Journal of proteomics最新文献

{"title":"“Phosphoproteomic quantification based on phosphopeptide intensity or occupancy? An evaluation based on casein kinase 2 downstream effects”","authors":"Arielis Rodríguez-Ulloa ,&nbsp;Mauro Rosales ,&nbsp;Yassel Ramos ,&nbsp;Osmany Guirola ,&nbsp;Luis J. González ,&nbsp;Jacek R. Wiśniewski ,&nbsp;Yasser Perera ,&nbsp;Silvio E. Perea ,&nbsp;Vladimir Besada","doi":"10.1016/j.jprot.2024.105269","DOIUrl":"10.1016/j.jprot.2024.105269","url":null,"abstract":"<div><p>Quantitative phosphoproteomic data has mostly been reported from experiments comparing relative phosphopeptides intensities in two or more different conditions, while the ideal parameter to compare is phosphopeptides occupancies. This term is scarcely used and therefore barely implemented in phosphoproteomics studies, and this should be of concern for the scientific journals. In order to demonstrate the relevance of this issue, here we show how the method of choice affects the interpretation of the data. The phosphoproteomic profile modulated in two AML cell lines after CK2 inhibition with CIGB-300 or CX-4945 is shown. Following the downstream action of CK2 the phosphosite intensity and occupancy results were compared to validate the best approach for quantitative phosphoproteomic studies. Even when the total number of quantified phosphopeptides was higher by using the intensity calculation, in all the cases the percent of CK2 consensus sequences which were down-regulated in response to CK2 inhibition was higher using the phosphosite occupancy quantification. To note, a high number of CK2 consensus sequences was found down-regulated with at least a 10% or 15% of phosphosite occupancy variation illustrating that low thresholds of occupancy modulation might be indicative of biological effect. Additionally, several biological processes only appear significantly over-represented in the phosphoproteome quantified by occupancy. The functional enrichment analysis per ranges of occupancy variations also illustrated clear differences among AML cell lines subjected to CK2 inhibition by CX-4945. A low overlap between the phosphoproteomes quantified by intensity and occupancy was obtained illustrating that new developments in proteomics techniques are needed to improve the performance of the occupancy approach. Even in such context, results indicate that occupancy quantification performs better than phosphorylation quantification based on intensity reinforcing the importance of such quantification approach to describe phosphoproteomic data.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"307 ","pages":"Article 105269"},"PeriodicalIF":2.8,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141889507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serum CD44 levels in early pregnancy and its genetic variants for increased risk of gestational diabetes mellitus in Chinese pregnant women","authors":"Ming Gao ,&nbsp;Hui Wang ,&nbsp;Ninghua Li ,&nbsp;Yijuan Qiao ,&nbsp;Hongyan Liu ,&nbsp;Weiqin Li ,&nbsp;Shuting Wang ,&nbsp;Jing Li ,&nbsp;Zhijie Yu ,&nbsp;Gang Hu ,&nbsp;Junhong Leng ,&nbsp;Xilin Yang","doi":"10.1016/j.jprot.2024.105268","DOIUrl":"10.1016/j.jprot.2024.105268","url":null,"abstract":"<div><p>This study aimed to explore associations of serum cluster of differentiation 44 (CD44) levels and its genetic variants in early pregnancy with gestational diabetes mellitus (GDM). We conducted a 1:1 case-control study (<em>n</em> = 414) nested in a prospective cohort of 22,302 pregnant women recruited from 2010 to 2012 in Tianjin, China. Blood samples were collected at the first antenatal care visit (at a median of 10^th gestational week). Binary conditional logistic regressions were performed to examine associations of serum CD44 levels and its genetic variants with increased risk of GDM. In this study, we found that serum CD44 levels in early pregnancy was associated with GDM risk in a U-shaped manner. High serum CD44 levels and its genetic risk score in early pregnancy were associated with markedly increased risk of GDM after adjustment for traditional confounders (OR: 1.95, 95%CI: 1.12–3.40 &amp; 1.95, 1.05–3.61). Furthermore, after adjustment for serum CD44 levels, the OR of CD44 genetic risk score for GDM was slightly attenuated but not significant (1.84, 0.98–3.48). In conclusion, serum CD44 levels and its genetic variants in early pregnancy were associated with GDM risk in Chinese pregnant women, with the effect of CD44 genetic variants being accounted for by serum CD44.</p></div><div><h3>Significance</h3><p>Recent studies suggested that pregnant women with GDM may have abnormal levels of CD44 and abnormal expression of CD44 gene, but it is uncertain whether abnormal CD44 plays a causal role in occurrence of GDM. Specifically, it remains unknown whether serum CD44 levels in early pregnancy and its genetic variants can predict the later occurrence of GDM. In this study, we found that high serum CD44 levels in early pregnancy and its genetic variants were associated with markedly increased risk of GDM in Chinese pregnant women, with the effect of CD44 genetic variants being largely accounted for by serum CD44 levels. Our study is the first reporting that serum CD44 levels and its genetic variants were associated with markedly increased risk of GDM. These multi-omics risk markers may be useful for identification of women at high risk of GDM in early pregnancy. Our findings also provide new insights into the disease mechanisms.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"307 ","pages":"Article 105268"},"PeriodicalIF":2.8,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141889508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The structure and proteomic analysis of byssus in Pteria penguin: Insights into byssus evolution and formation","authors":"Yi Chen ,&nbsp;Hengda Chen ,&nbsp;Changqing Han ,&nbsp;Huilong Ou ,&nbsp;Xin Zhan","doi":"10.1016/j.jprot.2024.105267","DOIUrl":"10.1016/j.jprot.2024.105267","url":null,"abstract":"<div><p>Byssus is a unique external structure in sessile bivalves and is critical for settlement and metamorphosis. However, little is known about the stout byssus in <em>Pteria penguin</em>. We explored the byssus structure and proteins using scanning electron microscopy and proteomics, respectively. The results revealed that <em>P. penguin</em> byssus has a dense and highly aligned fiber inner core, and the outer cuticle contains protein granules embedded in the protein matrix. Proteomic analysis revealed 31 proteins in the byssus, among which 15 differentially expressed proteins were mainly enriched in the EGF/EGF-like and laminin EGF-like domains. Foot proteins were enriched in the EF-hand, immunoglobulin, and fibronectin domains. All these domains can participate in protein-protein and/or protein-metal interactions in the extracellular matrix (ECM), which, together with the seven types of ECM proteins detected in the byssus, supports the hypothesis that the byssus is derived from the ECM. We also found that <em>in vitro</em> acellular structures of the byssus and the shell shared commonalities in their formation processes. These results are useful for further understanding byssus evolution and the characterization of byssus-related proteins.</p></div><div><h3>Significance</h3><p>This manuscript investigates the structure and the origin of <em>Pteria penguin</em> byssus, given that byssus is vital to provide critical protection for reproduction and even against environmental stresses that affect survival. However, there is rare research on byssus protein composition. Hence, though scanning electron microscopy and proteomic analysis, we discovered that <em>P. penguin</em> byssus possesses the dense and highly aligned fiber inner core, and the outer cuticle has protein granules embedded in the protein matrix. Proteomic analysis showed that there were 31 proteins in the byssus, among which 15 proteins were mainly enriched in the EGF/EGF-like and laminin EGF-like domains. Foot proteins closely related to byssus formation were enriched in EF hand, immunoglobulin, and fibronectin domains. These domains are able to participate in protein-protein and/or protein-metal interactions in the extracellular matrix (ECM), which together with the seven types of ECM proteins detected in byssus support the hypothesis that byssus derive from the ECM. We also found <em>in vitro</em> acellular structures the byssus and the shell share commonalities in their formation processes. These results were useful for further understanding the byssus evolution and the characterization of the byssus-related proteins.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"307 ","pages":"Article 105267"},"PeriodicalIF":2.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141875164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of the production system on the proteomics profiles of the Longissimus thoracis muscle in Arouquesa cattle","authors":"Laura Sacarrão-Birrento ,&nbsp;David M. Ribeiro ,&nbsp;Antje Dittmann ,&nbsp;Susana P. Alves ,&nbsp;Laura Kunz ,&nbsp;Severiano Silva ,&nbsp;Carlos A. Venâncio ,&nbsp;André M. de Almeida","doi":"10.1016/j.jprot.2024.105265","DOIUrl":"10.1016/j.jprot.2024.105265","url":null,"abstract":"<div><p><em>Arouquesa</em> cattle breed is an autochthonous Portuguese breed produced under a traditional mountain system that need improvement without affecting beef quality. The aim of this work is to compare the proteomics profiles of the <em>Longissimus thoracis</em> muscle from <em>Arouquesa</em> animals produced under different production systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF + S1) with weaning and slaughtering at 9 months, the S1 + S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF + S3 and S3). Upon slaughter, samples of L. <em>thoracis</em> were taken and analyzed using a shotgun proteomics workflow. Several putative markers of beef quality for the <em>Arouquesa</em> breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins are involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. We identified specific proteins for each group related to different metabolisms involved in several aspects that affect meat quality parameters. Our results demonstrate the link between production practices and putative meat characteristics, which have the potential to improve the traceability of certified products.</p></div><div><h3>Significance</h3><p><em>Arouquesa</em> breed is produced in a sustainable system using natural resources and contributing to the economy of low-populated rural regions in Northern Portugal. Besides their economic relevance, producing autochthonous breeds can counter rural depopulation and maintain local heritage. Additionally, consumer awareness about product quality is increasing and PDO products contribute to satisfying this demand. However, it is necessary to increase production so that it is possible to sell these products outside the production region. To ensure robust traceability and that PDO label characteristics are maintained despite increasing production yield, product analysis is of paramount importance. For this reason, proteomic approaches can provide insight into how production changes will affect beef quality and generate putative biomarkers of certified production systems.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"307 ","pages":"Article 105265"},"PeriodicalIF":2.8,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 low-abundance proteins in the royal jelly using the Osborne classification method","authors":"Pengfei Pei ,&nbsp;Wenxu Guo ,&nbsp;Mingxue Qi ,&nbsp;Jianhui Jiang ,&nbsp;Shan Feng ,&nbsp;Shi-Zhong Luo ,&nbsp;Long Chen","doi":"10.1016/j.jprot.2024.105266","DOIUrl":"10.1016/j.jprot.2024.105266","url":null,"abstract":"<div><p>Royal jelly (RJ) is recognized as healthy food, with a high content of proteins. These proteins play important roles in honeybee caste and human health, but the proteomic analysis of low-abundance proteins in RJ has long been a challenge. Herein, we used the Osborne classification method to separate the RJ proteins of Xinjiang black bees into various fractions. The globulin, ethanol-soluble protein, and glutelin fractions were further separated by SDS-PAGE, and proteomic analysis was carried out by LC-MS/MS and searched against the UniProt database. A total of 23 secretory proteins were identified by proteomic analysis, in which 7 proteins were identified for the first time in RJ. The Osborne classification method combining one-dimensional gel electrophoresis-based proteomic analysis allows the identification of low-abundance proteins in the RJ and greatly extends the knowledge about the components and functions of RJ proteins. The raw data are available via ProteomeXchange with the identifier <span><span>PXD023315</span><svg><path></path></svg></span>.</p></div><div><h3>Significance</h3><p>This study makes an important contribution to the research of the components and functions of low-abundance royal jelly proteins for the following reasons:</p><ul><li><span>1.</span><span><p>The Osborne method was applied to fractionize the royal jelly proteins, which benefits the identification of low-abundance proteins.</p></span></li><li><span>2.</span><span><p>23 secretory proteins were identified from the globulins, the ethanol-soluble proteins, and the glutelins of the RJ, and there were 7 proteins identified for the first time in royal jelly.</p></span></li><li><span>3.</span><span><p>This study extends the knowledge about the components and functions of royal jelly proteins.</p></span></li></ul></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"306 ","pages":"Article 105266"},"PeriodicalIF":2.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SWATH-proteomics reveals Mathurameha, a traditional anti-diabetic herbal formula, attenuates high glucose-induced endothelial dysfunction through the EGF/NO/IL-1β regulatory axis","authors":"Siripat Aluksanasuwan ,&nbsp;Keerakarn Somsuan ,&nbsp;Wararat Chiangjong ,&nbsp;Artitaya Rongjumnong ,&nbsp;Wuttichai Jaidee ,&nbsp;Narawadee Rujanapun ,&nbsp;Somchai Chutipongtanate ,&nbsp;Surat Laphookhieo ,&nbsp;Rawiwan Charoensup","doi":"10.1016/j.jprot.2024.105263","DOIUrl":"10.1016/j.jprot.2024.105263","url":null,"abstract":"<div><p>Mathurameha is a traditional Thai herbal formula with a clinically proven effect of blood sugar reduction in patients with diabetes mellitus, but its anti-diabetic complication potential is largely unknown. This study aimed to elucidate the effects of Mathurameha and its underlying mechanisms against high glucose-induced endothelial dysfunction in human endothelial EA.hy926 cells. After confirming no cytotoxic effects, the cells were treated with normal glucose (NG), high glucose (HG), or high glucose plus Mathurameha (HG + M) for 24 h. A quantitative label-free proteomic analysis using the sequential window acquisition of all theoretical mass spectra (SWATH-MS) approach identified 24 differentially altered proteins among the three groups: 7 between HG and NG, 9 between HG + M and NG, and 13 between HG + M and HG. Bioinformatic analyses suggested a potential anti-diabetic action through the epidermal growth factor (EGF) pathway. Subsequent functional validations demonstrated that Mathurameha reduced the EGF secretion and the intracellular reactive oxygen species (ROS) level in high glucose-treated cells. Mathurameha also exhibited a stimulatory effect on nitric oxide (NO) production while significantly reducing the secretion of endothelin-1 (ET-1) and interleukin-1β (IL-1β) in high glucose-treated cells. In conclusion, our findings demonstrated that Mathurameha attenuated high glucose-induced endothelial dysfunction through the EGF/NO/IL-1β regulatory axis.</p></div><div><h3>Significance</h3><p>This study reveals the potential of Mathurameha, a traditional Thai herbal formula, in mitigating high glucose-induced endothelial dysfunction, a common complication in diabetes mellitus. Using proteomics and bioinformatic analyses followed by functional validations, the present study highlights the protective effects of Mathurameha through the EGF/NO/IL-1β regulatory axis. These findings support its potential use as a therapeutic intervention for diabetic vascular complications and provide valuable information for developing more effective anti-diabetic drugs.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"306 ","pages":"Article 105263"},"PeriodicalIF":2.8,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Delineating protein biomarkers for gastric cancers: A catalogue of mass spectrometry-based markers and assessment of their suitability for targeted proteomics applications","authors":"Poornima Ramesh ,&nbsp;Mahammad Nisar ,&nbsp;Neha ,&nbsp;Shruthi Ammankallu ,&nbsp;Sreeranjini Babu ,&nbsp;Revathy Nandakumar ,&nbsp;Chandran S. Abhinand ,&nbsp;Thottethodi Subrahmanya Keshava Prasad ,&nbsp;Jalaluddin Akbar Kandel Codi ,&nbsp;Rajesh Raju","doi":"10.1016/j.jprot.2024.105262","DOIUrl":"10.1016/j.jprot.2024.105262","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Gastric cancer (GC) is a global health concern. To facilitate improved management of GCs, protein biomarkers have been identified through mass spectrometry-based proteomics platforms. In order to exhibit clinical utility of such data, we congregated over 6800 differentially regulated proteins in GCs from proteomics studies and recorded the mass spectrometry platforms, association of the protein with infectious agents, protein identifiers, sample size and clinical characters of samples used with details on validation. Development of targeted proteomics methods is the cornerstone for pursuing these markers into clinical utility. Therefore, we developed Protein Biomarker Matrix for Gastric Cancer (PBMGC), a simple catalogue of robustness of each protein. This analysis yielded the identification of robust tissue, serum, and urine diagnostic and prognostic protein biomarker panels which can be further tested for their clinical utility. We also ascertained proteotypic tryptic peptides of 5631 proteins suitable for developing multiple reaction monitoring (MRM) assays. Extensive characterization of these peptides was carried out to record peptide ions, mass/charge and enhanced specific peptide features. With the vision of catering to proteomics researchers, the data generated through this analysis has been catalogued at Gastric Cancer Proteomics DataBase (GCPDB) (&lt;span&gt;&lt;span&gt;https://ciods.in/gcpdb/&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;). Users can browse and download the data and improve GCPDB by submitting recently published data.&lt;/p&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;p&gt;Mass spectrometry-based proteomics platforms have accumulated substantial data on proteins differentially regulated in gastric cancer (GC) clinical samples. The utility of such data in clinical applications is limited by search for suitable biomarker panels for assessment of GCs.&lt;/p&gt;&lt;p&gt;We assembled over 6800 differentially regulated proteins in GCs from proteomics studies and recorded the corresponding details including mass spectrometry platforms, status on the association of the protein with infectious agents, protein identifiers from different databases, sample size and clinical characters of samples used in test and control conditions along with details on their validation.&lt;/p&gt;&lt;p&gt;Towards the vision of utilizing these markers in clinical assays, Protein Biomarker Matrix for Gastric Cancer (PBMGC) was developed and clinically relevant multi-protein panels were identified. We also demonstrated identification and characterization of tryptic proteotypic tryptic peptides of 5631 proteins biomarkers of GCs which are suitable for development of MRM assays in a SCIEX QTRAP instrument.&lt;/p&gt;&lt;p&gt;Aimed to caterproteomics researchers, the data generated through this analysis has been catalogued at Gastric Cancer Proteomics DataBase (GCPDB) (&lt;span&gt;&lt;span&gt;https://ciods.in/gcpdb/&lt;/span&gt;&lt;svg&gt;&lt;path&gt;&lt;/path&gt;&lt;/svg&gt;&lt;/span&gt;). The users can browse and download details on different markers and improve GCPD","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"306 ","pages":"Article 105262"},"PeriodicalIF":2.8,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of genetic diversity on the allergenicity of peanut (Arachis hypogaea) proteins: identification of the hypoallergenic accessions using BALB/c mice model and in silico analysis of Ara h 3 allergen cross-reactivity","authors":"Hanène Djeghim ,&nbsp;Ines Bellil ,&nbsp;Ouided Benslama ,&nbsp;Sabrina Lekmine ,&nbsp;Esma Temim ,&nbsp;Houda Boufendi ,&nbsp;Idoia Postigo ,&nbsp;Patricia Sánchez ,&nbsp;Douadi Khelifi","doi":"10.1016/j.jprot.2024.105264","DOIUrl":"10.1016/j.jprot.2024.105264","url":null,"abstract":"<div><p>This study investigated the effects of genetic diversity in the allergenicity of peanut and assessed the allergenic capacity of six <em>Arachis hypogaea</em> accessions using a Balb/c mouse model. It also explored potential cross-reactivities between Ara h 3 (peanut allergen) and Gly m (soybean allergen) using computational tools. Female Balb/c mice were injected with peanut protein extracts and alum. Serum-specific antibodies (IgE, IgGt, IgG1, IgG2a) were measured using ELISA, and allergic protein profiles were examined via western blot. Structural homology, B cell epitopes, and molecular interactions between Ara h 3 and Gly m with human IgE were also investigated. The mice developed high sIgE and sIgG1 responses, with antibodies recognizing 19 bands on western blot. Notably, Saharan accessions showed unique features such as no bands on western blot profiles, reduced anaphylactic symptoms, lower IgE titers, and less intestinal tissue damage. Molecular docking results suggest significant cross-allergenicity, supported by allergenicity predictions and structural homology analysis. This comprehensive analysis provides insights into shared epitopes, potential competition for binding sites, and molecular dynamics of cross-reactive responses, enhancing understanding of food allergen interactions. The study recommends using Algerian Sahara peanut accessions in breeding, genomics studies, and industry for safer peanut options for individuals with allergies.</p></div><div><h3>Significance</h3><p>The significance of this study lies in its contribution to addressing a major public health issue: peanut allergy, which represents a significant cause of anaphylaxis affecting numerous individuals and families worldwide. By exploring the genetic diversity of peanut proteins and identifying hypoallergenic accessions through experimental and computational approaches, this research offers valuable insights for mitigating allergic reactions. The findings highlight that certain accessions from the Saharan region exhibit reduced allergenicity, resulting in attenuated anaphylactic symptoms, lower IgE levels, and reduced intestinal damage in murine models. Furthermore, the study's in silico analysis sheds light on the issue of cross-reactivity between peanut and soybean allergens, providing crucial information for understanding allergen interactions at the molecular level. Overall, this research contributes to advancing knowledge in the field of food allergen research and has practical implications for improving the quality of life for individuals allergic to peanuts, particularly through the selection of safer peanut varieties and their cultivation.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"306 ","pages":"Article 105264"},"PeriodicalIF":2.8,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1874391924001969/pdfft?md5=6fd3072a8b3ca3c106535e8845d9ded7&pid=1-s2.0-S1874391924001969-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lipid metabolites abnormally expressed in pelvic fluid as potential biomarkers for ovarian cancer: A case-control study","authors":"Rongrong Tang ,&nbsp;Yunshan Zhu ,&nbsp;Lingfeng Chen ,&nbsp;Jinfei Tong ,&nbsp;Xudong Ma ,&nbsp;Fangying Sun ,&nbsp;Limei Zheng ,&nbsp;Hailan Yu ,&nbsp;Jianhua Yang","doi":"10.1016/j.jprot.2024.105261","DOIUrl":"10.1016/j.jprot.2024.105261","url":null,"abstract":"<div><h3>Background</h3><p>Ovarian cancer is insidious and usually detected in advanced stages of the disease. As the ovaries are pelvic organs, changes in their pelvic fluid metabolites may be associated with ovarian cancer.</p></div><div><h3>Methods</h3><p>Metabolomic changes in the pelvic fluid were detected using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in patients with ovarian cancer, ovarian cysts and uterine fibroids. Area under the curve (AUC) analysis was used to assess the diagnostic performance of lipid metabolites and blood tumor indices. The Pearson correlation algorithm was used to analyze the correlation between clinical characteristics and lipid metabolites in ovarian cancer patients.</p></div><div><h3>Results</h3><p>There were 24 lipid metabolites significantly changed in the pelvic fluid of ovarian cancer patients (<em>p</em> &lt; 0.05). Palmitoylcarnitine, lipoamide, lipid metabolites, and blood tumor indices (CA15–3 and CA125) showed AUC &gt; 0.8, with palmitoylcarnitine reaching a high of 0.942. In addition, we found that some lipid metabolites were significantly associated with the clinical stage, abdominal water volume, lymphatic metastasis, and recurrence (<em>p</em> &lt; 0.05, <em>r</em> &gt; 0.5).</p></div><div><h3>Conclusion</h3><p>Levels of specific lipid metabolites are potential biomarkers of ovarian cancer and may play a key role in the early diagnosis and prognostic assessment of ovarian cancer.</p></div><div><h3>Significance</h3><p>Our results showed that pelvic metabolites, especially some lipid metabolites, play an important role in the diagnosis of ovarian cancer. Meanwhile, partial lipid metabolites were closely associated with the clinical presentation and prognosis of patients with ovarian cancer. We believe that our study makes a significant contribution to the literature because it provides a potential approach that is more effective for ovarian cancer detection.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"307 ","pages":"Article 105261"},"PeriodicalIF":2.8,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141734453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic and Phosphoproteomic analysis of thyroid papillary carcinoma: Identification of potential biomarkers for metastasis","authors":"Lingyao Peng ,&nbsp;Zhenxian Zhang ,&nbsp;Wei Du ,&nbsp;Jiang Zhu ,&nbsp;Wenkai Duan","doi":"10.1016/j.jprot.2024.105260","DOIUrl":"10.1016/j.jprot.2024.105260","url":null,"abstract":"<div><p>Thyroid cancer has emerged as the most rapidly proliferating solid neoplasm. In this study, we included a cohort of patients who underwent sonographic assessment and surgical intervention at the Sir Run Run Shaw Hospital, associated with the School of Medicine at Zhejiang University, spanning from January 2019 to June 2020. Stratification of cases was based on a combination of preoperative ultrasonographic evaluations and postoperative histopathological diagnoses, resulting in three distinct groups: high-risk papillary thyroid carcinoma (PTC) labeled as C1, low-risk PTC designated as C2, and a control group (N) composed of benign thyroid tissue adjacent to the carcinoma. Proteomic and phosphoproteomic analyses were conducted on PTC specimens. The comparative assessment revealed that proteins up-regulated in the C1/N and C2/N groups were predominantly involved in functions such as amino acid binding, binding of phosphorylated compounds, and serine protease activity. Notably, proteins like NADH dehydrogenase, ATP synthase, oxidoreductases, and iron ion channels were significantly elevated in the C1 versus C2 comparative group. Through meticulous analysis of differential expression multiples, statistical significance, and involvement in metabolic pathways, this study identified eight potential biomarkers pertinent to PTC metastasis diagnostics, encompassing phosphorylated myosin 10, phosphorylated proline-directed protein kinase, leucine tRNA synthetase, 2-oxo-isovalerate dehydrogenase, succinic semialdehyde dehydrogenase, ADP/ATPtranslocase, pyruvate carboxylase, and fibrinogen. Therapeutic assays employing metformin, an AMP-activated protein kinase (AMPK) activator, alongside the phosphorylation-specific inhibitor ML-7 targeting Myosin10, demonstrated attenuated cellular proliferation, migration, and invasion capabilities in thyroid cancer cells, accompanied by a reduction in amino acid pools. Cellular colocalization and interaction studies elucidated that AMPK activation imposes an inhibitory influence on Myosin10 levels. The findings of this research corroborate the utility of proteomic and phosphoproteomic platforms in the identification of metastatic markers for PTC and suggest that modulation of AMPK activity, coupled with the inhibition of Myosin10 phosphorylation, may forge novel therapeutic avenues in the management of thyroid carcinoma.</p></div><div><h3>Significance</h3><p>The significance of our research lies in its potential to transform the current understanding and management of thyroid papillary carcinoma (PTC), particularly in its metastatic form. By integrating both proteomic and phosphoproteomic analyses, our study not only sheds light on the molecular alterations associated with PTC but also identifies eight novel biomarkers that could serve as indicators of metastatic potential.</p></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"306 ","pages":"Article 105260"},"PeriodicalIF":2.8,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}