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PKM2 promotes reductive glutamine metabolism

Cancer Biology & Medicine 2018年第4期15卷 389-399页

作者： Miao Liu Yuanyuan Wang Yuxia Ruan Changsen Bai Li Qiu Yanfen Cui Guoguang Ying Binghui Li department of Cancer Cell Biology Tianjin Medical University Cancer Institute and HospitalNational Clinical Research Center for CancerKey Laboratory of Cancer Prevention and TherapyTianjinTianjin’s Clinical Research Center for CancerTianjin 300060China department of biochemistry and Molecular Biology Capital Medical UniversityBeijing 100069China

Objective:Pyruvate kinases M(PKM),including the PKM1 and PKM2 isoforms,are critical factors in glucose ***2promotes aerobic glycolysis,a phenomenon known as"the Warburg effect".The purpose of this study was to identify the roles of PKM2 in regulating cellular ***:The CRISPR/Cas9 system was used to generate the PKM-knockout cell model to evaluate the role of PKM in cellular *** levels were measured by the Vitros LAC slide method on an autoanalyzer and glucose levels were measured by the autoanalyzer *** metabolism of ^(13)C_6-glucose or ^(13)C_5-glutamine was evaluated by liquid chromatography/mass spectrometry *** effects of PKM on tumor growth were detected in vivo in a tumor-bearing mouse ***:We found that both PKM1 and PKM2 enabled aerobic glycolysis,but PKM2 converted glucose to lactate much more efficiently than *** a result,PKM2 reduced glucose levels reserved for intracellular utilization,particularly for the production of citrate,and thus increased theα-ketoglutarate/citrate ratio to promote the generation of glutamine-derived acetylcoenzyme A through the reductive ***,reductive glutamine metabolism facilitated cell proliferation under hypoxia conditions,which supports in vivo tumor *** addition,PKM-deletion induced a reverse Warburg effect in tumorassociated stromal ***:PKM2 plays a critical role in promoting reductive glutamine metabolism and maintaining proton *** study is helpful to increase the understanding of the physiological role of PKM2 in cancer cells.

关键词： The Warburg effect the reverse Warburg effect PKM2 glucose metabolism proton homeostasis

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Ribotrap Analysis of Proteins Associated with FHL3 3'Untranslated Region in Glioma Cells

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Chinese Medical Sciences Journal 2014年第2期29卷 78-84页

作者： Wei Han Qing Xia Bin Yin Xiao-zhong Peng State Key Laboratory of Medical Molecular Biology Department of Biochemistry and Molecular Biology Institute of Basic Medical Sciences Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100005 China State Key Laboratory of Proteomics Institute of Basic Medical Sciences National Center of Biomedical Analysis Beijing 100850 China

Objective To screen the proteins associated with four-and-a-half LIM domains 3(FHL3) 3' untranslated region(3'UTR) in glioma cells. Methods Western blot was adopted to detect the regulatory effect of poly(C)-binding protein 2(PCBP2) on FHL3. Biotin pull-down and sliver staining were employed to screen and verify the candidate binding proteins of FHL3 3'UTR. Then liquid chromatography-tandem mass spectrometry(LC-MS/MS) and molecule annotation system were used to identify and analyze the candidate binding proteins. Immunoprecipitation was conducted to study the interaction between PCBP2 and polypyrimidine tract-binding protein 1(PTBP1), a binding protein identified by LC-MS/MS. Results PCBP2 could bind to FHL3 mRNA 3'UTR-A and inhibited the expression of FHL3 in T98 G glioms cells. 22 candidate binding proteins were identified. Among them, there were 11 RNA binding proteins, including PCBP2. PTBP1 associated with FHL3 mRNA 3'UTR and interacted with PCBP2 protein. Conclusion PCBP2 and PTBP1 can both associate with FHL3 mRNA 3'UTR through forming a protein complex.

关键词： FHL3 3'untranslated region poly(C)-binding protein 2 polypyrimidine tract-binding protein 1 liquid chromatography-tandem mass spectrometry

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Proteomic Portrait of Human Lymphoma Reveals Protein Molecular Fingerprint of Disease Specific Subtypes and Progression

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Phenomics 2023年第2期3卷 148-166页

作者： Xin Ku Jinghan Wang Haikuo Li Chen Meng Fang Yu Wenjuan Yu Zhongqi Li Ziqi Zhou Can Zhang Ying Hua Wei Yan Jie Jin Shanghai center for Systems Biomedicine Key Laboratory of Systems Biomedicine(Ministry of Education)Shanghai Jiao Tong UniversityShanghai 200240China department of Hematology The First Affiliated Hospital of Medical School of Zhejiang UniversityHangzhou 310003China Bavarian center for Biomolecular mass spectrometry Technical University of Munich85354 FreisingGermany Cancer center Zhejiang UniversityHangzhou 310003China department of Pathology The First Affiliated Hospital of Zhejiang UniversityHangzhou 310003China department of Surgical Oncology College of MedicineThe First Affiliated HospitalZhejiang UniversityHangzhou 310003China Key Laboratory of Hematologic Malignancies Diagnosis and TreatmentHangzhou 310003China Present Address:Division of Biology&biomedical Sciences Washington University in St.Louis School of MedicineSt.Louis 63130USA

An altered proteome in lymph nodes often suggests abnormal signaling pathways that may be associated with diverse lymphatic *** clinical biomarkers for histological classification of lymphomas have encountered many discrepancies,particularly for borderline ***,we launched a comprehensive proteomic study aimed to establish a proteomic landscape of patients with various lymphatic disorders and identify proteomic variations associated with different disease *** this study,109 fresh-frozen lymph node tissues from patients with various lymphatic disorders(with a focus on Non-Hodgkin’s Lymphoma)were analyzed by data-independent acquisition mass spectrometry.A quantitative proteomic landscape was comprehensively characterized,leading to the identification of featured protein profiles for each *** correlations between clinical outcomes and expression profiles of signature proteins were also *** representative signature proteins,phospholipid-binding proteins Annexin A6(ANXA6)and Phospholipase C Gamma 2(PLCG2),were successfully validated via *** also evaluated the capability of acquired proteomic signatures to segregate multiple lymphatic abnormalities and identified several core signature proteins,such as Sialic Acid Binding Ig Like Lectin 1(SIGLEC1)and GTPase of immunity-associated protein 5(GIMAP5).In summary,the established lympho-specific data resource provides a comprehensive map of protein expression in lymph nodes during multiple disease states,thus extending the existing human tissue proteome *** findings will be of great value in exploring protein expression and regulation underlying lymphatic malignancies,while also providing novel protein candidates to classify various lymphomas for more precise medical practice.

关键词： Lymphoma Non-Hodgkin’s Lymphoma Proteomics Stratification Molecular profiling

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Bone mineral density in lifelong trained male football players compared with young and elderly untrained men

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Journal of Sport and Health Science 2018年第2期7卷 159-168页

作者： Marie Hagman Eva Wulff Helge Therese Hornstrup Bjorn Fristrup Jens Jung Nielsen Niklas Rye Jorgensen Jesper Lovind Andersen Jorn Wulff Helge Peter Krustrup department of Sports Science and Clinical Biomechanics SDU Sport and Health Sciences Cluster (SHSC) University of Southern Denmark Odense 3450 Denmark department of Nutrition Exercise and Sports University of Copenhagen Copenhagen N 2200 Denmark Institute of Sports Medicine Copenhagen Bispebjerg Hospital Copenhagen NV 2400 Denmark department of Clinical biochemistry Rigshospitalet Research Center for Ageing and Osteoporosis Glostrup 2600 Denmark center of Healthy Aging Department of Biomedical Sciences University of Copenhagen Copenhagen N 2200 Denmark Sport and Health Sciences University of Exeter Exeter EX1 2LU UK

Purpose: The purpose of the present controlled cross-sectional study was to investigate proximal femur and whole-body bone mineral density(BMD), as well as bone turnover profile, in lifelong trained elderly male football players and young elite football players compared with untrained age-matched ***: One hundred and forty healthy, non-smoking men participated in the study, including lifelong trained football players(FTE, n = 35)aged 65—80 years, elite football players(FTY, n = 35) aged 18—30 years, as well as untrained age-matched elderly(UE, n = 35) and young(UY,n = 35) men. All participants underwent a regional dual-energy X-ray Absorptiometry(DXA) scan of the proximal femur and a whole-body DXA scan to determine BMD. From a resting blood sample, the bone turnover markers(BTMs) osteocalcin, carboxy-terminal type-1 collagen crosslinks(CTX-1), procollagen type-1 amino-terminal propeptide(P1NP), and sclerostin were ***: FTE had 7.3%—12.9% higher(p < 0.05) BMD of the femoral neck, wards, shaft, and total proximal femur in both legs compared to UE,and 9.3%—9.7% higher(p < 0.05) BMD in femoral trochanter in both legs compared to UY. FTY had 24.3%—37.4% higher(p < 0.001) BMD in all femoral regions and total proximal femur in both legs compared to UY. The whole-body DXA scan confirmed these results, with FTE showing similar whole-body BMD and 7.9% higher(p < 0.05) leg BMD compared to UY, and with FTY having 9.6% higher(p < 0.001) wholebody BMD and 18.2% higher(p < 0.001) leg BMD compared to UY. The plasma concentration of osteocalcin, CTX-1, and P1NP were 29%,53%, and 52% higher(p < 0.01), respectively, in FTY compared to ***: BMD of the proximal femur and whole-body BMD are markedly higher in lifelong trained male football players aged 65—80 years and young elite football players aged 18—30 years compared to age-matched untrained men. Elderly football players even show higher BMD in femoral trochanter and leg BMD than untrained young despi

关键词： Bone mass Bone turnover markers Dual-energy X-ray absorptiometry Proximal femur bone mineral density Soccer Whole-body bone mineral density

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mass spectrometry detection of basic drugs in fast chiral analyses with vancomycin stationary phases

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Journal of Pharmaceutical Analysis 2018年第5期8卷 324-332页

作者： Hongyue Guo M.Farooq Wahab Alain Berthod Daniel W.Armstrong department of Chemistry and biochemistry University of Texas at Arlington Institut des Sciences Analytiques CNRS Université de Lyon 1

Current trends in chiral analysis of pharmaceutical drugs are focused on faster separations and higher separation efficiencies, Core-shell or superficially porous particles （SPP） based chiral stationary phases （CSPs） provide reduced analysis times while maintaining high column efficiencies and sensitivity. In this study, mobile phase conditions suitable for chiral analyses with electrospray ionization LC-MS were systematically investigated using vancomycin as a representative CSP. The performance of a 2.7 μm SPP based vancomycin CSP （SPP-V） 10 cm ×0.21 cm column was compared to that of a corresponding 5 μm fully porous particles based analogue column. The results demonstrated that the SPP-V column provides higher efficiencies, 2-5 time greater sensitivity and shorter analysis time for a set of 22 basic pharma- ceutical drugs. The SPP-V was successfully applied for the analysis of the degradation products of racemic citalopram whose enantiomers could be selectively identified by MS.

关键词： mass spectrometry detection Chiral separation Basic drugs Beta-blockers Superficially porous particle Fully porous particle Fast separation Vancomycin

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In vivo detection of metabolic^(2)H-incorporation upon ingestion of^(2)H_(2)O

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Journal of Bio-X Research 2022年第2期5卷 81-89页

作者： Kim Arnold Xing Chen Hui Zhang Kapil Dev Singh Zhihong Yin Yao Yao Tiangang Luan Pablo Sinues Xue Li University of Basel Children’s Hospital(UKBB) Basel department of biomedical Engineering University of BaselAllschwilSwitzerland Institute of mass spectrometry and Atmospheric Environment Jinan University School of biomedical and Pharmaceutical Sciences Guangdong University of Technology Metabolic Innovation center Zhongshan School of MedicinePlatform of MetabolomicsCenter for Precision Medicine State Key Laboratory of Biocontrol School of Life SciencesSun Yat-sen University Institute of Environmental and Ecological Engineering Guangdong University of TechnologyGuangzhouGuangdong ProvinceChina

Objective:The aim of this work was to explore the feasibility of in vivo and non-invasive monitoring of deuterium/hydrogen(^(2)H/1H)exchange at the metabolic level upon exposure to heavy water(^(2)H_(2)O).Methods:The healthy female mice were randomly assigned to two groups after day 0 when both mice received standard drinking *** treated mouse was fed with^(2)H_(2)O(80%,v/v)and the control mouse fed with standard drinking water(H2O)over next ***-time mass spectrometric analysis of volatile metabolism emitted through breathing and the skin was performed on days 1,2,3,10,12,and *** experiment was approved by the Laboratory Animal Ethics Committee of Jinan University(approval No.20161117163322)on October 29,***:We observed a replacement of 1H by^(2)H in 52 mass spectral features(60^(2)H/1H isotopologue pairs)for the mouse fed with^(2)H_(2)O,but not for the control *** included pyruvic acid and lactic acid,lysine and methyl-lysine as well as short-chain fatty acids comprising acetic acid,propionic acid,butyric acid and valeric ***:Secondary electrospray ionization-high resolution mass spectrometry allows monitoring in vivo^(2)H-incorporation of metabolites in a non-invasive and real-time setup and opens new opportunities to use^(2)H tracing to extend current metabolic studies,especially those with a focus on anaerobic glycolysis,lysine methylation and gut microbiome via monitoring of short-chain fatty acids.

关键词： deuterium isotopes metabolomics non-invasive secondary electrospray ionization-high resolutionmass spectrometry

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Structural insights into the assembly of the 30S ribosomal subunit in vivo： functional role of S5 and location of the 17S rRNA precursor sequence

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Protein & Cell 2014年第5期5卷 394-407页

作者： Zhixiu Yang Qiang Guo Simon Goto Yuling Chen Ningning Li Kaige Yan Yixiao Zhang Akira Muto Haiteng Deng Hyouta Himeno Jianlin Lei Ning Gao Ministry of Education Key Laboratory of Protein Sciences Center for Structural Biology School of Life Sciences Tsinghua University Beijing 100084 China department of-biochemistry and Molecular Biology Faculty of Agriculture and Life Science Hirosaki University Hirosaki 036-8561 Japan

The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coil strain （ArsgAArbfA）. The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, inter- mediates derived under the two contrasting salt condi- tions （high and low） likely reflect two distinctive assembly stages, the relatively early and late stages of the 3＇ domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5＇ end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal thelocation of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mech- anisms on subunit production and protein translation.

关键词： RsgA RbfA ribosome assembly cryo-EM,quantitative mass spectrometry

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Proteomics of protein post-translational modifications implicated in neurodegeneration

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Translational Neurodegeneration 2014年第1期3卷 156-168页

作者： Ru-Jing Ren Eric B Dammer Gang Wang Nicholas T Seyfried Allan I Levey department of Neurology Center for Neurodegenerative DiseasesEmory University School of MedicineAtlantaGA 30322USA department of biochemistry Center for Neurodegenerative DiseasesEmory University School of MedicineAtlantaGA 30322USA department of Pharmacology Center for Neurodegenerative DiseasesEmory University School of MedicineAtlantaGA 30322USA Emory Proteomics Service center Center for Neurodegenerative DiseasesEmory University School of MedicineAtlantaGA 30322USA

mass spectrometry(MS)-based proteomics has developed into a battery of approaches that is exceedingly adept at identifying with high mass accuracy and precision any of the following:oxidative damage to proteins(redox proteomics),phosphorylation(phosphoproteomics),ubiquitination(diglycine remnant proteomics),protein fragmentation(degradomics),and other posttranslational modifications(PTMs).Many studies have linked these PTMs to pathogenic mechanisms of *** date,identifying PTMs on specific pathology-associated proteins has proven to be a valuable step in the evaluation of functional alteration of proteins and also elucidates biochemical and structural explanations for possible pathophysiological mechanisms of neurodegenerative *** review provides an overview of methods applicable to the identification and quantification of PTMs on proteins and enumerates historic,recent,and potential future research endeavours in the field of proteomics furthering the understanding of PTM roles in the pathogenesis of neurodegeneration.

关键词： Proteomics Protein posttranslational modifications Neurodegeneration Alzheimer’s disease Parkinson’s disease

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Radial Basis Function Networks Applied in Bacterial Classification Based on MALDI-TOF-MS

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Chemical Research in Chinese Universities 2002年第4期18卷 453-457页

作者： HARRINGTON Peter de B. VOORHEES Kent J. REES Jon Ohio University center for Intelligent Chemical Instrumentation Department of Chemistry and Biochemistry Ohio UniversityDepartment of Chemistry and Geochemistry Colorado School of MinesDepartment of Chemistry and Geochemistry Colorado School of Mines Athens Ohio 45701-2979 USA Golden CO 80401 USAGolden CO 80401 USA

The radial basis function networks were applied to bacterial classification based on the matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF-MS) data. The classification of bacteria cultured at different time was discussed and the effect of the network parameters on the classification was investigated. The cross-validation method was used to test the trained networks. The correctness of the classification of different bacteria investigated changes in a wide range from 61.5% to 92.8%. Owing to the complexity of biological effects in bacterial growth, the more rigid control of bacterial culture conditions seems to be a critical factor for improving the rate of correctness for bacterial classification.

关键词： Radial basis function network Matrix-assisted laser desorption/ionization Time-of-flight mass spectrometry Bacterium Classification

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High-throughput experimental methods for investigating biomolecular condensates

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Quantitative Biology 2021年第3期9卷 255-266页

作者： Taoyu Chen Qi Lei Minglei Shi Tingting Li department of biomedical Informatics School of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic&Systems BiologyTNLISTSchool of MedicineTsinghua UniversityBeijing 100084China

Background:The concept of biomolecular condensate was put forward recently to emphasize the ability of certain cellular compartments to concentrate molecules and comprise proteins and nucleic acids with specific biological functions,from ribosome genesis to RNA *** to their unique role in biological processes,it is crucial to investigate their compositions,which is a primary determinant of condensate ***:Since a wide range of macromolecules comprise biomolecular condensates,it is necessary for researchers to investigate them using high-throughput methodologies while low-throughput experiments are not efficient *** high-throughput methods usually purify interacting protein libraries from condensates before being scanned in mass *** is possible to extract organelles as a whole for specific condensates for further analysis,however,most condensates do not have a distinguishable marker or are sensitive to shear force to be extracted as a *** tagging allows a comprehensive view of interacting proteins of target molecule yet only proteins with strong bonds may be pulled *** labeling serves as a complementary method to label more dynamic proteins with weaker interactions,increasing sensitivity while decreasing ***-based fluorescent screening takes another path by scanning images automatically to illustrate the condensing state of biomolecules within membraneless organelles,which is a unique feature unlike the previous mass spectrometry-based ***:This review presents a rough glimpse into high-throughput methodologies for biomolecular condensate investigation to encourage usage of bioinformatic tools by researchers in relevant fields.

关键词： biomolecular condensates high-throughput phase separation interaction

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