PROTEOMICS – Clinical Applications最新文献

{"title":"Editorial Board: Proteomics 2'23","authors":"","doi":"10.1002/prca.202370022","DOIUrl":"https://doi.org/10.1002/prca.202370022","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"1 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83314839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics profiling of kidney brush border membrane from rats using LC-MS/MS analysis.","authors":"Aiying Yu,&nbsp;Jingfu Zhao,&nbsp;Wenjing Peng,&nbsp;Shiv Pratap S Yadav,&nbsp;Bruce A Molitoris,&nbsp;Mark C Wagner,&nbsp;Yehia Mechref","doi":"10.1002/prca.202200063","DOIUrl":"https://doi.org/10.1002/prca.202200063","url":null,"abstract":"<p><strong>Purpose: </strong>Chronic kidney disease (CKD) is defined by a reduced renal function, that is, glomerular filtration rate, and the extent of kidney damage is assessed by determining serum creatinine levels and proteins in urine, diagnosed as proteinuria/albuminuria. Albuminuria increases with age and can result from glomerular and/or proximal tubule (PT) alterations. Brush border membranes (BBMs) on PT cells are important in maintaining the stability of PT functions.</p><p><strong>Experimental design: </strong>An LC-MS/MS bottom-up proteomics analysis of BBMs from four groups of rat models was applied to investigate protein abundance alterations associated with CKD progression. Moreover, systems biology analyses were used to identify key proteins that can provide insight into the different regulated molecular pathways and processes associated with CKD.</p><p><strong>Results: </strong>Our results indicated that 303 proteins showed significantly altered expressions from the severe CKD BBM group when compared to the control. Focusing on renal diseases, several proteins including Ctnnb1, Fah, and Icam1 were annotated to kidney damage and urination disorder. The up-regulation of Ctnnb1 (β-catenin) could contribute to CKD through the regulation of the WNT signaling pathway.</p><p><strong>Conclusion and clinical relevance: </strong>Overall, the study of protein abundance changes in BBMs from rat models helps to reveal protein corrections with important pathways and regulator effects involved in CKD. Although this study is focused on rat models, the results provided more information for a deeper insight into possible CKD mechanisms in humans.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 2","pages":"e2200063"},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9271967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serum proteomics profiling identifies a preliminary signature for the diagnosis of early-stage lung cancer.","authors":"Roberto Gasparri,&nbsp;Roberta Noberini,&nbsp;Alessandro Cuomo,&nbsp;Avinash Yadav,&nbsp;Davide Tricarico,&nbsp;Carola Salvetto,&nbsp;Patrick Maisonneuve,&nbsp;Valentina Caminiti,&nbsp;Giulia Sedda,&nbsp;Angela Sabalic,&nbsp;Tiziana Bonaldi,&nbsp;Lorenzo Spaggiari","doi":"10.1002/prca.202200093","DOIUrl":"https://doi.org/10.1002/prca.202200093","url":null,"abstract":"<p><strong>Purpose: </strong>Lung cancer is the most common cause of death from cancer worldwide, largely due to late diagnosis. Thus, there is an urgent need to develop new approaches to improve the detection of early-stage lung cancer, which would greatly improve patient survival.</p><p><strong>Experimental design: </strong>The quantitative protein expression profiles of microvesicles isolated from the sera from 46 lung cancer patients and 41 high-risk non-cancer subjects were obtained using a mass spectrometry method based on a peptide library matching approach.</p><p><strong>Results: </strong>We identified 33 differentially expressed proteins that allow discriminating the two groups. We also built a machine learning model based on serum protein expression profiles that can correctly classify the majority of lung cancer cases and that highlighted a decrease in the levels of Arysulfatase A (ARSA) as the most discriminating factor found in tumors.</p><p><strong>Conclusions and clinical relevance: </strong>Our study identified a preliminary, non-invasive protein signature able to discriminate with high specificity and selectivity early-stage lung cancer patients from high-risk healthy subjects. These results provide the basis for future validation studies for the development of a non-invasive diagnostic tool for lung cancer.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 2","pages":"e2200093"},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9272979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Masthead: Proteomics 2'23","authors":"","doi":"10.1002/prca.202370023","DOIUrl":"https://doi.org/10.1002/prca.202370023","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"202 S606","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72407653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exosomal proteins as a source of biomarkers in colon cancer-derived peritoneal carcinomatosis - A pilot study.","authors":"Paul A Vallejos,&nbsp;Ryan N Fuller,&nbsp;Janviere Kabagwira,&nbsp;Mei Li Kwong,&nbsp;Amber Gonda,&nbsp;James R W McMullen,&nbsp;Natasha Le,&nbsp;Matthew J Selleck,&nbsp;Lance D Miller,&nbsp;Christopher C Perry,&nbsp;Maheswari Senthil,&nbsp;Nathan R Wall","doi":"10.1002/prca.202100085","DOIUrl":"https://doi.org/10.1002/prca.202100085","url":null,"abstract":"<p><strong>Purpose: </strong>Peritoneal carcinomatosis (PC), metastasized from colorectal cancer (CRC), remains a highly lethal disease. Outcomes of PC is significantly influenced by the amount of intra-abdominal tumor burden and therefore diagnostic tests that facilitate earlier diagnosis could improve PC treatment and patient outcomes.</p><p><strong>Experimental design: </strong>Using mass-spectrometry-based proteomics, we characterized the protein features of circulating exosomes in the context of CRC PC, CRC with liver metastasis, and primary CRC limited to the colon. We profiled exosomes isolated from patient plasma to identify exosome-associated protein cargoes released by these cancer types.</p><p><strong>Results: </strong>Analysis of the resulting data identified metastasis-specific exosome protein signatures. Bioinformatic analyses confirmed enrichment of proteins annotated to vesicle-associated processes and intracellular compartments, as well as representation of cancer hallmark functions and processes.</p><p><strong>Conclusion and clinical relevance: </strong>This research yielded distinct protein profiles for the CRC patient groups and suggests the utility of plasma exosome proteomic analysis for a better understanding of PC development and metastasis.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 2","pages":"e2100085"},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9620886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer.","authors":"Abhilash Barpanda,&nbsp;Chaitanya Tuckley,&nbsp;Arka Ray,&nbsp;Arghya Banerjee,&nbsp;Siddhartha P Duttagupta,&nbsp;Chetan Kantharia,&nbsp;Sanjeeva Srivastava","doi":"10.1002/prca.202200062","DOIUrl":"https://doi.org/10.1002/prca.202200062","url":null,"abstract":"<p><strong>Purpose: </strong>Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer.</p><p><strong>Experimental design: </strong>The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease.</p><p><strong>Results: </strong>The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 2","pages":"e2200062"},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9320458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma proteomics identify potential severity biomarkers from COVID-19 associated network.","authors":"Ayse Tugce Sahin,&nbsp;Ali Yurtseven,&nbsp;Sina Dadmand,&nbsp;Gulin Ozcan,&nbsp;Busra A Akarlar,&nbsp;Nazli Ezgi Ozkan Kucuk,&nbsp;Aydanur Senturk,&nbsp;Onder Ergonul,&nbsp;Fusun Can,&nbsp;Nurcan Tuncbag,&nbsp;Nurhan Ozlu","doi":"10.1002/prca.202200070","DOIUrl":"https://doi.org/10.1002/prca.202200070","url":null,"abstract":"<p><strong>Purpose: </strong>Coronavirus disease 2019 (COVID-19) continues to threaten public health globally. Severe acute respiratory coronavirus type 2 (SARS-CoV-2) infection-dependent alterations in the host cell signaling network may unveil potential target proteins and pathways for therapeutic strategies. In this study, we aim to define early severity biomarkers and monitor altered pathways in the course of SARS-CoV-2 infection.</p><p><strong>Experimental design: </strong>We systematically analyzed plasma proteomes of COVID-19 patients from Turkey by using mass spectrometry. Different severity grades (moderate, severe, and critical) and periods of disease (early, inflammatory, and recovery) are monitored. Significant alterations in protein expressions are used to reconstruct the COVID-19 associated network that was further extended to connect viral and host proteins.</p><p><strong>Results: </strong>Across all COVID-19 patients, 111 differentially expressed proteins were found, of which 28 proteins were unique to our study mainly enriching in immunoglobulin production. By monitoring different severity grades and periods of disease, CLEC3B, MST1, and ITIH2 were identified as potential early predictors of COVID-19 severity. Most importantly, we extended the COVID-19 associated network with viral proteins and showed the connectedness of viral proteins with human proteins. The most connected viral protein ORF8, which has a role in immune evasion, targets many host proteins tightly connected to the deregulated human plasma proteins.</p><p><strong>Conclusions and clinical relevance: </strong>Plasma proteomes from critical patients are intrinsically clustered in a distinct group than severe and moderate patients. Importantly, we did not recover any grouping based on the infection period, suggesting their distinct proteome even in the recovery phase. The new potential early severity markers can be further studied for their value in the clinics to monitor COVID-19 prognosis. Beyond the list of plasma proteins, our disease-associated network unravels altered pathways, and the possible therapeutic targets in SARS-CoV-2 infection by connecting human and viral proteins. Follow-up studies on the disease associated network that we propose here will be useful to determine molecular details of viral perturbation and to address how the infection affects human physiology.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 2","pages":"e2200070"},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9874836/pdf/PRCA-9999-2200070.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9635383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein sample preparation for tissue distribution study.","authors":"Linjia Cheng,&nbsp;Yilu Xu,&nbsp;Kangling Zhu,&nbsp;Bin Liang,&nbsp;Shuyan Zhang,&nbsp;Pingsheng Liu","doi":"10.1002/prca.202200088","DOIUrl":"https://doi.org/10.1002/prca.202200088","url":null,"abstract":"<p><strong>Purpose: </strong>The distribution and expression level of a protein among animal tissues is indicative of its possible roles. It is important to establish a generally applicable method to prepare protein samples with high-quality and achieve near 100% recovery of proteins from animal tissues.</p><p><strong>Experimental design: </strong>During preparation, to sufficiently dissolve and maintain stability of almost all proteins from tissues, as well as to avoid most contaminations affecting protein detection, 2×SDS Sample Buffer, sonication and trichloroacetic acid precipitation are applied.</p><p><strong>Results: </strong>Here we provide a relatively simple, reproducible, and broadly applicable method for studying protein distribution in most tissues, in which the issues resulting from protein degradation and modification during sample preparation and assay interference by other cellular components like neutral lipids and glycogen could be overcome. Furthermore, this method represents the protein content by equal wet tissue mass, which is a better means to present the expression level of a protein in various tissues. High-quality protein samples from almost all tissues could be prepared.</p><p><strong>Conclusions and clinical relevance: </strong>The samples produced are amenable to tissue distribution analysis by Western blotting and for silver/Coomassie staining, proteomics, and other protein analyses, which would contribute to potential biomarkers or treatments for a disease.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 2","pages":"e2200088"},"PeriodicalIF":2.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9259798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics of azoospermia: Towards the discovery of reliable markers for non-invasive diagnosis.","authors":"Aleksandar Rusevski,&nbsp;Dijana Plaseska-Karanfilska,&nbsp;Katarina Davalieva","doi":"10.1002/prca.202200060","DOIUrl":"https://doi.org/10.1002/prca.202200060","url":null,"abstract":"<p><strong>Purpose: </strong>Azoospermia, as the most severe form of male infertility, no longer indicates sterility due to modern medical advancements. The current diagnostic procedure based on testicular biopsy has several drawbacks which urges the development of novel, non-invasive diagnostic procedures based on biomarkers. In the last two decades, there have been many proteomics studies investigating potential azoospermia biomarkers. In this review, we aimed to provide a critical evaluation of these studies.</p><p><strong>Experimental design: </strong>Published articles were gathered by systematic literature search using Pubmed, Science Direct, and Google Scholar databases until March 2022 and were further preselected to include only studies on human samples.</p><p><strong>Results: </strong>A detailed review of these studies encompassed the proteomics platforms, sources of material, proposed candidate biomarkers, and their potential diagnostic specificity and sensitivity. In addition, emphasis was put on the top, most identified and validated biomarker candidates and their potential for discriminating azoospermia types and subtypes as well as predicting sperm retrieval success rate.</p><p><strong>Conclusions: </strong>Proteomics research of azoospermia has laid the groundwork for the development of a more streamlined biomarker testing. The future research should be focused on well-designed studies including samples from all types/subtypes as well as further testing of the most promising biomarkers identified so far.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 1","pages":"e2200060"},"PeriodicalIF":2.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10849645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tandem mass tag-based quantitative proteomic analysis of cervical cancer.","authors":"Mohammed F Aljawad,&nbsp;Abdul Hussein M Al Faisal,&nbsp;Mohammed F Alqanbar,&nbsp;Phillip A Wilmarth,&nbsp;Basima Q Hassan","doi":"10.1002/prca.202100105","DOIUrl":"https://doi.org/10.1002/prca.202100105","url":null,"abstract":"<p><strong>Background: </strong>Cervical cancer is a common cancer in women caused by high-risk human papillomavirus (Hr-HPV). Many potential biomarkers have been proposed for precancerous lesions and cancer diagnosis and some of these markers studied for prognosis. This study determined potential biomarkers for cervical cancer diagnosis in regard to HPV genotype by using isobaric labeling quantitative proteomics.</p><p><strong>Methods: </strong>in the current study, there were 75 formalin fixed paraffin embedded (FFPE) uterine cervical samples that used to determine the 14 HPV genotypes and the viral load of each genotype was determined. The tandem mass tag (TMT) proteomic work was performed on four FFPE samples of cervical cancer and four FFPE of control samples. The validation of biomarkers from cervical proteome were evaluated using Immunohistochemistry (IHC) testing.</p><p><strong>Results: </strong>The most frequent HPV genotype among all other genotypes was HPV 16. There were 2753 proteins quantified by TMT and 336 of these proteins had significant differential abundances. KPNA2, MCM2, COL1A1, and DCN were selected based on functional enrichment analysis and validated by Immunohistochemistry (IHC) testing. The staining of IHC confirmed the upregulation of KPNA2 and MCM2 expression in cervical neoplasia and the downregulation of DCN and COL1A1 in some cervical cancer group subjects.</p><p><strong>Conclusion: </strong>The KPNA2 marker was compared to other previously reported biomarkers and is a putative biomarker to be validated in further studies, specifically the relationship with HPV load.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 1","pages":"e2100105"},"PeriodicalIF":2.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10625309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}