1
|
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
|
2
|
Rais Y, Drabovich AP. Identification and Quantification of Human Relaxin Proteins by Immunoaffinity-Mass Spectrometry. J Proteome Res 2024. [PMID: 38739617 DOI: 10.1021/acs.jproteome.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The human relaxins belong to the Insulin/IGF/Relaxin superfamily of peptide hormones, and their physiological function is primarily associated with reproduction. In this study, we focused on a prostate tissue-specific relaxin RLN1 (REL1_HUMAN protein) and a broader tissue specificity RLN2 (REL2_HUMAN protein). Due to their structural similarity, REL1 and REL2 proteins were collectively named a 'human relaxin protein' in previous studies and were exclusively measured by immunoassays. We hypothesized that the highly selective and sensitive immunoaffinity-selected reaction monitoring (IA-SRM) assays would reveal the identity and abundance of the endogenous REL1 and REL2 in biological samples and facilitate the evaluation of these proteins for diagnostic applications. High levels of RLN1 and RLN2 transcripts were found in prostate and breast cancer cell lines by RT-PCR. However, no endogenous prorelaxin-1 or mature REL1 were detected by IA-SRM in cell lines, seminal plasma, or blood serum. The IA-SRM assay of REL2 demonstrated its undetectable levels (<9.4 pg/mL) in healthy control female and male sera and relatively high levels of REL2 in maternal sera across different gestational weeks (median 331 pg/mL; N = 120). IA-SRM assays uncovered potential cross-reactivity and nonspecific binding for relaxin immunoassays. The developed IA-SRM assays will facilitate the investigation of the physiological and pathological roles of REL1 and REL2 proteins.
Collapse
Affiliation(s)
- Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| |
Collapse
|
3
|
Shen L, Zhang Z, Wu P, Yang J, Cai Y, Chen K, Chai S, Zhao J, Chen H, Dai X, Yang B, Wei W, Dong L, Chen J, Jiang P, Cao C, Ma C, Xu C, Zou Y, Zhang J, Xiong W, Li Z, Xu S, Shu B, Wang M, Li Z, Wan Q, Xiong N, Chen S. Mechanistic insight into glioma through spatially multidimensional proteomics. SCIENCE ADVANCES 2024; 10:eadk1721. [PMID: 38363834 PMCID: PMC10871530 DOI: 10.1126/sciadv.adk1721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
Characterizing the tumor microenvironment at the molecular level is essential for understanding the mechanisms of tumorigenesis and evolution. However, the specificity of the blood proteome in localized region of the tumor and its linkages with other systems is difficult to investigate. Here, we propose a spatially multidimensional comparative proteomics strategy using glioma as an example. The blood proteome signature of tumor microenvironment was specifically identified by in situ collection of arterial and venous blood from the glioma region of the brain for comparison with peripheral blood. Also, by integrating with different dimensions of tissue and peripheral blood proteomics, the information on the genesis, migration, and exchange of glioma-associated proteins was revealed, which provided a powerful method for tumor mechanism research and biomarker discovery. The study recruited multidimensional clinical cohorts, allowing the proteomic results to corroborate each other, reliably revealing biological processes specific to gliomas, and identifying highly accurate biomarkers.
Collapse
Affiliation(s)
- Lei Shen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhourui Zhang
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Pengfei Wu
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Jingyi Yang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuankun Cai
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Keyu Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Songshan Chai
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jingwei Zhao
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongyu Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Xuan Dai
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bangkun Yang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lixin Dong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Pucha Jiang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Changjun Cao
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chao Ma
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chengshi Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yichun Zou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jibo Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenping Xiong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengwei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shuangxiang Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bing Shu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengyang Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zejin Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiongqiong Wan
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Nanxiang Xiong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Suming Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| |
Collapse
|
4
|
Chatanaka MK, Prassas I, Diamandis EP. Diagnostic and progression biomarkers in cerebrospinal fluid of Alzheimer's disease patients. BMC Med 2024; 22:60. [PMID: 38331825 PMCID: PMC10854014 DOI: 10.1186/s12916-024-03270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
In this commentary, we address a paper published by Johnson et al. by assessing the robustness of their method to discover diagnostic biomarkers in Alzheimer's disease (AD). In addition, we examine how these newly discovered and previously discovered biomarkers, can play a role in assisting patients with AD and those at risk for developing AD, with an emphasis on the translational hurdles that accompany such discoveries.
Collapse
Affiliation(s)
- Miyo K Chatanaka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ioannis Prassas
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | | |
Collapse
|
5
|
Walter J, Eludin Z, Drabovich AP. Redefining serological diagnostics with immunoaffinity proteomics. Clin Proteomics 2023; 20:42. [PMID: 37821808 PMCID: PMC10568870 DOI: 10.1186/s12014-023-09431-y] [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: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Serological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The advantages of straightforward setup and manufacturing, analytical sensitivity and specificity, affordability, and high-throughput measurements were accompanied by limitations such as semi-quantitative measurements, lack of universal reference standards, potential cross-reactivity, and challenges with multiplexing the complete panel of human immunoglobulin isotypes and subclasses. Redesign of conventional serological tests to include multiplex quantification of immunoglobulin isotypes and subclasses, utilize universal reference standards, and minimize cross-reactivity and non-specific binding will facilitate the development of assays with higher diagnostic specificity. Improved serological assays with higher diagnostic specificity will enable screenings of asymptomatic populations and may provide earlier detection of infectious diseases, autoimmune disorders, and cancer. In this review, we present the major clinical needs for serological diagnostics, overview conventional immunoassay detection techniques, present the emerging immunoassay detection technologies, and discuss in detail the advantages and limitations of mass spectrometry and immunoaffinity proteomics for serological diagnostics. Finally, we explore the design of novel immunoaffinity-proteomic assays to evaluate cell-mediated immunity and advance the sequencing of clinically relevant immunoglobulins.
Collapse
Affiliation(s)
- Jonathan Walter
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Zicki Eludin
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
| |
Collapse
|
6
|
Tsai FJ, Jaeger M, Coelho T, Powers ET, Kelly JW. Tafamidis concentration required for transthyretin stabilisation in cerebrospinal fluid. Amyloid 2023; 30:279-289. [PMID: 36691999 PMCID: PMC10363573 DOI: 10.1080/13506129.2023.2167595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/21/2022] [Accepted: 01/07/2023] [Indexed: 01/25/2023]
Abstract
BACKGROUND Hereditary transthyretin (TTR) amyloidosis (ATTRv) initially presents as a polyneuropathy and/or a cardiomyopathy. Central nervous system (CNS) pathology in ATTRv amyloidosis, including focal neurological episodes, dementia, cerebrovascular bleeding, and seizures, appears around a decade later. Wild-type (WT) TTR amyloidosis (ATTRwt) causes a cardiomyopathy. CNS pathology risk likely also increases in these patients as cardiomyopathy progresses. Herein, we study tafamidis-mediated TTR kinetic stabilisation in cerebrospinal fluid (CSF). METHODS Varying tafamidis concentrations (50-1000 nM) were added to CSF from healthy donors or ATTRv patients, and TTR stabilisation was measured via the decrease in dissociation rate. RESULTS Tafamidis meglumine (Vyndaqel) can be dosed at 20 or 80 mg QD. The latter dose is bioequivalent to a 61 mg QD dose of tafamidis free acid (Vyndamax). The tafamidis CSF concentration in ATTRv patients on 20 mg Vyndaqel is ∼125 nM. By linear extrapolation, we expect a CSF concentration of ∼500 nM at the higher dose. When tafamidis is added to healthy donor CSF at 125 or 500 nM, the WT TTR dissociation rate decreases by 42% or 87%, respectively. CONCLUSIONS Tafamidis stabilises TTR in CSF to what is likely a clinically meaningful extent at CSF concentrations achieved by the normal tafamidis dosing regimen.
Collapse
Affiliation(s)
- Felix J. Tsai
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Marcus Jaeger
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Teresa Coelho
- Unidade Corino de Andrade, Centro Hospitalar do Porto, Porto, Portugal
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, CA, USA
| |
Collapse
|
7
|
Chatanaka MK, Sohaei D, Diamandis EP, Prassas I. Beyond the amyloid hypothesis: how current research implicates autoimmunity in Alzheimer's disease pathogenesis. Crit Rev Clin Lab Sci 2023; 60:398-426. [PMID: 36941789 DOI: 10.1080/10408363.2023.2187342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023]
Abstract
The amyloid hypothesis has so far been at the forefront of explaining the pathogenesis of Alzheimer's Disease (AD), a progressive neurodegenerative disorder that leads to cognitive decline and eventual death. Recent evidence, however, points to additional factors that contribute to the pathogenesis of this disease. These include the neurovascular hypothesis, the mitochondrial cascade hypothesis, the inflammatory hypothesis, the prion hypothesis, the mutational accumulation hypothesis, and the autoimmunity hypothesis. The purpose of this review was to briefly discuss the factors that are associated with autoimmunity in humans, including sex, the gut and lung microbiomes, age, genetics, and environmental factors. Subsequently, it was to examine the rise of autoimmune phenomena in AD, which can be instigated by a blood-brain barrier breakdown, pathogen infections, and dysfunction of the glymphatic system. Lastly, it was to discuss the various ways by which immune system dysregulation leads to AD, immunomodulating therapies, and future directions in the field of autoimmunity and neurodegeneration. A comprehensive account of the recent research done in the field was extracted from PubMed on 31 January 2022, with the keywords "Alzheimer's disease" and "autoantibodies" for the first search input, and "Alzheimer's disease" with "IgG" for the second. From the first search, 19 papers were selected, because they contained recent research on the autoantibodies found in the biofluids of patients with AD. From the second search, four papers were selected. The analysis of the literature has led to support the autoimmune hypothesis in AD. Autoantibodies were found in biofluids (serum/plasma, cerebrospinal fluid) of patients with AD with multiple methods, including ELISA, Mass Spectrometry, and microarray analysis. Through continuous research, the understanding of the synergistic effects of the various components that lead to AD will pave the way for better therapeutic methods and a deeper understanding of the disease.
Collapse
Affiliation(s)
- Miyo K Chatanaka
- Department of Laboratory and Medicine Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Dorsa Sohaei
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory and Medicine Pathobiology, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Ioannis Prassas
- Laboratory Medicine Program, University Health Network, Toronto, Canada
| |
Collapse
|
8
|
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
|
9
|
Choi Y, Shin S, Son HJ, Lee NH, Myeong SH, Lee C, Jang H, Choi SJ, Kim HJ, Na DL. Identification of potential biomarkers related to mesenchymal stem cell response in patients with Alzheimer's disease. Stem Cell Res Ther 2023; 14:178. [PMID: 37468918 PMCID: PMC10357744 DOI: 10.1186/s13287-023-03410-8] [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: 07/01/2022] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Preclinical studies showed that mesenchymal stem cells (MSCs) ameliorate tau phosphorylation, amyloid-beta accumulation, and inflammation in Alzheimer's disease (AD) mouse models via secretion of neurotrophic factors and cytokines. We aimed to identify CSF biomarkers that can be used to predict or monitor the response to MSCs in patients with AD. METHODS AD patients were injected with human umbilical cord blood-MSCs (n = 22) or placebo (n = 12). The cerebrospinal fluid (CSF) samples were collected at baseline, one day after the first injection, and one day after the third injection. The patients injected with MSCs were classified into good responder (GR) or poor responder (PR) groups based on the rate of changes in the ratio of total-tau and phosphorylated-tau in the CSF. We selected three typical participants in each group, and their CSF protein levels were analyzed using liquid chromatography/tandem mass spectrometry (LC-MS/MS). RESULTS In the LC-MS/MS analysis, 1,667 proteins were identified. Eleven proteins showed significant differences between the typical GR and PR at baseline. Based on their significance level and known functions, two proteins, reticulocalbin-3 (RCN3) and follistatin-related protein 3 (FSTL3), were selected as potential biomarkers to predict MSC response. A total of 173 proteins showed significant change one day after the third injection compared to the baseline in typical GR. We excluded 45 proteins that showed significant change after the third injection compared to the baseline in the typical PR. Based on their significance level and known function, four proteins, scrapie-responsive protein 1 (SCRG1), neural proliferation differentiation and control protein (NPDC1), apolipoprotein E (ApoE), and cystatin C (CysC), were selected as potential biomarker to monitor MSC response. Additionally, functional analysis revealed that the increased CSF proteins after the third injection compared to the baseline in the typical GR were associated with synaptogenesis. CONCLUSIONS This study identified two proteins (RCN3 and FSTL3) that may be potential biomarkers for predicting MSC response and four proteins (SCRG1, NPDC1, ApoE, CysC) that may be potential biomarkers for monitoring MSC response in patients with AD. Further studies are needed to validate our results. Trial registration Clinical Trials.gov, NCT02054208. Registered on 4 February 2014. Samsung Medical Center IRB File No.2017-04-025. Registered on 20 June 2017.
Collapse
Affiliation(s)
- Yejoo Choi
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Sungho Shin
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Hyo Jin Son
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- School of Medicine, Sungkyunkwan University, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Neuroscience Center, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Na-Hee Lee
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06355, Republic of Korea
| | - Su Hyeon Myeong
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
| | - Cheolju Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Hyemin Jang
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Neuroscience Center, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Soo Jin Choi
- Biomedical Research Institute, MEDIPOST Co., Ltd., 21, Daewangpangyo-ro 644 Beon-gil, Seongnam-si, Gyeonggi-do, 13494, Republic of Korea
| | - Hee Jin Kim
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea.
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- School of Medicine, Sungkyunkwan University, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- Neuroscience Center, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06355, Republic of Korea.
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea.
| | - Duk L Na
- Cell and Gene Therapy Institute (CGTI), Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea.
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, Republic of Korea.
- Alzheimer's Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea.
| |
Collapse
|
10
|
Afridi R, Lee WH, Kim JH, Suk K. Utilizing databases for astrocyte secretome research. Expert Rev Proteomics 2023; 20:371-379. [PMID: 37978891 DOI: 10.1080/14789450.2023.2285311] [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: 06/26/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
INTRODUCTION Astrocytes are the most abundant cell type in the central nervous system (CNS). They play a pivotal role in supporting neuronal function and maintaining homeostasis by releasing a variety of bioactive proteins, collectively known as the astrocyte secretome. Investigating secretome provides insights into the molecular mechanisms underlying astrocyte function and dysfunction, as well as novel strategies to prevent and treat diseases affecting the CNS. AREAS COVERED Proteomics databases are a valuable resource for studying the role of astrocytes in healthy and diseased brain function, as they provide information about gene expression, protein expression, and cellular function. In this review, we discuss existing databases that are useful for astrocyte secretome research. EXPERT OPINION Astrocyte secretomics is a field that is rapidly progressing, yet the availability of dedicated databases is currently limited. To meet the increasing demand for comprehensive omics data in glia research, developing databases specifically focused on astrocyte secretome is crucial. Such databases would allow researchers to investigate the intricate molecular landscape of astrocytes and comprehend their involvement in diverse physiological and pathological processes. Expanding resources through the development of databases dedicated to the astrocyte secretome may facilitate further advancements in this field.
Collapse
Affiliation(s)
- Ruqayya Afridi
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Jong-Heon Kim
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
11
|
Zhang J, Kanoatov M, Jarvi K, Gauthier-Fisher A, Moskovtsev SI, Librach C, Drabovich AP. Germ cell-specific proteins AKAP4 and ASPX facilitate identification of rare spermatozoa in non-obstructive azoospermia. Mol Cell Proteomics 2023; 22:100556. [PMID: 37087050 DOI: 10.1016/j.mcpro.2023.100556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023] Open
Abstract
Non-obstructive azoospermia (NOA), the most severe form of male infertility, could be treated with intra-cytoplasmic sperm injection, providing spermatozoa were retrieved with the microdissection testicular sperm extraction (mTESE). We hypothesized that testis- and germ cell-specific proteins would facilitate flow cytometry-assisted identification of rare spermatozoa in semen cell pellets of NOA patients, thus enabling non-invasive diagnostics prior to mTESE. Data mining, targeted proteomics, and immunofluorescent microscopy identified and verified a panel of highly testis-specific proteins expressed at the continuum of germ cell differentiation. Late germ cell-specific proteins AKAP4_HUMAN and ASPX_HUMAN (ACRV1 gene) revealed exclusive localization in spermatozoa tails and acrosomes, respectively. A multiplex imaging flow cytometry assay facilitated fast and unambiguous identification of rare but morphologically intact AKAP4+/ASPX+/Hoechst+ spermatozoa within debris-laden semen pellets of NOA patients. While the previously suggested markers for spermatozoa retrieval suffered from low diagnostic specificity, the multi-step gating strategy and visualization of AKAP4+/ASPX+/Hoechst+ cells with elongated tails and acrosome-capped nuclei facilitated fast and unambiguous identification of the mature intact spermatozoa. AKAP4+/ASPX+/Hoechst+ assay may emerge as a non-invasive test to predict retrieval of morphologically intact spermatozoa by mTESE, thus improving diagnostics and treatment of severe forms of male infertility.
Collapse
Affiliation(s)
| | - Mirzo Kanoatov
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Keith Jarvi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Surgery, Division of Urology, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Sergey I Moskovtsev
- CReATe Fertility Centre, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Clifford Librach
- CReATe Fertility Centre, Toronto, ON, Canada; Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada; Department of Physiology, University of Toronto, Toronto, ON, Canada; Sunnybrook Research Institute, Toronto, ON, Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
12
|
Maity S, Mayer MG, Shu Q, Linh H, Bao D, Blair RV, He Y, Lyon CJ, Hu TY, Fischer T, Fan J. Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates. Mol Cell Proteomics 2023; 22:100523. [PMID: 36870567 PMCID: PMC9981268 DOI: 10.1016/j.mcpro.2023.100523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/18/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Neurologic manifestations are among the most frequently reported complications of COVID-19. However, given the paucity of tissue samples and the highly infectious nature of the etiologic agent of COVID-19, we have limited information to understand the neuropathogenesis of COVID-19. Therefore, to better understand the impact of COVID-19 on the brain, we used mass-spectrometry-based proteomics with a data-independent acquisition mode to investigate cerebrospinal fluid (CSF) proteins collected from two different nonhuman primates, Rhesus Macaque and African Green Monkeys, for the neurologic effects of the infection. These monkeys exhibited minimal to mild pulmonary pathology but moderate to severe central nervous system (CNS) pathology. Our results indicated that CSF proteome changes after infection resolution corresponded with bronchial virus abundance during early infection and revealed substantial differences between the infected nonhuman primates and their age-matched uninfected controls, suggesting these differences could reflect altered secretion of CNS factors in response to SARS-CoV-2-induced neuropathology. We also observed the infected animals exhibited highly scattered data distributions compared to their corresponding controls indicating the heterogeneity of the CSF proteome change and the host response to the viral infection. Dysregulated CSF proteins were preferentially enriched in functional pathways associated with progressive neurodegenerative disorders, hemostasis, and innate immune responses that could influence neuroinflammatory responses following COVID-19. Mapping these dysregulated proteins to the Human Brain Protein Atlas found that they tended to be enriched in brain regions that exhibit more frequent injury following COVID-19. It, therefore, appears reasonable to speculate that such CSF protein changes could serve as signatures for neurologic injury, identify important regulatory pathways in this process, and potentially reveal therapeutic targets to prevent or attenuate the development of neurologic injuries following COVID-19.
Collapse
Affiliation(s)
- Sudipa Maity
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Meredith G Mayer
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Qingbo Shu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Hellmers Linh
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Duran Bao
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Robert V Blair
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA
| | - Yanlin He
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Tracy Fischer
- Division of Comparative Pathology, National Primate Research Center, Covington, Louisiana, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA; Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA.
| |
Collapse
|
13
|
Behzad M, Zirak N, Madani GH, Baidoo L, Rezaei A, Karbasi S, Sadeghi M, Shafie M, Mayeli M, Alzheimer's Disease Neuroimaging Initiative. CSF-Targeted Proteomics Indicate Amyloid-Beta Ratios in Patients with Alzheimer's Dementia Spectrum. Int J Alzheimers Dis 2023; 2023:5336273. [PMID: 36793451 PMCID: PMC9925239 DOI: 10.1155/2023/5336273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 02/08/2023] Open
Abstract
Background According to recent studies, amyloid-β (Aβ) isoforms as cerebrospinal fluid (CSF) biomarkers have remarkable predictive value for cognitive decline in the early stages of Alzheimer's disease (AD). Herein, we aimed to investigate the correlations between several targeted proteomics in CSF samples with Aβ ratios and cognitive scores in patients in AD spectrum to search for potential early diagnostic utility. Methods A total of 719 participants were found eligible for inclusion. Patients were then categorized into cognitively normal (CN), mild cognitive impairment (MCI), and AD and underwent an assessment of Aβ and proteomics. Clinical Dementia Rating (CDR), Alzheimer's Disease Assessment Scale (ADAS), and Mini Mental State Exam (MMSE) were used for further cognitive assessment. The Aβ42, Aβ42/Aβ40, and Aβ42/38 ratios were considered as means of comparison to identify those peptides corresponding significantly to these established biomarkers and cognitive scores. The diagnostic utility of the IASNTQSR, VAELEDEK, VVSSIEQK, GDSVVYGLR, EPVAGDAVPGPK, and QETLPSK was assessed. Results All investigated peptides corresponded significantly to Aβ42 in controls. In those with MCI, VAELEDEK and EPVAGDAVPGPK were significantly correlated with Aβ42 (p value < 0.001). Additionally, IASNTQSR, VVSSIEQK, GDSVVYGLR, and QETLPSK were significantly correlated with Aβ42/Aβ40 and Aβ42/38 (p value < 0.001) in this group. This group of peptides similarly corresponded to Aβ ratios in those with AD. Eventually, IASNTQSR, VAELEDEK, and VVSSIEQK were significantly associated with CDR, ADAS-11, and ADAS-13, particularly in MCI group. Conclusion Our research suggests potential early diagnostic and prognostic utilities for certain peptides extracted from CSF-targeted proteomics research. The ethical approval of ADNI is available at ClinicalTrials.gov with Identifier: NCT00106899.
Collapse
Affiliation(s)
- Maryam Behzad
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Chemistery, University of Tehran, Iran
| | - Negin Zirak
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Educational Science and Psychology, University of Tabriz, Tabriz, Iran
| | - Ghazal Hamidi Madani
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Biology, Faculty of Sciences, University of Guilan, Iran
| | - Linda Baidoo
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Rezaei
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Karbasi
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Sadeghi
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahan Shafie
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa Mayeli
- NeuroTRACT Association, Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | |
Collapse
|
14
|
Bancroft EA, De La Mora M, Pandey G, Zarate SM, Srinivasan R. Extracellular S100B inhibits A-type voltage-gated potassium currents and increases L-type voltage-gated calcium channel activity in dopaminergic neurons. Glia 2022; 70:2330-2347. [PMID: 35916350 PMCID: PMC10738449 DOI: 10.1002/glia.24254] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/11/2022]
Abstract
Parkinson's disease (PD) is associated with an increase in secreted S100B within the midbrain and cerebrospinal fluid. In addition, S100B overexpression in mice accelerates the loss of substantia nigra pars compacta dopaminergic (DA) neurons, suggesting a role for this protein in PD pathogenesis. We found that in the mouse SNc, S100B labeled astrocytic processes completely envelop the somata of tyrosine hydroxylase (TH) expressing DA neurons only in male mice. These data suggest that an increase in S100B secretion by astrocytes within the midbrain could play a role in DA dysfunction during early PD. We therefore asked if acute exposure to extracellular S100B alters the activity of identified TH expressing DA neurons in primary mouse midbrain cultures. Acute exposure to 50 pM S100B specifically inhibited A-type voltage-gated potassium currents in TH+ , but not TH- neurons. This was accompanied by ~2-fold increases in the frequency of both intrinsic firing, as well as L-type voltage-gated calcium channel (VGCC)-mediated calcium fluxes only in TH+ neurons. Further, exposure to 100 μM 4-aminopyridine (4-AP), an A-type voltage-gated potassium channel inhibitor, mimicked the S100B mediated increase in intrinsic firing and L-type VGCC-mediated calcium fluxes in TH+ neurons. Taken together, our finding that extracellular S100B alters the activity of native DA neurons via an inhibition of A-type voltage-gated potassium channels has important implications for understanding the pathophysiology of early PD.
Collapse
Affiliation(s)
- Eric A. Bancroft
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
| | - Martha De La Mora
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
| | - Gauri Pandey
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
- Texas A&M Institute for Neuroscience (TAMIN), College Station, Texas, USA
| | - Sara M. Zarate
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
| | - Rahul Srinivasan
- Department of Neuroscience & Experimental Therapeutics, Texas A&M University School of Medicine, Bryan, Texas, USA
- Texas A&M Institute for Neuroscience (TAMIN), College Station, Texas, USA
| |
Collapse
|
15
|
Fu Z, Rais Y, Dara D, Jackson D, Drabovich AP. Rational Design and Development of SARS-CoV-2 Serological Diagnostics by Immunoprecipitation-Targeted Proteomics. Anal Chem 2022; 94:12990-12999. [PMID: 36095284 PMCID: PMC9523617 DOI: 10.1021/acs.analchem.2c01325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Current design of serological tests utilizes conservative
immunoassay
approaches and is focused on fast and convenient assay development,
throughput, straightforward measurements, and affordability. Limitations
of common serological assays include semiquantitative measurements,
cross-reactivity, lack of reference standards, and no differentiation
between human immunoglobulin subclasses. In this study, we suggested
that a combination of immunoaffinity enrichments with targeted proteomics
would enable rational design and development of serological assays
of infectious diseases, such as COVID-19. Immunoprecipitation-targeted
proteomic assays allowed for sensitive and specific measurements of
NCAP_SARS2 protein with a limit of detection of 313 pg/mL in serum
and enabled differential quantification of anti-SARS-CoV-2 antibody
isotypes (IgG, IgA, IgM, IgD, and IgE) and individual subclasses (IgG1-4
and IgA1-2) in plasma and saliva. Simultaneous evaluation of the numerous
antigen–antibody subclass combinations revealed a receptor-binding
domain (RBD)-IgG1 as a combination with the highest diagnostic performance.
Further validation revealed that anti-RBD IgG1, IgG3, IgM, and IgA1
levels were significantly elevated in convalescent plasma, while IgG2,
IgG4, and IgA2 were not informative. Anti-RBD IgG1 levels in convalescent
(2138 ng/mL) vs negative (95 ng/mL) plasma revealed 385 ng/mL as a
cutoff to detect COVID-19 convalescent plasma. Immunoprecipitation-targeted
proteomic assays will facilitate improvement and standardization of
the existing serological tests, enable rational design of novel tests,
and offer tools for the comprehensive investigation of immunoglobulin
subclass cooperation in immune response.
Collapse
Affiliation(s)
- Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Delaram Dara
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Dana Jackson
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| |
Collapse
|
16
|
Kalló G, Kumar A, Tőzsér J, Csősz É. Chemical Barrier Proteins in Human Body Fluids. Biomedicines 2022; 10:biomedicines10071472. [PMID: 35884778 PMCID: PMC9312486 DOI: 10.3390/biomedicines10071472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Abstract
Chemical barriers are composed of those sites of the human body where potential pathogens can contact the host cells. A chemical barrier is made up by different proteins that are part of the antimicrobial and immunomodulatory protein/peptide (AMP) family. Proteins of the AMP family exert antibacterial, antiviral, and/or antifungal activity and can modulate the immune system. Besides these proteins, a wide range of proteases and protease inhibitors can also be found in the chemical barriers maintaining a proteolytic balance in the host and/or the pathogens. In this review, we aimed to identify the chemical barrier components in nine human body fluids. The interaction networks of the chemical barrier proteins in each examined body fluid were generated as well.
Collapse
Affiliation(s)
- Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Correspondence: ; Tel.: +36-52-416432
| | - Ajneesh Kumar
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (A.K.); (J.T.); (É.C.)
- Biomarker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| |
Collapse
|
17
|
Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
Collapse
Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| |
Collapse
|
18
|
Klarić TS, Lauc G. The dynamic brain N-glycome. Glycoconj J 2022; 39:443-471. [PMID: 35334027 DOI: 10.1007/s10719-022-10055-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 01/17/2023]
Abstract
The attachment of carbohydrates to other macromolecules, such as proteins or lipids, is an important regulatory mechanism termed glycosylation. One subtype of protein glycosylation is asparagine-linked glycosylation (N-glycosylation) which plays a key role in the development and normal functioning of the vertebrate brain. To better understand the role of N-glycans in neurobiology, it's imperative we analyse not only the functional roles of individual structures, but also the collective impact of large-scale changes in the brain N-glycome. The systematic study of the brain N-glycome is still in its infancy and data are relatively scarce. Nevertheless, the prevailing view has been that the neuroglycome is inherently restricted with limited capacity for variation. The development of improved methods for N-glycomics analysis of brain tissue has facilitated comprehensive characterisation of the complete brain N-glycome under various experimental conditions on a larger scale. Consequently, accumulating data suggest that it's more dynamic than previously recognised and that, within a general framework, it has a given capacity to change in response to both intrinsic and extrinsic stimuli. Here, we provide an overview of the many factors that can alter the brain N-glycome, including neurodevelopment, ageing, diet, stress, neuroinflammation, injury, and disease. Given this emerging evidence, we propose that the neuroglycome has a hitherto underappreciated plasticity and we discuss the therapeutic implications of this regarding the possible reversal of pathological changes via interventions. We also briefly review the merits and limitations of N-glycomics as an analytical method before reflecting on some of the outstanding questions in the field.
Collapse
Affiliation(s)
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
19
|
Muk T, Stensballe A, Dmytriyeva O, Brunse A, Jiang PP, Thymann T, Sangild PT, Pankratova S. Differential Brain and Cerebrospinal Fluid Proteomic Responses to Acute Prenatal Endotoxin Exposure. Mol Neurobiol 2022; 59:2204-2218. [PMID: 35064541 DOI: 10.1007/s12035-022-02753-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
Abstract
Chorioamnionitis (CA) is a risk factor for preterm birth and is associated with neurodevelopmental delay and cognitive disorders. Prenatal inflammation-induced brain injury may resolve during the immediate postnatal period when rapid brain remodeling occurs. Cerebrospinal fluid (CSF) collected at birth may be a critical source of predictive biomarkers. Using pigs as a model of preterm infants exposed to CA, we hypothesized that prenatal lipopolysaccharide (LPS) exposure induces proteome changes in the CSF and brain at birth and postnatally. Fetal piglets (103 days gestation of full-term at 117 days) were administered intra-amniotic (IA) lipopolysaccharide (LPS) 3 days before preterm delivery by caesarian section. CSF and brain tissue were collected on postnatal Days 1 and 5 (P1 and P5). CSF and hippocampal proteins were profiled by LC-MS-based quantitative proteomics. Neuroinflammatory responses in the cerebral cortex, periventricular white matter and hippocampus were evaluated by immunohistochemistry, and gene expression was evaluated by qPCR. Pigs exposed to LPS in utero showed changes in CSF protein levels at birth but not at P5. Complement protein C3, hemopexin, vasoactive intestinal peptide, carboxypeptidase N subunit 2, ITIH1, and plasminogen expression were upregulated in the CSF, while proteins associated with axon growth and synaptic functions (FGFR1, BASP1, HSPD1, UBER2N, and RCN2), adhesion (talin1), and neuronal survival (Atox1) were downregulated. Microglia, but not astrocytes, were activated by LPS at P5 in the hippocampus but not in other brain regions. At this time, marginal increases in complement protein C3, LBP, HIF1a, Basp1, Minpp1, and FGFR1 transcription indicated hippocampal proinflammatory responses. In conclusion, few days exposure to endotoxin prenatally induce proteome changes in the CSF and brain at birth, but most changes resolve a few days later. The developing hippocampus has high neuronal plasticity in response to perinatal inflammation. Changes in CSF protein expression at birth may predict later structural brain damage in preterm infants exposed to variable types and durations of CA-related inflammation in utero.
Collapse
Affiliation(s)
- Tik Muk
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Oksana Dmytriyeva
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ping-Ping Jiang
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Thymann
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Per Torp Sangild
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark.,Department of Paediatrics, Odense University Hospital, Odense, Denmark
| | - Stanislava Pankratova
- Section of Comparative Pediatrics and Nutrition, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Frederiksberg C, Denmark.
| |
Collapse
|
20
|
Timsina J, Gomez-Fonseca D, Wang L, Do A, Western D, Alvarez I, Aguilar M, Pastor P, Henson RL, Herries E, Xiong C, Schindler SE, Fagan AM, Bateman RJ, Farlow M, Morris JC, Perrin R, Moulder K, Hassenstab J, Chhatwal J, Mori H, Sung YJ, Cruchaga C. Comparative Analysis of Alzheimer's Disease Cerebrospinal Fluid Biomarkers Measurement by Multiplex SOMAscan Platform and Immunoassay-Based Approach. J Alzheimers Dis 2022; 89:193-207. [PMID: 35871346 PMCID: PMC9562128 DOI: 10.3233/jad-220399] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND The SOMAscan assay has an advantage over immunoassay-based methods because it measures a large number of proteins in a cost-effective manner. However, the performance of this technology compared to the routinely used immunoassay techniques needs to be evaluated. OBJECTIVE We performed comparative analyses of SOMAscan and immunoassay-based protein measurements for five cerebrospinal fluid (CSF) proteins associated with Alzheimer's disease (AD) and neurodegeneration: NfL, Neurogranin, sTREM2, VILIP-1, and SNAP-25. METHODS We compared biomarkers measured in ADNI (N = 689), Knight-ADRC (N = 870), DIAN (N = 115), and Barcelona-1 (N = 92) cohorts. Raw protein values were transformed using z-score in order to combine measures from the different studies. sTREM2 and VILIP-1 had more than one analyte in SOMAscan; all available analytes were evaluated. Pearson's correlation coefficients between SOMAscan and immunoassays were calculated. Receiver operating characteristic curve and area under the curve were used to compare prediction accuracy of these biomarkers between the two platforms. RESULTS Neurogranin, VILIP-1, and NfL showed high correlation between SOMAscan and immunoassay measures (r > 0.9). sTREM2 had a fair correlation (r > 0.6), whereas SNAP-25 showed weak correlation (r = 0.06). Measures in both platforms provided similar predicted performance for all biomarkers except SNAP-25 and one of the sTREM2 analytes. sTREM2 showed higher AUC for SOMAscan based measures. CONCLUSION Our data indicate that SOMAscan performs as well as immunoassay approaches for NfL, Neurogranin, VILIP-1, and sTREM2. Our study shows promise for using SOMAscan as an alternative to traditional immunoassay-based measures. Follow-up investigation will be required for SNAP-25 and additional established biomarkers.
Collapse
Affiliation(s)
- Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Duber Gomez-Fonseca
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Anh Do
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ignacio Alvarez
- Memory Disorders Unit, Department of Neurology, University Hospital Mutua Terrassa, Terrassa, Spain
| | - Miquel Aguilar
- Memory Disorders Unit, Department of Neurology, University Hospital Mutua Terrassa, Terrassa, Spain
| | - Pau Pastor
- Memory Disorders Unit, Department of Neurology, University Hospital Mutua Terrassa, Terrassa, Spain
| | - Rachel L. Henson
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Elizabeth Herries
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Suzanne E. Schindler
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne M. Fagan
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- SILQ Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Randall J. Bateman
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- SILQ Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Martin Farlow
- Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Health, Indianapolis, IN, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- SILQ Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard Perrin
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Krista Moulder
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason Hassenstab
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jasmeer Chhatwal
- Massachusetts General Hospital, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hiroshi Mori
- Dept. of Clinical Neuroscience, Osaka City University Medical School, Nagaoka Sutoku University, Japan
| | | | | | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
| |
Collapse
|
21
|
Shao D, Huang L, Wang Y, Cui X, Li Y, Wang Y, Ma Q, Du W, Cui J. HBFP: a new repository for human body fluid proteome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6395039. [PMID: 34642750 PMCID: PMC8516408 DOI: 10.1093/database/baab065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Body fluid proteome has been intensively studied as a primary source for disease
biomarker discovery. Using advanced proteomics technologies, early research
success has resulted in increasingly accumulated proteins detected in different
body fluids, among which many are promising biomarkers. However, despite a
handful of small-scale and specific data resources, current research is clearly
lacking effort compiling published body fluid proteins into a centralized and
sustainable repository that can provide users with systematic analytic tools. In
this study, we developed a new database of human body fluid proteome (HBFP) that
focuses on experimentally validated proteome in 17 types of human body fluids.
The current database archives 11 827 unique proteins reported by 164
scientific publications, with a maximal false discovery rate of 0.01 on both the
peptide and protein levels since 2001, and enables users to query, analyze and
download protein entries with respect to each body fluid. Three unique features
of this new system include the following: (i) the protein annotation page
includes detailed abundance information based on relative qualitative measures
of peptides reported in the original references, (ii) a new score is calculated
on each reported protein to indicate the discovery confidence and (iii) HBFP
catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of
nine amino acids according to the Human Proteome Project Data Interpretation
Guidelines, while the remaining 4473 proteins have more than two unique peptides
without given sequence information. As an important resource for human protein
secretome, we anticipate that this new HBFP database can be a powerful tool that
facilitates research in clinical proteomics and biomarker discovery. Database URL:https://bmbl.bmi.osumc.edu/HBFP/
Collapse
Affiliation(s)
- Dan Shao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA.,Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China.,Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xueteng Cui
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yufei Li
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yao Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 310G Lincoln tower, 1800 cannon drive, Columbus, OH 43210, USA
| | - Wei Du
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA
| |
Collapse
|
22
|
Cicardi ME, Marrone L, Azzouz M, Trotti D. Proteostatic imbalance and protein spreading in amyotrophic lateral sclerosis. EMBO J 2021; 40:e106389. [PMID: 33792056 PMCID: PMC8126909 DOI: 10.15252/embj.2020106389] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/18/2020] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder whose exact causative mechanisms are still under intense investigation. Several lines of evidence suggest that the anatomical and temporal propagation of pathological protein species along the neural axis could be among the main driving mechanisms for the fast and irreversible progression of ALS pathology. Many ALS-associated proteins form intracellular aggregates as a result of their intrinsic prion-like properties and/or following impairment of the protein quality control systems. During the disease course, these mutated proteins and aberrant peptides are released in the extracellular milieu as soluble or aggregated forms through a variety of mechanisms. Internalization by recipient cells may seed further aggregation and amplify existing proteostatic imbalances, thus triggering a vicious cycle that propagates pathology in vulnerable cells, such as motor neurons and other susceptible neuronal subtypes. Here, we provide an in-depth review of ALS pathology with a particular focus on the disease mechanisms of seeding and transmission of the most common ALS-associated proteins, including SOD1, FUS, TDP-43, and C9orf72-linked dipeptide repeats. For each of these proteins, we report historical, biochemical, and pathological evidence of their behaviors in ALS. We further discuss the possibility to harness pathological proteins as biomarkers and reflect on the implications of these findings for future research.
Collapse
Affiliation(s)
- Maria Elena Cicardi
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Lara Marrone
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Mimoun Azzouz
- Department of NeuroscienceSheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Davide Trotti
- Department of NeuroscienceWeinberg ALS CenterVickie and Jack Farber Institute for NeuroscienceThomas Jefferson UniversityPhiladelphiaPAUSA
| |
Collapse
|
23
|
Andreadou EG, Katsipis G, Tsolaki M, Pantazaki AA. Involvement and relationship of bacterial lipopolysaccharides and cyclooxygenases levels in Alzheimer's Disease and Mild Cognitive Impairment patients. J Neuroimmunol 2021; 357:577561. [PMID: 34091099 DOI: 10.1016/j.jneuroim.2021.577561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/24/2021] [Accepted: 03/29/2021] [Indexed: 11/30/2022]
Abstract
This study reports elevated levels of bacterial lipopolysaccharides (LPSs) and cyclooxygenases (COX-1/2) in blood serum and cerebrospinal fluid (CSF) of Alzheimer's Disease (AD) and Mild Cognitive Impairment (MCI) patients compared to cognitively healthy individuals, indicating LPSs as promising biomarkers, especially in serum. LPSs, in both fluids, positively correlate with COX-1/2, Αβ42 and tau and negatively with mental state. Furthermore, COX-2 is the main determinant of LPSs presence in serum, whereas COX-1 in CSF. These results underline the significance of microbial/ inflammatory involvement in dementia and offer novel perspectives on the roles of LPSs and COX in pathogenesis of AD.
Collapse
Affiliation(s)
- Eleni G Andreadou
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), 57001 Thermi, Thessaloniki, Greece.
| | - Georgios Katsipis
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), 57001 Thermi, Thessaloniki, Greece
| | - Magda Tsolaki
- First Neurology Department, "AHEPA" University General Hospital of Thessaloniki, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Greek Association of Alzheimer's Disease and Related Disorders - GAADRD, Greece; Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), 57001 Thermi, Thessaloniki, Greece
| | - Anastasia A Pantazaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), 57001 Thermi, Thessaloniki, Greece.
| |
Collapse
|
24
|
Voukali E, Veetil NK, Němec P, Stopka P, Vinkler M. Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. Sci Rep 2021; 11:5312. [PMID: 33674647 PMCID: PMC7935914 DOI: 10.1038/s41598-021-84274-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/10/2021] [Indexed: 11/27/2022] Open
Abstract
Cerebrospinal fluid (CSF) proteins regulate neurogenesis, brain homeostasis and participate in signalling during neuroinflammation. Even though birds represent valuable models for constitutive adult neurogenesis, current proteomic studies of the avian CSF are limited to chicken embryos. Here we use liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to explore the proteomic composition of CSF and plasma in adult chickens (Gallus gallus) and evolutionarily derived parrots: budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus). Because cockatiel lacks a complete genome information, we compared the cross-species protein identifications using the reference proteomes of three model avian species: chicken, budgerigar and zebra finch (Taeniopygia guttata) and found the highest identification rates when mapping against the phylogenetically closest species, the budgerigar. In total, we identified 483, 641 and 458 unique proteins consistently represented in the CSF and plasma of all chicken, budgerigar and cockatiel conspecifics, respectively. Comparative pathways analyses of CSF and blood plasma then indicated clusters of proteins involved in neurogenesis, neural development and neural differentiation overrepresented in CSF in each species. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel evidence supporting the adult neurogenesis in birds.
Collapse
Affiliation(s)
- Eleni Voukali
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Nithya Kuttiyarthu Veetil
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| |
Collapse
|
25
|
Caicedo A, Zambrano K, Sanon S, Gavilanes AWD. Extracellular mitochondria in the cerebrospinal fluid (CSF): Potential types and key roles in central nervous system (CNS) physiology and pathogenesis. Mitochondrion 2021; 58:255-269. [PMID: 33662579 DOI: 10.1016/j.mito.2021.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
The cerebrospinal fluid (CSF) has an important role in the transport of nutrients and signaling molecules to the central nervous and immune systems through its circulation along the brain and spinal cord tissues. The mitochondrial activity in the central nervous system (CNS) is essential in processes such as neuroplasticity, neural differentiation and production of neurotransmitters. Interestingly, extracellular and active mitochondria have been detected in the CSF where they act as a biomarker for the outcome of pathologies such as subarachnoid hemorrhage and delayed cerebral ischemia. Additionally, cell-free-circulating mitochondrial DNA (ccf-mtDNA) has been detected in both the CSF of healthy donors and in that of patients with neurodegenerative diseases. Key questions arise as there is still much debate regarding if ccf-mtDNA detected in CSF is associated with a diversity of active or inactive extracellular mitochondria coexisting in distinct pathologies. Additionally, it is of great scientific and medical importance to identify the role of extracellular mitochondria (active and inactive) in the CSF and the difference between them being damage associated molecular patterns (DAMPs) or factors that promote homeostasis. This review analyzes the different types of extracellular mitochondria, methods for their identification and their presence in CSF. Extracellular mitochondria in the CSF could have an important implication in health and disease, which may lead to the development of medical approaches that utilize mitochondria as therapeutic agents.
Collapse
Affiliation(s)
- Andrés Caicedo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Sistemas Médicos SIME, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Kevin Zambrano
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands; Instituto de Neurociencias, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Serena Sanon
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Cornell University, Ithaca, United States
| | - Antonio W D Gavilanes
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| |
Collapse
|
26
|
Bruschi M, Petretto A, Cama A, Pavanello M, Bartolucci M, Morana G, Ramenghi LA, Garré ML, Ghiggeri GM, Panfoli I, Candiano G. Potential biomarkers of childhood brain tumor identified by proteomics of cerebrospinal fluid from extraventricular drainage (EVD). Sci Rep 2021; 11:1818. [PMID: 33469081 PMCID: PMC7815722 DOI: 10.1038/s41598-020-80647-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
Brain tumors are the most common solid tumors in childhood. There is the need for biomarkers of residual disease, therapy response and recurrence. Cerebrospinal fluid (CSF) is a source of brain tumor biomarkers. We analyzed the proteome of waste CSF from extraventricular drainage (EVD) from 29 children bearing different brain tumors and 17 controls needing EVD insertion for unrelated causes. 1598 and 1526 proteins were identified by liquid chromatography-coupled tandem mass spectrometry proteomics in CSF control and brain tumor patients, respectively, 263 and 191 proteins being exclusive of either condition. Bioinformatic analysis revealed promising protein biomarkers for the discrimination between control and tumor (TATA-binding protein-associated factor 15 and S100 protein B). Moreover, Thymosin beta-4 (TMSB4X) and CD109, and 14.3.3 and HSP90 alpha could discriminate among other brain tumors and low-grade gliomas plus glyoneuronal tumors/pilocytic astrocytoma, or embryonal tumors/medulloblastoma. Biomarkers were validated by ELISA assay. Our method was able to distinguish among brain tumor vs non-tumor/hemorrhagic conditions (controls) and to differentiate two large classes of brain tumors. Further prospective studies may assess whether the biomarkers proposed by our discovery approach can be identified in other bodily fluids, therefore less invasively, and are useful to guide therapy and predict recurrences.
Collapse
Affiliation(s)
- Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Andrea Petretto
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Armando Cama
- Department of Neurosurgery, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Pavanello
- Department of Neurosurgery, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Martina Bartolucci
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giovanni Morana
- Unit of Neuroradiology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Maria Luisa Garré
- Department of Neuroncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Gian Marco Ghiggeri
- UO of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Isabella Panfoli
- Dipartimento di Farmacia (DIFAR), Università di Genova, V.le Benedetto XV, 3, 16132, Genoa, Italy.
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| |
Collapse
|
27
|
Omiya H, Yamaguchi S, Watanabe T, Kuniya T, Harada Y, Kawaguchi D, Gotoh Y. BMP signaling suppresses Gemc1 expression and ependymal differentiation of mouse telencephalic progenitors. Sci Rep 2021; 11:613. [PMID: 33436697 PMCID: PMC7804439 DOI: 10.1038/s41598-020-79610-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 11/18/2020] [Indexed: 01/29/2023] Open
Abstract
The lateral ventricles of the adult mammalian brain are lined by a single layer of multiciliated ependymal cells, which generate a flow of cerebrospinal fluid through directional beating of their cilia as well as regulate neurogenesis through interaction with adult neural stem cells. Ependymal cells are derived from a subset of embryonic neural stem-progenitor cells (NPCs, also known as radial glial cells) that becomes postmitotic during the late embryonic stage of development. Members of the Geminin family of transcriptional regulators including GemC1 and Mcidas play key roles in the differentiation of ependymal cells, but it remains largely unclear what extracellular signals regulate these factors and ependymal differentiation during embryonic and early-postnatal development. We now show that the levels of Smad1/5/8 phosphorylation and Id1/4 protein expression-both of which are downstream events of bone morphogenetic protein (BMP) signaling-decline in cells of the ventricular-subventricular zone in the mouse lateral ganglionic eminence in association with ependymal differentiation. Exposure of postnatal NPC cultures to BMP ligands or to a BMP receptor inhibitor suppressed and promoted the emergence of multiciliated ependymal cells, respectively. Moreover, treatment of embryonic NPC cultures with BMP ligands reduced the expression level of the ependymal marker Foxj1 and suppressed the emergence of ependymal-like cells. Finally, BMP ligands reduced the expression levels of Gemc1 and Mcidas in postnatal NPC cultures, whereas the BMP receptor inhibitor increased them. Our results thus implicate BMP signaling in suppression of ependymal differentiation from NPCs through regulation of Gemc1 and Mcidas expression during embryonic and early-postnatal stages of mouse telencephalic development.
Collapse
Affiliation(s)
- Hanae Omiya
- grid.26999.3d0000 0001 2151 536XGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Shima Yamaguchi
- grid.26999.3d0000 0001 2151 536XGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Tomoyuki Watanabe
- grid.26999.3d0000 0001 2151 536XGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Takaaki Kuniya
- grid.26999.3d0000 0001 2151 536XGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yujin Harada
- grid.26999.3d0000 0001 2151 536XGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Daichi Kawaguchi
- grid.26999.3d0000 0001 2151 536XGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yukiko Gotoh
- grid.26999.3d0000 0001 2151 536XGraduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.26999.3d0000 0001 2151 536XInternational Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| |
Collapse
|
28
|
Di Meo A, Sohaei D, Batruch I, Alexandrou P, Prassas I, Diamandis EP. Proteomic Profiling of the Human Tissue and Biological Fluid Proteome. J Proteome Res 2020; 20:444-452. [PMID: 33107741 DOI: 10.1021/acs.jproteome.0c00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In-depth analysis of the human genome sequence has led to the annotation of approximately 20,000 human protein-coding genes. Although mass spectrometry (MS)-based workflows have made a great headway in achieving near genome-wide coverage, an equivalent complete map of the human proteome remains elusive. Delineating the spatial distribution of all human proteins at the organ, tissue, and cellular level can offer insight into health and disease and represents an excellent reference for the discovery of biomarkers and therapeutic targets. Here, we performed label-free liquid chromatography coupled to tandem MS (LC-MS/MS) to profile the normal human proteome. In total, we analyzed 117 samples from 46 normal tissues and organs at autopsy. Our high-resolution MS approach allowed for the quantification of 10,438 unique proteins. In order to expand our coverage of the human proteome, we combined our previously published biological fluid proteomic data from healthy individuals. We considered data from seven biological fluids, including urine, cerebrospinal fluid, synovial fluid, seminal plasma, sweat, cervical vaginal fluid, and nipple aspirate fluid. Overall, we generated tandem mass spectra corresponding to 13,028 unique human protein-coding genes. Although our analysis did not accomplish complete proteome coverage, it should be an important complementary resource for future biomarker discovery.
Collapse
Affiliation(s)
- Ashley Di Meo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Dorsa Sohaei
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Pantelis Alexandrou
- Department of Forensic Medicine and Toxicology, School of Medicine, University of Athens, Athens 157 72, Greece
| | - Ioannis Prassas
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON M5S, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto M5G 2C4, Canada
| |
Collapse
|
29
|
Macron C, Núñez Galindo A, Cominetti O, Dayon L. A Versatile Workflow for Cerebrospinal Fluid Proteomic Analysis with Mass Spectrometry: A Matter of Choice between Deep Coverage and Sample Throughput. Methods Mol Biol 2020; 2044:129-154. [PMID: 31432411 DOI: 10.1007/978-1-4939-9706-0_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human cerebrospinal fluid (CSF) is a sample of choice in the study of brain disorders. This biological fluid circulates in the brain and the spinal cord and contains tissue-specific proteins, indicative of health and disease conditions. Despite its potential as a valid source of biological markers, CSF remains largely understudied as compared to blood, in particular due to its more invasive way of sampling.Challenges remain when performing proteomic analysis in clinical research studies. State-of-the-art mass spectrometry (MS) enables deep characterization of the human proteome. But some technical limitations are cardinal to be addressed, such as the capacity to routinely analyze large cohorts of samples. Importantly, a trade-off still needs to be made between the proteome coverage depth and the number of measured samples. In this context, we developed a scalable automated proteomic pipeline for the analysis of CSF. Because of its versatility, this workflow can be adapted to accommodate proteome coverage and/or sample throughput. It allows us to prepare and quantitatively analyze hundreds to thousands of CSF samples; it can also allow identification of more than 3000 proteins in a CSF sample when coupled with isoelectric focusing fractionation.In this chapter, we describe an end-to-end pipeline for the proteomic analysis of CSF. The main steps of the sample preparation comprise spiking of a standard, protein digestion, isobaric labeling, and purification; these are performed in a 96-well plate format enabling automation. Depending on the targeted depth of the CSF proteome, optional analytical steps can be included, such as the removal of abundant proteins and sample pre-fractionation. Liquid chromatography tandem MS as well as data processing and analysis complete the pipeline.
Collapse
Affiliation(s)
- Charlotte Macron
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
| |
Collapse
|
30
|
Batruch I, Lim B, Soosaipillai A, Brinc D, Fiala C, Diamandis EP. Mass Spectrometry-Based Assay for Targeting Fifty-Two Proteins of Brain Origin in Cerebrospinal Fluid. J Proteome Res 2020; 19:3060-3071. [PMID: 32315192 DOI: 10.1021/acs.jproteome.0c00087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cerebrospinal fluid (CSF) is a circulatory fluid of the central nervous system and it can reflect the biochemical changes occurring in the brain. Although CSF retrieval through lumbar puncture is invasive, it remains the most commonly used fluid in exploring brain pathology as it is less complex and contains a higher concentration of brain-derived proteins than plasma (Reiber, H. Clin. Chim. Acta 2001, 310, 173-186; Macron et al. J. Proteome Res. 2018, 17, 4315-4319). We hypothesize that proteins produced by the brain will have diagnostic significance for brain pathologies. Hence, we expanded the previously in-house-developed 31-protein panel with more proteins classified as brain-specific by the Human Protein Atlas (HPA). Using the HPA, we selected 76 protein coding genes and screened CSF using liquid chromatography-mass spectrometry (LC-MS) and narrowed the protein list to candidates identified endogenously in CSF. Next, we developed a parallel reaction monitoring (PRM) assay for the 21 new proteins and merged it with the 31-protein assay developed earlier. In the process, we evaluated different screening strategies and optimized MS collision energies and ion isolation windows to achieve the highest possible analyte signal resulting in the PRM assay with an average linear dynamic range of 4.3 × 103. We also assessed the extent of Asn (N)-Gln (Q) deamidation, N-terminal pyro-Glu (E) conversion, and Met (M) oxidation and found that deamidation can be misassigned without high mass accuracy and high-resolution settings. We also assessed how many of these proteins could be reliably measured in 10 individual patient CSF samples. Our approach allows us to measure the relative levels of 52 brain-derived proteins in CSF by a single LC-MS method. This new assay may have important applications in discovering CSF biomarkers for various neurological diseases.
Collapse
Affiliation(s)
- Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada
| | - Bryant Lim
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5G 1X5, Canada
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto M5G 2C4, Canada
| | - Clare Fiala
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5G 1X5, Canada
| | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5T 3L9, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto M5G 1X5, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto M5G 2C4, Canada
| |
Collapse
|
31
|
Guha D, Lorenz DR, Misra V, Chettimada S, Morgello S, Gabuzda D. Proteomic analysis of cerebrospinal fluid extracellular vesicles reveals synaptic injury, inflammation, and stress response markers in HIV patients with cognitive impairment. J Neuroinflammation 2019; 16:254. [PMID: 31805958 PMCID: PMC6896665 DOI: 10.1186/s12974-019-1617-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/10/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) are nano-sized particles present in most body fluids including cerebrospinal fluid (CSF). Little is known about CSF EV proteins in HIV+ individuals. Here, we characterize the CSF EV proteome in HIV+ subjects and its relationship to neuroinflammation, stress responses, and HIV-associated neurocognitive disorders (HAND). METHODS CSF EVs isolated from 20 HIV+ subjects with (n = 10) or without (n = 10) cognitive impairment were characterized by electron microscopy, nanoparticle tracking analysis, immunoblotting, and untargeted LC/MS/MS mass spectrometry. Functional annotation was performed by gene ontology (GO) mapping and expression annotation using Biobase Transfac and PANTHER software. Cultured astrocytic U87 cells were treated with hydrogen peroxide for 4 h to induce oxidative stress and EVs isolated by ultracentrifugation. Selected markers of astrocytes (GFAP, GLUL), inflammation (CRP), and stress responses (PRDX2, PARK7, HSP70) were evaluated in EVs released by U87 cells following induction of oxidative stress and in CSF EVs from HIV+ patients by immunoblotting. RESULTS Mass spectrometry identified 2727 and 1626 proteins in EV fractions and EV-depleted CSF samples, respectively. CSF EV fractions were enriched with exosomal markers including Alix, syntenin, tetraspanins, and heat-shock proteins and a subset of neuronal, astrocyte, oligodendrocyte, and choroid plexus markers, in comparison to EV-depleted CSF. Proteins related to synapses, immune/inflammatory responses, stress responses, metabolic processes, mitochondrial functions, and blood-brain barrier were also identified in CSF EV fractions by GO mapping. HAND subjects had higher abundance of CSF EVs and proteins mapping to GO terms for synapses, glial cells, inflammation, and stress responses compared to those without HAND. GFAP, GLUL, CRP, PRDX2, PARK7, and HSP70 were confirmed by immunoblotting of CSF EVs from subjects with HAND and were also detected in EVs released by U87 cells under oxidative stress. CONCLUSIONS These findings suggest that CSF EVs derived from neurons, glial cells, and choroid plexus carry synaptic, immune/inflammation-related, and stress response proteins in HIV+ individuals with cognitive impairment, representing a valuable source for biomarker discovery.
Collapse
Affiliation(s)
- Debjani Guha
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - David R Lorenz
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Vikas Misra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Sukrutha Chettimada
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Susan Morgello
- Departments of Neurology, Neuroscience and Pathology, Mount Sinai Medical Center, New York, NY, USA
| | - Dana Gabuzda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
32
|
Pronker MF, van den Hoek H, Janssen BJC. Design and structural characterisation of olfactomedin-1 variants as tools for functional studies. BMC Mol Cell Biol 2019; 20:50. [PMID: 31726976 PMCID: PMC6857237 DOI: 10.1186/s12860-019-0232-1] [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: 05/29/2019] [Accepted: 10/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Olfactomedin-1 (Olfm1; also known as Noelin or Pancortin) is a highly-expressed secreted brain and retina protein and its four isoforms have different roles in nervous system development and function. Structural studies showed that the long Olfm1 isoform BMZ forms a disulfide-linked tetramer with a V-shaped architecture. The tips of the Olfm1 "V" each consist of two C-terminal β-propeller domains that enclose a calcium binding site. Functional characterisation of Olfm1 may be aided by new biochemical tools derived from these core structural elements. RESULTS Here we present the production, purification and structural analysis of three novel monomeric, dimeric and tetrameric forms of mammalian Olfm1 for functional studies. We characterise these constructs structurally by high-resolution X-ray crystallography and small-angle X-ray scattering. The crystal structure of the Olfm1 β-propeller domain (to 1.25 Å) represents the highest-resolution structure of an olfactomedin family member to date, revealing features such as a hydrophilic tunnel containing water molecules running into the core of the domain where the calcium binding site resides. The shorter Olfactomedin-1 isoform BMY is a disulfide-linked tetramer with a shape similar to the corresponding region in the longer BMZ isoform. CONCLUSIONS These recombinantly-expressed protein tools should assist future studies, for example of biophysical, electrophysiological or morphological nature, to help elucidate the functions of Olfm1 in the mature mammalian brain. The control over the oligomeric state of Olfm1 provides a firm basis to better understand the role of Olfm1 in the (trans-synaptic) tethering or avidity-mediated clustering of synaptic receptors such as post-synaptic AMPA receptors and pre-synaptic amyloid precursor protein. In addition, the variation in domain composition of these protein tools provides a means to dissect the Olfm1 regions important for receptor binding.
Collapse
Affiliation(s)
- Matti F Pronker
- MRC Laboratory of Molecular Biology, Division of Neurobiology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. .,Bijvoet Center for Biomolecular Research, Utrecht University, Crystal and Structural Chemistry, Kruytgebouw, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Hugo van den Hoek
- Bijvoet Center for Biomolecular Research, Utrecht University, Crystal and Structural Chemistry, Kruytgebouw, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Department of Molecular Structural Biology, Max Planck institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Bert J C Janssen
- Bijvoet Center for Biomolecular Research, Utrecht University, Crystal and Structural Chemistry, Kruytgebouw, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| |
Collapse
|
33
|
Goldhardt O, Warnhoff I, Yakushev I, Begcevic I, Förstl H, Magdolen V, Soosaipillai A, Diamandis E, Alexopoulos P, Grimmer T. Kallikrein-related peptidases 6 and 10 are elevated in cerebrospinal fluid of patients with Alzheimer's disease and associated with CSF-TAU and FDG-PET. Transl Neurodegener 2019; 8:25. [PMID: 31467673 PMCID: PMC6712703 DOI: 10.1186/s40035-019-0168-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/13/2019] [Indexed: 12/20/2022] Open
Abstract
Background Alterations in the expression of human kallikrein-related peptidases (KLKs) have been described in patients with Alzheimer’s disease (AD). We elucidated the suitability of KLK6, KLK8 and KLK10 to distinguish AD from NC and explored associations with established AD biomarkers. Methods KLK levels in cerebrospinal fluid (CSF), as determined by ELISA, were compared between 32 AD patients stratified to A/T/(N) system with evidence for amyloid pathology and of 23 normal controls with normal AD biomarkers. Associations between KLK levels and clinical severity, CSF and positron emission tomography (PET) based AD biomarkers were tested for. Results Levels of KLK6 and KLK10 were significantly increased in AD. KLK6 differed significantly between AD A+/T+/N+ and AD A+/T−/N+ or NC with an AUC of 0.922. CSF pTau and tTau levels were significantly associated with KLK6 in AD. Conclusions KLK6 deserves further investigations as a potential biomarker of Tau pathology in AD. Electronic supplementary material The online version of this article (10.1186/s40035-019-0168-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Oliver Goldhardt
- 1Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Ismaninger Str. 22, 81675 Munich, Germany
| | - Inanna Warnhoff
- 1Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Ismaninger Str. 22, 81675 Munich, Germany
| | - Igor Yakushev
- 2Department of Nuclear Medicine, TUM-NIC, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Ismaninger Str. 22, 81675 Munich, Germany
| | - Ilijana Begcevic
- 5Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario M5S 1A8 Canada
| | - Hans Förstl
- 1Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Ismaninger Str. 22, 81675 Munich, Germany
| | - Viktor Magdolen
- 3Department of Obstetrics & Gynecology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Ismaninger Str. 22, 81675 Munich, Germany
| | - Antoninus Soosaipillai
- 4Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
| | - Eleftherios Diamandis
- 4Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray St., Toronto, Ontario M5T 3L9 Canada.,5Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario M5S 1A8 Canada
| | - Panagiotis Alexopoulos
- 1Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Ismaninger Str. 22, 81675 Munich, Germany.,6Department of Psychiatry, University hospital of Rion, University of Patras, 26500 Rion Patras, Patras, Greece
| | - Timo Grimmer
- 1Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Ismaninger Str. 22, 81675 Munich, Germany
| |
Collapse
|
34
|
Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Balateu-Paños D, Colom-Cadena M, Gomez-Giro G, Muñoz L, Querol-Vilaseca M, Pegueroles J, Rami L, Lladó A, Molinuevo JL, Tainta M, Clarimón J, Spires-Jones T, Blesa R, Fortea J, Martínez-Lage P, Sánchez-Valle R, Sabidó E, Bayés À, Belbin O. Changes in Synaptic Proteins Precede Neurodegeneration Markers in Preclinical Alzheimer's Disease Cerebrospinal Fluid. Mol Cell Proteomics 2019; 18:546-560. [PMID: 30606734 PMCID: PMC6398205 DOI: 10.1074/mcp.ra118.001290] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
A biomarker of synapse loss, an early event in Alzheimer's disease (AD) pathophysiology that precedes neuronal death and symptom onset, would be a much-needed prognostic biomarker. With direct access to the brain interstitial fluid, the cerebrospinal fluid (CSF) is a potential source of synapse-derived proteins. In this study, we aimed to identify and validate novel CSF biomarkers of synapse loss in AD. Discovery: Combining shotgun proteomics of the CSF with an exhaustive search of the literature and public databases, we identified 251 synaptic proteins, from which we selected 22 for further study. Verification: Twelve proteins were discarded because of poor detection by Selected Reaction Monitoring (SRM). We confirmed the specific expression of 9 of the remaining proteins (Calsynytenin-1, GluR2, GluR4, Neurexin-2A, Neurexin-3A, Neuroligin-2, Syntaxin-1B, Thy-1, Vamp-2) at the human synapse using Array Tomography microscopy and biochemical fractionation methods. Exploration: Using SRM, we monitored these 9 synaptic proteins (20 peptides) in a cohort of CSF from cognitively normal controls and subjects in the pre-clinical and clinical AD stages (n = 80). Compared with controls, peptides from 8 proteins were elevated 1.3 to 1.6-fold (p < 0.04) in prodromal AD patients. Validation: Elevated levels of a GluR4 peptide at the prodromal stage were replicated (1.3-fold, p = 0.04) in an independent cohort (n = 60). Moreover, 7 proteins were reduced at preclinical stage 1 (0.6 to 0.8-fold, p < 0.04), a finding that was replicated (0.7 to 0.8-fold, p < 0.05) for 6 proteins in a third cohort (n = 38). In a cross-cohort meta-analysis, 6 synaptic proteins (Calsyntenin-1, GluR4, Neurexin-2A, Neurexin-3A, Syntaxin-1B and Thy-1) were reduced 0.8-fold (p < 0.05) in preclinical AD, changes that precede clinical symptoms and CSF markers of neurodegeneration. Therefore, these proteins could have clinical value for assessing disease progression, especially in preclinical stages of AD.
Collapse
Affiliation(s)
- Alberto Lleó
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain;
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Raúl Núñez-Llaves
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Daniel Alcolea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Cristina Chiva
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | | | - Martí Colom-Cadena
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Gemma Gomez-Giro
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Laia Muñoz
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Marta Querol-Vilaseca
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Jordi Pegueroles
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Lorena Rami
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Albert Lladó
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - José L Molinuevo
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Mikel Tainta
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
- ¶¶Servicio de Neurologia, Organización Sanitaria Integrada Goierri-Alto Urola, Osakidetza, Zumárraga, España
| | - Jordi Clarimón
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Tara Spires-Jones
- ‖‖Centre for Discovery Brain Sciences and UK Dementia Research Institute, University of Edinburgh EH8 9JZ, UK
| | - Rafael Blesa
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Juan Fortea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Pablo Martínez-Lage
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
| | - Raquel Sánchez-Valle
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Eduard Sabidó
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | - Àlex Bayés
- ***Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025, Barcelona, Spain
- ‡‡‡Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Olivia Belbin
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain;
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| |
Collapse
|
35
|
Jankovska E, Svitek M, Holada K, Petrak J. Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage. Clin Proteomics 2019; 16:9. [PMID: 30890900 PMCID: PMC6390343 DOI: 10.1186/s12014-019-9229-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the central nervous system. This makes human CSF an attractive source of potential biomarkers for neurologic diseases. Similarly to blood plasma, proteomic analysis of CSF is complicated by a high dynamic range of individual protein concentrations and by the presence of several highly abundant proteins. To deal with the abundant human CSF proteins, methods developed for blood plasma/serum are routinely used. Multiple affinity removal systems and protein enrichment of less abundant proteins using a combinatorial peptide ligand library are among the most frequent approaches. However, their relative impact on CSF proteome coverage has never been evaluated side-by-side in a single study. Therefore, we explored the effect of CSF depletion using MARS 14 cartridge and ProteoMiner ligand library on the number of CSF proteins identified in subsequent LC–MS/MS analysis. LC–MS/MS analysis of crude (non-treated) CSF provided roughly 500 identified proteins. Depletion of CSF by MARS 14 cartridge increased the number of identifications to nearly 800, while treatment of CSF using ProteoMiner enabled identification of 600 proteins. To explore the potential losses of CSF proteins during the depletion process, we also analyzed the “waste” fractions generated by both methods, i.e., proteins retained by the MARS 14 cartridge, and the molecules present in the flow-through fraction from ProteoMiner. More than 250 proteins were bound to MARS 14 cartridge, 100 of those were not identified in the corresponding depleted CSF. Similarly, analysis of the waste fraction in ProteoMiner workflow provided almost 70 unique proteins not found in the CSF depleted by the ligand library. Both depletion strategies significantly increased the number of identified CSF proteins compared to crude CSF. However, MARS 14 depletion provided a markedly higher number of identified proteins (773) compared to ProteoMiner (611). Further, we showed that CSF proteins are lost due to co-depletion (MARS 14) or exclusion (ProteoMiner) during the depletion process. This suggests that the routinely discarded “waste” fractions contain proteins of potential interest and should be included in CSF biomarker studies.
Collapse
Affiliation(s)
- Eliska Jankovska
- 1BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marek Svitek
- 2Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University, Prague, Czech Republic.,3General University Hospital, Prague, Czech Republic
| | - Karel Holada
- 4Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jiri Petrak
- 1BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic
| |
Collapse
|
36
|
Schiza C, Korbakis D, Jarvi K, Diamandis EP, Drabovich AP. Identification of TEX101-associated Proteins Through Proteomic Measurement of Human Spermatozoa Homozygous for the Missense Variant rs35033974. Mol Cell Proteomics 2019; 18:338-351. [PMID: 30429210 PMCID: PMC6356071 DOI: 10.1074/mcp.ra118.001170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Indexed: 01/19/2023] Open
Abstract
TEX101 is a germ-cell-specific protein and a validated biomarker of male infertility. Mouse TEX101 was found essential for male fertility and was suggested to function as a cell surface chaperone involved in maturation of proteins required for sperm migration and sperm-oocyte interaction. However, the precise functional role of human TEX101 is not known and cannot be studied in vitro due to the lack of human germ cell lines. Here, we genotyped 386 men for a common missense variant rs35033974 of TEX101 and identified 52 heterozygous and 4 homozygous men. We then discovered by targeted proteomics that the variant allele rs35033974 was associated with the near-complete degradation (>97%) of the corresponding G99V TEX101 form and suggested that spermatozoa of homozygous men could serve as a knockdown model to study TEX101 function in humans. Differential proteomic profiling with label-free quantification measured 8,046 proteins in spermatozoa of eight men and identified eight cell-surface and nine secreted testis-specific proteins significantly down-regulated in four patients homozygous for rs35033974. Substantially reduced levels of testis-specific cell-surface proteins potentially involved in sperm migration and sperm-oocyte interaction (including LY6K and ADAM29) were confirmed by targeted proteomics and Western blotting assays. Because recent population-scale genomic data revealed homozygous fathers with biological children, rs35033974 is not a monogenic factor of male infertility in humans. However, median TEX101 levels in seminal plasma were found fivefold lower (p = 0.0005) in heterozygous than in wild-type men of European ancestry. We conclude that spermatozoa of rs35033974 homozygous men have substantially reduced levels of TEX101 and could be used as a model to elucidate the precise TEX101 function, which will advance biology of human reproduction.
Collapse
Affiliation(s)
- Christina Schiza
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada;; Department of Pathology and Laboratory Medicine
| | - Dimitrios Korbakis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada;; Lunenfeld-Tanenbaum Research Institute
| | - Keith Jarvi
- Lunenfeld-Tanenbaum Research Institute,; Department of Surgery, Division of Urology, Mount Sinai Hospital, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada;; Department of Pathology and Laboratory Medicine,; Lunenfeld-Tanenbaum Research Institute,; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada;; Department of Pathology and Laboratory Medicine,; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
| |
Collapse
|
37
|
Dayon L, Cominetti O, Wojcik J, Galindo AN, Oikonomidi A, Henry H, Migliavacca E, Kussmann M, Bowman GL, Popp J. Proteomes of Paired Human Cerebrospinal Fluid and Plasma: Relation to Blood–Brain Barrier Permeability in Older Adults. J Proteome Res 2019; 18:1162-1174. [DOI: 10.1021/acs.jproteome.8b00809] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | | | | | | | | | - Hugues Henry
- Department of Laboratories, CHUV, 1011 Lausanne, Switzerland
| | | | - Martin Kussmann
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV, 1011 Lausanne, Switzerland
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, HUG, 1226 Geneva, Switzerland
| |
Collapse
|
38
|
Analyzing Cerebrospinal Fluid Proteomes to Characterize Central Nervous System Disorders: A Highly Automated Mass Spectrometry-Based Pipeline for Biomarker Discovery. Methods Mol Biol 2019; 1959:89-112. [PMID: 30852817 DOI: 10.1007/978-1-4939-9164-8_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Over the past decade, liquid chromatography tandem mass spectrometry (LC MS/MS)-based workflows become standard for biomarker discovery in proteomics. These medium- to high-throughput (in terms of protein content) profiling approaches have been applied to clinical research. As a result, human proteomes have been characterized to a greater extent than ever before. However, proteomics in clinical research and biomarker discovery studies has generally been performed with small cohorts of subjects (or pooled samples from larger cohorts). This is problematic, as when aiming to identify novel biomarkers, small studies suffer from inherent and important limitations, as a result of the reduced biological diversity and representativity of human populations. Consequently, larger-scale proteomics will be key to delivering robust biomarker candidates and enabling translation to clinical practice.Cerebrospinal fluid (CSF) is a highly clinically relevant body fluid, and an important source of potential biomarkers for brain-associated damage, such as that induced by traumatic brain injury and stroke, and brain diseases, such as Alzheimer's disease and Parkinson's disease. We have developed a scalable automated proteomic pipeline (ASAP2) for biomarker discovery. This workflow is compatible with larger clinical research studies in terms of sample size, while still allowing several hundred proteins to be measured in CSF by MS. In this chapter, we describe the whole proteomic workflow to analyze human CSF. We further illustrate our protocol with some examples from an analysis of hundreds of human CSF samples, in the specific context of biomarker discovery to characterize central nervous system disorders.
Collapse
|
39
|
Abstract
Protein profiling enabled through affinity proteomics represents a powerful strategy for analysis of complex samples such as human body fluids. Cerebrospinal fluid (CSF) is the proximal fluid of the central nervous system and is commonly analyzed in the context of neurological diseases. Through the presence of brain-derived proteins, this fluid can offer insight into the physiological state of the brain. Here, we describe multiplex and flexible protein and autoantibody profiling approaches using suspension bead arrays. Through minimal sample processing, these methods enable high-throughput analysis of hundreds of samples and proteins in one single assay and thereby provide powerful approaches for discovery of disease-associated proteins and autoantigens.
Collapse
|
40
|
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: 29] [Impact Index Per Article: 4.8] [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
|
41
|
Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Vatunga G, Ndung'u J, Boudot C, Bisser S, Courtioux B. Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects. J Proteomics 2018; 196:150-161. [PMID: 30414516 DOI: 10.1016/j.jprot.2018.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/02/2018] [Accepted: 11/05/2018] [Indexed: 02/04/2023]
Abstract
Human African trypanosomiasis (HAT) is a neglected tropical disease that is endemic in sub-Saharan Africa. Control of the disease has been recently improved by better screening and treatment strategies, and the disease is on the WHO list of possible elimination. However, some physiopathological aspects of the disease transmission and progression remain unclear. We propose a new proteomic approach to identify new targets and thus possible new biomarkers of the disease. We also focused our attention on fluids classically associated with HAT (serum and cerebrospinal fluid (CSF)) and on the more easily accessible biological fluids urine and saliva. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) established the proteomic profile of patients with early and late stage disease. The serum, CSF, urine and saliva of 3 uninfected controls, 3 early stage patients and 4 late stage patients were analyzed. Among proteins identified, in CSF, urine and saliva, respectively, 37, 8 and 24 proteins were differentially expressed and showed particular interest with regards to their function. The most promising proteins (Neogenin, Neuroserpin, secretogranin 2 in CSF; moesin in urine and intelectin 2 in saliva) were quantified by enzyme-linked immunosorbent assay in a confirmatory cohort of 14 uninfected controls, 23 patients with early stage disease and 43 patients with late stage disease. The potential of two proteins, neuroserpin and moesin, with the latter present in urine, were further characterized. Our results showed the potential of proteomic analysis to discover new biomarkers and provide the basis of the establishment of a new proteomic catalogue applied to HAT-infected subjects and controls. SIGNIFICANCE: Sleeping sickness, also called Human African Trypanosomiasis (HAT), is a parasitic infection caused by a parasitic protozoan, Trypanosoma brucei gambiense or T. b. rhodesiense which are transmitted via an infected tsetse fly: Glossina. For both, the haemolymphatic stage (or first stage) signs and symptoms are intermittent fever, lymphadenopathy, hepatosplenomegaly, headaches, pruritus, and for T. b. rhodesiense infection a chancre is often formed at the bite site. Meningoencephalitic stage (or second stage) occurs when parasites invade the CNS, it is characterised by neurological signs and symptoms such as altered gait, tremors, neuropathy, somnolence which can lead to coma and death if untreated. first stage of the disease is characterizing by fevers, headaches, itchiness, and joint pains and progressive lethargy corresponding to the second stage with confusion, poor coordination, numbness and trouble sleeping. Actually, diagnosing HAT requires specialized expertise and significant resources such as well-equipped health centers and qualified staff. Such resources are lacking in many endemic areas that are often in rural locales, so many individuals with HAT die before the diagnosis is established. In this study, we analysed by mass spectrometry the entire proteome of serum, CSF, urine and saliva samples from infected and non-infected Angolan individuals to define new biomarkers of the disease. This work of proteomics analysis is a preliminary stage to the characterization of the whole proteome, of these 4 biological fluids, of HAT patients. We have identified 69 new biomarkers. Five of them have been thoroughly investigated by ELISA quantification. Neuroserpine and Moesin are respectively promising new biomarkers in CSF and urine's patient for a better diagnosis.
Collapse
Affiliation(s)
- Julien Bonnet
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR 1094 Tropical Neuroepidemiology, Limoges, France.
| | - Camille Garcia
- Jacques Monod Institute, Proteomics Facility, University Paris Diderot Sorbonne Paris Cité, Paris, France..
| | - Thibaut Leger
- Jacques Monod Institute, Proteomics Facility, University Paris Diderot Sorbonne Paris Cité, Paris, France..
| | - Marie-Pauline Couquet
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR 1094 Tropical Neuroepidemiology, Limoges, France.
| | - Philippe Vignoles
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR 1094 Tropical Neuroepidemiology, Limoges, France.
| | - Gedeao Vatunga
- Instituto de Combate e controlo das Tripanossomiases (ICCT), Luanda, Angola.
| | - Joseph Ndung'u
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland.
| | - Clotilde Boudot
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR 1094 Tropical Neuroepidemiology, Limoges, France.
| | - Sylvie Bisser
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR 1094 Tropical Neuroepidemiology, Limoges, France; Pasteur Institute in French Guiana, 23 Boulevard Pasteur, 973006, Cayenne Cedex, French Guiana.
| | - Bertrand Courtioux
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR 1094 Tropical Neuroepidemiology, Limoges, France.
| |
Collapse
|
42
|
Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J, Eisenacher M, Marcus K. Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry. J Proteome Res 2018; 17:3418-3430. [PMID: 30207155 DOI: 10.1021/acs.jproteome.8b00308] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the brain and serves as a valuable specimen to examine diseases of the central nervous system through analyzing its components. These include the analysis of metabolites, cells as well as proteins. For identifying new suitable diagnostic protein biomarkers bottom-up data-dependent acquisition (DDA) mass spectrometry-based approaches are most popular. Drawbacks of this method are stochastic and irreproducible precursor ion selection. Recently, data-independent acquisition (DIA) emerged as an alternative method. It overcomes several limitations of DDA, since it combines the benefits of DDA and targeted methods like selected reaction monitoring (SRM). We established a DIA method for in-depth proteome analysis of CSF. For this, four spectral libraries were generated with samples from native CSF ( n = 5), CSF fractionation (15 in total) and substantia nigra fractionation (54 in total) and applied to three CSF DIA replicates. The DDA and DIA methods for CSF were conducted with the same nanoLC parameters using a 180 min gradient. Compared to a conventional DDA method, our DIA approach increased the number of identified protein groups from 648 identifications in DDA to 1574 in DIA using a comprehensive spectral library generated with DDA measurements from five native CSF and 54 substantia nigra fractions. We also could show that a sample specific spectral library generated from native CSF only increased the identification reproducibility from three DIA replicates to 90% (77% with a DDA method). Moreover, by utilizing a substantia nigra specific spectral library for CSF DIA, over 60 brain-originated proteins could be identified compared to only 11 with DDA. In conclusion, the here presented optimized DIA method substantially outperforms DDA and could develop into a powerful tool for biomarker discovery in CSF. Data are available via ProteomeXchange with the identifiers PXD010698, PXD010708, PXD010690, PXD010705, and PXD009624.
Collapse
Affiliation(s)
- Katalin Barkovits
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Andreas Linden
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Sara Galozzi
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Lukas Schilde
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Sandra Pacharra
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik , Klinikstraße 16 , D-34128 Kassel , Germany
| | - Nadine Stoepel
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Simone Steinbach
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Caroline May
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Julian Uszkoreit
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Martin Eisenacher
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Katrin Marcus
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| |
Collapse
|
43
|
Macron C, Lane L, Núñez Galindo A, Dayon L. Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification. J Proteome Res 2018; 17:4113-4126. [PMID: 30124047 DOI: 10.1021/acs.jproteome.8b00300] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cerebrospinal fluid (CSF) is a body fluid of choice for biomarker studies of brain disorders but remains relatively under-studied compared with other biological fluids such as plasma, partly due to the more invasive means of its sample collection. The present study establishes an in-depth CSF proteome through the analysis of a unique CSF sample from a pool of donors. After immunoaffinity depletion, the CSF sample was fractionated using off-gel electrophoresis and analyzed with liquid chromatography tandem mass spectrometry (MS) using the latest generation of hybrid Orbitrap mass spectrometers. The shotgun proteomic analysis allowed the identification of 20 689 peptides mapping on 3379 proteins. To the best of our knowledge, the obtained data set constitutes the largest CSF proteome published so far. Among the CSF proteins identified, 34% correspond to genes whose transcripts are highly expressed in brain according to the Human Protein Atlas. The principal Alzheimer's disease biomarkers (e.g., tau protein, amyloid-β, apolipoprotein E, and neurogranin) were detected. Importantly, our data set significantly contributes to the Chromosome-centric Human Proteome Project (C-HPP), and 12 proteins considered as missing are proposed for validation in accordance with the HPP guidelines. Of these 12 proteins, 8 proteins are based on 2 to 6 uniquely mapping peptides from this CSF analysis, and 4 match a new peptide with a "stranded" single peptide in PeptideAtlas from previous CSF studies. The MS proteomic data are available to the ProteomeXchange Consortium ( http://www.proteomexchange.org/ ) with the data set identifier PXD009646.
Collapse
Affiliation(s)
- Charlotte Macron
- Proteomics , Nestlé Institute of Health Sciences , 1015 Lausanne , Switzerland
| | - Lydie Lane
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics , CMU, rue Michel-Servet 1 , 1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , rue Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| | | | - Loïc Dayon
- Proteomics , Nestlé Institute of Health Sciences , 1015 Lausanne , Switzerland
| |
Collapse
|
44
|
Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP. Discovery of a Human Testis-specific Protein Complex TEX101-DPEP3 and Selection of Its Disrupting Antibodies. Mol Cell Proteomics 2018; 17:2480-2495. [PMID: 30097533 DOI: 10.1074/mcp.ra118.000749] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/11/2018] [Indexed: 01/01/2023] Open
Abstract
TEX101 is a testis-specific protein expressed exclusively in male germ cells and is a validated biomarker of male infertility. Studies in mice suggest that TEX101 is a cell-surface chaperone which regulates, through protein-protein interactions, the maturation of proteins involved in spermatozoa transit and oocyte binding. Male TEX101-null mice are sterile. Here, we identified by co-immunoprecipitation-mass spectrometry the interactome of human TEX101 in testicular tissues and spermatozoa. The testis-specific cell-surface dipeptidase 3 (DPEP3) emerged as the top hit. We further validated the TEX101-DPEP3 complex by using hybrid immunoassays. Combinations of antibodies recognizing different epitopes of TEX101 and DPEP3 facilitated development of a simple immunoassay to screen for disruptors of TEX101-DPEP3 complex. As a proof-of-a-concept, we demonstrated that anti-TEX101 antibody T4 disrupted the native TEX101-DPEP3 complex. Disrupting antibodies may be used to study the human TEX101-DPEP3 complex, and to develop modulators for male fertility.
Collapse
Affiliation(s)
- Christina Schiza
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Dimitrios Korbakis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Efstratia Panteleli
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Keith Jarvi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Surgery, Division of Urology, Mount Sinai Hospital, Toronto, Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
| |
Collapse
|
45
|
Dayon L, Núñez Galindo A, Wojcik J, Cominetti O, Corthésy J, Oikonomidi A, Henry H, Kussmann M, Migliavacca E, Severin I, Bowman GL, Popp J. Alzheimer disease pathology and the cerebrospinal fluid proteome. Alzheimers Res Ther 2018; 10:66. [PMID: 30021611 PMCID: PMC6052524 DOI: 10.1186/s13195-018-0397-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/11/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Altered proteome profiles have been reported in both postmortem brain tissues and body fluids of subjects with Alzheimer disease (AD), but their broad relationships with AD pathology, amyloid pathology, and tau-related neurodegeneration have not yet been fully explored. Using a robust automated MS-based proteomic biomarker discovery workflow, we measured cerebrospinal fluid (CSF) proteomes to explore their association with well-established markers of core AD pathology. METHODS Cross-sectional analysis was performed on CSF collected from 120 older community-dwelling adults with normal (n = 48) or impaired cognition (n = 72). LC-MS quantified hundreds of proteins in the CSF. CSF concentrations of β-amyloid 1-42 (Aβ1-42), tau, and tau phosphorylated at threonine 181 (P-tau181) were determined with immunoassays. First, we explored proteins relevant to biomarker-defined AD. Then, correlation analysis of CSF proteins with CSF markers of amyloid pathology, neuronal injury, and tau hyperphosphorylation (i.e., Aβ1-42, tau, P-tau181) was performed using Pearson's correlation coefficient and Bonferroni correction for multiple comparisons. RESULTS We quantified 790 proteins in CSF samples with MS. Four CSF proteins showed an association with CSF Aβ1-42 levels (p value ≤ 0.05 with correlation coefficient (R) ≥ 0.38). We identified 50 additional CSF proteins associated with CSF tau and 46 proteins associated with CSF P-tau181 (p value ≤ 0.05 with R ≥ 0.37). The majority of those proteins that showed such associations were brain-enriched proteins. Gene Ontology annotation revealed an enrichment for synaptic proteins and proteins originating from reelin-producing cells and the myelin sheath. CONCLUSIONS We used an MS-based proteomic workflow to profile the CSF proteome in relation to cerebral AD pathology. We report strong evidence of previously reported CSF proteins and several novel CSF proteins specifically associated with amyloid pathology or neuronal injury and tau hyperphosphorylation.
Collapse
Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | | | | | - John Corthésy
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Hugues Henry
- Department of Laboratories, CHUV, Lausanne, Switzerland
| | - Martin Kussmann
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Present address: Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - India Severin
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV, Lausanne, Switzerland
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, HUG, Geneva, Switzerland
| |
Collapse
|
46
|
Begcevic I, Tsolaki M, Brinc D, Brown M, Martinez-Morillo E, Lazarou I, Kozori M, Tagaraki F, Nenopoulou S, Gkioka M, Lazarou E, Lim B, Batruch I, Diamandis EP. Neuronal pentraxin receptor-1 is a new cerebrospinal fluid biomarker of Alzheimer's disease progression. F1000Res 2018; 7:1012. [PMID: 30191060 PMCID: PMC6081984 DOI: 10.12688/f1000research.15095.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Background: Alzheimer's disease (AD) is the most common type of dementia, with progressive onset of clinical symptoms. The main pathological hallmarks are brain deposits of extracellular amyloid beta plaques and intracellular neurofibrillary tangles (NFT). Cerebrospinal fluid reflects pathological changes in the brain; amyloid beta 1-42 is a marker of amyloid plaques, while total and phosphorylated tau are markers of NFT formation. Additional biomarkers associated with disease pathogenesis are needed, for better prognosis, more specific diagnosis, prediction of disease severity and progression and for improved patient classification in clinical trials. The aim of the present study was to evaluate brain-specific proteins as potential biomarkers of progression of AD. Methods: Overall, 30 candidate proteins were quantified in cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment (MCI) and mild, moderate and severe AD dementia (n=101) using mass spectrometry-based selected reaction monitoring assays. ELISA was used for neuronal pentraxin receptor-1 (NPTXR) confirmation. Results: The best discrimination between MCI and more advanced AD stages (moderate and severe dementia) was observed for protein NPTXR (area under the curve, AUC=0.799). A statistically different abundance of this protein was observed between the two groups, with severe AD patients having progressively lower levels (p<0.05). ELISA confirmed lower levels in AD, in a separate cohort that included controls, MCI and AD patients. Conclusions: We conclude that NPTXR protein in CSF is a novel potential biomarker of AD progression and could have important utility in assessing treatment success in clinical trials.
Collapse
Affiliation(s)
- Ilijana Begcevic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Magda Tsolaki
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Marshall Brown
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eduardo Martinez-Morillo
- Laboratory of Medicine, Department of Clinical Biochemistry, Hospital Universitario Central, Oviedo, Spain
| | - Ioulietta Lazarou
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mahi Kozori
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fani Tagaraki
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stella Nenopoulou
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mara Gkioka
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eutichia Lazarou
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Bryant Lim
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Ihor Batruch
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| |
Collapse
|
47
|
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: 14] [Impact Index Per Article: 2.3] [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
|
48
|
Begcevic I, Brinc D, Brown M, Martinez-Morillo E, Goldhardt O, Grimmer T, Magdolen V, Batruch I, Diamandis EP. Brain-related proteins as potential CSF biomarkers of Alzheimer's disease: A targeted mass spectrometry approach. J Proteomics 2018; 182:12-20. [PMID: 29684683 DOI: 10.1016/j.jprot.2018.04.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/15/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia, characterized by progressive cognitive decline. The main disease hallmarks include amyloid beta aggregates and neurofibrillary tangles. Brain pathology is reflected in cerebrospinal fluid (CSF); the core biomarkers amyloid beta 1-42, total and phosphorylated tau protein levels are changed, relative to cognitively normal elderly. Still, there is a need for additional biomarkers which could identify disease more accurately and at an earlier stage, predict severity and be used in research settings. Here we evaluated 30 brain-related proteins as candidate biomarkers of AD. Proteins were quantified in CSF samples from cognitively healthy individuals (n = 23) and patients with mild cognitive impairment (MCI) due to AD (n = 20) or dementia due to AD (n = 10) using selected reaction monitoring mass spectrometry assays. APLP1 protein was increased in MCI relative to control (p < 0.001). The best discrimination between MCI vs. controls was observed with a model combining APLP1 and SPP1 proteins (area under the curve, AUC = 0.84). The strongest associations between protein abundance and disease severity were found for APLP1, CNTN2 and SPP1 proteins, which had a significant correlation with MMSE and CDR tests (p < 0.05). This study identifies new proteins with biomarker potential at various stages of AD severity. SIGNIFICANCE The current study evaluated 30 brain-related, highly specific proteins as candidate biomarkers of AD diagnosis. Protein APLP1 showed promise as early AD biomarker; protein panel APLP1 and SPP1 had the best diagnostic potential in discriminating MCI from control group, while proteins APLP1, SPP1 and CNTN2 may be indicators of disease progression, demonstrating weak to moderate correlation with cognitive tests. This study therefore identifies new proteins with biomarker potential at early AD stage. If the performance of proposed biomarkers is further confirmed, these proteins may add value in the clinic or clinical trial settings as diagnostic biomarkers (alone or in combination with the existing biomarkers) of the prodromal AD stage, and in monitoring disease progression.
Collapse
Affiliation(s)
- Ilijana Begcevic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Marshall Brown
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eduardo Martinez-Morillo
- Laboratory of Medicine, Department of Clinical Biochemistry, Hospital Universitario Central, Oviedo, Spain
| | - Oliver Goldhardt
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Viktor Magdolen
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Ihor Batruch
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
| |
Collapse
|
49
|
Waldera-Lupa DM, Etemad-Parishanzadeh O, Brocksieper M, Kirchgaessler N, Seidel S, Kowalski T, Montesinos-Rongen M, Deckert M, Schlegel U, Stühler K. Proteomic changes in cerebrospinal fluid from primary central nervous system lymphoma patients are associated with protein ectodomain shedding. Oncotarget 2017; 8:110118-110132. [PMID: 29299134 PMCID: PMC5746369 DOI: 10.18632/oncotarget.22654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
Primary central nervous system lymphomas (PCNSLs) are mature B-cell lymphomas confined to the central nervous system (CNS). Blood-brain barrier (BBB) dysfunction drastically alters the cerebrospinal fluid (CSF) proteome in PCNSL patients. To reveal the interaction of PCNSL tumors with CNS structures and the vasculature, we conducted a whole-proteome analysis of CSF from PCNSL patients (n = 17 at initial diagnosis) and tumor-free controls (n = 10) using label-free quantitative mass spectrometry. We identified 601 proteins in the CSF proteome using a one-step approach without further prefractionation, and quantified 438 proteins in detail using the Hi-N method. An immunoassay revealed that 70% of the patients in our unselected PCNSL patient cohort had BBB dysfunction. Correlation analysis indicated that 127 (30%) of the quantified proteins were likely increased in PCSNL patients due to BBB dysfunction. After the exclusion of these proteins, 66 were found to differ in abundance (fold-change > 2.0, p < 0.05) between PCNSL and control CSF proteomes, and most of those were associated with the CNS. These data also provide the first evidence that proteomic changes in CSF from PCNSL patients are mainly associated with protein ectodomain shedding, and that shedding of human leukocyte antigen class 2 proteins is a mechanism of tumor-cell immune evasion.
Collapse
Affiliation(s)
- Daniel Michael Waldera-Lupa
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Omid Etemad-Parishanzadeh
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Mareike Brocksieper
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Nina Kirchgaessler
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Sabine Seidel
- Department of Neurology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Thomas Kowalski
- Department of Neurology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | | | - Martina Deckert
- Institute of Neuropathology, University of Cologne, Cologne, Germany
| | - Uwe Schlegel
- Department of Neurology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany.,Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
50
|
Gao L, Zhong JC, Huang WT, Dang YW, Kang M, Chen G. Integrative analysis of BSG expression in NPC through immunohistochemistry and public high-throughput gene expression data. Am J Transl Res 2017; 9:4574-4592. [PMID: 29118919 PMCID: PMC5666066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Though basigin (BSG) was reported to be overexpressed in nasopharyngeal carcinoma (NPC) and correlate with the development of NPC, the molecular basis of BSG in NPC remained elusive. The aim of the research was to investigate BSG expression in NPC and the potential molecular mechanism underlying it. MATERIALS AND METHODS BSG expression in NPC tissues was detected with immunohistochemistry. Chi-square test, Kruskal-Wallis test and Spearman correlation test were performed to examine the relationship between BSG expression and the clinico-pathological features as well as EGFR and P-53 expression in NPC. In addition, data from the Human Protein Atlas (HPA) database and oncomine were collected to validate BSG expression in NPC. Meta-analysis was conducted to investigate the association between BSG expression and the clinico-pathological variables of NPC. The prognostic value and the alteration of BSG gene status were also analyzed with data from The Cancer Genome Atlas (TCGA). RESULTS BSG presented notably higher expression in NPC tissues than in non-cancer tissues. Moreover, IHC results showed that BSG expression was significantly correlated with tumor progression. A positive correlation was also found between BSG expression and EGFR, P53 expression. Meta-analysis confirmed that BSG was indicative of lymph node metastasis and TNM stage in NPC. Additionally, data from cBioPortal indicated that alteration of BSG gene existed in 5% of NPC cases and BSG correlative genes were obtained from the Co-expression Analysis in TCGA. CONCLUSION BSG was overexpressed in NPC and might have an oncogenic effect on the tumorigenesis and progression of NPC.
Collapse
Affiliation(s)
- Li Gao
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, P. R. China
| | - Jin-Cai Zhong
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, P. R. China
| | - Wen-Ting Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, P. R. China
| | - Min Kang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, P. R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical UniversityNanning, P. R. China
| |
Collapse
|