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Lapehn S, Colacino JA, Harris C. Spatiotemporal protein dynamics during early organogenesis in mouse conceptuses treated with valproic acid. Neurotoxicol Teratol 2023; 99:107286. [PMID: 37442398 PMCID: PMC10697214 DOI: 10.1016/j.ntt.2023.107286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Valproic acid (VPA) is an anti-epileptic medication that increases the risk of neural tube defect (NTD) outcomes in infants exposed during gestation. Previous studies into VPA's mechanism of action have focused on alterations in gene expression and metabolism but have failed to consider how exposure changes the abundance of critical developmental proteins over time. This study evaluates the effects of VPA on protein abundance in the developmentally distinct tissues of the mouse visceral yolk sac (VYS) and embryo proper (EMB) using mouse whole embryo culture. Embryos were exposed to 600 μM VPA at 2 h intervals over 10 h during early organogenesis with the aim of identifying protein pathways relevant to VPA's mechanism of action in failed NTC. Protein abundance was measured through tandem mass tag (TMT) labeling followed by liquid chromatography and mass spectrometry. Overall, there were over 1500 proteins with altered abundance after VPA exposure in the EMB or VYS with 428 of these proteins showing previous gene expression associations with VPA exposure. Limited overlap of significant proteins between tissues supported the conclusion of independent roles for the VYS and EMB in response to VPA. Pathway analysis of proteins with increased or decreased abundance identified multiple pathways with mechanistic relevance to NTC and embryonic development including convergent extension, Wnt Signaling/planar cell polarity, cellular migration, cellular proliferation, cell death, and cytoskeletal organization processes as targets of VPA. Clustering of co-regulated proteins to identify shared patterns of protein abundance over time highlighted 4 h and 6/10 h as periods of divergent protein abundance between control and VPA-treated samples in the VYS and EMB, respectively. Overall, this study demonstrated that VPA temporally alters protein content in critical developmental pathways in the VYS and the EMB during early organogenesis in mice.
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Affiliation(s)
- Samantha Lapehn
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Craig Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
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Horánszky A, Shashikadze B, Elkhateib R, Lombardo SD, Lamberto F, Zana M, Menche J, Fröhlich T, Dinnyés A. Proteomics and disease network associations evaluation of environmentally relevant Bisphenol A concentrations in a human 3D neural stem cell model. Front Cell Dev Biol 2023; 11:1236243. [PMID: 37664457 PMCID: PMC10472293 DOI: 10.3389/fcell.2023.1236243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Bisphenol A (BPA) exposure is associated with a plethora of neurodevelopmental abnormalities and brain disorders. Previous studies have demonstrated BPA-induced perturbations to critical neural stem cell (NSC) characteristics, such as proliferation and differentiation, although the underlying molecular mechanisms remain under debate. The present study evaluated the effects of a repeated-dose exposure of environmentally relevant BPA concentrations during the in vitro 3D neural induction of human induced pluripotent stem cells (hiPSCs), emulating a chronic exposure scenario. Firstly, we demonstrated that our model is suitable for NSC differentiation during the early stages of embryonic brain development. Our morphological image analysis showed that BPA exposure at 0.01, 0.1 and 1 µM decreased the average spheroid size by day 21 (D21) of the neural induction, while no effect on cell viability was detected. No alteration to the rate of the neural induction was observed based on the expression of key neural lineage and neuroectodermal transcripts. Quantitative proteomics at D21 revealed several differentially abundant proteins across all BPA-treated groups with important functions in NSC proliferation and maintenance (e.g., FABP7, GPC4, GAP43, Wnt-8B, TPPP3). Additionally, a network analysis demonstrated alterations to the glycolytic pathway, potentially implicating BPA-induced changes to glycolytic signalling in NSC proliferation impairments, as well as the pathophysiology of brain disorders including intellectual disability, autism spectrum disorders, and amyotrophic lateral sclerosis (ALS). This study enhances the current understanding of BPA-related NSC aberrations based mostly on acute, often high dose exposures of rodent in vivo and in vitro models and human GWAS data in a novel human 3D cell-based model with real-life scenario relevant prolonged and low-level exposures, offering further mechanistic insights into the ramifications of BPA exposure on the developing human brain and consequently, later life neurological disorders.
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Affiliation(s)
- Alex Horánszky
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Bachuki Shashikadze
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Radwa Elkhateib
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Salvo Danilo Lombardo
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Federica Lamberto
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | | | - Jörg Menche
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - András Dinnyés
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Department of Cell Biology and Molecular Medicine, University of Szeged, Szeged, Hungary
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Boschetti E, Righetti PG. Low-Abundance Protein Enrichment for Medical Applications: The Involvement of Combinatorial Peptide Library Technique. Int J Mol Sci 2023; 24:10329. [PMID: 37373476 DOI: 10.3390/ijms241210329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The discovery of low- and very low-abundance proteins in medical applications is considered a key success factor in various important domains. To reach this category of proteins, it is essential to adopt procedures consisting of the selective enrichment of species that are present at extremely low concentrations. In the past few years pathways towards this objective have been proposed. In this review, a general landscape of the enrichment technology situation is made first with the presentation and the use of combinatorial peptide libraries. Then, a description of this peculiar technology for the identification of early-stage biomarkers for well-known pathologies with concrete examples is given. In another field of medical applications, the determination of host cell protein traces potentially present in recombinant therapeutic proteins, such as antibodies, is discussed along with their potentially deleterious effects on the health of patients on the one hand, and on the stability of these biodrugs on the other hand. Various additional applications of medical interest are disclosed for biological fluids investigations where the target proteins are present at very low concentrations (e.g., protein allergens).
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Abstract
Mass spectrometry-based protein methodologies have revolutionized the field of analytical biochemistry and enable the identification of hundreds to thousands of proteins in biological fluids, cell lines, and tissue. This methodology requires the initial separation of a protein constellation, and this has been successfully achieved using gel-based techniques, particularly that of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). However, given the complexity of the proteome, fractionation techniques may be required to optimize the detection of low-abundance proteins, which are often underrepresented but which may represent important players in health and disease. Such subcellular fractionation protocols typically utilize density-gradient centrifugation and have enabled the enrichment of crude microsomes, the cytosol, the plasmalemma, the nuclei, and the mitochondria. In this chapter, we describe the experimental steps involved in the enrichment of crude microsomes from the skeletal muscle using differential centrifugation and subsequent verification of enrichment by gel electrophoresis and immunoblotting, prior to comparative 2D-DIGE analysis.
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Möller L, Vainstein Y, Wöhlbrand L, Dörries M, Meyer B, Sohn K, Rabus R. Transcriptome-proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes. Proteomics 2022; 22:e2100404. [PMID: 35778945 DOI: 10.1002/pmic.202100404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean that uses an arsenal of hydrolases for biomacromolecule decomposition to effectively digest its omnivorous diet. The present study builds on a hybrid-assembled transcriptome (13,671 ORFs) combined with comprehensive proteome profiling. The analysis of individual krill compartments allowed detection of significantly more different proteins compared to that of the entire animal (1,464 vs. 294 proteins). The nearby krill sampling stations in the Bransfield Strait (Antarctic Peninsula) yielded rather uniform proteome datasets. Proteins related to energy production and lipid degradation were particularly abundant in the abdomen, agreeing with the high energy demand of muscle tissue. A total of 378 different biomacromolecule hydrolysing enzymes were detected, including 250 proteases, 99 CAZymes, 14 nucleases and 15 lipases. The large repertoire in proteases is in accord with the protein-rich diet affiliated with E. superba's omnivorous lifestyle and complex biology. The richness in chitin-degrading enzymes allows not only digestion of zooplankton diet, but also the utilization of the discharged exoskeleton after moulting. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Lars Möller
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Yeheven Vainstein
- In-Vitro-Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Marvin Dörries
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.,Biodiversity Change, Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Bettina Meyer
- Biodiversity and Biological Processes in Polar Oceans, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.,Ecophysiology of Pelagic Key Species, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Biodiversity Change, Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Kai Sohn
- In-Vitro-Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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Kriel NL, Newton-Foot M, Bennion OT, Aldridge BB, Mehaffy C, Belisle JT, Walzl G, Warren RM, Sampson SL, Gey van Pittius NC. Localization of EccA 3 at the growing pole in Mycobacterium smegmatis. BMC Microbiol 2022; 22:140. [PMID: 35590245 PMCID: PMC9118679 DOI: 10.1186/s12866-022-02554-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background Bacteria require specialized secretion systems for the export of molecules into the extracellular space to modify their environment and scavenge for nutrients. The ESX-3 secretion system is required by mycobacteria for iron homeostasis. The ESX-3 operon encodes for one cytoplasmic component (EccA3) and five membrane components (EccB3 – EccE3 and MycP3). In this study we sought to identify the sub-cellular location of EccA3 of the ESX-3 secretion system in mycobacteria. Results Fluorescently tagged EccA3 localized to a single pole in the majority of Mycobacterium smegmatis cells and time-lapse fluorescent microscopy identified this pole as the growing pole. Deletion of ESX-3 did not prevent polar localization of fluorescently tagged EccA3, suggesting that EccA3 unipolar localization is independent of other ESX-3 components. Affinity purification - mass spectrometry was used to identify EccA3 associated proteins which may contribute to the localization of EccA3 at the growing pole. EccA3 co-purified with fatty acid metabolism proteins (FAS, FadA3, KasA and KasB), mycolic acid synthesis proteins (UmaA, CmaA1), cell division proteins (FtsE and FtsZ), and cell shape and cell cycle proteins (MurS, CwsA and Wag31). Secretion system related proteins Ffh, SecA1, EccA1, and EspI were also identified. Conclusions Time-lapse microscopy demonstrated that EccA3 is located at the growing pole in M. smegmatis. The co-purification of EccA3 with proteins known to be required for polar growth, mycolic acid synthesis, the Sec secretion system (SecA1), and the signal recognition particle pathway (Ffh) also suggests that EccA3 is located at the site of active cell growth. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02554-6.
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Affiliation(s)
- Nastassja L Kriel
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Mae Newton-Foot
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Owen T Bennion
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Carolina Mehaffy
- Mycobacteria Research Laboratories, Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - John T Belisle
- Mycobacteria Research Laboratories, Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Samantha L Sampson
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nico C Gey van Pittius
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Jahangir S, John P, Bhatti A, Aslam MM, Mehmood Malik J, Anderson JR, Peffers MJ. LC-MS/MS-Based Serum Protein Profiling for Identification of Candidate Biomarkers in Pakistani Rheumatoid Arthritis Patients. Life (Basel) 2022; 12:life12030464. [PMID: 35330214 PMCID: PMC8955720 DOI: 10.3390/life12030464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Rheumatoid arthritis is an autoimmune disorder of complex disease etiology. Currently available serological diagnostic markers lack in terms of sensitivity and specificity and thus additional biomarkers are warranted for early disease diagnosis and management. We aimed to screen and compare serum proteome profiles of rheumatoid arthritis serotypes with healthy controls in the Pakistani population for identification of potential disease biomarkers. Serum samples from rheumatoid arthritis patients and healthy controls were enriched for low abundance proteins using ProteoMinerTM columns. Rheumatoid arthritis patients were assigned to one of the four serotypes based on anti-citrullinated peptide antibodies and rheumatoid factor. Serum protein profiles were analyzed via liquid chromatography-tandem mass spectrometry. The changes in the protein abundances were determined using label-free quantification software ProgenesisQITM followed by pathway analysis. Findings were validated in an independent cohort of patients and healthy controls using an enzyme-linked immunosorbent assay. A total of 213 proteins were identified. Comparative analysis of all groups (false discovery rate < 0.05, >2-fold change, and identified with ≥2 unique peptides) identified ten proteins that were differentially expressed between rheumatoid arthritis serotypes and healthy controls including pregnancy zone protein, selenoprotein P, C4b-binding protein beta chain, apolipoprotein M, N-acetylmuramoyl-L-alanine amidase, catalytic chain, oncoprotein-induced transcript 3 protein, Carboxypeptidase N subunit 2, Apolipoprotein C-I and Apolipoprotein C-III. Pathway analysis predicted inhibition of liver X receptor/retinoid X receptor activation pathway and production of nitric oxide and reactive oxygen species pathway in macrophages in all serotypes. A catalogue of potential serum biomarkers for rheumatoid arthritis were identified. These biomarkers can be further evaluated in larger cohorts from different populations for their diagnostic and prognostic potential.
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Affiliation(s)
- Sidrah Jahangir
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan; (S.J.); (A.B.)
| | - Peter John
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan; (S.J.); (A.B.)
- Correspondence: ; Tel.: +92-051-9085-6151
| | - Attya Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan; (S.J.); (A.B.)
| | - Muhammad Muaaz Aslam
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15216, USA;
| | | | - James R. Anderson
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK; (J.R.A.); (M.J.P.)
| | - Mandy J. Peffers
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK; (J.R.A.); (M.J.P.)
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A Bioinformatics Approach to Mine the Microbial Proteomic Profile of COVID-19 Mass Spectrometry Data. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2010010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS) is one of the key technologies used in proteomics. The majority of studies carried out using proteomics have focused on identifying proteins in biological samples such as human plasma to pin down prognostic or diagnostic biomarkers associated with particular conditions or diseases. This study aims to quantify microbial (viral and bacterial) proteins in healthy human plasma. MS data of healthy human plasma were searched against the complete proteomes of all available viruses and bacteria. With this baseline established, the same strategy was applied to characterize the metaproteomic profile of different SARS-CoV-2 disease stages in the plasma of patients. Two SARS-CoV-2 proteins were detected with a high confidence and could serve as the early markers of SARS-CoV-2 infection. The complete bacterial and viral protein content in SARS-CoV-2 samples was compared for the different disease stages. The number of viral proteins was found to increase significantly with the progression of the infection, at the expense of bacterial proteins. This strategy can be extended to aid in the development of early diagnostic tests for other infectious diseases based on the presence of microbial biomarkers in human plasma samples.
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Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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Leprêtre M, Faury N, Segarra A, Claverol S, Degremont L, Palos-Ladeiro M, Armengaud J, Renault T, Morga B. Comparative Proteomics of Ostreid Herpesvirus 1 and Pacific Oyster Interactions With Two Families Exhibiting Contrasted Susceptibility to Viral Infection. Front Immunol 2021; 11:621994. [PMID: 33537036 PMCID: PMC7848083 DOI: 10.3389/fimmu.2020.621994] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Massive mortality outbreaks affecting Pacific oysters (Crassostrea gigas) spat/juveniles are often associated with the detection of a herpesvirus called ostreid herpesvirus type 1 (OsHV-1). In this work, experimental infection trials of C. gigas spat with OsHV-1 were conducted using two contrasted Pacific oyster families for their susceptibility to viral infection. Live oysters were sampled at 12, 26, and 144 h post infection (hpi) to analyze host-pathogen interactions using comparative proteomics. Shotgun proteomics allowed the detection of seven viral proteins in infected oysters, some of them with potential immunomodulatoy functions. Viral proteins were mainly detected in susceptible oysters sampled at 26 hpi, which correlates with the mortality and viral load observed in this oyster family. Concerning the Pacific oyster proteome, more than 3,000 proteins were identified and contrasted proteomic responses were observed between infected A- and P-oysters, sampled at different post-injection times. Gene ontology (GO) and KEGG pathway enrichment analysis performed on significantly modulated proteins uncover the main immune processes (such as RNA interference, interferon-like pathway, antioxidant defense) which contribute to the defense and resistance of Pacific oysters to viral infection. In the more susceptible Pacific oysters, results suggest that OsHV-1 manipulate the molecular machinery of host immune response, in particular the autophagy system. This immunomodulation may lead to weakening and consecutively triggering death of Pacific oysters. The identification of several highly modulated and defense-related Pacific oyster proteins from the most resistant oysters supports the crucial role played by the innate immune system against OsHV-1 and the viral infection. Our results confirm the implication of proteins involved in an interferon-like pathway for efficient antiviral defenses and suggest that proteins involved in RNA interference process prevent viral replication in C. gigas. Overall, this study shows the interest of multi-omic approaches applied on groups of animals with differing sensitivities and provides novel insight into the interaction between Pacific oyster and OsHV-1 with key proteins involved in viral infection resistance.
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Affiliation(s)
- Maxime Leprêtre
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, Reims, France
| | - Nicole Faury
- SG2M-LGPMM, Laboratoire De Génétique Et Pathologie Des Mollusques Marins, Ifremer, La Tremblade, France
| | - Amélie Segarra
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Stéphane Claverol
- Centre Génomique Fonctionnelle de Bordeaux, Plateforme Protéome, Université de Bordeaux, Bordeaux, France
| | - Lionel Degremont
- SG2M-LGPMM, Laboratoire De Génétique Et Pathologie Des Mollusques Marins, Ifremer, La Tremblade, France
| | - Mélissa Palos-Ladeiro
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO Unité Stress Environnementaux et BIOsurveillance des milieux aquatiques, UFR Sciences Exactes et Naturelles, Campus du Moulin de la Housse, Reims, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, DépartementMédicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Tristan Renault
- Département Ressources Biologiques Et Environnement, Ifremer, Nantes, France
| | - Benjamin Morga
- SG2M-LGPMM, Laboratoire De Génétique Et Pathologie Des Mollusques Marins, Ifremer, La Tremblade, France
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Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122453. [PMID: 33279813 DOI: 10.1016/j.jchromb.2020.122453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/29/2022]
Abstract
Shotgun proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed, comparing FASP-GPF, SDS-PAGE and FASP-HpH using a Q Exactive Orbitrap mass spectrometer. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a substantial increase in protein identifications, and an even greater increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dylan H Multari
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
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12
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Wang B, Hao J, Pan N, Wang Z, Chen Y, Wan C. Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell. J Proteomics 2020; 230:103965. [PMID: 32891891 DOI: 10.1016/j.jprot.2020.103965] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/25/2020] [Accepted: 08/31/2020] [Indexed: 02/05/2023]
Abstract
The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and characterize SEPs in Hep3B cell line, we developed an optimized peptidomic assay by combining different peptide extraction and separation methods. The organic solvent precipitation method in peptidomic showed promotion in the enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high-quality MS/MS spectra. Furthermore, different strategies exhibited good complementarity in improving the total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Results in this work provide robust evidence to date that the human proteome is more complicated than previously appreciated, and this will be a benefit to discoveries of proteins without function annotation. SIGNIFICANCE: In this work, methods were optimized to identify SEPs in Hep3B. The organic solvent precipitation presents promotion in enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high quality MS/MS spectra. Different strategies exhibited good complementarity in improving total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Furthermore, 22 SEPs generated from the uORF may has potential effect in translation control, and 149 newly identified SEPs have known functional domains or cross-species conservation. Results in this work present robust evidence for the coding potential of the ignored region of human genomes and may provide additional insights into tumor biology.
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Affiliation(s)
- Bing Wang
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Junhui Hao
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Ni Pan
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Zhiwei Wang
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Yinxuan Chen
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China
| | - Cuihong Wan
- Hubei Key Lab of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, No. 152 Luoyu Road, Wuhan 430079, PR China.
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13
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Marchat LA, Hernández-de la Cruz ON, Ramírez-Moreno E, Silva-Cázares MB, López-Camarillo C. Proteomics approaches to understand cell biology and virulence of Entamoeba histolytica protozoan parasite. J Proteomics 2020; 226:103897. [PMID: 32652218 DOI: 10.1016/j.jprot.2020.103897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/09/2020] [Accepted: 07/06/2020] [Indexed: 11/19/2022]
Abstract
Entamoeba histolytica is the primitive eukaryotic parasite responsible of human amoebiasis, a disease characterized by bloody intestinal diarrhea and invasive extraintestinal illness. The knowledge of the complete genome sequence of virulent E. histolytica and related non-pathogenic species allowed the development of novel genome-wide methodological approaches including protein expression profiling and cellular proteomics in the so called post-genomic era. Proteomics studies have greatly increased our understanding of the cell biology of this ancient parasite. This review summarizes the current works concerning proteomics studies on cell biology, life cycle, virulence and pathogenesis, novel therapies, and protein expression regulation mechanisms in E. histolytica parasite. Also, we discuss the use of proteomics data for the development of novel therapies, the identification of potential disease biomarkers and differential diagnosis between species. SIGNIFICANCE: Entamoeba histolytica is the unicellular protozoan parasite responsible of human amoebiasis, a serious disease with worldwide distribution characterized by bloody intestinal diarrhea and invasive extraintestinal illness including peritonitis and liver, pulmonary and brain abscesses. The post-genomic era allowed the development of proteomic studies including protein expression profiling and cellular proteomics. These proteomics studies have greatly increased our understanding on cell biology, life cycle (cyst-trophozoite conversion), virulence, pathogenesis, novel therapies, and protein expression regulation mechanisms in E. histolytica. Importantly, proteomics has revealed the identity of proteins related to novel therapies, and the identification of potential disease biomarkers and proteins with use in diagnosis between species. Hopefully in the coming years, and through the use of more sophisticated omics tools, including deep proteomics, a more complete set of proteins involved in the aforementioned cellular processes can be obtained to understand the biology of this ancient eukaryote.
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Affiliation(s)
- Laurence A Marchat
- Programa en Biomedicina Molecular y Red de Biotecnología, ENMH-Instituto Politécnico Nacional, CDMX, México.
| | | | - Esther Ramírez-Moreno
- Programa en Biomedicina Molecular y Red de Biotecnología, ENMH-Instituto Politécnico Nacional, CDMX, México
| | - Macrina B Silva-Cázares
- Doctorado Institucional en Ingeniería y Ciencias de Materiales, Coordinación Académica Región Altiplano, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, CDMX, México.
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14
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Anderson J, Phelan MM, Rubio-Martinez LM, Fitzgerald MM, Jones SW, Clegg PD, Peffers MJ. Optimization of Synovial Fluid Collection and Processing for NMR Metabolomics and LC-MS/MS Proteomics. J Proteome Res 2020; 19:2585-2597. [PMID: 32227958 PMCID: PMC7341532 DOI: 10.1021/acs.jproteome.0c00035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Synovial fluid (SF) is of great interest for the investigation of orthopedic pathologies, as it is in close proximity to various tissues that are primarily altered during these disease processes and can be collected using minimally invasive protocols. Multi-"omic" approaches are commonplace, although little consideration is often given for multiple analysis techniques at sample collection. Nuclear magnetic resonance (NMR) metabolomics and liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics are two complementary techniques particularly suited to the study of SF. However, currently there are no agreed upon standard protocols that are published for SF collection and processing for use with NMR metabolomic analysis. Furthermore, the large protein concentration dynamic range present within SF can mask the detection of lower abundance proteins in proteomics. While combinational ligand libraries (ProteoMiner columns) have been developed to reduce this dynamic range, their reproducibility when used in conjunction with SF, or on-bead protein digestion protocols, has yet to be investigated. Here we employ optimized protocols for the collection, processing, and storage of SF for NMR metabolite analysis and LC-MS/MS proteome analysis, including a Lys-C endopeptidase digestion step prior to tryptic digestion, which increased the number of protein identifications and improved reproducibility for on-bead ProteoMiner digestion.
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Affiliation(s)
- James
R. Anderson
- Institute
of Ageing and Chronic Disease, University
of Liverpool, Liverpool L69 3BX, U.K.
| | - Marie M. Phelan
- Institute
of Integrative Biology, University of Liverpool, Liverpool L69 3BX, U.K.,HLS
Technology Directorate, University of Liverpool, Liverpool L69 3BX, U.K.
| | - Luis M. Rubio-Martinez
- Institute
of Ageing and Chronic Disease, University
of Liverpool, Liverpool L69 3BX, U.K.,Institute
of Veterinary Science, University of Liverpool, Leahurst Campus, Neston CH64 7TE, U.K.
| | - Matthew M. Fitzgerald
- Institute
of Veterinary Science, University of Liverpool, Leahurst Campus, Neston CH64 7TE, U.K.
| | - Simon W. Jones
- Institute
of Inflammation and Ageing, University of
Birmingham, Birmingham B15 2TT, U.K.
| | - Peter D. Clegg
- Institute
of Ageing and Chronic Disease, University
of Liverpool, Liverpool L69 3BX, U.K.
| | - Mandy J. Peffers
- Institute
of Ageing and Chronic Disease, University
of Liverpool, Liverpool L69 3BX, U.K.,. Tel: 07872692102
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15
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Bousalis D, Lacko CS, Hlavac N, Alkassis F, Wachs RA, Mobini S, Schmidt CE, Kasahara H. Extracellular Matrix Disparities in an Nkx2-5 Mutant Mouse Model of Congenital Heart Disease. Front Cardiovasc Med 2020; 7:93. [PMID: 32548129 PMCID: PMC7272573 DOI: 10.3389/fcvm.2020.00093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 12/19/2022] Open
Abstract
Congenital heart disease (CHD) affects almost one percent of all live births. Despite diagnostic and surgical reparative advances, the causes and mechanisms of CHD are still primarily unknown. The extracellular matrix plays a large role in cell communication, function, and differentiation, and therefore likely plays a role in disease development and pathophysiology. Cell adhesion and gap junction proteins, such as integrins and connexins, are also essential to cellular communication and behavior, and could interact directly (integrins) or indirectly (connexins) with the extracellular matrix. In this work, we explore disparities in the expression and spatial patterning of extracellular matrix, adhesion, and gap junction proteins between wild type and Nkx2-5 +/R52G mutant mice. Decellularization and proteomic analysis, Western blotting, histology, immunostaining, and mechanical assessment of embryonic and neonatal wild type and Nkx2-5 mutant mouse hearts were performed. An increased abundance of collagen IV, fibronectin, and integrin β-1 was found in Nkx2-5 mutant neonatal mouse hearts, as well as increased expression of connexin 43 in embryonic mutant hearts. Furthermore, a ventricular noncompaction phenotype was observed in both embryonic and neonatal mutant hearts, as well as spatial disorganization of ECM proteins collagen IV and laminin in mutant hearts. Characterizing such properties in a mutant mouse model provides valuable information that can be applied to better understanding the mechanisms of congenital heart disease.
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Affiliation(s)
- Deanna Bousalis
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Christopher S Lacko
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Nora Hlavac
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Fariz Alkassis
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, United States
| | - Rebecca A Wachs
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Sahba Mobini
- Instituto de Micro y Nanotecnología, IMN-CNM, CSIC (CEI UAM+CSIC), Madrid, Spain.,Centro de Biología Molecular Severo Ochoa (CBMSO, UAM-CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Christine E Schmidt
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States
| | - Hideko Kasahara
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL, United States
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16
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Boschetti E, Righetti PG. Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods. Methods Mol Biol 2020; 2139:381-404. [PMID: 32462601 DOI: 10.1007/978-1-0716-0528-8_28] [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] [Indexed: 06/11/2023]
Abstract
The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries. This methodology, allowing for an enhancement of low-abundance proteins, has been extensively applied with the advantage of deciphering the proteome composition of various plant organs. This general methodology is here described extensively along with a number of possible variations. Specific guidelines are suggested to cover peculiar situations or to comply with other associated analytical methods.
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17
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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18
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Tomin T, Schittmayer M, Honeder S, Heininger C, Birner-Gruenberger R. Irreversible oxidative post-translational modifications in heart disease. Expert Rev Proteomics 2019; 16:681-693. [PMID: 31361162 PMCID: PMC6816499 DOI: 10.1080/14789450.2019.1645602] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Development of specific biomarkers aiding early diagnosis of heart failure is an ongoing challenge. Biomarkers commonly used in clinical routine usually act as readouts of an already existing acute condition rather than disease initiation. Functional decline of cardiac muscle is greatly aggravated by increased oxidative stress and damage of proteins. Oxidative post-translational modifications occur already at early stages of tissue damage and are thus regarded as potential up-coming disease markers. Areas covered: Clinical practice regarding commonly used biomarkers for heart disease is briefly summarized. The types of oxidative post-translational modification in cardiac pathologies are discussed with a special focus on available quantitative techniques and characteristics of individual modifications with regard to their stability and analytical accessibility. As irreversible oxidative modifications trigger protein degradation pathways or cause protein aggregation, both influencing biomarker abundance, a chapter is dedicated to their regulation in the heart.
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Affiliation(s)
- Tamara Tomin
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
| | - Matthias Schittmayer
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
| | - Sophie Honeder
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria
| | - Christoph Heininger
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria
| | - Ruth Birner-Gruenberger
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
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19
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Backus KM, Cao J, Maddox SM. Opportunities and challenges for the development of covalent chemical immunomodulators. Bioorg Med Chem 2019; 27:3421-3439. [PMID: 31204229 DOI: 10.1016/j.bmc.2019.05.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/24/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
Abstract
Compounds that react irreversibly with cysteines have reemerged as potent and selective tools for altering protein function, serving as chemical probes and even clinically approved drugs. The exquisite sensitivity of human immune cell signaling pathways to oxidative stress indicates the likely, yet still underexploited, general utility of covalent probes for selective chemical immunomodulation. Here, we provide an overview of immunomodulatory cysteines, including identification of electrophilic compounds available to label these residues. We focus our discussion on three protein classes essential for cell signaling, which span the 'druggability' spectrum from amenable to chemical probes (kinases), somewhat druggable (proteases), to inaccessible (phosphatases). Using existing inhibitors as a guide, we identify general strategies to guide the development of covalent probes for selected undruggable classes of proteins and propose the application of such compounds to alter immune cell functions.
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Affiliation(s)
- Keriann M Backus
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA.
| | - Jian Cao
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA
| | - Sean M Maddox
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA
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20
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Adhikari S, Sharma S, Ahn SB, Baker MS. In Silico Peptide Repertoire of Human Olfactory Receptor Proteomes on High-Stringency Mass Spectrometry. J Proteome Res 2019; 18:4117-4123. [PMID: 31046287 DOI: 10.1021/acs.jproteome.8b00494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Human olfactory receptors (ORs) are seven-pass transmembrane G-protein coupled receptors (GPCR) involved in smell perception and many other signaling pathways. They are primarily expressed in the olfactory epithelium and ectopically expressed in several other organs and tissues. neXtProt contains 4 PE1 (protein existence 1, evidenced at the protein level) ORs, determined on the basis of either protein interaction data (i.e., OR1D4 and OR2AG1) or convincing genetic, haplotype, or biochemical data (i.e., OR1D2 and OR2J3). Not a single OR currently qualifies for neXtProt PE1 status based on mass spectrometry (MS) evidence. Many reasons for this absence of MS-based identification have been proposed, including (i) confined or spatiotemporal or developmental expression, (ii) low copy number, (iii) OR repertoire gene silencing, and (iv) limited tissue availability. OR transmembrane domains (TMDs) inherently limit MS identification because the hydrophobic nature restricts the access of trypsin to potential cleavage sites. Equally, the extremely low frequency or lack of accessible arginine and lysine residues in TMDs renders trypsin cleavage ineffective. Here, we demonstrate an analytical approach specifically focused on the hydrophilic (trypsin-accessible) domains of ORs [i.e., with all transmembrane segments and anchored peptides excluded). We predicted the ability of OR soluble (hydrophilic) domains to yield 2 or more >9 amino acids (aa) length unique mapping (unique to a protein only), non-nested (peptides with varying length at the N or C terminal but containing the same core sequence), leucine/isoleucine (I/L) switch examined (I and L have same mass and cannot be distinguished by MS) tryptic peptides. Our analysis showed that ∼58% of the human OR proteome could potentially generate tryptic peptides that satisfy current the Human Proteome Project data interpretation guidelines (version 2.1) when no missed cleavages are allowed and increases to ∼78% when one missed cleavage is allowed. The utilization of current biological data (adjuvant genomics, expression profile, transcriptomics, epigenome silencing data, etc.) and the adoption of a non-conventional proteomics approach (e.g., Confetti multiprotease digestion, CNBr cleavage of TMDs, and more-extreme chromatographic and MS methods) could aid in the detection of the remaining ORs.
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Affiliation(s)
- Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Samridhi Sharma
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia
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21
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Scheidler CM, Kick LM, Schneider S. Ribosomal Peptides and Small Proteins on the Rise. Chembiochem 2019; 20:1479-1486. [PMID: 30648812 DOI: 10.1002/cbic.201800715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 11/05/2022]
Abstract
Genetically encoded and ribosomally synthesised peptides and small proteins act as important regulators in fundamental cellular processes, including gene expression, development, signalling and metabolism. Moreover, they also play a crucial role in eukaryotic and prokaryotic defence against microorganisms. Extremely diverse in size and structure, they are often subject to extensive post-translational modification. Recent technological advances are now allowing the analysis of the whole cellular transcriptome and proteome, revealing the presence of hundreds of long-overlooked alternative and short open reading frames (short ORFs, or sORFs) in mRNA and supposedly noncoding RNAs. However, in many instances the biological roles of their translational products remain to be elucidated. Here we provide an overview on the intriguing structural and functional diversity of ribosomally synthesised peptides and newly discovered peptides and small proteins.
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Affiliation(s)
- Christopher M Scheidler
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Leonhard M Kick
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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22
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Peffers MJ, Smagul A, Anderson JR. Proteomic analysis of synovial fluid: current and potential uses to improve clinical outcomes. Expert Rev Proteomics 2019; 16:287-302. [PMID: 30793992 DOI: 10.1080/14789450.2019.1578214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Synovial fluid (SF) is in close proximity to tissues which are primarily altered during articular disease and has significant potential to better understand the underlying disease pathogeneses of articular pathologies and biomarker discovery. Although development of mass spectrometry-based methods has allowed faster and higher sensitivity techniques, interrogation of the SF proteome has been hindered by its large protein concentration dynamic range, impeding quantification of lower abundant proteins. Areas covered: Recent advances have developed methodologies to reduce the large protein concentration dynamic range of SF and subsequently allow deeper exploration of the SF proteome. This review concentrates on methods to overcome biofluid complexity, mass spectrometry proteomics methodologies, extracellular vesicles proteomics and the application of advances within the field in clinical disease, including osteoarthritis, rheumatoid arthritis, spondyloarthritis and juvenile arthritis. A narrative review was conducted with articles searched using PubMed, 1991-2018. Expert opinion: The SF proteomics field faces various challenges, including the requirement for rigorous and standardised methods of sample collection/storage, the sensitivity and specificity of proteomic assays, techniques to combat the large protein concentration dynamic range and comprehensive data analysis to reduce falsely identified markers. Additionally, there are challenges in developing multi 'omic' integration techniques, with computational integration enhancing analysis.
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Affiliation(s)
- Mandy Jayne Peffers
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - Aibek Smagul
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
| | - James Ross Anderson
- a Comparative Musculoskeletal Biology, Institute of Ageing and Chronic Disease , University of Liverpool , Liverpool , UK
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23
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Harpole M, Davis J, Espina V. Current state of the art for enhancing urine biomarker discovery. Expert Rev Proteomics 2017; 13:609-26. [PMID: 27232439 DOI: 10.1080/14789450.2016.1190651] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Urine is a highly desirable biospecimen for biomarker analysis because it can be collected recurrently by non-invasive techniques, in relatively large volumes. Urine contains cellular elements, biochemicals, and proteins derived from glomerular filtration of plasma, renal tubule excretion, and urogenital tract secretions that reflect, at a given time point, an individual's metabolic and pathophysiologic state. AREAS COVERED High-resolution mass spectrometry, coupled with state of the art fractionation systems are revealing the plethora of diagnostic/prognostic proteomic information existing within urinary exosomes, glycoproteins, and proteins. Affinity capture pre-processing techniques such as combinatorial peptide ligand libraries and biomarker harvesting hydrogel nanoparticles are enabling measurement/identification of previously undetectable urinary proteins. Expert commentary: Future challenges in the urinary proteomics field include a) defining either single or multiple, universally applicable data normalization methods for comparing results within and between individual patients/data sets, and b) defining expected urinary protein levels in healthy individuals.
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Affiliation(s)
- Michael Harpole
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin Davis
- b Department of Chemistry/Biochemistry , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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24
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Boschetti E, D'Amato A, Candiano G, Righetti PG. Protein biomarkers for early detection of diseases: The decisive contribution of combinatorial peptide ligand libraries. J Proteomics 2017; 188:1-14. [PMID: 28882677 DOI: 10.1016/j.jprot.2017.08.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/09/2017] [Accepted: 08/13/2017] [Indexed: 12/31/2022]
Abstract
The present review deals with biomarker discovery, especially in regard to sample treatment via combinatorial peptide ligand libraries, perhaps the only technique at present allowing deep exploration of biological fluids and tissue extracts in search for low- to very-low-abundance proteins, which could possibly mark the onset of most pathologies. Early-stage biomarkers, in fact, might be the only way to detect the beginning of most diseases thus permitting proper intervention and care. The following cancers are reviewed, with lists of potential biomarkers suggested in various reports: hepatocellular carcinoma, ovarian cancer, breast cancer and pancreatic cancer, together with some other interesting applications. Although panels of proteins have been presented, with robust evidence, as potential early-stage biomarkers in these different pathologies, their approval by FDA as novel biomarkers in routine clinical chemistry settings would require plenty of additional work and efforts from the pharma industry. The science environment in universities could simply not afford such heavy monetary investments. SIGNIFICANCE After more than 16years of search for novel biomarkers, to be used in a clinical chemistry set-up, via proteomic analysis (mostly in biological fluids) it was felt a critical review was due. In the present report, though, only papers reporting biomarker discovery via combinatorial peptide ligand libraries are listed and assessed, since this methodology seems to be the most advanced one for digging in depth into low-to very-low-abundance proteins, which might represent important biomarkers for the onset of pathologies. In particular, a large survey has been made for the following diseases, since they appear to have a large incidence on human population and/or represent fatal diseases: ovarian cancer, breast cancer, pancreatic cancer and hepatocellular carcinoma.
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Affiliation(s)
| | - Alfonsina D'Amato
- Quadram Institute of Bioscience, Norwich Research Park, NR4 7UA Norwich, UK
| | - Giovanni Candiano
- Nephrology, Dialysis, Transplantation Unit and Laboratory on Pathophysiology of Uremia, Istituto Giannina Gaslini, Genoa, Italy
| | - Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Via Mancinelli 7, Milano 20131, Italy.
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IEF peptide fractionation method combined to shotgun proteomics enhances the exploration of rice milk proteome. Anal Biochem 2017; 537:72-77. [PMID: 28864145 DOI: 10.1016/j.ab.2017.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/27/2017] [Indexed: 01/03/2023]
Abstract
We conducted a proteomics study in order to detect the proteomic method which provides the most complete characterization of the proteins of rice milk. In particular, we compared the results obtained from LC-MS/MS after protein precipitation with acetone or TCA, as well as the results obtained from LC-MS/MS after protein prefractionation based on SDS-PAGE (GeLC-MS/MS) or ProteoMiner™ technology (ProteoMiner-LC-MS/MS), and after peptide prefractionation based on IEF (pIEF-LC-MS/MS). A total of 158 protein species have been detect in rice milk. The physical-chemical analysis and classification of the identified proteins were also reported. In particular, we showed that pIEF-LC-MS/MS method led to a significant increase in the proteome coverage, allowing the identification of a total of 96 proteins of milk rice. This study demonstrates the utility of a prefractionation step based on pIEF before the shotgun proteomic analysis and offers an in-depth insight into the rice milk proteome.
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Limonier F, Van Steendam K, Waeterloos G, Brusselmans K, Sneyers M, Deforce D. An application of mass spectrometry for quality control of biologicals: Highly sensitive profiling of plasma residuals in human plasma-derived immunoglobulin. J Proteomics 2017; 152:312-320. [DOI: 10.1016/j.jprot.2016.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 01/02/2023]
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27
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Ye Z, Sangireddy S, Okekeogbu I, Zhou S, Yu CL, Hui D, Howe KJ, Fish T, Thannhauser TW. Drought-Induced Leaf Proteome Changes in Switchgrass Seedlings. Int J Mol Sci 2016; 17:ijms17081251. [PMID: 27490537 PMCID: PMC5000649 DOI: 10.3390/ijms17081251] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/24/2016] [Accepted: 07/27/2016] [Indexed: 11/16/2022] Open
Abstract
Switchgrass (Panicum virgatum) is a perennial crop producing deep roots and thus highly tolerant to soil water deficit conditions. However, seedling establishment in the field is very susceptible to prolonged and periodic drought stress. In this study, a “sandwich” system simulating a gradual water deletion process was developed. Switchgrass seedlings were subjected to a 20-day gradual drought treatment process when soil water tension was increased to 0.05 MPa (moderate drought stress) and leaf physiological properties had expressed significant alteration. Drought-induced changes in leaf proteomes were identified using the isobaric tags for relative and absolute quantitation (iTRAQ) labeling method followed by nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) analysis. Additionally, total leaf proteins were processed using a combinatorial library of peptide ligands to enrich for lower abundance proteins. Both total proteins and those enriched samples were analyzed to increase the coverage of the quantitative proteomics analysis. A total of 7006 leaf proteins were identified, and 257 (4% of the leaf proteome) expressed a significant difference (p < 0.05, fold change <0.6 or >1.7) from the non-treated control to drought-treated conditions. These proteins are involved in the regulation of transcription and translation, cell division, cell wall modification, phyto-hormone metabolism and signaling transduction pathways, and metabolic pathways of carbohydrates, amino acids, and fatty acids. A scheme of abscisic acid (ABA)-biosynthesis and ABA responsive signal transduction pathway was reconstructed using these drought-induced significant proteins, showing systemic regulation at protein level to deploy the respective mechanism. Results from this study, in addition to revealing molecular responses to drought stress, provide a large number of proteins (candidate genes) that can be employed to improve switchgrass seedling growth and establishment under soil drought conditions (Data are available via ProteomeXchange with identifier PXD004675).
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Affiliation(s)
- Zhujia Ye
- Department of Agricultural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Sasikiran Sangireddy
- Department of Agricultural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Ikenna Okekeogbu
- Department of Agricultural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Suping Zhou
- Department of Agricultural Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Chih-Li Yu
- Department of Biological Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA.
| | - Kevin J Howe
- Functional & Comparative Proteomics Center, USDA-ARS, Cornell University, Ithaca, NY 14853, USA.
| | - Tara Fish
- Functional & Comparative Proteomics Center, USDA-ARS, Cornell University, Ithaca, NY 14853, USA.
| | - Theodore W Thannhauser
- Functional & Comparative Proteomics Center, USDA-ARS, Cornell University, Ithaca, NY 14853, USA.
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28
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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29
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Wewer Albrechtsen NJ, Hornburg D, Albrechtsen R, Svendsen B, Toräng S, Jepsen SL, Kuhre RE, Hansen M, Janus C, Floyd A, Lund A, Vilsbøll T, Knop FK, Vestergaard H, Deacon CF, Meissner F, Mann M, Holst JJ, Hartmann B. Oxyntomodulin Identified as a Marker of Type 2 Diabetes and Gastric Bypass Surgery by Mass-spectrometry Based Profiling of Human Plasma. EBioMedicine 2016; 7:112-20. [PMID: 27322465 PMCID: PMC4909640 DOI: 10.1016/j.ebiom.2016.03.034] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/02/2016] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
Low-abundance regulatory peptides, including metabolically important gut hormones, have shown promising therapeutic potential. Here, we present a streamlined mass spectrometry-based platform for identifying and characterizing low-abundance regulatory peptides in humans. We demonstrate the clinical applicability of this platform by studying a hitherto neglected glucose- and appetite-regulating gut hormone, namely, oxyntomodulin. Our results show that the secretion of oxyntomodulin in patients with type 2 diabetes is significantly impaired, and that its level is increased by more than 10-fold after gastric bypass surgery. Furthermore, we report that oxyntomodulin is co-distributed and co-secreted with the insulin-stimulating and appetite-regulating gut hormone glucagon-like peptide-1 (GLP-1), is inactivated by the same protease (dipeptidyl peptidase-4) as GLP-1 and acts through its receptor. Thus, oxyntomodulin may participate with GLP-1 in the regulation of glucose metabolism and appetite in humans. In conclusion, this mass spectrometry-based platform is a powerful resource for identifying and characterizing metabolically active low-abundance peptides.
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Affiliation(s)
- Nicolai J Wewer Albrechtsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Hornburg
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Reidar Albrechtsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Sciences and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Berit Svendsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Signe Toräng
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara L Jepsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune E Kuhre
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie Hansen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Janus
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Floyd
- Department of Surgery, Division of Bariatric Surgery, Køge Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Asger Lund
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Tina Vilsbøll
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Filip K Knop
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carolyn F Deacon
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Felix Meissner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Bolette Hartmann
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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30
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Weng Y, Sui Z, Shan Y, Jiang H, Zhou Y, Zhu X, Liang Z, Zhang L, Zhang Y. In-Depth Proteomic Quantification of Cell Secretome in Serum-Containing Conditioned Medium. Anal Chem 2016; 88:4971-8. [DOI: 10.1021/acs.analchem.6b00910] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yejing Weng
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yichu Shan
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hao Jiang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Zhou
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xudong Zhu
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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31
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Prefractionation methods for individual adult fruit fly hemolymph proteomic analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1015-1016:74-81. [DOI: 10.1016/j.jchromb.2016.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 02/06/2016] [Accepted: 02/08/2016] [Indexed: 11/23/2022]
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32
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Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
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Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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33
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Mining the human plasma proteome with three-dimensional strategies by high-resolution Quadrupole Orbitrap Mass Spectrometry. Anal Chim Acta 2015; 904:65-75. [PMID: 26724764 DOI: 10.1016/j.aca.2015.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
Human plasma is a readily available clinical sample that reflects the status of the body in normal physiological and disease states. Although the wide dynamic range and immense complexity of plasma proteins are obstacles, comprehensive proteomic analysis of human plasma is necessary for biomarker discovery and further verification. Various methods such as immunodepletion, protein equalization and hyper fractionation have been applied to reduce the influence of high-abundance proteins (HAPs) and to reduce the high level of complexity. However, the depth at which the human plasma proteome has been explored in a relatively short time frame has been limited, which impedes the transfer of proteomic techniques to clinical research. Development of an optimal strategy is expected to improve the efficiency of human plasma proteome profiling. Here, five three-dimensional strategies combining HAP depletion (the 1st dimension) and protein fractionation (the 2nd dimension), followed by LC-MS/MS analysis (the 3rd dimension) were developed and compared for human plasma proteome profiling. Pros and cons of the five strategies are discussed for two issues: HAP depletion and complexity reduction. Strategies A and B used proteome equalization and tandem Seppro IgY14 immunodepletion, respectively, as the first dimension. Proteome equalization (strategy A) was biased toward the enrichment of basic and low-molecular weight proteins and had limited ability to enrich low-abundance proteins. By tandem removal of HAPs (strategy B), the efficiency of HAP depletion was significantly increased, whereas more off-target proteins were subtracted simultaneously. In the comparison of complexity reduction, strategy D involved a deglycosylation step before high-pH RPLC separation. However, the increase in sequence coverage did not increase the protein number as expected. Strategy E introduced SDS-PAGE separation of proteins, and the results showed oversampling of HAPs and identification of fewer proteins. Strategy C combined single Seppro IgY14 immunodepletion, high-pH RPLC fractionation and LC-MS/MS analysis. It generated the largest dataset, containing 1544 plasma protein groups and 258 newly identified proteins in a 30-h-machine-time analysis, making it the optimum three-dimensional strategy in our study. Further analysis of the integrated data from the five strategies showed identical distribution patterns in terms of sequence features and GO functional analysis with the 1929-plasma-protein dataset, further supporting the reliability of our plasma protein identifications. The characterization of 20 cytokines in the concentration range from sub-nanograms/milliliter to micrograms/milliliter demonstrated the sensitivity of the current strategies.
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34
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Undin T, Lind SB, Dahlin AP. MS for investigation of time-dependent protein adsorption on surfaces in complex biological samples. Future Sci OA 2015; 1:FSO32. [PMID: 28031905 PMCID: PMC5137957 DOI: 10.4155/fso.15.32] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIM This study aims at developing a nondestructive way for investigating protein adsorption on surfaces such as biomaterials using mass spectrometry. METHODS Ventricular cerebrospinal fluid in contact with poly carbonate membranes were used as adsorption templates and on-surface enzymatic digestion was applied to desorb proteins and cleave them into peptides. Mass spectrometric analysis provided both protein identification and determination of protein specific adsorption behavior. RESULTS In general, the adsorption increased with incubation time but also protein-specific time-resolved adsorption patterns from the complex protein solution were discovered. CONCLUSION The method developed is a promising tool for the characterization of biofouling, which sometimes causes rejection and encapsulation of implants and can be used as complement to other surface analytical techniques.
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Affiliation(s)
- Torgny Undin
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, PO Box 599, SE-751 24 Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, PO Box 599, SE-751 24 Uppsala, Sweden
| | - Andreas P Dahlin
- Department of Engineering Sciences, Uppsala University, PO Box 534, SE-751 21 Uppsala, Sweden
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35
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Melani RD, Araujo GD, Carvalho PC, Goto L, Nogueira FC, Junqueira M, Domont GB. Seeing beyond the tip of the iceberg: A deep analysis of the venome of the Brazilian Rattlesnake, Crotalus durissus terrificus. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Fernandez-Irigoyen J, Labarga A, Zabaleta A, de Morentin XM, Perez-Valderrama E, Zelaya MV, Santamaria E. Toward defining the anatomo-proteomic puzzle of the human brain: An integrative analysis. Proteomics Clin Appl 2015; 9:796-807. [PMID: 25418211 DOI: 10.1002/prca.201400127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/17/2014] [Accepted: 11/18/2014] [Indexed: 01/18/2023]
Abstract
The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections that, in turn, define ∼900 neuroanatomical subdivisions in the adult brain (Hawrylycz et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revealed specific regional transcriptional signatures that are regulated in a spatiotemporal manner, increasing the complexity of the structural and molecular organization of this organ (Kang et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478, 483-489). During the last decade, neuroproteomics has emerged as a powerful approach to profile neural proteomes using shotgun-based MS, providing complementary information about protein content and function at a global level. Here, we revise recent proteome profiling studies performed in human brain, with special emphasis on proteome mapping of anatomical macrostructures, specific subcellular compartments, and cerebrospinal fluid. Moreover, we have performed an integrative functional analysis of the protein compilation derived from these large-scale human brain proteomic studies in order to obtain a comprehensive view of human brain biology. Finally, we also discuss the potential contribution of our meta-analysis to the Chromosome-centric Human Proteome Project initiative.
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Affiliation(s)
- Joaquín Fernandez-Irigoyen
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Alberto Labarga
- Bioinformatics Unit, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Aintzane Zabaleta
- Biofunctional Nanomaterials Laboratory, CIC Biomagune, San Sebastian, Spain
| | - Xabier Martínez de Morentin
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Estela Perez-Valderrama
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | | | - Enrique Santamaria
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
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37
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Zeng Q, Smith DJ, Shippy SA. Proteomic analysis of individual fruit fly hemolymph. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 981-982:33-9. [DOI: 10.1016/j.jchromb.2014.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 11/12/2014] [Accepted: 11/25/2014] [Indexed: 11/16/2022]
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38
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Boschetti E, Righetti PG. Mixed-bed affinity chromatography: principles and methods. Methods Mol Biol 2015; 1286:131-158. [PMID: 25749952 DOI: 10.1007/978-1-4939-2447-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mixed-bed chromatography is far from being a well-established technology within the panoply of bioseparation tools. Composed of an assembly of distinct sorbents that are mixed in a single bed, they have been mostly developed in the last decade for the reduction of dynamic concentration range where they allowed discovering many low-copy proteins within very complex proteomes. Other interesting preparative applications of mixed-bed chromatography have since been developed. In this chapter the basic concepts first and then detailed application recipes are described for (1) the reduction of protein dynamic concentration range, (2) the removal of impurity traces at the last stage of a biopurification process, and (3) the selection and use of sorbents as mixed bed in protein purification.
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Affiliation(s)
- Egisto Boschetti
- JAM-Conseil, 9-11 rue Boutard, 92200, Neuilly sur Seine, France,
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39
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Righetti PG, Boschetti E. Sample treatment methods involving combinatorial peptide ligand libraries for improved proteomes analyses. Methods Mol Biol 2015; 1243:55-82. [PMID: 25384740 DOI: 10.1007/978-1-4939-1872-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
If used in an optimized manner, the technology of combinatorial peptide solid-phase libraries can easily improve the analytical determinations of proteomes by several factors. The discovery of novel species and of early stage biomarkers becomes thus reachable with a simple sample treatment. This report describes the most important point to consider (overloading and full recovery) along with a minimum scientific background and gives then detailed recipes to laboratory technicians. Orientations for optional routes are also given according to the objective of the experimental investigations. This covers different approaches to capture proteins of very low abundance. Total protein harvestings to prevent partial losses are also described such as single exhaustive desorption and fractionated elutions for more detailed analyses. Documented results are also reported demonstrating the capability of the technology well beyond what is the common assumption.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, Milan, 20131, Italy
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40
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Righetti PG, Candiano G, Citterio A, Boschetti E. Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics. Anal Chem 2014; 87:293-305. [DOI: 10.1021/ac502171b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Pier Giorgio Righetti
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
| | - Giovanni Candiano
- Laboratory on Pathophysiology of Uremia
and Department of Nephrology, Istituto Giannina Gaslini, Genova, Italy
| | - Attilio Citterio
- Politecnico di Milano, Department of Chemistry, Materials and Chemical Engineering “Giulio
Natta”, Via Mancinelli
7, Milano 20131, Italy
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41
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Barkla BJ, Vera-Estrella R, Pantoja O. Progress and challenges for abiotic stress proteomics of crop plants. Proteomics 2014; 13:1801-15. [PMID: 23512887 DOI: 10.1002/pmic.201200401] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 12/12/2022]
Abstract
Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome.
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Affiliation(s)
- Bronwyn J Barkla
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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Abstract
The question of low-abundance proteins from biological tissues is still a major issue. Technologies have been devised to improve the situation and in the last few years a method based on solid-phase combinatorial peptide ligand libraries has been extensively applied to animal extracts. This method has also been extended to plant extracts taking advantage of findings from previous experience. Detailed methods are described and their pertinence highlighted according to various situations of plant sample origin, size of the sample, and analytical methods intended to be used for protein identifications.
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Park E, Drakakaki G. Proteomics of endosomal compartments from plants case study: isolation of trans-Golgi network vesicles. Methods Mol Biol 2014; 1209:179-187. [PMID: 25117284 DOI: 10.1007/978-1-4939-1420-3_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A detailed understanding of endomembrane processes and their biological roles is vital for a complete picture of plant growth and development; however their highly dynamic nature has complicated comprehensive and rigorous studies so far. Recent pioneering efforts have demonstrated that isolation of vesicles in their native state, paired with a quantitative identification of their cargo, offers a viable and practicable approach for the dissection of endomembrane trafficking pathways. The protocol presented in this chapter describes in detail the isolation of the SYP61 trans-Golgi network vesicles from Arabidopsis. With minor alterations, in a few key parameters, it can be adopted to yield a universal procedure for the broad spectrum of plant vesicles.
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Affiliation(s)
- Eunsook Park
- Department of Plant sciences, University of California Davis, Asmundson Hall, One Shields Avenue, Davis, CA, 95616, USA
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44
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Petriz BA, Franco OL. Application of Cutting-Edge Proteomics Technologies for Elucidating Host–Bacteria Interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:1-24. [DOI: 10.1016/b978-0-12-800453-1.00001-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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45
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Laskay ÜA, Lobas AA, Srzentić K, Gorshkov MV, Tsybin YO. Proteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments. J Proteome Res 2013; 12:5558-69. [DOI: 10.1021/pr400522h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ünige A. Laskay
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 2 av. Forel, 1015 Lausanne, Switzerland
| | - Anna A. Lobas
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskii Prospect 38, Bldg. 2,119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., 141707 Dolgoprudny, Moscow
Region, Russia
| | - Kristina Srzentić
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 2 av. Forel, 1015 Lausanne, Switzerland
| | - Mikhail V. Gorshkov
- Institute
for Energy Problems of Chemical Physics, Russian Academy of Sciences, Leninskii Prospect 38, Bldg. 2,119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., 141707 Dolgoprudny, Moscow
Region, Russia
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 2 av. Forel, 1015 Lausanne, Switzerland
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46
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Optimized sample treatment protocol by solid-phase peptide libraries to enrich for protein traces. Amino Acids 2013; 45:1431-42. [DOI: 10.1007/s00726-013-1596-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/12/2013] [Indexed: 12/11/2022]
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47
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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48
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Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring. J Proteomics 2013; 89:215-26. [DOI: 10.1016/j.jprot.2013.05.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/03/2013] [Accepted: 05/29/2013] [Indexed: 11/18/2022]
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49
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Fasoli E, Colzani M, Aldini G, Citterio A, Righetti PG. Lemon peel and Limoncello liqueur: A proteomic duet. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1484-91. [DOI: 10.1016/j.bbapap.2013.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/23/2022]
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50
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Omasits U, Quebatte M, Stekhoven DJ, Fortes C, Roschitzki B, Robinson MD, Dehio C, Ahrens CH. Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Res 2013; 23:1916-27. [PMID: 23878158 PMCID: PMC3814891 DOI: 10.1101/gr.151035.112] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ∼90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.
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Affiliation(s)
- Ulrich Omasits
- Quantitative Model Organism Proteomics, Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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