PROTEOMICS – Clinical Applications最新文献

{"title":"Editorial Board: Proteomics 4'23","authors":"","doi":"10.1002/prca.202370042","DOIUrl":"https://doi.org/10.1002/prca.202370042","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"29 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88801977","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 4'23","authors":"","doi":"10.1002/prca.202370043","DOIUrl":"https://doi.org/10.1002/prca.202370043","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87202427","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":"Analytical validation of a multi-protein, serum-based assay for disease activity assessments in multiple sclerosis.","authors":"Ferhan Qureshi,&nbsp;Wayne Hu,&nbsp;Louisa Loh,&nbsp;Hemali Patel,&nbsp;Maria DeGuzman,&nbsp;Michael Becich,&nbsp;Fatima Rubio da Costa,&nbsp;Victor Gehman,&nbsp;Fujun Zhang,&nbsp;John Foley,&nbsp;Tanuja Chitnis","doi":"10.1002/prca.202200018","DOIUrl":"https://doi.org/10.1002/prca.202200018","url":null,"abstract":"<p><strong>Purpose: </strong>To characterize and analytically validate the MSDA Test, a multi-protein, serum-based biomarker assay developed using Olink^® PEA methodology.</p><p><strong>Experimental design: </strong>Two lots of the MSDA Test panel were manufactured and subjected to a comprehensive analytical characterization and validation protocol to detect biomarkers present in the serum of patients with multiple sclerosis (MS). Biomarker concentrations were incorporated into a final algorithm used for calculating four Disease Pathway scores (Immunomodulation, Neuroinflammation, Myelin Biology, and Neuroaxonal Integrity) and an overall Disease Activity score.</p><p><strong>Results: </strong>Analytical characterization demonstrated that the multi-protein panel satisfied the criteria necessary for a fit-for-purpose validation considering the assay's intended clinical use. This panel met acceptability criteria for 18 biomarkers included in the final algorithm out of 21 biomarkers evaluated. VCAN was omitted based on factors outside of analytical validation; COL4A1 and GH were excluded based on imprecision and diurnal variability, respectively. Performance of the four Disease Pathway and overall Disease Activity scores met the established acceptability criteria.</p><p><strong>Conclusions and clinical relevance: </strong>Analytical validation of this multi-protein, serum-based assay is the first step in establishing its potential utility as a quantitative, minimally invasive, and scalable biomarker panel to enhance the standard of care for patients with MS.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 3","pages":"e2200018"},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9627145","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":"Two effective models based on comprehensive lipidomics and metabolomics can distinguish BC versus HCs, and TNBC versus non-TNBC.","authors":"Yu Jin,&nbsp;Shuoqing Fan,&nbsp;Wenna Jiang,&nbsp;Jingya Zhang,&nbsp;Lexin Yang,&nbsp;Jiawei Xiao,&nbsp;Haohua An,&nbsp;Li Ren","doi":"10.1002/prca.202200042","DOIUrl":"https://doi.org/10.1002/prca.202200042","url":null,"abstract":"<p><strong>Background: </strong>Lipidomics and metabolomics are closely related to tumor phenotypes, and serum lipoprotein subclasses and small-molecule metabolites are considered as promising biomarkers for breast cancer (BC) diagnosis. This study aimed to explore potential biomarker models based on lipidomic and metabolomic analysis that could distinguish BC from healthy controls (HCs) and triple-negative BC (TNBC) from non-TNBC.</p><p><strong>Methods: </strong>Blood samples were collected from 114 patients with BC and 75 HCs. A total of 112 types of lipoprotein subclasses and 30 types of small-molecule metabolites in the serum were detected by ¹ H-NMR. All lipoprotein subclasses and small-molecule metabolites were subjected to a three-step screening process in the order of significance (p < 0.05), univariate regression (p < 0.1), and lasso regression (nonzero coefficient). Discriminant models of BC versus HCs and TNBC versus non-TNBC were established using binary logistic regression.</p><p><strong>Results: </strong>We developed a valid discriminant model based on three-biomarker panel (formic acid, TPA2, and L6TG) that could distinguish patients with BC from HCs. The area under the receiver operating characteristic curve (AUC) was 0.999 (95% confidence interval [CI]: 0.995-1.000) and 0.990 (95% CI: 0.959-1.000) in the training and validation sets, respectively. Based on the panel (D-dimer, CA15-3, CEA, L5CH, glutamine, and ornithine), a discriminant model was established to differentiate between TNBC and non-TNBC, with AUC of 0.892 (95% CI: 0.778-0.967) and 0.905 (95% CI: 0.754-0.987) in the training and validation sets, respectively.</p><p><strong>Conclusion: </strong>This study revealed lipidomic and metabolomic differences between BC versus HCs and TNBC versus non-TNBC. Two validated discriminatory models established against lipidomic and metabolomic differences can accurately distinguish BC from HCs and TNBC from non-TNBC.</p><p><strong>Impact: </strong>Two validated discriminatory models can be used for early BC screening and help BC patients avoid time-consuming, expensive, and dangerous BC screening.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 3","pages":"e2200042"},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9991340","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 3'23","authors":"","doi":"10.1002/prca.202370033","DOIUrl":"https://doi.org/10.1002/prca.202370033","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"12 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81131272","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":"Fast and straightforward simultaneous quantification of multiple apolipoproteins in human serum on a high-throughput LC-MS/MS platform.","authors":"Hyojin Kim,&nbsp;Won Suk Yang,&nbsp;Dongheui An,&nbsp;Sang-Guk Lee,&nbsp;Je-Hyun Baek","doi":"10.1002/prca.202200056","DOIUrl":"https://doi.org/10.1002/prca.202200056","url":null,"abstract":"<p><strong>Purpose: </strong>Apolipoprotein monitoring is useful for diagnosing cardiovascular diseases, as they are risk factors of arteriosclerosis and other neutral fat-related diseases. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is advantageous for simultaneous apolipoprotein quantification, differentiation, and standardization including their isoforms. However, fast and straightforward sample preparation that retains quantification accuracy remains challenging in clinical MS.</p><p><strong>Experimental design: </strong>We developed a simultaneous assay for serum apolipoprotein A-I (ApoA-I), apolipoprotein B100 family, and apolipoprotein C-III (ApoC-III) using a high-throughput LC-MS/MS platform coupled with a BRAVO system. The assay was simplified by using sodium deoxycholate and trypsin/lys-C without reduction and alkylation steps.</p><p><strong>Results: </strong>Simple sample preparation reduced turnaround time by 1.5 h and neat goat serum was chosen as an optimal calibration matrix for accurate protein quantification. Assay precision, linearity, correlation, accuracy, limit of detection (LOD), limit of quantitation (LOQ), and carryover were validated according to CLSI guidelines over 41 days using more than 100 human serum samples. Good correlation compared with turbidimetric immunoassay (TIA) was observed by Deming regression for all analytes.</p><p><strong>Conclusions and clinical relevance: </strong>A high-throughput LC-MS/MS and BRAVO assay for simultaneous apolipoprotein analysis was validated using a simple preparation method with a human serum calibrator in goat serum matrix. The assay is readily expandable to include other target serum proteins and/or their isoforms.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 3","pages":"e2200056"},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9626614","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":"Optimised plasma sample preparation and LC-MS analysis to support large-scale proteomic analysis of clinical trial specimens: Application to the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial.","authors":"Matthew B O'Rourke, Andrzej S Januszewski, David R Sullivan, Imre Lengyel, Alan J Stewart, Swati Arya, Ronald C Ma, Sanjeev Galande, Anandwardhan A Hardikar, Mugdha V Joglekar, Anthony C Keech, Alicia J Jenkins, Mark P Molloy","doi":"10.1002/prca.202200106","DOIUrl":"10.1002/prca.202200106","url":null,"abstract":"<p><strong>Purpose: </strong>Robust, affordable plasma proteomic biomarker workflows are needed for large-scale clinical studies. We evaluated aspects of sample preparation to allow liquid chromatography-mass spectrometry (LC-MS) analysis of more than 1500 samples from the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial of adults with type 2 diabetes.</p><p><strong>Methods: </strong>Using LC-MS with data-independent acquisition we evaluated four variables: plasma protein depletion, EDTA or citrated anti-coagulant blood collection tubes, plasma lipid depletion strategies and plasma freeze-thaw cycles. Optimised methods were applied in a pilot study of FIELD participants.</p><p><strong>Results: </strong>LC-MS of undepleted plasma conducted over a 45 min gradient yielded 172 proteins after excluding immunoglobulin isoforms. Cibachrome-blue-based depletion yielded additional proteins but with cost and time expenses, while immunodepleting albumin and IgG provided few additional identifications. Only minor variations were associated with blood collection tube type, delipidation methods and freeze-thaw cycles. From 65 batches involving over 1500 injections, the median intra-batch quantitative differences in the top 100 proteins of the plasma external standard were less than 2%. Fenofibrate altered seven plasma proteins.</p><p><strong>Conclusions and clinical relevance: </strong>A robust plasma handling and LC-MS proteomics workflow for abundant plasma proteins has been developed for large-scale biomarker studies that balance proteomic depth with time and resource costs.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 3","pages":"e2200106"},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10909541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10008445","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":"Integrated glycomics strategy for galactosylated-N-glycans recognized by Bandeiraea Simplicifolia Lectin I in salivary proteins associated with lung cancer.","authors":"Fan Zhang,&nbsp;Mingyuan Xie,&nbsp;Zhen Tang,&nbsp;Hailong Xie,&nbsp;Lixin Yue,&nbsp;Xilong Wang,&nbsp;Jiajun Yang,&nbsp;Yanhua Chen,&nbsp;Zheng Li","doi":"10.1002/prca.202200012","DOIUrl":"https://doi.org/10.1002/prca.202200012","url":null,"abstract":"<p><strong>Purpose: </strong>Lung cancer (LC) is the leading cause of cancer-related deaths worldwide, mainly due to late diagnosis and poor prognosis. Saliva is an important source for discovering biomarkers and contains an abundance of biological information. The purpose of this study was to determine whether galactosylation levels of salivary proteins are associated with LC.</p><p><strong>Experimental design: </strong>First, we analyzed the alterations of the glycopatterns recognized by Bandeiraea Simplicifolia Lectin I (BS-I) in five groups (healthy volunteers [HV]: 28, benign pulmonary disease [BPD]: 27, lung adenocarcinoma [ADC]: 39, squamous cell carcinoma [SCC]: 28, small-cell lung cancer [SCLC]: 22) of 144 saliva samples using lectin microarrays. Pooled samples from each group were subsequently validated by the lectin blotting technique. Finally, the N-glycan profiles of their salivary glycoproteins isolated by the BS-I-magnetic particle conjugates from pooled samples for each group were analyzed by MALDI-TOF/TOF-MS.</p><p><strong>Results: </strong>The results showed that the expression level of galactosylated glycans recognized by BS-I was significantly increased in patients with LC compared with BPD and HV. Receiver operating characteristic (ROC) analysis indicated that the levels of salivary glycopattern recognized by BS-I could discriminate lung disease (BPD, ADC, SCC, and SCLC) and HV with an AUC of 0.700 (95% CI: 0.589-0.812), and discriminate LC and BPD with an AUC of 0.860 (95% CI: 0.763-0.956). Also, the proportion of galactosylated N-glycans in ADC (38.4%), SCC (43.1%), and SCLC (39.5%) increased compared to HV (30.1%) and BPD (33.7%), and two galactosylated N-glycan peaks (m/z 1828.683, 2418.853) could be identified only in the LC groups (ADC, SCC, and SCLC).</p><p><strong>Conclusions and clinical relevance: </strong>These findings could provide crucial information on galactosylated N-linked glycans associated with LC and facilitate the study of LC biomarkers based on precise alterations of galactosylated N-glycans in saliva.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 3","pages":"e2200012"},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9634433","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":"Tape stripped stratum corneum samples are suitable for diagnosis and comprehensive proteomic investigation in mycosis fungoides.","authors":"Hafsa Anees Qureshi,&nbsp;Ali Azimi,&nbsp;Jillian Wells,&nbsp;Pablo Fernandez-Penas","doi":"10.1002/prca.202200039","DOIUrl":"https://doi.org/10.1002/prca.202200039","url":null,"abstract":"<p><strong>Background: </strong>Mycosis Fungoides (MF) is a common cutaneous T-cell lymphoma. It can sometimes be challenging to diagnose MF using current clinico-histopathological criteria. Non-invasive molecular profiling analysis has the potential to aid the diagnosis and understanding of MF.</p><p><strong>Method: </strong>Lesional and body site matched normal stratum corneum samples were obtained from the same MF patients (n = 28) using adhesive discs, followed by proteomic analyses using data-independent acquisition mass spectrometry (DIA-MS). Differential abundance analyses and bioinformatic analyses were performed to identify differentially abundant proteins and altered biofunctions between the MF and normal stratum corneum samples.</p><p><strong>Results: </strong>In total, 1303 proteins were identified, of which 290 proteins were significantly changed in the MF cohort compared to the normal stratum corneum. Ingenuity pathway analysis (IPA) predicted the significant inhibition of cell death of cancer cells and significant activation of immune-related activities and viral infection in the MF lesions. MF lesions were also associated with upstream regulators relating to immuno-oncologic dysfunctions. The top-250 variating proteins efficiently separated normal stratum corneum from matched MF samples.</p><p><strong>Conclusion: </strong>Non-invasive proteomic analysis could transform the diagnosis of MF by reducing the need for invasive biopsy. The identification of altered biological functions may serve as useful biomarkers to predict MF progression.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 3","pages":"e2200039"},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9639325","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":"Editorial Board: Proteomics 3'23","authors":"","doi":"10.1002/prca.202370032","DOIUrl":"https://doi.org/10.1002/prca.202370032","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"29 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89561369","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}