

Proteomes Pub Date : 2022-04-30 DOI: 10.3390/proteomes10020014

Vikrant Rai, D. Agrawal

{"title":"Transcriptional and Epigenetic Factors Associated with Early Thrombosis of Femoral Artery Involved in Arteriovenous Fistula","authors":"Vikrant Rai, D. Agrawal","doi":"10.3390/proteomes10020014","DOIUrl":"https://doi.org/10.3390/proteomes10020014","url":null,"abstract":"Arteriovenous fistulas (AVFs), created for hemodialysis in end-stage renal disease patients, mature through the outward remodeling of the outflow vein. However, early thrombosis and chronic inflammation are detrimental to the process of AVF maturation and precipitate AVF maturation failure. For the successful remodeling of the outflow vein, blood flow through the fistula is essential, but early arterial thrombosis attenuates this blood flow, and the vessels become thrombosed and stenosed, leading to AVF failure. The altered expression of various proteins involved in maintaining vessel patency or thrombosis is regulated by genes of which the expression is regulated by transcription factors and microRNAs. In this study, using thrombosed and stenosed arteries following AVF creation, we delineated transcription factors and microRNAs associated with differentially expressed genes in bulk RNA sequencing data using upstream and causal network analysis. We observed changes in many transcription factors and microRNAs that are involved in angiogenesis; vascular smooth muscle cell proliferation, migration, and phenotypic changes; endothelial cell function; hypoxia; oxidative stress; vessel remodeling; immune responses; and inflammation. These factors and microRNAs play a critical role in the underlying molecular mechanisms in AVF maturation. We also observed epigenetic factors involved in gene regulation associated with these molecular mechanisms. The results of this study indicate the importance of investigating the transcriptional and epigenetic regulation of AVF maturation and maturation failure and targeting factors precipitating early thrombosis and stenosis.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43126381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Insights on Proteomics-Driven Body Fluid-Based Biomarkers of Cervical Cancer 癌症蛋白质组学驱动的体液生物标志物研究进展

IF 3.3

Proteomes Pub Date : 2022-04-29 DOI: 10.3390/proteomes10020013

A. Mukherjee, Chinmay Pednekar, Siddhant Sujit Kolke, Megha Kattimani, Subhiksha Duraisamy, A. Burli, Sudeep Gupta, Sanjeeva Srivastava

{"title":"Insights on Proteomics-Driven Body Fluid-Based Biomarkers of Cervical Cancer","authors":"A. Mukherjee, Chinmay Pednekar, Siddhant Sujit Kolke, Megha Kattimani, Subhiksha Duraisamy, A. Burli, Sudeep Gupta, Sanjeeva Srivastava","doi":"10.3390/proteomes10020013","DOIUrl":"https://doi.org/10.3390/proteomes10020013","url":null,"abstract":"Cervical cancer is one of the top malignancies in women around the globe, which still holds its place despite being preventable at early stages. Gynecological conditions, even maladies like cervical cancer, still experience scrutiny from society owing to prevalent taboo and invasive screening methods, especially in developing economies. Additionally, current diagnoses lack specificity and sensitivity, which prolong diagnosis until it is too late. Advances in omics-based technologies aid in discovering differential multi-omics profiles between healthy individuals and cancer patients, which could be utilized for the discovery of body fluid-based biomarkers. Body fluids are a promising potential alternative for early disease detection and counteracting the problems of invasiveness while also serving as a pool of potential biomarkers. In this review, we will provide details of the body fluids-based biomarkers that have been reported in cervical cancer. Here, we have presented our perspective on proteomics for global biomarker discovery by addressing several pertinent problems, including the challenges that are confronted in cervical cancer. Further, we also used bioinformatic methods to undertake a meta-analysis of significantly up-regulated biomolecular profiles in CVF from cervical cancer patients. Our analysis deciphered alterations in the biological pathways in CVF such as immune response, glycolytic processes, regulation of cell death, regulation of structural size, protein polymerization disease, and other pathways that can cumulatively contribute to cervical cancer malignancy. We believe, more extensive research on such biomarkers, will speed up the road to early identification and prevention of cervical cancer in the near future.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41970898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multi-Omics Integrative Approach of Extracellular Vesicles: A Future Challenging Milestone 细胞外囊泡的多组学综合方法:未来具有挑战性的里程碑

IF 3.3

Proteomes Pub Date : 2022-04-22 DOI: 10.3390/proteomes10020012

E. Shaba, L. Vantaggiato, L. Governini, A. Haxhiu, G. Sebastiani, Daniela Fignani, G. Grieco, L. Bergantini, L. Bini, C. Landi

{"title":"Multi-Omics Integrative Approach of Extracellular Vesicles: A Future Challenging Milestone","authors":"E. Shaba, L. Vantaggiato, L. Governini, A. Haxhiu, G. Sebastiani, Daniela Fignani, G. Grieco, L. Bergantini, L. Bini, C. Landi","doi":"10.3390/proteomes10020012","DOIUrl":"https://doi.org/10.3390/proteomes10020012","url":null,"abstract":"In the era of multi-omic sciences, dogma on singular cause-effect in physio-pathological processes is overcome and system biology approaches have been providing new perspectives to see through. In this context, extracellular vesicles (EVs) are offering a new level of complexity, given their role in cellular communication and their activity as mediators of specific signals to target cells or tissues. Indeed, their heterogeneity in terms of content, function, origin and potentiality contribute to the cross-interaction of almost every molecular process occurring in a complex system. Such features make EVs proper biological systems being, therefore, optimal targets of omic sciences. Currently, most studies focus on dissecting EVs content in order to either characterize it or to explore its role in various pathogenic processes at transcriptomic, proteomic, metabolomic, lipidomic and genomic levels. Despite valuable results being provided by individual omic studies, the categorization of EVs biological data might represent a limit to be overcome. For this reason, a multi-omic integrative approach might contribute to explore EVs function, their tissue-specific origin and their potentiality. This review summarizes the state-of-the-art of EVs omic studies, addressing recent research on the integration of EVs multi-level biological data and challenging developments in EVs origin.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45778232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

In-Depth Quantitative Proteomics Characterization of In Vitro Selected Miltefosine Resistance in Leishmania infantum 婴儿利什曼原虫米特氟辛体外抗性的深度定量蛋白质组学分析

IF 3.3

Proteomes Pub Date : 2022-03-31 DOI: 10.3390/proteomes10020010

L. Saboia-Vahia, P. Cuervo, J. Wiśniewski, G. Dias-Lopes, Nathalia Pinho, G. Padrón, Fernando de Pilla Varotti, S. Murta/

{"title":"In-Depth Quantitative Proteomics Characterization of In Vitro Selected Miltefosine Resistance in Leishmania infantum","authors":"L. Saboia-Vahia, P. Cuervo, J. Wiśniewski, G. Dias-Lopes, Nathalia Pinho, G. Padrón, Fernando de Pilla Varotti, S. Murta/","doi":"10.3390/proteomes10020010","DOIUrl":"https://doi.org/10.3390/proteomes10020010","url":null,"abstract":"Visceral leishmaniasis (VL) is a neglected disease caused by Leishmania parasites. Although significant morbidity and mortality in tropical and subtropical regions of the world are associated with VL, the low investment for developing new treatment measures is chronic. Moreover, resistance and treatment failure are increasing for the main medications, but the emergence of resistance phenotypes is poorly understood at the protein level. Here, we analyzed the development of resistance to miltefosine upon experimental selection in a L. infantum strain. Time to miltefosine resistance emergence was ~six months and label-free quantitative mass-spectrometry-based proteomics analyses revealed that this process involves a remodeling of components of the membrane and mitochondrion, with significant increase in oxidative phosphorylation complexes, particularly on complex IV and ATP synthase, accompanied by increased energy metabolism mainly dependent on β-oxidation of fatty acids. Proteins canonically involved in ROS detoxification did not contribute to the resistant process whereas sterol biosynthesis enzymes could have a role in this development. Furthermore, changes in the abundance of proteins known to be involved in miltefosine resistance such as ABC transporters and phospholipid transport ATPase were detected. Together, our data show a more complete picture of the elements that make up the miltefosine resistance phenotype in L. infantum.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48108486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Molecular Dynamics Study of Citrullinated Proteins Associated with the Development of Rheumatoid Arthritis 瓜氨酸蛋白与类风湿性关节炎发生的分子动力学研究

IF 3.3

Proteomes Pub Date : 2022-02-11 DOI: 10.3390/proteomes10010008

A. Taldaev, V. Rudnev, L. Kulikova, K. Nikolsky, A. Efimov, K. Malsagova, A. Kaysheva

{"title":"Molecular Dynamics Study of Citrullinated Proteins Associated with the Development of Rheumatoid Arthritis","authors":"A. Taldaev, V. Rudnev, L. Kulikova, K. Nikolsky, A. Efimov, K. Malsagova, A. Kaysheva","doi":"10.3390/proteomes10010008","DOIUrl":"https://doi.org/10.3390/proteomes10010008","url":null,"abstract":"Biological activity regulation by protein post-translational modification (PTM) is critical for cell function, development, differentiation, and survival. Dysregulation of PTM proteins is present in various pathological conditions, including rheumatoid arthritis (RA). RA is a systemic autoimmune disease that primarily affects joints, and there are three main types of protein PTMs associated with the development of this disease, namely, glycosylation, citrullination, and carbamylation. Glycosylation is important for the processing and presentation of antigen fragments on the cell surface and can modulate immunoglobulin activity. The citrullination of autoantigens is closely associated with RA, as evidenced by the presence of antibodies specific to citrullinated proteins in the serum of patients. Carbamylation and dysregulation have recently been associated with RA development in humans.In this study, we performed an overview analysis of proteins with post-translational modifications associated with the development of RA adverted in peer-reviewed scientific papers for the past 20 years. As a result of the search, a list of target proteins and corresponding amino acid sequences with PTM in RA was formed. Structural characteristics of the listed modified proteins were extracted from the Protein Data Bank. Then, molecular dynamics experiments of intact protein structures and corresponding structures with PTMs were performed regarding structures in the list announced in the ProtDB service. This study aimed to conduct a molecular dynamics study of intact proteins and proteins, including post-translational modification and protein citrullination, likely associated with RA development. We observed another exhibition of the fundamental physics concept, symmetry, at the submolecular level, unveiled as the autonomous repetitions of outside the protein structural motif performance globule corresponding to those in the whole protein molecule.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41694332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Bovine Peripheral Blood Derived Lymphocyte Proteome and Secretome Show Divergent Reaction of Bovine Immune Phenotypes after Stimulation with Pokeweed Mitogen 美洲商陆有丝分裂原刺激后牛外周血淋巴细胞蛋白质组和分泌组表现出不同的免疫表型反应

IF 3.3

Proteomes Pub Date : 2022-02-08 DOI: 10.3390/proteomes10010007

K. J. Kleinwort, Roxane L Degroote, S. Hirmer, Lucia Korbonits, Lea Lorenz, Armin M Scholz, S. Hauck, C. Deeg

{"title":"Bovine Peripheral Blood Derived Lymphocyte Proteome and Secretome Show Divergent Reaction of Bovine Immune Phenotypes after Stimulation with Pokeweed Mitogen","authors":"K. J. Kleinwort, Roxane L Degroote, S. Hirmer, Lucia Korbonits, Lea Lorenz, Armin M Scholz, S. Hauck, C. Deeg","doi":"10.3390/proteomes10010007","DOIUrl":"https://doi.org/10.3390/proteomes10010007","url":null,"abstract":"We recently identified a deviant bovine immune phenotype characterized by hyperproliferation of lymphocytes after polyclonal stimulation. This phenotype was first discovered in dams that responded to PregSure BVD vaccination by producing pathological antibodies, triggering the fatal disease “bovine neonatal pancytopenia” in calves. The aim of the study was to gain deeper insights into molecular processes occurring in lymphocytes of immune phenotypes and the effect on their secretome after immune stimulation. Two discovery proteomic experiments were performed with unstimulated and Pokeweed Mitogen (PWM) stimulated lymphocytes, using label-free LC-MS/MS. In lymphocytes, 2447 proteins were quantified, and 1204 proteins were quantified in the secretome. Quantitative proteome analysis of immune deviant and control samples after PWM stimulation revealed clear differences. The increase in abundance of IL17A, IL17F, IL8, CCL5, LRRC59, and CLIC4 was higher in controls through mitogenic stimulation. In contrast, the abundance of IFNγ, IL2, IL2RA, CD83, and CD200 increased significantly more in immune deviant lymphocytes. Additional pathway enrichment analysis of differentially secreted proteins also yielded fundamental differences between the immune phenotypes. Our study provides a comprehensive dataset, which gives novel insights into proteome changes of lymphocytes from different bovine immune phenotypes. These differences point to the development of diverse immune responses of bovine immune phenotypes after immune stimulation.","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2022-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47850802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Acknowledgment to Reviewers of Proteomes in 2021 2021年蛋白质组评审员致谢

IF 3.3

Proteomes Pub Date : 2022-01-25 DOI: 10.3390/proteomes10010006

引用次数: 0

Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions. 霰弹枪蛋白质组学是研究植物蛋白质组学及其病原体和植物-病原体相互作用的有力工具

IF 4

Proteomes Pub Date : 2022-01-19 DOI: 10.3390/proteomes10010005

Sadegh Balotf, Richard Wilson, Robert S Tegg, David S Nichols, Calum R Wilson

{"title":"Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions.","authors":"Sadegh Balotf, Richard Wilson, Robert S Tegg, David S Nichols, Calum R Wilson","doi":"10.3390/proteomes10010005","DOIUrl":"10.3390/proteomes10010005","url":null,"abstract":"<p><p>The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.</p>","PeriodicalId":20877,"journal":{"name":"Proteomes","volume":"10 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2022-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8883913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69807240","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}

引用次数: 0