1
|
Manolis D, Hasan S, Maraveyas A, O'Brien DP, Kessler BM, Kramer H, Nikitenko LL. Quantitative proteomics reveals CLR interactome in primary human cells. J Biol Chem 2024; 300:107399. [PMID: 38777147 PMCID: PMC11231609 DOI: 10.1016/j.jbc.2024.107399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/03/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The G protein-coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) mediates essential functions in several cell types and is implicated in cardiovascular pathologies, skin diseases, migraine, and cancer. To date, the network of proteins interacting with CLR ("CLR interactome") in primary cells, where this GPCR is expressed at endogenous (physiologically relevant) levels, remains unknown. To address this knowledge gap, we established a novel integrative methodological workflow/approach for conducting a comprehensive/proteome-wide analysis of Homo sapiens CLR interactome. We used primary human dermal lymphatic endothelial cells and combined immunoprecipitation utilizing anti-human CLR antibody with label-free quantitative nano LC-MS/MS and quantitative in situ proximity ligation assay. By using this workflow, we identified 37 proteins interacting with endogenously expressed CLR amongst 4902 detected members of the cellular proteome (by quantitative nano LC-MS/MS) and revealed direct interactions of two kinases and two transporters with this GPCR (by in situ proximity ligation assay). All identified interactors have not been previously reported as members of CLR interactome. Our approach and findings uncover the hitherto unrecognized compositional complexity of the interactome of endogenously expressed CLR and contribute to fundamental understanding of the biology of this GPCR. Collectively, our study provides a first-of-its-kind integrative methodological approach and datasets as valuable resources and robust platform/springboard for advancing the discovery and comprehensive characterization of physiologically relevant CLR interactome at a proteome-wide level in a range of cell types and diseases in future studies.
Collapse
Affiliation(s)
- Dimitrios Manolis
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull, UK
| | - Shirin Hasan
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull, UK
| | - Anthony Maraveyas
- Queens Centre for Oncology and Haematology, Castle Hill Hospital, Hull University Teaching Hospitals NHS Teaching Trust, Hull, UK
| | - Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Holger Kramer
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Leonid L Nikitenko
- Centre for Biomedicine, Hull York Medical School, University of Hull, Hull, UK.
| |
Collapse
|
2
|
Md Dom ZI, Pipino C, Krolewski B, O'Neil K, Satake E, Krolewski AS. Effect of TNFα stimulation on expression of kidney risk inflammatory proteins in human umbilical vein endothelial cells cultured in hyperglycemia. Sci Rep 2021; 11:11133. [PMID: 34045516 PMCID: PMC8160214 DOI: 10.1038/s41598-021-90496-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
We recently identified a kidney risk inflammatory signature (KRIS), comprising 6 TNF receptors (including TNFR1 and TNFR2) and 11 inflammatory proteins. Elevated levels of these proteins in circulation were strongly associated with risk of the development of end-stage kidney disease (ESKD) during 10-year follow-up. It has been hypothesized that elevated levels of these proteins in circulation might reflect (be markers of) systemic exposure to TNFα. In this in vitro study, we examined intracellular and extracellular levels of these proteins in human umbilical vein endothelial cells (HUVECs) exposed to TNFα in the presence of hyperglycemia. KRIS proteins as well as 1300 other proteins were measured using the SOMAscan proteomics platform. Four KRIS proteins (including TNFR1) were down-regulated and only 1 protein (IL18R1) was up-regulated in the extracellular fraction of TNFα-stimulated HUVECs. In the intracellular fraction, one KRIS protein was down-regulated (CCL14) and 1 protein was up-regulated (IL18R1). The levels of other KRIS proteins were not affected by exposure to TNFα. HUVECs exposed to a hyperglycemic and inflammatory environment also showed significant up-regulation of a distinct set of 53 proteins (mainly in extracellular fraction). In our previous study, circulating levels of these proteins were not associated with progression to ESKD in diabetes.
Collapse
Affiliation(s)
- Zaipul I Md Dom
- Research Division, Joslin Diabetes Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Caterina Pipino
- Research Division, Joslin Diabetes Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Medical, Oral and Biotechnological Sciences, Center for Advanced Studies and Technology, University G. D'Annunzio of Chieti-Pescara, Chieti, Italy
| | - Bozena Krolewski
- Research Division, Joslin Diabetes Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Eiichiro Satake
- Research Division, Joslin Diabetes Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrzej S Krolewski
- Research Division, Joslin Diabetes Center, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Section on Genetics and Epidemiology, Joslin Diabetes Center, One Joslin Place, Boston, MA, 02215, USA.
| |
Collapse
|
3
|
Yan Q, Ma S, Nan W, Chen H, Zhang Q. Label-free mass spectrometry-based proteomics for investigating the therapeutic mechanism of Sijunzi decoction on spleen deficiency syndrome. Microchem J 2021. [DOI: 10.1016/j.microc.2021.105944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
4
|
Klein J, Caubet C, Camus M, Makridakis M, Denis C, Gilet M, Feuillet G, Rascalou S, Neau E, Garrigues L, Thillaye du Boullay O, Mischak H, Monsarrat B, Burlet-Schiltz O, Vlahou A, Saulnier-Blache JS, Bascands JL, Schanstra JP. Connectivity mapping of glomerular proteins identifies dimethylaminoparthenolide as a new inhibitor of diabetic kidney disease. Sci Rep 2020; 10:14898. [PMID: 32913274 PMCID: PMC7484761 DOI: 10.1038/s41598-020-71950-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/18/2020] [Indexed: 01/09/2023] Open
Abstract
While blocking the renin angiotensin aldosterone system (RAAS) has been the main therapeutic strategy to control diabetic kidney disease (DKD) for many years, 25-30% of diabetic patients still develop the disease. In the present work we adopted a systems biology strategy to analyze glomerular protein signatures to identify drugs with potential therapeutic properties in DKD acting through a RAAS-independent mechanism. Glomeruli were isolated from wild type and type 1 diabetic (Ins2Akita) mice treated or not with the angiotensin-converting enzyme inhibitor (ACEi) ramipril. Ramipril efficiently reduced the urinary albumin/creatine ratio (ACR) of Ins2Akita mice without modifying DKD-associated renal-injuries. Large scale quantitative proteomics was used to identify the DKD-associated glomerular proteins (DKD-GPs) that were ramipril-insensitive (RI-DKD-GPs). The raw data are publicly available via ProteomeXchange with identifier PXD018728. We then applied an in silico drug repurposing approach using a pattern-matching algorithm (Connectivity Mapping) to compare the RI-DKD-GPs's signature with a collection of thousands of transcriptional signatures of bioactive compounds. The sesquiterpene lactone parthenolide was identified as one of the top compounds predicted to reverse the RI-DKD-GPs's signature. Oral treatment of 2 months old Ins2Akita mice with dimethylaminoparthenolide (DMAPT, a water-soluble analogue of parthenolide) for two months at 10 mg/kg/d by gavage significantly reduced urinary ACR. However, in contrast to ramipril, DMAPT also significantly reduced glomerulosclerosis and tubulointerstitial fibrosis. Using a system biology approach, we identified DMAPT, as a compound with a potential add-on value to standard-of-care ACEi-treatment in DKD.
Collapse
Affiliation(s)
- Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Cécile Caubet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
- Evotec (France) SAS, Toulouse, France
| | - Mylène Camus
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
| | - Manousos Makridakis
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Marion Gilet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Simon Rascalou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Eric Neau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Luc Garrigues
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
- Evotec (France) SAS, Toulouse, France
| | | | | | - Bernard Monsarrat
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
| | - Antonia Vlahou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jean Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.
- Université Toulouse III Paul-Sabatier, Toulouse, France.
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1188 - Université de La Réunion, Saint-Denis, France.
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.
- Université Toulouse III Paul-Sabatier, Toulouse, France.
| |
Collapse
|
5
|
Wang X, Shen S, Rasam SS, Qu J. MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts. MASS SPECTROMETRY REVIEWS 2019; 38:461-482. [PMID: 30920002 PMCID: PMC6849792 DOI: 10.1002/mas.21595] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/28/2019] [Indexed: 05/04/2023]
Abstract
The rapidly-advancing field of pharmaceutical and clinical research calls for systematic, molecular-level characterization of complex biological systems. To this end, quantitative proteomics represents a powerful tool but an optimal solution for reliable large-cohort proteomics analysis, as frequently involved in pharmaceutical/clinical investigations, is urgently needed. Large-cohort analysis remains challenging owing to the deteriorating quantitative quality and snowballing missing data and false-positive discovery of altered proteins when sample size increases. MS1 ion current-based methods, which have become an important class of label-free quantification techniques during the past decade, show considerable potential to achieve reproducible protein measurements in large cohorts with high quantitative accuracy/precision. Nonetheless, in order to fully unleash this potential, several critical prerequisites should be met. Here we provide an overview of the rationale of MS1-based strategies and then important considerations for experimental and data processing techniques, with the emphasis on (i) efficient and reproducible sample preparation and LC separation; (ii) sensitive, selective and high-resolution MS detection; iii)accurate chromatographic alignment; (iv) sensitive and selective generation of quantitative features; and (v) optimal post-feature-generation data quality control. Prominent technical developments in these aspects are discussed. Finally, we reviewed applications of MS1-based strategy in disease mechanism studies, biomarker discovery, and pharmaceutical investigations.
Collapse
Affiliation(s)
- Xue Wang
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
| | - Shichen Shen
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
| | - Sailee Suryakant Rasam
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
| | - Jun Qu
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
| |
Collapse
|
6
|
Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado‐Torres L, Halushka MK, Kim M, Pandey A. Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics 2019; 19:e1800315. [PMID: 30983154 PMCID: PMC6812510 DOI: 10.1002/pmic.201800315] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/17/2019] [Indexed: 01/11/2023]
Abstract
Understanding the molecular profile of every human cell type is essential for understanding its role in normal physiology and disease. Technological advancements in DNA sequencing, mass spectrometry, and computational methods allow us to carry out multiomics analyses although such approaches are not routine yet. Human umbilical vein endothelial cells (HUVECs) are a widely used model system to study pathological and physiological processes associated with the cardiovascular system. In this study, next-generation sequencing and high-resolution mass spectrometry to profile the transcriptome and proteome of primary HUVECs is employed. Analysis of 145 million paired-end reads from next-generation sequencing confirmed expression of 12 186 protein-coding genes (FPKM ≥0.1), 439 novel long non-coding RNAs, and revealed 6089 novel isoforms that were not annotated in GENCODE. Proteomics analysis identifies 6477 proteins including confirmation of N-termini for 1091 proteins, isoforms for 149 proteins, and 1034 phosphosites. A database search to specifically identify other post-translational modifications provide evidence for a number of modification sites on 117 proteins which include ubiquitylation, lysine acetylation, and mono-, di- and tri-methylation events. Evidence for 11 "missing proteins," which are proteins for which there was insufficient or no protein level evidence, is provided. Peptides supporting missing protein and novel events are validated by comparison of MS/MS fragmentation patterns with synthetic peptides. Finally, 245 variant peptides derived from 207 expressed proteins in addition to alternate translational start sites for seven proteins and evidence for novel proteoforms for five proteins resulting from alternative splicing are identified. Overall, it is believed that the integrated approach employed in this study is widely applicable to study any primary cell type for deeper molecular characterization.
Collapse
Affiliation(s)
- Anil K. Madugundu
- Center for Molecular MedicineNational Institute of Mental Health and NeurosciencesHosur RoadBangalore560029KarnatakaIndia
- Institute of BioinformaticsInternational Technology ParkBangalore560066KarnatakaIndia
- Manipal Academy of Higher EducationManipal576104KarnatakaIndia
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
| | - Chan Hyun Na
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- NeurologyInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Raja Sekhar Nirujogi
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Santosh Renuse
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
| | - Kwang Pyo Kim
- Department of Applied ChemistryKyung Hee UniversityYonginGyeonggi17104Republic of Korea
| | - Kathleen H. Burns
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMD21205USA
- High Throughput Biology CenterJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Christopher Wilks
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
| | - Ben Langmead
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
| | - Shannon E. Ellis
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
- Department of BiostatisticsJohns Hopkins Bloomberg School of Public HealthBaltimoreMD21205USA
| | - Leonardo Collado‐Torres
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
- Lieber Institute for Brain DevelopmentJohns Hopkins Medical CampusBaltimoreMD21205USA
| | - Marc K. Halushka
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Min‐Sik Kim
- Department of Applied ChemistryKyung Hee UniversityYonginGyeonggi17104Republic of Korea
- Department of New BiologyDGISTDaegu42988Republic of Korea
| | - Akhilesh Pandey
- Center for Molecular MedicineNational Institute of Mental Health and NeurosciencesHosur RoadBangalore560029KarnatakaIndia
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
- NeurologyInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of Biological ChemistryJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of OncologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
| |
Collapse
|
7
|
Xiao R, Li L, Ma Y. A label-free proteomic approach differentiates between conventional and organic rice. J Food Compost Anal 2019. [DOI: 10.1016/j.jfca.2019.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
8
|
Smith JR, David LL, Appukuttan B, Wilmarth PA. Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Retinal and Choroidal Vascular Endothelial Cells: Potential Targets for New Biologic Drugs. Am J Ophthalmol 2018; 193:197-229. [PMID: 29559410 PMCID: PMC6109601 DOI: 10.1016/j.ajo.2018.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/19/2022]
Abstract
PURPOSE Diseases that involve retinal or choroidal vascular endothelial cells are leading causes of vision loss: age-related macular degeneration, retinal ischemic vasculopathies, and noninfectious posterior uveitis. Proteins differentially expressed by these endothelial cell populations are potential drug targets. We used deep proteomic profiling to define the molecular phenotype of human retinal and choroidal endothelial cells at the protein level. METHODS Retinal and choroidal vascular endothelial cells were separately isolated from 5 human eye pairs by selection on CD31. Total protein was extracted and digested, and peptide fractions were analyzed by reverse-phase liquid chromatography tandem mass spectrometry. Peptide sequences were assigned to fragment ion spectra, and proteins were inferred from openly accessible protein databases. Protein abundance was determined by spectral counting. Publicly available software packages were used to identify proteins that were differentially expressed between human retinal and choroidal endothelial cells, and to classify proteins that were highly abundant in each endothelial cell population. RESULTS Human retinal and/or choroidal vascular endothelial cells expressed 5042 nonredundant proteins. Setting the differential expression false discovery rate at 0.05, 498 proteins of 3454 quantifiable proteins (14.4%) with minimum mean spectral counts of 2.5 were differentially abundant in the 2 cell populations. Retinal and choroidal endothelial cells were enriched in angiogenic proteins, and retinal endothelial cells were also enriched in immunologic proteins. CONCLUSIONS This work describes the different protein expression profiles of human retinal and choroidal vascular endothelial cells, and provides multiple candidates for further study as novel treatments or drug targets for posterior eye diseases. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.
Collapse
Affiliation(s)
- Justine R Smith
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA.
| | - Larry L David
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA
| | - Binoy Appukuttan
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA
| | - Phillip A Wilmarth
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA
| |
Collapse
|
9
|
Heimroth RD, Casadei E, Salinas I. Effects of Experimental Terrestrialization on the Skin Mucus Proteome of African Lungfish ( Protopterus dolloi). Front Immunol 2018; 9:1259. [PMID: 29915597 PMCID: PMC5994560 DOI: 10.3389/fimmu.2018.01259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/18/2018] [Indexed: 11/13/2022] Open
Abstract
Animal mucosal barriers constantly interact with the external environment, and this interaction is markedly different in aquatic and terrestrial environments. Transitioning from water to land was a critical step in vertebrate evolution, but the immune adaptations that mucosal barriers such as the skin underwent during that process are essentially unknown. Vertebrate animals such as the African lungfish have a bimodal life, switching from freshwater to terrestrial habitats when environmental conditions are not favorable. African lungfish skin mucus secretions contribute to the terrestrialization process by forming a cocoon that surrounds and protects the lungfish body. The goal of this study was to characterize the skin mucus immunoproteome of African lungfish, Protopterus dolloi, before and during the induction phase of terrestrialization as well as the immunoproteome of the gill mucus during the terrestrialization induction phase. Using LC-MS/MS, we identified a total of 974 proteins using a lungfish Illumina RNA-seq database, 1,256 proteins from previously published lungfish sequence read archive and 880 proteins using a lungfish 454 RNA-seq database for annotation in the three samples analyzed (free-swimming skin mucus, terrestrialized skin mucus, and terrestrialized gill mucus). The terrestrialized skin mucus proteome was enriched in proteins with known antimicrobial functions such as histones and S100 proteins compared to free-swimming skin mucus. In support, gene ontology analyses showed that the terrestrialized skin mucus proteome has predicted functions in processes such as viral process, defense response to Gram-negative bacterium, and tumor necrosis factor-mediated signaling. Importantly, we observed a switch in immunoglobulin heavy chain secretion upon terrestrialization, with IgW1 long form (IgW1L) and IgM1 present in free-swimming skin mucus and IgW1L, IgM1, and IgM2 in terrestrialized skin mucus. Combined, these results indicate an increase in investment in the production of unique immune molecules in P. dolloi skin mucus in response to terrestrialization that likely better protects lungfish against external aggressors found in land.
Collapse
Affiliation(s)
| | | | - Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, NM, United States
| |
Collapse
|
10
|
Zhang M, An B, Qu Y, Shen S, Fu W, Chen YJ, Wang X, Young R, Canty JM, Balthasar JP, Murphy K, Bhattacharyya D, Josephs J, Ferrari L, Zhou S, Bansal S, Vazvaei F, Qu J. Sensitive, High-Throughput, and Robust Trapping-Micro-LC-MS Strategy for the Quantification of Biomarkers and Antibody Biotherapeutics. Anal Chem 2018; 90:1870-1880. [PMID: 29276835 PMCID: PMC5960441 DOI: 10.1021/acs.analchem.7b03949] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
For LC-MS-based targeted quantification of biotherapeutics and biomarkers in clinical and pharmaceutical environments, high sensitivity, high throughput, and excellent robustness are all essential but remain challenging. For example, though nano-LC-MS has been employed to enhance analytical sensitivity, it falls short because of its low loading capacity, poor throughput, and low operational robustness. Furthermore, high chemical noise in protein bioanalysis typically limits the sensitivity. Here we describe a novel trapping-micro-LC-MS (T-μLC-MS) strategy for targeted protein bioanalysis, which achieves high sensitivity with exceptional robustness and high throughput. A rapid, high-capacity trapping of biological samples is followed by μLC-MS analysis; dynamic sample trapping and cleanup are performed using pH, column chemistry, and fluid mechanics separate from the μLC-MS analysis, enabling orthogonality, which contributes to the reduction of chemical noise and thus results in improved sensitivity. Typically, the selective-trapping and -delivery approach strategically removes >85% of the matrix peptides and detrimental components, markedly enhancing sensitivity, throughput, and operational robustness, and narrow-window-isolation selected-reaction monitoring further improves the signal-to-noise ratio. In addition, unique LC-hardware setups and flow approaches eliminate gradient shock and achieve effective peak compression, enabling highly sensitive analyses of plasma or tissue samples without band broadening. In this study, the quantification of 10 biotherapeutics and biomarkers in plasma and tissues was employed for method development. As observed, a significant sensitivity gain (up to 25-fold) compared with that of conventional LC-MS was achieved, although the average run time was only 8 min/sample. No appreciable peak deterioration or loss of sensitivity was observed after >1500 injections of tissue and plasma samples. The developed method enabled, for the first time, ultrasensitive LC-MS quantification of low levels of a monoclonal antibody and antigen in a tumor and cardiac troponin I in plasma after brief cardiac ischemia. This strategy is valuable when highly sensitive protein quantification in large sample sets is required, as is often the case in typical biomarker validation and pharmaceutical investigations of antibody therapeutics.
Collapse
Affiliation(s)
- Ming Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Bo An
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Yang Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Wei Fu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
- Department of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuan-Ju Chen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xue Wang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Rebeccah Young
- Division of Cardiovascular Medicine, Western New York Department of Veterans of Affairs Medical Center, Buffalo, New York 14203, United States
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, United States
| | - John M Canty
- Division of Cardiovascular Medicine, Western New York Department of Veterans of Affairs Medical Center, Buffalo, New York 14203, United States
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, United States
| | - Joseph P Balthasar
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Keeley Murphy
- Thermo Scientific, San Jose, California 95134, United States
| | | | | | - Luca Ferrari
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Shaolian Zhou
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel CH-4070, Switzerland
| | - Surendra Bansal
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Faye Vazvaei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| |
Collapse
|
11
|
Miller M, Chen A, Gobert V, Augé B, Beau M, Burlet-Schiltz O, Haenlin M, Waltzer L. Control of RUNX-induced repression of Notch signaling by MLF and its partner DnaJ-1 during Drosophila hematopoiesis. PLoS Genet 2017; 13:e1006932. [PMID: 28742844 PMCID: PMC5549762 DOI: 10.1371/journal.pgen.1006932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/08/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
A tight regulation of transcription factor activity is critical for proper development. For instance, modifications of RUNX transcription factors dosage are associated with several diseases, including hematopoietic malignancies. In Drosophila, Myeloid Leukemia Factor (MLF) has been shown to control blood cell development by stabilizing the RUNX transcription factor Lozenge (Lz). However, the mechanism of action of this conserved family of proteins involved in leukemia remains largely unknown. Here we further characterized MLF's mode of action in Drosophila blood cells using proteomic, transcriptomic and genetic approaches. Our results show that MLF and the Hsp40 co-chaperone family member DnaJ-1 interact through conserved domains and we demonstrate that both proteins bind and stabilize Lz in cell culture, suggesting that MLF and DnaJ-1 form a chaperone complex that directly regulates Lz activity. Importantly, dnaj-1 loss causes an increase in Lz+ blood cell number and size similarly as in mlf mutant larvae. Moreover we find that dnaj-1 genetically interacts with mlf to control Lz level and Lz+ blood cell development in vivo. In addition, we show that mlf and dnaj-1 loss alters Lz+ cell differentiation and that the increase in Lz+ blood cell number and size observed in these mutants is caused by an overactivation of the Notch signaling pathway. Finally, using different conditions to manipulate Lz activity, we show that high levels of Lz are required to repress Notch transcription and signaling. All together, our data indicate that the MLF/DnaJ-1-dependent increase in Lz level allows the repression of Notch expression and signaling to prevent aberrant blood cell development. Thus our findings establish a functional link between MLF and the co-chaperone DnaJ-1 to control RUNX transcription factor activity and Notch signaling during blood cell development in vivo.
Collapse
Affiliation(s)
- Marion Miller
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Aichun Chen
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Vanessa Gobert
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Benoit Augé
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Mathilde Beau
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marc Haenlin
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucas Waltzer
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| |
Collapse
|
12
|
Ahsan N, Belmont J, Chen Z, Clifton JG, Salomon AR. Highly reproducible improved label-free quantitative analysis of cellular phosphoproteome by optimization of LC-MS/MS gradient and analytical column construction. J Proteomics 2017. [PMID: 28634120 DOI: 10.1016/j.jprot.2017.06.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Expanding the sequencing depth of the peptides with a statistically significant quantitative change derived from a biological stimulation is critical. Here we demonstrate that optimization of LC gradient and analytical column construction can reveal over 30,000 unique peptides and 23,000 phosphopeptides at high confidence. The quantitative reproducibility of different analytical workflows was evaluated by comparing the phosphoproteome of CD3/4 stimulated and unstimulated T-cells as a model system. A fritless, 50cm-long column packed with 1.9μm particles operated with a standard pressure HPLC significantly improved the sequencing depth 51% and decreased the selected ion chromatogram peak spreading. Most importantly, under the optimal workflow we observed an improvement of over 300% in detection of significantly changed phosphopeptides in the stimulated cells compared with the other workflows. The discovery power of the optimized column configuration was illustrated by identification of significantly altered phosphopeptides harboring novel sites from proteins previously established as important in T cell signaling including A-Raf, B-Raf, c-Myc, CARMA1, Fyn, ITK, LAT, NFAT1/2/3, PKCα, PLCγ1/2, RAF1, and SOS1. Taken together, our results reveal the analytical power of optimized chromatography using sub 2μm particles for the analysis of the T cell phosphoproteome to reveal a vast landscape of significantly altered phosphorylation changes in response to T cell receptor stimulation.
Collapse
Affiliation(s)
- Nagib Ahsan
- Division of Biology and Medicine, Brown University, Providence, RI 02903, USA; Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA
| | - Judson Belmont
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Zhuo Chen
- Department of Chemistry, Brown University, Providence, RI 02912, USA
| | - James G Clifton
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown, University, Providence, RI 02912, USA
| | - Arthur R Salomon
- Center for Cancer Research Development, Proteomics Core Facility, Rhode Island Hospital, Providence, RI 02903, USA; Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA; Department of Chemistry, Brown University, Providence, RI 02912, USA.
| |
Collapse
|
13
|
Muller L, Fornecker L, Van Dorsselaer A, Cianférani S, Carapito C. Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics. Proteomics 2016; 16:2953-2961. [DOI: 10.1002/pmic.201600288] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/23/2016] [Accepted: 10/12/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Leslie Muller
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Luc Fornecker
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| |
Collapse
|
14
|
Extracellular IL-33 cytokine, but not endogenous nuclear IL-33, regulates protein expression in endothelial cells. Sci Rep 2016; 6:34255. [PMID: 27694941 PMCID: PMC5046127 DOI: 10.1038/srep34255] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/08/2016] [Indexed: 12/17/2022] Open
Abstract
IL-33 is a nuclear cytokine from the IL-1 family that plays important roles in health and disease. Extracellular IL-33 activates a growing number of target cells, including group 2 innate lymphoid cells, mast cells and regulatory T cells, but it remains unclear whether intracellular nuclear IL-33 has additional functions in the nucleus. Here, we used a global proteomic approach based on high-resolution mass spectrometry to compare the extracellular and intracellular roles of IL-33 in primary human endothelial cells, a major source of IL-33 protein in human tissues. We found that exogenous extracellular IL-33 cytokine induced expression of a distinct set of proteins associated with inflammatory responses in endothelial cells. In contrast, knockdown of endogenous nuclear IL-33 expression using two independent RNA silencing strategies had no reproducible effect on the endothelial cell proteome. These results suggest that IL-33 acts as a cytokine but not as a nuclear factor regulating gene expression in endothelial cells.
Collapse
|
15
|
Morimoto H, Kadoya R, Takahashi K, Kasahara Y. Proteome analysis of Pseudomonas putida F1 genes induced in soil environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:825-832. [PMID: 27452675 DOI: 10.1111/1758-2229.12445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Knowledge of the gene expression dynamics of a single soil bacterial strain contributes to the understanding of its behaviour, physiological state and surrounding microenvironment. Genes expressed in soil environments rather than in laboratory media are considered to particularly relevant. Here, we compared genome-wide gene expression profiles of the bacterium Pseudomonas putida F1 inoculated in three different types of nonsterile soils deduced using proteome analysis via sodium dodecyl sulfate-polyacrylamide gel electrophoresis combined with liquid chromatography-tandem mass spectrometry. Proteins commonly detected in all three samples and involved with bacterial growth and fundamental metabolism were excluded. Nine proteins were identified as specifically expressed in soil including an aldehyde dehydrogenase, a nitric oxide dioxygenase and five proteins encoded by a cluster of metabolism-associated genes. Expression factor analysis revealed that the nitric oxide dioxygenase-coding gene was induced by nitric oxide and the five clustered genes were induced under phosphate starvation. The expression of these genes can be attributed to response to soil environmental stimuli surrounding the F1 cells. These results strongly suggest that our soil metaproteome approach is useful for understanding the autecology and lifestyle of a single bacterial strain in soil environments and allows the prediction of the microenvironment surrounding the bacterial cells.
Collapse
Affiliation(s)
- Hajime Morimoto
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Ryosuke Kadoya
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Kazuhiro Takahashi
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| | - Yasuhiro Kasahara
- Institute of Low Temperature Science, Hokkaido University, Kita 19, Nishi 8, Kita-ku, Sapporo 060-0819, Japan
| |
Collapse
|
16
|
Sheta R, Woo CM, Roux-Dalvai F, Fournier F, Bourassa S, Droit A, Bertozzi CR, Bachvarov D. A metabolic labeling approach for glycoproteomic analysis reveals altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. J Proteomics 2016; 145:91-102. [PMID: 27095597 PMCID: PMC5436706 DOI: 10.1016/j.jprot.2016.04.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/31/2016] [Accepted: 04/12/2016] [Indexed: 12/29/2022]
Abstract
UNLABELLED Epithelial ovarian cancer (EOC) is a disease responsible for more deaths among women in the Western world than all other gynecologic malignancies. There is urgent need for new therapeutic targets and a better understanding of EOC initiation and progression. We have previously identified the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) gene, a member of the GalNAc-transferases (GalNAc-Ts) gene family, as hypomethylated and overexpressed in high-grade serous EOC tumors, compared to low malignant potential EOC tumors and normal ovarian tissues. This data also suggested for a role of GALNT3 in aberrant EOC glycosylation, possibly implicated in disease progression. To evaluate differential glycosylation in EOC caused by modulations in GALNT3 expression, we used a metabolic labeling strategy for enrichment and mass spectrometry-based characterization of glycoproteins following GALNT3 gene knockdown (KD) in A2780s EOC cells. A total of 589 differentially expressed glycoproteins were identified upon GALNT3 KD. Most identified proteins were involved in mechanisms of cellular metabolic functions, post-translational modifications, and some have been reported to be implicated in EOC etiology. The GALNT3-dependent glycoproteins identified by this metabolic labeling approach support the oncogenic role of GALNT3 in EOC dissemination and may be pursued as novel EOC biomarkers and/or therapeutic targets. BIOLOGICAL SIGNIFICANCE Knowledge of the O-glycoproteome has been relatively elusive, and the functions of the individual polypeptide GalNAc-Ts have been poorly characterized. Alterations in GalNAc-Ts expression were shown to provide huge variability in the O-glycoproteome in various pathologies, including cancer. The application of a chemical biology approach for the metabolic labeling and subsequent characterization of O-glycoproteins in EOC using the Ac4GalNAz metabolite has provided a strategy allowing for proteomic discovery of GalNAc-Ts specific functions. Our study supports an essential role of one of the GalNAc-Ts - GALNT3, in EOC dissemination, including its implication in modulating PTMs and EOC metabolism. Our approach validates the use of the applied metabolic strategy to identify important functions of GalNAc-Ts in normal and pathological conditions.
Collapse
Affiliation(s)
- Razan Sheta
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, PQ, Canada
| | - Christina M Woo
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - Sylvie Bourassa
- Centre de recherche du CHU de Québec, CHUL, Québec, PQ, Canada
| | - Arnaud Droit
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, CHUL, Québec, PQ, Canada
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Dimcho Bachvarov
- Department of Molecular Medicine, Laval University, Québec, PQ, Canada; Centre de recherche du CHU de Québec, L'Hôtel-Dieu de Québec, Québec, PQ, Canada
| |
Collapse
|
17
|
Comparative analysis of novel autoantibody isotypes against citrullinated-inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3)542–556 peptide in serum from Taiwanese females with rheumatoid arthritis, primary Sjögren's syndrome and secondary Sjögren's syndrome in rheumatoid arthritis. J Proteomics 2016; 141:1-11. [DOI: 10.1016/j.jprot.2016.03.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 03/10/2016] [Accepted: 03/16/2016] [Indexed: 12/29/2022]
|
18
|
Proteomic dataset for altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. Data Brief 2016; 8:342-9. [PMID: 27331112 PMCID: PMC4908283 DOI: 10.1016/j.dib.2016.05.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/12/2016] [Accepted: 05/24/2016] [Indexed: 01/20/2023] Open
Abstract
This article contains raw and processed data related to research published in "Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin O-glycosylation" [1]. The data presented here was obtained with the application of a bioorthogonal chemical reporter strategy analyzing differential glycoprotein expression following the knock-down (KD) of the GALNT3 gene in the epithelial ovarian cancer (EOC) cell line A2780s. LC-MS/MS mass spectrometry analysis was then performed and the processed data related to the identified glycoproteins show that several hundred proteins are differentially expressed between control and GALNT3 KD A2780s cells. The obtained data also uncover numerous novel glycoproteins; some of which could represent new potential EOC biomarkers and/or therapeutic targets.
Collapse
|
19
|
Comparative shotgun proteomic analysis of wild and domesticated Opuntia spp. species shows a metabolic adaptation through domestication. J Proteomics 2016; 143:353-364. [PMID: 27072113 DOI: 10.1016/j.jprot.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/01/2023]
Abstract
UNLABELLED The Opuntia genus is widely distributed in America, but the highest richness of wild species are found in Mexico, as well as the most domesticated Opuntia ficus-indica, which is the most domesticated species and an important crop in agricultural economies of arid and semiarid areas worldwide. During domestication process, the Opuntia morphological characteristics were favored, such as less and smaller spines in cladodes and less seeds in fruits, but changes at molecular level are almost unknown. To obtain more insights about the Opuntia molecular changes through domestication, a shotgun proteomic analysis and database-dependent searches by homology was carried out. >1000 protein species were identified and by using a label-free quantitation method, the Opuntia proteomes were compared in order to identify differentially accumulated proteins among wild and domesticated species. Most of the changes were observed in glucose, secondary, and 1C metabolism, which correlate with the observed protein, fiber and phenolic compounds accumulation in Opuntia cladodes. Regulatory proteins, ribosomal proteins, and proteins related with response to stress were also observed in differential accumulation. These results provide new valuable data that will help to the understanding of the molecular changes of Opuntia species through domestication. BIOLOGICAL SIGNIFICANCE Opuntia species are well adapted to dry and warm conditions in arid and semiarid regions worldwide, and they are highly productive plants showing considerable promises as an alternative food source. However, there is a gap regarding Opuntia molecular mechanisms that enable them to grow in extreme environmental conditions and how the domestication processes has changed them. In the present study, a shotgun analysis was carried out to characterize the proteomes of five Opuntia species selected by its domestication degree. Our results will help to a better understanding of proteomic features underlying the selection and specialization under evolution and domestication of Opuntia and will provide a platform for basic biology research and gene discovery.
Collapse
|
20
|
He Y, Cao X, Zhang S, Rogers J, Hartson S, Jiang H. Changes in the Plasma Proteome of Manduca sexta Larvae in Relation to the Transcriptome Variations after an Immune Challenge: Evidence for High Molecular Weight Immune Complex Formation. Mol Cell Proteomics 2016; 15:1176-87. [PMID: 26811355 DOI: 10.1074/mcp.m115.054296] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 11/06/2022] Open
Abstract
Manduca sextais a lepidopteran model widely used to study insect physiological processes, including innate immunity. In this study, we explored the proteomes of cell-free hemolymph from larvae injected with a sterile buffer (C for control) or a mixture of bacteria (I for induced). Of the 654 proteins identified, 70 showed 1.67 to >200-fold abundance increases after the immune challenge; 51 decreased to 0-60% of the control levels. While there was no strong parallel between plasma protein levels and their transcript levels in hemocytes or fat body, the mRNA level changes (i.e.I/C ratios of normalized read numbers) in the tissues concurred with their protein level changes (i.e.I/C ratios of normalized spectral counts) with correlation coefficients of 0.44 and 0.57, respectively. Better correlations support that fat body contributes a more significant portion of the plasma proteins involved in various aspects of innate immunity. Consistently, ratios of mRNA and protein levels were better correlated for immunity-related proteins than unrelated ones. There is a set of proteins whose apparent molecular masses differ considerably from the calculatedMr's, suggestive of posttranslational modifications. In addition, some lowMrproteins were detected in the range of 80 to >300 kDa on a reducing SDS-polyacrylamide gel, indicating the existence of highMrcovalent complexes. We identified 30 serine proteases and their homologs, 11 of which are known members of an extracellular immune signaling network. Along with our quantitative transcriptome data, the protein identification, inducibility, and association provide leads toward a focused exploration of humoral immunity inM. sexta.
Collapse
Affiliation(s)
- Yan He
- From the ‡Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Xiaolong Cao
- From the ‡Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078; §Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078
| | - Shuguang Zhang
- From the ‡Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078
| | - Janet Rogers
- §Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078
| | - Steve Hartson
- §Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078
| | - Haobo Jiang
- From the ‡Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078;
| |
Collapse
|
21
|
Laurent V, Guérard A, Mazerolles C, Le Gonidec S, Toulet A, Nieto L, Zaidi F, Majed B, Garandeau D, Socrier Y, Golzio M, Cadoudal T, Chaoui K, Dray C, Monsarrat B, Schiltz O, Wang YY, Couderc B, Valet P, Malavaud B, Muller C. Periprostatic adipocytes act as a driving force for prostate cancer progression in obesity. Nat Commun 2016; 7:10230. [PMID: 26756352 PMCID: PMC4729927 DOI: 10.1038/ncomms10230] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 11/18/2015] [Indexed: 02/06/2023] Open
Abstract
Obesity favours the occurrence of locally disseminated prostate cancer in the periprostatic adipose tissue (PPAT) surrounding the prostate gland. Here we show that adipocytes from PPAT support the directed migration of prostate cancer cells and that this event is strongly promoted by obesity. This process is dependent on the secretion of the chemokine CCL7 by adipocytes, which diffuses from PPAT to the peripheral zone of the prostate, stimulating the migration of CCR3 expressing tumour cells. In obesity, higher secretion of CCL7 by adipocytes facilitates extraprostatic extension. The observed increase in migration associated with obesity is totally abrogated when the CCR3/CCL7 axis is inhibited. In human prostate cancer tumours, expression of the CCR3 receptor is associated with the occurrence of aggressive disease with extended local dissemination and a higher risk of biochemical recurrence, highlighting the potential benefit of CCR3 antagonists in the treatment of prostate cancer.
Collapse
Affiliation(s)
- Victor Laurent
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Adrien Guérard
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Catherine Mazerolles
- Département d'Anatomo-Pathologie, Institut Universitaire du Cancer, Toulouse cedex 9 31059, France
| | - Sophie Le Gonidec
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Tissu Adipeux, Obésité et Diabète”, Institut National de la Santé et de la Recherche Médicale, INSERM U1048, Toulouse F-31432, France
| | - Aurélie Toulet
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Laurence Nieto
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Falek Zaidi
- Département d'Anatomo-Pathologie, Institut Universitaire du Cancer, Toulouse cedex 9 31059, France
| | - Bilal Majed
- Centre Hospitalier de la Région de Saint-Omer (CHRSO), Route de Blendecques, BP 60357, Saint-Omer Cedex 62505, France
| | - David Garandeau
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Youri Socrier
- Département d'Anatomo-Pathologie, Institut Universitaire du Cancer, Toulouse cedex 9 31059, France
| | - Muriel Golzio
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Thomas Cadoudal
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Tissu Adipeux, Obésité et Diabète”, Institut National de la Santé et de la Recherche Médicale, INSERM U1048, Toulouse F-31432, France
| | - Karima Chaoui
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Cedric Dray
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Tissu Adipeux, Obésité et Diabète”, Institut National de la Santé et de la Recherche Médicale, INSERM U1048, Toulouse F-31432, France
| | - Bernard Monsarrat
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Odile Schiltz
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Yuan Yuan Wang
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| | - Bettina Couderc
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Tumeur et Environnement”, Centre de Recherche en Cancérologie de Toulouse (CRCT), Toulouse Cedex 1 F-31037, France
| | - Philippe Valet
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Tissu Adipeux, Obésité et Diabète”, Institut National de la Santé et de la Recherche Médicale, INSERM U1048, Toulouse F-31432, France
| | - Bernard Malavaud
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département d'Urologie, Institut Universitaire du Cancer, Toulouse cedex 9 31059, France
| | - Catherine Muller
- Université de Toulouse, UPS, Toulouse F-31077, France
- Département “Biologie du Cancer” et “Biologie Structurale et Biophysique”, CNRS; Institut de Pharmacologie et de Biologie Structurale, Toulouse F-31077, France
| |
Collapse
|
22
|
Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Van Dorssaeler A, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A. Benchmarking quantitative label-free LC–MS data processing workflows using a complex spiked proteomic standard dataset. J Proteomics 2016; 132:51-62. [DOI: 10.1016/j.jprot.2015.11.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/04/2015] [Accepted: 11/08/2015] [Indexed: 10/22/2022]
|
23
|
Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssié D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianférani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Couté Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief 2015; 6:286-94. [PMID: 26862574 PMCID: PMC4706616 DOI: 10.1016/j.dib.2015.11.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 11/23/2015] [Indexed: 11/30/2022] Open
Abstract
This data article describes a controlled, spiked proteomic dataset for which the “ground truth” of variant proteins is known. It is based on the LC-MS analysis of samples composed of a fixed background of yeast lysate and different spiked amounts of the UPS1 mixture of 48 recombinant proteins. It can be used to objectively evaluate bioinformatic pipelines for label-free quantitative analysis, and their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. More specifically, it can be useful for tuning software tools parameters, but also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. The raw MS files can be downloaded from ProteomeXchange with identifier PXD001819. Starting from some raw files of this dataset, we also provide here some processed data obtained through various bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, to exemplify the use of such data in the context of software benchmarking, as discussed in details in the accompanying manuscript [1]. The experimental design used here for data processing takes advantage of the different spike levels introduced in the samples composing the dataset, and processed data are merged in a single file to facilitate the evaluation and illustration of software tools results for the detection of variant proteins with different absolute expression levels and fold change values.
Collapse
Affiliation(s)
- Claire Ramus
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Agnès Hovasse
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Marlène Marcellin
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Anne-Marie Hesse
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Emmanuelle Mouton-Barbosa
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - David Bouyssié
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Sebastian Vaca
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Christine Carapito
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Karima Chaoui
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Christophe Bruley
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Jérôme Garin
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Sarah Cianférani
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Myriam Ferro
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Alain Van Dorssaeler
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Odile Burlet-Schiltz
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| | - Christine Schaeffer
- ProFi, Proteomic French Infrastructure, France; Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Yohann Couté
- ProFi, Proteomic French Infrastructure, France; CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, Grenoble F-38054, France; INSERM U1038, Grenoble F-38054, France; Université Grenoble, F-38054, France
| | - Anne Gonzalez de Peredo
- ProFi, Proteomic French Infrastructure, France; CNRS UMR5089 Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, 31077 Toulouse, France; Université de Toulouse, 118 Route de Narbonne, 31077 Toulouse, France
| |
Collapse
|
24
|
Role of Calprotectin as a Modulator of the IL27-Mediated Proinflammatory Effect on Endothelial Cells. Mediators Inflamm 2015; 2015:737310. [PMID: 26663990 PMCID: PMC4664814 DOI: 10.1155/2015/737310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/21/2015] [Indexed: 01/05/2023] Open
Abstract
An underlying endothelial dysfunction plays a fundamental role in the pathogenesis of cardiovascular events and is the central feature of atherosclerosis. The protein-based communication between leukocytes and inflamed endothelial cells leading to diapedesis has been largely investigated and several key players such as IL6, TNFα, or the damage associated molecular pattern molecule (DAMP) calprotectin are now well identified. However, regarding cytokine IL27, the controversial current knowledge about its inflammatory role and the involved regulatory elements requires clarification. Therefore, we examined the inflammatory impact of IL27 on primary endothelial cells and the potentially modulatory effect of calprotectin on both transcriptome and proteome levels. A qPCR-based screening demonstrated high IL27-mediated gene expression of IL7, IL15, CXCL10, and CXCL11. Calprotectin time-dependent downregulatory effects were observed on IL27-induced IL15 and CXCL10 gene expression. A mass spectrometry-based approach of IL27 ± calprotectin cell stimulation enlightened a calprotectin modulatory role in the expression of 28 proteins, mostly involved in the mechanism of leukocyte transmigration. Furthermore, we showed evidence for STAT1 involvement in this process. Our findings provide new evidence about the IL27-dependent proinflammatory signaling which may be under the control of calprotectin and highlight the need for further investigations on molecules which might have antiatherosclerotic functions.
Collapse
|
25
|
Spinner CA, Uttenweiler-Joseph S, Metais A, Stella A, Burlet-Schiltz O, Moog-Lutz C, Lamsoul I, Lutz PG. Substrates of the ASB2α E3 ubiquitin ligase in dendritic cells. Sci Rep 2015; 5:16269. [PMID: 26537633 PMCID: PMC4633680 DOI: 10.1038/srep16269] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/12/2015] [Indexed: 11/17/2022] Open
Abstract
Conventional dendritic cells (cDCs) comprise distinct populations with specialized immune functions that are mediators of innate and adaptive immune responses. Transcriptomic and proteomic approaches have been used so far to identify transcripts and proteins that are differentially expressed in these subsets to understand the respective functions of cDCs subsets. Here, we showed that the Cullin 5-RING E3 ubiquitin ligase (E3) ASB2α, by driving degradation of filamin A (FLNa) and filamin B (FLNb), is responsible for the difference in FLNa and FLNb abundance in the different spleen cDC subsets. Importantly, the ability of these cDC subsets to migrate correlates with the level of FLNa. Furthermore, our results strongly point to CD4 positive and double negative cDCs as distinct populations. Finally, we develop quantitative global proteomic approaches to identify ASB2α substrates in DCs using ASB2 conditional knockout mice. As component of the ubiquitin-proteasome system (UPS) are amenable to pharmacological manipulation, these approaches aimed to the identification of E3 substrates in physiological relevant settings could potentially lead to novel targets for therapeutic strategies.
Collapse
Affiliation(s)
- Camille A Spinner
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Sandrine Uttenweiler-Joseph
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Arnaud Metais
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Alexandre Stella
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Odile Burlet-Schiltz
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Christel Moog-Lutz
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Isabelle Lamsoul
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Pierre G Lutz
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne BP 64182, F-31077 Toulouse, France.,Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| |
Collapse
|
26
|
Muhseen ZT, Xiong Q, Chen Z, Ge F. Proteomics studies on stress responses in diatoms. Proteomics 2015; 15:3943-53. [PMID: 26364674 DOI: 10.1002/pmic.201500165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/09/2015] [Accepted: 09/09/2015] [Indexed: 01/09/2023]
Abstract
Diatoms are a highly diverse group of eukaryotic phytoplankton that are distributed throughout marine and freshwater environments and are believed to be responsible for approximately 40% of the total marine primary productivity. The ecological success of diatoms suggests that they have developed a range of strategies to cope with various biotic and abiotic stress factors. It is of great interest to understand the adaptive responses of diatoms to different stresses in the marine environment. Proteomic technologies have been applied to the adaptive responses of marine diatoms under different growth conditions in recent years such as nitrogen starvation, iron limitation and phosphorus deficiency. These studies have provided clues to elucidate the sophisticated sensing mechanisms that control their adaptive responses. Although only a very limited number of proteomic studies were conducted in diatoms, the obtained data have led to a better understanding of the biochemical processes that contribute to their ecological success. This review presents the current status of proteomic studies of diatom stress responses and discusses the novel developments and applications for the analysis of protein post-translational modification in diatoms. The potential future application of proteomics could contribute to a better understanding of the physiological mechanisms underlying diatom acclimation to a given stress and the acquisition of an enhanced diatom stress tolerance. Future challenges and research opportunities in the proteomics studies of diatoms are also discussed.
Collapse
Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| |
Collapse
|
27
|
Shen X, Hu Q, Li J, Wang J, Qu J. Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics. J Proteome Res 2015; 14:4147-57. [PMID: 26051676 DOI: 10.1021/acs.jproteome.5b00200] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Comprehensive and accurate evaluation of data quality and false-positive biomarker discovery is critical to direct the method development/optimization for quantitative proteomics, which nonetheless remains challenging largely due to the high complexity and unique features of proteomic data. Here we describe an experimental null (EN) method to address this need. Because the method experimentally measures the null distribution (either technical or biological replicates) using the same proteomic samples, the same procedures and the same batch as the case-vs-contol experiment, it correctly reflects the collective effects of technical variability (e.g., variation/bias in sample preparation, LC-MS analysis, and data processing) and project-specific features (e.g., characteristics of the proteome and biological variation) on the performances of quantitative analysis. To show a proof of concept, we employed the EN method to assess the quantitative accuracy and precision and the ability to quantify subtle ratio changes between groups using different experimental and data-processing approaches and in various cellular and tissue proteomes. It was found that choices of quantitative features, sample size, experimental design, data-processing strategies, and quality of chromatographic separation can profoundly affect quantitative precision and accuracy of label-free quantification. The EN method was also demonstrated as a practical tool to determine the optimal experimental parameters and rational ratio cutoff for reliable protein quantification in specific proteomic experiments, for example, to identify the necessary number of technical/biological replicates per group that affords sufficient power for discovery. Furthermore, we assessed the ability of EN method to estimate levels of false-positives in the discovery of altered proteins, using two concocted sample sets mimicking proteomic profiling using technical and biological replicates, respectively, where the true-positives/negatives are known and span a wide concentration range. It was observed that the EN method correctly reflects the null distribution in a proteomic system and accurately measures false altered proteins discovery rate (FADR). In summary, the EN method provides a straightforward, practical, and accurate alternative to statistics-based approaches for the development and evaluation of proteomic experiments and can be universally adapted to various types of quantitative techniques.
Collapse
Affiliation(s)
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute , Elm and Carlton Streets, Buffalo, New York 14263, United States
| | | | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute , Elm and Carlton Streets, Buffalo, New York 14263, United States
| | | |
Collapse
|
28
|
Moulédous L, Froment C, Burlet-Schiltz O, Schulz S, Mollereau C. Phosphoproteomic analysis of the mouse brain mu-opioid (MOP) receptor. FEBS Lett 2015; 589:2401-8. [PMID: 26226422 DOI: 10.1016/j.febslet.2015.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/03/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022]
Abstract
Many in vitro data have shown that the efficacy of several opioid drugs is correlated with differential mu-opioid (MOP) receptor phosphorylation. Label-free semiquantitative on-line nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) analyses were performed to compare the endogenous MOP receptor phosphorylation patterns of mice administered with morphine, etonitazene and fentanyl. The analysis identified S363, T370 and S375 as phosphorylated residues in the carboxy-terminus. Only T370 and S375 were regulated by agonists, with a higher propensity to promote double phosphorylation for high efficacy agonists. Our study provides confirmation that differential agonist-driven multi-site phosphorylation of MOP receptor occurs in vivo and validate the use of MS to study endogenous GPCR phosphorylation.
Collapse
Affiliation(s)
- Lionel Moulédous
- Institut de Pharmacologie et Biologie Structurale CNRS/Université de Toulouse, 205 route de Narbonne, 31077 Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale CNRS/Université de Toulouse, 205 route de Narbonne, 31077 Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale CNRS/Université de Toulouse, 205 route de Narbonne, 31077 Toulouse, France
| | - Stefan Schulz
- Institute of Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Strasse 1, 07747 Jena, Germany.
| | - Catherine Mollereau
- Institut de Pharmacologie et Biologie Structurale CNRS/Université de Toulouse, 205 route de Narbonne, 31077 Toulouse, France.
| |
Collapse
|
29
|
Decourcelle M, Perez-Fons L, Baulande S, Steiger S, Couvelard L, Hem S, Zhu C, Capell T, Christou P, Fraser P, Sandmann G. Combined transcript, proteome, and metabolite analysis of transgenic maize seeds engineered for enhanced carotenoid synthesis reveals pleotropic effects in core metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3141-50. [PMID: 25796085 PMCID: PMC4449536 DOI: 10.1093/jxb/erv120] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The aim of this study was to assess whether endosperm-specific carotenoid biosynthesis influenced core metabolic processes in maize embryo and endosperm and how global seed metabolism adapted to this expanded biosynthetic capacity. Although enhancement of carotenoid biosynthesis was targeted to the endosperm of maize kernels, a concurrent up-regulation of sterol and fatty acid biosynthesis in the embryo was measured. Targeted terpenoid analysis, and non-targeted metabolomic, proteomic, and transcriptomic profiling revealed changes especially in carbohydrate metabolism in the transgenic line. In-depth analysis of the data, including changes of metabolite pools and increased enzyme and transcript concentrations, gave a first insight into the metabolic variation precipitated by the higher up-stream metabolite demand by the extended biosynthesis capacities for terpenoids and fatty acids. An integrative model is put forward to explain the metabolic regulation for the increased provision of terpenoid and fatty acid precursors, particularly glyceraldehyde 3-phosphate and pyruvate or acetyl-CoA from imported fructose and glucose. The model was supported by higher activities of fructokinase, glucose 6-phosphate isomerase, and fructose 1,6-bisphosphate aldolase indicating a higher flux through the glycolytic pathway. Although pyruvate and acetyl-CoA utilization was higher in the engineered line, pyruvate kinase activity was lower. A sufficient provision of both metabolites may be supported by a by-pass in a reaction sequence involving phosphoenolpyruvate carboxylase, malate dehydrogenase, and malic enzyme.
Collapse
Affiliation(s)
- Mathilde Decourcelle
- Unité de Biochimie et Physiologie Moléculaire des Plantes, INRA, 34060 Montpellier, France
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 OEX, UK
| | | | - Sabine Steiger
- Biosynthesis Group, Institute of Molecular Biosciences, Goethe University Frankfurt/M, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | | | - Sonia Hem
- Unité de Biochimie et Physiologie Moléculaire des Plantes, INRA, 34060 Montpellier, France
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, 25198 Lleida, Spain Institució Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 OEX, UK
| | - Gerhard Sandmann
- Biosynthesis Group, Institute of Molecular Biosciences, Goethe University Frankfurt/M, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| |
Collapse
|
30
|
Geiger A, Hamidou Soumana I, Tchicaya B, Rofidal V, Decourcelle M, Santoni V, Hem S. Differential expression of midgut proteins in Trypanosoma brucei gambiense-stimulated vs. non-stimulated Glossina palpalis gambiensis flies. Front Microbiol 2015; 6:444. [PMID: 26029185 PMCID: PMC4428205 DOI: 10.3389/fmicb.2015.00444] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/24/2015] [Indexed: 11/13/2022] Open
Abstract
The unicellular pathogenic protozoan Trypanosoma brucei gambiense is responsible for the chronic form of sleeping sickness. This vector-borne disease is transmitted to humans by the tsetse fly of the group Glossina palpalis, including the subspecies G. p. gambiensis, in which the parasite completes its developmental cycle. Sleeping sickness control strategies can therefore target either the human host or the fly vector. Indeed, suppression of one step in the parasite developmental cycle could abolish parasite transmission to humans, with consequences on the spreading of the disease. In order to develop this type of approach, we have identified, at the proteome level, events resulting from the tripartite interaction between the tsetse fly G. p. gambiensis, its microbiome, and the trypanosome. Proteomes were analyzed from four biological replicates of midguts from flies sampled 3 days post-feeding on either a trypanosome-infected (stimulated flies) or a non-infected (non-stimulated flies) bloodmeal. Over 500 proteins were identified in the midguts of flies from both feeding groups, 13 of which were shown to be differentially expressed in trypanosome-stimulated vs. non-stimulated flies. Functional annotation revealed that several of these proteins have important functions that could be involved in modulating the fly infection process by trypanosomes (and thus fly vector competence), including anti-oxidant and anti-apoptotic, cellular detoxifying, trypanosome agglutination, and immune stimulating or depressive effects. The results show a strong potential for diminishing or even disrupting fly vector competence, and their application holds great promise for improving the control of sleeping sickness.
Collapse
Affiliation(s)
- Anne Geiger
- UMR 177, Institut de Recherche pour le Développement-CIRAD, CIRAD TA A-17/G Montpellier, France
| | | | - Bernadette Tchicaya
- UMR 177, Institut de Recherche pour le Développement-CIRAD, CIRAD TA A-17/G Montpellier, France
| | - Valérie Rofidal
- Plateforme de Spectrométrie de Masse Protéomique - MSPP, Biochimie et Physiologie Moléculaire des Plantes - UMR 5004 Centre National de la Recherche Scientifique/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier II Montpellier, France
| | - Mathilde Decourcelle
- Plateforme de Spectrométrie de Masse Protéomique - MSPP, Biochimie et Physiologie Moléculaire des Plantes - UMR 5004 Centre National de la Recherche Scientifique/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier II Montpellier, France
| | - Véronique Santoni
- Plateforme de Spectrométrie de Masse Protéomique - MSPP, Biochimie et Physiologie Moléculaire des Plantes - UMR 5004 Centre National de la Recherche Scientifique/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier II Montpellier, France
| | - Sonia Hem
- Plateforme de Spectrométrie de Masse Protéomique - MSPP, Biochimie et Physiologie Moléculaire des Plantes - UMR 5004 Centre National de la Recherche Scientifique/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier II Montpellier, France
| |
Collapse
|
31
|
Tu C, Beharry KD, Shen X, Li J, Wang L, Aranda JV, Qu J. Proteomic profiling of the retinas in a neonatal rat model of oxygen-induced retinopathy with a reproducible ion-current-based MS1 approach. J Proteome Res 2015; 14:2109-2120. [PMID: 25780855 DOI: 10.1021/pr501238m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Investigation of the retina proteome during hypoxia-induced retinal neovascularization is valuable for understanding pathogenesis of retinopathy of prematurity (ROP). Here we employed a reproducible ion-current-based MS1 quantification approach (ICB) to explore the retinal proteomic changes in early stage of ROP in a rat model of oxygen-induced retinopathy (OIR). Retina proteins, which are rich in membrane proteins, were efficiently extracted by a detergent-cocktail and subjected to precipitation/on-pellet-digestion, followed by nano-LC-MS analysis on a 75-cm column with a 7-h gradient. The high reproducibility of sample preparation and chromatography separation enabled excellent peak alignment and contributed to the superior performance of ICB over parallel label-free approaches. In this study, sum-of-intensity with rejection was incorporated to determine the protein ratios. In total, 1325 unique protein groups were quantified from rat retinas (n = 4/group) with at least two distinct peptides at a protein FDR of 1%. Thirty-two significantly altered proteins were observed with confidence, and the elevated glial fibrillary acidic protein and decreased crystalline proteins in OIR retinas agree well with previous studies. Selected key alterations were further validated by Western blot analysis. Interestingly, Rab21/RhoA/ROCK2/moesin signaling pathway was found to be involved in retinal neovascularization of OIR. Moreover, highly elevated annexin A3, a potential angiogenic mediator, was observed in OIR retinas and may serve as a potential therapeutic target. In conclusion, reproducible ICB profiling enabled reliable discovery of many altered mediators and pathways in OIR retinas, thereby providing new insights into molecular mechanisms involved in pathogenesis of ROP.
Collapse
Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Kay D Beharry
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,Department of Ophthalmology, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,SUNY Eye Institute, Syracuse, New York 13202, United States
| | - Xiaomeng Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Lianshui Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Jacob V Aranda
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,Department of Ophthalmology, State University of New York, Downstate Medical Center, Brooklyn, New York 11203, United States.,SUNY Eye Institute, Syracuse, New York 13202, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| |
Collapse
|
32
|
Bouyssié D, Dubois M, Nasso S, Gonzalez de Peredo A, Burlet-Schiltz O, Aebersold R, Monsarrat B. mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets. Mol Cell Proteomics 2015; 14:771-81. [PMID: 25505153 PMCID: PMC4349994 DOI: 10.1074/mcp.o114.039115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 11/27/2014] [Indexed: 01/14/2023] Open
Abstract
The analysis and management of MS data, especially those generated by data independent MS acquisition, exemplified by SWATH-MS, pose significant challenges for proteomics bioinformatics. The large size and vast amount of information inherent to these data sets need to be properly structured to enable an efficient and straightforward extraction of the signals used to identify specific target peptides. Standard XML based formats are not well suited to large MS data files, for example, those generated by SWATH-MS, and compromise high-throughput data processing and storing. We developed mzDB, an efficient file format for large MS data sets. It relies on the SQLite software library and consists of a standardized and portable server-less single-file database. An optimized 3D indexing approach is adopted, where the LC-MS coordinates (retention time and m/z), along with the precursor m/z for SWATH-MS data, are used to query the database for data extraction. In comparison with XML formats, mzDB saves ∼25% of storage space and improves access times by a factor of twofold up to even 2000-fold, depending on the particular data access. Similarly, mzDB shows also slightly to significantly lower access times in comparison with other formats like mz5. Both C++ and Java implementations, converting raw or XML formats to mzDB and providing access methods, will be released under permissive license. mzDB can be easily accessed by the SQLite C library and its drivers for all major languages, and browsed with existing dedicated GUIs. The mzDB described here can boost existing mass spectrometry data analysis pipelines, offering unprecedented performance in terms of efficiency, portability, compactness, and flexibility.
Collapse
Affiliation(s)
- David Bouyssié
- From the ‡CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France; §Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France;
| | - Marc Dubois
- From the ‡CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France; §Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Sara Nasso
- ¶Department of Biology, Institute of Molecular Systems Biology, ETH, Auguste-Piccard-Hof 1, ETH Hönggerberg, CH-8093 Zürich, Switzerland
| | - Anne Gonzalez de Peredo
- From the ‡CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France; §Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France; §Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Ruedi Aebersold
- ¶Department of Biology, Institute of Molecular Systems Biology, ETH, Auguste-Piccard-Hof 1, ETH Hönggerberg, CH-8093 Zürich, Switzerland; ‖Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Bernard Monsarrat
- From the ‡CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France; §Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| |
Collapse
|
33
|
Fabre B, Lambour T, Garrigues L, Amalric F, Vigneron N, Menneteau T, Stella A, Monsarrat B, Van den Eynde B, Burlet-Schiltz O, Bousquet-Dubouch MP. Deciphering preferential interactions within supramolecular protein complexes: the proteasome case. Mol Syst Biol 2015; 11:771. [PMID: 25561571 PMCID: PMC4332148 DOI: 10.15252/msb.20145497] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In eukaryotic cells, intracellular protein breakdown is mainly performed by the ubiquitin-proteasome system. Proteasomes are supramolecular protein complexes formed by the association of multiple sub-complexes and interacting proteins. Therefore, they exhibit a very high heterogeneity whose function is still not well understood. Here, using a newly developed method based on the combination of affinity purification and protein correlation profiling associated with high-resolution mass spectrometry, we comprehensively characterized proteasome heterogeneity and identified previously unknown preferential associations within proteasome sub-complexes. In particular, we showed for the first time that the two main proteasome subtypes, standard proteasome and immunoproteasome, interact with a different subset of important regulators. This trend was observed in very diverse human cell types and was confirmed by changing the relative proportions of both 20S proteasome forms using interferon-γ. The new method developed here constitutes an innovative and powerful strategy that could be broadly applied for unraveling the dynamic and heterogeneous nature of other biologically relevant supramolecular protein complexes.
Collapse
Affiliation(s)
- Bertrand Fabre
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - Thomas Lambour
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - Luc Garrigues
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - François Amalric
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - Nathalie Vigneron
- Ludwig Institute for Cancer Research, Brussels, Belgium WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium de Duve Institute Université catholique de Louvain, Brussels, Belgium
| | - Thomas Menneteau
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - Alexandre Stella
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - Bernard Monsarrat
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - Benoît Van den Eynde
- Ludwig Institute for Cancer Research, Brussels, Belgium WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium de Duve Institute Université catholique de Louvain, Brussels, Belgium
| | - Odile Burlet-Schiltz
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| | - Marie-Pierre Bousquet-Dubouch
- CNRS IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France Université de Toulouse UPS IPBS, Toulouse, France
| |
Collapse
|
34
|
Yin X, Zhang Y, Liu X, Chen C, Lu H, Shen H, Yang P. Systematic comparison between SDS-PAGE/RPLC and high-/low-pH RPLC coupled tandem mass spectrometry strategies in a whole proteome analysis. Analyst 2015; 140:1314-22. [DOI: 10.1039/c4an02119c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Systematic comparison of two fractionation methods, which are SDS-PAGE in the protein level and high-pH RPLC in the peptide level.
Collapse
Affiliation(s)
- Xuefei Yin
- Department of Chemistry and Institutes of Biomedical Science Shanghai Medical School
- Fudan University
- Shanghai 200032
- China
| | - Yang Zhang
- Department of Chemistry and Institutes of Biomedical Science Shanghai Medical School
- Fudan University
- Shanghai 200032
- China
| | - Xiaohui Liu
- Department of Chemistry and Institutes of Biomedical Science Shanghai Medical School
- Fudan University
- Shanghai 200032
- China
| | - Chen Chen
- Department of Chemistry and Institutes of Biomedical Science Shanghai Medical School
- Fudan University
- Shanghai 200032
- China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Science Shanghai Medical School
- Fudan University
- Shanghai 200032
- China
| | - Huali Shen
- Department of Chemistry and Institutes of Biomedical Science Shanghai Medical School
- Fudan University
- Shanghai 200032
- China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Science Shanghai Medical School
- Fudan University
- Shanghai 200032
- China
| |
Collapse
|
35
|
Tu C, Sheng Q, Li J, Shen X, Zhang M, Shyr Y, Qu J. ICan: an optimized ion-current-based quantification procedure with enhanced quantitative accuracy and sensitivity in biomarker discovery. J Proteome Res 2014; 13:5888-97. [PMID: 25285707 PMCID: PMC4261937 DOI: 10.1021/pr5008224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
The
rapidly expanding availability of high-resolution mass spectrometry
has substantially enhanced the ion-current-based relative quantification
techniques. Despite the increasing interest in ion-current-based methods,
quantitative sensitivity, accuracy, and false discovery rate remain
the major concerns; consequently, comprehensive evaluation and development
in these regards are urgently needed. Here we describe an integrated,
new procedure for data normalization and protein ratio estimation,
termed ICan, for improved ion-current-based analysis of data generated
by high-resolution mass spectrometry (MS). ICan achieved significantly
better accuracy and precision, and lower false-positive rate for discovering
altered proteins, over current popular pipelines. A spiked-in experiment
was used to evaluate the performance of ICan to detect small changes.
In this study E. coli extracts were spiked with moderate-abundance
proteins from human plasma (MAP, enriched by IgY14-SuperMix procedure)
at two different levels to set a small change of 1.5-fold. Forty-five
(92%, with an average ratio of 1.71 ± 0.13) of 49 identified
MAP protein (i.e., the true positives) and none of the reference proteins
(1.0-fold) were determined as significantly altered proteins, with
cutoff thresholds of ≥1.3-fold change and p ≤ 0.05. This is the first study to evaluate and prove competitive
performance of the ion-current-based approach for assigning significance
to proteins with small changes. By comparison, other methods showed
remarkably inferior performance. ICan can be broadly applicable to
reliable and sensitive proteomic survey of multiple biological samples
with the use of high-resolution MS. Moreover, many key features evaluated
and optimized here such as normalization, protein ratio determination,
and statistical analyses are also valuable for data analysis by isotope-labeling
methods.
Collapse
Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York , Kapoor 318, North Campus, Buffalo, New York 14260, United States
| | | | | | | | | | | | | |
Collapse
|
36
|
Rabilloud T, Lescuyer P. Proteomics in mechanistic toxicology: History, concepts, achievements, caveats, and potential. Proteomics 2014; 15:1051-74. [DOI: 10.1002/pmic.201400288] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/25/2014] [Accepted: 08/25/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals; CNRS UMR; 5249 Grenoble France
- Laboratory of Chemistry and Biology of Metals; Université Grenoble Alpes; Grenoble France
- Laboratory of Chemistry and Biology of Metals; CEA Grenoble; iRTSV/CBM; Grenoble France
| | - Pierre Lescuyer
- Department of Human Protein Sciences; Clinical Proteomics and Chemistry Group; Geneva University; Geneva Switzerland
- Toxicology and Therapeutic Drug Monitoring Laboratory; Department of Genetic and Laboratory Medicine; Geneva University Hospitals; Geneva Switzerland
| |
Collapse
|
37
|
Bray L, Froment C, Pardo P, Candotto C, Burlet-Schiltz O, Zajac JM, Mollereau C, Moulédous L. Identification and functional characterization of the phosphorylation sites of the neuropeptide FF2 receptor. J Biol Chem 2014; 289:33754-66. [PMID: 25326382 DOI: 10.1074/jbc.m114.612614] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The neuropeptide FF2 (NPFF2) receptor belongs to the rhodopsin family of G protein-coupled receptors and mediates the effects of several related RFamide neuropeptides. One of the main pharmacological interests of this system resides in its ability to regulate endogenous opioid systems, making it a potential target to reduce the negative effects of chronic opioid use. Phosphorylation of intracellular residues is the most extensively studied post-translational modification regulating G protein-coupled receptor activity. However, until now, no information concerning NPFF2 receptor phosphorylation is available. In this study, we combined mass spectrometric analysis and site-directed mutagenesis to analyze for the first time the phosphorylation pattern of the NPFF2 receptor and the role of the various phosphorylation sites in receptor signaling, desensitization, and trafficking in a SH-SY5Y model cell line. We identified the major, likely GRK-dependent, phosphorylation cluster responsible for acute desensitization, (412)TNST(415) at the end of the C terminus of the receptor, and additional sites involved in desensitization ((372)TS(373)) and internalization (Ser(395)). We thus demonstrate the key role played by phosphorylation in the regulation of NPFF2 receptor activity and trafficking. Our data also provide additional evidence supporting the concept that desensitization and internalization are partially independent processes relying on distinct phosphorylation patterns.
Collapse
Affiliation(s)
- Lauriane Bray
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Carine Froment
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Pardo
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Cédric Candotto
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Jean-Marie Zajac
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Catherine Mollereau
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| | - Lionel Moulédous
- From the Institut de Pharmacologie et Biologie Structurale, UMR5089 CNRS, Université de Toulouse, 31077 Toulouse, France
| |
Collapse
|
38
|
Wen YT, Wang JS, Tsai SH, Chuan CN, Wu JJ, Liao PC. Label-free proteomic analysis of environmental acidification-influenced Streptococcus pyogenes secretome reveals a novel acid-induced protein histidine triad protein A (HtpA) involved in necrotizing fasciitis. J Proteomics 2014; 109:90-103. [DOI: 10.1016/j.jprot.2014.06.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 06/11/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
|
39
|
Martinez-Pinna R, de Peredo AG, Monsarrat B, Burlet-Schiltz O, Martin-Ventura JL. Label-free quantitative proteomic analysis of human plasma-derived microvesicles to find protein signatures of abdominal aortic aneurysms. Proteomics Clin Appl 2014; 8:620-5. [DOI: 10.1002/prca.201400010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/25/2014] [Accepted: 05/26/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Roxana Martinez-Pinna
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse France
- UPS, IPBS; Université de Toulouse; Toulouse France
| | - Anne Gonzalez de Peredo
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse France
- UPS, IPBS; Université de Toulouse; Toulouse France
| | - Bernard Monsarrat
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse France
- UPS, IPBS; Université de Toulouse; Toulouse France
| | - Odile Burlet-Schiltz
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse France
- UPS, IPBS; Université de Toulouse; Toulouse France
| | | |
Collapse
|
40
|
Yin X, Liu X, Zhang Y, Yan G, Wang F, Lu H, Shen H, Yang P. Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation. Proteomics 2014; 14:2008-16. [PMID: 25044409 DOI: 10.1002/pmic.201300510] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 06/11/2014] [Accepted: 07/03/2014] [Indexed: 01/05/2023]
Abstract
In this paper, we demonstrate a rapid and reproducible 1D LC-MS/MS workflow for fast quantitative proteomic research. We have optimized the LC-MS/MS conditions, including digestion and gradient conditions, sample loading amount, and MS parameter settings. As a result, we were able to obtain twice as many protein identifications compared with the LC-MS/MS conditions before optimization. More than 4500 protein groups and 50 000 peptides were identified in less than 8 h without any fractionation. This 1D workflow was then applied to the analysis of the MLN4924 treated/untreated human umbilical vein endothelial cell (HUVEC) samples with label-free quantification. In these experiments, a total of 179 proteins showed a statistically significant expression change after the MLN4924 treatment. Functional analysis showed that these proteins are associated with cell death and survival; gene expression; cell cycle; and DNA replication, recombination, and repair.
Collapse
Affiliation(s)
- Xuefei Yin
- Department of Chemistry and Institutes of Biomedical Sciences Shanghai Medical School, Fudan University, Shanghai, P. R. China
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Shen X, Young R, Canty JM, Qu J. Quantitative proteomics in cardiovascular research: global and targeted strategies. Proteomics Clin Appl 2014; 8:488-505. [PMID: 24920501 DOI: 10.1002/prca.201400014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/02/2014] [Accepted: 06/06/2014] [Indexed: 11/05/2022]
Abstract
Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here, we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation.
Collapse
Affiliation(s)
- Xiaomeng Shen
- Department of Biochemistry, University at Buffalo, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | | | | | | |
Collapse
|
42
|
Giorgianni F, Koirala D, Weber KT, Beranova-Giorgianni S. Proteome analysis of subsarcolemmal cardiomyocyte mitochondria: a comparison of different analytical platforms. Int J Mol Sci 2014; 15:9285-301. [PMID: 24865490 PMCID: PMC4100094 DOI: 10.3390/ijms15069285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/05/2023] Open
Abstract
Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease.
Collapse
Affiliation(s)
- Francesco Giorgianni
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Diwa Koirala
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Karl T Weber
- Division of Cardiology, Department of Medicine, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| |
Collapse
|
43
|
Fabre B, Lambour T, Garrigues L, Ducoux-Petit M, Amalric F, Monsarrat B, Burlet-Schiltz O, Bousquet-Dubouch MP. Label-Free Quantitative Proteomics Reveals the Dynamics of Proteasome Complexes Composition and Stoichiometry in a Wide Range of Human Cell Lines. J Proteome Res 2014; 13:3027-37. [DOI: 10.1021/pr500193k] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Bertrand Fabre
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Thomas Lambour
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Luc Garrigues
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Manuelle Ducoux-Petit
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - François Amalric
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Bernard Monsarrat
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Odile Burlet-Schiltz
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Marie-Pierre Bousquet-Dubouch
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); 205 route de Narbonne, F-31077 Toulouse, France
- Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| |
Collapse
|
44
|
Talamantes T, Ughy B, Domonkos I, Kis M, Gombos Z, Prokai L. Label-free LC-MS/MS identification of phosphatidylglycerol-regulated proteins in Synechocystis
sp. PCC6803. Proteomics 2014; 14:1053-7. [DOI: 10.1002/pmic.201300372] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/04/2014] [Accepted: 02/20/2014] [Indexed: 01/21/2023]
Affiliation(s)
- Tatjana Talamantes
- Department of Molecular Biology and Immunology; University of North Texas Health Science Center; Fort Worth TX USA
| | - Bettina Ughy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Plant Biology; Szeged Hungary
| | - Ildikó Domonkos
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Plant Biology; Szeged Hungary
| | - Mihály Kis
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Plant Biology; Szeged Hungary
| | - Zoltán Gombos
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Plant Biology; Szeged Hungary
| | - Laszlo Prokai
- Department of Molecular Biology and Immunology; University of North Texas Health Science Center; Fort Worth TX USA
| |
Collapse
|
45
|
Alberio T, Bondi H, Colombo F, Alloggio I, Pieroni L, Urbani A, Fasano M. Mitochondrial proteomics investigation of a cellular model of impaired dopamine homeostasis, an early step in Parkinson's disease pathogenesis. MOLECULAR BIOSYSTEMS 2014; 10:1332-44. [PMID: 24675778 DOI: 10.1039/c3mb70611g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Impaired dopamine homeostasis is an early event in the pathogenesis of Parkinson's disease. Generation of intracellular reactive oxygen species consequent to dopamine oxidation leads to mitochondrial dysfunction and eventually cell death. Alterations in the mitochondrial proteome due to dopamine exposure were investigated in the SH-SY5Y human neuroblastoma cell line. The combination of two orthogonal proteomic approaches, two-dimensional electrophoresis and shotgun proteomics (proteomeXchange dataset PXD000838), was used to highlight the specific pathways perturbed by the increase of intracellular dopamine, in comparison with those perturbed by a specific mitochondrial toxin (4-methylphenylpyridinium, MPP(+)), a neurotoxin causing Parkinsonism-like symptoms in animal models. Proteins altered by MPP(+) did not completely overlap with those affected by dopamine treatment. In particular, the MPP(+) target complex I component NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 was not affected by dopamine together with 26 other proteins. The comparison of proteomics approaches highlighted the fragmentation of some mitochondrial proteins, suggesting an alteration of the mitochondrial protease activity. Pathway and disease association analysis of the proteins affected by dopamine revealed the overrepresentation of the Parkinson's disease and the parkin-ubiquitin proteasomal system pathways and of gene ontologies associated with generation of precursor metabolites and energy, response to topologically incorrect proteins and programmed cell death. These alterations may be globally interpreted in part as the result of a direct effect of dopamine on mitochondria (e.g. alteration of the mitochondrial protease activity) and in part as the effect on mitochondria of a general activation of cellular processes (e.g. regulation of programmed cell death).
Collapse
Affiliation(s)
- Tiziana Alberio
- Biomedical Research Division, Department of Theoretical and Applied Sciences, University of Insubria, Busto Arsizio, Italy.
| | | | | | | | | | | | | |
Collapse
|
46
|
Tu C, Li J, Sheng Q, Zhang M, Qu J. Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data. J Proteome Res 2014; 13:2069-79. [PMID: 24635752 PMCID: PMC3993956 DOI: 10.1021/pr401206m] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Survey-scan-based label-free method
have shown no compelling benefit
over fragment ion (MS2)-based approaches when low-resolution mass
spectrometry (MS) was used, the growing prevalence of high-resolution
analyzers may have changed the game. This necessitates an updated,
comparative investigation of these approaches for data acquired by
high-resolution MS. Here, we compared survey scan-based (ion current,
IC) and MS2-based abundance features including spectral-count (SpC)
and MS2 total-ion-current (MS2-TIC), for quantitative analysis using
various high-resolution LC/MS data sets. Key discoveries include:
(i) study with seven different biological data sets revealed only
IC achieved high reproducibility for lower-abundance proteins; (ii)
evaluation with 5-replicate analyses of a yeast sample showed IC provided
much higher quantitative precision and lower missing data; (iii) IC,
SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range;
(iv)
both MS2-TIC and IC showed good linear response to various protein
loading amounts but not SpC; (v) quantification using a well-characterized
CPTAC data set showed that IC exhibited markedly higher quantitative
accuracy, higher sensitivity, and lower false-positives/false-negatives
than both SpC and MS2-TIC. Therefore, IC achieved an overall superior
performance than the MS2-based strategies in terms of reproducibility,
missing data, quantitative dynamic range, quantitative accuracy, and
biomarker discovery.
Collapse
Affiliation(s)
- Chengjian Tu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York , Buffalo, NY 14260, United States
| | | | | | | | | |
Collapse
|
47
|
Siguier B, Haon M, Nahoum V, Marcellin M, Burlet-Schiltz O, Coutinho PM, Henrissat B, Mourey L, O'Donohue MJ, Berrin JG, Tranier S, Dumon C. First structural insights into α-L-arabinofuranosidases from the two GH62 glycoside hydrolase subfamilies. J Biol Chem 2014; 289:5261-73. [PMID: 24394409 DOI: 10.1074/jbc.m113.528133] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
α-L-arabinofuranosidases are glycoside hydrolases that specifically hydrolyze non-reducing residues from arabinose-containing polysaccharides. In the case of arabinoxylans, which are the main components of hemicellulose, they are part of microbial xylanolytic systems and are necessary for complete breakdown of arabinoxylans. Glycoside hydrolase family 62 (GH62) is currently a small family of α-L-arabinofuranosidases that contains only bacterial and fungal members. Little is known about the GH62 mechanism of action, because only a few members have been biochemically characterized and no three-dimensional structure is available. Here, we present the first crystal structures of two fungal GH62 α-L-arabinofuranosidases from the basidiomycete Ustilago maydis (UmAbf62A) and ascomycete Podospora anserina (PaAbf62A). Both enzymes are able to efficiently remove the α-L-arabinosyl substituents from arabinoxylan. The overall three-dimensional structure of UmAbf62A and PaAbf62A reveals a five-bladed β-propeller fold that confirms their predicted classification into clan GH-F together with GH43 α-L-arabinofuranosidases. Crystallographic structures of the complexes with arabinose and cellotriose reveal the important role of subsites +1 and +2 for sugar binding. Intriguingly, we observed that PaAbf62A was inhibited by cello-oligosaccharides and displayed binding affinity to cellulose although no activity was observed on a range of cellulosic substrates. Bioinformatic analyses showed that UmAbf62A and PaAbf62A belong to two distinct subfamilies within the GH62 family. The results presented here provide a framework to better investigate the structure-function relationships within the GH62 family.
Collapse
Affiliation(s)
- Béatrice Siguier
- From the Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Swift J, Harada T, Buxboim A, Shin JW, Tang HY, Speicher DW, Discher DE. Label-free mass spectrometry exploits dozens of detected peptides to quantify lamins in wildtype and knockdown cells. Nucleus 2013; 4:450-9. [PMID: 24448480 DOI: 10.4161/nucl.27413] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Label-free quantitation and characterization of proteins by mass spectrometry (MS) is now feasible, especially for moderately expressed structural proteins such as lamins that typically yield dozens of tryptic peptides from tissue cells. Using standard cell culture samples, we describe general algorithms for quantitative analysis of peptides identified in liquid chromatography tandem mass spectrometry (LC-MS/MS). The algorithms were foundational to the discovery that the absolute stoichiometry of A-type to B-type lamins scales with tissue stiffness (Swift et al., Science 2013). Isoform dominance helps make sense of why mutations and changes with age of mechanosensitive lamin-A,C only affect "stiff" tissues such as heart, muscle, bone, or even fat, but not brain. A Peak Ratio Fingerprinting (PRF) algorithm is elaborated here through its application to lamin-A,C knockdown. After demonstrating the large dynamic range of PRF using calibrated mixtures of human and mouse lysates, we validate measurements of partial knockdown with standard cell biology analyses using quantitative immunofluorescence and immunoblotting. Optimal sets of MS-detected peptides as determined by PRF demonstrate that the strongest peptide signals are not necessarily the most reliable for quantitation. After lamin-A,C knockdown, PRF computes an invariant set of "housekeeping" proteins as part of a broader proteomic analysis that also shows the proteome of mesenchymal stem cells (MSCs) is more broadly perturbed than that of a human epithelial cancer line (A549s), with particular variation in nuclear and cytoskeletal proteins. These methods offer exciting prospects for basic and clinical studies of lamin-A,C as well as other MS-detectable proteins.
Collapse
Affiliation(s)
- Joe Swift
- Molecular & Cell Biophysics Laboratory, University of Pennsylvania; Philadelphia PA USA; Center for Systems and Computational Biology; Wistar Institute; Philadelphia PA USA
| | - Takamasa Harada
- Molecular & Cell Biophysics Laboratory, University of Pennsylvania; Philadelphia PA USA
| | - Amnon Buxboim
- Molecular & Cell Biophysics Laboratory, University of Pennsylvania; Philadelphia PA USA
| | - Jae-Won Shin
- Molecular & Cell Biophysics Laboratory, University of Pennsylvania; Philadelphia PA USA
| | - Hsin-Yao Tang
- Center for Systems and Computational Biology; Wistar Institute; Philadelphia PA USA
| | - David W Speicher
- Center for Systems and Computational Biology; Wistar Institute; Philadelphia PA USA
| | - Dennis E Discher
- Molecular & Cell Biophysics Laboratory, University of Pennsylvania; Philadelphia PA USA; Center for Systems and Computational Biology; Wistar Institute; Philadelphia PA USA
| |
Collapse
|
49
|
ELL, a novel TFIIH partner, is involved in transcription restart after DNA repair. Proc Natl Acad Sci U S A 2013; 110:17927-32. [PMID: 24127601 DOI: 10.1073/pnas.1305009110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA lesions that block transcription may cause cell death even when repaired, if transcription does not restart to reestablish cellular metabolism. However, transcription resumption after individual DNA-lesion repair remains poorly described in mechanistic terms and its players are largely unknown. The general transcription factor II H (TFIIH) is a major actor of both nucleotide excision repair subpathways of which transcription-coupled repair highlights the interplay between DNA repair and transcription. Using an unbiased proteomic approach, we have identified the protein eleven-nineteen lysine-rich leukemia (ELL) as a TFIIH partner. Here we show that ELL is recruited to UV-damaged chromatin in a Cdk7- dependent manner (a component of the cyclin-dependent activating kinase subcomplex of TFIIH). We demonstrate that depletion of ELL strongly hinders RNA polymerase II (RNA Pol II) transcription resumption after lesion removal and DNA gap filling. Lack of ELL was also observed to increase RNA Pol II retention to the chromatin during this process. Identifying ELL as an essential player for RNA Pol II restart during cellular DNA damage response opens the way to obtaining a mechanistic description of transcription resumption after DNA repair.
Collapse
|
50
|
Megger DA, Bracht T, Meyer HE, Sitek B. Label-free quantification in clinical proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1581-90. [DOI: 10.1016/j.bbapap.2013.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 03/26/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
|