1
|
Xu T, Wang Q, Wang Q, Sun L. Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4664-4682. [PMID: 38973469 PMCID: PMC11257149 DOI: 10.1039/d4ay00651h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
Proteoforms are all forms of protein molecules from the same gene because of variations at the DNA, RNA, and protein levels, e.g., alternative splicing and post-translational modifications (PTMs). Delineation of proteins in a proteoform-specific manner is crucial for understanding their biological functions. Mass spectrometry (MS)-intensive top-down proteomics (TDP) is promising for comprehensively characterizing intact proteoforms in complex biological systems. It has achieved substantial progress in technological development, including sample preparation, proteoform separations, MS instrumentation, and bioinformatics tools. In a single TDP study, thousands of proteoforms can be identified and quantified from a cell lysate. It has also been applied to various biomedical research to better our understanding of protein function in regulating cellular processes and to discover novel proteoform biomarkers of diseases for early diagnosis and therapeutic development. This review covers the most recent technological development and biomedical applications of MS-intensive TDP.
Collapse
Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| |
Collapse
|
2
|
Apolipoprotein A-II, a Player in Multiple Processes and Diseases. Biomedicines 2022; 10:biomedicines10071578. [PMID: 35884883 PMCID: PMC9313276 DOI: 10.3390/biomedicines10071578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022] Open
Abstract
Apolipoprotein A-II (apoA-II) is the second most abundant apolipoprotein in high-density lipoprotein (HDL) particles, playing an important role in lipid metabolism. Human and murine apoA-II proteins have dissimilar properties, partially because human apoA-II is dimeric whereas the murine homolog is a monomer, suggesting that the role of apoA-II may be quite different in humans and mice. As a component of HDL, apoA-II influences lipid metabolism, being directly or indirectly involved in vascular diseases. Clinical and epidemiological studies resulted in conflicting findings regarding the proatherogenic or atheroprotective role of apoA-II. Human apoA-II deficiency has little influence on lipoprotein levels with no obvious clinical consequences, while murine apoA-II deficiency causes HDL deficit in mice. In humans, an increased plasma apoA-II concentration causes hypertriglyceridemia and lowers HDL levels. This dyslipidemia leads to glucose intolerance, and the ensuing high blood glucose enhances apoA-II transcription, generating a vicious circle that may cause type 2 diabetes (T2D). ApoA-II is also used as a biomarker in various diseases, such as pancreatic cancer. Herein, we provide a review of the most recent findings regarding the roles of apoA-II and its functions in various physiological processes and disease states, such as cardiovascular disease, cancer, amyloidosis, hepatitis, insulin resistance, obesity, and T2D.
Collapse
|
3
|
Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
Collapse
Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
4
|
The Secretome Deregulations in a Rat Model of Endotoxemic Shock. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6650464. [PMID: 34349874 PMCID: PMC8328724 DOI: 10.1155/2021/6650464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/13/2021] [Indexed: 12/21/2022]
Abstract
Introduction Septic shock is a systemic inflammatory response syndrome associated with organ failures. Earlier clinical diagnosis would be of benefit to a decrease in the mortality rate. However, there is currently a lack of predictive biomarkers. The secretome is the set of proteins secreted by a cell, tissue, or organism at a given time and under certain conditions. The plasma secretome is easily accessible from biological fluids and represents a good opportunity to discover new biomarkers that can be studied with nontargeted “omic” strategies. Aims To identify relevant deregulated proteins (DEP) in the secretome of a rat endotoxemic shock model. Methods Endotoxemic shock was induced in rats by intravenous injection of lipopolysaccharides (LPS, S. enterica typhi, 0.5 mg/kg) and compared to controls (Ringer Lactate, iv). Under isoflurane anesthesia, carotid cannulation allowed mean arterial blood pressure (MAP) and heart rate (HR) monitoring and blood sampling at different time points (T0 and T50 or T0 and T90, with EDTA and protease inhibitor). Samples were prepared for large-scale tandem mass spectrometry (MS-MS) based on a label-free quantification to allow identification of the proteins deregulated upon endotoxemic conditions. A Gene Ontology (GO) analysis defined several clusters of biological processes (BP) in which the DEP are involved. Results Ninety minutes after shock induction, the LPS group presents a reduction in MAP (-45%, p < 0.05) and increased lactate levels (+27.5%, p < 0.05) compared to the control group. Proteomic analyses revealed 10 and 33 DEP in the LPS group, respectively, at 50 and 90 minutes after LPS injection. At these time points, GO-BP showed alterations in pathways involved in oxidative stress response and coagulation. Conclusion This study proposes an approach to identify relevant DEP in septic shock and brings new insights into the understanding of the secretome adaptations upon sepsis.
Collapse
|
5
|
Demus D, Naber A, Dotz V, Jansen BC, Bladergroen MR, Nouta J, Sijbrands EJG, Van Hoek M, Nicolardi S, Wuhrer M. Large-Scale Analysis of Apolipoprotein CIII Glycosylation by Ultrahigh Resolution Mass Spectrometry. Front Chem 2021; 9:678883. [PMID: 34026735 PMCID: PMC8138127 DOI: 10.3389/fchem.2021.678883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 01/10/2023] Open
Abstract
Apolipoprotein-CIII (apo-CIII) is a glycoprotein involved in lipid metabolism and its levels are associated with cardiovascular disease risk. Apo-CIII sialylation is associated with improved plasma triglyceride levels and its glycosylation may have an effect on the clearance of triglyceride-rich lipoproteins by directing these particles to different metabolic pathways. Large-scale sample cohort studies are required to fully elucidate the role of apo-CIII glycosylation in lipid metabolism and associated cardiovascular disease. In this study, we revisited a high-throughput workflow for the analysis of intact apo-CIII by ultrahigh-resolution MALDI FT-ICR MS. The workflow includes a chemical oxidation step to reduce methionine oxidation heterogeneity and spectrum complexity. Sinapinic acid matrix was used to minimize the loss of sialic acids upon MALDI. MassyTools software was used to standardize and automate MS data processing and quality control. This method was applied on 771 plasma samples from individuals without diabetes allowing for an evaluation of the expression levels of apo-CIII glycoforms against a panel of lipid biomarkers demonstrating the validity of the method. Our study supports the hypothesis that triglyceride clearance may be regulated, or at least strongly influenced by apo-CIII sialylation. Interestingly, the association of apo-CIII glycoforms with triglyceride levels was found to be largely independent of body mass index. Due to its precision and throughput, the new workflow will allow studying the role of apo-CIII in the regulation of lipid metabolism in various disease settings.
Collapse
Affiliation(s)
- Daniel Demus
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands.,Ludger Ltd., Culham Science Centre, Abingdon, United Kingdom
| | - Annemieke Naber
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Viktoria Dotz
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Bas C Jansen
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands.,Ludger Ltd., Culham Science Centre, Abingdon, United Kingdom
| | - Marco R Bladergroen
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Jan Nouta
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Eric J G Sijbrands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mandy Van Hoek
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Simone Nicolardi
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, Netherlands
| |
Collapse
|
6
|
Hu Y, Meuret C, Martinez A, Yassine HN, Nedelkov D. Distinct patterns of apolipoprotein C-I, C-II, and C-III isoforms are associated with markers of Alzheimer's disease. J Lipid Res 2020; 62:100014. [PMID: 33518512 PMCID: PMC7859854 DOI: 10.1194/jlr.ra120000919] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Apolipoproteins C-I, C-II, and C-III interact with ApoE to regulate lipoprotein metabolism and contribute to Alzheimer's disease pathophysiology. In plasma, apoC-I and C-II exist as truncated isoforms, while apoC-III exhibits multiple glycoforms. This study aimed to 1) delineate apoC-I, C-II, and C-III isoform profiles in cerebrospinal fluid (CSF) and plasma in a cohort of nondemented older individuals (n = 61), and 2) examine the effect of APOE4 on these isoforms and their correlation with CSF Aβ42, a surrogate of brain amyloid accumulation. The isoforms of the apoCs were immunoaffinity enriched and measured with MALDI-TOF mass spectrometry, revealing a significantly higher percentage of truncated apoC-I and apoC-II in CSF compared with matched plasma, with positive correlation between CSF and plasma. A greater percentage of monosialylated and disialylated apoC-III isoforms was detected in CSF, accompanied by a lower percentage of the two nonsialylated apoC-III isoforms, with significant linear correlations between CSF and plasma. Furthermore, a greater percentage of truncated apoC-I in CSF and apoC-II in plasma and CSF was observed in individuals carrying at least one APOE Ɛ4 allele. Increased apoC-I and apoC-II truncations were associated with lower CSF Aβ42. Finally, monosialylated apoC-III was lower, and disialylated apoC-III greater in the CSF of Ɛ4 carriers. Together, these results reveal distinct patterns of the apoCs isoforms in CSF, implying CSF-specific apoCs processing. These patterns were accentuated in APOE Ɛ4 allele carriers, suggesting an association between APOE4 genotype and Alzheimer's disease pathology with apoCs processing and function in the brain.
Collapse
Affiliation(s)
| | | | - Ashley Martinez
- University of Southern California, Los Angeles, California, USA
| | | | | |
Collapse
|
7
|
Blanchard V, Garçon D, Jaunet C, Chemello K, Billon-Crossouard S, Aguesse A, Garfa A, Famchon G, Torres A, Le May C, Pichelin M, Bigot-Corbel E, Lambert G, Cariou B, Hadjadj S, Krempf M, Bach-Ngohou K, Croyal M. A high-throughput mass spectrometry-based assay for large-scale profiling of circulating human apolipoproteins. J Lipid Res 2020; 61:1128-1139. [PMID: 32404332 DOI: 10.1194/jlr.d120000835] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/08/2020] [Indexed: 12/20/2022] Open
Abstract
Apolipoproteins govern lipoprotein metabolism and are promising biomarkers of metabolic and cardiovascular diseases. Unlike immunoassays, MS enables the quantification and phenotyping of multiple apolipoproteins. Hence, here, we aimed to develop a LC-MS/MS assay that can simultaneously quantitate 18 human apolipoproteins [A-I, A-II, A-IV, A-V, B48, B100, C-I, C-II, C-III, C-IV, D, E, F, H, J, L1, M, and (a)] and determined apoE, apoL1, and apo(a) phenotypes in human plasma and serum samples. The plasma and serum apolipoproteins were trypsin digested through an optimized procedure and peptides were extracted and analyzed by LC-MS/MS. The method was validated according to standard guidelines in samples spiked with known peptide amounts. The LC-MS/MS results were compared with those obtained with other techniques, and reproducibility, dilution effects, and stabilities were also assessed. Peptide markers were successfully selected for targeted apolipoprotein quantification and phenotyping. After optimization, the assay was validated for linearity, lower limits of quantification, accuracy (biases: -14.8% to 12.1%), intra-assay variability [coefficients of variation (CVs): 1.5-14.2%], and inter-assay repeatability (CVs: 4.1-14.3%). Bland-Altman plots indicated no major statistically significant differences between LC-MS/MS and other techniques. The LC-MS/MS results were reproducible over five repeated experiments (CVs: 1.8-13.7%), and we identified marked differences among the plasma and serum samples. The LC-MS/MS assay developed here is rapid, requires only small sampling volumes, and incurs reasonable costs, thus making it amenable for a wide range of studies of apolipoprotein metabolism. We also highlight how this assay can be implemented in laboratories.
Collapse
Affiliation(s)
- Valentin Blanchard
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Réunion Océan Indien (DéTROI), Plateforme CYROI, Saint-Denis de La Réunion, France. mailto:
| | - Damien Garçon
- L'Institut du Thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | | | - Kevin Chemello
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Réunion Océan Indien (DéTROI), Plateforme CYROI, Saint-Denis de La Réunion, France
| | - Stéphanie Billon-Crossouard
- NUN, INRA, CHU Nantes, UMR 1280, PhAN, IMAD, CRNH-O, Nantes, France; CRNH-O Mass Spectrometry Core Facility, Nantes, France
| | - Audrey Aguesse
- NUN, INRA, CHU Nantes, UMR 1280, PhAN, IMAD, CRNH-O, Nantes, France; CRNH-O Mass Spectrometry Core Facility, Nantes, France
| | - Aya Garfa
- CRNH-O Mass Spectrometry Core Facility, Nantes, France
| | | | - Amada Torres
- NUN, INRA, CHU Nantes, UMR 1280, PhAN, IMAD, CRNH-O, Nantes, France
| | - Cédric Le May
- L'Institut du Thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - Matthieu Pichelin
- L'Institut du Thorax, INSERM, CNRS, University of Nantes, CHU Nantes, Nantes, France
| | | | - Gilles Lambert
- Université de La Réunion, INSERM, UMR 1188 Diabète athérothrombose Réunion Océan Indien (DéTROI), Plateforme CYROI, Saint-Denis de La Réunion, France
| | - Bertrand Cariou
- L'Institut du Thorax, INSERM, CNRS, University of Nantes, CHU Nantes, Nantes, France
| | - Samy Hadjadj
- CRNH-O Mass Spectrometry Core Facility, Nantes, France; L'Institut du Thorax, INSERM, CNRS, University of Nantes, CHU Nantes, Nantes, France
| | - Michel Krempf
- NUN, INRA, CHU Nantes, UMR 1280, PhAN, IMAD, CRNH-O, Nantes, France; CRNH-O Mass Spectrometry Core Facility, Nantes, France; ELSAN, Clinique Bretéché, Nantes, France
| | - Kalyane Bach-Ngohou
- Department of Biochemistry, CHU de Nantes, France; INSERM U1235, University of Nantes, Nantes, France
| | - Mikaël Croyal
- NUN, INRA, CHU Nantes, UMR 1280, PhAN, IMAD, CRNH-O, Nantes, France; CRNH-O Mass Spectrometry Core Facility, Nantes, France
| |
Collapse
|
8
|
Poverennaya EV, Kiseleva OI, Ivanov AS, Ponomarenko EA. Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms. BIOCHEMISTRY (MOSCOW) 2020; 85:68-79. [PMID: 32079518 DOI: 10.1134/s000629792001006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a single gene often have different functions, which implies different protein partners. By interacting with each other, proteoforms create a network reflecting the dynamics of cellular processes in an organism. Perturbations of protein-protein interactions change the network topology, which often triggers pathological processes. Studying proteoforms is a relatively new research area in proteomics, and this is why there are comparatively few experimental studies on the interaction of proteoforms. Bioinformatics tools can facilitate such studies by providing valuable complementary information to the experimental data and, in particular, expanding the possibilities of the studies of proteoform interactions.
Collapse
Affiliation(s)
| | - O I Kiseleva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | | |
Collapse
|
9
|
Jacobs-Cachá C, Puig-Gay N, Helm D, Rettel M, Sellarès J, Meseguer A, Savitski MM, Moreso FJ, Soler MJ, Seron D, Lopez-Hellin J. A misprocessed form of Apolipoprotein A-I is specifically associated with recurrent Focal Segmental Glomerulosclerosis. Sci Rep 2020; 10:1159. [PMID: 31980684 PMCID: PMC6981185 DOI: 10.1038/s41598-020-58197-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/10/2020] [Indexed: 12/29/2022] Open
Abstract
Apolipoprotein A-Ib (ApoA-Ib) is a high molecular weight form of Apolipoprotein A-I (ApoA-I) found specifically in the urine of kidney-transplanted patients with recurrent idiopathic focal segmental glomerulosclerosis (FSGS). To determine the nature of the modification present in ApoA-Ib, we sequenced the whole APOA1 gene in ApoA-Ib positive and negative patients, and we also studied the protein primary structure using mass spectrometry. No genetic variations in the APOA1 gene were found in the ApoA-Ib positive patients that could explain the increase in its molecular mass. The mass spectrometry analysis revealed three extra amino acids at the N-Terminal end of ApoA-Ib that were not present in the standard plasmatic form of ApoA-I. These amino acids corresponded to half of the propeptide sequence of the immature form of ApoA-I (proApoA-I) indicating that ApoA-Ib is a misprocessed form of proApoA-I. The description of ApoA-Ib could be relevant not only because it can allow the automated analysis of this biomarker in the clinical practice but also because it has the potential to shed light into the molecular mechanisms that cause idiopathic FSGS, which is currently unknown.
Collapse
Affiliation(s)
- Conxita Jacobs-Cachá
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain. .,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain.
| | - Natàlia Puig-Gay
- Renal Physiopathology Group-CIBBIM. Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joana Sellarès
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Anna Meseguer
- Renal Physiopathology Group-CIBBIM. Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Mikhail M Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany.,Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Francesc J Moreso
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Maria José Soler
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Daniel Seron
- Nephrology Research Group, Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Nephrology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Joan Lopez-Hellin
- Renal Physiopathology Group-CIBBIM. Hospital Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain. .,Biochemistry Department, Hospital Vall d'Hebrón, Barcelona, Spain.
| |
Collapse
|
10
|
Hu Y, Meuret C, Go S, Yassine HN, Nedelkov D. Simple and Fast Assay for Apolipoprotein E Phenotyping and Glycotyping: Discovering Isoform-Specific Glycosylation in Plasma and Cerebrospinal Fluid. J Alzheimers Dis 2020; 76:883-893. [PMID: 32568201 PMCID: PMC7504994 DOI: 10.3233/jad-200203] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND The mechanisms of how APOEɛ4 allele (APOE4) increases the risk of Alzheimer's disease (AD) pathology have not been fully elucidated. In cerebrospinal fluid (CSF), apoE is heavily glycosylated. OBJECTIVE To determine the impact of APOE genotype on the relative abundance of apoE protein isoforms and their specific glycosylation patterns in CSF and plasma via a newly developed mass spectrometric immunoassay (MSIA) assay. METHODS Total glycosylation and isoform-specific glycosylation were analyzed in plasma and CSF from a group of non-demented older individuals (n = 22), consisting of homozygous ɛ3 and ɛ4 or heterozygous ɛ3/ɛ4, ɛ2/ɛ3, or ɛ2/ɛ4 carriers. The glycan structures were further confirmed after treatment with sialidase. RESULTS In heterozygous individuals, the apoE3/E2, E4/E2, and E4/E3 isoform ratios were all significantly lower in plasma compared to CSF. For all individuals, a single O-linked glycan was observed in plasma, while two glycans (of the same type) per apoE were observed in CSF. The ratio of glycosylated to total apoE was greater in CSF compared to plasma for all apoE isoforms. In plasma and CSF, a trend of decreasing glycosylation was observed from apoE2 > apoE3 > apoE4. The difference in the percentage of secondary glycosylation in CSF was significantly greater in apoE4 compared to the other isoforms. CONCLUSION The new MSIA apoE assay robustly distinguishes among apoE isoforms and glycoforms in plasma and CSF. ApoE4 is the predominant isoform and least glycosylated in CSF. Assessing apoE isoform-specific glycosylation by MSIA may help clarify brain apoE metabolism and AD risk.
Collapse
|
11
|
Emerging evidences for the opposite role of apolipoprotein C3 and apolipoprotein A5 in lipid metabolism and coronary artery disease. Lipids Health Dis 2019; 18:220. [PMID: 31836003 PMCID: PMC6909560 DOI: 10.1186/s12944-019-1166-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022] Open
Abstract
Apolipoprotein C3 (apoC3) and apolipoprotein A5 (apoA5), encoded by APOA1/C3/A4/A5 gene cluster, are two critical regulators of plasma triglyceride (TG) metabolism. Deficiency of apoC3 or apoA5 led to significant decreased or increased plasma TG levels, respectively. Recent studies indicated apoC3 and apoA5 also played roles in plasma remnant cholesterol, high density lipoprotein (HDL) and hepatic TG metabolisms. Moreover, large scale population genetic studies indicated that loss of function mutations in APOC3 and APOA5 gene conferred decreased and increased risk of coronary artery disease (CAD), respectively. This manuscript mainly reviewed existing evidences suggesting the opposite role of apoC3 and apoA5 in lipid metabolism and CAD risk, and discussed the potential correlation between these two apolipoproteins.
Collapse
|
12
|
Wang T, Turko IV. Proteomic Toolbox To Standardize the Separation of Extracellular Vesicles and Lipoprotein Particles. J Proteome Res 2018; 17:3104-3113. [PMID: 30080417 DOI: 10.1021/acs.jproteome.8b00225] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Circulating in blood, extracellular vesicles (EVs) and lipoprotein particles (LPs) have diagnostic and prognostic value. To unambiguously define their functions, separation protocols need to be developed. However, because of their similar size and density, traditional approaches to separate EVs and LPs often fail to provide the required resolution. Further development and standardization of affinity-based protocols is necessary, and a quantitative method is needed to assess the efficiency of LP depletion from EV samples. In the present study, we propose the simultaneous quantification of three groups of proteins by mass spectrometry as a toolbox to evaluate prospective separation protocols. We generated 15N-labeled internal standards for quantification of (i) EV-specific proteins, (ii) all classes and subclasses of apolipoproteins constituting LPs, and (iii) several major serum proteins. These standards were then used in multiple reaction monitoring assay to evaluate the performance of size-exclusion chromatography, heparin-Sepharose, lipopolysaccharide-Sepharose, (2-hydroxypropyl)-β-cyclodextrin-Sepharose, and concanavalin A-Sepharose in separating serum EVs and LPs. The efficiency of a resin to separate EVs from non-EV substances could be jeopardized by simultaneous EV aggregation. Therefore, dynamic light scattering analysis was used in this study in addition to the proteomic toolbox when making a recommendation to use particular resin for EV isolation. On the basis of our measurements, we concluded that none of the individual separation protocols used in this study resulted in LP-free EVs, and the combination of two protocols may be complex due to low EV yield. Overall, this further points to the importance of proposed proteomic toolbox for the future evaluation of EV separation protocols.
Collapse
Affiliation(s)
- Tingting Wang
- Biomolecular Measurement Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States.,Institute for Bioscience and Biotechnology Research , Rockville , Maryland 20850 , United States
| | - Illarion V Turko
- Biomolecular Measurement Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States.,Institute for Bioscience and Biotechnology Research , Rockville , Maryland 20850 , United States
| |
Collapse
|
13
|
Looße C, Swieringa F, Heemskerk JWM, Sickmann A, Lorenz C. Platelet proteomics: from discovery to diagnosis. Expert Rev Proteomics 2018; 15:467-476. [PMID: 29787335 DOI: 10.1080/14789450.2018.1480111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Platelets are the smallest cells within the circulating blood with key roles in physiological hemostasis and pathological thrombosis regulated by the onset of activating/inhibiting processes via receptor responses and signaling cascades. Areas covered: Proteomics as well as genomic approaches have been fundamental in identifying and quantifying potential targets for future diagnostic strategies in the prevention of bleeding and thrombosis, and uncovering the complexity of platelet functions in health and disease. In this article, we provide a critical overview on current functional tests used in diagnostics and the future perspectives for platelet proteomics in clinical applications. Expert commentary: Proteomics represents a valuable tool for the identification of patients with diverse platelet associated defects. In-depth validation of identified biomarkers, e.g. receptors, signaling proteins, post-translational modifications, in large cohorts is decisive for translation into routine clinical diagnostics.
Collapse
Affiliation(s)
- Christina Looße
- a Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund , Germany
| | - Frauke Swieringa
- a Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund , Germany
| | - Johan W M Heemskerk
- b Department of Biochemistry , CARIM, Maastricht University , Maastricht , The Netherlands
| | - Albert Sickmann
- a Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund , Germany.,c Medizinisches Proteom-Center , Medizinische Fakultät, Ruhr-Universität Bochum , Bochum , Germany.,d Department of Chemistry, College of Physical Sciences , University of Aberdeen , Aberdeen , UK
| | - Christin Lorenz
- a Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund , Germany
| |
Collapse
|