1
|
Doroszkiewicz J, Mroczko J, Winkel I, Mroczko B. Metabolic and Immune System Dysregulation: Unraveling the Connections between Alzheimer's Disease, Diabetes, Inflammatory Bowel Diseases, and Rheumatoid Arthritis. J Clin Med 2024; 13:5057. [PMID: 39274269 PMCID: PMC11396443 DOI: 10.3390/jcm13175057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/16/2024] Open
Abstract
Alzheimer's disease (AD), diabetes mellitus (DM), inflammatory bowel diseases (IBD), and rheumatoid arthritis (RA) are chronic conditions affecting millions globally. Despite differing clinical symptoms, these diseases share pathophysiological mechanisms involving metabolic and immune system dysregulation. This paper examines the intricate connections between these disorders, focusing on shared pathways such as insulin resistance, lipid metabolism dysregulation, oxidative stress, and chronic inflammation. An important aspect is the role of amyloid-beta plaques and tau protein tangles, which are hallmark features of AD. These protein aggregates are influenced by metabolic dysfunction and inflammatory processes similar to those seen in DM, RA, and IBD. This manuscript explores how amyloid and tau pathologies may be exacerbated by shared metabolic and immune dysfunction. Additionally, this work discusses the gut-brain axis and the influence of gut microbiota in mediating disease interactions. Understanding these commonalities opens new avenues for multi-targeted therapeutic approaches that address the root causes rather than merely the symptoms of these conditions. This integrative perspective could lead to more effective interventions and improved patient outcomes, emphasizing the importance of a unified approach in managing these interconnected diseases.
Collapse
Affiliation(s)
- Julia Doroszkiewicz
- Department of Neurodegeneration Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Jan Mroczko
- Department of Neurodegeneration Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Izabela Winkel
- Dementia Disorders Centre, Medical University of Wroclaw, 50-425 Scinawa, Poland
| | - Barbara Mroczko
- Department of Neurodegeneration Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Biochemical Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland
| |
Collapse
|
2
|
Chen X, Cai L, Fan W, Yang Q, Mao X, Yao L. Causal relationships between rheumatoid arthritis and neurodegenerative diseases: a two-sample univariable and multivariable Mendelian randomization study. Front Med (Lausanne) 2024; 11:1439344. [PMID: 39193017 PMCID: PMC11347450 DOI: 10.3389/fmed.2024.1439344] [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: 05/27/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
Background Observational research has highlighted a potential relationship between rheumatoid arthritis (RA) and neurodegenerative diseases (NDs). However, the confirmation of a causal connection is impeded by the inherent limitations of such studies, including vulnerability to confounding factors and the possibility of reverse causality. This study employs a two-sample Mendelian randomization (MR) approach to assess the causal impact of RA on three NDs, including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). Methods We aggregated data from genome-wide association studies (GWASs) targeting RA or NDs within populations of European descent. Single nucleotide polymorphisms (SNPs) with robust associations to RA were identified as instrumental variables (IVs). To estimate the association between RA and AD, PD, and ALS, we utilized the inverse variance weighted (IVW) method in our univariable MR (UVMR) analysis. Validation of the IVW results ensued through supplementary analyses using MR-Egger and weighted median methods. The multivariable MR (MVMR) analysis was conducted, adjusting for body mass index (BMI), alcohol drinking, and type 2 diabetes mellitus (T2DM). Results The UVMR analysis, based on the IVW method, revealed a significantly positive causal association between RA and late-onset (LO) AD (OR [95% CI] = 1.084 [1.020-1.153]; p = 9.980 × 10-3), while suggesting a possible inverse relationship with PD (OR [95% CI] = 0.727 [0.563-0.938]; p = 0.014). Our study did not detect any causal connections between RA and early-onset (EO) AD, atypical or mixed (AM) AD, and ALS (all p > 0.05). The MVMR analysis results indicated that after adjusting for alcohol drinking, RA remains a risk factor for LOAD (OR [95% CI] = 1.094 [1.024-1.169]; p = 0.008). However, MVMR analysis revealed no causal connections between RA and PD after adjustments for BMI, alcohol drinking, or T2DM (all p > 0.05). Sensitivity analyses showed no evidence of heterogeneity and horizontal pleiotropy. Conclusions This research provides genetic evidence indicating that RA potentially causes an increased risk of developing LOAD and PD. Such a revelation underscores the importance for individuals suffering from RA to be vigilant about the potential emergence of LOAD and PD. Ongoing monitoring and prompt detection are essential for successfully managing and intervening in this possible risk.
Collapse
Affiliation(s)
- Xingyu Chen
- Department of Neurology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Li Cai
- Department of Neurology, The Third Hospital of Changsha, Changsha, China
| | - Weibing Fan
- Department of Neurology, The Third Hospital of Changsha, Changsha, China
| | - Qian Yang
- Department of Neurology, The Third Hospital of Changsha, Changsha, China
| | - Xinfa Mao
- Department of Neurology, The Third Hospital of Changsha, Changsha, China
| | - Liping Yao
- Department of Neurology, The Third Hospital of Changsha, Changsha, China
| |
Collapse
|
3
|
Yang L, Stanisheuski S, Song Z, Bracha S, Maier CS. Top-down mass spectrometry for characterizing the low molecular weight proteome of canine osteosarcoma cell phenotypes. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:313-325. [PMID: 37724027 DOI: 10.1177/14690667231202766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Osteosarcoma (OS) is the most common primary malignant tumor of bone, which occupying about 20% of all bone cancers. To increase understanding of the biology of OS, we developed and evaluated a top-down mass spectrometry approach to detect, identify and quantify low molecular weight (MW) proteins (i.e., 1 kDa < MW < 30 kDa) in osteosarcoma cells. Top-down proteomic (TDP) data was acquired using reversed phase nano-liquid chromatography in conjunction with high-resolution mass spectrometry and resulted in the assignment of 328 proteins and 820 proteoforms or degradation products with high confidence. Eight post-translational modifications (PTMs) were identified in the present study, including N-terminal acetylation, lysine acetylation, succinylation, malonylation, serine/tyrosine phosphorylation, histidine methylation and N-acetylleucine. We confirmed that a truncated N-terminal proteoform lost 73 Da of mass through removal of the N-terminal Met (-131 Da), acetylation of the second amino acid (+42 Da), and Met oxidation (+16 Da). The results showed that the levels of proteoforms/biodegradable peptides correlated with the metastatic phenotypes of osteosarcoma cell lines. This study demonstrates the benefits of TDP for the characterization and relative quantification of proteoforms with relevance to OS biology and the potential of small molecular weight proteoforms to serve as a still underappreciated source of biomarkers.
Collapse
Affiliation(s)
- Liping Yang
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
| | | | - Zifeng Song
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
| | - Shay Bracha
- Department of Clinical Sciences, Oregon State University, Corvallis, OR, USA
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
4
|
Trzeciak P, Herbet M, Dudka J. Common Factors of Alzheimer's Disease and Rheumatoid Arthritis-Pathomechanism and Treatment. Molecules 2021; 26:6038. [PMID: 34641582 PMCID: PMC8512006 DOI: 10.3390/molecules26196038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
The accumulation of amyloid plaques, or misfolded fragments of proteins, leads to the development of a condition known as amyloidosis, which is clinically recognized as a systemic disease. Amyloidosis plays a special role in the pathogenesis of neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease, and rheumatoid arthritis (RA). The occurrence of amyloidosis correlates with the aging process of the organism, and since nowadays, old age is determined by the comfort of functioning and the elimination of unpleasant disease symptoms in the elderly, exposure to this subject is justified. In Alzheimer's disease, amyloid plaques negatively affect glutaminergic and cholinergic transmission and loss of sympathetic protein, while in RA, amyloids stimulated by the activity of the immune system affect the degradation of the osteoarticular bond. The following monograph draws attention to the over-reactivity of the immune system in AD and RA, describes the functionality of the blood-brain barrier as an intermediary medium between RA and AD, and indicates the direction of research to date, focusing on determining the relationship and the cause-effect link between these disorders. The paper presents possible directions for the treatment of amyloidosis, with particular emphasis on innovative therapies.
Collapse
Affiliation(s)
| | - Mariola Herbet
- Chair and Department of Toxicology, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 8b Street, 20-090 Lublin, Poland; (P.T.)
| | | |
Collapse
|
5
|
Foreman RE, George AL, Reimann F, Gribble FM, Kay RG. Peptidomics: A Review of Clinical Applications and Methodologies. J Proteome Res 2021; 20:3782-3797. [PMID: 34270237 DOI: 10.1021/acs.jproteome.1c00295] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Improvements in both liquid chromatography (LC) and mass spectrometry (MS) instrumentation have greatly enhanced proteomic and small molecule metabolomic analysis in recent years. Less focus has been on the improved capability to detect and quantify small bioactive peptides, even though the exact sequences of the peptide species produced can have important biological consequences. Endogenous bioactive peptide hormones, for example, are generated by the targeted and regulated cleavage of peptides from their prohormone sequence. This process may include organ specific variants, as proglucagon is converted to glucagon in the pancreas but glucagon-like peptide-1 (GLP-1) in the small intestine, with glucagon raising, whereas GLP-1, as an incretin, lowering blood glucose. Therefore, peptidomics workflows must preserve the structure of the processed peptide products to prevent the misidentification of ambiguous peptide species. The poor in vivo and in vitro stability of peptides in biological matrices is a major factor that needs to be considered when developing methods to study them. The bioinformatic analysis of peptidomics data sets requires the inclusion of specific post-translational modifications, which are critical for the function of many bioactive peptides. This review aims to discuss and contrast the various extraction, analytical, and bioinformatics approaches used for human peptidomics studies in a multitude of matrices.
Collapse
Affiliation(s)
- Rachel E Foreman
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Amy L George
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Frank Reimann
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Fiona M Gribble
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Richard G Kay
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| |
Collapse
|
6
|
Diurnal variation of inflammatory plasma proteins involved in pain. Pain Rep 2019; 4:e776. [PMID: 31875183 PMCID: PMC6882578 DOI: 10.1097/pr9.0000000000000776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/19/2022] Open
Abstract
Supplemental Digital Content is Available in the Text. Introduction: Proteomics is a powerful approach for biochemical research because it directly studies the main functional components of biochemical systems. The understanding of the normal fluctuations of the proteome in health is essential to identify pain-specific biomarkers. Objective: To investigate fluctuations of the plasma proteome in healthy pain-free individuals. Methods: Blood samples were structurally collected in the early morning and evening from 10 clinically healthy individuals (26.3 ± 3.3 years). High abundant proteins were removed from plasma, and proteins were then analysed by nanoliquid chromatography combined with mass spectrometry. In addition, an assay of 71 cytokines/chemokines/growth factors was analysed. Results: Multivariate statistical analysis displayed that there were up to 64 proteins whose expression levels were significantly altered between the plasma samples collected during the morning and evening; no changes existed for the assay. The levels of 34 proteins were increased and 30 proteins were decreased during the evening compared with the morning sample. The increased proteins were involved in the biological processes such as protein activation cascade, complement activation, and stress response. The decreased proteins were involved in regulation of endopeptidase activity, inflammatory response, and protein metabolic processes. Conclusion: The circadian variations in the plasma proteome stress the need to collect blood samples of both patients and controls at a fixed time of the day. The results in this study might be useful for better understanding of the complexity of individual variation in the human plasma proteome over time and provide a baseline for improved pain biomarker discovery.
Collapse
|
7
|
Tan WKY, Purnamawati K, Pakkiri LS, Tan SH, Yang X, Chan MY, Drum CL. Sources of variability in quantifying circulating thymosin beta-4: literature review and recommendations. Expert Opin Biol Ther 2018; 18:141-147. [DOI: 10.1080/14712598.2018.1448382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Warren K. Y. Tan
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Cardiovascular Research Institute, National University Health System, Singapore
| | - Kristy Purnamawati
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore
| | - Leroy S. Pakkiri
- Cardiovascular Research Institute, National University Health System, Singapore
| | - Sock Hwee Tan
- Cardiovascular Research Institute, National University Health System, Singapore
| | - Xiaoxun Yang
- Cardiovascular Research Institute, National University Health System, Singapore
| | - Mark Y. Chan
- Cardiovascular Research Institute, National University Health System, Singapore
| | - Chester L. Drum
- Cardiovascular Research Institute, National University Health System, Singapore
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| |
Collapse
|
8
|
Kim KS, Yang HI. Thymosin β4 in rheumatoid arthritis: Friend or foe. Biomed Rep 2017; 7:205-208. [PMID: 28808568 DOI: 10.3892/br.2017.952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 12/21/2022] Open
Abstract
Rheumatoid arthritis (RA) has characteristic pannus tissues, which show tumor-like growth of the synovium through chronic joint inflammation. The synovium is highly penetrated by various immune cells, and the synovial lining becomes hyperplastic due to increased numbers of macrophage-like and fibroblast-like synoviocytes. Thus, a resultant hypoxic condition stimulates the expression of inflammation-related genes in various cells, in particular, vascular endothelial growth factor. Thymosin β4 (Tβ4), a 5-kDa protein, is known to play a significant role in various biological activities, such as actin sequestering, cell motility, migration, inflammation, and damage repair. Recent studies have provided evidence that Tβ4 may have a role in RA pathogenesis. The Tβ4 level has been shown to increase significantly in the joint fluid and serum of RA patients. However, whether Tβ4 stimulates or inhibits activation of RA immune responses remains to be determined. In the present study, we discuss the logical and clinical justifications for Tβ4 as a potential target for RA therapeutics.
Collapse
Affiliation(s)
- Kyoung Soo Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 134-727, Republic of Korea.,East-West Bone and Joint Disease Research Institute, Kyung Hee University Hospital at Gangdong, Seoul 134-727, Republic of Korea
| | - Hyung-In Yang
- East-West Bone and Joint Disease Research Institute, Kyung Hee University Hospital at Gangdong, Seoul 134-727, Republic of Korea.,Division of Rheumatology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul 134-727, Republic of Korea
| |
Collapse
|
9
|
Lourido L, Blanco FJ, Ruiz-Romero C. Defining the proteomic landscape of rheumatoid arthritis: progress and prospective clinical applications. Expert Rev Proteomics 2017; 14:431-444. [PMID: 28425787 DOI: 10.1080/14789450.2017.1321481] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The heterogeneity of Rheumatoid Arthritis (RA) and the absence of clinical tests accurate enough to identify the early stages of this disease have hampered its management. Therefore, proteomics research is increasingly focused on the discovery of novel biological markers, which would not only be able make an early diagnosis, but also to gain insight into the different pathological mechanisms underlying the heterogeneity of RA and also to stratify patients, which is critical to enabling effective treatments. Areas covered: The proteomic approaches that have been utilised to provide knowledge about RA pathogenesis, and to identify biomarkers for RA diagnosis, prognosis, disease monitoring and prediction of response to therapy, are summarized. Expert commentary: Although each proteomic study is unique in its design, all of them have contributed to the understanding of RA pathogenesis and the discovery of promising biomarkers for patient stratification, which would improve clinical care of RA patients. Still, efforts need to be made to validate these findings and translate them into clinical practice.
Collapse
Affiliation(s)
- Lucía Lourido
- a Rheumatology Division, ProteoRed/ISCIII Proteomics Group , INIBIC - Hospital Universitario de A Coruña , A Coruña , Spain.,b RIER-RED de Inflamación y Enfermedades Reumáticas , INIBIC-CHUAC , A Coruña , Spain
| | - Francisco J Blanco
- a Rheumatology Division, ProteoRed/ISCIII Proteomics Group , INIBIC - Hospital Universitario de A Coruña , A Coruña , Spain.,b RIER-RED de Inflamación y Enfermedades Reumáticas , INIBIC-CHUAC , A Coruña , Spain
| | - Cristina Ruiz-Romero
- a Rheumatology Division, ProteoRed/ISCIII Proteomics Group , INIBIC - Hospital Universitario de A Coruña , A Coruña , Spain.,c CIBER-BBN Instituto de Salud Carlos III , INIBIC-CHUAC , A Coruña , Spain
| |
Collapse
|
10
|
Abstract
Precision medicine is an emerging approach for prevention and treatment of diseases considering individuals’ uniqueness. Omics provide one step forward toward advanced precision medicine and include technologies such as genomics, proteomics and metabolomics generating valuable data through characterization of entire biological systems. With the aid of omics, a major shift has been started to occur in understanding of diseases followed by potential fundamental changes in medical care strategies. This short review aims at providing some examples of current omics that are applied in the field of pain in terms of new biomarkers for diagnosis of different pain types, stratification of patients and new therapeutic targets. Implementation of omics would most likely offer breakthrough in the future of pain management.
Collapse
Affiliation(s)
- Parisa Gazerani
- Department of Health Science & Technology, Faculty of Medicine, Aalborg University, Frederik Bajers Vej 7A2-A2-208, 9220 Aalborg East, Denmark
| | - Hye Sook Han Vinterhøj
- Department of Health Science & Technology, Faculty of Medicine, Aalborg University, Frederik Bajers Vej 7A2-A2-208, 9220 Aalborg East, Denmark
| |
Collapse
|
11
|
Eakin AJ, Bustard MJ, McGeough CM, Ahmed T, Bjourson AJ, Gibson DS. Siglec-1 and -2 as potential biomarkers in autoimmune disease. Proteomics Clin Appl 2016; 10:635-44. [DOI: 10.1002/prca.201500069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/25/2015] [Accepted: 01/05/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Amanda J. Eakin
- Northern Ireland Centre for Stratified Medicine; Altnagelvin Hospital Campus; Ulster University; Londonderry Northern Ireland UK
| | - Michael J. Bustard
- Northern Ireland Centre for Stratified Medicine; Altnagelvin Hospital Campus; Ulster University; Londonderry Northern Ireland UK
| | - Cathy M. McGeough
- Northern Ireland Centre for Stratified Medicine; Altnagelvin Hospital Campus; Ulster University; Londonderry Northern Ireland UK
| | - Tahanver Ahmed
- Northern Ireland Centre for Stratified Medicine; Altnagelvin Hospital Campus; Ulster University; Londonderry Northern Ireland UK
| | - Anthony J. Bjourson
- Northern Ireland Centre for Stratified Medicine; Altnagelvin Hospital Campus; Ulster University; Londonderry Northern Ireland UK
| | - David S. Gibson
- Northern Ireland Centre for Stratified Medicine; Altnagelvin Hospital Campus; Ulster University; Londonderry Northern Ireland UK
| |
Collapse
|
12
|
Márquez A, Martín J, Carmona FD. Emerging aspects of molecular biomarkers for diagnosis, prognosis and treatment response in rheumatoid arthritis. Expert Rev Mol Diagn 2016; 16:663-75. [DOI: 10.1080/14737159.2016.1174579] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
13
|
Clement CC, Becerra A, Yin L, Zolla V, Huang L, Merlin S, Follenzi A, Shaffer SA, Stern LJ, Santambrogio L. The Dendritic Cell Major Histocompatibility Complex II (MHC II) Peptidome Derives from a Variety of Processing Pathways and Includes Peptides with a Broad Spectrum of HLA-DM Sensitivity. J Biol Chem 2016; 291:5576-5595. [PMID: 26740625 DOI: 10.1074/jbc.m115.655738] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/26/2022] Open
Abstract
The repertoire of peptides displayed in vivo by MHC II molecules derives from a wide spectrum of proteins produced by different cell types. Although intracellular endosomal processing in dendritic cells and B cells has been characterized for a few antigens, the overall range of processing pathways responsible for generating the MHC II peptidome are currently unclear. To determine the contribution of non-endosomal processing pathways, we eluted and sequenced over 3000 HLA-DR1-bound peptides presented in vivo by dendritic cells. The processing enzymes were identified by reference to a database of experimentally determined cleavage sites and experimentally validated for four epitopes derived from complement 3, collagen II, thymosin β4, and gelsolin. We determined that self-antigens processed by tissue-specific proteases, including complement, matrix metalloproteases, caspases, and granzymes, and carried by lymph, contribute significantly to the MHC II self-peptidome presented by conventional dendritic cells in vivo. Additionally, the presented peptides exhibited a wide spectrum of binding affinity and HLA-DM susceptibility. The results indicate that the HLA-DR1-restricted self-peptidome presented under physiological conditions derives from a variety of processing pathways. Non-endosomal processing enzymes add to the number of epitopes cleaved by cathepsins, altogether generating a wider peptide repertoire. Taken together with HLA-DM-dependent and-independent loading pathways, this ensures that a broad self-peptidome is presented by dendritic cells. This work brings attention to the role of "self-recognition" as a dynamic interaction between dendritic cells and the metabolic/catabolic activities ongoing in every parenchymal organ as part of tissue growth, remodeling, and physiological apoptosis.
Collapse
Affiliation(s)
| | | | | | | | | | - Simone Merlin
- the School of Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Antonia Follenzi
- From the Departments of Pathology and; the School of Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Scott A Shaffer
- Biochemistry and Molecular Pharmacology and; the Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Lawrence J Stern
- the Departments of Pathology and; Biochemistry and Molecular Pharmacology and
| | - Laura Santambrogio
- From the Departments of Pathology and; Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461,.
| |
Collapse
|
14
|
Cheon DH, Nam EJ, Park KH, Woo SJ, Lee HJ, Kim HC, Yang EG, Lee C, Lee JE. Comprehensive Analysis of Low-Molecular-Weight Human Plasma Proteome Using Top-Down Mass Spectrometry. J Proteome Res 2015; 15:229-44. [DOI: 10.1021/acs.jproteome.5b00773] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dong Huey Cheon
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Interdisciplinary
Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Republic of Korea
| | - Eun Ji Nam
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Kyu Hyung Park
- Department
of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 463-707, Republic of Korea
| | - Se Joon Woo
- Department
of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 463-707, Republic of Korea
| | - Hye Jin Lee
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Hee Cheol Kim
- Department
of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
| | - Eun Gyeong Yang
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| | - Cheolju Lee
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
- Department
of Biological Chemistry, University of Science and Technology, Daejeon 305-333, Republic of Korea
| | - Ji Eun Lee
- Center
for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
| |
Collapse
|
15
|
Park YJ, Chung MK, Hwang D, Kim WU. Proteomics in Rheumatoid Arthritis Research. Immune Netw 2015; 15:177-85. [PMID: 26330803 PMCID: PMC4553255 DOI: 10.4110/in.2015.15.4.177] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/16/2015] [Accepted: 07/31/2015] [Indexed: 12/20/2022] Open
Abstract
Although rheumatoid arthritis (RA) is the most common chronic inflammatory autoimmune disease, diagnosis of RA is currently based on clinical manifestations, and there is no simple, practical assessment tool in the clinical field to assess disease activity and severity. Recently, there has been increasing interest in the discovery of new diagnostic RA biomarkers that can assist in evaluating disease activity, severity, and treatment response. Proteomics, the large-scale study of the proteome, has emerged as a powerful technique for protein identification and characterization. For the past 10 years, proteomic techniques have been applied to different biological samples (synovial tissue/fluid, blood, and urine) from RA patients and experimental animal models. In this review, we summarize the current state of the application of proteomics in RA and its importance in identifying biomarkers and treatment targets.
Collapse
Affiliation(s)
- Yune-Jung Park
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon 16247, Korea. ; POSTECH-CATHOLIC Biomedical Engineering Institute, The Catholic University of Korea, Seoul 06591, Korea
| | - Min Kyung Chung
- Division of Rheumatology, Department of Internal Medicine, St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Daehee Hwang
- Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, Daegu Gyeongbuk Institute of Science and Technology, Daegu 43014, Korea
| | - Wan-Uk Kim
- POSTECH-CATHOLIC Biomedical Engineering Institute, The Catholic University of Korea, Seoul 06591, Korea. ; Division of Rheumatology, Department of Internal Medicine, St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| |
Collapse
|
16
|
Cabras T, Iavarone F, Martelli C, Delfino D, Rossetti DV, Inserra I, Manconi B, Desiderio C, Messana I, Hannappel E, Faa G, Castagnola M. High-resolution mass spectrometry for thymosins detection and characterization. Expert Opin Biol Ther 2015; 15 Suppl 1:S191-201. [PMID: 26095945 DOI: 10.1517/14712598.2015.1009887] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVES The aim of this study was to characterize β and α thymosins and their proteoforms in various tissues and bodily fluids by mass spectrometry and to look at their association with a wide variety of pathologies. METHODS A top-down proteomic platform based on high-performance liquid chromatography (HPLC) coupled to high-resolution LTQ-Orbitrap mass spectrometry (MS) was applied to the characterization of naturally occurring peptides. RESULTS In addition to thymosin β4 (Tβ4) and β10 (Tβ10), several post-translational modifications of both these peptides were identified not only in bodily fluids but also in normal and pathological tissues of different origins. The analysis of tissue specimens allowed the characterization of different C-terminal truncated forms of Tβ4 and Tβ10 together with other proteolytic fragments. The sulfoxide derivative of both Tβ4 and Tβ10 and the acetylated derivatives at lysine residues of Tβ4 were also characterized. Different proteoforms of prothymosin α, parathymosin α, thymosin α1 and thymosin α11 together with diverse proteolytic fragments were identified too. CONCLUSION The clinical and prognostic significance and the origin of these proteoforms have to be deeply investigated.
Collapse
Affiliation(s)
- Tiziana Cabras
- Università di Cagliari, Dipartimento di Scienze della Vita e dell'Ambiente , Cagliari , Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Park HJ, Yang K, Kim MJ, Jang J, Lee M, Kim DW, Lee H, Cho SW. Bio-inspired oligovitronectin-grafted surface for enhanced self-renewal and long-term maintenance of human pluripotent stem cells under feeder-free conditions. Biomaterials 2015; 50:127-39. [PMID: 25736503 DOI: 10.1016/j.biomaterials.2015.01.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 01/08/2015] [Accepted: 01/20/2015] [Indexed: 12/26/2022]
Abstract
Current protocols for human pluripotent stem cell (hPSC) expansion require feeder cells or matrices from animal sources that have been the major obstacle to obtain clinical grade hPSCs due to safety issues, difficulty in quality control, and high expense. Thus, feeder-free, chemically defined synthetic platforms have been developed, but are mostly confined to typical polystyrene culture plates. Here, we report a chemically defined, material-independent, bio-inspired surface coating allowing for feeder-free expansion and maintenance of self-renewal and pluripotency of hPSCs on various polymer substrates and devices. Polydopamine (pDA)-mediated immobilization of vitronectin (VN) peptides results in surface functionalization of VN-dimer/pDA conjugates. The engineered surfaces facilitate adhesion, proliferation, and colony formation of hPSCs via enhanced focal adhesion, cell-cell interaction, and biophysical signals, providing a chemically defined, xeno-free culture system for clonal expansion and long-term maintenance of hPSCs. This surface engineering enables the application of clinically-relevant hPSCs to a variety of biomedical systems such as tissue-engineering scaffolds and medical devices.
Collapse
Affiliation(s)
- Hyun-Ji Park
- Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Kisuk Yang
- Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Mun-Jung Kim
- Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Jiho Jang
- Department of Physiology, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Mihyun Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Dong-Wook Kim
- Department of Physiology, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Haeshin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.
| |
Collapse
|
18
|
Development of an improved fractionation of the human plasma proteome by a combination of abundant proteins depletion and multi-lectin affinity chromatography. Bioanalysis 2014; 6:2537-48. [DOI: 10.4155/bio.14.217] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: Current analytical tools lack the required capacity to reduce the complexity of the plasma proteome and identify low-level proteins of clinical interest. Hence, the need to develop a fractionation approach to provide adequate throughput for a clinical study and minimize the loss and improve the detection of low abundance proteins. Materials & methods: We present the development of an analytical platform that combines the depletion of 12 high abundance proteins and multi-lectin affinity chromatography (12P-M-LAC) fractionation. Results & conclusion: We validated the highly specific, stable and robust 12P-M-LAC platform using human plasma. An improved enrichment of low abundance proteins and glycoproteins with minimum sample loss was achieved demonstrating the suitability of this platform in future biomarker discovery studies.
Collapse
|
19
|
Gbormittah FO, Lee LY, Taylor K, Hancock WS, Iliopoulos O. Comparative studies of the proteome, glycoproteome, and N-glycome of clear cell renal cell carcinoma plasma before and after curative nephrectomy. J Proteome Res 2014; 13:4889-900. [PMID: 25184692 PMCID: PMC4227548 DOI: 10.1021/pr500591e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Clear cell renal cell carcinoma
is the most prevalent of all reported kidney cancer cases, and currently
there are no markers for early diagnosis. This has stimulated great
research interest recently because early detection of the disease
can significantly improve the low survival rate. Combining the proteome,
glycoproteome, and N-glycome data from clear cell renal cell carcinoma
plasma has the potential of identifying candidate markers for early
diagnosis and prognosis and/or to monitor disease recurrence. Here,
we report on the utilization of a multi-dimensional fractionation
approach (12P-M-LAC) and LC–MS/MS to comprehensively investigate
clear cell renal cell carcinoma plasma collected before (disease)
and after (non-disease) curative nephrectomy (n =
40). Proteins detected in the subproteomes were investigated via label-free
quantification. Protein abundance analysis revealed a number of low-level
proteins with significant differential expression levels in disease
samples, including HSPG2, CD146, ECM1, SELL, SYNE1, and VCAM1. Importantly,
we observed a strong correlation between differentially expressed
proteins and clinical status of the patient. Investigation of the
glycoproteome returned 13 candidate glycoproteins with significant
differential M-LAC column binding. Qualitative analysis indicated
that 62% of selected candidate glycoproteins showed higher levels
(upregulation) in M-LAC bound fraction of disease samples. This observation
was further confirmed by released N-glycans data in which 53% of identified
N-glycans were present at different levels in plasma in the disease
vs non-disease samples. This striking result demonstrates the potential
for significant protein glycosylation alterations in clear cell renal
cell carcinoma cancer plasma. With future validation in a larger cohort,
information derived from this study may lead to the development of
clear cell renal cell carcinoma candidate biomarkers.
Collapse
Affiliation(s)
- Francisca O Gbormittah
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | | | | | | | | |
Collapse
|
20
|
Cheng Y, Chen Y, Sun X, Li Y, Huang C, Deng H, Li Z. Identification of Potential Serum Biomarkers for Rheumatoid Arthritis by High-Resolution Quantitative Proteomic Analysis. Inflammation 2014; 37:1459-67. [DOI: 10.1007/s10753-014-9871-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
21
|
Clement CC, Santambrogio L. The lymph self-antigen repertoire. Front Immunol 2013; 4:424. [PMID: 24379811 PMCID: PMC3864156 DOI: 10.3389/fimmu.2013.00424] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/20/2013] [Indexed: 01/26/2023] Open
Abstract
The lymphatic fluid originates from the interstitial fluid which bathes every parenchymal organ and reflects the “omic” composition of the tissue from which it originates in its physiological or pathological signature. Several recent proteomic analyses have mapped the proteome-degradome and peptidome of this immunologically relevant fluid pointing to the lymph as an important source of tissue-derived self-antigens. A vast array of lymph-circulating peptides have been mapped deriving from a variety of processing pathways including caspases, cathepsins, MMPs, ADAMs, kallikreins, calpains, and granzymes, among others. These self peptides can be directly loaded on circulatory dendritic cells and expand the self-antigenic repertoire available for central and peripheral tolerance.
Collapse
Affiliation(s)
- Cristina C Clement
- Department of Pathology, Albert Einstein College of Medicine , New York, NY , USA ; Department of Microbiology and Immunology, Albert Einstein College of Medicine , New York, NY , USA
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine , New York, NY , USA ; Department of Microbiology and Immunology, Albert Einstein College of Medicine , New York, NY , USA
| |
Collapse
|
22
|
Santambrogio L, Stern LJ. Carrying yourself: self antigen composition of the lymphatic fluid. Lymphat Res Biol 2013; 11:149-54. [PMID: 24024574 DOI: 10.1089/lrb.2013.0009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Advances in proteomics methodology and instrumentation have allowed detailed characterization of the composition of lymph. Far from being a simple ultrafiltrate of blood plasma, lymph has been shown to carry a rich repertoire of proteins and peptides reflecting the tissue of origin and its physiological state. Peptides derived from lymph can be loaded on the MHCII proteins, particularly those present on immature and/or inactivated antigen presenting cells, and may play an important role in maintenance of peripheral tolerance.
Collapse
Affiliation(s)
- Laura Santambrogio
- 1 Department of Pathology, Microbiology and Immunology, Albert Einstein College of Medicine , New York, New York
| | | |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
| |
Collapse
|
24
|
Ortea I, Roschitzki B, Ovalles JG, Longo JL, de la Torre I, González I, Gómez-Reino JJ, González A. Discovery of serum proteomic biomarkers for prediction of response to infliximab (a monoclonal anti-TNF antibody) treatment in rheumatoid arthritis: An exploratory analysis. J Proteomics 2012; 77:372-82. [DOI: 10.1016/j.jprot.2012.09.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 12/22/2022]
|
25
|
Tsai MH, Chang CL, Yu YS, Lin TY, Chong CP, Lin YS, Su MY, Yang JY, Shu TY, Lu X, Chen CH, Liu MY. Chemical analysis of C-reactive protein synthesized by human aortic endothelial cells under oxidative stress. Anal Chem 2012; 84:9646-54. [PMID: 23046186 DOI: 10.1021/ac302856v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
C-reactive protein (CRP) is a clinical biomarker of inflammation, and high levels of CRP correlate with cardiovascular disease. The objectives of this study were to test our hypothesis that oxidized low-density lipoprotein (ox-LDL) induces the release of CRP from human aortic endothelial cells (HAECs) and to optimize several analytical methods to identify CRP released from cultured cells in a model of atherogenic stress. HAECs were incubated with copper-oxidized LDL, and the supernatant was subsequently purified by diethylaminoethyl chromatography and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). We identified an optimal buffer for the elution of CRP, which contained 0.05 M sodium phosphate and 2.0 M NaCl (pH 4.5). Purified CRP was digested with trypsin and subjected to high-performance LC with an optimal mobile phase of acetonitrile-water containing 0.1% formic acid (50:50, v/v) and an optimal mobile phase flow rate of 0.2 mL/min. We identified optimal parameters for MS/MS analysis of CRP, including sheath gas pressure (80 psi), capillary temperature (275 °C), collision energy (25%), tube lens offset (-5 V), auxiliary gas pressure (0 psi), and isolation width of parent ion (m/z value = 3). Characterization of CRP was based on the extracted ion chromatograms and selected multiple-reaction monitoring spectra of three peptides (peptide-1, -2, and -3) derived from trypsin-digested intact CRP standard. CRP peptide-2 and peptide-3 were identified in the supernatant of ox-LDL-treated HAECs. Confirmation of CRP was based on LC-MS/MS and enzyme-linked immunosorbent assay analysis of CRP in purified HAEC supernatant, as well as real-time PCR analysis of CRP mRNA levels in HAECs.
Collapse
Affiliation(s)
- Ming-Hua Tsai
- Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Kriegsmann M, Seeley EH, Schwarting A, Kriegsmann J, Otto M, Thabe H, Dierkes B, Biehl C, Sack U, Wellmann A, Kahaly GJ, Schwamborn K, Caprioli RM. MALDI MS imaging as a powerful tool for investigating synovial tissue. Scand J Rheumatol 2012; 41:305-9. [PMID: 22639849 DOI: 10.3109/03009742.2011.647925] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To identify and image protein biomarker candidates in the synovial tissue of patients with rheumatoid arthritis (RA) and patients with osteoarthritis (OA). METHODS A novel matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) technique was applied to the analysis of synovial tissue. Patients were classified according to the American College of Rheumatology (ACR) criteria for RA. Frozen sections were stained to obtain morphological data. Serial sections were desiccated, and spotted with matrix for MALDI analysis. Ions generated by laser irradiation of the tissue were separated in time, based on their m/z ratio, and were subsequently detected. IMS was used in a 'profiling' mode to detect discrete spots for rapid evaluation of proteomic patterns in various tissue compartments. Photomicrographs of the stained tissue images were reviewed by a pathologist. Areas of interest (10 discrete areas/compartment) were marked digitally and the histology-annotated images were merged to form a photomicrograph of the section taken before the MALDI measurement. Pixel coordinates of these areas were transferred to a robotic spotter, the matrix was spotted, and the coordinates of the spots were transferred to a mass spectrometer for spectral acquisition. The data generated were then subjected to biocomputation analysis to reveal the biomarker candidates. RESULTS Several peaks (m/z) consistent in mass with calgranulins, defensins, and thymosins were detected and their distribution in various synovial compartments (synovial lining and sublining layer) was demonstrated. CONCLUSION MALDI IMS is a powerful tool for the rapid detection of numerous proteins (in situ proteomics) and was applied here for the analysis of the distribution of proteins in synovial tissue sections.
Collapse
Affiliation(s)
- M Kriegsmann
- Department of Clinical Immunology, Medical Faculty, University of Leipzig, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
A general approach for the purification and quantitative glycomic analysis of human plasma. Anal Bioanal Chem 2012; 402:2687-700. [DOI: 10.1007/s00216-012-5712-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/28/2011] [Accepted: 01/04/2012] [Indexed: 11/26/2022]
|
28
|
Zhu GT, Li XS, Gao Q, Zhao NW, Yuan BF, Feng YQ. Pseudomorphic synthesis of monodisperse magnetic mesoporous silica microspheres for selective enrichment of endogenous peptides. J Chromatogr A 2011; 1224:11-8. [PMID: 22218330 DOI: 10.1016/j.chroma.2011.12.045] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Revised: 12/06/2011] [Accepted: 12/13/2011] [Indexed: 01/16/2023]
Abstract
In this work, we describe a novel synthetic strategy of magnetic mesoporous silica spheres (Fe3O4@mSiO2) for the selective enrichment of endogenous peptides. Fe3O4 particles were coated with silica shell by a sol-gel method, followed by pseudomorphic synthesis to transform nonporous silica shell into ordered mesoporous silica shell. The core/shell structure and mesostructure were individually fabricated in two steps, which can be expedient to independently optimize the properties of monodispersion, magnetization and mesostructure. Actually, it was confirmed that the produced Fe3O4@mSiO2 particles possess good monodispersion, high magnetization, superparamagnetism, uniform accessible mesopores, and large surface area and pore volume. With these good properties, Fe3O4@mSiO2 spheres were applied to the rapid enrichment of peptides. Based on the size-exclusion mechanism and hydrophobic interaction with siloxane bridge group mainly on the surface of inside pores, Fe3O4@mSiO2 can selectively capture peptides and exclude high-MW proteins and salts. Furthermore, peptides in human plasma were successfully enriched by Fe3O4@mSiO2.
Collapse
Affiliation(s)
- Gang-Tian Zhu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | | | | | | | | | | |
Collapse
|
29
|
Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
Collapse
Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
| | | | | | | |
Collapse
|
30
|
Choi HM, Lee YA, Yang HI, Yoo MC, Kim KS. Increased levels of thymosin β4 in synovial fluid of patients with rheumatoid arthritis: association of thymosin β4 with other factors that are involved in inflammation and bone erosion in joints. Int J Rheum Dis 2011; 14:320-4. [PMID: 22004227 DOI: 10.1111/j.1756-185x.2011.01652.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIM Thymosin (Tβ4) may have various biological effects that are relevant to the pathogenesis of rheumatoid arthritis (RA). This study was performed to gain insight into the relevance of Tβ4 in the pathogenesis of inflammatory arthritis. METHOD The level of Tβ4 in synovial fluid from patients with osteoarthritis (OA) or RA was measured by enzyme-linked immunosorbent assay. An association between Tβ4 and matrix metalloproteinase (MMP)-1 and MMP-13 (collagenases), MMP-2 and MMP-9 (gelatinases), MMP-7, adiponectin, lactoferrin, vascular endothelial growth factor (VEGF), urokinase-type plasminogen activator (uPA), interleukin (IL)-6, IL-8 and prostaglandin E2 (PGE(2) ) in synovial joint fluids from OA and RA patients were investigated. RESULTS The level of Tβ4 in the synovial joint fluid of patients with OA and RA was (mean ± SD) 145 ± 88 and 1359 ± 1685 ng/mL, respectively. The level of Tβ4 in the synovial joint fluid of RA patients was significantly associated with the levels of MMP-9, MMP-13, VEGF, uPA, IL-6 and IL-8, but not with MMP-1, MMP-2, MMP-7, adiponectin and lactoferrin. In contrast, the level of Tβ4 in the synovial joint fluid of patients with OA was not associated with any of these molecules. CONCLUSIONS The results suggest that Tβ4 may play an important role in bone degradation and inflammation in RA but not OA, although nothing is known about the molecular mechanisms mediating Tβ4 in arthritic joints. The role of Tβ4 in arthritis should be studied to understand its relevance to the pathogenic processes in arthritis.
Collapse
Affiliation(s)
- Hyun M Choi
- East-West Bone & Joint Research Institute, Kyung Hee University, Seoul, Korea
| | | | | | | | | |
Collapse
|
31
|
Saroha A, Biswas S, Chatterjee BP, Das HR. Altered glycosylation and expression of plasma alpha-1-acid glycoprotein and haptoglobin in rheumatoid arthritis. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:1839-43. [DOI: 10.1016/j.jchromb.2011.04.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 11/30/2022]
|
32
|
Millioni R, Tolin S, Puricelli L, Sbrignadello S, Fadini GP, Tessari P, Arrigoni G. High abundance proteins depletion vs low abundance proteins enrichment: comparison of methods to reduce the plasma proteome complexity. PLoS One 2011; 6:e19603. [PMID: 21573190 PMCID: PMC3087803 DOI: 10.1371/journal.pone.0019603] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/06/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND To date, the complexity of the plasma proteome exceeds the analytical capacity of conventional approaches to isolate lower abundance proteins that may prove to be informative biomarkers. Only complex multistep separation strategies have been able to detect a substantial number of low abundance proteins (<100 ng/ml). The first step of these protocols is generally the depletion of high abundance proteins by the use of immunoaffinity columns or, alternatively, the enrichment of by the use of solid phase hexapeptides ligand libraries. METHODOLOGY/PRINCIPAL FINDINGS Here we present a direct comparison of these two approaches. Following either approach, the plasma sample was further fractionated by SCX chromatography and analyzed by RP-LC-MS/MS with a Q-TOF mass spectrometer. The depletion of the 20 most abundant plasma proteins allowed the identification of about 25% more proteins than those detectable following low abundance proteins enrichment. The two datasets are partially overlapping and the identified proteins belong to the same order of magnitude in terms of plasma concentration. CONCLUSIONS/SIGNIFICANCE Our results show that the two approaches give complementary results. However, the enrichment of low abundance proteins has the great advantage of obtaining much larger amount of material that can be used for further fractionations and analyses and emerges also as a cheaper and technically simpler approach. Collectively, these data indicate that the enrichment approach seems more suitable as the first stage of a complex multi-step fractionation protocol.
Collapse
Affiliation(s)
- Renato Millioni
- Department of Clinical and Experimental Medicine, Division of Metabolism, University of Padua, Padua, Italy.
| | | | | | | | | | | | | |
Collapse
|
33
|
De Santis M, Inzitari R, Bosello SL, Peluso G, Fanali C, Iavarone F, Zizzo G, Bocci M, Cabras T, Messana I, Fuso L, Varone F, Pagliari G, Castagnola M, Ferraccioli G. β-Thymosins and interstitial lung disease: study of a scleroderma cohort with a one-year follow-up. Respir Res 2011; 12:22. [PMID: 21314931 PMCID: PMC3045324 DOI: 10.1186/1465-9921-12-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 02/11/2011] [Indexed: 11/29/2022] Open
Abstract
Background β-thymosins play roles in cytoskeleton rearrangement, angiogenesis, fibrosis and reparative process, thus suggesting a possible involvement in the pathogenesis of systemic sclerosis. The aim of the study was to investigate the presence of thymosins β4, β4 sulfoxide, and β10 in bronchoalveolar lavage fluid of scleroderma patients with interstitial lung disease and the relation of these factors with pulmonary functional and radiological parameters. Methods β-thymosins concentrations were determined by Reverse Phase-High Performance Liquid Chromatography-Electrospray-Mass Spectrometry in the bronchoalveolar lavage fluid of 46 scleroderma patients with lung involvement and of 15 controls. Results Thymosin β4, β4 sulfoxide, and β10 were detectable in bronchoalveolar lavage fluid of patients and controls. Thymosin β4 levels were significantly higher in scleroderma patients than in controls. In addition, analyzing the progression of scleroderma lung disease at one-year follow-up, we have found that higher thymosin β4 levels seem to have a protective role against lung tissue damage. Thymosin β4 sulfoxide levels were higher in the smokers and in the scleroderma patients with alveolitis. Conclusions We describe for the first time β-thymosins in bronchoalveolar lavage fluid and their possible involvement in the pathogenesis of scleroderma lung disease. Thymosin β4 seems to have a protective role against lung tissue damage, while its oxidation product mirrors an alveolar inflammatory status.
Collapse
Affiliation(s)
- Maria De Santis
- Department of Rheumatology, Catholic University, Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
De Franceschi L, Bosello S, Scambi C, Biasi D, De Santis M, Caramaschi P, Peluso G, La Verde V, Bambara LM, Ferraccioli G. Proteome analysis of biological fluids from autoimmune-rheumatological disorders. Proteomics Clin Appl 2011; 5:78-89. [PMID: 21246742 DOI: 10.1002/prca.201000069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/27/2010] [Accepted: 11/01/2010] [Indexed: 11/10/2022]
Abstract
Autoimmune-rheumatological diseases are worldwide distributed disorders and represent a complex array of illnesses characterized by autoreactivity (reactivity against self-antigens) of T-B lymphocytes and by the synthesis of autoantibodies crucial for diagnosis (biomarkers). Yet, the effects of the autoimmune chronic inflammation on the infiltrated tissues and organs generally lead to profound tissue and organ damage with loss of function (i.e., lung, kidney, joints, exocrine glands). Although progresses have been made on the knowledge of these disorders, much still remains to be investigated on their pathogenesis and identification of new biomarkers useful in clinical practice. The rationale of using proteomics in autoimmune-rheumatological diseases has been the unmet need to collect, from biological fluids that are easily obtainable, a summary of the final biochemical events that represent the effects of the interplay between immune cells, mesenchymal cells and endothelial cells. Proteomic analysis of these fluids shows encouraging results and in this review, we addressed four major autoimmune-rheumatological diseases investigated through proteomic techniques and provide evidence-based data on the highlights obtained in systemic sclerosis, primary and secondary Sjogren's syndrome, systemic lupus erythematosus and rheumatoid arthritis.
Collapse
Affiliation(s)
- Lucia De Franceschi
- Department of Medicine, Section of Internal Medicine, University of Verona, Verona, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Tousi F, Hancock WS, Hincapie M. Technologies and strategies for glycoproteomics and glycomics and their application to clinical biomarker research. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2011; 3:20-32. [PMID: 32938106 DOI: 10.1039/c0ay00413h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Several approaches and technologies are currently available to study the glycosylated proteome (glycoproteomics) or the entire repertoire of glycans in a biological system (glycomics). The biological importance of glycosylation has driven the development of novel, sensitive separation and detection methods. New and improved methodologies, such as high throughput array systems and liquid chromatography-mass spectrometry for glycan profiling and sequencing, are emerging and are being applied in clinical research. A major thrust of glycoproteomics and glycomic clinical research is the application of these analytical tools to cancer research and is aimed at the discovery of glycan-based biomarkers for diagnosis of early stage human cancers, monitoring disease progression, measuring response to therapy, and detecting recurrence. The identification of cancer biomarkers requires a multidisciplinary approach and therefore this review discusses the strategies, technologies and methods currently used for N-glycoprotein/glycanbiomarker research.
Collapse
Affiliation(s)
- Fateme Tousi
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - Marina Hincapie
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| |
Collapse
|
36
|
Vanarsa K, Mohan C. Proteomics in rheumatology: the dawn of a new era. F1000 MEDICINE REPORTS 2010; 2:87. [PMID: 21283596 PMCID: PMC3026622 DOI: 10.3410/m2-87] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most rheumatic autoimmune diseases are complex in terms of their genetic origins and underlying pathogenic processes. Non-hypothesis-driven scanning platforms are adding novel insights to our understanding of these multifactorial diseases. This review summarizes the handful of recent proteomic studies that have been executed using samples from patients with rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis, osteoarthritis, or Sjogren's syndrome. The candidate biomarkers that have been uncovered in the reviewed studies have potential applications in diagnosis, prognosis, and theranostics. Though we are at the infancy of the proteomics era in rheumatology, the limited number of molecules uncovered thus far already hold promise. Ongoing research in proteomics holds tremendous potential for shaping how rheumatic diseases are diagnosed, prognosticated, and managed clinically over the coming years.
Collapse
Affiliation(s)
- Kamala Vanarsa
- Department of Internal Medicine, Rheumatic Divisions Department, UT Southwestern Medical Center 5323 Harry Hines Boulevard, Dallas, TX 75390-8884 USA
| | | |
Collapse
|
37
|
Liumbruno G, D’Alessandro A, Grazzini G, Zolla L. How has proteomics informed transfusion biology so far? Crit Rev Oncol Hematol 2010; 76:153-72. [DOI: 10.1016/j.critrevonc.2010.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 12/22/2009] [Accepted: 01/07/2010] [Indexed: 01/06/2023] Open
|
38
|
Beaudry F. Stability comparison between sample preparation procedures for mass spectrometry-based targeted or shotgun peptidomic analysis. Anal Biochem 2010; 407:290-2. [DOI: 10.1016/j.ab.2010.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 07/30/2010] [Accepted: 08/12/2010] [Indexed: 12/16/2022]
|
39
|
Abstract
Thymosin beta(4) as well as the other members of the beta-thymosin family are important G-actin sequestering peptides. The chemical properties, the biosynthesis, and posttranslational modifications (PTMs) of these peptides are discussed. During biosynthesis of thymosin beta(4) the initiator methionine is removed and the N-terminus is acetylated. Research on proteomics revealed several acetylated lysine residues and two phosphorylated threonine residues. The enormous number of phosphorylable and acetylable sites in the human proteome raises the question about the biological significance of these PTMs in the context of beta-thymosins. Presently, this question cannot be answered because neither the concentration of these modified beta-thymosins in cells is known nor the consequences of the modifications on the biological function(s) of beta-thymosins have been studied yet. Thymosin beta(4) is also posttranslationally modified by transglutaminase forming covalent bonds with other molecules. Prolyl oligopeptidase generates ac-SDKP from thymosin beta(4). The concentration of C-terminal peptide fragments of thymosin beta(4) is elevated in the blood of patients with rheumatoid arthritis.
Collapse
Affiliation(s)
- E Hannappel
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany.
| |
Collapse
|
40
|
Proteomics for quality-control processes in transfusion medicine. Anal Bioanal Chem 2010; 398:111-24. [DOI: 10.1007/s00216-010-3799-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/24/2010] [Accepted: 04/27/2010] [Indexed: 12/23/2022]
|
41
|
Pemberton AD, Brown JK. In vitro interactions of extracellular histones with LDL suggest a potential pro-atherogenic role. PLoS One 2010; 5:e9884. [PMID: 20360839 PMCID: PMC2845606 DOI: 10.1371/journal.pone.0009884] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 03/08/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Nuclear histones have previously been shown to aggregate LDL in vitro, suggestive of a possible pro-atherogenic role. Recent studies indicate that histones are released during acute inflammation, and therefore might interact with circulating lipoproteins in vivo. In view of the associative link between inflammation and cardiovascular disease, the behaviour of histones was investigated using in vitro models of LDL retention and foam cell formation. METHODOLOGY/PRINCIPAL FINDINGS Heparin agarose beads were used as a model of a matrix rich in sulphated glycosaminoglycans, to which histones bind strongly. Histone-modified beads were observed to pull down more LDL from solution than untreated beads, indicating that histones can function as bridging molecules, enhancing LDL retention. Furthermore, addition of heparin inhibited histone-induced aggregation of LDL. To model foam cell formation, murine RAW 264.7 macrophages were incubated for 24 h in the presence of LDL, histones, LDL plus histones or vehicle control. Cells incubated with LDL in the presence of histones accumulated significantly more intracellular lipid than with LDL or histone alone. CONCLUSIONS/SIGNIFICANCE These results are consistent with a potential pro-atherogenic role for extracellular histones, which should be investigated further.
Collapse
Affiliation(s)
- Alan D Pemberton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom.
| | | |
Collapse
|
42
|
Tucholska M, Florentinus A, Williams D, Marshall JG. The endogenous peptides of normal human serum extracted from the acetonitrile-insoluble precipitate using modified aqueous buffer with analysis by LC-ESI-Paul ion trap and Qq-TOF. J Proteomics 2010; 73:1254-69. [PMID: 20211283 DOI: 10.1016/j.jprot.2010.02.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 01/10/2023]
Abstract
Many peptides of biological or medicinal importance may be derived from proteolytic actions and are found at low concentrations in human blood fluids. Endogenous polypeptides from human serum were precipitated in acetonitrile and the precipitate was then selectively extracted with water modified by organic solvents and collected over C18 resin. Extraction of serum with C18 alone, and the acetonitrile supernatant or ultrafiltration collected over C18, served as controls. The samples were analyzed by SDS-PAGE, or C18 high pressure liquid chromatography with electrospray ionization using a Paul ion trap and Qq-TOF. Spectra were correlated without specifying an enzyme using the X!TANDEM or the Paragon algorithms. Multiple endogenous peptides from plasminogen, coagulation factors, collagens, serum amyloid, receptors, zinc finger/bromo peptide proteins, ryanodine receptor, calmodulin binding activator, erythroid differentiation factor, testes cancer antigen, extracellular matrix protein, myeloid/lymphoid leukemia 2 and many low abundance proteins were correlated by X!TANDEM with protein expect values of approximately E-16 or less. Proteins with binding sites for nucleic acids, phosphoinositides, and other cellular locations were also observed using the Qq-TOF and Paragon algorithm. Proteins with low expectation scores and overlapping peptides sequences were observed. The existence of these proteins in serum has been confirmed by tryptic digestion and LC-ESI-MS/MS. The presence of plasminogen, serum amyloid and zinc finger RNA binding proteins were confirmed by Western blot. There was agreement on the detection of endogenous peptides from low abundance proteins associated with the biology of cancer from the examination of the blood peptides by ion trap and Qq-TOF, tryptic digests of blood proteins, and Western blot.
Collapse
Affiliation(s)
- Monika Tucholska
- Department of Chemistry and Biology, Faculty of Engineering and Applied Science, 350 Victoria Street, Toronto, ON, Canada M5B 2K3
| | | | | | | |
Collapse
|
43
|
Martins-De-Souza D, Dias-Neto E, Schmitt A, Falkai P, Gormanns P, Maccarrone G, Turck CW, Gattaz WF. Proteome analysis of schizophrenia brain tissue. World J Biol Psychiatry 2010; 11:110-20. [PMID: 20109112 DOI: 10.3109/15622970903490626] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Proteome analysis has emerged as a promising strategy to the identification of potential biomarkers and to further confirm the importance of certain pathways in the schizophrenia (SCZ) pathophysiology. Reviewing the results of 13 proteome studies in SCZ brain tissue, we aimed to provide information regarding potential proteins biomarkers as well as information about the pathophysiology of the disease. METHODS AND RESULTS Using two-dimensional gel electrophoresis and shotgun mass spectrometry, 31 proteins were consistently found differentially expressed in the brains of SCZ patients. The most frequent protein alterations reported in SCZ were related to brain energy metabolism, brain plasticity, and synaptic function, processes that are thought to belong to the core of the biology of this disease. The recurrent identification and validation of inter-related protein clusters, determined in different samples and approaches, strongly reinforces the putative involvement of certain pathways in SCZ. CONCLUSIONS The availability of reliable markers not only paves the way to the development of new therapeutic strategies but also points out the possibility of their use as peripheral blood markers that may potentially contribute to the early SCZ detection and early therapeutic intervention, both of which can reduce the social and cognitive consequences of the disease.
Collapse
|
44
|
Blood-related proteomics. J Proteomics 2009; 73:483-507. [PMID: 19567275 DOI: 10.1016/j.jprot.2009.06.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 12/12/2022]
Abstract
Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups has contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of the usefulness of proteomics in blood-related research is accurately given. In particular, proteomic tools could be adopted to follow the main steps of the blood-banking production processes (a comparison of collection methods, pathogen inactivation techniques, storage protocols). Thus proteomics has been recently transformed from a mere basic-research extremely-expensive toy into a dramatically-sensitive and efficient eye-lens to either delve into the depths of the molecular mechanisms of blood and blood components or to establish quality parameters in the blood-banking production chain totally anew.
Collapse
|