PROTEOMICS – Clinical Applications最新文献

{"title":"Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin-Fixed Paraffin-Embedded Tissue.","authors":"Stefanie K Schwab, Peter S Harris, Cole Michel, Courtney D McGinnis, Rooban B Nahomi, Mohammed A Assiri, Richard Reisdorph, Kammi Henriksen, David J Orlicky, Moshe Levi, Avi Rosenberg, Ram H Nagaraj, Kristofer S Fritz","doi":"10.1002/prca.202400018","DOIUrl":"10.1002/prca.202400018","url":null,"abstract":"<p><strong>Purpose: </strong>Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end-stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post-translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism.</p><p><strong>Experimental design: </strong>A novel extraction and LC-MS/MS approach was adapted to quantify sites of lysine acetylation from formalin-fixed paraffin-embedded (FFPE) kidney tissue and from patients with DKD and non-diabetic donors (n = 5 and n = 7, respectively).</p><p><strong>Results: </strong>Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis.</p><p><strong>Conclusions and clinical relevance: </strong>A quantitative acetylomics platform was developed for protein biomarker discovery in formalin-fixed and paraffin-embedded biopsies of kidney transplant patients suffering from DKD.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458931","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":"Pressure Cycling Technology Combined With MicroLC-SWATH Mass Spectrometry for the Analysis of Sex-Related Differences Between Male and Female Cerebella: A Promising Approach to Investigating Proteomics Differences in Psychiatric and Neurodegenerative Diseases.","authors":"Katarzyna Macur, Anna Roszkowska, Paulina Czaplewska, Natalia Miękus-Purwin, Ilona Klejbor, Janusz Moryś, Tomasz Bączek","doi":"10.1002/prca.202400001","DOIUrl":"10.1002/prca.202400001","url":null,"abstract":"<p><strong>Purpose: </strong>Pressure cycling technology (PCT) coupled with data-independent sequential window acquisition of all theoretical mass spectra (SWATH-MS) can be a powerful tool for identifying and quantifying biomarkers (e.g., proteins) in complex biological samples. Mouse models are frequently used in brain studies, including those focusing on different neurodevelopmental and psychiatric disorders. More and more pieces of evidence have suggested that sex-related differences in the brain impact the rates, clinical manifestations, and therapy outcomes of these disorders. However, sex-based differences in the proteomic profiles of mouse cerebella have not been widely investigated.</p><p><strong>Experimental design: </strong>In this pilot study, we evaluate the applicability of coupling PCT sample preparation with microLC-SWATH-MS analysis to map and identify differences in the proteomes of two female and two male mice cerebellum samples.</p><p><strong>Results: </strong>We identified and quantified 174 proteins in mice cerebella. A comparison of the proteomic profiles revealed that the levels of 11 proteins in the female and male mice cerebella varied significantly.</p><p><strong>Conclusions and clinical relevance: </strong>Although this study utilizes a small sample, our results indicate that the studied male and female mice cerebella possessed differing proteome compositions, mainly with respect to energy metabolism processes.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142111311","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":"Comparative salivary proteomics analysis of children with and without early childhood caries using the DIA approach: A pilot study.","authors":"Jinxiang Ye, Fangfang Zhang, Zhouyuan Luo, Xiaoyan Ou","doi":"10.1002/prca.202400006","DOIUrl":"10.1002/prca.202400006","url":null,"abstract":"<p><strong>Objective: </strong>To screen differentially expressed proteins (DEPs) in the saliva of Early childhood caries (ECC) with different degrees of severity.</p><p><strong>Methods: </strong>The proteomic profiles of salivary of children with ECC of varying severity by data independent acquisition data independent acquisition (DIA) technique. A total of 12 preschool children aged 3-5 years were included in this study.</p><p><strong>Results: </strong>In this study, a total of 15,083 peptides and 1944 proteins were quantified; The results of DEPs screening showed that 34 DEPs were identified between the group H and the group LC, including 18 up-regulated proteins and 16 down-regulated proteins; 34 DEPs were screened between the group H and the group HC, including 17 up-regulated proteins and 17 down-regulated proteins; 42 DEPs were screened between the group LC and the group HC, including 18 up-regulated proteins and 24 down-regulated proteins. Among these DEPs, we screened several key proteins that may play a role in ECC, such as MK, histone H4, TGFβ3, ZG16B, MUC20, and SMR-3B.</p><p><strong>Conclusion: </strong>Salivary proteins, as important host factors of caries, are differentially expressed between the saliva of ECC children and healthy children. Specific DEPs are expected to become potential biomarkers for the diagnosis of ECC.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071854","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":"Correction to \"Identification of Novel Biomarkers for Frailty Diagnosis Via Serum Amino Acids Metabolomic Analysis Using UPLC-MS/MS\".","authors":"","doi":"10.1002/prca.202400084","DOIUrl":"10.1002/prca.202400084","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293932","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":"Understanding LC/MS-Based Metabolomics: A Detailed Reference for Natural Product Analysis.","authors":"Jyotirmay Sarkar, Rajveer Singh, Shivani Chandel","doi":"10.1002/prca.202400048","DOIUrl":"https://doi.org/10.1002/prca.202400048","url":null,"abstract":"<p><p>Liquid chromatography, when used in conjunction with mass spectrometry (LC/MS), is a powerful tool for conducting accurate and reproducible investigations of numerous metabolites in natural products (NPs). LC/MS has gained prominence in metabolomic research due to its high throughput, the availability of multiple ionization techniques and its ability to provide comprehensive metabolite coverage. This unique method can significantly influence various scientific domains. This review offers a comprehensive overview of the current state of LC/MS-based metabolomics in the investigation of NPs. This review provides a thorough overview of the state of the art in LC/MS-based metabolomics for the investigation of NPs. It covers the principles of LC/MS, various aspects of LC/MS-based metabolomics such as sample preparation, LC modes, method development, ionization techniques and data pre-processing. Moreover, it presents the applications of LC/MS-based metabolomics in numerous fields of NPs research such as including biomarker discovery, the agricultural research, food analysis, the study of marine NPs and microbiological research. Additionally, this review discusses the challenges and limitations of LC/MS-based metabolomics, as well as emerging trends and developments in this field.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546981","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":"Proteomic Analysis of Fibroblasts Exposed to Resin Composite Release.","authors":"Yohann Flottes, Elisabeth Dursun","doi":"10.1002/prca.202400049","DOIUrl":"https://doi.org/10.1002/prca.202400049","url":null,"abstract":"<p><strong>Objective: </strong>To investigate the potential effects of products released by a resin composite on the proteome of human gingival fibroblasts.</p><p><strong>Methods: </strong>Fifteen resin composite cylinders of a Bis-GMA-based resin composite (Tetric EvoCeram, Ivoclar) were made and placed in a culture medium for 24 h. Then, 30 mL of this medium was placed for 72 h in contact with human gingival fibroblasts and a second control group consisted of cells placed in culture medium only. Afterward, cells were collected, washed, and their proteins extracted. Three two-dimensional electrophoresis were performed per condition. Image analysis of the gels was carried out to highlight the differential protein spots. These spots were then analyzed by an ESI/qTOF mass spectrometer. Finally, specific databases provided protein identification, their interactions, and the pathways where they are implicated.</p><p><strong>Results: </strong>Delta2D software allowed the detection of 21 spots of different proteins. The MASCOT identified 28 proteins. Five proteins from four spots were upregulated, 23 proteins from 17 spots were downregulated. The UniProt database showed that all these proteins were involved in cellular architecture, structural modifications and quality control of proteins, cellular homeostasis, and metabolic pathways. The STRING database revealed the interactions between the regulated proteins. The GO enrichment analysis showed that 19 pathways were affected.</p><p><strong>Significance: </strong>The products released from the resin composite tested led to changes in the fibroblast proteome. Under the conditions of this study, resin composite released products can cause early adverse effects on cells, but without complete inhibition of their cellular functions.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473127","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":"TMT-Based Quantitative Proteomic Profiling of Human Esophageal Cancer Cells Reveals the Potential Mechanism and Potential Therapeutic Targets Associated With Radioresistance.","authors":"Aidi Gao, Chao He, Hengrui Chen, Qianlin Liu, Yin Chen, Jianying Sun, Chuanfeng Wu, Ya Pan, Sonia Rocha, Mu Wang, Jundong Zhou","doi":"10.1002/prca.202400010","DOIUrl":"https://doi.org/10.1002/prca.202400010","url":null,"abstract":"<p><strong>Purpose: </strong>The recurrence of esophageal squamous cell carcinoma (ESCC) in radiation therapy treatment presents a complex challenge due to its resistance to radiation. However, the mechanism underlying the development of radioresistance in ESCC remains unclear. In this study, we aim to uncover the mechanisms underlying radioresistance in ESCC cells and identify potential targets for radiosensitization.</p><p><strong>Methods: </strong>We established two radio-resistant cell lines, TE-1R and KYSE-150R, from the parental ESCC cell lines TE-1 and KYSE-150 through fractionated irradiation. A TMT-based quantitative proteomic profiling approach was applied to identify changes in protein expression patterns. Cell Counting Kit-8, colony formation, γH2AX foci immunofluorescence and comet assays were utilized to validate our findings. The downstream effectors of the DNA repair pathway were confirmed using an HR/NHEJ reporter assay and Western blot analysis. Furthermore, we evaluated the expression of potential targets in ESCC tissues through immunohistochemistry combined with mass spectrometry.</p><p><strong>Results: </strong>Over 2,000 proteins were quantitatively identified in the ESCC cell lysates. A comparison with radio-sensitive cells revealed 61 up-regulated and 14 down-regulated proteins in the radio-resistant cells. Additionally, radiation treatment induced 24 up-regulated and 12 down-regulated proteins in the radio-sensitive ESCC cells. Among the differentially expressed proteins, S100 calcium binding protein A6 (S100A6), glutamine gamma-glutamyltransferase 2 (TGM2), glycogen phosphorylase, brain form (PYGB), and Thymosin Beta 10 (TMSB10) were selected for further validation studies as they were found to be over-expressed in the accumulated radio-resistant ESCC cells and radio-resistant cells. Importantly, high S100A6 expression showed a positive correlation with cancer recurrence in ESCC patients. Our results suggest that several key proteins, including S100A6, TGM2, and PYGB, play a role in the development of radioresistance in ESCC.</p><p><strong>Conclusions: </strong>Our results revealed that several proteins including Protein S100-A6 (S100A6), Protein-glutamine gamma-glutamyltransferase 2 (TGM2), Glycogen phosphorylase, brain form (PYGB) were involved in radio-resistance development. These proteins could potentially serve as biomarkers for ESCC radio-resistance and as therapeutic targets to treat radio-resistant ESCC cells.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142392707","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 4'24","authors":"","doi":"10.1002/prca.202470043","DOIUrl":"https://doi.org/10.1002/prca.202470043","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141743645","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 4'24","authors":"","doi":"10.1002/prca.202470042","DOIUrl":"https://doi.org/10.1002/prca.202470042","url":null,"abstract":"","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141743644","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":"Spindle apparatus coiled-coil protein 1 (SPDL1) serves as a novel prognostic biomarker in triple-negative breast cancer.","authors":"Xian-Yan Yang, Xiao-Xia Zheng, Xue-Jia Zhai, Tao Tang, Shi-Cang Yu","doi":"10.1002/prca.202300002","DOIUrl":"10.1002/prca.202300002","url":null,"abstract":"<p><strong>Background: </strong>Triple-negative breast cancer (TNBC) has a poor prognosis, an ineffective diagnosis, and a high degree of aggressiveness. Therefore, novel therapeutic targets for TNBC urgently need to be identified.</p><p><strong>Methods: </strong>Through a series of bioinformatics analyses, including analysis of differential gene expression, protein-protein interaction (PPI) network, univariate cox regression, immune infiltration, pathway enrichment, etc, as well as auxiliary immunohistochemistry (IHC) and protein quantitativae analysis, to explore prognostic marker for TNBC.</p><p><strong>Results: </strong>In TNBC tissues, we found that SPDL1 (CCDC99) was considerably overexpressed at both the mRNA and protein levels compared to that in normal and non-TNBC tissues. Additionally, we found that SPDL1-high expression was strongly linked to poor prognosis in TNBC patients. Excessive SPDL1 expression was positively correlated with tumor growth and strongly linked to the cell cycle, DNA replication, and the p53 signaling pathway. In addition, CIBERSORT analysis revealed that SPDL1 can affect the tumor immune microenvironment (TME) in TNBC, encourage the development of TNBC and act as a potential prognostic biomarker for TNBC. Patients with SPDL1-high expression were more sensitive to AZD8055. Notably, we discovered that SPDL1 is highly expressed in the majority of malignancies and may have an impact on the pancancer prognosis.</p><p><strong>Conclusions: </strong>SPDL1 can serve as a novel prognostic marker for TNBC and pancancer patients.</p>","PeriodicalId":20571,"journal":{"name":"PROTEOMICS – Clinical Applications","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139692787","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}