1
|
Sousa-Pinto B, Palamarchuk Y, Leemann L, Jankin S, Basagaña X, Ballester J, Bedbrook A, Czarlewski W, Almeida R, Haahtela T, Haveri H, Prass M, Henriques T, Vieira RJ, Klimek L, Ollert M, Shamji MH, Jutel M, Del Giacco S, Torres MJ, Zuberbier T, Fonseca JA, Sofiev M, Anto JM, Bousquet J. From MASK-air and SILAM to CATALYSE (Climate Action To Advance HeaLthY Societies in Europe). J Investig Allergol Clin Immunol 2024; 34:12-19. [PMID: 37498647 DOI: 10.18176/jiaci.0923] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
Plant species vary under different climatic conditions and the distribution of pollen in the air. Trends in pollen distribution can be used to assess the impact of climate change on public health. In 2015, the Mobile Airways Sentinel networK for rhinitis and asthma (MASK-air®) was launched as a project of the European Innovation Partnership on Active and Healthy Ageing (EIP-on-AHA, DG Santé and DG CONNECT). This project aimed to develop a warning system to inform patients about the onset of the pollen season, namely, the System for Integrated modeLling of Atmospheric coMposition (SILAM). A global-to-meso-scale dispersion model was developed by the Finnish Meteorological Institute (FMI). It provides quantitative information on atmospheric pollution of anthropogenic and natural origins, particularly on allergenic pollens. Impact of Air Pollution on Asthma and Rhinitis (POLLAR, EIT Health) has combined MASK-air clinical data with SILAM forecasts. A new Horizon Europe grant (Climate Action to Advance HeaLthY Societies in Europe [CATALYSE]; grant agreement number 101057131), which came into force in September 2022, aims to improve our understanding of climate change and help us find ways to counteractit. One objective of this project is to develop early warning systems and predictive models to improve the effectiveness of strategies for adapting to climate change. One of the warning systems is focused on allergic rhinitis (CATALYSE Task 3.2), with a collaboration between the FMI (Finland), Porto University (Portugal), MASK-air SAS (France), ISGlobal (Spain), Hertie School (Germany), and the University of Zurich (Switzerland). It is to be implemented with the support of the European Academy of Allergy and Clinical Immunology. This paper reports the planning of CATALYSE Task 3.2.
Collapse
Affiliation(s)
- B Sousa-Pinto
- MEDCIDS - Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS@RISE - Center for Health Technology and Services Research, Health Research Network, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Y Palamarchuk
- Finnish Meteorological Institute (FMI), Helsinki, Finland
| | - L Leemann
- Department of Political Science, University of Zürich, Zurich, Switzerland
| | - S Jankin
- Data Science Lab, Hertie School, Berlin, Germany
| | - X Basagaña
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - J Ballester
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
| | | | - W Czarlewski
- MASK-air SAS, Montpellier, France
- Medical Consulting Czarlewski, Levallois, France
| | - R Almeida
- MEDCIDS - Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS@RISE - Center for Health Technology and Services Research, Health Research Network, Faculty of Medicine, University of Porto, Porto, Portugal
- Medical Consulting Czarlewski, Levallois, France
| | - T Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - H Haveri
- Health and Hospital Care Services, Wellbeing services county of Päijät-Häme, Lahti, Finland
| | - M Prass
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
- Coordination Unit, Lahti University Campus, Lahti, Finland
| | - T Henriques
- MEDCIDS - Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS@RISE - Center for Health Technology and Services Research, Health Research Network, Faculty of Medicine, University of Porto, Porto, Portugal
| | - R J Vieira
- MEDCIDS - Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS@RISE - Center for Health Technology and Services Research, Health Research Network, Faculty of Medicine, University of Porto, Porto, Portugal
| | - L Klimek
- Department of Otolaryngology, Head and Neck Surgery, Universitätsmedizin Mainz, Germany
- Center for Rhinology and Allergology, Wiesbaden, Germany
| | - M Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis (ORCA), Odense, Denmark
- Department of Dermatology and Allergy Center, Odense University Hospital, Odense, Denmark
| | - M H Shamji
- National Heart and Lung Institute, Imperial College, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - M Jutel
- Department of Clinical Immunology, Wrocław Medical University, Wroclaw, Poland
- ALL-MED Medical Research Institute, Wroclaw, Poland
| | - S Del Giacco
- Department of Medical Sciences and Public Health and Unit of Allergy and Clinical Immunology, University Hospital "Duilio Casula", University of Cagliari, Cagliari, Italy
| | - M J Torres
- Allergy Unit, Regional University Hospital of Malaga, Malaga University, ARADyAL, Malaga, Spain
| | - T Zuberbier
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany
| | - J A Fonseca
- MEDCIDS - Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS@RISE - Center for Health Technology and Services Research, Health Research Network, Faculty of Medicine, University of Porto, Porto, Portugal
| | - M Sofiev
- Finnish Meteorological Institute (FMI), Helsinki, Finland
| | - J M Anto
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - J Bousquet
- MASK-air SAS, Montpellier, France
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany
- University Hospital Montpellier, Montpellier, France
| |
Collapse
|
2
|
Andrews B, Murphy AE, Stofella M, Maslen S, Almeida-Souza L, Skehel JM, Skene NG, Sobott F, Frank RAW. Multidimensional dynamics of the proteome in the neurodegenerative and aging mammalian brain. Mol Cell Proteomics 2021; 21:100192. [PMID: 34979241 PMCID: PMC8816717 DOI: 10.1016/j.mcpro.2021.100192] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 12/03/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic labeling in live mice with global proteomic profiling to simultaneously quantify both the flux and amount of proteins in mouse models of neurodegeneration. In multiple models, protein turnover increases were associated with increasing pathology. This method distinguishes changes in protein expression mediated by synthesis from those mediated by degradation. In the AppNL-F knockin mouse model of Alzheimer’s disease, increased turnover resulted from imbalances in both synthesis and degradation, converging on proteins associated with synaptic vesicle recycling (Dnm1, Cltc, Rims1) and mitochondria (Fis1, Ndufv1). In contrast to disease models, aging in wild-type mice caused a widespread decrease in protein recycling associated with a decrease in autophagic flux. Overall, this simple multidimensional approach enables a comprehensive mapping of proteome dynamics and identifies affected proteins in mouse models of disease and other live animal test settings. Multidimensional proteomic screen to detect imbalances in mouse models of disease. Increased proteome turnover in multiple symptomatic neurodegeneration mouse models. Healthy aging is associated with a global decrease in protein turnover.
Collapse
Affiliation(s)
- Byron Andrews
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alan E Murphy
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Michele Stofella
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Leonardo Almeida-Souza
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Helsinki Institute of Life Science - HiLIFE, Institute of Biotechnology and Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, 00790, Helsinki, Finland
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nathan G Skene
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Frank Sobott
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - René A W Frank
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
| |
Collapse
|
3
|
Mimić G, Podraščanin Z, Lugonja P, Šikoparija B. The influence of source maps on SILAM performance in modeling ragweed pollen concentrations in the area of a major European source. Int J Biometeorol 2021; 65:917-928. [PMID: 33474614 DOI: 10.1007/s00484-021-02075-3] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
The Pannonian Plain is one of the centers of ragweed distribution in Europe. The province of Vojvodina (Serbia) is located on the southern part of the Pannonian Plain, representing a highly infested region. In this study, we have used the SILAM atmospheric dispersion model to simulate ragweed pollen concentrations during the season 2016 in the Vojvodina region. SILAM was tested with three different source maps of ragweed distribution in Vojvodina only: (1) map used in operational SILAM, which was calibrated with the SILAM model and observations, (2) map derived using "top-down" approach with land cover data inventory, and (3) map obtained with "top-down" approach using crop classification from the satellite data. Additionally, the sensitivity studies were done using two modified maps to study the effect of the source strength and long-range transport. Results of simulations were validated with the bi-hourly, daily, and seasonal pollen concentrations measured at five stations in Vojvodina. Overall Pearson correlation coefficients were 0.51 (Map 1), 0.50 (Map 2), and 0.42 (Map 3), while debiased scores were 232.95 pollen m-3 (Map 1), 245.59 pollen m-3 (Map 2), and 258.24 pollen m-3 (Map 3). Even though Vojvodina is in the area of a major European source, regional transport of ragweed pollen from a few hundred kilometers of the surrounding area was important in explaining the presence of pollen in the afternoon hours, although it could not completely explain total pollen quantity. The results confirmed that it is vital to calibrate source maps using atmospheric dispersion model with the observed pollen data.
Collapse
Affiliation(s)
- Gordan Mimić
- BioSense Institute, University of Novi Sad, Novi Sad, Serbia.
| | - Zorica Podraščanin
- Faculty of Sciences, Department of Physics, University of Novi Sad, Novi Sad, Serbia
| | - Predrag Lugonja
- BioSense Institute, University of Novi Sad, Novi Sad, Serbia
| | - Branko Šikoparija
- BioSense Institute, University of Novi Sad, Novi Sad, Serbia
- Faculty of Sciences, Laboratory for palynology, University of Novi Sad, Novi Sad, Serbia
| |
Collapse
|
4
|
Heibel SK, McGuire PJ, Haskins N, Datta Majumdar H, Rayavarapu S, Nagaraju K, Hathout Y, Brown K, Tuchman M, Caldovic L. AMP-activated protein kinase signaling regulated expression of urea cycle enzymes in response to changes in dietary protein intake. J Inherit Metab Dis 2019; 42:1088-1096. [PMID: 31177541 PMCID: PMC7385982 DOI: 10.1002/jimd.12133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/02/2019] [Accepted: 06/05/2019] [Indexed: 12/30/2022]
Abstract
Abundance of urea cycle enzymes in the liver is regulated by dietary protein intake. Although urea cycle enzyme levels rise in response to a high-protein (HP) diet, signaling networks that sense dietary protein intake and trigger changes in expression of urea cycle genes have not been identified. The aim of this study was to identify signaling pathway(s) that respond to changes in protein intake and regulate expression of urea cycle genes in mice and human hepatocytes. Mice were adapted to either HP or low-protein diets followed by isolation of liver protein and mRNA and integrated analysis of the proteomic and transcriptomic data. HP diet led to increased expression of mRNA and enzymes in amino acid degradation pathways and decreased expression of mRNA and enzymes in carbohydrate and fat metabolism, which implicated adenosine monophosphate-activated protein kinase (AMPK) as a possible regulator. Primary human hepatocytes, treated with 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) an activator of AMPK, were used to test whether AMPK regulates expression of urea cycle genes. The abundance of carbamoylphosphate synthetase 1 and ornithine transcarbamylase mRNA increased in hepatocytes treated with AICAR, which supports a role for AMPK signaling in regulation of the urea cycle. Because AMPK is either a target of drugs used to treat type-2 diabetes, these drugs might increase the expression of urea cycle enzymes in patients with partial urea cycle disorders, which could be the basis of a new therapeutic approach.
Collapse
Affiliation(s)
- Sandra Kirsch Heibel
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave NW, Washington DC, USA
| | | | - Nantaporn Haskins
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave NW, Washington DC, USA
| | - Himani Datta Majumdar
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave NW, Washington DC, USA
| | - Sree Rayavarapu
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave NW, Washington DC, USA
| | - Kanneboyina Nagaraju
- Department of Pharmaceutical Sciences, Binghamton University, Binghamton NY, USA
| | - Yetrib Hathout
- Department of Pharmaceutical Sciences, Binghamton University, Binghamton NY, USA
| | - Kristy Brown
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave NW, Washington DC, USA
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave NW, Washington DC, USA
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave NW, Washington DC, USA
| |
Collapse
|
5
|
Wang T, Wang J, Wang J, Mao L, Tang B, Vanderklish PW, Liao X, Xiong ZQ, Liao L. HAP1 is an in vivo UBE3A target that augments autophagy in a mouse model of Angelman syndrome. Neurobiol Dis 2019; 132:104585. [PMID: 31445164 DOI: 10.1016/j.nbd.2019.104585] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 04/15/2019] [Revised: 07/25/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023] Open
Abstract
Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by maternal mutation and paternal imprinting of the gene encoding UBE3A, an E3 ubiquitin ligase. Although several potential target proteins of UBE3A have been reported, how these proteins regulate neuronal development remains unclear. We performed a large-scale quantitative proteomic analysis using stable-isotope labeling of amino acids in mammals (SILAM) in mice with maternal Ube3a mutation. We identified huntingtin (Htt)-associated protein (HAP1), a protein that is involved in Huntington's disease (HD), as a new target of UBE3A. We demonstrate that HAP1 regulates autophagy at the initiation stage by promoting PtdIns3K complex formation and enhancing its activity. HAP1 also co-localized with MAP1LC3 (LC3) and other proteins involved in autophagosome expansion. As a result, HAP1 increased autophagy flux. Strikingly, knocking down of HAP1 alleviated aberrant autophagy in primary neurons from AS mice. Concordantly, treatment of AS neurons with an autophagy inhibitor alleviated the reduction in density of dendritic spines. Furthermore, autophagy inhibition in AS mice partially alleviated a social interaction deficit as shown in open field test. Thus, our results identify HAP1 as an in vivo UBE3A target that contributes to deregulated autophagy and synaptic dysfunction in the central nervous system of AS mouse.
Collapse
Affiliation(s)
- Tingting Wang
- Shanghai Key Laboratory of Regulatory Biology, Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jingyu Wang
- Shanghai Key Laboratory of Regulatory Biology, Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jie Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Mao
- Shanghai Key Laboratory of Regulatory Biology, Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Bin Tang
- Shanghai Key Laboratory of Regulatory Biology, Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Peter W Vanderklish
- Department of Molecular Medicine, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhi-Qi Xiong
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Sciences, East China Normal University, Shanghai 200241, China.
| |
Collapse
|
6
|
Xu Z, Zhai L, Yi T, Gao H, Fan F, Li Y, Wang Y, Li N, Xing X, Su N, Wu F, Chang L, Chen X, Dai E, Zhao C, Yang X, Cui C, Xu P. Hepatitis B virus X induces inflammation and cancer in mice liver through dysregulation of cytoskeletal remodeling and lipid metabolism. Oncotarget 2018; 7:70559-70574. [PMID: 27708241 PMCID: PMC5342574 DOI: 10.18632/oncotarget.12372] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022] Open
Abstract
Hepatitis B virus X protein (HBx) participates in the occurrence and development processes of hepatocellular carcinoma (HCC) as a multifunctional regulation factor. However, the underlying molecular mechanism remains obscure. Here, we describe the use of p21HBx/+ mouse and SILAM (Stable Isotope Labeling in Mammals) strategy to define the pathological mechanisms for the occurrence and development of HBx induced liver cancer. We systematically compared a series of proteome samples from regular mice, 12- and 24-month old p21HBx/+ mice representing the inflammation and HCC stages of liver disease respectively and their nontransgenic wild-type (WT) littermates. Totally we identified 22 and 97 differentially expressed proteins out of a total of 2473 quantified proteins. Bioinformatics analysis suggested that the lipid metabolism and CDC42-induced cytoskeleton remodeling pathways were strongly activated by the HBx transgene. Interestingly, the protein-protein interaction MS study revealed that HBx directly interacted with multiple proteins in these two pathways. The same effect of up-regulation of cytoskeleton and lipid metabolism related proteins, including CDC42, CFL1, PPARγ and ADFP, was also observed in the Huh-7 cells transfected with HBx. More importantly, CFL1 and ADFP were specifically accumulated in HBV-associated HCC (HBV-HCC) patient samples, and their expression levels were positively correlated with the severity of HBV-related liver disease. These results provide evidence that HBx induces the dysregulation of cytoskeleton remodeling and lipid metabolism and leads to the occurrence and development of liver cancer. The CFL1 and ADFP might be served as potential biomarkers for prognosis and diagnosis of HBV-HCC.
Collapse
Affiliation(s)
- Zhongwei Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China.,Central Laboratory, Logistics University of Chinese People's Armed Police Force, Tianjin, 300309, P.R. China
| | - Linghui Zhai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Tailong Yi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China.,Anhui Medical University, Hefei, 230032, P.R. China
| | - Huiying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Fengxu Fan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China.,Anhui Medical University, Hefei, 230032, P.R. China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Youliang Wang
- Beijing Institute of Bioengineering, Beijing, 100071, P. R. China
| | - Ning Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Xiaohua Xing
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Na Su
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Feilin Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Xiuli Chen
- The Fifth Hospital of Shijiazhuang City, Shijiazhuang, 050021, P.R. China
| | - Erhei Dai
- The Fifth Hospital of Shijiazhuang City, Shijiazhuang, 050021, P.R. China
| | - Chao Zhao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, and Research Center on Aging and Medicine, Fudan University, Shanghai, 200032, P.R. China
| | - Xiao Yang
- Beijing Institute of Bioengineering, Beijing, 100071, P. R. China
| | - Chunping Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences Beijing, Institute of Radiation Medicine, Beijing, 102206, P.R. China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430072, P. R. China.,Anhui Medical University, Hefei, 230032, P.R. China
| |
Collapse
|
7
|
Moody LR, Barrett-Wilt GA, Sussman MR, Messing A. Glial fibrillary acidic protein exhibits altered turnover kinetics in a mouse model of Alexander disease. J Biol Chem 2017; 292:5814-5824. [PMID: 28223355 DOI: 10.1074/jbc.m116.772020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 12/12/2016] [Revised: 02/15/2017] [Indexed: 12/27/2022] Open
Abstract
Mutations in the astrocyte-specific intermediate filament glial fibrillary acidic protein (GFAP) lead to the rare and fatal disorder, Alexander disease (AxD). A prominent feature of the disease is aberrant accumulation of GFAP. It has been proposed that this accumulation occurs because of an increase in gene transcription coupled with impaired proteasomal degradation, yet this hypothesis remains untested. We therefore sought to directly investigate GFAP turnover in a mouse model of AxD that is heterozygous for a disease-causing point mutation (GfapR236H/+) (and thus expresses both wild-type and mutant protein). Stable isotope labeling by amino acids in cell culture, using primary cortical astrocytes, indicated that the in vitro half-lives of total GFAP in astrocytes from wild-type and mutant mice were similar at ∼3-4 days. Surprisingly, results obtained with stable isotope labeling of mammals revealed that, in vivo, the half-life of GFAP in mutant mice (15.4 ± 0.5 days) was much shorter than that in wild-type mice (27.5 ± 1.6 days). These unexpected in vivo data are most consistent with a model in which synthesis and degradation are both increased. Our work reveals that an AxD-causing mutation alters GFAP turnover kinetics in vivo and provides an essential foundation for future studies aimed at preventing or reducing the accumulation of GFAP. In particular, these data suggest that elimination of GFAP might be possible and occurs more quickly than previously surmised.
Collapse
Affiliation(s)
| | | | | | - Albee Messing
- From the Waisman Center, .,Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin 53705
| |
Collapse
|
8
|
Mayers MD, Moon C, Stupp GS, Su AI, Wolan DW. Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease. J Proteome Res 2017; 16:1014-1026. [PMID: 28052195 DOI: 10.1021/acs.jproteome.6b00938] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across two mouse cohorts as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control, thereby limiting genetic and environmental variables that influence microbiome composition. The data generated highlight quantitative alterations in both host and microbial proteins due to intestinal inflammation and corroborates the observed phylogenetic changes in bacteria that accompany IBD in humans and mouse models. The combination of isotope labeling with shotgun proteomics resulted in the total identification of 4434 protein clusters expressed in the microbial proteomic environment, 276 of which demonstrated differential abundance between control and IBD mice. Notably, application of a novel cysteine-reactive probe uncovered several microbial proteases and hydrolases overrepresented in the IBD mice. Implementation of these methods demonstrated that substantial insights into the identity and dysregulation of host and microbial proteins altered in IBD can be accomplished and can be used in the interrogation of other microbiome-related diseases.
Collapse
Affiliation(s)
- Michael D Mayers
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Clara Moon
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gregory S Stupp
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andrew I Su
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis W Wolan
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
9
|
Savas JN, Park SK, Yates JR 3rd. Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry Analysis. Methods Mol Biol 2016; 1410:293-304. [PMID: 26867752 DOI: 10.1007/978-1-4939-3524-6_18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The analysis of protein half-life and degradation dynamics has proven critically important to our understanding of a broad and diverse set of biological conditions ranging from cancer to neurodegeneration. Historically these protein turnover measures have been performed in cells by monitoring protein levels after "pulse" labeling of newly synthesized proteins and subsequent chase periods. Comparing the level of labeled protein remaining as a function of time to the initial level reveals the protein's half-life. In this method we provide a detailed description of the workflow required for the determination of protein turnover rates on a whole proteome scale in vivo. Our approach starts with the metabolic labeling of whole rodents by restricting all the nitrogen in their diet to exclusively nitrogen-15 in the form of spirulina algae. After near complete organismal labeling with nitrogen-15, the rodents are then switched to a normal nitrogen-14 rich diet for time periods of days to years. Tissues are harvested, the extracts are fractionated, and the proteins are digested to peptides. Peptides are separated by multidimensional liquid chromatography and analyzed by high resolution orbitrap mass spectrometry (MS). The nitrogen-15 containing proteins are then identified and measured by the bioinformatic proteome analysis tools Sequest, DTASelect2, and Census. In this way, our metabolic pulse-chase approach reveals in vivo protein decay rates proteome-wide.
Collapse
|
10
|
Miller RA, Winrow CJ, Spellman DS, Song Q, Reiss DR, Conway JP, Taylor RR, Coleman PJ, Hendrickson RC, Renger JJ. Quantitative proteomics in laser capture microdissected sleep nuclei from rat brain. J Neurogenet 2014; 28:136-45. [PMID: 24579665 PMCID: PMC4075250 DOI: 10.3109/01677063.2014.883389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The combination of stable isotope labeling of amino acids in mammals (SILAM) and laser capture microdissection (LCM) for selective proteomic analysis of the targeted tissues holds tremendous potential for refined characterization of proteome changes within complex tissues such as the brain. The authors have applied this approach to measure changes in relative protein abundance in ventral tegmental area (VTA) of the rat brain that correlate to pharmacological perturbations. Enriched 13C615N2-lysine was introduced in vivo via diet. These animals were sacrificed during the middle of the 12-hour light period to extract isotopically “heavy” proteins, which were then used as a reference for extracts from dosed, unlabeled rats. Animals were administered an orexin peptide (Ox-B), an orexin receptor antagonist (ORA), or a mixture of both (Ox-B + ORA). All samples were obtained at same phase of the sleep cycle. Labeled-pair identification and differential quantitation provided protein identification and expression ratio data. Five proteins were found to exhibit decreased relative abundance after administration of an ORA, including α-synuclein and rat myelin basic protein. Conversely, six proteins showed increased relative abundance upon antagonist treatment, including 2’,3’-cyclic nucleotide 3’-phosphodiesterase.
Collapse
Affiliation(s)
- Ronald A Miller
- Department of Proteomics, Molecular Profiling and Research Informatics, Merck Research Laboratories , West Point, Pennsylvania , USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|