1
|
Wang D, Chen Z, Li L. Profiling Human Cerebrospinal Fluid (CSF) Endogenous Peptidome in Alzheimer's Disease. Methods Mol Biol 2024; 2758:445-455. [PMID: 38549029 DOI: 10.1007/978-1-0716-3646-6_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Human cerebrospinal fluid (CSF) is a rich source for central nervous system (CNS)-related disease biomarker discovery due to its direct interchange with the extracellular fluid of the CNS. Though extensive proteome-level profiling has been conducted for CSF, studies targeting at its endogenous peptidome is still limited. It is more difficult to include the post-translational modifications (PTMs) characterization of the peptidome in the mass spectrometry (MS) analysis because of their low abundance and the challenge of data interpretation. In this chapter, we present a peptidomic workflow that combines molecular weight cut-off (MWCO) separation, electron-transfer and higher-energy collision dissociation (EThcD) fragmentation, and a three-step database searching strategy for comprehensive PTM analysis of endogenous peptides including both N-glycosylation and O-glycosylation and other common peptide PTMs. The method has been successfully adopted to analyze CSF samples from healthy donors, mild cognitive impairment (MCI), and Alzheimer's disease (AD) patients to provide a landscape of peptidome in different disease states.
Collapse
Affiliation(s)
- Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
2
|
Kajana X, Spinelli S, Garbarino A, Balagura G, Bartolucci M, Petretto A, Pavanello M, Candiano G, Panfoli I, Bruschi M. Identification of Central Nervous System Oncologic Disease Biomarkers in EVs from Cerebrospinal Fluid (CSF) of Pediatric Patients: A Pilot Neuro-Proteomic Study. Biomolecules 2023; 13:1730. [PMID: 38136601 PMCID: PMC10741637 DOI: 10.3390/biom13121730] [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: 10/25/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Cerebrospinal fluid (CSF) is a biochemical-clinical window into the brain. Unfortunately, its wide dynamic range, low protein concentration, and small sample quantity significantly limit the possibility of using it routinely. Extraventricular drainage (EVD) of CSF allows us to solve quantitative problems and to study the biological role of extracellular vesicles (EVs). In this study, we implemented bioinformatic analysis of our previous data of EVD of CSF and its EVs obtained from congenital hydrocephalus with the aim of identifying a comprehensive list of potential tumor and non-tumor biomarkers of central nervous system diseases. Among all proteins identified, those enriched in EVs are associated with synapses, synaptosomes, and nervous system diseases including gliomas, embryonal tumors, and epilepsy. Among these EV-enriched proteins, given the broad consensus present in the recent scientific literature, we validated syntaxin-binding protein 1 (STXBP1) as a marker of malignancy in EVD of CSF and its EVs from patients with pilocytic astrocytoma and medulloblastoma. Our results show that STXBP1 is negatively enriched in EVs compared to non-tumor diseases and its downregulation correlates with adverse outcomes. Further experiments are needed to validate this and other EV markers in the blood of pediatric patients for translational medicine applications.
Collapse
Affiliation(s)
- Xhuliana Kajana
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy (S.S.)
| | - Sonia Spinelli
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy (S.S.)
| | - Andrea Garbarino
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy (S.S.)
| | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, University of Genoa, 16132 Genoa, Italy
| | - Martina Bartolucci
- Proteomics and Clinical Metabolomics Unit at the Core Facilities, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.B.)
| | - Andrea Petretto
- Proteomics and Clinical Metabolomics Unit at the Core Facilities, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (M.B.)
| | - Marco Pavanello
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy (S.S.)
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy (S.S.)
| | - Isabella Panfoli
- Department of Pharmacy (DIFAR), School of Medical and Pharmaceutical Sciences, University of Genoa, 16132 Genoa, Italy
| | - Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy (S.S.)
- Department of Experimental Medicine (DIMES), University of Genoa, 16132 Genoa, Italy
| |
Collapse
|
3
|
Chen Z, Wang D, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Yu Q, Zetterberg H, Asthana S, Carlsson C, Okonkwo O, Li L. In-Depth Site-Specific O-Glycosylation Analysis of Glycoproteins and Endogenous Peptides in Cerebrospinal Fluid (CSF) from Healthy Individuals, Mild Cognitive Impairment (MCI), and Alzheimer's Disease (AD) Patients. ACS Chem Biol 2022; 17:3059-3068. [PMID: 34964596 PMCID: PMC9240109 DOI: 10.1021/acschembio.1c00932] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Site-specific O-glycoproteome mapping in complex biological systems provides a molecular basis for understanding the structure-function relationships of glycoproteins and their roles in physiological and pathological processes. Previous O-glycoproteome analysis in cerebrospinal fluid (CSF) focused on sialylated glycoforms, while missing information on other glycosylation types. In order to achieve an unbiased O-glycosylation profile, we developed an integrated strategy combining universal boronic acid enrichment, high-pH fractionation, and electron-transfer and higher-energy collision dissociation (EThcD) for enhanced intact O-glycopeptide analysis. We applied this strategy to analyze the O-glycoproteome in CSF, resulting in the identification of 308 O-glycopeptides from 110 O-glycoproteins, covering both sialylated and nonsialylated glycoforms. To our knowledge, this is the largest data set of O-glycoproteins and O-glycosites reported for CSF to date. We also developed a peptidomics workflow that utilized the EThcD and a three-step database searching strategy for comprehensive PTM analysis of endogenous peptides, including N-glycosylation, O-glycosylation, and other common peptide PTMs. Interestingly, among the 1411 endogenous peptides identified, 89 were O-glycosylated, and only one N-glycosylated peptide was found, indicating that CSF endogenous peptides were predominantly O-glycosylated. Analyses of the O-glycoproteome and endogenous peptidome PTMs were also conducted in the CSF of MCI and AD patients to provide a landscape of glycosylation patterns in different disease states. Our results showed a decreasing trend in fucosylation and an increasing trend of endogenous peptide O-glycosylation, which may play an important role in AD progression.
Collapse
Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Danqing Wang
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Richard Shipman
- Applied Science Program, University of Wisconsin-Stout, Menomonie, WI 54751, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 43180, Mölndal, Sweden,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 43180, Mölndal, Sweden,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, United Kingdom,UK Dementia Research Institute at UCL, London, WC1E 6BT, United Kingdom
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA,School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA,Correspondence: Professor Lingjun Li, School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, , Fax: +1-608-262-5345, Phone: +1-608-265-8491
| |
Collapse
|
4
|
Weighted Gene Co-Expression Network Analysis and Support Vector Machine Learning in the Proteomic Profiling of Cerebrospinal Fluid from Extraventricular Drainage in Child Medulloblastoma. Metabolites 2022; 12:metabo12080724. [PMID: 36005596 PMCID: PMC9412589 DOI: 10.3390/metabo12080724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/25/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
Medulloblastoma (MB) is the most common pediatric malignant central nervous system tumor. Overall survival in MB depends on treatment tuning. There is aneed for biomarkers of residual disease and recurrence. We analyzed the proteome of waste cerebrospinal fluid (CSF) from extraventricular drainage (EVD) from six children bearing various subtypes of MB and six controls needing EVD insertion for unrelated causes. Samples included total CSF, microvesicles, exosomes, and proteins captured by combinatorial peptide ligand library (CPLL). Liquid chromatography-coupled tandem mass spectrometry proteomics identified 3560 proteins in CSF from control and MB patients, 2412 (67.7%) of which were overlapping, and 346 (9.7%) and 805 (22.6%) were exclusive. Multidimensional scaling analysis discriminated samples. The weighted gene co-expression network analysis (WGCNA) identified those modules functionally associated with the samples. A ranked core of 192 proteins allowed distinguishing between control and MB samples. Machine learning highlighted long-chain fatty acid transport protein 4 (SLC27A4) and laminin B-type (LMNB1) as proteins that maximized the discrimination between control and MB samples. Machine learning WGCNA and support vector machine learning were able to distinguish between MB versus non-tumor/hemorrhagic controls. The two potential protein biomarkers for the discrimination between control and MB may guide therapy and predict recurrences, improving the MB patients' quality of life.
Collapse
|
5
|
Muqaku B, Oeckl P. Peptidomic Approaches and Observations in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23137332. [PMID: 35806335 PMCID: PMC9266836 DOI: 10.3390/ijms23137332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/16/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Mass spectrometry (MS), with its immense technological developments over the last two decades, has emerged as an unavoidable technique in analyzing biomolecules such as proteins and peptides. Its multiplexing capability and explorative approach make it a valuable tool for analyzing complex clinical samples concerning biomarker research and investigating pathophysiological mechanisms. Peptides regulate various biological processes, and several of them play a critical role in many disease-related pathological conditions. One important example in neurodegenerative diseases is the accumulation of amyloid-beta peptides (Aβ) in the brain of Alzheimer’s disease (AD) patients. When investigating brain function and brain-related pathologies, such as neurodegenerative diseases, cerebrospinal fluid (CSF) represents the most suitable sample because of its direct contact with the brain. In this review, we evaluate publications applying peptidomics analysis to CSF samples, focusing on neurodegenerative diseases. We describe the methodology of peptidomics analysis and give an overview of the achievements of CSF peptidomics over the years. Finally, publications reporting peptides regulated in AD are discussed.
Collapse
Affiliation(s)
- Besnik Muqaku
- German Center for Neurodegenerative Diseases (DZNE e.V.), 89081 Ulm, Germany;
| | - Patrick Oeckl
- German Center for Neurodegenerative Diseases (DZNE e.V.), 89081 Ulm, Germany;
- Department of Neurology, Ulm University Hospital, 89081 Ulm, Germany
- Correspondence: ; Tel.: +49-731-500-63143
| |
Collapse
|
6
|
Xiao H, Jiang H, Tu H, Jia Y, Wang H, Lü X, Fang R, Xiao G. Extraction, Isolation and Identification of Low Molecular Weight Peptides in Human Milk. Foods 2022; 11:foods11131836. [PMID: 35804652 PMCID: PMC9265843 DOI: 10.3390/foods11131836] [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: 06/08/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
Human milk contains numerous free low molecular weight peptides (LMWPs), which may play an important role in infant health and growth. The bioactivities of LMWPs are determined by their structures, especially the amino acid sequences. In the present study, 81 human milk samples were collected and purified by cation-exchange solid-phase extraction (SPE). Ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) was used for the separation and detection of free LMWPs in human milk. A total of 56 LMWPs were identified and quantified. These LMWPs were mainly derived from 3 regions of β-casein, which were the amino acid fragments of 16–40, 85–110, and 205–226. The predominant LMWPs were RETIESLSSSEESITEYK, RETIESLSSSEESITEYKQKVEKVK, ETIESLSSSEESITEYK, TQPLAPVHNPIS, and QPLAPVHNPISV with molecular weights of 2247.9573, 2860.2437, 2091.8591, 1372.7666, and 1271.7212, respectively. The results indicated that the technique based on SPE and UPLC-QTOF-MS might greatly facilitate the analysis of LMWPs in human milk.
Collapse
Affiliation(s)
- Hailong Xiao
- Key Laboratory of Agricultural Products Chemical and Biological Processing Technology, Zhejiang University of Science and Technology, Hangzhou 310023, China; (H.X.); (R.F.)
- Hangzhou Institute for Food and Drug Control, Hangzhou 310017, China; (H.J.); (H.T.); (Y.J.); (H.W.)
- Zhejiang Market Bureau Supervision Key Laboratory of Dairy and Dairy Products, Hangzhou 310017, China
| | - He Jiang
- Hangzhou Institute for Food and Drug Control, Hangzhou 310017, China; (H.J.); (H.T.); (Y.J.); (H.W.)
- Zhejiang Market Bureau Supervision Key Laboratory of Dairy and Dairy Products, Hangzhou 310017, China
| | - Haiyun Tu
- Hangzhou Institute for Food and Drug Control, Hangzhou 310017, China; (H.J.); (H.T.); (Y.J.); (H.W.)
- Zhejiang Market Bureau Supervision Key Laboratory of Dairy and Dairy Products, Hangzhou 310017, China
| | - Yanbo Jia
- Hangzhou Institute for Food and Drug Control, Hangzhou 310017, China; (H.J.); (H.T.); (Y.J.); (H.W.)
- Zhejiang Market Bureau Supervision Key Laboratory of Dairy and Dairy Products, Hangzhou 310017, China
| | - Hongqing Wang
- Hangzhou Institute for Food and Drug Control, Hangzhou 310017, China; (H.J.); (H.T.); (Y.J.); (H.W.)
- Zhejiang Market Bureau Supervision Key Laboratory of Dairy and Dairy Products, Hangzhou 310017, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China;
| | - Ruosi Fang
- Key Laboratory of Agricultural Products Chemical and Biological Processing Technology, Zhejiang University of Science and Technology, Hangzhou 310023, China; (H.X.); (R.F.)
| | - Gongnian Xiao
- Key Laboratory of Agricultural Products Chemical and Biological Processing Technology, Zhejiang University of Science and Technology, Hangzhou 310023, China; (H.X.); (R.F.)
- Correspondence: ; Tel./Fax: +86-571-85070370
| |
Collapse
|
7
|
Abstract
Peptides play a crucial role in many vitally important functions of living organisms. The goal of peptidomics is the identification of the "peptidome," the whole peptide content of a cell, organ, tissue, body fluid, or organism. In peptidomic or proteomic studies, capillary electrophoresis (CE) is an alternative technique for liquid chromatography. It is a highly efficient and fast separation method requiring extremely low amounts of sample. In peptidomic approaches, CE is commonly combined with mass spectrometric (MS) detection. Most often, CE is coupled with electrospray ionization MS and less frequently with matrix-assisted laser desorption/ionization MS. CE-MS has been employed in numerous studies dealing with determination of peptide biomarkers in different body fluids for various diseases, or in food peptidomic research for the analysis and identification of peptides with special biological activities. In addition to the above topics, sample preparation techniques commonly applied in peptidomics before CE separation and possibilities for peptide identification and quantification by CE-MS or CE-MS/MS methods are discussed in this chapter.
Collapse
|
8
|
Yu S, Lu Y, Su A, Chen J, Li J, Zhou B, Liu X, Xia Q, Li Y, Li J, Huang M, Ye Y, Zhao Q, Jiang S, Yan X, Wang X, Di C, Pan J, Su S. A CD10-OGP Membrane Peptolytic Signaling Axis in Fibroblasts Regulates Lipid Metabolism of Cancer Stem Cells via SCD1. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101848. [PMID: 34363355 PMCID: PMC8498877 DOI: 10.1002/advs.202101848] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Carcinoma-associated fibroblasts (CAFs) consist of heterogeneous subpopulations that play a critical role in the dynamics of the tumor microenvironment. The extracellular signals of CAFs have been attributed to the extracellular matrix, cytokines, cell surface checkpoints, and exosomes. In the present study, it is demonstrated that the CD10 transmembrane hydrolase expressed on a subset of CAFs supports tumor stemness and induces chemoresistance. Mechanistically, CD10 degenerates an antitumoral peptide termed osteogenic growth peptide (OGP). OGP restrains the expression of rate-limiting desaturase SCD1 and inhibits lipid desaturation, which is required for cancer stem cells (CSCs). Targeting CD10 significantly improves the efficacy of chemotherapy in vivo. Clinically, CD10-OGP signals are associated with the response to neoadjuvant chemotherapy in patients with breast cancer. The collective data suggest that a nexus between the niche and lipid metabolism in CSCs is a promising therapeutic target for breast cancer.
Collapse
Affiliation(s)
- Shubin Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Yiwen Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - An Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Jianing Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Jiang Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Boxuan Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Xinwei Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Qidong Xia
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Yihong Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Jiaqian Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Min Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Yingying Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Qiyi Zhao
- Department of Infectious Diseasesthe Third Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510630China
- Guangdong Provincial Key Laboratory of Liver Disease Researchthe Third Affiliated HospitalSun Yat‐sen UniversityGuangzhou510630China
- Key Laboratory of Tropical Disease Control (Sun Yat‐sen University)Ministry of EducationGuangzhouGuangdong510080China
| | - Sushi Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Xiaoqing Yan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Xiaojuan Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Can Di
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Jiayao Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationMedical Research CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Breast Tumor CenterSun Yat‐Sen Memorial HospitalSun Yat‐Sen UniversityGuangzhou510120China
- Department of Infectious Diseasesthe Third Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510630China
- Department of ImmunologyZhongshan School of MedicineSun Yat‐Sen UniversityGuangzhou510080China
| |
Collapse
|
9
|
van der Plas MJA, Cai J, Petrlova J, Saleh K, Kjellström S, Schmidtchen A. Method development and characterisation of the low-molecular-weight peptidome of human wound fluids. eLife 2021; 10:e66876. [PMID: 34227939 PMCID: PMC8260221 DOI: 10.7554/elife.66876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/03/2021] [Indexed: 01/13/2023] Open
Abstract
The normal wound healing process is characterised by proteolytic events, whereas infection results in dysfunctional activations by endogenous and bacterial proteases. Peptides, downstream reporters of these proteolytic actions, could therefore serve as a promising tool for diagnosis of wounds. Using mass-spectrometry analyses, we here for the first time characterise the peptidome of human wound fluids. Sterile post-surgical wound fluids were found to contain a high degree of peptides in comparison to human plasma. Analyses of the peptidome from uninfected healing wounds and Staphylococcus aureus -infected wounds identify unique peptide patterns of various proteins, including coagulation and complement factors, proteases, and antiproteinases. Together, the work defines a workflow for analysis of peptides derived from wound fluids and demonstrates a proof-of-concept that such fluids can be used for analysis of qualitative differences of peptide patterns from larger patient cohorts, providing potential biomarkers for wound healing and infection.
Collapse
Affiliation(s)
- Mariena JA van der Plas
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund UniversityLundSweden
- LEO Foundation Center for Cutaneous Drug Delivery, Department of Pharmacy, University of CopenhagenCopenhagenDenmark
| | - Jun Cai
- LEO Foundation Center for Cutaneous Drug Delivery, Department of Pharmacy, University of CopenhagenCopenhagenDenmark
| | - Jitka Petrlova
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund UniversityLundSweden
| | - Karim Saleh
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund UniversityLundSweden
- Dermatology, Skane University HospitalLundSweden
| | - Sven Kjellström
- Division of Mass Spectrometry, Department of Clinical Sciences, Lund UniversityLundSweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund UniversityLundSweden
- Dermatology, Skane University HospitalLundSweden
- Copenhagen Wound Healing Center, Bispebjerg Hospital, Department of Biomedical Sciences, University of CopenhagenCopenhagenDenmark
| |
Collapse
|
10
|
Uddin MS, Kabir MT, Jakaria M, Sobarzo-Sánchez E, Barreto GE, Perveen A, Hafeez A, Bin-Jumah MN, Abdel-Daim MM, Ashraf GM. Exploring the Potential of Neuroproteomics in Alzheimer's Disease. Curr Top Med Chem 2021; 20:2263-2278. [PMID: 32493192 DOI: 10.2174/1568026620666200603112030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/27/2020] [Accepted: 05/08/2020] [Indexed: 12/25/2022]
Abstract
Alzheimer's disease (AD) is progressive brain amyloidosis that damages brain regions associated with memory, thinking, behavioral and social skills. Neuropathologically, AD is characterized by intraneuronal hyperphosphorylated tau inclusions as neurofibrillary tangles (NFTs), and buildup of extracellular amyloid-beta (Aβ) peptide as senile plaques. Several biomarker tests capturing these pathologies have been developed. However, for the full clinical expression of the neurodegenerative events of AD, there exist other central molecular pathways. In terms of understanding the unidentified underlying processes for the progression and development of AD, a complete comprehension of the structure and composition of atypical aggregation of proteins is essential. Presently, to aid the prognosis, diagnosis, detection, and development of drug targets in AD, neuroproteomics is elected as one of the leading essential tools for the efficient exploratory discovery of prospective biomarker candidates estimated to play a crucial role. Therefore, the aim of this review is to present the role of neuroproteomics to analyze the complexity of AD.
Collapse
Affiliation(s)
- Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh,Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | | | - Md Jakaria
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Eduardo Sobarzo-Sánchez
- Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile,Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Spain
| | - George E Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland,Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Saharanpur, India
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Saharanpur, India
| | - May N Bin-Jumah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia,Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ghulam M Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
11
|
Peptidomic profiling of cerebrospinal fluid from patients with intracranial saccular aneurysms. J Proteomics 2021; 240:104188. [PMID: 33781962 DOI: 10.1016/j.jprot.2021.104188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023]
Abstract
Intracranial saccular aneurysms (ISA) represent 90%-95% of all intracranial aneurysm cases, characterizing abnormal pockets at arterial branch points. Ruptures lead to subarachnoid hemorrhages (SAH) and poor prognoses. We applied mass spectrometry-based peptidomics to investigate the peptidome of twelve cerebrospinal fluid (CSF) samples collected from eleven patients diagnosed with ISA. For peptide profile analyses, participants were classified into: 1) ruptured intracranial saccular aneurysms (RIA), 2) unruptured intracranial saccular aneurysms (UIA), and late-ruptured intracranial saccular aneurysms (LRIA). Altogether, a total of 2199 peptides were detected by both Mascot and Peaks software, from which 484 (22.0%) were unique peptides. All unique peptides presented conserved chains, domains, regions of protein modulation and/or post-translational modification sites related to human diseases. Gene Ontology (GO) analyses of peptide precursor proteins showed that 42% are involved in binding, 56% in cellular anatomical entities, and 39% in intercellular signaling molecules. Unique peptides identified in patients diagnosed with RIA have a larger molecular weight and a distinctive developmental process compared to UIA and LRIA (P ≤ 0.05). Continued investigations will allow the characterization of the biological and clinical significance of the peptides identified in the present study, as well as identify prototypes for peptide-based pharmacological therapies to treat ISA. SIGNIFICANCE.
Collapse
|
12
|
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: 15] [Impact Index Per Article: 5.0] [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
|
13
|
Hou X, Yuan Z, Wang X, Cheng R, Zhou X, Qiu J. Peptidome analysis of cerebrospinal fluid in neonates with hypoxic-ischemic brain damage. Mol Brain 2020; 13:133. [PMID: 33008433 PMCID: PMC7531121 DOI: 10.1186/s13041-020-00671-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/18/2020] [Indexed: 12/20/2022] Open
Abstract
Hypoxic-ischemic brain injury (HIBD) causes neonatal death and serious neurological disability; however, there are currently no promising therapies for it excepting cooling. Therefore, in this study, we used peptidome analysis to identify differentially expressed peptides in cerebrospinal fluid (CSF) of neonates with HIBD or controls, which may give a foundation for finding new promising drugs of neonatal HIBD. CSF samples were collected from neonates with HIBD (n = 4) or controls (n = 4). ITRAQ LC-MS/MS was used to identify differentially expressed peptides between two groups. A total of 35 differentially expressed peptides from 25 precursor proteins were identified. The 2671.5 Da peptide (HSQFIGYPITLFVEKER), one of the down-regulated peptides in neonatal HIBD, is a fragment of heat shock protein 90-alpha (HSP90α/HSP90AA1). Results of bioinformatics analysis showed that HSP90α/HSP90AA1 was located in the protein-protein interaction (PPI) network hub and was involved in the NOD-LIKE receptor (NLR) signaling pathway. This peptide, we named it Hypoxic-Ischemic Brain Damage Associated Peptide (HIBDAP), is a hydrophilic peptide with high stability and has a long half-life of 3.5 h in mammalian reticulocytes. It was demonstrated that TAT-HIBDAP could successfully enter PC12 cells and further into the nucleus. After HIBDAP pretreatment and 6 h of OGD treatment, low concentrations of HIBDAP increased the survival rate of cells, except 40 μM had a toxic effect. Safe concentrations of HIBDAP reduced pyroptosis of PC12 cells under OGD, except 20 μM had no effect, by suppressing expressions of NLRP3, ASC and Caspase-1 except NLRP1. The results of our study identified the characterization and expression profiles of peptides in CSF of neonatal HIBD. Several meaningful peptides such as HIBDAP may play significant roles in neonatal HIBD and provide new therapeutic targets for neonatal HIBD.
Collapse
Affiliation(s)
- Xuewen Hou
- Department of Newborn Infants, Children's Hospital of Nanjing Medical University, Nanjing, 210008, Jiangsu, China
| | - Zijun Yuan
- Department of Newborn Infants, Children's Hospital of Nanjing Medical University, Nanjing, 210008, Jiangsu, China
| | - Xuan Wang
- Department of Newborn Infants, Children's Hospital of Nanjing Medical University, Nanjing, 210008, Jiangsu, China
| | - Rui Cheng
- Department of Newborn Infants, Children's Hospital of Nanjing Medical University, Nanjing, 210008, Jiangsu, China
| | - Xiaoguang Zhou
- Department of Newborn Infants, Children's Hospital of Nanjing Medical University, Nanjing, 210008, Jiangsu, China.
| | - Jie Qiu
- Department of Newborn Infants, Children's Hospital of Nanjing Medical University, Nanjing, 210008, Jiangsu, China.
| |
Collapse
|
14
|
van Huizen NA, Ijzermans JNM, Burgers PC, Luider TM. Collagen analysis with mass spectrometry. MASS SPECTROMETRY REVIEWS 2020; 39:309-335. [PMID: 31498911 DOI: 10.1002/mas.21600] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Mass spectrometry-based techniques can be applied to investigate collagen with respect to identification, quantification, supramolecular organization, and various post-translational modifications. The continuous interest in collagen research has led to a shift from techniques to analyze the physical characteristics of collagen to methods to study collagen abundance and modifications. In this review, we illustrate the potential of mass spectrometry for in-depth analyses of collagen.
Collapse
Affiliation(s)
- Nick A van Huizen
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Jan N M Ijzermans
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Peter C Burgers
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
15
|
Fleites LA, Johnson R, Kruse AR, Nachman RJ, Hall DG, MacCoss M, Heck ML. Peptidomics Approaches for the Identification of Bioactive Molecules from Diaphorina citri. J Proteome Res 2020; 19:1392-1408. [PMID: 32037832 DOI: 10.1021/acs.jproteome.9b00509] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Huanglongbing (HLB), a deadly citrus disease, is primarily associated with Candidatus Liberibacter asiaticus (CLas) and spread by the hemipteran insect Diaphorina citri. Control strategies to combat HLB are urgently needed. In this work, we developed and compared workflows for the extraction of the D. citri peptidome, a dynamic set of polypeptides produced by proteolysis and other cellular processes. High-resolution mass spectrometry revealed bias among methods reflecting the physiochemical properties of the peptides: while TCA/acetone-based methods resulted in enrichment of C-terminally amidated peptides, a modification characteristic of bioactive peptides, larger peptides were overrepresented in the aqueous phase of chloroform/methanol extracts, possibly indicative of reduced co-analytical degradation during sample preparation. Parallel reaction monitoring (PRM) was used to validate the structure and upregulation of peptides derived from hemocyanin, a D. citri immune system protein, in insects reared on healthy and CLas-infected trees. Mining of the data sets also revealed 122 candidate neuropeptides, including PK/PBAN family neuropeptides and kinins, biostable analogs of which have known insecticidal properties. Taken together, this information yields new, in-depth insights into peptidomics methodology. Additionally, the putative neuropeptides identified may lead to psyllid mortality if applied to or expressed in citrus, consequently blocking the spread of HLB disease in citrus groves.
Collapse
Affiliation(s)
- Laura A Fleites
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853-2901, United States.,Department of Plant Pathology and Plant Microbe Biology, Cornell University, Ithaca, New York 14850-5905, United States
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Angela R Kruse
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,Department of Plant Pathology and Plant Microbe Biology, Cornell University, Ithaca, New York 14850-5905, United States
| | - Ronald J Nachman
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, Texas 77845, United States
| | - David G Hall
- USDA Agricultural Research Service, US Horticulture Research Laboratory, Fort Pierce, Florida 34945, United States
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michelle L Heck
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, United States.,USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853-2901, United States.,Department of Plant Pathology and Plant Microbe Biology, Cornell University, Ithaca, New York 14850-5905, United States
| |
Collapse
|
16
|
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
|
17
|
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
|
18
|
Sogorb-Esteve A, García-Ayllón MS, Gobom J, Alom J, Zetterberg H, Blennow K, Sáez-Valero J. Levels of ADAM10 are reduced in Alzheimer's disease CSF. J Neuroinflammation 2018; 15:213. [PMID: 30045733 PMCID: PMC6060469 DOI: 10.1186/s12974-018-1255-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022] Open
Abstract
Background The disintegrin metalloproteinase 10 (ADAM10) is the main α-secretase acting in the non-amyloidogenic processing of the amyloid precursor protein. This study assesses whether ADAM10 is present in cerebrospinal fluid (CSF), and whether it has potential as a biomarker for Alzheimer’s disease (AD). Methods ADAM10 was characterized in human CSF samples by immunoprecipitation and western blotting using antibodies specific for different domains of the protein and by ultracentrifugation in sucrose density gradients. Samples from AD patients (n = 20) and age-matched non-AD controls (n = 20) were characterized for classical CSF biomarkers, Aβ42, T-tau, or P-tau by ELISA, and assayed for soluble ADAM10 levels by western blotting. Results We found that ADAM10 is present in human CSF as several distinct species: an immature form retaining the prodomain (proADAM10; ~ 80 kDa), a mature unprocessed full-length form (ADAM10f; ~ 55 kDa), and a truncated large soluble form released from the membrane (sADAM10; ~ 50 kDa). Fractionation by ultracentrifugation on sucrose density gradients showed that the ADAM10f and sADAM10 species form large complexes. Immunoblotting revealed a significant decrease in ADAM10f and sADAM10 in AD CSF compared to control CSF, while proADAM10 levels remained unaltered. Conclusions Several forms of ADAM10 are present in CSF, mainly assembled as high-molecular weight complexes. The determination of the levels of mature forms of CSF-ADAM10 may be useful as a biomarker for AD. Electronic supplementary material The online version of this article (10.1186/s12974-018-1255-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aitana Sogorb-Esteve
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, Av. Ramón y Cajal s/n, Sant Joan d'Alacant, E-03550, Alicante, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d'Alacant, Spain
| | - María-Salud García-Ayllón
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, Av. Ramón y Cajal s/n, Sant Joan d'Alacant, E-03550, Alicante, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d'Alacant, Spain.,Unidad de Investigación, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria Biomédica de la Comunidad Valenciana (FISABIO), Elche, Spain
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Jordi Alom
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d'Alacant, Spain.,Servicio de Neurología, Hospital General Universitario de Elche, Fundación para el Fomento de la Investigación Sanitaria Biomédica de la Comunidad Valenciana (FISABIO), Elche, Spain
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Javier Sáez-Valero
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, Av. Ramón y Cajal s/n, Sant Joan d'Alacant, E-03550, Alicante, Spain. .,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Sant Joan d'Alacant, Spain.
| |
Collapse
|
19
|
Spreafico F, Bongarzone I, Pizzamiglio S, Magni R, Taverna E, De Bortoli M, Ciniselli CM, Barzanò E, Biassoni V, Luchini A, Liotta LA, Zhou W, Signore M, Verderio P, Massimino M. Proteomic analysis of cerebrospinal fluid from children with central nervous system tumors identifies candidate proteins relating to tumor metastatic spread. Oncotarget 2018; 8:46177-46190. [PMID: 28526811 PMCID: PMC5542258 DOI: 10.18632/oncotarget.17579] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Central nervous system (CNS) tumors are the most common solid tumors in childhood. Since the sensitivity of combined cerebrospinal fluid (CSF) cytology and radiological neuroimaging in detecting meningeal metastases remains relatively low, we sought to characterize the CSF proteome of patients with CSF tumors to identify biomarkers predictive of metastatic spread. CSF samples from 27 children with brain tumors and 13 controls (extra-CNS non-Hodgkin lymphoma) were processed using core-shell hydrogel nanoparticles, and analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS). Candidate proteins were identified with Fisher's exact test and/or a univariate logistic regression model. Reverse phase protein array (RPPA), Western blot (WB), and ELISA were used in the training set and in an independent set of CFS samples (60 cases, 14 controls) to validate our discovery findings. Among the 558 non-redundant proteins identified by LC-MS/MS, 147 were missing from the CSF database at http://www.biosino.org. Fourteen of the 26 final top-candidate proteins were chosen for validation with WB, RPPA and ELISA methods. Six proteins (type 1 collagen, insulin-like growth factor binding protein 4, procollagen C-endopeptidase enhancer 1, glial cell-line derived neurotrophic factor receptor α2, inter-alpha-trypsin inhibitor heavy chain 4, neural proliferation and differentiation control protein-1) revealed the ability to discriminate metastatic cases from controls. Combining a unique dataset of CSFs from pediatric CNS tumors with a novel enabling nanotechnology led us to identify CSF proteins potentially related to metastatic status.
Collapse
Affiliation(s)
- Filippo Spreafico
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Italia Bongarzone
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ruben Magni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Elena Taverna
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maida De Bortoli
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara M Ciniselli
- Unit of Medical Statistics, Biometry and Bioinformatics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Barzanò
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronica Biassoni
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Weidong Zhou
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Michele Signore
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
20
|
Cui X, Li Y, Yang L, You L, Wang X, Shi C, Ji C, Guo X. Peptidome analysis of human milk from women delivering macrosomic fetuses reveals multiple means of protection for infants. Oncotarget 2018; 7:63514-63525. [PMID: 27566575 PMCID: PMC5325381 DOI: 10.18632/oncotarget.11532] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/13/2016] [Indexed: 01/11/2023] Open
Abstract
Breastfeeding is associated with a lower incidence of obesity, diabetes, and cardiovascular disease later in life. While macrosomic infants have a higher risk of developing obesity and other metabolic disorders. Breast milk may contain special nutrients to meet the different growth needs of different infants. Whether mothers make breast milk different to meet the requirement of macrosomic infants is still unknown. Here, we conducted a comparison between mothers delivering macrosomic and non-macrosomic infants in colostrum endogenous peptides. More than 400 peptides, originating from at least 34 protein precursors, were identified by Liquid Chromatography/Mass Spectrometry (LC/MS). Out of these, 29 peptides found to be significant differently expressed (|fold change| ≥ 3, P < 0.01). Blastp analysis revealed 41 peptides may have established biological activities, which exhibit immunomodulating, antibacterial action, antioxidation, opioid agonist and antihypertensive activity. Furthermore, we found that peptide located at β-Casein 24-38 AA has antimicrobial effect against E. coli, Y. enterocolitica and S. aureus. While, κ-Casein 89-109 AA-derived peptide plays as a regulator of preadipocyte proliferation. The profile of endogenous peptides from macrosomic term infants is different from non-macrosomic terms. This different peptide expression potentially has specific physiological function to benefit macrosomic infants. Finally, we believe that our research is a meaningfull finding which may add to the understanding of milk peptide physiological action.
Collapse
Affiliation(s)
- Xianwei Cui
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| | - Yun Li
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| | - Lei Yang
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| | - Lianghui You
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| | - Xing Wang
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| | - Chunmei Shi
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| | - Chenbo Ji
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| | - Xirong Guo
- From Nanjing Maternal and Child Health Medical Institute, Nanjing Medical University Affiliated Nanjing Maternal and Child Health Hospital
| |
Collapse
|
21
|
Lista S, Zetterberg H, O'Bryant SE, Blennow K, Hampel H. Evolving Relevance of Neuroproteomics in Alzheimer's Disease. Methods Mol Biol 2018; 1598:101-115. [PMID: 28508359 DOI: 10.1007/978-1-4939-6952-4_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Substantial progress in the understanding of the biology of Alzheimer's disease (AD) has been achieved over the past decades. The early detection and diagnosis of AD and other age-related neurodegenerative diseases, however, remain a challenging scientific frontier. Therefore, the comprehensive discovery (relating to all individual, converging or diverging biochemical disease mechanisms), development, validation, and qualification of standardized biological markers with diagnostic and prognostic functions with a precise performance profile regarding specificity, sensitivity, and positive and negative predictive value are warranted.Methodological innovations in the area of exploratory high-throughput technologies, such as sequencing, microarrays, and mass spectrometry-based analyses of proteins/peptides, have led to the generation of large global molecular datasets from a multiplicity of biological systems, such as biological fluids, cells, tissues, and organs. Such methodological progress has shifted the attention to the execution of hypothesis-independent comprehensive exploratory analyses (opposed to the classical hypothesis-driven candidate approach), with the aim of fully understanding the biological systems in physiology and disease as a whole. The systems biology paradigm integrates experimental biology with accurate and rigorous computational modelling to describe and foresee the dynamic features of biological systems. The use of dynamically evolving technological platforms, including mass spectrometry, in the area of proteomics has enabled to rush the process of biomarker discovery and validation for refining significantly the diagnosis of AD. Currently, proteomics-which is part of the systems biology paradigm-is designated as one of the dominant matured sciences needed for the effective exploratory discovery of prospective biomarker candidates expected to play an effective role in aiding the early detection, diagnosis, prognosis, and therapy development in AD.
Collapse
Affiliation(s)
- Simone Lista
- AXA Research Fund & UPMC Chair, Paris, France. .,Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris 06, Inserm, CNRS, Institut du cerveau et dela moelle (ICM), Département de Neurologie, Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), HôpitalPitié-Salpêtrière, Boulevard de l'hôpital, F-75013, Paris, France.
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Sid E O'Bryant
- Institute for Healthy Aging, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,The Torsten Söderberg Professorship in Medicine at the Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Harald Hampel
- AXA Research Fund & UPMC Chair, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie, Paris 06, Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A) & Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France; Département de Neurologie, Hôpital de la Pitié-Salpêtrière, Boulevard de l'hôpital, F-75013, Paris, France
| |
Collapse
|
22
|
EndoProteoFASP as a Tool to Unveil the Peptidome-Protease Profile: Application to Salivary Diagnostics. Methods Mol Biol 2018; 1719:293-310. [PMID: 29476519 DOI: 10.1007/978-1-4939-7537-2_19] [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: 01/13/2023]
Abstract
In the quest to fully comprehend the proteolytic events leading to the generation of the salivary peptidome, we have developed a method for the sequential elution of salivary peptides throughout progressive endogenous proteolysis. By screening the time-dependent changes in the salivary peptidome we can predict the activity pattern of salivary proteases responsible for such peptide fingerprint and identify susceptible protein targets. Herein, we describe a step-by-step tutorial based on a filter-aided sample preparation (FASP) method, taking advantage of the endogenous salivary proteases armamentarium (endoProteoFASP), to produce new peptides from the salivary proteins, adding to those present in the sample at the time of collection. In this protocol, the different sets of peptides retrieved after sample elution are identified following a liquid chromatography-tandem mass spectrometry approach. The likelihood of a large set of endogenous proteases (collected from several public sources) to be responsible for the generation of such peptides can be predicted by the analysis of the cleavage site specificity by Proteasix ( http://proteasix.cs.man.ac.uk /) algorithm. The attained peptidome-protease profile can be useful to elucidate the peptidome dynamics and the proteolytic events underpinning pathophysiological phenomena taking place locally within the oral cavity. This may help clinicians to diagnose oral pathologies and develop preventive therapeutic plans.
Collapse
|
23
|
Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources mainly by HPLC and mass spectrometry. Mass spectrometry allows the detection of a multitude of single peptides in complex mixtures. The term first appeared in full papers in the year 2001, after over 100 years of peptide research with a main focus on one or a few specific peptides. Within the last 15 years, this new field has grown to over 1200 publications. Mass spectrometry techniques, in combination with other analytical methods, were developed for the fast and comprehensive analysis of peptides in proteomics and specifically adjusted to implement peptidomics technologies. Although peptidomics is closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. The development of peptidomics is described, including the most important implementations for its technological basis. Different strategies are covered which are applied to several important applications, such as neuropeptidomics and discovery of bioactive peptides or biomarkers. This overview includes links to all other chapters in the book as well as recent developments of separation, mass spectrometric, and data processing technologies. Additionally, some new applications in food and plant peptidomics as well as immunopeptidomics are introduced.
Collapse
|
24
|
Hansson KT, Skillbäck T, Pernevik E, Holmén-Larsson J, Brinkmalm G, Blennow K, Zetterberg H, Gobom J. Sample Preparation for Endopeptidomic Analysis in Human Cerebrospinal Fluid. J Vis Exp 2017. [PMID: 29286401 DOI: 10.3791/56244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
This protocol describes a method developed to identify endogenous peptides in human cerebrospinal fluid (CSF). For this purpose, a previously developed method based on molecular weight cut-off (MWCO) filtration and mass spectrometric analysis was combined with an offline high-pH reverse phase HPLC pre-fractionation step. Secretion into CSF is the main pathway for removal of molecules shed by cells of the central nervous system. Thus, many processes in the central nervous system are reflected in the CSF, rendering it a valuable diagnostic fluid. CSF has a complex composition, containing proteins that span a concentration range of 8 - 9 orders of magnitude. Besides proteins, previous studies have also demonstrated the presence of a large number of endogenous peptides. While less extensively studied than proteins, these may also hold potential interest as biomarkers. Endogenous peptides were separated from the CSF protein content through MWCO filtration. By removing a majority of the protein content from the sample, it is possible to increase the sample volume studied and thereby also the total amount of the endogenous peptides. The complexity of the filtrated peptide mixture was addressed by including a reverse phase (RP) HPLC pre-fractionation step at alkaline pH prior to LC-MS analysis. The fractionation was combined with a simple concatenation scheme where 60 fractions were pooled into 12, analysis time consumption could thereby be reduced while still largely avoiding co-elution. Automated peptide identification was performed by using three different peptide/protein identification software programs and subsequently combining the results. The different programs were complementary rather than comparable with less than 15% of the identifications overlapped between the three.
Collapse
Affiliation(s)
- Karl T Hansson
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg;
| | - Tobias Skillbäck
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital
| | - Elin Pernevik
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg
| | - Jessica Holmén-Larsson
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg
| | - Gunnar Brinkmalm
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg
| | - Kaj Blennow
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital
| | - Henrik Zetterberg
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital; Department of Molecular Neuroscience, UCL Institute of Neurology
| | - Johan Gobom
- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, Sahlgrenska Academy at University of Gothenburg; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital
| |
Collapse
|
25
|
Bosso M, Ständker L, Kirchhoff F, Münch J. Exploiting the human peptidome for novel antimicrobial and anticancer agents. Bioorg Med Chem 2017; 26:2719-2726. [PMID: 29122440 DOI: 10.1016/j.bmc.2017.10.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 10/28/2017] [Indexed: 12/22/2022]
Abstract
Infectious diseases and cancers are leading causes of death and pose major challenges to public health. The human peptidome encompasses millions of compounds that display an enormous structural and functional diversity and represents an excellent source for the discovery of endogenous agents with antimicrobial and/or anticancer activity. Here, we discuss how to exploit the human peptidome for novel antimicrobial and anticancer agents through the generation of peptide libraries from human body fluids and tissues and stepwise purification of bioactive compounds.
Collapse
Affiliation(s)
- Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstrasse 1, 89081 Ulm, Germany
| | - Ludger Ständker
- Ulm Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany; Core Facility Functional Peptidomics, Ulm University Medical Center, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstrasse 1, 89081 Ulm, Germany; Ulm Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstrasse 1, 89081 Ulm, Germany; Ulm Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany; Core Facility Functional Peptidomics, Ulm University Medical Center, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
| |
Collapse
|
26
|
Hansson KT, Skillbäck T, Pernevik E, Kern S, Portelius E, Höglund K, Brinkmalm G, Holmén-Larsson J, Blennow K, Zetterberg H, Gobom J. Expanding the cerebrospinal fluid endopeptidome. Proteomics 2017; 17. [PMID: 28044435 DOI: 10.1002/pmic.201600384] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 11/11/2022]
Abstract
Biomarkers of neurodegenerative disorders are needed to assist in diagnosis, to monitor disease progression and therapeutic interventions, and to provide insight into disease mechanisms. One route to identify such biomarkers is by proteomic and peptidomic analysis of cerebrospinal fluid (CSF). In the current study, we performed an in-depth analysis of the human CSF endopeptidome to establish an inventory that may serve as a basis for future targeted biomarker studies. High-pH RP HPLC was employed for off-line sample prefractionation followed by low-pH nano-LC-MS analysis. Different software programs and scoring algorithms for peptide identification were employed and compared. A total of 18 031 endogenous peptides were identified at a FDR of 1%, increasing the number of known endogenous CSF peptides 10-fold compared to previous studies. The peptides were derived from 2 053 proteins of which more than 60 have been linked to neurodegeneration. Notably, among the findings were six peptides derived from microtubule-associated protein tau, three of which span the diagnostically interesting threonine-181 (Tau-F isoform). Also, 213 peptides from amyloid precursor protein were identified, 58 of which were partially or completely within the sequence of amyloid β 1-40/42, as well as 109 peptides from apolipoprotein E, spanning sequences that discriminate between the E2/E3/E4 isoforms of the protein.
Collapse
Affiliation(s)
- Karl T Hansson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
| | - Tobias Skillbäck
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Elin Pernevik
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
| | - Silke Kern
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Erik Portelius
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Kina Höglund
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
| | - Jessica Holmén-Larsson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| |
Collapse
|
27
|
Flagmeier P, De S, Wirthensohn DC, Lee SF, Vincke C, Muyldermans S, Knowles TPJ, Gandhi S, Dobson CM, Klenerman D. Ultrasensitive Measurement of Ca 2+
Influx into Lipid Vesicles Induced by Protein Aggregates. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick Flagmeier
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Suman De
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - David C. Wirthensohn
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Steven F. Lee
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology; Vrije Universiteit Brussel; Brussels Belgium
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology; Vrije Universiteit Brussel; Brussels Belgium
| | - Tuomas P. J. Knowles
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Sonia Gandhi
- Department of Molecular Neuroscience; Institute of Neurology; University College London; Queen Square London WC1N 3BG UK
| | - Christopher M. Dobson
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - David Klenerman
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|
28
|
Majerova P, Barath P, Michalicova A, Katina S, Novak M, Kovac A. Changes of Cerebrospinal Fluid Peptides due to Tauopathy. J Alzheimers Dis 2017; 58:507-520. [DOI: 10.3233/jad-170110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Peter Barath
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Alena Michalicova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Stanislav Katina
- AXON Neuroscience R&D, Bratislava, Slovak Republic
- Institute of Mathematics and Statistics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Novak
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
- Department of Pharmacology and Toxicology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovak Republic
| |
Collapse
|
29
|
Flagmeier P, De S, Wirthensohn DC, Lee SF, Vincke C, Muyldermans S, Knowles TPJ, Gandhi S, Dobson CM, Klenerman D. Ultrasensitive Measurement of Ca 2+ Influx into Lipid Vesicles Induced by Protein Aggregates. Angew Chem Int Ed Engl 2017; 56:7750-7754. [PMID: 28474754 PMCID: PMC5615231 DOI: 10.1002/anie.201700966] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/23/2017] [Indexed: 12/15/2022]
Abstract
To quantify and characterize the potentially toxic protein aggregates associated with neurodegenerative diseases, a high‐throughput assay based on measuring the extent of aggregate‐induced Ca2+ entry into individual lipid vesicles has been developed. This approach was implemented by tethering vesicles containing a Ca2+ sensitive fluorescent dye to a passivated surface and measuring changes in the fluorescence as a result of membrane disruption using total internal reflection microscopy. Picomolar concentrations of Aβ42 oligomers could be observed to induce Ca2+ influx, which could be inhibited by the addition of a naturally occurring chaperone and a nanobody designed to bind to the Aβ peptide. We show that the assay can be used to study aggregates from other proteins, such as α‐synuclein, and to probe the effects of complex biofluids, such as cerebrospinal fluid, and thus has wide applicability.
Collapse
Affiliation(s)
- Patrick Flagmeier
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Suman De
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David C Wirthensohn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sonia Gandhi
- Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| |
Collapse
|
30
|
Wang J, Cunningham R, Zetterberg H, Asthana S, Carlsson C, Okonkwo O, Li L. Label-free quantitative comparison of cerebrospinal fluid glycoproteins and endogenous peptides in subjects with Alzheimer's disease, mild cognitive impairment, and healthy individuals. Proteomics Clin Appl 2016; 10:1225-1241. [DOI: 10.1002/prca.201600009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/18/2016] [Accepted: 11/08/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Jingxin Wang
- Neuroscience Training Program; University of Wisconsin-Madison; Madison WI USA
| | | | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory; Sahlgrenska University Hospital; Mölndal Sweden
- Department of Psychiatry and Neurochemistry; Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg; Mölndal Sweden
- Department of Molecular Neuroscience; UCL Institute of Neurology; Queen Square London UK
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center; University of Wisconsin School of Medicine and Public Health; Madison WI USA
- Geriatric Research Education and Clinical Center; Wm. S. Middleton Veterans Hospital; Madison WI USA
- Wisconsin Alzheimer's Institute; University of Wisconsin School of Medicine and Public Health; Madison WI USA
| | - Cynthia Carlsson
- Wisconsin Alzheimer's Disease Research Center; University of Wisconsin School of Medicine and Public Health; Madison WI USA
- Geriatric Research Education and Clinical Center; Wm. S. Middleton Veterans Hospital; Madison WI USA
- Wisconsin Alzheimer's Institute; University of Wisconsin School of Medicine and Public Health; Madison WI USA
| | - Ozioma Okonkwo
- Neuroscience Training Program; University of Wisconsin-Madison; Madison WI USA
- Wisconsin Alzheimer's Disease Research Center; University of Wisconsin School of Medicine and Public Health; Madison WI USA
- Geriatric Research Education and Clinical Center; Wm. S. Middleton Veterans Hospital; Madison WI USA
- Wisconsin Alzheimer's Institute; University of Wisconsin School of Medicine and Public Health; Madison WI USA
| | - Lingjun Li
- Neuroscience Training Program; University of Wisconsin-Madison; Madison WI USA
- School of Pharmacy; University of Wisconsin-Madison; Madison WI USA
- Department of Chemistry; University of Wisconsin-Madison; Madison WI USA
- School of Life Sciences; Tianjin University; Tianjin China
| |
Collapse
|
31
|
Morell-Garcia D, Bauça JM, Sastre MP, Yañez A, Llompart I. Sample-dependent diagnostic accuracy of prostaglandin D synthase in cerebrospinal fluid leak. Clin Biochem 2016; 50:27-31. [PMID: 27614217 DOI: 10.1016/j.clinbiochem.2016.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/01/2016] [Accepted: 09/05/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Prostaglandin D2 synthase, commonly known as β-trace protein (βTP), is an excellent biomarker for the assessment of cerebrospinal fluid (CSF) leaks. Despite being widely used, the limits for the diagnostic values of βTP are not well established to date, and currently suggested cut-off values in literature range from 0.25 to 6.0mg/L. Sample-specific and more accurate thresholds are a current need. METHODS A retrospective observational study, performed in a tertiary-care hospital, between January 2006 and January 2014. A total of 74 patients were included, with a definitive diagnosis after initial leak suspicion and at least one determination of βTP using a nephelometry-based assay. A total of 46 CSF samples were included in the control group. Samples were obtained from nasal secretions, ear secretions or spinal surgical injury, directly using sterile Eppendorf tubes. The analysis of 3 different cut-off values was performed and the receiver operating curve (ROC) analyses were calculated. RESULTS Initial diagnostic suspicion was confirmed in 51% of cases, most of which were of postoperative origin (51%) and traumatic (26%). The βTP median concentration in different samples was significantly higher in the presence of cerebrospinal fluid fistula, regardless of sample type (22.0mg/L vs. 0.24mg/L, 95% confidence interval: 19.0-30.8 vs. 0.08-0.40; p<0.001). Data from contingency tables show 100% sensitivity and specificity, depending on sample type and the cut-off value used: for rhinorrhea and otorrhea samples, the most appropriate it was 0.7mg/L, while values >2.0mg/L could be used for spine postoperative fluid leakage samples. CONCLUSIONS The cut off value for βTP in the diagnosis and follow-up of cerebrospinal fluid leaks should be modified depending on the type of secretion (sample type), for a better diagnostic accuracy.
Collapse
Affiliation(s)
- Daniel Morell-Garcia
- Department of Laboratory Medicine, Hospital Universitari Son Espases, Palma de Mallorca, Balearic Islands, Spain; Institut d'Investigació Sanitària de Palma (IdISPa), Palma de Mallorca, Balearic Islands, Spain.
| | - Josep Miquel Bauça
- Department of Laboratory Medicine, Hospital Universitari Son Espases, Palma de Mallorca, Balearic Islands, Spain; Institut d'Investigació Sanitària de Palma (IdISPa), Palma de Mallorca, Balearic Islands, Spain
| | - M Pilar Sastre
- Department of Laboratory Medicine, Hospital Universitari Son Espases, Palma de Mallorca, Balearic Islands, Spain
| | - Aina Yañez
- Institut d'Investigació Sanitària de Palma (IdISPa), Palma de Mallorca, Balearic Islands, Spain
| | - Isabel Llompart
- Department of Laboratory Medicine, Hospital Universitari Son Espases, Palma de Mallorca, Balearic Islands, Spain
| |
Collapse
|
32
|
Meo AD, Pasic MD, Yousef GM. Proteomics and peptidomics: moving toward precision medicine in urological malignancies. Oncotarget 2016; 7:52460-52474. [PMID: 27119500 PMCID: PMC5239567 DOI: 10.18632/oncotarget.8931] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/16/2016] [Indexed: 12/31/2022] Open
Abstract
Urological malignancies are a major cause of morbidity and mortality worldwide. Advances in early detection, diagnosis, prognosis and prediction of treatment response can significantly improve patient care. Proteomic and peptidomic profiling studies are at the center of kidney, prostate and bladder cancer biomarker discovery and have shown great promise for improved clinical assessment. Mass spectrometry (MS) is the most widely employed method for proteomic and peptidomic analyses. A number of MS platforms have been developed to facilitate accurate identification of clinically relevant markers in various complex biological samples including tissue, urine and blood. Furthermore, protein profiling studies have been instrumental in the successful introduction of several diagnostic multimarker tests into the clinic. In this review, we will provide a brief overview of high-throughput technologies for protein and peptide based biomarker discovery. We will also examine the current state of kidney, prostate and bladder cancer biomarker research as well as review the journey toward successful clinical implementation.
Collapse
Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Maria D. Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, Ontario, Canada
| | - George M. Yousef
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
33
|
Guillot A, Boulay M, Chambellon É, Gitton C, Monnet V, Juillard V. Mass Spectrometry Analysis of the Extracellular Peptidome of Lactococcus lactis: Lines of Evidence for the Coexistence of Extracellular Protein Hydrolysis and Intracellular Peptide Excretion. J Proteome Res 2016; 15:3214-24. [DOI: 10.1021/acs.jproteome.6b00424] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alain Guillot
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Mylène Boulay
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Émilie Chambellon
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Christophe Gitton
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Véronique Monnet
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| | - Vincent Juillard
- UMR Micalis,
INRA, AgroParisTech, Université Paris Saclay, F-78350 Jouy-en-Josas, France
| |
Collapse
|
34
|
Ziganshin RH, Ivanova OM, Lomakin YA, Belogurov AA, Kovalchuk SI, Azarkin IV, Arapidi GP, Anikanov NA, Shender VO, Piradov MA, Suponeva NA, Vorobyeva AA, Gabibov AG, Ivanov VT, Govorun VM. The Pathogenesis of the Demyelinating Form of Guillain-Barre Syndrome (GBS): Proteo-peptidomic and Immunological Profiling of Physiological Fluids. Mol Cell Proteomics 2016; 15:2366-78. [PMID: 27143409 PMCID: PMC4937510 DOI: 10.1074/mcp.m115.056036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 04/27/2016] [Indexed: 01/06/2023] Open
Abstract
Acute inflammatory demyelinating polyneuropathy (AIDP) - the main form of Guillain-Barre syndrome-is a rare and severe disorder of the peripheral nervous system with an unknown etiology. One of the hallmarks of the AIDP pathogenesis is a significantly elevated cerebrospinal fluid (CSF) protein level. In this paper CSF peptidome and proteome in AIDP were analyzed and compared with multiple sclerosis and control patients. A total protein concentration increase was shown to be because of even changes in all proteins rather than some specific response, supporting the hypothesis of protein leakage from blood through the blood-nerve barrier. The elevated CSF protein level in AIDP was complemented by activization of protein degradation and much higher peptidome diversity. Because of the studies of the acute motor axonal form, Guillain-Barre syndrome as a whole is thought to be associated with autoimmune response against neurospecific molecules. Thus, in AIDP, autoantibodies against cell adhesion proteins localized at Ranvier's nodes were suggested as possible targets in AIDP. Indeed, AIDP CSF peptidome analysis revealed cell adhesion proteins degradation, however no reliable dependence on the corresponding autoantibodies levels was found. Proteome analysis revealed overrepresentation of Gene Ontology groups related to responses to bacteria and virus infections, which were earlier suggested as possible AIDP triggers. Immunoglobulin blood serum analysis against most common neuronal viruses did not reveal any specific pathogen; however, AIDP patients were more immunopositive in average and often had polyinfections. Cytokine analysis of both AIDP CSF and blood did not show a systemic adaptive immune response or general inflammation, whereas innate immunity cytokines were up-regulated. To supplement the widely-accepted though still unproven autoimmunity-based AIDP mechanism we propose a hypothesis of the primary peripheral nervous system damaging initiated as an innate immunity-associated local inflammation following neurotropic viruses egress, whereas the autoantibody production might be an optional complementary secondary process.
Collapse
Affiliation(s)
- Rustam H Ziganshin
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation;
| | - Olga M Ivanova
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Yakov A Lomakin
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Alexey A Belogurov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Sergey I Kovalchuk
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Igor V Azarkin
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Georgij P Arapidi
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation; §Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudny 141700, Russian Federation
| | - Nikolay A Anikanov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Victoria O Shender
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Mikhail A Piradov
- ¶Research Center of Neurology, Volokolamskoye highway, 80, Moscow 125367, Russian Federation
| | - Natalia A Suponeva
- ¶Research Center of Neurology, Volokolamskoye highway, 80, Moscow 125367, Russian Federation
| | - Anna A Vorobyeva
- ¶Research Center of Neurology, Volokolamskoye highway, 80, Moscow 125367, Russian Federation
| | - Alexander G Gabibov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Vadim T Ivanov
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation
| | - Vadim M Govorun
- From the ‡Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya str., 16/10, Moscow 117997, Russian Federation; §Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudny 141700, Russian Federation; ‖Research Institute of Physical Chemical Medicine, Malaya Pirogovskaya str., 1a, Moscow 119435, Russian Federation
| |
Collapse
|
35
|
Hölttä M, Dean RA, Siemers E, Mawuenyega KG, Sigurdson W, May PC, Holtzman DM, Portelius E, Zetterberg H, Bateman RJ, Blennow K, Gobom J. A single dose of the γ-secretase inhibitor semagacestat alters the cerebrospinal fluid peptidome in humans. Alzheimers Res Ther 2016; 8:11. [PMID: 26948580 PMCID: PMC4780148 DOI: 10.1186/s13195-016-0178-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/29/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND In Alzheimer's disease, beta-amyloid peptides in the brain aggregate into toxic oligomers and plaques, a process which is associated with neuronal degeneration, memory loss, and cognitive decline. One therapeutic strategy is to decrease the production of potentially toxic beta-amyloid species by the use of inhibitors or modulators of the enzymes that produce beta-amyloid from amyloid precursor protein (APP). The failures of several such drug candidates by lack of effect or undesired side-effects underscore the importance to monitor the drug effects in the brain on a molecular level. Here we evaluate if peptidomic analysis in cerebrospinal fluid (CSF) can be used for this purpose. METHODS Fifteen human healthy volunteers, divided into three groups, received a single dose of placebo or either 140 mg or 280 mg of the γ-secretase inhibitor semagacestat (LY450139). Endogenous peptides in CSF, sampled prior to administration of the drug and at six subsequent time points, were analyzed by liquid chromatography coupled to mass spectrometry, using isobaric labeling based on the tandem mass tag approach for relative quantification. RESULTS Out of 302 reproducibly detected peptides, 11 were affected by the treatment. Among these, one was derived from APP and one from amyloid precursor-like protein 1. Nine peptides were derived from proteins that may not be γ-secretase substrates per se, but that are regulated in a γ-secretase-dependent manner. CONCLUSIONS These results indicate that a CSF peptidomic approach may be a valuable tool both to verify target engagement and to identify other pharmacodynamic effects of the drug. Data are available via ProteomeXchange with identifier PXD003075. TRIAL REGISTRATION NCT00765115 , registered 30/09/2008.
Collapse
Affiliation(s)
- Mikko Hölttä
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
| | - Robert A Dean
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Headquarters, Indianapolis, IN, 46285, USA.
| | - Eric Siemers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Headquarters, Indianapolis, IN, 46285, USA.
| | - Kwasi G Mawuenyega
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Wendy Sigurdson
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Alzheimer's Disease Research Center, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Patrick C May
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Headquarters, Indianapolis, IN, 46285, USA.
| | - David M Holtzman
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Alzheimer's Disease Research Center, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Erik Portelius
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
- UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
| | - Randall J Bateman
- Department of Neurology, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Alzheimer's Disease Research Center, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, 660 South Euclid, Campus Box 8111, St. Louis, MO, 63110, USA.
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, SU/Mölndal Hospital, 431 80, Mölndal, Sweden.
| |
Collapse
|
36
|
Sjödin S, Andersson KKA, Mercken M, Zetterberg H, Borghys H, Blennow K, Portelius E. APLP1 as a cerebrospinal fluid biomarker for γ-secretase modulator treatment. ALZHEIMERS RESEARCH & THERAPY 2015; 7:77. [PMID: 26689589 PMCID: PMC4687145 DOI: 10.1186/s13195-015-0160-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/28/2015] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Alzheimer's disease brains are characterized by extracellular plaques containing the aggregated amyloid β42 (Aβ42) peptide and intraneuronal tangles containing hyperphosphorylated tau. Aβ42 is produced by sequential processing of the amyloid precursor protein (APP) by β-secretase followed by γ-secretase. Substantial efforts have been put into developing pharmaceuticals preventing the production or increasing the clearance of Aβ42. However, treatments inhibiting γ-secretase have proven disappointing due to off-target effects. To circumvent these effects, γ-secretase modulators (GSMs) have been developed, which rather than inhibiting γ-secretase shift its preference into producing less aggregation-prone shorter Aβ peptides. Belonging to the same family of proteins as APP, amyloid-like protein 1 (APLP1) is also a substrate for γ-secretase. Herein we investigated whether the GSM E2012 affects APLP1 processing in the central nervous system by measuring APLP1 peptide levels in cerebrospinal fluid (CSF) before and after E2012 treatment in dogs. METHODS An in-house monoclonal APLP1 antibody, AP1, was produced and utilized for immunopurification of APLP1 from human and dog CSF in a hybrid immuno-affinity mass spectrometric method. Seven dogs received a single dose of 20 or 80 mg/kg of E2012 in a randomized cross-over design and CSF was collected prior to and 4, 8 and 24 hours after dosing. RESULTS We have identified 14 CSF APLP1 peptides in humans and 12 CSF APLP1 peptides in dogs. Of these, seven were reproducibly detectable in dogs who received E2012. We found a dose-dependent relative increase of the CSF peptides APLP1β17, 1β18 and 1β28 accompanied with a decrease of 1β25 and 1β27 in response to E2012 treatment. All peptides reverted to baseline over the time of sample collection. CONCLUSION We show an in vivo effect of the GSM E2012 on the processing of APLP1 which is measurable in CSF. These data suggest that APLP1 peptides may be used as biomarkers to monitor drug effects of GSMs on γ-secretase processing in clinical trials. However, this requires further investigation in larger cohorts, including studies in man.
Collapse
Affiliation(s)
- Simon Sjödin
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Mölndal, S-431 80, Sweden.
| | - Kerstin K A Andersson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Mölndal, S-431 80, Sweden.
| | - Marc Mercken
- Janssen Research and Development, Beerse, Belgium.
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Mölndal, S-431 80, Sweden. .,UCL Institute of Neurology, University College London, London, UK.
| | | | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Mölndal, S-431 80, Sweden.
| | - Erik Portelius
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Mölndal, S-431 80, Sweden.
| |
Collapse
|
37
|
Gobom J. Advancing cerebrospinal fluid biomarker discovery by mass spectrometry. Neurodegener Dis Manag 2015; 5:371-3. [PMID: 26477620 DOI: 10.2217/nmt.15.35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Johan Gobom
- Institute of Neuroscience & Physiology, Department of Psychiatry & Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital/Molndal, V-huset, Molndal, SE-431 80, Sweden
| |
Collapse
|
38
|
Häggmark A, Schwenk JM, Nilsson P. Neuroproteomic profiling of human body fluids. Proteomics Clin Appl 2015; 10:485-502. [PMID: 26286680 DOI: 10.1002/prca.201500065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/17/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
Analysis of protein expression and abundance provides a possibility to extend the current knowledge on disease-associated processes and pathways. The human brain is a complex organ and dysfunction or damage can give rise to a variety of neurological diseases. Although many proteins potentially reflecting disease progress are originating from brain, the scarce availability of human tissue material has lead to utilization of body fluids such as cerebrospinal fluid and blood in disease-related research. Within the most common neurological disorders, much effort has been spent on studying the role of a few hallmark proteins in disease pathogenesis but despite extensive investigation, the signatures they provide seem insufficient to fully understand and predict disease progress. In order to expand the view the field of neuroproteomics has lately emerged alongside developing technologies, such as affinity proteomics and mass spectrometry, for multiplexed and high-throughput protein profiling. Here, we provide an overview of how such technologies have been applied to study neurological disease and we also discuss some important considerations concerning discovery of disease-associated profiles.
Collapse
Affiliation(s)
- Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
39
|
Mesbah K, Verpillot R, Chiari M, Pallandre A, Taverna M. Neutral polymers as coatings for high resolution electrophoretic separation of Aβ peptides on glass microchips. Analyst 2015; 139:6547-55. [PMID: 25356444 DOI: 10.1039/c4an01296h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study reports a comparison of the performances of two neutral polymers, poly ethylene-oxide (PEO) and poly(dimethylacrylamide-co-allyl glycidyl ether) (EpDMA), in glass microchips to achieve zone electrophoresis separation of several truncated forms of beta amyloid (Aβ) peptides, sharing very similar structures. The peptides were derivatized by FluoProbes 488 NHS to allow their fluorescence detection. Two protocols based either on PEO or EpDMA led to good pH stabilities in addition to a significant reduction of the electroosmotic flow. These two polymer coatings allowed repeatable analyses and high resolution for the simultaneous analysis of three Aβ peptides, Aβ 1-38, Aβ 1-40 and Aβ 1-42, considered as potential biomarkers of Alzheimer's disease. A recovery study showed that EpDMA was superior in reducing the adsorption of the Aβ peptides on the coated inner wall. Finally, the separation method relying on the EpDMA coated microchips was validated as linear using a calibration curve and the LOD was estimated to be close to 200 nM. Despite very short migration distances, different N-terminal or C-terminal truncated Aβ peptides, corresponding to promising biomarker combinations for the future diagnostic, were fully resolved. The method was successfully applied to detect these peptides in spiked cerebrospinal fluid and has provided a first achievement towards the development of a microsystem that would integrate preconcentration and separation steps.
Collapse
Affiliation(s)
- Kiarach Mesbah
- Protéines et Nanotechnologies en Sciences Séparatives CNRS UMR 8612, Institut Galien de Paris-Sud, Univ Paris-Sud, Faculté de pharmacie, 92296 Chatenay-Malabry, France.
| | | | | | | | | |
Collapse
|
40
|
Romanova EV, Sweedler JV. Peptidomics for the discovery and characterization of neuropeptides and hormones. Trends Pharmacol Sci 2015; 36:579-86. [PMID: 26143240 DOI: 10.1016/j.tips.2015.05.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/31/2022]
Abstract
The discovery of neuropeptides as signaling molecules with paracrine or hormonal regulatory functions has led to trailblazing advances in physiology and fostered the characterization of numerous neuropeptide-binding G protein-coupled receptors (GPCRs) as potential drug targets. The impact on human health has been tremendous: approximately 30% of commercial drugs act via the GPCR pathway. However, about 25% of the GPCRs encoded by the mammalian genome still lack their pharmacological identity. Searching for the orphan GPCR endogenous ligands that are likely to be neuropeptides has proved to be a formidable task. Here we describe the mass spectrometry (MS)-based technologies and experimental strategies that have been successful in achieving high-throughput characterization of endogenous peptides in nervous and endocrine systems.
Collapse
Affiliation(s)
- Elena V Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|
41
|
Dallas DC, Guerrero A, Parker EA, Robinson RC, Gan J, German JB, Barile D, Lebrilla CB. Current peptidomics: applications, purification, identification, quantification, and functional analysis. Proteomics 2015; 15:1026-38. [PMID: 25429922 PMCID: PMC4371869 DOI: 10.1002/pmic.201400310] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/24/2014] [Indexed: 12/28/2022]
Abstract
Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.
Collapse
Affiliation(s)
- David C. Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Evan A. Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Randall C. Robinson
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Junai Gan
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| |
Collapse
|
42
|
Brinkmalm A, Portelius E, Öhrfelt A, Brinkmalm G, Andreasson U, Gobom J, Blennow K, Zetterberg H. Explorative and targeted neuroproteomics in Alzheimer's disease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:769-78. [PMID: 25619854 DOI: 10.1016/j.bbapap.2015.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/23/2014] [Accepted: 01/16/2015] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is a progressive brain amyloidosis that injures brain regions involved in memory consolidation and other higher brain functions. Neuropathologically, the disease is characterized by accumulation of a 42 amino acid peptide called amyloid β (Aβ42) in extracellular senile plaques, intraneuronal inclusions of hyperphosphorylated tau protein in neurofibrillary tangles, and neuronal and axonal degeneration and loss. Biomarker assays capturing these pathologies have been developed for use on cerebrospinal fluid samples but there are additional molecular pathways that most likely contribute to the neurodegeneration and full clinical expression of AD. One way of learning more about AD pathogenesis is to identify novel biomarkers for these pathways and examine them in longitudinal studies of patients in different stages of the disease. Here, we discuss targeted proteomic approaches to study AD and AD-related pathologies in closer detail and explorative approaches to discover novel pathways that may contribute to the disease. This article is part of a Special Issue entitled: Neuroproteomics: Applications in neuroscience and neurology.
Collapse
Affiliation(s)
- Ann Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden.
| | - Erik Portelius
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Annika Öhrfelt
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Ulf Andreasson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Johan Gobom
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden; UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom.
| |
Collapse
|
43
|
Hanrieder J, Malmberg P, Ewing AG. Spatial neuroproteomics using imaging mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:718-31. [PMID: 25582083 DOI: 10.1016/j.bbapap.2014.12.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/11/2014] [Accepted: 12/19/2014] [Indexed: 12/12/2022]
Abstract
The nervous system constitutes arguably the most complicated and least understood cellular network in the human body. This consequently manifests itself in the fact that the molecular bases of neurodegenerative diseases remain unknown. The limited understanding of neurobiological mechanisms relates directly to the lack of appropriate bioanalytical technologies that allow highly resolved, sensitive, specific and comprehensive molecular imaging in complex biological matrices. Imaging mass spectrometry (IMS) is an emerging technique for molecular imaging. The technique is characterized by its high chemical specificity allowing comprehensive, spatial protein and peptide profiling in situ. Imaging MS represents therefore a powerful approach for investigation of spatio-temporal protein and peptide regulations in CNS derived tissue and cells. This review aims to provide a concise overview of major developments and applications concerning imaging mass spectrometry based protein and peptide profiling in neurobiological and biomedical research. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
Collapse
Affiliation(s)
- Jörg Hanrieder
- National Center for Imaging Mass Spectrometry, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden; Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Institute of Neuroscience and Physiology, Department Psychiatry and Neurochemistry, University of Gothenburg, Sahlgrenska University Hospital Mölndal, Mölndal, Sweden
| | - Per Malmberg
- National Center for Imaging Mass Spectrometry, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden; Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew G Ewing
- National Center for Imaging Mass Spectrometry, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden; Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
44
|
Hölttä M, Minthon L, Hansson O, Holmén-Larsson J, Pike I, Ward M, Kuhn K, Rüetschi U, Zetterberg H, Blennow K, Gobom J. An Integrated Workflow for Multiplex CSF Proteomics and Peptidomics—Identification of Candidate Cerebrospinal Fluid Biomarkers of Alzheimer’s Disease. J Proteome Res 2014; 14:654-63. [DOI: 10.1021/pr501076j] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mikko Hölttä
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Lennart Minthon
- Clinical
Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, 221 00 Lund, Sweden
| | - Oskar Hansson
- Clinical
Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, 221 00 Lund, Sweden
| | - Jessica Holmén-Larsson
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Ian Pike
- Proteome
Sciences
PLC, KT11 3EP London, United Kingdom
| | - Malcolm Ward
- Proteome
Sciences
PLC, KT11 3EP London, United Kingdom
| | - Karsten Kuhn
- Proteome Science R&D GmbH&CoKG, 60438 Frankfurt am Main, Germany
| | - Ulla Rüetschi
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
- UCL Institute of Neurology, Queen Square, WC1N 3BG London, United Kingdom
| | - Kaj Blennow
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Johan Gobom
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| |
Collapse
|
45
|
Podvin S, Dang X, Meads M, Kurabi A, Costantini T, Eliceiri BP, Baird A, Coimbra R. Esophageal cancer-related gene-4 (ECRG4) interactions with the innate immunity receptor complex. Inflamm Res 2014; 64:107-18. [PMID: 25511108 DOI: 10.1007/s00011-014-0789-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/04/2014] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE AND DESIGN The human c2orf40 gene encodes a tumor suppressor gene called esophageal cancer-related gene-4 (ECRG4) with pro- and anti-inflammatory activities that depend on cell surface processing. Here, we investigated its physical and functional association with the innate immunity receptor complex. METHODS Interactions between ECRG4 and the innate immunity receptor complex were assessed by flow cytometry, immunohistochemistry, confocal microscopy, and co-immunoprecipitation. Phage display was used for ligand targeting to cells that overexpress the TLR4-MD2-CD14. RESULTS Immunoprecipitation and immunohistochemical studies demonstrate a physical interaction between ECRG4 and TLR4-MD2-CD14 on human granulocytes. Flow cytometry shows ECRG4 on the cell surface of a subset of CD14(+) and CD16(+) leukocytes. In a cohort of trauma patients, the C-terminal 16 amino acid domain of ECRG4 (ECRG4(133-148)) appears to be processed and shed, presumably at a thrombin-like consensus sequence. Phage targeting this putative ligand shows that this peptide sequence internalizes into cells through the TLR4/CD14/MD2 complex, but modulates inflammation through non-canonical, NFκB signal transduction. CONCLUSIONS ECRG4 is present on the surface of human monocytes and granulocytes. Its interaction with the human innate immunity receptor complex supports a role for cell surface activation of ECRG4 during inflammation and implicates this receptor in its mechanism of action.
Collapse
Affiliation(s)
- Sonia Podvin
- Division of Trauma, Surgical Critical Care, Burns, and Acute Care Surgery, Department of Surgery, University of California, San Diego, San Diego, CA, USA
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Bauça JM, Martínez-Morillo E, Diamandis EP. Peptidomics of Urine and Other Biofluids for Cancer Diagnostics. Clin Chem 2014; 60:1052-61. [DOI: 10.1373/clinchem.2013.211714] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Cancer is a leading cause of death worldwide. The low diagnostic sensitivity and specificity of most current cancer biomarkers make early cancer diagnosis a challenging task. The comprehensive study of peptides and small proteins in a living system, known as “peptidomics,” represents an alternative technological approach to the discovery of potential biomarkers for the assessment of a wide variety of pathologies. This review examines the current status of peptidomics for several body fluids, with a focus on urine, for cancer diagnostics applications.
CONTENT
Several studies have used high-throughput technologies to characterize the peptide content of different body fluids. Because of its noninvasive collection and high stability, urine is a valuable source of candidate cancer biomarkers. A wide variety of preanalytical issues concerning patient selection and sample handling need to be considered, because not doing so can affect the quality of the results by introducing bias and artifacts. Optimization of both the analytical strategies and the processing of bioinformatics data is also essential to minimize the false-discovery rate.
SUMMARY
Peptidomics-based studies of urine and other body fluids have yielded a number of biomolecules and peptide panels with potential for diagnosing different types of cancer, especially of the ovary, prostate, and bladder. Large-scale studies are needed to validate these molecules as cancer biomarkers.
Collapse
Affiliation(s)
- Josep Miquel Bauça
- Servei d'Anàlisis Clíniques, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Eduardo Martínez-Morillo
- Samuel Lunenfeld Research Institute, Joseph and Wolf Lebovic Health Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| |
Collapse
|
47
|
Smith CR, Batruch I, Bauça JM, Kosanam H, Ridley J, Bernardini MQ, Leung F, Diamandis EP, Kulasingam V. Deciphering the peptidome of urine from ovarian cancer patients and healthy controls. Clin Proteomics 2014; 11:23. [PMID: 24982608 PMCID: PMC4065538 DOI: 10.1186/1559-0275-11-23] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 04/17/2014] [Indexed: 01/05/2023] Open
Abstract
Background Ovarian cancer (OvCa) is the most lethal gynecological malignancy. The emergence of high-throughput technologies, such as mass spectrometry, has allowed for a paradigm shift in the way we search for novel biomarkers. Urine-based peptidomic profiling is a novel approach that may result in the discovery of noninvasive biomarkers for diagnosing patients with OvCa. In this study, the peptidome of urine from 6 ovarian cancer patients and 6 healthy controls was deciphered. Results Urine samples underwent ultrafiltration and the filtrate was subjected to solid phase extraction, followed by fractionation using strong cation exchange chromatography. These fractions were analyzed using an Orbitrap mass spectrometer. Over 4600 unique endogenous urine peptides arising from 713 proteins were catalogued, representing the largest urine peptidome reported to date. Each specimen was processed in triplicate and reproducibility at the protein (69-76%) and peptide (58-63%) levels were noted. More importantly, over 3100 unique peptides were detected solely in OvCa specimens. One such promising biomarker was leucine-rich alpha-2-glycoprotein (LRG1), where multiple peptides were found in all urines from OvCa patients, but only one peptide was found in one healthy control urine sample. Conclusions Mining the urine peptidome may yield highly promising novel OvCa biomarkers.
Collapse
Affiliation(s)
- Christopher R Smith
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ihor Batruch
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Josep Miquel Bauça
- Servei d'Anàlisis Clíniques, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Hari Kosanam
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Julia Ridley
- Department of Psychosocial Oncology and Palliative Care, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada ; Division of Palliative Care, Department of Community and Palliative Medicine, University of Toronto, Toronto, ON, Canada
| | - Marcus Q Bernardini
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
| | - Felix Leung
- Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
| | - Eleftherios P Diamandis
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Samuel Lunenfeld Research Institute, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
| | - Vathany Kulasingam
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, 200 Elizabeth Street, Room 3 EB 362A, Toronto, ON M5G 2C4, Canada
| |
Collapse
|
48
|
Calias P, Banks WA, Begley D, Scarpa M, Dickson P. Intrathecal delivery of protein therapeutics to the brain: a critical reassessment. Pharmacol Ther 2014; 144:114-22. [PMID: 24854599 DOI: 10.1016/j.pharmthera.2014.05.009] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/12/2014] [Indexed: 12/25/2022]
Abstract
Disorders of the central nervous system (CNS), including stroke, neurodegenerative diseases, and brain tumors, are the world's leading causes of disability. Delivery of drugs to the CNS is complicated by the blood-brain barriers that protect the brain from the unregulated leakage and entry of substances, including proteins, from the blood. Yet proteins represent one of the most promising classes of therapeutics for the treatment of CNS diseases. Many strategies for overcoming these obstacles are in development, but the relatively straightforward approach of bypassing these barriers through direct intrathecal administration has been largely overlooked. Originally discounted because of its lack of usefulness for delivering small, lipid-soluble drugs to the brain, the intrathecal route has emerged as a useful, in some cases perhaps the ideal, route of administration for certain therapeutic protein and targeted disease combinations. Here, we review blood-brain barrier functions and cerebrospinal fluid dynamics and their relevance to drug delivery via the intrathecal route, discuss animal and human studies that have investigated intrathecal delivery of protein therapeutics, and outline several characteristics of protein therapeutics that can allow them to be successfully delivered intrathecally.
Collapse
Affiliation(s)
| | - William A Banks
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care Center, Seattle, WA, USA; Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - David Begley
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Maurizio Scarpa
- Department of Paediatrics, University of Padova, Padova, Italy
| | - Patricia Dickson
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, USA
| |
Collapse
|
49
|
Abstract
Neurodevelopmental disorders affect a substantial minority of the general population. Their origins are still largely unknown, but a complex interplay of genetic and environmental factors causing disturbances of the central nervous system's maturation and a variety of higher cognitive skills is presumed. Only limited research of rather small sample size and narrow scope has been conducted in neurodevelopmental disorders using a twin-differences design. The Roots of Autism and ADHD Twin Study in Sweden (RATSS) is an ongoing project targeting monozygotic twins discordant for categorical or dimensional autistic and inattentive/hyperactive-impulsive phenotypes as well as other neurodevelopmental disorders, and typically developing twin controls. Included pairs are 9 years of age or older, and comprehensively assessed for psychopathology, medical history, neuropsychology, and dysmorphology, as well as structural, functional, and molecular brain imaging. Specimens are collected for induced pluripotent (iPS) and neuroepithelial stem cells, genetic, gut bacteria, protein-/monoamine, and electron microscopy analyses. RATSS's objective is to generate a launch pad for novel surveys to understand the complexity of genotype-environment-phenotype interactions in autism spectrum disorder and attention-deficit hyperactivity disorder (ADHD). By October 2013, RATSS had collected data from 55 twin pairs, among them 10 monozygotic pairs discordant for autism spectrum disorder, seven for ADHD, and four for other neurodevelopmental disorders. This article describes the design, recruitment, data collection, measures, collected pairs' characteristics, as well as ongoing and planned analyses in RATSS. Potential gains of the study comprise the identification of environmentally mediated biomarkers, the emergence of candidates for drug development, translational modeling, and new leads for prevention of incapacitating outcomes.
Collapse
|
50
|
Yau Y, Leong RW, Zeng M, Wasinger VC. Proteomics and metabolomics in inflammatory bowel disease. J Gastroenterol Hepatol 2013; 28:1076-86. [PMID: 23489082 DOI: 10.1111/jgh.12193] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2013] [Indexed: 12/16/2022]
Abstract
Genome-wide studies in inflammatory bowel disease (IBD) have allowed us to understand Crohn's disease and ulcerative colitis as forms of related autoinflammatory disorders that arise from a multitude of pathogenic origins. Proteomics and metabolomics are the offspring of genomics that possess unprecedented possibilities to characterize unknown pathogenic pathways. It has been about a decade since proteomics was first applied to IBD, and 5 years for metabolomics. These techniques have yielded novel and potentially important findings, but turning these results into beneficial patient outcomes remains challenging. This review recounts the history and context of clinical IBD developments before and after proteomics and metabolomics IBD in this field, discusses the challenges in consolidating high complexity data with physiological understanding, and provides an outlook on the emerging principles that will help interface the bioanalytical laboratory with IBD prognosis.
Collapse
Affiliation(s)
- Yunki Yau
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, Australia
| | | | | | | |
Collapse
|