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Zhang F, Rakhimbekova A, Lashley T, Madl T. Brain regions show different metabolic and protein arginine methylation phenotypes in frontotemporal dementias and Alzheimer's disease. Prog Neurobiol 2023; 221:102400. [PMID: 36581185 DOI: 10.1016/j.pneurobio.2022.102400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/05/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022]
Abstract
Frontotemporal dementia (FTD) is a heterogeneous neurodegenerative disease with multiple histopathological subtypes. FTD patients share similar symptoms with Alzheimer's disease (AD). Hence, FTD patients are commonly misdiagnosed as AD, despite the consensus clinical diagnostic criteria. It is therefore of great clinical need to identify a biomarker that can distinguish FTD from AD and control individuals, and potentially further differentiate between FTD pathological subtypes. We conducted a metabolomic analysis on post-mortem human brain tissue from three regions: cerebellum, frontal cortex and occipital cortex from control, FTLD-TDP type A, type A-C9, type C and AD. Our results indicate that the brain subdivisions responsible for different functions show different metabolic patterns. We further explored the region-specific metabolic characteristics of different FTD subtypes and AD patients. Different FTD subtypes and AD share similar metabolic phenotypes in the cerebellum, but AD exhibited distinct metabolic patterns in the frontal and occipital regions compared to FTD. The identified brain region-specific metabolite biomarkers could provide a tool for distinguishing different FTD subtypes and AD and provide the first insights into the metabolic changes of FTLD-TDP type A, type A-C9, type C and AD in different regions of the brain. The importance of protein arginine methylation in neurodegenerative disease has come to light, so we investigated whether the arginine methylation level contributes to disease pathogenesis. Our findings provide new insights into the relationship between arginine methylation and metabolic changes in FTD subtypes and AD that could be further explored, to study the molecular mechanism of pathogenesis.
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Affiliation(s)
- Fangrong Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, China; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Anastasia Rakhimbekova
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK; Queen Square Brain Bank for Neurological Diseases, UCL Queen Square Institute of Neurology, London, UK.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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Zhang J, Rakhimbekova A, Duan X, Yin Q, Foss CA, Fan Y, Xu Y, Li X, Cai X, Kutil Z, Wang P, Yang Z, Zhang N, Pomper MG, Wang Y, Bařinka C, Yang X. A prostate-specific membrane antigen activated molecular rotor for real-time fluorescence imaging. Nat Commun 2021; 12:5460. [PMID: 34526506 PMCID: PMC8443597 DOI: 10.1038/s41467-021-25746-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/25/2021] [Indexed: 12/03/2022] Open
Abstract
Surgery is an efficient way to treat localized prostate cancer (PCa), however, it is challenging to demarcate rapidly and accurately the tumor boundary intraoperatively, as existing tumor detection methods are seldom performed in real-time. To overcome those limitations, we develop a fluorescent molecular rotor that specifically targets the prostate-specific membrane antigen (PSMA), an established marker for PCa. The probes have picomolar affinity (IC50 = 63-118 pM) for PSMA and generate virtually instantaneous onset of robust fluorescent signal proportional to the concentration of the PSMA-probe complex. In vitro and ex vivo experiments using PCa cell lines and clinical samples, respectively, indicate the utility of the probe for biomedical applications, including real-time monitoring of endocytosis and tumor staging. Experiments performed in a PCa xenograft model reveal suitability of the probe for imaging applications in vivo.
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Affiliation(s)
- Jingming Zhang
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China
| | - Anastasia Rakhimbekova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 25250, Vestec, Czech Republic
| | - Xiaojiang Duan
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China
| | - Qingqing Yin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100191, Beijing, China
| | - Catherine A Foss
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yan Fan
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China
| | - Yangyang Xu
- Department of Urology, Peking University First Hospital, 100034, Beijing, China
- The Institute of Urology, Peking University, 100034, Beijing, China
- National Urological Cancer Center, 100034, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, 10034, Beijing, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, 100034, Beijing, China
- The Institute of Urology, Peking University, 100034, Beijing, China
- National Urological Cancer Center, 100034, Beijing, China
- Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, 10034, Beijing, China
| | - Xuekang Cai
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China
| | - Zsofia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 25250, Vestec, Czech Republic
| | - Pengyuan Wang
- Department of General Surgery, Peking University First Hospital, 100034, Beijing, China
| | - Zhi Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/ Beijing), Department of Nuclear Medicine, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Ning Zhang
- Translational Cancer Research Center, Peking University First Hospital, 100034, Beijing, China
| | - Martin G Pomper
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yiguang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100191, Beijing, China.
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 25250, Vestec, Czech Republic.
| | - Xing Yang
- Department of Nuclear Medicine, Peking University First Hospital, 100034, Beijing, China.
- Institute of Medical Technology, Peking University Health Science Center, 100191, Beijing, China.
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Rakhimbekova A, Akhmetshin TN, Minibaeva GI, Nugmanov RI, Gimadiev TR, Madzhidov TI, Baskin II, Varnek A. Cross-validation strategies in QSPR modelling of chemical reactions. SAR QSAR Environ Res 2021; 32:207-219. [PMID: 33601989 DOI: 10.1080/1062936x.2021.1883107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
In this article, we consider cross-validation of the quantitative structure-property relationship models for reactions and show that the conventional k-fold cross-validation (CV) procedure gives an 'optimistically' biased assessment of prediction performance. To address this issue, we suggest two strategies of model cross-validation, 'transformation-out' CV, and 'solvent-out' CV. Unlike the conventional k-fold cross-validation approach that does not consider the nature of objects, the proposed procedures provide an unbiased estimation of the predictive performance of the models for novel types of structural transformations in chemical reactions and reactions going under new conditions. Both the suggested strategies have been applied to predict the rate constants of bimolecular elimination and nucleophilic substitution reactions, and Diels-Alder cycloaddition. All suggested cross-validation methodologies and tutorial are implemented in the open-source software package CIMtools (https://github.com/cimm-kzn/CIMtools).
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Affiliation(s)
- A Rakhimbekova
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | - T N Akhmetshin
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
- Laboratory of Chemoinformatics, UMR 7140 CNRS, University of Strasbourg, Strasbourg, France
| | - G I Minibaeva
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | - R I Nugmanov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | - T R Gimadiev
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
| | - T I Madzhidov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
| | - I I Baskin
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russia
- Department of Materials Science and Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - A Varnek
- Laboratory of Chemoinformatics, UMR 7140 CNRS, University of Strasbourg, Strasbourg, France
- Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
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Yakimova LS, Shurpik DN, Gilmanova LH, Makhmutova AR, Rakhimbekova A, Stoikov II. Highly selective binding of methyl orange dye by cationic water-soluble pillar[5]arenes. Org Biomol Chem 2016; 14:4233-8. [DOI: 10.1039/c6ob00539j] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The bulky/negatively charged substituents of guest anions hinder the substrate entering the π-electron rich pillar[5]arene cavity.
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Affiliation(s)
- L. S. Yakimova
- Kazan Federal University
- A.M. Butlerov Chemical Institute
- Kazan
- Russian Federation
| | - D. N. Shurpik
- Kazan Federal University
- A.M. Butlerov Chemical Institute
- Kazan
- Russian Federation
| | - L. H. Gilmanova
- Kazan Federal University
- A.M. Butlerov Chemical Institute
- Kazan
- Russian Federation
| | - A. R. Makhmutova
- Kazan Federal University
- A.M. Butlerov Chemical Institute
- Kazan
- Russian Federation
| | - A. Rakhimbekova
- Kazan Federal University
- A.M. Butlerov Chemical Institute
- Kazan
- Russian Federation
| | - I. I. Stoikov
- Kazan Federal University
- A.M. Butlerov Chemical Institute
- Kazan
- Russian Federation
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