Journal of Proteome Research最新文献_第4页

Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer. FFPE组织样本的蛋白质组学分析确定了直肠癌放射治疗耐药的潜在分子机制。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-01 Epub Date: 2025-06-26 DOI: 10.1021/acs.jproteome.5c00114

Tobias Zott, Michael Wolf, Günter Plessl-Walder, Heinz Regele, Michael Bergmann, Samuel M Meier-Menches, Christopher Gerner, Gerd R Silberhumer, Andrea Bileck

{"title":"Proteomic Analysis of FFPE Tissue Samples Identifies Potential Molecular Mechanisms Mediating Resistance to Radiotherapy in Rectal Cancer.","authors":"Tobias Zott, Michael Wolf, Günter Plessl-Walder, Heinz Regele, Michael Bergmann, Samuel M Meier-Menches, Christopher Gerner, Gerd R Silberhumer, Andrea Bileck","doi":"10.1021/acs.jproteome.5c00114","DOIUrl":"10.1021/acs.jproteome.5c00114","url":null,"abstract":"Chemoradiation prior to surgery in locally advanced rectal cancer is the current standard therapy but is not effective in all rectal cancer patients. Prognostic markers supporting patient stratification with respect to clinical response would therefore be desirable. The aim of this study was to investigate pathophysiological mechanisms underlying radioresistance and to identify potential prognostic markers by comparative proteome profiling. Therefore, formalin fixed paraffin-embedded tissue (FFPE) samples from rectal tumors (n = 50) and normal control tissue (n = 39) of nonresponders and responders to neoadjuvant chemoradiation were analyzed. As a result, 1685 robustly identified proteins were further evaluated. Comparing tumor with corresponding control samples revealed 221 differentially expressed proteins (FDR < 0.05) with FTL, PCOLCE, and RCN3 being most striking in tumor tissue. CEACAM 1, 5, and 6, as well as MCM protein complex components, were significantly up-regulated in tumor tissue of nonresponders. The autophagic activity-related and DNA damage repair proteins TOM1, CAPNS1, TP53BP1, HS1BP3, as well as COTL1 and DCPS, discriminated non- and nearly complete from complete responders. In the tumor-surrounding tissue of nonresponders, the innate immune response-suppressing protein CD55 was found specifically up-regulated. These proteins may serve as prognostic markers and potential therapeutic targets, requiring further validation in prospective studies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"3990-4001"},"PeriodicalIF":3.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504175","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}

引用次数: 0

Acute Metabolic Effects in Brazilian A-29 Fighter Pilots by NMR-Based Metabolomics. 基于核磁共振代谢组学的巴西A-29战斗机飞行员急性代谢效应

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-01 Epub Date: 2025-07-21 DOI: 10.1021/acs.jproteome.5c00129

Roberta Verissimo França de Oliveira, Grace Barros de Sá, Alanny Cristine Dos Santos Pinheiro, Antonia Claudia Jácome da Câmara, Palmielly Diógenes, Adriano Percival Calderaro Calvo, Laila Ribeiro Fernandes, Luísa Soares da Silva, Rafael Loureiro Simões, Verônica Morandi, Gilson Costa Dos Santos, Paulo Farinatti

{"title":"Acute Metabolic Effects in Brazilian A-29 Fighter Pilots by NMR-Based Metabolomics.","authors":"Roberta Verissimo França de Oliveira, Grace Barros de Sá, Alanny Cristine Dos Santos Pinheiro, Antonia Claudia Jácome da Câmara, Palmielly Diógenes, Adriano Percival Calderaro Calvo, Laila Ribeiro Fernandes, Luísa Soares da Silva, Rafael Loureiro Simões, Verônica Morandi, Gilson Costa Dos Santos, Paulo Farinatti","doi":"10.1021/acs.jproteome.5c00129","DOIUrl":"10.1021/acs.jproteome.5c00129","url":null,"abstract":"Operating an aircraft imposes significant physical and mental demands on pilots, particularly those in military aviation. These challenges include circadian disruptions, irregular working hours, and exposure to G-forces. This study investigates the acute metabolic effects of flight in the A-29 fighter pilots of the Brazilian Air Force (FAB). Blood, urine, and saliva samples were collected from 32 pilots, trainees (n = 12; aged 23-26 years) and instructors (n = 20; aged 25-41 years), immediately before and after flights. Assessments included anthropometric measurements, complete blood count (CBC), circulating endothelial cells (CECs), coagulogram, lipidogram, urinalysis, and nuclear magnetic resonance (NMR)-based metabolomics. After flights, trainees showed a 12% increase in the number of segmented neutrophils, while instructors exhibited a 15% increase in the number of lymphocyte counts. Serum lactate levels decreased in both groups (23% in trainees and 12% in instructors). Salivary glucose increased by 49% in trainees, whereas instructors demonstrated decreases in metabolites such as choline (23%) and lactate (15%). Urinary trigonelline levels increased by 53% in instructors. The observed changes were more pronounced in instructors vs trainees, indicating a degree of metabolic adaptation associated with greater flight experience. These findings highlight NMR-based metabolomics as a valuable tool for monitoring acute metabolic changes in fighter pilots.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"4033-4043"},"PeriodicalIF":3.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673323","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}

引用次数: 0

OCIAD2 Promotes Cancer Progression via Metabolic Reprogramming in Lung Adenocarcinoma. OCIAD2在肺腺癌中通过代谢重编程促进癌症进展。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-01 Epub Date: 2025-07-21 DOI: 10.1021/acs.jproteome.5c00273

Yi-Hui Huang, Wen-Hsin Chang, Chi-Ya Shen, Kang-Yi Su, Gee-Chen Chang, Jin-Shing Chen, Wen-Yao Lee, Yu-Ju Chen, Sung-Liang Yu

{"title":"OCIAD2 Promotes Cancer Progression via Metabolic Reprogramming in Lung Adenocarcinoma.","authors":"Yi-Hui Huang, Wen-Hsin Chang, Chi-Ya Shen, Kang-Yi Su, Gee-Chen Chang, Jin-Shing Chen, Wen-Yao Lee, Yu-Ju Chen, Sung-Liang Yu","doi":"10.1021/acs.jproteome.5c00273","DOIUrl":"10.1021/acs.jproteome.5c00273","url":null,"abstract":"Given the limited proteomic insights and high incidence of lung adenocarcinoma, further investigation of uncharacterized proteins in cancer progression remains crucial. In this study, a poorly characterized protein, OCIA domain-containing 2 (OCIAD2), encoded by chromosome 4 was identified as being upregulated in lung adenocarcinoma from our previous proteogenomics data using the Taiwan Cancer Moonshot cohort. OCIAD2 was highly expressed in tumor tissues in 95.5% of lung adenocarcinoma patients in our cohort, with elevated expression correlating with worse survival. Functional studies revealed that the silencing of the OCIAD2 decreased cell migration, invasion, and colony-forming abilities. Gene Set Enrichment Analysis (GSEA) indicated the involvement of OCIAD2 in oxidative phosphorylation (OXPHOS). Subsequently, mitochondrial metabolic assay demonstrated that OCIAD2 impairs OXPHOS function, accompanied by a metabolic shift toward glycolysis. These findings suggest that OCIAD2 promotes cancer progression through metabolic reprogramming, highlighting the role of OCIAD2 as a potential biomarker and therapeutic target for lung adenocarcinoma.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"4139-4153"},"PeriodicalIF":3.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673361","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}

引用次数: 0

Identifying lncRNA-Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry. 利用杂交捕获和质谱技术鉴定造血祖细胞中lncrna -蛋白的相互作用。

IF 3.6 2区生物学

Journal of Proteome Research Pub Date : 2025-08-01 DOI: 10.1021/acs.jproteome.5c00334

Yuling Dai, Jeong-Ah Kim, Isabella T Whitworth, Mark Scalf, Mabel M Jung, Brian L Frey, Emery H Bresnick, Lloyd M Smith

{"title":"Identifying lncRNA-Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry.","authors":"Yuling Dai, Jeong-Ah Kim, Isabella T Whitworth, Mark Scalf, Mabel M Jung, Brian L Frey, Emery H Bresnick, Lloyd M Smith","doi":"10.1021/acs.jproteome.5c00334","DOIUrl":"https://doi.org/10.1021/acs.jproteome.5c00334","url":null,"abstract":"Long noncoding RNAs (lncRNAs) exert regulatory functions in a wide spectrum of biological contexts, and certain regulatory functions involve the formation of RNA-protein complexes. Discovering the structure and function of these complexes may unveil important functional insights. The DDX41 gene encoding the DEAD-box RNA helicase 41 protein (DDX41) is subject to extensive germline genetic variation, and certain variants create a predisposition to develop myelodysplastic syndrome and acute myeloid leukemia. While the importance of DDX41 for the control of hematopoiesis is established, many questions remain regarding the mechanisms of how DDX41 functions in hematopoietic stem and progenitor cells. Previously, we identified a DDX41-regulated lncRNA, growth-arrest-specific 5 (Gas5). As the Gas5 function in hematopoiesis is unknown, we analyzed the protein interactors of Gas5 lncRNA using HyPR-MS (hybridization purification of RNA-protein complexes, followed by mass spectrometry). A total of 303 proteins were identified as Gas5 lncRNA interactors, five of which were experimentally validated as Gas5 lncRNA interactors by RNA immunoprecipitation qPCR (RIP-qPCR) analysis. The identification of protein interactors with a DDX41-regulated lncRNA establishes a foundation on which to guide future mechanistic and biological studies.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758723","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}

引用次数: 0

IF 3.6 2区生物学