1
|
Chen C, Shu Y, Yan C, Li H, Huang Z, Shen S, Liu C, Jiang Y, Huang S, Wang Z, Mei F, Qin F, Liu X, Qiu W. Astrocyte-derived clusterin disrupts glial physiology to obstruct remyelination in mouse models of demyelinating diseases. Nat Commun 2024; 15:7791. [PMID: 39242637 PMCID: PMC11379856 DOI: 10.1038/s41467-024-52142-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 08/26/2024] [Indexed: 09/09/2024] Open
Abstract
Multiple sclerosis (MS) is a debilitating demyelinating disease characterized by remyelination failure attributed to inadequate oligodendrocyte precursor cells (OPCs) differentiation and aberrant astrogliosis. A comprehensive cell atlas reanalysis of clinical specimens brings to light heightened clusterin (CLU) expression in a specific astrocyte subtype links to active lesions in MS patients. Our investigation reveals elevated astrocytic CLU levels in both active lesions of patient tissues and female murine MS models. CLU administration stimulates primary astrocyte proliferation while concurrently impeding astrocyte-mediated clearance of myelin debris. Intriguingly, CLU overload directly impedes OPC differentiation and induces OPCs and OLs apoptosis. Mechanistically, CLU suppresses PI3K-AKT signaling in primary OPCs via very low-density lipoprotein receptor. Pharmacological activation of AKT rescues the damage inflicted by excess CLU on OPCs and ameliorates demyelination in the corpus callosum. Furthermore, conditional knockout of CLU emerges as a promising intervention, showcasing improved remyelination processes and reduced severity in murine MS models.
Collapse
Affiliation(s)
- Chen Chen
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Department of Neurosurgery, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yaqing Shu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chengkai Yan
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huilu Li
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhenchao Huang
- Department of Neurosurgery, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - ShiShi Shen
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chunxin Liu
- Department of Emergency, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanjun Jiang
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong SAR, China
- Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shixiong Huang
- Department of Neurology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, China
| | - Zhanhang Wang
- Department of Neurology, 999 Brain Hospital, Guangzhou, China
| | - Feng Mei
- Department of Histology and Embryology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Feng Qin
- Department of Neurosurgery, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Xiaodong Liu
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Wei Qiu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
2
|
Wurtz LI, Knyazhanskaya E, Sohaei D, Prassas I, Pittock S, Willrich MAV, Saadeh R, Gupta R, Atkinson HJ, Grill D, Stengelin M, Thebault S, Freedman MS, Diamandis EP, Scarisbrick IA. Identification of brain-enriched proteins in CSF as biomarkers of relapsing remitting multiple sclerosis. Clin Proteomics 2024; 21:42. [PMID: 38880880 PMCID: PMC11181608 DOI: 10.1186/s12014-024-09494-5] [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: 03/15/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a clinically and biologically heterogenous disease with currently unpredictable progression and relapse. After the development and success of neurofilament as a cerebrospinal fluid (CSF) biomarker, there is reinvigorated interest in identifying other markers of or contributors to disease. The objective of this study is to probe the predictive potential of a panel of brain-enriched proteins on MS disease progression and subtype. METHODS This study includes 40 individuals with MS and 14 headache controls. The MS cohort consists of 20 relapsing remitting (RR) and 20 primary progressive (PP) patients. The CSF of all individuals was analyzed for 63 brain enriched proteins using a method of liquid-chromatography tandem mass spectrometry. Wilcoxon rank sum test, Kruskal-Wallis one-way ANOVA, logistic regression, and Pearson correlation were used to refine the list of candidates by comparing relative protein concentrations as well as relation to known imaging and molecular biomarkers. RESULTS We report 30 proteins with some relevance to disease, clinical subtype, or severity. Strikingly, we observed widespread protein depletion in the disease CSF as compared to control. We identified numerous markers of relapsing disease, including KLK6 (kallikrein 6, OR = 0.367, p < 0.05), which may be driven by active disease as defined by MRI enhancing lesions. Other oligodendrocyte-enriched proteins also appeared at reduced levels in relapsing disease, namely CNDP1 (carnosine dipeptidase 1), LINGO1 (leucine rich repeat and Immunoglobin-like domain-containing protein 1), MAG (myelin associated glycoprotein), and MOG (myelin oligodendrocyte glycoprotein). Finally, we identified three proteins-CNDP1, APLP1 (amyloid beta precursor like protein 1), and OLFM1 (olfactomedin 1)-that were statistically different in relapsing vs. progressive disease raising the potential for use as an early biomarker to discriminate clinical subtype. CONCLUSIONS We illustrate the utility of targeted mass spectrometry in generating potential targets for future biomarker studies and highlight reductions in brain-enriched proteins as markers of the relapsing remitting disease stage.
Collapse
Affiliation(s)
- Lincoln I Wurtz
- Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Dorsa Sohaei
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Ioannis Prassas
- Mount Sinai Hospital, Toronto, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Sean Pittock
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, USA
| | | | - Ruba Saadeh
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ruchi Gupta
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Hunter J Atkinson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Diane Grill
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - Simon Thebault
- Department of Medicine and The Ottawa Research Institute, Ottawa, Canada
- Division of Multiple Sclerosis, Department of Neurology, The University of Pennsylvania, Philadelphia, USA
| | - Mark S Freedman
- Department of Medicine and The Ottawa Research Institute, Ottawa, Canada
| | | | - Isobel A Scarisbrick
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, USA.
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, 55905, USA.
| |
Collapse
|
3
|
Ponzini E. Tear biomarkers. Adv Clin Chem 2024; 120:69-115. [PMID: 38762243 DOI: 10.1016/bs.acc.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
An extensive exploration of lacrimal fluid molecular biomarkers in understanding and diagnosing a spectrum of ocular and systemic diseases is presented. The chapter provides an overview of lacrimal fluid composition, elucidating the roles of proteins, lipids, metabolites, and nucleic acids within the tear film. Pooled versus single-tear analysis is discussed to underline the benefits and challenges associated with both approaches, offering insights into optimal strategies for tear sample analysis. Subsequently, an in-depth analysis of tear collection methods is presented, with a focus on Schirmer's test strips and microcapillary tubes methods. Alternative tear collection techniques are also explored, shedding light on their applicability and advantages. Variability factors, including age, sex, and diurnal fluctuations, are examined in the context of their impact on tear biomarker analysis. The main body of the chapter is dedicated to discussing specific biomarkers associated with ocular discomfort and a wide array of ocular diseases. From dry eye disease and thyroid-associated ophthalmopathy to keratoconus, age-related macular degeneration, diabetic retinopathy, and glaucoma, the intricate relationship between molecular biomarkers and these conditions is thoroughly dissected. Expanding beyond ocular pathologies, the chapter explores the applicability of tear biomarkers in diagnosing systemic diseases such as multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer's disease, Parkinson's disease, and cancer. This broader perspective underscores the potential of lacrimal fluid analysis in offering non-invasive diagnostic tools for conditions with far-reaching implications.
Collapse
Affiliation(s)
- Erika Ponzini
- Department of Materials Science, University of Milano Bicocca, Milan, Italy; COMiB Research Center, University of Milano Bicocca, Milan, Italy.
| |
Collapse
|
4
|
Sohaei D, Thebault S, Avery LM, Batruch I, Lam B, Xu W, Saadeh RS, Scarisbrick IA, Diamandis EP, Prassas I, Freedman MS. Cerebrospinal fluid camk2a levels at baseline predict long-term progression in multiple sclerosis. Clin Proteomics 2023; 20:33. [PMID: 37644477 PMCID: PMC10466840 DOI: 10.1186/s12014-023-09418-9] [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: 03/17/2022] [Accepted: 06/28/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) remains a highly unpredictable disease. Many hope that fluid biomarkers may contribute to better stratification of disease, aiding the personalisation of treatment decisions, ultimately improving patient outcomes. OBJECTIVE The objective of this study was to evaluate the predictive value of CSF brain-specific proteins from early in the disease course of MS on long term clinical outcomes. METHODS In this study, 34 MS patients had their CSF collected and stored within 5 years of disease onset and were then followed clinically for at least 15 years. CSF concentrations of 64 brain-specific proteins were analyzed in the 34 patient CSF, as well as 19 age and sex-matched controls, using a targeted liquid-chromatography tandem mass spectrometry approach. RESULTS We identified six CSF brain-specific proteins that significantly differentiated MS from controls (p < 0.05) and nine proteins that could predict disease course over the next decade. CAMK2A emerged as a biomarker candidate that could discriminate between MS and controls and could predict long-term disease progression. CONCLUSION Targeted approaches to identify and quantify biomarkers associated with MS in the CSF may inform on long term MS outcomes. CAMK2A may be one of several candidates, warranting further exploration.
Collapse
Affiliation(s)
- Dorsa Sohaei
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Simon Thebault
- Department of Medicine, The Ottawa Hospital, 01 Smyth Road, Box 601, Ottawa, ON, K1H 8L6, Canada
- The Ottawa Hospital Research Institute, Ottawa, Canada
| | - Lisa M Avery
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Department of Biostatistics, The Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Ihor Batruch
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Brian Lam
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, United States of America
| | - Wei Xu
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Department of Biostatistics, The Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Rubah S Saadeh
- Department of Physical Medicine and Rehabilitation, Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Isobel A Scarisbrick
- Department of Physical Medicine and Rehabilitation, Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Ioannis Prassas
- Mount Sinai Hospital, Joseph & Wolf Lebovic Ctr, 60 Murray St [Box 32]; Flr 6 - Rm L6-201, Toronto, ON, M5T 3L9, Canada.
- Laboratory Medicine Program, University Health Network, Toronto, Canada.
| | - Mark S Freedman
- Department of Medicine, The Ottawa Hospital, 01 Smyth Road, Box 601, Ottawa, ON, K1H 8L6, Canada.
- The Ottawa Hospital Research Institute, Ottawa, Canada.
| |
Collapse
|
5
|
Steinskog ESS, Finne K, Enger M, Helgeland L, Iversen PO, McCormack E, Wiig H, Tenstad O. Isolation of lymph shows dysregulation of STAT3 and CREB pathways in the spleen and liver during leukemia development in a rat model. Microcirculation 2023; 30:e12800. [PMID: 36702790 DOI: 10.1111/micc.12800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND AND AIMS Acute myeloid leukemia (AML) is a heterogeneous malignant condition characterized by massive infiltration of poorly differentiated white blood cells in the blood stream, bone marrow, and extramedullary sites. During leukemic development, hepatosplenomegaly is expected to occur because large blood volumes are continuously filtered through these organs. We asked whether infiltration of leukemic blasts initiated a response that could be detected in the interstitial fluid phase of the spleen and liver. MATERIAL AND METHODS We used a rat model known to mimic human AML in growth characteristics and behavior. By cannulating efferent lymphatic vessels from the spleen and liver, we were able to monitor the response of the microenvironment during AML development. RESULTS AND DISCUSSION Flow cytometric analysis of lymphocytes showed increased STAT3 and CREB signaling in spleen and depressed signaling in liver, and proteins related to these pathways were identified with a different profile in lymph and plasma in AML compared with control. Additionally, several proteins were differently regulated in the microenvironment of spleen and liver in AML when compared with control. CONCLUSION Interstitial fluid, and its surrogate efferent lymph, can be used to provide unique information about responses in AML-infiltered organs and substances released to the general circulation during leukemia development.
Collapse
Affiliation(s)
| | - Kenneth Finne
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marianne Enger
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Lars Helgeland
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Per Ole Iversen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Emmet McCormack
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | - Helge Wiig
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Olav Tenstad
- Department of Biomedicine, University of Bergen, Bergen, Norway
| |
Collapse
|
6
|
Li Y, Hu F, Deng J, Huang X, Zhou C, Wu M, Duan D. Proteomic analysis of radioiodine-refractory differentiated thyroid cancer identifies CHI3L1 upregulation in association with dysfunction of the sodium-iodine symporter. Oncol Lett 2022; 25:36. [PMID: 36589664 PMCID: PMC9773326 DOI: 10.3892/ol.2022.13622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Radioiodine refractory differentiated thyroid cancer (RR-DTC) is the main factor adversely affecting the overall survival rate of patients with thyroid cancer. The aim of the present study was to investigate the underlying molecular mechanism of pathogenesis of RR-DTC and to explore novel therapeutic targets for clinical treatment. A proteomic analysis was performed using the tumor tissues of patients with RR-DTC. A total of 6 metastatic lymph nodes were collected during lymph node dissection, 3 from patients with RR-DTC and 3 from patients with papillary thyroid cancer. The expression of chitinase-3-like 1 (CHI3L1) and sodium-iodine symporter (NIS) in the tumor tissue was detected by immunohistochemistry (IHC). Western blotting was used to detect the expression of CHI3L1, phosphorylated (p)-MEK and p-ERK1/2 in PTC-K1 cells transfected with CHI3L1 overexpression vector. The proteomic analysis identified 665 differentially expressed proteins (DEPs), including 327 upregulated and 338 downregulated proteins in the RR-DTC group, which were enriched in 59 signaling pathways by Kyoto Encyclopedia of Genes and Genomes database analysis. In particular, CHI3L1 was demonstrated to be significantly upregulated in RR-DTC as evidenced by quantitative proteomic analysis and IHC. Western blotting suggested that the overexpression of CHI3L1 activated the MEK/ERK1/2 signaling pathway, which may lead to NIS dysfunction. In conclusion, the present study suggests that CHI3L1 is a potential molecular target for the radiotherapy of patients with RR-DTC.
Collapse
Affiliation(s)
- Yunjie Li
- Department of Nuclear Medicine, The Second People's Hospital of Shenzhen, Shenzhen, Guangdong 518035, P.R. China
| | - Fengqiong Hu
- Department of Nuclear Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jie Deng
- Department of Nuclear Medicine, The Second Affiliated Hospital of Army Medical University, Chongqing 400037, P.R. China
| | - Xin Huang
- Department of Nuclear Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Chunyan Zhou
- Department of Nuclear Medicine, Chongqing General Hospital, Chongqing 401147, P.R. China
| | - Mengxue Wu
- Department of Nuclear Medicine, The First Hospital Affiliated to Army Medical University, Chongqing 400038, P.R. China
| | - Dong Duan
- Department of Nuclear Medicine, Chongqing General Hospital, Chongqing 401147, P.R. China,Correspondence to: Dr Dong Duan, Department of Nuclear Medicine, Chongqing General Hospital, 118 Xingguang Avenue, Yubei, Chongqing 401147, P.R. China, E-mail:
| |
Collapse
|
7
|
Almuslehi MSM, Sen MK, Shortland PJ, Mahns DA, Coorssen JR. Histological and Top-Down Proteomic Analyses of the Visual Pathway in the Cuprizone Demyelination Model. J Mol Neurosci 2022; 72:1374-1401. [PMID: 35644788 PMCID: PMC9170674 DOI: 10.1007/s12031-022-01997-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/07/2022] [Indexed: 10/27/2022]
Abstract
Abstract
A change in visual perception is a frequent early symptom of multiple sclerosis (MS), the pathoaetiology of which remains unclear. Following a slow demyelination process caused by 12 weeks of low-dose (0.1%) cuprizone (CPZ) consumption, histology and proteomics were used to investigate components of the visual pathway in young adult mice. Histological investigation did not identify demyelination or gliosis in the optic tracts, pretectal nuclei, superior colliculi, lateral geniculate nuclei or visual cortices. However, top-down proteomic assessment of the optic nerve/tract revealed a significant change in the abundance of 34 spots in high-resolution two-dimensional (2D) gels. Subsequent liquid chromatography-tandem mass spectrometry (LC-TMS) analysis identified alterations in 75 proteoforms. Literature mining revealed the relevance of these proteoforms in terms of proteins previously implicated in animal models, eye diseases and human MS. Importantly, 24 proteoforms were not previously described in any animal models of MS, eye diseases or MS itself. Bioinformatic analysis indicated involvement of these proteoforms in cytoskeleton organization, metabolic dysregulation, protein aggregation and axonal support. Collectively, these results indicate that continuous CPZ-feeding, which evokes a slow demyelination, results in proteomic changes that precede any clear histological changes in the visual pathway and that these proteoforms may be potential early markers of degenerative demyelinating conditions.
Collapse
|
8
|
Liu H, Wang Z, Li H, Li M, Han B, Qi Y, Wang H, Gao J. Label-free Quantitative Proteomic Analysis of Cerebrospinal Fluid and Serum in Patients With Relapse-Remitting Multiple Sclerosis. Front Genet 2022; 13:892491. [PMID: 35571066 PMCID: PMC9092947 DOI: 10.3389/fgene.2022.892491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The lack of effective serum and cerebrospinal fluid (CSF) biomarkers remains a barrier to early diagnosis and treatment of multiple sclerosis (MS). The study is to identify the diagnostic biomarkers of serum and CSF in patients who suffered MS. Methods: At first, we performed differential analysis of CSF and serum proteomics on control and relapse-remitting multiple sclerosis (RRMS) patients. Secondly, CSF and serum’s differential proteins were compared, in order to identify the significative proteins. Finally, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis were performed on the differential proteins in serum and CSF respectively to clarify their common biological functions and pathways. Results: At the first step, in CSF, 73 proteins were significantly differentially expressed in the RRMS set compared with the controls. In serum, 22 proteins were differentially expressed. Secondly, we found MMP2 C8G and CFH were the same high expression trend in CSF and serum. Finally, we found the differential proteins in serum and CSF are mostly participated in biological processes: immuno-inflammatory response, neuronal development, cell adhesion and signaling. Conclusion: MMP2, C8G and CFH may participate in the pathogenesis of RRMS, which are the potential diagnostic biomarkers of the disease.
Collapse
Affiliation(s)
- Haijie Liu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ziwen Wang
- Department of Neurology, Baoding No. 1 Central Hospital, Baoding, China
| | - He Li
- Department of Automation, College of Information Science and Engineering, Tianjin Tianshi College, Tianjin, China
| | - Meijie Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Bo Han
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yuan Qi
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Huailu Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Juan Gao
- Department of Neurology, Baoding No. 1 Central Hospital, Baoding, China
| |
Collapse
|
9
|
Jin Y, Wang W, Wang Q, Zhang Y, Zahid KR, Raza U, Gong Y. Alpha-1-antichymotrypsin as a novel biomarker for diagnosis, prognosis, and therapy prediction in human diseases. Cancer Cell Int 2022; 22:156. [PMID: 35439996 PMCID: PMC9019971 DOI: 10.1186/s12935-022-02572-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/06/2022] [Indexed: 12/15/2022] Open
Abstract
The glycoprotein alpha-1-antichymotrypsin (AACT), a serine protease inhibitor, is mainly synthesized in the liver and then secreted into the blood and is involved in the acute phase response, inflammation, and proteolysis. The dysregulation of AACT and its glycosylation levels are associated with tumor progression and recurrence, and could be used as a biomarker for tumor monitoring. In this review, we summarized the expression level, glycosylation modification, and biological characteristics of AACT during inflammation, neurodegenerative or other elderly diseases, and tumorigenesis, as well as, focused on the biological roles of AACT in cancer. The aberrant expression of AACT in cancer might be due to genetic alterations and/or immune by bioinformatics analysis. Moreover, AACT may serve as a diagnostic or prognostic biomarker or therapeutic target in tumors. Furthermore, we found that the expression of AACT was associated with the overall survival of patients with human cancers. Decreased AACT expression was associated with poor survival in patients with liver cancer, increased AACT expression was associated with shorter survival in patients with pancreatic cancer, and decreased AACT expression was associated with shorter survival in patients with early lung cancer. The review confirmed the key roles of AACT in tumorigenesis, suggesting that the glycoprotein AACT may serve as a biomarker for tumor diagnosis and prognosis, and could be a potential therapeutic target for human diseases.
Collapse
Affiliation(s)
- Yanxia Jin
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Weidong Wang
- College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China.
| | - Qiyun Wang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Yueyang Zhang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Kashif Rafiq Zahid
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science and Oceanography, Carson International Cancer Center, Shenzhen University, Shenzhen, Guangdong, China
| | - Umar Raza
- Department of Biological Sciences, National University of Medical Sciences (NUMS), PWD Campus, Rawalpindi, Pakistan
| | - Yongsheng Gong
- Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, No.26 Daoqian Street, Suzhou, 215002, China.
| |
Collapse
|
10
|
Salazar IL, Lourenço AST, Manadas B, Baldeiras I, Ferreira C, Teixeira AC, Mendes VM, Novo AM, Machado R, Batista S, Macário MDC, Grãos M, Sousa L, Saraiva MJ, Pais AACC, Duarte CB. Posttranslational modifications of proteins are key features in the identification of CSF biomarkers of multiple sclerosis. J Neuroinflammation 2022; 19:44. [PMID: 35135578 PMCID: PMC8822857 DOI: 10.1186/s12974-022-02404-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
Background Multiple sclerosis is an inflammatory and degenerative disease of the central nervous system (CNS) characterized by demyelination and concomitant axonal loss. The lack of a single specific test, and the similarity to other inflammatory diseases of the central nervous system, makes it difficult to have a clear diagnosis of multiple sclerosis. Therefore, laboratory tests that allows a clear and definite diagnosis, as well as to predict the different clinical courses of the disease are of utmost importance. Herein, we compared the cerebrospinal fluid (CSF) proteome of patients with multiple sclerosis (in the relapse–remitting phase of the disease) and other diseases of the CNS (inflammatory and non-inflammatory) aiming at identifying reliable biomarkers of multiple sclerosis. Methods CSF samples from the discovery group were resolved by 2D-gel electrophoresis followed by identification of the protein spots by mass spectrometry. The results were analyzed using univariate (Student’s t test) and multivariate (Hierarchical Cluster Analysis, Principal Component Analysis, Linear Discriminant Analysis) statistical and numerical techniques, to identify a set of protein spots that were differentially expressed in CSF samples from patients with multiple sclerosis when compared with other two groups. Validation of the results was performed in samples from a different set of patients using quantitative (e.g., ELISA) and semi-quantitative (e.g., Western Blot) experimental approaches. Results Analysis of the 2D-gels showed 13 protein spots that were differentially expressed in the three groups of patients: Alpha-1-antichymotrypsin, Prostaglandin-H2-isomerase, Retinol binding protein 4, Transthyretin (TTR), Apolipoprotein E, Gelsolin, Angiotensinogen, Agrin, Serum albumin, Myosin-15, Apolipoprotein B-100 and EF-hand calcium-binding domain—containing protein. ELISA experiments allowed validating part of the results obtained in the proteomics analysis and showed that some of the alterations in the CSF proteome are also mirrored in serum samples from multiple sclerosis patients. CSF of multiple sclerosis patients was characterized by TTR oligomerization, thus highlighting the importance of analyzing posttranslational modifications of the proteome in the identification of novel biomarkers of the disease. Conclusions The model built based on the results obtained upon analysis of the 2D-gels and in the validation phase attained an accuracy of about 80% in distinguishing multiple sclerosis patients and the other two groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02404-2.
Collapse
Affiliation(s)
- Ivan L Salazar
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Ana S T Lourenço
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Inês Baldeiras
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Cláudia Ferreira
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Anabela Claro Teixeira
- Molecular Neurobiology Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Vera M Mendes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ana Margarida Novo
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Rita Machado
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Sónia Batista
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria do Carmo Macário
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Mário Grãos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.,Biocant-Associação de Transferência de Tecnologia, Cantanhede, Portugal
| | - Lívia Sousa
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria João Saraiva
- Molecular Neurobiology Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Alberto A C C Pais
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Carlos B Duarte
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
| |
Collapse
|
11
|
Sanchez D, Ganfornina MD. The Lipocalin Apolipoprotein D Functional Portrait: A Systematic Review. Front Physiol 2021; 12:738991. [PMID: 34690812 PMCID: PMC8530192 DOI: 10.3389/fphys.2021.738991] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022] Open
Abstract
Apolipoprotein D is a chordate gene early originated in the Lipocalin protein family. Among other features, regulation of its expression in a wide variety of disease conditions in humans, as apparently unrelated as neurodegeneration or breast cancer, have called for attention on this gene. Also, its presence in different tissues, from blood to brain, and different subcellular locations, from HDL lipoparticles to the interior of lysosomes or the surface of extracellular vesicles, poses an interesting challenge in deciphering its physiological function: Is ApoD a moonlighting protein, serving different roles in different cellular compartments, tissues, or organisms? Or does it have a unique biochemical mechanism of action that accounts for such apparently diverse roles in different physiological situations? To answer these questions, we have performed a systematic review of all primary publications where ApoD properties have been investigated in chordates. We conclude that ApoD ligand binding in the Lipocalin pocket, combined with an antioxidant activity performed at the rim of the pocket are properties sufficient to explain ApoD association with different lipid-based structures, where its physiological function is better described as lipid-management than by long-range lipid-transport. Controlling the redox state of these lipid structures in particular subcellular locations or extracellular structures, ApoD is able to modulate an enormous array of apparently diverse processes in the organism, both in health and disease. The new picture emerging from these data should help to put the physiological role of ApoD in new contexts and to inspire well-focused future research.
Collapse
Affiliation(s)
- Diego Sanchez
- Instituto de Biologia y Genetica Molecular, Unidad de Excelencia, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas, Valladolid, Spain
| | - Maria D Ganfornina
- Instituto de Biologia y Genetica Molecular, Unidad de Excelencia, Universidad de Valladolid-Consejo Superior de Investigaciones Cientificas, Valladolid, Spain
| |
Collapse
|
12
|
Bjørkum AA, Carrasco Duran A, Frode B, Sinha Roy D, Rosendahl K, Birkeland E, Stuhr L. Human blood serum proteome changes after 6 hours of sleep deprivation at night. SLEEP SCIENCE AND PRACTICE 2021. [DOI: 10.1186/s41606-021-00066-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Abstract
Background
The aim of this study was to discover significantly changed proteins in human blood serum after loss of 6 h sleep at night. Furthermore, to reveal affected biological process- and molecular function categories that might be clinically relevant, by exploring systems biological databases.
Methods
Eight females were recruited by volunteer request. Peripheral venous whole blood was sampled at 04:00 am, after 6 h of sleep and after 6 h of sleep deprivation. We used within-subjects design (all subjects were their own control). Blood serum from each subject was depleted before protein digestion by trypsin and iTRAQ labeling. Labled peptides were analyzed by mass spectrometry (LTQ OritrapVelos Elite) connected to a LC system (Dionex Ultimate NCR-3000RS).
Results
We identified 725 proteins in human blood serum. 34 proteins were significantly differentially expressed after 6 h of sleep deprivation at night. Out of 34 proteins, 14 proteins were up-regulated, and 20 proteins were down-regulated. We emphasized the functionality of the 16 proteins commonly differentiated in all 8 subjects and the relation to pathological conditions. In addition, we discussed Histone H4 (H4) and protein S100-A6/Calcyclin (S10A6) that were upregulated more than 1.5-fold. Finally, we discussed affected biological process- and molecular function categories.
Conclusions
Overall, our study suggest that acute sleep deprivation, at least in females, affects several known biological processes- and molecular function categories and associates to proteins that also are changed under pathological conditions like impaired coagulation, oxidative stress, immune suppression, neurodegenerative related disorder, and cancer. Data are available via ProteomeXchange with identifier PXD021004.
Collapse
|
13
|
Proteomics of Multiple Sclerosis: Inherent Issues in Defining the Pathoetiology and Identifying (Early) Biomarkers. Int J Mol Sci 2021; 22:ijms22147377. [PMID: 34298997 PMCID: PMC8306353 DOI: 10.3390/ijms22147377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple Sclerosis (MS) is a demyelinating disease of the human central nervous system having an unconfirmed pathoetiology. Although animal models are used to mimic the pathology and clinical symptoms, no single model successfully replicates the full complexity of MS from its initial clinical identification through disease progression. Most importantly, a lack of preclinical biomarkers is hampering the earliest possible diagnosis and treatment. Notably, the development of rationally targeted therapeutics enabling pre-emptive treatment to halt the disease is also delayed without such biomarkers. Using literature mining and bioinformatic analyses, this review assessed the available proteomic studies of MS patients and animal models to discern (1) whether the models effectively mimic MS; and (2) whether reasonable biomarker candidates have been identified. The implication and necessity of assessing proteoforms and the critical importance of this to identifying rational biomarkers are discussed. Moreover, the challenges of using different proteomic analytical approaches and biological samples are also addressed.
Collapse
|
14
|
Cao A, Chen Y, Ni Z, Zhang C, Cao M, Cai L. Production mechanism of semicarbazide from protein in Chinese softshell turtles at different drying temperatures based on TMT-tagged quantitative proteomics. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
15
|
Aït Amiri S, Deboux C, Soualmia F, Chaaya N, Louet M, Duplus E, Betuing S, Nait Oumesmar B, Masurier N, El Amri C. Identification of First-in-Class Inhibitors of Kallikrein-Related Peptidase 6 That Promote Oligodendrocyte Differentiation. J Med Chem 2021; 64:5667-5688. [PMID: 33949859 DOI: 10.1021/acs.jmedchem.0c02175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune demyelinating disease of the central nervous system (CNS) that causes severe motor, sensory, and cognitive impairments. Kallikrein-related peptidase (KLK)6 is the most abundant serine protease secreted in the CNS, mainly by oligodendrocytes, the myelin-producing cells of the CNS, and KLK6 is assumed to be a robust biomarker of MS, since it is highly increased in the cerebrospinal fluid (CSF) of MS patients. Here, we report the design and biological evaluation of KLK6's low-molecular-weight inhibitors, para-aminobenzyl derivatives. Interestingly, selected hit compounds were selective of the KLK6 proteolytic network encompassing KLK1 and plasmin that also participate in the development of MS physiopathology. Moreover, hits were found noncytotoxic on primary cultures of murine neurons and oligodendrocyte precursor cells (OPCs). Among them, two compounds (32 and 42) were shown to promote the differentiation of OPCs into mature oligodendrocytes in vitro constituting thus emerging leads for the development of regenerative therapies.
Collapse
Affiliation(s)
- Sabrina Aït Amiri
- Faculty of Sciences and Engineering, IBPS, UMR 8256 CNRS-UPMC, ERL INSERM U1164, Biological Adaptation and Ageing, Sorbonne Université, F-75252 Paris, France
| | - Cyrille Deboux
- Institut du Cerveau, Inserm U 1127, CNRS UMR 7725, Sorbonne Université, F-75013 Paris, France
| | - Feryel Soualmia
- Faculty of Sciences and Engineering, IBPS, UMR 8256 CNRS-UPMC, ERL INSERM U1164, Biological Adaptation and Ageing, Sorbonne Université, F-75252 Paris, France
| | - Nancy Chaaya
- Faculty of Sciences and Engineering, IBPS, UMR 8256 CNRS-UPMC, ERL INSERM U1164, Biological Adaptation and Ageing, Sorbonne Université, F-75252 Paris, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, F-34093 Montpellier, France
| | - Eric Duplus
- Faculty of Sciences and Engineering, IBPS, UMR 8256 CNRS-UPMC, ERL INSERM U1164, Biological Adaptation and Ageing, Sorbonne Université, F-75252 Paris, France
| | - Sandrine Betuing
- Faculty of Sciences and Engineering, IBPS, UMR 8246-CNRS/INSERM U1130, Neurosciences Paris Seine, Sorbonne Université, F-75252 Paris, France
| | - Brahim Nait Oumesmar
- Institut du Cerveau, Inserm U 1127, CNRS UMR 7725, Sorbonne Université, F-75013 Paris, France
| | - Nicolas Masurier
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, F-34093 Montpellier, France
| | - Chahrazade El Amri
- Faculty of Sciences and Engineering, IBPS, UMR 8256 CNRS-UPMC, ERL INSERM U1164, Biological Adaptation and Ageing, Sorbonne Université, F-75252 Paris, France
| |
Collapse
|
16
|
van Lierop ZY, Wieske L, Koel-Simmelink MJ, Chatterjee M, Dekker I, Leurs CE, Willemse EA, Moraal B, Barkhof F, Eftimov F, Uitdehaag BM, Killestein J, Teunissen CE. Serum contactin-1 as a biomarker of long-term disease progression in natalizumab-treated multiple sclerosis. Mult Scler 2021; 28:102-110. [PMID: 33890520 PMCID: PMC8689420 DOI: 10.1177/13524585211010097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Natalizumab treatment provides a model for non-inflammation-induced disease progression in multiple sclerosis (MS). OBJECTIVE To study serum contactin-1 (sCNTN1) as a novel biomarker for disease progression in natalizumab-treated relapsing-remitting MS (RRMS) patients. METHODS Eighty-nine natalizumab-treated RRMS patients with minimum follow-up of 3 years were included. sCNTN1 was analyzed at baseline (before natalizumab initiation), 3, 12, 24 months (M) and last follow-up (median 5.2 years) and compared to 222 healthy controls (HC) and 15 primary progressive MS patients (PPMS). Results were compared between patients with progressive, stable, or improved disability according to EDSS-plus criteria. RESULTS Median sCNTN1 levels (ng/mL,) in RRMS (baseline: 10.7, 3M: 9.7, 12M: 10.4, 24M: 10.8; last follow-up: 9.7) were significantly lower compared to HC (12.5; p ⩽ 0.001). It was observed that 48% of patients showed progression during follow-up, 11% improved, and 40% remained stable. sCNTN1 levels were significantly lower in progressors both at baseline and at 12M compared to non-progressors. A 1 ng/mL decrease in baseline sCNTN1 was consistent with an odds ratio of 1.23 (95% confidence interval 1.04-1.45) (p = 0.017) for progression during follow-up. CONCLUSION Lower baseline sCNTN1 concentrations were associated with long-term disability progression during natalizumab treatment, making it a possible blood-based prognostic biomarker for RRMS.
Collapse
Affiliation(s)
- Zoë Ygj van Lierop
- Department of Neurology, Amsterdam UMC, Vrije Universiteit Amsterdam, MS Center Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Luuk Wieske
- Department of Neurology and Neurophysiology, Amsterdam UMC, Academisch Medisch Centrum, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Marleen Ja Koel-Simmelink
- Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Neurochemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Madhurima Chatterjee
- Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Neurochemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Iris Dekker
- Department of Neurology, Amsterdam UMC, Vrije Universiteit Amsterdam, MS Center Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands/Department of Rehabilitation Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Cyra E Leurs
- Department of Neurology, Amsterdam UMC, Vrije Universiteit Amsterdam, MS Center Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Eline Aj Willemse
- Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Neurochemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Bastiaan Moraal
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, MS Center Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, MS Center Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands/Institutes of Neurology and Healthcare Engineering, University College London, London, UK
| | - Filip Eftimov
- Department of Neurology and Neurophysiology, Amsterdam UMC, Academisch Medisch Centrum, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Bernhard Mj Uitdehaag
- Department of Neurology, Amsterdam UMC, Vrije Universiteit Amsterdam, MS Center Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- Department of Neurology, Amsterdam UMC, Vrije Universiteit Amsterdam, MS Center Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte E Teunissen
- Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Neurochemistry Laboratory and Biobank, Amsterdam Neuroscience, Amsterdam, The Netherlands
| |
Collapse
|
17
|
Guldbrandsen A, Lereim RR, Jacobsen M, Garberg H, Kroksveen AC, Barsnes H, Berven FS. Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis. Clin Proteomics 2020; 17:33. [PMID: 32963504 PMCID: PMC7499868 DOI: 10.1186/s12014-020-09296-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/08/2020] [Indexed: 12/25/2022] Open
Abstract
Background Verification of cerebrospinal fluid (CSF) biomarkers for multiple sclerosis and other neurological diseases is a major challenge due to a large number of candidates, limited sample material availability, disease and biological heterogeneity, and the lack of standardized assays. Furthermore, verification studies are often based on a low number of proteins from a single discovery experiment in medium-sized cohorts, where antibodies and surrogate peptides may differ, thus only providing an indication of proteins affected by the disease and not revealing the bigger picture or concluding on the validity of the markers. We here present a standard approach for locating promising biomarker candidates based on existing knowledge, resulting in high-quality assays covering the main biological processes affected by multiple sclerosis for comparable measurements over time. Methods Biomarker candidates were located in CSF-PR (proteomics.uib.no/csf-pr), and further filtered based on estimated concentration in CSF and biological function. Peptide surrogates for internal standards were selected according to relevant criteria, parallel reaction monitoring (PRM) assays created, and extensive assay quality testing performed, i.e. intra- and inter-day variation, trypsin digestion status over time, and whether the peptides were able to separate multiple sclerosis patients and controls. Results Assays were developed for 25 proteins, represented by 72 peptides selected according to relevant guidelines and available literature and tested for assay peptide suitability. Stability testing revealed 64 peptides with low intra- and inter-day variations, with 44 also being stably digested after 16 h of trypsin digestion, and 37 furthermore showing a significant difference between multiple sclerosis and controls, thereby confirming literature findings. Calibration curves and the linear area of measurement have, so far, been determined for 17 of these peptides. Conclusions We present 37 high-quality PRM assays across 21 CSF-proteins found to be affected by multiple sclerosis, along with a recommended workflow for future development of new assays. The assays can directly be used by others, thus enabling better comparison between studies. Finally, the assays can robustly and stably monitor biological processes in multiple sclerosis patients over time, thus potentially aiding in diagnosis and prognosis, and ultimately in treatment decisions.
Collapse
Affiliation(s)
- Astrid Guldbrandsen
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Mari Jacobsen
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Hilde Garberg
- Biobank Haukeland, Haukeland University Hospital, Bergen, Norway
| | | | - Harald Barsnes
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway
| |
Collapse
|
18
|
Kuiperij HB, Hondius DC, Kersten I, Versleijen AAM, Rozemuller AJM, Greenberg SM, Schreuder FHBM, Klijn CJM, Verbeek MM. Apolipoprotein D: a potential biomarker for cerebral amyloid angiopathy. Neuropathol Appl Neurobiol 2020; 46:431-440. [PMID: 31872472 DOI: 10.1111/nan.12595] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/18/2019] [Indexed: 01/08/2023]
Abstract
AIMS We investigated the potential of apolipoprotein D (apoD) as cerebrospinal fluid (CSF) biomarker for cerebral amyloid angiopathy (CAA) after confirmation of its association with CAA pathology in human brain tissue. METHODS The association of apoD with CAA pathology was analysed in human occipital lobe tissue of CAA (n = 9), Alzheimer's disease (AD) (n = 11) and healthy control cases (n = 11). ApoD levels were quantified in an age- and sex-matched CSF cohort of CAA patients (n = 31), AD patients (n = 27) and non-neurological controls (n = 67). The effects of confounding factors (age, sex, serum levels) on apoD levels were studied using CSF of non-neurological controls (age range 16-85 years), and paired CSF and serum samples. RESULTS ApoD was strongly associated with amyloid deposits in vessels, but not with parenchymal plaques in human brain tissue. CSF apoD levels correlated with age and were higher in men than women in subjects >50 years. The apoD CSF/serum ratio correlated with the albumin ratio. When controlling for confounding factors, CSF apoD levels were significantly lower in CAA patients compared with controls and compared with AD patients (P = 0.0008). CONCLUSIONS Our data show that apoD is specifically associated with CAA pathology and may be a CSF biomarker for CAA, but clinical application is complicated due to dependency on age, sex and blood-CSF barrier integrity. Well-controlled follow-up studies are required to determine whether apoD can be used as reliable biomarker for CAA.
Collapse
Affiliation(s)
- H B Kuiperij
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud Alzheimer Centre, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - D C Hondius
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.,Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - I Kersten
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud Alzheimer Centre, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A A M Versleijen
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A J M Rozemuller
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - S M Greenberg
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - F H B M Schreuder
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud Alzheimer Centre, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C J M Klijn
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud Alzheimer Centre, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M M Verbeek
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud Alzheimer Centre, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
19
|
Dynamics of clusterin protein expression in the brain and plasma following experimental traumatic brain injury. Sci Rep 2019; 9:20208. [PMID: 31882899 PMCID: PMC6934775 DOI: 10.1038/s41598-019-56683-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022] Open
Abstract
Progress in the preclinical and clinical development of neuroprotective and antiepileptogenic treatments for traumatic brain injury (TBI) necessitates the discovery of prognostic biomarkers for post-injury outcome. Our previous mRNA-seq data revealed a 1.8–2.5 fold increase in clusterin mRNA expression in lesioned brain areas in rats with lateral fluid-percussion injury (FPI)-induced TBI. On this basis, we hypothesized that TBI leads to increases in the brain levels of clusterin protein, and consequently, increased plasma clusterin levels. For evaluation, we induced TBI in adult male Sprague-Dawley rats (n = 80) by lateral FPI. We validated our mRNA-seq findings with RT-qPCR, confirming increased clusterin mRNA levels in the perilesional cortex (FC 3.3, p < 0.01) and ipsilateral thalamus (FC 2.4, p < 0.05) at 3 months post-TBI. Immunohistochemistry revealed a marked increase in extracellular clusterin protein expression in the perilesional cortex and ipsilateral hippocampus (7d to 1 month post-TBI), and ipsilateral thalamus (14d to 12 months post-TBI). In the thalamus, punctate immunoreactivity was most intense around activated microglia and mitochondria. Enzyme-linked immunoassays indicated that an acute 15% reduction, rather than an increase in plasma clusterin levels differentiated animals with TBI from sham-operated controls (AUC 0.851, p < 0.05). Our findings suggest that plasma clusterin is a candidate biomarker for acute TBI diagnosis.
Collapse
|
20
|
Chatterjee M, Koel-Simmelink MJ, Verberk IM, Killestein J, Vrenken H, Enzinger C, Ropele S, Fazekas F, Khalil M, Teunissen CE. Contactin-1 and contactin-2 in cerebrospinal fluid as potential biomarkers for axonal domain dysfunction in multiple sclerosis. Mult Scler J Exp Transl Clin 2018; 4:2055217318819535. [PMID: 30627437 PMCID: PMC6305953 DOI: 10.1177/2055217318819535] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/31/2018] [Accepted: 11/22/2018] [Indexed: 01/06/2023] Open
Abstract
Background Contactin-1 and contactin-2 are important for the maintenance of axonal integrity. Objective To investigate the cerebrospinal fluid levels of contactin-1 and contactin-2 in multiple sclerosis patients and controls, and their potential use as prognostic markers for neurodegeneration. Methods Cerebrospinal fluid contactin-1 and contactin-2 were measured in relapsing–remitting multiple sclerosis (n = 41), secondary progressive multiple sclerosis (n = 26) and primary progressive multiple sclerosis patients (n = 13) and controls (n = 18), and in a second cohort with clinically isolated syndrome patients (n = 88, median clinical follow-up period of 2.3 years) and controls (n = 20). Correlations/linear regressions were analysed with other baseline cerebrospinal fluid axonal damage markers and cross-sectional/longitudinal magnetic resonance imaging features. Results Contactin-1 and contactin-2 levels were up to 1.4-fold reduced in relapsing–remitting multiple sclerosis (contactin-1: p = 0.01, contactin-2: p = 0.02) and secondary progressive multiple sclerosis (contactin-1: p = 0.05, contactin-2: p = 0.02) compared to controls. In clinically isolated syndrome patients, contactin-1 tended to increase when compared to controls (p = 0.07). Both contactin-1 and contactin-2 correlated with neurofilament light, neurofilament heavy and magnetic resonance imaging metrics differently depending on the disease stage. In clinically isolated syndrome patients, baseline contactin-2 level (β = –0.42, p = 0.04) predicted the longitudinal decline in cortex volume. Conclusion Cerebrospinal fluid contactin-1 and contactin-2 reveal axonal dysfunction in various stages of multiple sclerosis and their inclusion to the biomarker panel may provide better insight into the extent of axonal damage/dysfunction.
Collapse
Affiliation(s)
- Madhurima Chatterjee
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, The Netherlands
| | - Marleen Ja Koel-Simmelink
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, The Netherlands
| | - Inge Mw Verberk
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, The Netherlands
| | - Joep Killestein
- Department of Neurology, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, The Netherlands
| | - Hugo Vrenken
- Department of Radiology, VU University Medical Center, Amsterdam UMC, The Netherlands
| | | | - Stefan Ropele
- Department of Neurology, Medical University of Graz, Austria
| | - Franz Fazekas
- Department of Neurology, Medical University of Graz, Austria
| | - Michael Khalil
- Department of Neurology, Medical University of Graz, Austria
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam UMC, The Netherlands
| |
Collapse
|
21
|
Schilde LM, Kösters S, Steinbach S, Schork K, Eisenacher M, Galozzi S, Turewicz M, Barkovits K, Mollenhauer B, Marcus K, May C. Protein variability in cerebrospinal fluid and its possible implications for neurological protein biomarker research. PLoS One 2018; 13:e0206478. [PMID: 30496192 PMCID: PMC6264484 DOI: 10.1371/journal.pone.0206478] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/12/2018] [Indexed: 11/19/2022] Open
Abstract
Cerebrospinal fluid is investigated in biomarker studies for various neurological disorders of the central nervous system due to its proximity to the brain. Currently, only a limited number of biomarkers have been validated in independent studies. The high variability in the protein composition and protein abundance of cerebrospinal fluid between as well as within individuals might be an important reason for this phenomenon. To evaluate this possibility, we investigated the inter- and intraindividual variability in the cerebrospinal fluid proteome globally, with a specific focus on disease biomarkers described in the literature. Cerebrospinal fluid from a longitudinal study group including 12 healthy control subjects was analyzed by label-free quantification (LFQ) via LC-MS/MS. Data were quantified via MaxQuant. Then, the intra- and interindividual variability and the reference change value were calculated for every protein. We identified and quantified 791 proteins, and 216 of these proteins were abundant in all samples and were selected for further analysis. For these proteins, we found an interindividual coefficient of variation of up to 101.5% and an intraindividual coefficient of variation of up to 29.3%. Remarkably, these values were comparably high for both proteins that were published as disease biomarkers and other proteins. Our results support the hypothesis that natural variability greatly impacts cerebrospinal fluid protein biomarkers because high variability can lead to unreliable results. Thus, we suggest controlling the variability of each protein to distinguish between good and bad biomarker candidates, e.g., by utilizing reference change values to improve the process of evaluating potential biomarkers in future studies.
Collapse
Affiliation(s)
- Lukas M. Schilde
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Steffen Kösters
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Simone Steinbach
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Karin Schork
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Sara Galozzi
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Michael Turewicz
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Klinikstraße, Kassel, and University Medical Center Göttingen, Department of Neurology, Göttingen, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| | - Caroline May
- Medizinisches Proteom-Center, Ruhr-University Bochum, Universitaetsstrasse, Bochum, Germany
| |
Collapse
|
22
|
Song H, Zhou H, Qu Z, Hou J, Chen W, Cai W, Cheng Q, Chuang DY, Chen S, Li S, Li J, Cheng J, Greenlief CM, Lu Y, Simonyi A, Sun GY, Wu C, Cui J, Gu Z. From Analysis of Ischemic Mouse Brain Proteome to Identification of Human Serum Clusterin as a Potential Biomarker for Severity of Acute Ischemic Stroke. Transl Stroke Res 2018; 10:546-556. [PMID: 30465328 DOI: 10.1007/s12975-018-0675-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/01/2018] [Accepted: 11/11/2018] [Indexed: 12/22/2022]
Abstract
Ischemic stroke is a devastating neurological disease that can cause permanent brain damage, but to date, few biomarkers are available to reliably assess the severity of injury during acute onset. In this study, quantitative proteomic analysis of ischemic mouse brain detected the increase in expression levels of clusterin (CLU) and cystatin C (CST3). Since CLU is a secretary protein, serum samples (n = 70) were obtained from acute ischemic stroke (AIS) patients within 24 h of stroke onset and together with 70 matched health controls. Analysis of CLU levels indicated significantly higher levels in AIS patients than healthy controls (14.91 ± 4.03 vs. 12.79 ± 2.22 ng/L; P = 0.0004). Analysis of serum CST3 also showed significant increase in AIS patients as compared with healthy controls (0.90 ± 0.19 vs. 0.84 ± 0.12 ng/L; P = 0.0064). The serum values of CLU were also positively correlated with the NIH Stroke Scale (NIHSS) scores, the time interval after stroke onset, as well as major stroke risk factors associated with lipid profile. These data demonstrate that elevated levels of serum CLU and CST3 are independently associated with AIS and may serve as peripheral biomarkers to aid clinical assessment of AIS and its severity. This pilot study thus contributes to progress toward preclinical proteomic screening by using animal models and allows translation of results from bench to bedside.
Collapse
Affiliation(s)
- Hailong Song
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA.,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA
| | - Hui Zhou
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA.,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA
| | - Zhe Qu
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA.,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA
| | - Jie Hou
- Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.,Computer Science, University of Missouri, Columbia, MO, 65211, USA
| | - Weilong Chen
- Department of Neurology, the Second Affiliated Clinical College of Fujian University of Traditional Chinese Medicine, Fuzhou, 350001, China
| | - Weiwu Cai
- Department of Neurology, the Second Affiliated Clinical College of Fujian University of Traditional Chinese Medicine, Fuzhou, 350001, China
| | - Qiong Cheng
- Department of Neurology, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Dennis Y Chuang
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA.,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.,Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Shanyan Chen
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA.,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA
| | - Shuwei Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Jilong Li
- Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.,Computer Science, University of Missouri, Columbia, MO, 65211, USA
| | - Jianlin Cheng
- Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.,Computer Science, University of Missouri, Columbia, MO, 65211, USA
| | | | - Yuan Lu
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, 78666, USA
| | - Agnes Simonyi
- Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.,Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Grace Y Sun
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA.,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.,Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Chenghan Wu
- Department of Neurology, the Second Affiliated Clinical College of Fujian University of Traditional Chinese Medicine, Fuzhou, 350001, China
| | - Jiankun Cui
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA.,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA
| | - Zezong Gu
- Department of Pathology & Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA. .,Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
23
|
Martin NA, Nawrocki A, Molnar V, Elkjaer ML, Thygesen EK, Palkovits M, Acs P, Sejbaek T, Nielsen HH, Hegedus Z, Sellebjerg F, Molnar T, Barbosa EGV, Alcaraz N, Gallyas F, Svenningsen AF, Baumbach J, Lassmann H, Larsen MR, Illes Z. Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes. PLoS One 2018; 13:e0202530. [PMID: 30114292 PMCID: PMC6095600 DOI: 10.1371/journal.pone.0202530] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/03/2018] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Here, we applied a multi-omics approach (i) to examine molecular pathways related to de- and remyelination in multiple sclerosis (MS) lesions; and (ii) to translate these findings to the CSF proteome in order to identify molecules that are differentially expressed among MS subtypes. METHODS To relate differentially expressed genes in MS lesions to de- and remyelination, we compared transcriptome of MS lesions to transcriptome of cuprizone (CPZ)-induced de- and remyelination. Protein products of the overlapping orthologous genes were measured within the CSF by quantitative proteomics, parallel reaction monitoring (PRM). Differentially regulated proteins were correlated with molecular markers of inflammation by using MesoScale multiplex immunoassay. Expression kinetics of differentially regulated orthologous genes and proteins were examined in the CPZ model. RESULTS In the demyelinated and remyelinated corpus callosum, we detected 1239 differentially expressed genes; 91 orthologues were also differentially expressed in MS lesions. Pathway analysis of these orthologues suggested that the TYROBP (DAP12)-TREM2 pathway, TNF-receptor 1, CYBA and the proteasome subunit PSMB9 were related to de- and remyelination. We designed 129 peptides representing 51 orthologous proteins, measured them by PRM in 97 individual CSF, and compared their levels between relapsing (n = 40) and progressive MS (n = 57). Four proteins were differentially regulated among relapsing and progressive MS: tyrosine protein kinase receptor UFO (UFO), TIMP-1, apolipoprotein C-II (APOC2), and beta-2-microglobulin (B2M). The orthologous genes/proteins in the mouse brain peaked during acute remyelination. UFO, TIMP-1 and B2M levels correlated inversely with inflammation in the CSF (IL-6, MCP-1/CCL2, TARC/CCL17). APOC2 showed positive correlation with IL-2, IL-16 and eotaxin-3/CCL26. CONCLUSIONS Pathology-based multi-omics identified four CSF markers that were differentially expressed in MS subtypes. Upregulated TIMP-1, UFO and B2M orthologues in relapsing MS were associated with reduced inflammation and reflected reparatory processes, in contrast to the upregulated orthologue APOC2 in progressive MS that reflected changes in lipid metabolism associated with increased inflammation.
Collapse
Affiliation(s)
- Nellie A. Martin
- Department of Neurology, Odense University Hospital, Odense, Denmark
| | - Arkadiusz Nawrocki
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Viktor Molnar
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Maria L. Elkjaer
- Department of Neurology, Odense University Hospital, Odense, Denmark
| | - Eva K. Thygesen
- Department of Neurology, Odense University Hospital, Odense, Denmark
| | - Miklos Palkovits
- Laboratory of Neuromorphology and Human Brain Tissue Bank/Microdissection Laboratory, Semmelweis University, Budapest, Hungary
| | - Peter Acs
- Department of Neurology, University of Pecs, Pecs, Hungary
| | - Tobias Sejbaek
- Department of Neurology, Odense University Hospital, Odense, Denmark
| | - Helle H. Nielsen
- Department of Neurology, Odense University Hospital, Odense, Denmark
| | - Zoltan Hegedus
- Laboratory of Bioinformatics, Biological Research Centre, Szeged, Hungary
| | - Finn Sellebjerg
- Danish Multiple Sclerosis Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tihamer Molnar
- Department of Anaesthesiology and Intensive Therapy, University of Pecs, Pecs, Hungary
| | - Eudes G. V. Barbosa
- Computational Biology Group, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Nicolas Alcaraz
- Computational Biology Group, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ferenc Gallyas
- Department of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
- Nuclear-Mitochondrial Interactions Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Asa F. Svenningsen
- Department of Neurobiology Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Computational Biology Group, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Hans Lassmann
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Zsolt Illes
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Department of Neurology, University of Pecs, Pecs, Hungary
- Department of Clinical Research, BRIDGE, University of Southern Denmark, Odense, Denmark
- * E-mail:
| |
Collapse
|
24
|
Begcevic I, Brinc D, Dukic L, Simundic AM, Zavoreo I, Basic Kes V, Martinez-Morillo E, Batruch I, Drabovich AP, Diamandis EP. Targeted Mass Spectrometry-Based Assays for Relative Quantification of 30 Brain-Related Proteins and Their Clinical Applications. J Proteome Res 2018; 17:2282-2292. [PMID: 29708756 DOI: 10.1021/acs.jproteome.7b00768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cerebrospinal fluid (CSF) is a promising clinical sample for identification of novel biomarkers for various neurological disorders. Considering its direct contact with brain tissue, CSF represents a valuable source of brain-related and brain-specific proteins. Multiple sclerosis is an inflammatory, demyelinating neurological disease affecting the central nervous system, and so far there are no diagnostic or prognostic disease specific biomarkers available in the clinic. The primary aim of the present study was to develop a targeted mass spectrometry assay for simultaneous quantification of 30 brain-related proteins in CSF and subsequently to demonstrate assay feasibility in neurological samples derived from multiple sclerosis patients. Our multiplex selected reaction monitoring assay had wide dynamic range (median fold range across peptides = 8.16 × 103) and high assay reproducibility (median across peptides CV = 4%). Candidate biomarkers were quantified in CSF samples from neurologically healthy individuals (n = 9) and patients diagnosed with clinically isolated syndrome (n = 29) or early multiple sclerosis (n = 15).
Collapse
Affiliation(s)
- Ilijana Begcevic
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada.,Department of Clinical Biochemistry , University Health Network , Toronto , Ontario M5G 2C4 , Canada
| | - Lora Dukic
- Department of Medical Laboratory Diagnostics , University Hospital "Sveti Duh" , 10000 Zagreb , Croatia
| | - Ana-Maria Simundic
- Department of Medical Laboratory Diagnostics , University Hospital "Sveti Duh" , 10000 Zagreb , Croatia
| | - Iris Zavoreo
- University Department of Neurology , Medical School University Hospital "Sestre milosrdnice" , 10000 Zagreb , Croatia
| | - Vanja Basic Kes
- University Department of Neurology , Medical School University Hospital "Sestre milosrdnice" , 10000 Zagreb , Croatia
| | - Eduardo Martinez-Morillo
- Laboratory of Medicine, Department of Clinical Biochemistry , Hospital Universitario Central de Asturias , 33011 Oviedo , Spain
| | - Ihor Batruch
- Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Clinical Biochemistry , University Health Network , Toronto , Ontario M5G 2C4 , Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada.,Department of Clinical Biochemistry , University Health Network , Toronto , Ontario M5G 2C4 , Canada
| |
Collapse
|
25
|
Stoop MP, Runia TF, Stingl C, van der Vuurst de Vries RM, Luider TM, Hintzen RQ. Decreased Neuro-Axonal Proteins in CSF at First Attack of Suspected Multiple Sclerosis. Proteomics Clin Appl 2017; 11. [PMID: 28941200 DOI: 10.1002/prca.201700005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/23/2017] [Indexed: 01/10/2023]
Abstract
The pathology of multiple sclerosis is located in the central nervous system, therefore cerebrospinal fluid (CSF) is an attractive biofluid for biomarker research for proteins related to the early stages of this disease. In this study, the CSF proteome of patients with a clinically isolated syndrome of demyelination (CIS, a first attack of multiple sclerosis) is compared to the CSF proteome of control patients to identify differentially abundant proteins. CSF samples of 47 CIS patients and 45 control subjects are enzymatically digested and subsequently measured by LC-MS/MS (LTQ-Orbitrap). Following mass spectrometry differential abundances of the identified proteins between groups are investigated. A total of 3159 peptides are identified, relating to 485 proteins. One protein is significantly more abundant in CSF of CIS patients than in controls: Ig kappa chain C region. In contrast, 35 proteins are significantly lower in CIS patients than controls, most of them with functions in nervous system development and function, such as amyloid-like protein 1 (validated by ELISA in an independent sample set (p < 0.01)), contactin 1, contactin 2 and neuronal cell adhesion molecule. A remarkably lower abundance of neuro-axonal proteins is observed in patients with a first demyelinating event compared to controls.
Collapse
Affiliation(s)
- Marcel P Stoop
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Tessel F Runia
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Christoph Stingl
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Theo M Luider
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Rogier Q Hintzen
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands.,Departments of Immunology, Erasmus MC, Rotterdam, the Netherlands
| |
Collapse
|
26
|
Bastos P, Ferreira R, Manadas B, Moreira PI, Vitorino R. Insights into the human brain proteome: Disclosing the biological meaning of protein networks in cerebrospinal fluid. Crit Rev Clin Lab Sci 2017; 54:185-204. [PMID: 28393582 DOI: 10.1080/10408363.2017.1299682] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers. Bioinformatics analysis of data retrieved from 99 mass spectrometry (MS)-based studies on CSF profiling highlighted 1985 differentially expressed proteins across 49 diseases. A large percentage of the modulated proteins originate from exosome vesicles, and the majority are involved in either neuronal cell growth, development, maturation, migration, or neurotransmitter-mediated cellular communication. Nevertheless, some diseases present a unique CSF proteome profile, which were critically analyzed in the present study. For instance, 48 proteins were found exclusively upregulated in the CSF of patients with Alzheimer's disease and are mainly involved in steroid esterification and protein activation cascade processes. A higher number of exclusively upregulated proteins were found in the CSF of patients with multiple sclerosis (76 proteins) and with bacterial meningitis (70 proteins). Whereas in multiple sclerosis, these proteins are mostly involved in the regulation of RNA metabolism and apoptosis, in bacterial meningitis the exclusively upregulated proteins participate in inflammation and antibacterial humoral response, reflecting disease pathogenesis. The exploration of the contribution of exclusively upregulated proteins to disease pathogenesis will certainly help to envision potential biomarkers in the CSF for the clinical management of nervous system diseases.
Collapse
Affiliation(s)
- Paulo Bastos
- a Department of Chemistry , University of Aveiro , Aveiro , Portugal.,b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal
| | - Rita Ferreira
- c QOPNA, Department of Chemistry , University of Aveiro , Aveiro , Portugal
| | - Bruno Manadas
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal
| | - Paula I Moreira
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal.,e Laboratory of Physiology, Faculty of Medicine , University of Coimbra , Coimbra , Portugal
| | - Rui Vitorino
- b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal.,f Departmento de Cirurgia e Fisiologia, Faculdade de Medicina , Unidade de Investigação Cardiovascular, Universidade do Porto , Porto , Portugal
| |
Collapse
|
27
|
Abstract
PURPOSE OF REVIEW Mass spectrometry is an ever evolving technology that is equipped with a variety of tools for protein research. Some lipoprotein studies, especially those pertaining to HDL biology, have been exploiting the versatility of mass spectrometry to understand HDL function through its proteome. Despite the role of mass spectrometry in advancing research as a whole, however, the technology remains obscure to those without hands on experience, but still wishing to understand it. In this review, we walk the reader through the coevolution of common mass spectrometry workflows and HDL research, starting from the basic unbiased mass spectrometry methods used to profile the HDL proteome to the most recent targeted methods that have enabled an unprecedented view of HDL metabolism. RECENT FINDINGS Unbiased global proteomics have demonstrated that the HDL proteome is organized into subgroups across the HDL size fractions providing further evidence that HDL functional heterogeneity is in part governed by its varying protein constituents. Parallel reaction monitoring, a novel targeted mass spectrometry method, was used to monitor the metabolism of HDL apolipoproteins in humans and revealed that apolipoproteins contained within the same HDL size fraction exhibit diverse metabolic properties. SUMMARY Mass spectrometry provides a variety of tools and strategies to facilitate understanding, through its proteins, the complex biology of HDL.
Collapse
Affiliation(s)
- Sasha A. Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Center for Excellence in Vascular Biology, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
28
|
Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS. Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics 2016; 16:1154-65. [PMID: 26841090 DOI: 10.1002/pmic.201500284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 11/05/2022]
Abstract
The aims of the study were to: (i) identify differentially regulated proteins in cerebrospinal fluid (CSF) between multiple sclerosis (MS) patients and non-MS controls; (ii) examine the effect of matching the CSF samples on either total protein amount or volume, and compare four protein normalization strategies for CSF protein quantification. CSF from MS patients (n = 37) and controls (n = 64), consisting of other noninflammatory neurological diseases (n = 50) and non neurological spinal anesthetic subjects (n = 14), were analyzed using label-free proteomics, quantifying almost 800 proteins. In total, 122 proteins were significantly regulated (p < 0.05), where 77 proteins had p-value <0.01 or AUC value >0.75. Hierarchical clustering indicated that there were two main groups of MS patients, those with increased levels of inflammatory response proteins and decreased levels of proteins involved in neuronal tissue development (n = 30), and those with normal protein levels for both of these protein groups (n = 7). The main subgroup of controls clustering with the MS patients showing increased inflammation and decreased neuronal tissue development were patients suffering from chronic fatigue. Our data indicate that the preferable way to quantify proteins in CSF is to first match the samples on total protein amount and then normalize the data based on the median intensities, preferably from the CNS-enriched proteins.
Collapse
Affiliation(s)
- Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Elise Aasebø
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Vincent Van Pesch
- Neurology Department, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Diego Franciotta
- Laboratory of Neuroimmunology, IRCCS, "C. Mondino" National Neurological Institute, Pavia, Italy
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Magnus Berle
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| |
Collapse
|
29
|
Guldbrandsen A, Farag Y, Kroksveen AC, Oveland E, Lereim RR, Opsahl JA, Myhr KM, Berven FS, Barsnes H. CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders. Mol Cell Proteomics 2016; 16:300-309. [PMID: 27890865 DOI: 10.1074/mcp.o116.064477] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/18/2016] [Indexed: 01/23/2023] Open
Abstract
The rapidly growing number of biomedical studies supported by mass spectrometry based quantitative proteomics data has made it increasingly difficult to obtain an overview of the current status of the research field. A better way of organizing the biomedical proteomics information from these studies and making it available to the research community is therefore called for. In the presented work, we have investigated scientific publications describing the analysis of the cerebrospinal fluid proteome in relation to multiple sclerosis, Parkinson's disease and Alzheimer's disease. Based on a detailed set of filtering criteria we extracted 85 data sets containing quantitative information for close to 2000 proteins. This information was made available in CSF-PR 2.0 (http://probe.uib.no/csf-pr-2.0), which includes novel approaches for filtering, visualizing and comparing quantitative proteomics information in an interactive and user-friendly environment. CSF-PR 2.0 will be an invaluable resource for anyone interested in quantitative proteomics on cerebrospinal fluid.
Collapse
Affiliation(s)
- Astrid Guldbrandsen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Yehia Farag
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Ann Cathrine Kroksveen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Eystein Oveland
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Ragnhild R Lereim
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Jill A Opsahl
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Kjell-Morten Myhr
- §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway.,¶Norwegian Multiple Sclerosis Registry and Biobank, Haukeland University Hospital, 5021 Bergen, Norway
| | - Frode S Berven
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway; .,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway.,‖Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Harald Barsnes
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,**Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,‡‡Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| |
Collapse
|
30
|
Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS. In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis. J Proteome Res 2016; 16:179-194. [PMID: 27728768 DOI: 10.1021/acs.jproteome.6b00659] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry and pathway analysis. More than 2000 proteins and 1700 deglycopeptides were quantified, with 484 proteins and 180 deglycopeptides significantly changed between pools of RRMS and pools of controls. Approximately 300 of the significantly changed proteins were assigned to various biological processes including inflammation, extracellular matrix organization, cell adhesion, immune response, and neuron development. Ninety-six significantly changed deglycopeptides mapped to proteins that were not found changed in the global protein study. In addition, four mapped to the proteins oligo-myelin glycoprotein and noelin, which were found oppositely changed in the global study. Both are ligands to the nogo receptor, and the glycosylation of these proteins appears to be affected by RRMS. Our study gives the most extensive overview of the RRMS affected processes observed from the CSF proteome to date, and the list of differential proteins will have great value for selection of biomarker candidates for further verification.
Collapse
Affiliation(s)
- Ann Cathrine Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Kjell-Morten Myhr
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Øivind Torkildsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| |
Collapse
|
31
|
van Luijn MM, van Meurs M, Stoop MP, Verbraak E, Wierenga-Wolf AF, Melief MJ, Kreft KL, Verdijk RM, 't Hart BA, Luider TM, Laman JD, Hintzen RQ. Elevated Expression of the Cerebrospinal Fluid Disease Markers Chromogranin A and Clusterin in Astrocytes of Multiple Sclerosis White Matter Lesions. J Neuropathol Exp Neurol 2016; 75:86-98. [PMID: 26683597 DOI: 10.1093/jnen/nlv004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Using proteomics, we previously identified chromogranin A (CgA) and clusterin (CLU) as disease-related proteins in the cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS). CgA and CLU are involved in cell survival and are implicated in neurodegenerative disorders and may also have roles in MS pathophysiology. We investigated CgA and CLU expression in lesions and nonlesional regions in postmortem brains of MS patients and controls and in the brains of marmosets with experimental autoimmune encephalomyelitis. By quantitative PCR, mRNA levels of CgA and CLU were elevated in white matter but not in grey matter of MS patients. In situ analyses showed greater expression of CgA and CLU in white matter lesions than in normal-appearing regions in MS patients and in the marmosets, primarily in or adjacent to perivascular spaces and inflammatory infiltrates. Both proteins were expressed by glial fibrillary acidic protein-positive astrocytes. CgA was more localized in astrocytic processes and endfeet surrounding blood vessels and was abundant in the superficial glia limitans and ependyma, 2 CSF-brain borders. Increased expression of CgA and CLU in reactive astrocytes in MS white matter lesions supports a role for these molecules as neuro-inflammatory mediators and their potential as CSF markers of active pathological processes in MS patients.
Collapse
|
32
|
Pavelek Z, Vyšata O, Tambor V, Pimková K, Vu DL, Kuča K, Šťourač P, Vališ M. Proteomic analysis of cerebrospinal fluid for relapsing-remitting multiple sclerosis and clinically isolated syndrome. Biomed Rep 2016; 5:35-40. [PMID: 27347402 PMCID: PMC4906564 DOI: 10.3892/br.2016.668] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/25/2016] [Indexed: 01/21/2023] Open
Abstract
Early diagnosis and treatment of multiple sclerosis (MS) in the initial stages of the disease can significantly retard its progression. The aim of the present study was to identify changes in the cerebrospinal fluid proteome in patients with relapsing-remitting MS and clinically isolated MS syndrome who are at high risk of developing MS (case group) compared to healthy population (control) in order to identify potential new markers, which could ultimately aid in early diagnosis of MS. The protein concentrations of each of the 11 case and 15 control samples were determined using a bicinchoninic acid assay. Nanoscale liquid chromatography coupled with tandem mass spectrometry was used for protein identification. Proteomics data were processed using the Perseus software suite and R. The results were filtered using the Benjamini-Hochberg procedure for the false discovery rate (FDR) correction (FDR<0.05). The results showed that, 26 proteins were significantly dysregulated in case samples compared to the controls. Nine proteins were found to be significantly less abundant in case samples, while the abundance of 17 proteins was significantly increased in case samples compared to controls. Three of the proteins were previously linked to RR MS, including immunoglobulin (Ig) γ-1 chain C region, Ig heavy chain V–III region BRO and Ig κ chain C region. Three proteins that were uniquely expressed in patients with RR MS were identified and these proteins may serve as prognostic biomarkers for identifying patients with a high risk of developing RR MS.
Collapse
Affiliation(s)
- Zbyšek Pavelek
- Department of Neurology, Faculty of Medicine and University Hospital Hradec Králové, Charles University in Prague, CZ-500 05 Hradec Králové, Czech Republic
| | - Oldřich Vyšata
- Department of Neurology, Faculty of Medicine and University Hospital Hradec Králové, Charles University in Prague, CZ-500 05 Hradec Králové, Czech Republic
| | - Vojtěch Tambor
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Kristýna Pimková
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Dai Long Vu
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Kamil Kuča
- Biomedical Research Center, University Hospital Hradec Králové, CZ-500 05 Hradec Králové, Czech Republic
| | - Pavel Šťourač
- Department of Neurology, Faculty of Medicine and University Hospital Brno, CZ-639 00 Brno, Czech Republic
| | - Martin Vališ
- Department of Neurology, Faculty of Medicine and University Hospital Hradec Králové, Charles University in Prague, CZ-500 05 Hradec Králové, Czech Republic
| |
Collapse
|
33
|
Distinct protein signature of hypertension-induced damage in the renal proteome of the two-kidney, one-clip rat model. J Hypertens 2016; 33:126-35. [PMID: 25304470 DOI: 10.1097/hjh.0000000000000370] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Hypertensive nephrosclerosis is one of the most frequent causes of chronic kidney failure. Proteome analysis potentially improves the pathophysiological understanding and diagnostic precision of this disorder. In the present exploratory study, we investigated experimental nephrosclerosis in the two-kidney, one-clip (2K1C) hypertensive rat model. METHODS The renal cortex proteome from juxtamedullary cortex and outer cortex of 2K1C male Wistar-Hannover rats (n = 4) was compared with the sham-operated controls (n = 6), using mass spectrometry-based quantitative proteomics. We combined a high abundant plasma protein depletion strategy with an extended liquid chromatographic gradient to improve peptide and protein identification. Immunohistology was used for independent confirmation of abundance. RESULTS We identified 1724 proteins, of which 1434 were quantified with at least two unique peptides. Comparative proteomics revealed 608 proteins, including the platelet-derived growth factor receptor-β signalling pathway, with different abundances between the non-clipped kidney of hypertensive 2K1C rats and the corresponding kidney of the normotensive controls (P < 0.05, absolute fold change ≥1.5). Among the most significantly altered proteins in the whole cortex were periostin, transgelin, and creatine kinase B-type. Relative abundance of periostin alone allowed clear classification of 2K1C and controls. Enrichment of periostin in 2K1C rats was verified by immunohistology, showing positivity especially around the fibrotic vessels. CONCLUSION The proteome is altered in hypertension-induced kidney damage. We propose periostin, especially in combination with transgelin and creatine kinase B-type, as possible proteomic classifier to distinguish hypertensive nephrosclerosis from the normal tissue. This classifier needs to be further validated with respect to early diagnosis of fibrosis, prognosis, and its potential as a novel molecular target for pharmacological interventions.
Collapse
|
34
|
Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
Collapse
Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
| |
Collapse
|
35
|
Borràs E, Cantó E, Choi M, Maria Villar L, Álvarez-Cermeño JC, Chiva C, Montalban X, Vitek O, Comabella M, Sabidó E. Protein-Based Classifier to Predict Conversion from Clinically Isolated Syndrome to Multiple Sclerosis. Mol Cell Proteomics 2016; 15:318-28. [PMID: 26552840 PMCID: PMC4762525 DOI: 10.1074/mcp.m115.053256] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/25/2015] [Indexed: 11/06/2022] Open
Abstract
Multiple sclerosis is an inflammatory, demyelinating, and neurodegenerative disease of the central nervous system. In most patients, the disease initiates with an episode of neurological disturbance referred to as clinically isolated syndrome, but not all patients with this syndrome develop multiple sclerosis over time, and currently, there is no clinical test that can conclusively establish whether a patient with a clinically isolated syndrome will eventually develop clinically defined multiple sclerosis. Here, we took advantage of the capabilities of targeted mass spectrometry to establish a diagnostic molecular classifier with high sensitivity and specificity able to differentiate between clinically isolated syndrome patients with a high and a low risk of developing multiple sclerosis. Based on the combination of abundances of proteins chitinase 3-like 1 and ala-β-his-dipeptidase in cerebrospinal fluid, we built a statistical model able to assign to each patient a precise probability of conversion to clinically defined multiple sclerosis. Our results are of special relevance for patients affected by multiple sclerosis as early treatment can prevent brain damage and slow down the disease progression.
Collapse
Affiliation(s)
- Eva Borràs
- From the ‡Proteomics Unit, Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; §Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ester Cantó
- ¶Servei de Neurologia-Neuroimmunologia. Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Receca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona. Barcelona, Spain
| | - Meena Choi
- ‖Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Luisa Maria Villar
- **Department of Neurology and Immunology, Hospital Ramón y Cajal, Ctra. de Colmenar Viejo, km. 9,100, Madrid, 28034, Spain
| | - José Carlos Álvarez-Cermeño
- **Department of Neurology and Immunology, Hospital Ramón y Cajal, Ctra. de Colmenar Viejo, km. 9,100, Madrid, 28034, Spain
| | - Cristina Chiva
- From the ‡Proteomics Unit, Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; §Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Xavier Montalban
- ¶Servei de Neurologia-Neuroimmunologia. Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Receca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona. Barcelona, Spain
| | - Olga Vitek
- ‖Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Manuel Comabella
- ¶Servei de Neurologia-Neuroimmunologia. Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Receca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona. Barcelona, Spain;
| | - Eduard Sabidó
- From the ‡Proteomics Unit, Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; §Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain;
| |
Collapse
|
36
|
Del Campo M, Jongbloed W, Twaalfhoven HAM, Veerhuis R, Blankenstein MA, Teunissen CE. Facilitating the Validation of Novel Protein Biomarkers for Dementia: An Optimal Workflow for the Development of Sandwich Immunoassays. Front Neurol 2015; 6:202. [PMID: 26483753 PMCID: PMC4586418 DOI: 10.3389/fneur.2015.00202] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/31/2015] [Indexed: 01/11/2023] Open
Abstract
Different neurodegenerative disorders, such as Alzheimer’s disease (AD) and frontotemporal dementia (FTD), lead to dementia syndromes. Dementia will pose a huge impact on society and thus it is essential to develop novel tools that are able to detect the earliest, most sensitive, discriminative, and dynamic biomarkers for each of the disorders. To date, the most common assays used in large-scale protein biomarker analysis are enzyme-linked immunosorbent assays (ELISA), such as the sandwich immunoassays, which are sensitive, practical, and easily implemented. However, due to the novelty of many candidate biomarkers identified during proteomics screening, such assays or the antibodies that specifically recognize the desired marker are often not available. The development and optimization of a new ELISA should be carried out with considerable caution since a poor planning can be costly, ineffective, time consuming, and it may lead to a misinterpretation of the findings. Previous guidelines described either the overall biomarker development in more general terms (i.e., the process from biomarker discovery to validation) or the specific steps of performing an ELISA procedure. However, a workflow describing and guiding the main issues in the development of a novel ELISA is missing. Here, we describe a specific and detailed workflow to develop and validate new ELISA for a successful and reliable validation of novel dementia biomarkers. The proposed workflow highlights the main issues in the development of an ELISA and covers several critical aspects, including production, screening, and selection of specific antibodies until optimal fine-tuning of the assay. Although these recommendations are designed to analyze novel biomarkers for dementia in cerebrospinal fluid, they are generally applicable for the development of immunoassays for biomarkers in other human body fluids or tissues. This workflow is designed to maximize the quality of the developed ELISA using a time- and cost-efficient strategy. This will facilitate the validation of the dementia biomarker candidates ultimately allowing accurate diagnostic conclusions.
Collapse
Affiliation(s)
- Marta Del Campo
- Neurochemistry Laboratory, VU University Medical Center , Amsterdam , Netherlands ; Department of Clinical Chemistry, VU University Medical Center , Amsterdam , Netherlands
| | - Wesley Jongbloed
- Department of Clinical Chemistry, VU University Medical Center , Amsterdam , Netherlands
| | - Harry A M Twaalfhoven
- Neurochemistry Laboratory, VU University Medical Center , Amsterdam , Netherlands ; Department of Clinical Chemistry, VU University Medical Center , Amsterdam , Netherlands
| | - Robert Veerhuis
- Neurochemistry Laboratory, VU University Medical Center , Amsterdam , Netherlands ; Department of Psychiatry, VU University Medical Center , Amsterdam , Netherlands
| | - Marinus A Blankenstein
- Department of Clinical Chemistry, VU University Medical Center , Amsterdam , Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, VU University Medical Center , Amsterdam , Netherlands ; Department of Clinical Chemistry, VU University Medical Center , Amsterdam , Netherlands
| |
Collapse
|
37
|
Kroksveen AC, Jaffe JD, Aasebø E, Barsnes H, Bjørlykke Y, Franciotta D, Keshishian H, Myhr KM, Opsahl JA, van Pesch V, Teunissen CE, Torkildsen Ø, Ulvik RJ, Vethe H, Carr SA, Berven FS. Quantitative proteomics suggests decrease in the secretogranin-1 cerebrospinal fluid levels during the disease course of multiple sclerosis. Proteomics 2015; 15:3361-9. [DOI: 10.1002/pmic.201400142] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 03/12/2015] [Accepted: 07/01/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Ann C. Kroksveen
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
| | - Jacob D. Jaffe
- Broad Institute of MIT and Harvard; 7 Cambridge Center; Cambridge MA USA
| | - Elise Aasebø
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- Computational Biology Unit, Department of Informatics; University of Bergen; Bergen Norway
| | - Yngvild Bjørlykke
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- Department of Clinical Science; University of Bergen; Bergen Norway
| | - Diego Franciotta
- Laboratory of Neuroimmunology; “C. Mondino” National Neurological Institute; Pavia Italy
| | - Hasmik Keshishian
- Broad Institute of MIT and Harvard; 7 Cambridge Center; Cambridge MA USA
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- The Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - Jill A. Opsahl
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
| | - Vincent van Pesch
- Neurochemistry Unit; Institute of Neuroscience, Université Catholique de Louvain; Brussels Belgium
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory and Biobank; Department of Clinical Chemistry; VU University Medical Center; Amsterdam The Netherlands
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- The Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - Rune J. Ulvik
- Department of Clinical Medicine; University of Bergen; Bergen Norway
- Laboratory of Clinical Biochemistry; Haukeland University Hospital; Bergen Norway
| | - Heidrun Vethe
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- Department of Clinical Science; University of Bergen; Bergen Norway
| | - Steven A. Carr
- Broad Institute of MIT and Harvard; 7 Cambridge Center; Cambridge MA USA
| | - Frode S. Berven
- The KG Jebsen Centre for MS-research; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Proteomics Unit (PROBE); Department of Biomedicine; University of Bergen; Bergen Norway
- The Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| |
Collapse
|
38
|
de Bang TC, Petersen J, Pedas PR, Rogowska-Wrzesinska A, Jensen ON, Schjoerring JK, Jensen PE, Thelen JJ, Husted S. A laser ablation ICP-MS based method for multiplexed immunoblot analysis: applications to manganese-dependent protein dynamics of photosystem II in barley (Hordeum vulgare L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:555-565. [PMID: 26095749 DOI: 10.1111/tpj.12906] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/04/2015] [Indexed: 06/04/2023]
Abstract
Manganese (Mn) constitutes an essential co-factor in the oxygen-evolving complex of photosystem II (PSII). Consequently, Mn deficiency reduces photosynthetic efficiency and leads to changes in PSII composition. In order to study these changes, multiplexed protein assays are advantageous. Here, we developed a multiplexed antibody-based assay and analysed selected PSII subunits in barley (Hordeum vulgare L.). A selection of antibodies were labelled with specific lanthanides and immunoreacted with thylakoids exposed to Mn deficiency after western blotting. Subsequently, western blot membranes were analysed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), which allowed selective and relative quantitative analysis via the different lanthanides. The method was evaluated against established liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) methods, based on data-dependent acquisition (DDA) and selected reaction monitoring (SRM). Manganese deficiency resulted in a general decrease in PSII protein abundances, an effect that was shown to be reversible upon Mn re-supplementation. Specifically, the extrinsic proteins PsbP and PsbQ showed Mn-dependent changes in abundances. Similar trends in the response to Mn deficiency at the protein level were observed when comparing DDA, SRM and LA-ICP-MS results. A biologically important exception to this trend was the loss of PsbO in the SRM analysis, which highlights the necessity of validating protein changes by more than one technique. The developed method enables a higher number of proteins to be multiplexed in comparison to existing immunoassays. Furthermore, multiplexed protein analysis by LA-ICP-MS provides an analytical platform with high throughput appropriate for screening large collections of plants.
Collapse
Affiliation(s)
- Thomas Christian de Bang
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Jørgen Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark, Denmark
| | - Pai Rosager Pedas
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark, Denmark
| | - Ole Noerregaard Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark, Denmark
| | - Jan Kofod Schjoerring
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Jay J Thelen
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO 65211, USA
| | - Søren Husted
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| |
Collapse
|
39
|
Shevchenko G, Konzer A, Musunuri S, Bergquist J. Neuroproteomics tools in clinical practice. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:705-17. [PMID: 25680928 DOI: 10.1016/j.bbapap.2015.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/30/2015] [Indexed: 12/13/2022]
Abstract
Neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are characterized by neuronal impairment that leads to disease-specific changes in the neuronal proteins. The early diagnosis of these disorders is difficult, thus, the need for identifying, developing and using valid clinically applicable biomarkers that meet the criteria of precision, specificity and repeatability is very vital. The application of rapidly emerging technology such as mass spectrometry (MS) in proteomics has opened new avenues to accelerate biomarker discovery, both for diagnostic as well as for prognostic purposes. This review summarizes the most recent advances in the mass spectrometry-based neuroproteomics and analyses the current and future directions in the biomarker discovery for the neurodegenerative diseases. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
Collapse
Affiliation(s)
- Ganna Shevchenko
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Anne Konzer
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Sravani Musunuri
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden.
| |
Collapse
|
40
|
Hölttä M, Minthon L, Hansson O, Holmén-Larsson J, Pike I, Ward M, Kuhn K, Rüetschi U, Zetterberg H, Blennow K, Gobom J. An Integrated Workflow for Multiplex CSF Proteomics and Peptidomics—Identification of Candidate Cerebrospinal Fluid Biomarkers of Alzheimer’s Disease. J Proteome Res 2014; 14:654-63. [DOI: 10.1021/pr501076j] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mikko Hölttä
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Lennart Minthon
- Clinical
Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, 221 00 Lund, Sweden
| | - Oskar Hansson
- Clinical
Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, 221 00 Lund, Sweden
| | - Jessica Holmén-Larsson
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Ian Pike
- Proteome
Sciences
PLC, KT11 3EP London, United Kingdom
| | - Malcolm Ward
- Proteome
Sciences
PLC, KT11 3EP London, United Kingdom
| | - Karsten Kuhn
- Proteome Science R&D GmbH&CoKG, 60438 Frankfurt am Main, Germany
| | - Ulla Rüetschi
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
- UCL Institute of Neurology, Queen Square, WC1N 3BG London, United Kingdom
| | - Kaj Blennow
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Johan Gobom
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| |
Collapse
|
41
|
Kroksveen AC, Opsahl JA, Guldbrandsen A, Myhr KM, Oveland E, Torkildsen Ø, Berven FS. Cerebrospinal fluid proteomics in multiple sclerosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:746-56. [PMID: 25526888 DOI: 10.1016/j.bbapap.2014.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/27/2014] [Accepted: 12/11/2014] [Indexed: 12/31/2022]
Abstract
Multiple sclerosis (MS) is an immune mediated chronic inflammatory disease of the central nervous system usually initiated during young adulthood, affecting approximately 2.5 million people worldwide. There is currently no cure for MS, but disease modifying treatment has become increasingly more effective, especially when started in the first phase of the disease. The disease course and prognosis are often unpredictable and it can be challenging to determine an early diagnosis. The detection of novel biomarkers to understand more of the disease mechanism, facilitate early diagnosis, predict disease progression, and find treatment targets would be very attractive. Over the last decade there has been an increasing effort toward finding such biomarker candidates. One promising strategy has been to use state-of-the-art quantitative proteomics approaches to compare the cerebrospinal fluid (CSF) proteome between MS and control patients or between different subgroups of MS. In this review we summarize and discuss the status of CSF proteomics in MS, including the latest findings with a focus on the last five years. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
Collapse
Affiliation(s)
- Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Eystein Oveland
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway.
| |
Collapse
|
42
|
Suliman S, Xing Z, Wu X, Xue Y, Pedersen TO, Sun Y, Døskeland AP, Nickel J, Waag T, Lygre H, Finne-Wistrand A, Steinmüller-Nethl D, Krueger A, Mustafa K. Release and bioactivity of bone morphogenetic protein-2 are affected by scaffold binding techniques in vitro and in vivo. J Control Release 2014; 197:148-57. [PMID: 25445698 DOI: 10.1016/j.jconrel.2014.11.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 11/02/2014] [Accepted: 11/03/2014] [Indexed: 11/15/2022]
Abstract
A low dose of 1μg rhBMP-2 was immobilised by four different functionalising techniques on recently developed poly(l-lactide)-co-(ε-caprolactone) [(poly(LLA-co-CL)] scaffolds. It was either (i) physisorbed on unmodified scaffolds [PHY], (ii) physisorbed onto scaffolds modified with nanodiamond particles [nDP-PHY], (iii) covalently linked onto nDPs that were used to modify the scaffolds [nDP-COV] or (iv) encapsulated in microspheres distributed on the scaffolds [MICS]. Release kinetics of BMP-2 from the different scaffolds was quantified using targeted mass spectrometry for up to 70days. PHY scaffolds had an initial burst of release while MICS showed a gradual and sustained increase in release. In contrast, NDP-PHY and nDP-COV scaffolds showed no significant release, although nDP-PHY scaffolds maintained bioactivity of BMP-2. Human mesenchymal stem cells cultured in vitro showed upregulated BMP-2 and osteocalcin gene expression at both week 1 and week 3 in the MICS and nDP-PHY scaffold groups. These groups also demonstrated the highest BMP-2 extracellular protein levels as assessed by ELISA, and mineralization confirmed by Alizarin red. Cells grown on the PHY scaffolds in vitro expressed collagen type 1 alpha 2 early but the scaffold could not sustain rhBMP-2 release to express mineralization. After 4weeks post-implantation using a rat mandible critical-sized defect model, micro-CT and Masson trichrome results showed accelerated bone regeneration in the PHY, nDP-PHY and MICS groups. The results demonstrate that PHY scaffolds may not be desirable for clinical use, since similar osteogenic potential was not seen under both in vitro and in vivo conditions, in contrast to nDP-PHY and MICS groups, where continuous low doses of BMP-2 induced satisfactory bone regeneration in both conditions. The nDP-PHY scaffolds used here in critical-sized bone defects for the first time appear to have promise compared to growth factors adsorbed onto a polymer alone and the short distance effect prevents adverse systemic side effects.
Collapse
Affiliation(s)
- Salwa Suliman
- Department of Clinical Dentistry, Center for Clinical Dental Research, University of Bergen, Norway.
| | - Zhe Xing
- Department of Clinical Dentistry, Center for Clinical Dental Research, University of Bergen, Norway
| | - Xujun Wu
- Department of Cranio-Maxillofacial and Oral Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Ying Xue
- Department of Clinical Dentistry, Center for Clinical Dental Research, University of Bergen, Norway
| | - Torbjorn O Pedersen
- Department of Clinical Dentistry, Center for Clinical Dental Research, University of Bergen, Norway
| | - Yang Sun
- Department of Fibre and Polymer Technology, Royal Institute of Technology, KTH, Stockholm, Sweden
| | | | - Joachim Nickel
- Chair Tissue Engineering and Regenerative Medicine, University Hospital of Würzburg, Germany; Fraunhofer Project Group Regenerative Technologies in Oncology, Würzburg, Germany
| | - Thilo Waag
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
| | - Henning Lygre
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna Finne-Wistrand
- Department of Fibre and Polymer Technology, Royal Institute of Technology, KTH, Stockholm, Sweden
| | | | - Anke Krueger
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
| | - Kamal Mustafa
- Department of Clinical Dentistry, Center for Clinical Dental Research, University of Bergen, Norway.
| |
Collapse
|
43
|
Bjorlykke Y, Vethe H, Vaudel M, Barsnes H, Berven FS, Tjora E, Raeder H. Carboxyl-Ester Lipase Maturity-Onset Diabetes of the Young Disease Protein Biomarkers in Secretin-Stimulated Duodenal Juice. J Proteome Res 2014; 14:521-30. [DOI: 10.1021/pr500750z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yngvild Bjorlykke
- KG
Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Jonas Lies Vei 65, Bergen 5021, Norway
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
| | - Heidrun Vethe
- KG
Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Jonas Lies Vei 65, Bergen 5021, Norway
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
| | - Marc Vaudel
- Proteomics
Unit (PROBE), Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Harald Barsnes
- Proteomics
Unit (PROBE), Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Frode S. Berven
- Proteomics
Unit (PROBE), Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Erling Tjora
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
| | - Helge Raeder
- KG
Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Jonas Lies Vei 65, Bergen 5021, Norway
- Department
of Pediatrics, Haukeland University Hospital, Jonas Lies vei 65, Bergen 5021, Norway
| |
Collapse
|
44
|
Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS. In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR). Mol Cell Proteomics 2014; 13:3152-63. [PMID: 25038066 PMCID: PMC4223498 DOI: 10.1074/mcp.m114.038554] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF proteome, and hydrazide-based glycopeptide capture for mapping glycopeptides. A maximal protein set of 3081 proteins (28,811 peptide sequences) was identified, of which 520 were identified as glycoproteins from the glycopeptide enrichment strategy, including 1121 glycopeptides and their glycosylation sites. To our knowledge, this is the largest number of identified proteins and glycopeptides reported for CSF, including 417 glycosylation sites not previously reported. From parallel plasma samples, we identified 1050 proteins (9739 peptide sequences). An overlap of 877 proteins was found between the two body fluids, whereas 2204 proteins were identified only in CSF and 173 only in plasma. All mapping results are freely available via the new CSF Proteome Resource (http://probe.uib.no/csf-pr), which can be used to navigate the CSF proteome and help guide the selection of signature peptides in targeted quantitative proteomics.
Collapse
Affiliation(s)
- Astrid Guldbrandsen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Heidrun Vethe
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Yehia Farag
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; ¶Department of Informatics, University of Bergen, Bergen, Norway
| | - Eystein Oveland
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‖Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hilde Garberg
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Magnus Berle
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; **Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Kjell-Morten Myhr
- §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‡‡Norwegian Multiple Sclerosis Registry and Biobank, Haukeland University Hospital, Bergen, Norway
| | - Jill A Opsahl
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; §§Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
45
|
Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| |
Collapse
|
46
|
Scorilas A, Mavridis K. Predictions for the future of kallikrein-related peptidases in molecular diagnostics. Expert Rev Mol Diagn 2014; 14:713-22. [PMID: 24927162 DOI: 10.1586/14737159.2014.928207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Kallikrein-related peptidases (KLKs) form a cancer-related ensemble of serine proteases. This multigene family hosts the most widely used cancer biomarker that is PSA-KLK3, with millions of tests performed annually worldwide. The present report provides an overview of the biomarker potential of the extended KLK family (KLK1-KLK15) in various disease settings and envisages approaches that could lead to additional KLK-driven applications in future molecular diagnostics. Particular focus is given on the inclusion of KLKs into multifaceted cancer biomarker panels that provide enhanced diagnostic, prognostic and/or predictive accuracy in several human malignancies. Such panels have been described so far for prostate, ovarian, lung and colorectal cancers. The role of KLKs as biomarkers in non-malignant disease settings, such as Alzheimer's disease and multiple sclerosis, is also commented upon. Predictions are given on the challenges and future directions regarding clinically oriented KLK research.
Collapse
Affiliation(s)
- Andreas Scorilas
- Department of Biochemistry and Molecular Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
| | | |
Collapse
|
47
|
Malekzadeh A, Teunissen C. Recent progress in omics-driven analysis of MS to unravel pathological mechanisms. Expert Rev Neurother 2014; 13:1001-16. [PMID: 24053344 DOI: 10.1586/14737175.2013.835602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At present, the pathophysiology and specific biological markers reflecting pathology of multiple sclerosis (MS) remain undetermined. The risk of developing MS is considered to depend on genetic susceptibility and environmental factors. The interaction of environmental factors with epigenetic mechanisms could affect the transcriptional level and therefore also the translational level. In the last decade, growing amount of hypothesis-free 'omics' studies have shed light on the potential MS mechanisms and raised potential biomarker targets. To understand MS pathophysiology and discover a subset of biomarkers, it is becoming essential to take a step forward and integrate the findings of the different fields of 'omics' into a systems biology network. In this review, we will discuss the recent findings of the genomic, transcriptomic and proteomic fields for MS and aim to make a unifying model.
Collapse
Affiliation(s)
- Arjan Malekzadeh
- Department of Clinical Chemistry, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | | |
Collapse
|
48
|
Salvisberg C, Tajouri N, Hainard A, Burkhard PR, Lalive PH, Turck N. Exploring the human tear fluid: discovery of new biomarkers in multiple sclerosis. Proteomics Clin Appl 2014; 8:185-94. [PMID: 24488530 DOI: 10.1002/prca.201300053] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/19/2013] [Accepted: 01/22/2014] [Indexed: 12/19/2022]
Abstract
PURPOSE Multiple sclerosis is the first cause of progressive neurological disability among young adults living in Western countries. Its diagnosis is mostly based on clinical evaluation, neuroimaging, and in some cases cerebrospinal fluid (CSF) analysis, but no definitive diagnostic test exists. We proposed here that the exploration of tears from multiple sclerosis patients could lead to the discovery of new biomarkers. EXPERIMENTAL DESIGN Thirty multiple sclerosis patients (20% men) recruited to the Geneva University Hospitals were included in our study (mean age ± SD [years]: 42.4 ± 15.9). Twenty-five control patients (32% men) were also enrolled (mean age ± SD [years]: 42.7±15.1). Tears, CSF or blood was collected for each patient. Three independent quantitative (tandem mass tag) experiments were carried out between tears from multiple sclerosis and control patients. Protein verification was performed by Western blot on tears and CSF and by ELISA on serum samples. RESULTS Combined proteomics analyses provided 185 identified tear proteins. Among the differential proteins, alpha-1 antichymotrypsin was the only one to be significantly increased in the three experiments with similar ratios (ratios 1.6 to 2.5, p < 0.05). Its tear, CSF and serum elevation were further confirmed by Western blot and ELISA, respectively. CONCLUSIONS AND CLINICAL RELEVANCE This study supports the concept that modifications of the tear proteome can reflect biological abnormalities associated with multiple sclerosis and perhaps other inflammatory conditions affecting the CNS. In addition, alpha-1 antichymotrypsin elevation in tear fluid emerges as a promising biomarker for the diagnosis of multiple sclerosis.
Collapse
Affiliation(s)
- Cindy Salvisberg
- Translational Biomarker Group, Department of Human Protein Sciences, Medical University Center, Geneva, Switzerland
| | | | | | | | | | | |
Collapse
|
49
|
Effects of blood contamination and the rostro-caudal gradient on the human cerebrospinal fluid proteome. PLoS One 2014; 9:e90429. [PMID: 24599184 PMCID: PMC3943968 DOI: 10.1371/journal.pone.0090429] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/30/2014] [Indexed: 11/19/2022] Open
Abstract
Over the last years there has been an increased focus on the importance of knowing the effect of pre-analytical influence on the proteomes under study, particularly in the field of biomarker discovery. We present three proteomics studies examining the effect of blood contamination and the rostro-caudal gradient (RCG) on the cerebrospinal fluid (CSF) proteome, in addition to plasma/CSF protein ratios. The studies showed that the central nervous system (CNS) derived proteins appeared to be unaffected by the RCG, while the plasma-derived proteins showed an increase in concentration towards the lumbar area. This implies that the concentration of the plasma-derived proteins in CSF will vary depending on the volume of CSF that is collected. In the CSF samples spiked with blood, 262 of 814 quantified proteins showed an abundance increase of more than 1.5 fold, while 403 proteins had a fold change of less than 1.2 and appeared to be unaffected by blood contamination. Proteins with a high plasma/CSF ratio appeared to give the largest effect on the CSF proteome upon blood contamination. The results give important background information on how factors like blood contamination, RCG and blood-CNS-barrier influences the CSF proteome. This information is particularly important in the field of biomarker discovery, but also for routine clinical measurements. The data from the blood contamination and RCG discovery studies have been deposited to the ProteomeXchange with identifier PXD000401.
Collapse
|
50
|
Hölper S, Ruhs A, Krüger M. Stable isotope labeling for proteomic analysis of tissues in mouse. Methods Mol Biol 2014; 1188:95-106. [PMID: 25059607 DOI: 10.1007/978-1-4939-1142-4_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Since the first metabolic labeling experiments with stable isotopes beginning of the last century, several approaches were pursued to monitor protein dynamics in living animals. Today, almost all model organisms from bacteria to rodents can be fully labeled with SILAC (stable isotope labeling of amino acids in cell culture) amino acids. The development of special media and diets containing the labeled amino acids provides an efficient way to metabolically label prokaryotic and eukaryotic organisms. Preferentially, the essential amino acid lysine ((13)C6-lysine) is used to label mice (Mus musculus) and after one generation the natural isotope is fully replaced by the stable (13)C6-lysine isotope. So far, the SILAC mouse approach has been used to analyze several transgenic and knockout mouse models. Spike-in of labeled proteins into non-labeled samples provides an accurate relative protein quantification method without any chemical modification. Here we describe how to establish a SILAC mouse colony and describe the analysis of skeletal muscle tissue with different metabolic and contractile profiles.
Collapse
Affiliation(s)
- Soraya Hölper
- Max Planck Institute for Heart and Lung Research, Lugwigstr. 43, 61231, Bad Nauheim, Germany
| | | | | |
Collapse
|