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Qin XP, Lu QJ, Yang CH, Wang J, Chen JF, Liu K, Chen X, Zhou J, Pan YH, Li YH, Ren SC, Liu JM, Liu WP, Qian HJ, Yi XL, Lai CY, Qu LJ, Gao X, Xu YS, Chen Z, Zhuo YM. CRMP4 CpG Hypermethylation Predicts Upgrading to Gleason Score ≥ 8 in Prostate Cancer. Front Oncol 2022; 12:840950. [PMID: 35359369 PMCID: PMC8960729 DOI: 10.3389/fonc.2022.840950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/21/2022] [Indexed: 01/07/2023] Open
Abstract
Background This study determined the predictive value of CRMP4 promoter methylation in prostate tissues collected by core needle biopsies for a postoperative upgrade of Gleason Score (GS) to ≥8 in patients with low-risk PCa. Method A retrospective analysis of the clinical data was conducted from 631 patients diagnosed with low-risk PCa by core needle biopsy at multiple centers and then underwent Radical Prostatectomy (RP) from 2014-2019. Specimens were collected by core needle biopsy to detect CRMP4 promoter methylation. The pathologic factors correlated with the postoperative GS upgrade to ≥8 were analyzed by logistic regression. The cut-off value for CRMP4 promoter methylation in the prostate tissues collected by core needle biopsy was estimated from the ROC curve in patients with a postoperative GS upgrade to ≥8. Result Multivariate logistic regression showed that prostate volume, number of positive cores, and CRMP4 promoter methylation were predictive factors for a GS upgrade to ≥8 (OR: 0.94, 95% CI: 0.91-0.98, P=0.003; OR: 3.16, 95% CI: 1.81-5.53, P<0.001; and OR: 1.43, 95% CI: 1.32-1.55, P<0.001, respectively). The positive predictive rate was 85.2%, the negative predictive rate was 99.3%, and the overall predictive rate was 97.9%. When the CRMP4 promoter methylation rate was >18.00%, the low-risk PCa patients were more likely to escalate to high-risk patients. The predictive sensitivity and specificity were 86.9% and 98.8%, respectively. The area under the ROC curve (AUC) was 0.929 (95% CI: 0.883-0.976; P<0.001). The biochemical recurrence (BCR)-free survival, progression-free survival (PFS), and cancer-specific survival (CSS) were worse in patients with CRMP4 methylation >18.0% and postoperative GS upgrade to ≥8 than in patients without an upgrade (P ≤ 0.002). Conclusion A CRMP4 promoter methylation rate >18.00% in prostate cancer tissues indicated that patients were more likely to escalate from low-to-high risk after undergoing an RP. We recommend determining CRMP4 promoter methylation before RP for low-risk PCa patients.
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Affiliation(s)
- Xiao-Ping Qin
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qi-Ji Lu
- Department of Urology, Affiliated Xiaolan Hospital, Southern Medical University, Zhongshan, China
| | - Cheng-Huizi Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jue Wang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jian-Fan Chen
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Kan Liu
- Department of Urology, The Third Medical Centre, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Xin Chen
- Department of Pathology, The Third Medical Centre, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Jing Zhou
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu-Hang Pan
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yong-Hong Li
- Department of Urology, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Shan-Cheng Ren
- Department of Urology, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jiu-Min Liu
- Department of Urology, Guangdong General Hospital, Guangzhou, China
| | - Wei-Peng Liu
- Department of Urology, The First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Hui-Jun Qian
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xian-Lin Yi
- Department of Urology, Cancer Hospital, Guangxi Medical University, Nanning, China
| | - Cai-Yong Lai
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Li-Jun Qu
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xin Gao
- Department of Urology, The Third Affiliated Hospital of Sun Yet-Sen University, Guangzhou, China
| | - Yu-Sheng Xu
- Department of Emergency, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zheng Chen
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yu-Min Zhuo
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Turck CW, Webhofer C, Reckow S, Moy J, Wang M, Guillermier C, Poczatek JC, Filiou MD. Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry. Proteomics 2022; 22:e2100244. [PMID: 35355420 DOI: 10.1002/pmic.202100244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022]
Abstract
A major challenge in managing depression is that antidepressant drugs take a long time to exert their therapeutic effects. For the development of faster acting therapies, it is crucial to get an improved understanding of the molecular mechanisms underlying antidepressant mode of action. Here, we used a novel mass spectrometry-based workflow to investigate how antidepressant treatment affects brain protein turnover at single cell and subcellular resolution. We combined stable isotope metabolic labeling, quantitative Tandem Mass Spectrometry (qTMS) and Multi-isotope Imaging Mass Spectrometry (MIMS) to simultaneously quantify and image protein synthesis and turnover in hippocampi of mice treated with the antidepressant paroxetine. We identified changes in turnover of individual hippocampal proteins that reveal altered metabolism-mitochondrial processes and report on subregion-specific turnover patterns upon paroxetine treatment. This workflow can be used to investigate brain protein turnover changes upon pharmacological interventions at a resolution and precision that has not been possible with other methods to date. Our results reveal acute paroxetine effects on brain protein turnover and shed light on antidepressant mode of action. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Christian Webhofer
- Max Planck Institute of Psychiatry, Munich, Germany.,Present address: Amgen Research GmbH, Munich, Germany
| | | | - Jeffrey Moy
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,National Resource for Imaging Mass Spectrometry (NRIMS), Cambridge, MA, USA
| | - Mei Wang
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,National Resource for Imaging Mass Spectrometry (NRIMS), Cambridge, MA, USA
| | - Christelle Guillermier
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,National Resource for Imaging Mass Spectrometry (NRIMS), Cambridge, MA, USA
| | - J Collin Poczatek
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,National Resource for Imaging Mass Spectrometry (NRIMS), Cambridge, MA, USA
| | - Michaela D Filiou
- Max Planck Institute of Psychiatry, Munich, Germany.,Department of Biological Applications and Technology, School of Health Sciences, University of Ioannina, Ioannina, Greece.,Biomedical Research Institute, Foundation for Research and Technology-Hellas (FORTH), Ioannina, Greece
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Valdés A, Bergström Lind S. Mass Spectrometry-Based Analysis of Time-Resolved Proteome Quantification. Proteomics 2019; 20:e1800425. [PMID: 31652013 DOI: 10.1002/pmic.201800425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/20/2019] [Indexed: 11/09/2022]
Abstract
The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time-dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners-both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS-based analysis of time-resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.
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Affiliation(s)
- Alberto Valdés
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, 75124, Uppsala, Sweden
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Liu H, Wang Y, Liu J, Fu W. Proteomics analysis of fetal growth restriction and taurine‑treated fetal growth restriction rat brain tissue by 2D DIGE and MALDI‑TOF/TOF MS analysis. Int J Mol Med 2019; 44:207-217. [PMID: 31115483 PMCID: PMC6559329 DOI: 10.3892/ijmm.2019.4182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 04/23/2019] [Indexed: 02/05/2023] Open
Abstract
Fetal growth restriction (FGR) is caused by placental insufficiency and can lead to short and long‑term neurodevelopmental delays. Taurine, one of the most abundant amino acids in the brain, is critical for the normal growth and development of the nervous system; however, the mechanistic role of taurine in neural growth and development remains unknown. The present study investigated the role of taurine in FGR. Specifically, we explored the proteomic profiles of fetal rats at 6 h postpartum by two‑dimensional difference gel electrophoresis combined with matrix assisted laser desorption ionization‑time‑of‑flight (TOF)/TOF tandem mass spectrometry; the findings were verified via reverse transcription‑quantitative polymerase chain reaction. A total of 31 differentially expressed protein spots were selected. Among these, 31 were matched, including dihydropyrimidinase‑related protein 2 and , CRK and peroxiredoxin 2. Functional analysis using the Gene Ontology database and Ingenuity Pathway Analysis demonstrated that the differentially expressed proteins were mainly associated with neuronal differentiation, 'metabolic process', 'biological regulation' and developmental processes. The present study identified several proteins that were differentially expressed in rats with FGR in the presence or absence of taurine administration. The results of the present study suggest a potential role for taurine in the treatment and prevention of FGR.
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Affiliation(s)
- Haifeng Liu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515
- Department of Neonatology, The First People's Hospital of Chenzhou, Chenzhou, Hunan 423000
- Department of Neonatology and NICU of Bayi Children's Hospital, The Army General Hospital of The Chinese PLA, Beijing 100700
- Department of Neonatology and NICU, Beijing Chaoyang District Maternal and Child Healthcare Hospital, Beijing 100101
| | - Yan Wang
- NICU of Taian City Central Hospital, Taian, Shandong 271000, P.R. China
| | - Jing Liu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510515
- Department of Neonatology and NICU of Bayi Children's Hospital, The Army General Hospital of The Chinese PLA, Beijing 100700
- Department of Neonatology and NICU, Beijing Chaoyang District Maternal and Child Healthcare Hospital, Beijing 100101
- Correspondence to: Dr Jing Liu, The Second School of Clinical Medicine, Southern Medical University, 1023-1063 South Shatai Road, Baiyun, Guangzhou, Guangdong 510515, P.R. China, E-mail:
| | - Wei Fu
- Department of Neonatology and NICU, Beijing Chaoyang District Maternal and Child Healthcare Hospital, Beijing 100101
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5
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Cohen LD, Ziv NE. Neuronal and synaptic protein lifetimes. Curr Opin Neurobiol 2019; 57:9-16. [PMID: 30677713 DOI: 10.1016/j.conb.2018.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/14/2018] [Indexed: 01/08/2023]
Abstract
Neuronal proteostasis is uniquely challenged by the extraordinary architecture of neurons, the vast number of synapses they form, and the need to precisely preserve function at individual synapses. Quantitative information on protein lifetimes can provide clues as to how these challenges are met. Advances in proteomics and mass spectrometry, which now enable comprehensive lifetime estimations for thousands of proteins, suggest that neuronal and synaptic protein lifetimes are unusually long, with half-lives typically ranging from days to weeks, even months and beyond for certain protein families. Half-lives in vivo are several-fold longer than those in cell culture, tend to cluster for proteins belonging to multimolecular complexes, are affected by developmental stage, and possibly by environmental conditions and activity levels.
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Affiliation(s)
- Laurie D Cohen
- Technion Faculty of Medicine, Rappaport Institute and Network Biology Research Laboratories, Fishbach Building, Technion City, Haifa, 32000, Israel
| | - Noam E Ziv
- Technion Faculty of Medicine, Rappaport Institute and Network Biology Research Laboratories, Fishbach Building, Technion City, Haifa, 32000, Israel.
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Stastna M, Gottlieb RA, Van Eyk JE. Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. Expert Rev Proteomics 2017; 14:529-543. [PMID: 28532181 DOI: 10.1080/14789450.2017.1333424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation. The methods that identify both regulatory proteins associated with translational components and newly synthesized proteins are discussed. Expert commentary: Emerging proteomic approaches make it possible to monitor protein dynamics in cells, tissues and whole animals. The ability to detect alteration in protein abundance soon after their synthesis enables earlier recognition of disease causing factors and candidates to prevent/rectify disease phenotype.
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Affiliation(s)
- Miroslava Stastna
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,c Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i ., Brno , Czech Republic
| | - Roberta A Gottlieb
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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Duque-Guimarães D, Ong TP, de Almeida-Faria J, Guest PC, Ozanne SE. SILAC Mass Spectrometry Profiling: A Psychiatric Disorder Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 974:289-298. [PMID: 28353248 DOI: 10.1007/978-3-319-52479-5_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Stable isotope labelling by amino acids in cell culture (SILAC) is a technique that allows proteomic profiling of cells. In this chapter we describe a protocol for the identification and quantification of newly synthesised proteins. The methodology can be applied to any cultured cell system with relevance to schizophrenia, affective disorders and autism spectrum conditions including those addressing responses to pharmacological stimuli.
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Affiliation(s)
- Daniella Duque-Guimarães
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thomas Prates Ong
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
- Food Research Center (FoRC) and Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Juliana de Almeida-Faria
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
- Department of Pharmacology, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255 F/01, Cidade Universitária ZeferinoVaz, 13083-862, Campinas, Brazil
| | - Susan E Ozanne
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
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