PROTEOMICS – Clinical Applications最新文献

{"title":"Comparative proteomics of saliva of healthy and gingivitis individuals from Rio de Janeiro.","authors":"Carlos Vinicius Ferreira da Silva, Youssef Bacila Sade, Sandra Mara Naressi Scapin, Carina M da Silva-Boghossian, Eidy de Oliveira Santos","doi":"10.1002/prca.202200098","DOIUrl":"10.1002/prca.202200098","url":null,"abstract":"In this work, we identified human and bacterial proteomes in the saliva from volunteers with gingivitis or healthy.","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 5","pages":"e2200098"},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10217199","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":"Mass spectrometry-based proteomic profiling of sonicate fluid differentiates Staphylococcus aureus periprosthetic joint infection from non-infectious failure: A pilot study.","authors":"Cody R Fisher,&nbsp;Kiran K Mangalaparthi,&nbsp;Kerryl E Greenwood-Quaintance,&nbsp;Matthew P Abdel,&nbsp;Akhilesh Pandey,&nbsp;Robin Patel","doi":"10.1002/prca.202200071","DOIUrl":"10.1002/prca.202200071","url":null,"abstract":"<p><strong>Purpose: </strong>This pilot study aimed to use proteomic profiling of sonicate fluid samples to compare host response during Staphylococcus aureus-associated periprosthetic joint infection (PJI) and non-infected arthroplasty failure (NIAF) and identify potential novel biomarkers differentiating the two.</p><p><strong>Experimental design: </strong>In this pilot study, eight sonicate fluid samples (four from NIAF and four from S. aureus PJI) were studied. Samples were reduced, alkylated, and trypsinized overnight, followed by analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a high-resolution Orbitrap Eclipse mass spectrometer. MaxQuant software suite was used for protein identification, filtering, and label-free quantitation.</p><p><strong>Results: </strong>Principal component analysis of the identified proteins clearly separated S. aureus PJI and NIAF samples. Overall, 810 proteins were identified based on their detection in at least three out of four samples from each group; 35 statistically significant differentially abundant proteins (DAPs) were found (two-sample t-test p-values ≤0.05 and log₂ fold-change values ≥2 or ≤-2). Gene ontology pathway analysis found that microbial defense responses, specifically those related to neutrophil activation, to be increased in S. aureus PJI compared to NIAF samples.</p><p><strong>Conclusion and clinical relevance: </strong>Proteomic profiling of sonicate fluid using LC-MS/MS differentiated S. aureus PJI and NIAF in this pilot study. Further work is needed using a larger sample size and including non-S. aureus PJI and a diversty of NIAF-types.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 5","pages":"e2200071"},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10509319/pdf/nihms-1890045.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10271512","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":"Masthead: Proteomics 5'23","authors":"","doi":"10.1002/prca.202370053","DOIUrl":"https://doi.org/10.1002/prca.202370053","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"116 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139344553","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":"Association analysis of hepatocellular carcinoma-related hub proteins and hub genes.","authors":"Xinhong Zhang,&nbsp;Boyan Zhang,&nbsp;Yawei Zhang,&nbsp;Fan Zhang","doi":"10.1002/prca.202200090","DOIUrl":"10.1002/prca.202200090","url":null,"abstract":"<p><strong>Purpose: </strong>Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. The occurrence and development of HCC are closely related to epigenetic modifications. Epigenetic modifications can regulate gene expression and related functions through DNA methylation. This paper presents an association analysis method of HCC-related hub proteins and hub genes.</p><p><strong>Experimental design: </strong>Bioinformatics analysis of HCC-related DNA methylation data is carried out to clarify the molecular mechanism of HCC-related genes and to find hub genes (genes with more connections in the network) by constructing in the gene interaction network. This paper proposes an accurate prediction method of protein-protein interaction (PPI) based on deep learning model DeepSG2PPI. The trained DeepSG2PPI model predicts the interaction relationship between the synthetic proteins regulated by HCC-related genes.</p><p><strong>Results: </strong>This paper finds that four genes are the intersection of hub genes and hub proteins. The four genes are: FBL, CCNB2, ALDH18A1, and RPLP0. The association of RPLP0 gene with HCC is a new finding of this study. RPLP0 is expected to become a new biomarker for the treatment, diagnosis, and prognosis of HCC. The four proteins corresponding to the four genes are: ENSP00000221801, ENSP00000288207, ENSP00000360268, and ENSP00000449328.</p><p><strong>Conclusions and clinical relevance: </strong>The association between the hub genes with the hub proteins is analyzed. The mutual verification of the hub genes and the hub proteins can obtain more credible HCC-related genes and proteins, which is helpful for the diagnosis, treatment, and drug development of HCC.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 5","pages":"e2200090"},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10217718","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":"Quantitative proteomic analysis of bronchoalveolar lavage fluids from patients with small cell lung cancers.","authors":"Hung M Vu,&nbsp;Hazara Begum Mohammad,&nbsp;Thy N C Nguyen,&nbsp;Jun Hyung Lee,&nbsp;Yeji Do,&nbsp;Ji-Youn Sung,&nbsp;Seung Hyeun Lee,&nbsp;Min-Sik Kim","doi":"10.1002/prca.202300011","DOIUrl":"10.1002/prca.202300011","url":null,"abstract":"<p><strong>Purpose: </strong>Small cell lung cancer (SCLC) is one of the malignant cancers with aggressive progression and poor prognosis. Bronchoalveolar lavage fluid (BALF) has been arising recently as a potential source of biomarkers for lung cancers. In this study, we performed quantitative BALF proteomic analysis to identify potential biomarkers for SCLC.</p><p><strong>Experimental design: </strong>BALF were collected from tumor-bearing lungs and non-tumor lungs of five SCLC patients. Then, BALF proteomes were prepared for a TMT-based quantitative mass spectrometry analysis. Differentially expressed proteins (DEP) were identified when considering individual variation. Potential SCLC biomarker candidates were validated by immunohistochemistry (IHC). A public database of multiple SCLC cell lines was used to evaluate the correlation of these markers with SCLC subtypes and chemo-drug responses.</p><p><strong>Results: </strong>We identified 460 BALF proteins in SCLC patients and observed considerable individual variation among the patients. Immunohistochemical analysis and bioinformatics resulted in the identification of CNDP2 and RNPEP as potential subtype markers for ASCL1 and NEUROD1, respectively. In addition, CNDP2 was found to be positively correlated with responses to etoposide, carboplatin, and irinotecan.</p><p><strong>Conclusions and clinical relevance: </strong>BALF is an emerging source of biomarkers, making it useful for the diagnosis and prognosis of lung cancers. We characterized the proteomes of paired BALF samples collected from tumor-bearing and non-tumor lungs of SCLC patients. Several proteins were found elevated in tumor-bearing BALF, and especially CNDP2 and RNPEP appeared to be potential indicators for ASLC1-high and NEUROD1-high subtypes of SCLC, respectively. The positive correlation of CNDP2 with chemo-drug responses would help to make decisions for treatment of SCLC patients. These putative biomarkers could be comprehensively investigated for a clinical use towards precision medicine.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 5","pages":"e2300011"},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10566906","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":"The crosstalking of lactate-Histone lactylation and tumor.","authors":"Yao Rong,&nbsp;Fengyuan Dong,&nbsp;Guiqian Zhang,&nbsp;Mingzheng Tang,&nbsp;Xiashuang Zhao,&nbsp;Yan Zhang,&nbsp;Pengxian Tao,&nbsp;Hui Cai","doi":"10.1002/prca.202200102","DOIUrl":"10.1002/prca.202200102","url":null,"abstract":"<p><p>Lactate was once considered to be a by-product of energy metabolism, but its unique biological value was only gradually explored with the advent of the Warburg effect. As an end product of glycolysis, lactate can act as a substrate for energy metabolism, a signal transduction molecule, a regulator of the tumor microenvironment and immune cells, and a regulator of the deubiquitination of specific enzymes, and is involved in various biological aspects of tumor regulation, including energy shuttling, growth and invasion, angiogenesis and immune escape. Furthermore, we describe a novel lactate-dependent epigenetic modification, namely histone lactylation modification, and review the progress of its study in tumors, mainly involving the reprogramming of tumor phenotypes, regulation of related gene expression, mediation of the glycolytic process in tumor stem cells (CSCs) and influence on the tumor immune microenvironment. The study of epigenetic regulation of tumor genes by histone modification is still in its infancy, and we expect that by summarizing the effects of lactate and histone modification on tumor and related gene regulation, we will clarify the scientific significance of future histone modification studies and the problems to be solved, and open up new fields for targeted tumor therapy.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 5","pages":"e2200102"},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10215867","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":"Intraoperative plasma proteomic changes in cardiac surgery: In search of biomarkers of post-operative delirium.","authors":"Kwame Wiredu,&nbsp;Sean O'Connor,&nbsp;Heba Naseem,&nbsp;Brooke L Brauer,&nbsp;Arminja N Kettenbach,&nbsp;Hildreth R Frost,&nbsp;Shahzad Shaefi,&nbsp;Scott A Gerber","doi":"10.1002/prca.202200066","DOIUrl":"10.1002/prca.202200066","url":null,"abstract":"<p><strong>Purpose: </strong>Delirium presents a significant healthcare burden. It complicates post-operative care in up to 50% of cardiac surgical patients with worse outcomes, longer hospital stays and higher cost of care. Moreover, the nature of delirium following cardiac surgery with cardiopulmonary bypass (CPB) remains unclear, the underlying pathobiology is poorly understood, status quo diagnostic methods are subjective, and diagnostic biomarkers are currently lacking.</p><p><strong>Objective: </strong>To identify diagnostic biomarkers of delirium and for insights into possible neuronal pathomechanisms.</p><p><strong>Experimental design: </strong>Comparative proteomic analyses were performed on plasma samples from a nested matched cohort of patients who underwent cardiac surgery. Validation by targeted proteomics was performed in an independent set of samples. Biomarkers were assessed for biological functions and diagnostic accuracy.</p><p><strong>Results: </strong>Forty-seven percent of subjects demonstrated delirium. Of 3803 proteins identified from patient samples by multiplexed quantitative proteomics, 16 were identified as signatures of exposure to CPB, and 11 biomarkers distinguished delirium cases from non-cases (AuROC = 93%). Notable among these biomarkers are C-reactive protein, serum amyloid A-1 and cathepsin-B.</p><p><strong>Conclusions and clinical relevance: </strong>The interplay of systemic and central inflammatory markers sheds new light on delirium pathogenesis. This work suggests that accurate identification of cases may be achievable using panels of biomarkers.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 4","pages":"e2200066"},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10290728/pdf/nihms-1897022.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9869692","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":"Proteoglycans in breast cancer, identification and characterization by LC-MS/MS assisted proteomics approach: A review.","authors":"K K Ajeeshkumar,&nbsp;Ankita Sahu,&nbsp;Astha Singh,&nbsp;A R Nisha,&nbsp;Niladri Sekhar Chatterjee,&nbsp;Suseela Mathew,&nbsp;Saurabh Verma","doi":"10.1002/prca.202200046","DOIUrl":"https://doi.org/10.1002/prca.202200046","url":null,"abstract":"<p><strong>Purpose: </strong>Proteoglycans (PGs) are negatively charged macromolecules containing a core protein and single or several glycosaminoglycan chains attached by covalent bond. They are distributed in all tissues, including extracellular matrix (ECM), cell surface, and basement membrane. They are involved in major pathways and cell signalling cascades which modulate several vital physiological functions of the body. They have also emerged as a target molecule for cancer treatment and as possible biomarkers for early cancer detection. Among cancers, breast cancer is a highly invasive and heterogenous type and has become the major cause of mortality especially among women. So, this review revisits the studies on PGs characterization in breast cancer using LC-MS/MS-based proteomics approach, which will be further helpful for identification of potential PGs-based biomarkers or therapeutic targets.</p><p><strong>Experimental design: </strong>There is a lack of comprehensive knowledge on the use of LC-MS/MS-based proteomics approaches to identify and characterize PGs in breast cancer.</p><p><strong>Results: </strong>LC-MS/MS assisted PGs characterization in breast cancer revealed the vital PGs in breast cancer invasion and progression. In addition, comprehensive profiling and characterization of PGs in breast cancer are efficiently carried out by this approach.</p><p><strong>Conclusions: </strong>Proteomics techniques including LC-MS/MS-based identification of proteoglycans is effectively carried out in breast cancer research. Identification of expression at different stages of breast cancer is a major challenge, and LC-MS/MS-based profiling of PGs can boost novel strategies to treat breast cancer, which involve targeting PGs, and also aid early diagnosis using PGs as biomarkers.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 4","pages":"e2200046"},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10230282","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":"Urinary collagen peptides: Source of markers for bone metabolic processes in kidney transplant recipients.","authors":"David Marx,&nbsp;Dany Anglicheau,&nbsp;Sophie Caillard,&nbsp;Bruno Moulin,&nbsp;Audrey Kochman,&nbsp;Harald Mischak,&nbsp;Agnieszka Latosinska,&nbsp;Frank Bienaimé,&nbsp;Dominique Prié,&nbsp;Pierre Marquet,&nbsp;Peggy Perrin,&nbsp;Wilfried Gwinner,&nbsp;Jochen Metzger","doi":"10.1002/prca.202200118","DOIUrl":"https://doi.org/10.1002/prca.202200118","url":null,"abstract":"<p><strong>Introduction: </strong>Kidney transplant recipients (KTRs) are at an increased risk of fractures. Total urinary hydroxyproline excretion served as marker for bone resorption (BR) but was replaced by β-CrossLaps (CTX), a C-terminal collagen α-1(I) chain (COL1A1) telopeptide. We investigated the low-molecular-weight urinary proteome for peptides associated with changes in bone metabolism after kidney transplantation.</p><p><strong>Methods: </strong>Clinical and laboratory data including serum levels of CTX in 96 KTR from two nephrology centers were correlated with signal intensities of urinary peptides identified by capillary electrophoresis mass spectrometry.</p><p><strong>Results: </strong>Eighty-two urinary peptides were significantly correlated with serum CTX levels. COL1A1 was the predominant peptide source. Oral bisphosphonates were administered for decreased bone density in an independent group of 11 KTR and their effect was evaluated on the aforementioned peptides. Study of the peptides cleavage sites revealed a signature of Cathepsin K and MMP9. Seventeen of these peptides were significantly associated with bisphosphonate treatment, all showing a marked reduction in their excretion levels compared to baseline.</p><p><strong>Discussion: </strong>This study provides strong evidence for the presence of collagen peptides in the urine of KTR that are associated with BR and that are sensitive to bisphosphonate treatment. Their assessment might become a valuable tool to monitor bone status in KTR.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 4","pages":"e2200118"},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9873121","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":"Identification of potential extracellular vesicle protein markers altered in osteosarcoma from public databases.","authors":"Jinhe Zhang,&nbsp;Huiyan Li","doi":"10.1002/prca.202200084","DOIUrl":"https://doi.org/10.1002/prca.202200084","url":null,"abstract":"<p><strong>Purpose: </strong>Extracellular vesicles (EVs) have become promising biomarkers for cancer management. Particularly, the molecular cargo such as proteins carried by EVs are similar to their cells of origin, providing important information that can be used for cancer diagnostics, prognosis, and treatment monitoring. However, to date, molecular analysis on EVs is still challenging, limited by the availability of efficient analytical technologies, largely due to the small size of EVs. In this work, we developed a computational workflow for in silico identification of potential EV protein markers from genomic and proteomic databases, and applied it for the discovery of osteosarcoma (OS) EV protein markers.</p><p><strong>Experimental design: </strong>Both mRNA and protein data were computed and compared from publicly accessible databases, and top markers with high differential expression levels were selected.</p><p><strong>Results: </strong>Thirty nine markers were identified overexpressed and seven found to be downregulated. These identified markers have been found to be associated with OS on different aspects in literature, demonstrating the usability of this workflow.</p><p><strong>Conclusions and clinical relevance: </strong>This work provides a list of potential EV protein markers that are either overexpressed or downregulated in OS for further experimental validation for improved clinical management of OS.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":"17 4","pages":"e2200084"},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9869691","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}