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Yang JC, Chen SP, Wang YF, Chang CH, Chang KH, Fuh JL, Chow LH, Han CL, Chen YJ, Wang SJ. Cerebrospinal Fluid Proteome Map Reveals Molecular Signatures of Reversible Cerebral Vasoconstriction Syndrome. Mol Cell Proteomics 2024; 23:100794. [PMID: 38839039 PMCID: PMC11263949 DOI: 10.1016/j.mcpro.2024.100794] [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: 10/06/2023] [Revised: 04/08/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Reversible cerebral vasoconstriction syndrome (RCVS) is a complex neurovascular disorder characterized by repetitive thunderclap headaches and reversible cerebral vasoconstriction. The pathophysiological mechanism of this mysterious syndrome remains underexplored and there is no clinically available molecular biomarker. To provide insight into the pathogenesis of RCVS, this study reported the first landscape of dysregulated proteome of cerebrospinal fluid (CSF) in patients with RCVS (n = 21) compared to the age- and sex-matched controls (n = 20) using data-independent acquisition mass spectrometry. Protein-protein interaction and functional enrichment analysis were employed to construct functional protein networks using the RCVS proteome. An RCVS-CSF proteome library resource of 1054 proteins was established, which illuminated large groups of upregulated proteins enriched in the brain and blood-brain barrier (BBB). Personalized RCVS-CSF proteomic profiles from 17 RCVS patients and 20 controls reveal proteomic changes involving the complement system, adhesion molecules, and extracellular matrix, which may contribute to the disruption of BBB and dysregulation of neurovascular units. Moreover, an additional validation cohort validated a panel of biomarker candidates and a two-protein signature predicted by machine learning model to discriminate RCVS patients from controls with an area under the curve of 0.997. This study reveals the first RCVS proteome and a potential pathogenetic mechanism of BBB and neurovascular unit dysfunction. It also nominates potential biomarker candidates that are mechanistically plausible for RCVS, which may offer potential diagnostic and therapeutic opportunities beyond the clinical manifestations.
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Affiliation(s)
- Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Shih-Pin Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Clinical Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Yen-Feng Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chan-Hua Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Central University, Taoyuan, Taiwan
| | - Kun-Hao Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Department of Chemistry, Institute of Chemistry, Academia Sinica, Naitonal Tsing Hua University, Hsinchu, Taiwan
| | - Jong-Ling Fuh
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Lok-Hi Chow
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Anesthesiology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| | - Shuu-Jiun Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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2
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Zeiler FA, Iturria-Medina Y, Thelin EP, Gomez A, Shankar JJ, Ko JH, Figley CR, Wright GEB, Anderson CM. Integrative Neuroinformatics for Precision Prognostication and Personalized Therapeutics in Moderate and Severe Traumatic Brain Injury. Front Neurol 2021; 12:729184. [PMID: 34557154 PMCID: PMC8452858 DOI: 10.3389/fneur.2021.729184] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/09/2021] [Indexed: 01/13/2023] Open
Abstract
Despite changes in guideline-based management of moderate/severe traumatic brain injury (TBI) over the preceding decades, little impact on mortality and morbidity have been seen. This argues against the “one-treatment fits all” approach to such management strategies. With this, some preliminary advances in the area of personalized medicine in TBI care have displayed promising results. However, to continue transitioning toward individually-tailored care, we require integration of complex “-omics” data sets. The past few decades have seen dramatic increases in the volume of complex multi-modal data in moderate and severe TBI care. Such data includes serial high-fidelity multi-modal characterization of the cerebral physiome, serum/cerebrospinal fluid proteomics, admission genetic profiles, and serial advanced neuroimaging modalities. Integrating these complex and serially obtained data sets, with patient baseline demographics, treatment information and clinical outcomes over time, can be a daunting task for the treating clinician. Within this review, we highlight the current status of such multi-modal omics data sets in moderate/severe TBI, current limitations to the utilization of such data, and a potential path forward through employing integrative neuroinformatic approaches, which are applied in other neuropathologies. Such advances are positioned to facilitate the transition to precision prognostication and inform a top-down approach to the development of personalized therapeutics in moderate/severe TBI.
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Affiliation(s)
- Frederick A Zeiler
- Section of Neurosurgery, Department of Surgery, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Biomedical Engineering, Faculty of Engineering, University of Manitoba, Winnipeg, MB, Canada.,Centre on Aging, University of Manitoba, Winnipeg, MB, Canada.,Division of Anaesthesia, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Yasser Iturria-Medina
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada.,McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, QC, Canada.,Ludmer Centre for Neuroinformatics and Mental Health, Montreal, QC, Canada
| | - Eric P Thelin
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Alwyn Gomez
- Section of Neurosurgery, Department of Surgery, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jai J Shankar
- Department of Radiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ji Hyun Ko
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg, MB, Canada
| | - Chase R Figley
- Department of Radiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg, MB, Canada
| | - Galen E B Wright
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg, MB, Canada.,Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Chris M Anderson
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg, MB, Canada.,Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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3
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Lindblad C, Pin E, Just D, Al Nimer F, Nilsson P, Bellander BM, Svensson M, Piehl F, Thelin EP. Fluid proteomics of CSF and serum reveal important neuroinflammatory proteins in blood-brain barrier disruption and outcome prediction following severe traumatic brain injury: a prospective, observational study. Crit Care 2021; 25:103. [PMID: 33712077 PMCID: PMC7955664 DOI: 10.1186/s13054-021-03503-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Severe traumatic brain injury (TBI) is associated with blood-brain barrier (BBB) disruption and a subsequent neuroinflammatory process. We aimed to perform a multiplex screening of brain enriched and inflammatory proteins in blood and cerebrospinal fluid (CSF) in order to study their role in BBB disruption, neuroinflammation and long-term functional outcome in TBI patients and healthy controls. METHODS We conducted a prospective, observational study on 90 severe TBI patients and 15 control subjects. Clinical outcome data, Glasgow Outcome Score, was collected after 6-12 months. We utilized a suspension bead antibody array analyzed on a FlexMap 3D Luminex platform to characterize 177 unique proteins in matched CSF and serum samples. In addition, we assessed BBB disruption using the CSF-serum albumin quotient (QA), and performed Apolipoprotein E-genotyping as the latter has been linked to BBB function in the absence of trauma. We employed pathway-, cluster-, and proportional odds regression analyses. Key findings were validated in blood samples from an independent TBI cohort. RESULTS TBI patients had an upregulation of structural CNS and neuroinflammatory pathways in both CSF and serum. In total, 114 proteins correlated with QA, among which the top-correlated proteins were complement proteins. A cluster analysis revealed protein levels to be strongly associated with BBB integrity, but not carriage of the Apolipoprotein E4-variant. Among cluster-derived proteins, innate immune pathways were upregulated. Forty unique proteins emanated as novel independent predictors of clinical outcome, that individually explained ~ 10% additional model variance. Among proteins significantly different between TBI patients with intact or disrupted BBB, complement C9 in CSF (p = 0.014, ΔR2 = 7.4%) and complement factor B in serum (p = 0.003, ΔR2 = 9.2%) were independent outcome predictors also following step-down modelling. CONCLUSIONS This represents the largest concomitant CSF and serum proteomic profiling study so far reported in TBI, providing substantial support to the notion that neuroinflammatory markers, including complement activation, predicts BBB disruption and long-term outcome. Individual proteins identified here could potentially serve to refine current biomarker modelling or represent novel treatment targets in severe TBI.
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Affiliation(s)
- Caroline Lindblad
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Elisa Pin
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - David Just
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Faiez Al Nimer
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Center for Neurology, Academic Specialist Center, Stockholm Health Services, Stockholm, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Bo-Michael Bellander
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Svensson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Piehl
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Center for Neurology, Academic Specialist Center, Stockholm Health Services, Stockholm, Sweden
| | - Eric Peter Thelin
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
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4
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Saber M, Pathak KV, McGilvrey M, Garcia-Mansfield K, Harrison JL, Rowe RK, Lifshitz J, Pirrotte P. Proteomic analysis identifies plasma correlates of remote ischemic conditioning in the context of experimental traumatic brain injury. Sci Rep 2020; 10:12989. [PMID: 32737368 PMCID: PMC7395133 DOI: 10.1038/s41598-020-69865-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/20/2020] [Indexed: 12/02/2022] Open
Abstract
Remote ischemic conditioning (RIC), transient restriction and recirculation of blood flow to a limb after traumatic brain injury (TBI), can modify levels of pathology-associated circulating protein. This study sought to identify TBI-induced molecular alterations in plasma and whether RIC would modulate protein and metabolite levels at 24 h after diffuse TBI. Adult male C57BL/6 mice received diffuse TBI by midline fluid percussion or were sham-injured. Mice were assigned to treatment groups 1 h after recovery of righting reflex: sham, TBI, sham RIC, TBI RIC. Nine plasma metabolites were significantly lower post-TBI (six amino acids, two acylcarnitines, one carnosine). RIC intervention returned metabolites to sham levels. Using proteomics analysis, twenty-four putative protein markers for TBI and RIC were identified. After application of Benjamini–Hochberg correction, actin, alpha 1, skeletal muscle (ACTA1) was found to be significantly increased in TBI compared to both sham groups and TBI RIC. Thus, identified metabolites and proteins provide potential biomarkers for TBI and therapeutic RIC in order to monitor disease progression and therapeutic efficacy.
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Affiliation(s)
- Maha Saber
- BARROW Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA.,Child Health, University of Arizona College of Medicine-Phoenix, 425 N 5th street ABC1, Phoenix, AZ, USA
| | - Khyati V Pathak
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Marissa McGilvrey
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Krystine Garcia-Mansfield
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jordan L Harrison
- BARROW Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA.,Child Health, University of Arizona College of Medicine-Phoenix, 425 N 5th street ABC1, Phoenix, AZ, USA
| | - Rachel K Rowe
- BARROW Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA.,Child Health, University of Arizona College of Medicine-Phoenix, 425 N 5th street ABC1, Phoenix, AZ, USA.,Phoenix VA Health Care System, Phoenix, AZ, USA
| | - Jonathan Lifshitz
- BARROW Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, USA. .,Child Health, University of Arizona College of Medicine-Phoenix, 425 N 5th street ABC1, Phoenix, AZ, USA. .,Phoenix VA Health Care System, Phoenix, AZ, USA.
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, Phoenix, AZ, USA
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5
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Jankovska E, Svitek M, Holada K, Petrak J. Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage. Clin Proteomics 2019; 16:9. [PMID: 30890900 PMCID: PMC6390343 DOI: 10.1186/s12014-019-9229-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the central nervous system. This makes human CSF an attractive source of potential biomarkers for neurologic diseases. Similarly to blood plasma, proteomic analysis of CSF is complicated by a high dynamic range of individual protein concentrations and by the presence of several highly abundant proteins. To deal with the abundant human CSF proteins, methods developed for blood plasma/serum are routinely used. Multiple affinity removal systems and protein enrichment of less abundant proteins using a combinatorial peptide ligand library are among the most frequent approaches. However, their relative impact on CSF proteome coverage has never been evaluated side-by-side in a single study. Therefore, we explored the effect of CSF depletion using MARS 14 cartridge and ProteoMiner ligand library on the number of CSF proteins identified in subsequent LC–MS/MS analysis. LC–MS/MS analysis of crude (non-treated) CSF provided roughly 500 identified proteins. Depletion of CSF by MARS 14 cartridge increased the number of identifications to nearly 800, while treatment of CSF using ProteoMiner enabled identification of 600 proteins. To explore the potential losses of CSF proteins during the depletion process, we also analyzed the “waste” fractions generated by both methods, i.e., proteins retained by the MARS 14 cartridge, and the molecules present in the flow-through fraction from ProteoMiner. More than 250 proteins were bound to MARS 14 cartridge, 100 of those were not identified in the corresponding depleted CSF. Similarly, analysis of the waste fraction in ProteoMiner workflow provided almost 70 unique proteins not found in the CSF depleted by the ligand library. Both depletion strategies significantly increased the number of identified CSF proteins compared to crude CSF. However, MARS 14 depletion provided a markedly higher number of identified proteins (773) compared to ProteoMiner (611). Further, we showed that CSF proteins are lost due to co-depletion (MARS 14) or exclusion (ProteoMiner) during the depletion process. This suggests that the routinely discarded “waste” fractions contain proteins of potential interest and should be included in CSF biomarker studies.
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Affiliation(s)
- Eliska Jankovska
- 1BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marek Svitek
- 2Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University, Prague, Czech Republic.,3General University Hospital, Prague, Czech Republic
| | - Karel Holada
- 4Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jiri Petrak
- 1BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic
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6
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Halford J, Shen S, Itamura K, Levine J, Chong AC, Czerwieniec G, Glenn TC, Hovda DA, Vespa P, Bullock R, Dietrich WD, Mondello S, Loo JA, Wanner IB. New astroglial injury-defined biomarkers for neurotrauma assessment. J Cereb Blood Flow Metab 2017; 37:3278-3299. [PMID: 28816095 PMCID: PMC5624401 DOI: 10.1177/0271678x17724681] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/01/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
Abstract
Traumatic brain injury (TBI) is an expanding public health epidemic with pathophysiology that is difficult to diagnose and thus treat. TBI biomarkers should assess patients across severities and reveal pathophysiology, but currently, their kinetics and specificity are unclear. No single ideal TBI biomarker exists. We identified new candidates from a TBI CSF proteome by selecting trauma-released, astrocyte-enriched proteins including aldolase C (ALDOC), its 38kD breakdown product (BDP), brain lipid binding protein (BLBP), astrocytic phosphoprotein (PEA15), glutamine synthetase (GS) and new 18-25kD-GFAP-BDPs. Their levels increased over four orders of magnitude in severe TBI CSF. First post-injury week, ALDOC levels were markedly high and stable. Short-lived BLBP and PEA15 related to injury progression. ALDOC, BLBP and PEA15 appeared hyper-acutely and were similarly robust in severe and mild TBI blood; 25kD-GFAP-BDP appeared overnight after TBI and was rarely present after mild TBI. Using a human culture trauma model, we investigated biomarker kinetics. Wounded (mechanoporated) astrocytes released ALDOC, BLBP and PEA15 acutely. Delayed cell death corresponded with GFAP release and proteolysis into small GFAP-BDPs. Associating biomarkers with cellular injury stages produced astroglial injury-defined (AID) biomarkers that facilitate TBI assessment, as neurological deficits are rooted not only in death of CNS cells, but also in their functional compromise.
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Affiliation(s)
- Julia Halford
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Sean Shen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Kyohei Itamura
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Jaclynn Levine
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Albert C Chong
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Gregg Czerwieniec
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Thomas C Glenn
- Department of Neurosurgery, Brain Injury Research Center, Department of Molecular and Medical Pharmacology
| | - David A Hovda
- Department of Neurosurgery, Brain Injury Research Center, Department of Molecular and Medical Pharmacology
| | - Paul Vespa
- Department of Neurology, UCLA-David Geffen School of Medicine, Los Angeles, CA, USA
| | - Ross Bullock
- Department of Neurological Surgery, Jackson Memorial Hospital, Miami, FL, USA
| | - W Dalton Dietrich
- The Miami Project to Cure Paralysis, University of Miami-Miller School of Medicine, Miami, FL, USA
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Ina-Beate Wanner
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
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7
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Ercole A, Magnoni S, Vegliante G, Pastorelli R, Surmacki J, Bohndiek SE, Zanier ER. Current and Emerging Technologies for Probing Molecular Signatures of Traumatic Brain Injury. Front Neurol 2017; 8:450. [PMID: 28912750 PMCID: PMC5582086 DOI: 10.3389/fneur.2017.00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/14/2017] [Indexed: 01/10/2023] Open
Abstract
Traumatic brain injury (TBI) is understood as an interplay between the initial injury, subsequent secondary injuries, and a complex host response all of which are highly heterogeneous. An understanding of the underlying biology suggests a number of windows where mechanistically inspired interventions could be targeted. Unfortunately, biologically plausible therapies have to-date failed to translate into clinical practice. While a number of stereotypical pathways are now understood to be involved, current clinical characterization is too crude for it to be possible to characterize the biological phenotype in a truly mechanistically meaningful way. In this review, we examine current and emerging technologies for fuller biochemical characterization by the simultaneous measurement of multiple, diverse biomarkers. We describe how clinically available techniques such as cerebral microdialysis can be leveraged to give mechanistic insights into TBI pathobiology and how multiplex proteomic and metabolomic techniques can give a more complete description of the underlying biology. We also describe spatially resolved label-free multiplex techniques capable of probing structural differences in chemical signatures. Finally, we touch on the bioinformatics challenges that result from the acquisition of such large amounts of chemical data in the search for a more mechanistically complete description of the TBI phenotype.
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Affiliation(s)
- Ari Ercole
- Division of Anaesthesia, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Sandra Magnoni
- Department of Anesthesiology and Intensive Care, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Gloria Vegliante
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Roberta Pastorelli
- Unit of Gene and Protein Biomarkers, Laboratory of Mass Spectrometry, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Jakub Surmacki
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Elizabeth Bohndiek
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Elisa R. Zanier
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
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8
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Sharma R, Rosenberg A, Bennett ER, Laskowitz DT, Acheson SK. A blood-based biomarker panel to risk-stratify mild traumatic brain injury. PLoS One 2017; 12:e0173798. [PMID: 28355230 PMCID: PMC5371303 DOI: 10.1371/journal.pone.0173798] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 02/27/2017] [Indexed: 11/19/2022] Open
Abstract
Mild traumatic brain injury (TBI) accounts for the vast majority of the nearly two million brain injuries suffered in the United States each year. Mild TBI is commonly classified as complicated (radiographic evidence of intracranial injury) or uncomplicated (radiographically negative). Such a distinction is important because it helps to determine the need for further neuroimaging, potential admission, or neurosurgical intervention. Unfortunately, imaging modalities such as computed tomography (CT) and magnetic resonance imaging (MRI) are costly and not without some risk. The purpose of this study was to screen 87 serum biomarkers to identify a select panel of biomarkers that would predict the presence of intracranial injury as determined by initial brain CT. Serum was collected from 110 patients who sustained a mild TBI within 24 hours of blood draw. Two models were created. In the broad inclusive model, 72kDa type IV collagenase (MMP-2), C-reactive protein (CRP), creatine kinase B type (CKBB), fatty acid binding protein-heart (hFABP), granulocyte-macrophage colony-stimulating factor (GM-CSF) and malondialdehyde modified low density lipoprotein (MDA-LDL) significantly predicted injury visualized on CT, yielding an overall c-statistic of 0.975 and a negative predictive value (NPV) of 98.6. In the parsimonious model, MMP-2, CRP, and CKBB type significantly predicted injury visualized on CT, yielding an overall c-statistic of 0.964 and a negative predictive value (NPV) of 97.2. These results suggest that a serum based biomarker panel can accurately differentiate patients with complicated mild TBI from those with uncomplicated mild TBI. Such a panel could be useful to guide early triage decisions, including the need for further evaluation or admission, especially in those environments in which resources are limited.
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Affiliation(s)
- Richa Sharma
- School of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Alexandra Rosenberg
- School of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ellen R. Bennett
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Daniel T. Laskowitz
- School of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Shawn K. Acheson
- Durham VA Medical Center, Durham, North Carolina, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, North Carolina, United States of America
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9
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Levine J, Kwon E, Paez P, Yan W, Czerwieniec G, Loo JA, Sofroniew MV, Wanner IB. Traumatically injured astrocytes release a proteomic signature modulated by STAT3-dependent cell survival. Glia 2015; 64:668-94. [PMID: 26683444 DOI: 10.1002/glia.22953] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/20/2015] [Indexed: 01/02/2023]
Abstract
Molecular markers associated with CNS injury are of diagnostic interest. Mechanical trauma generates cellular deformation associated with membrane permeability with unknown molecular consequences. We used an in vitro model of stretch-injury and proteomic analyses to determine protein changes in murine astrocytes and their surrounding fluids. Abrupt pressure-pulse stretching resulted in the rapid release of 59 astrocytic proteins with profiles reflecting cell injury and cell death, i.e., mechanoporation and cell lysis. This acute trauma-release proteome was overrepresented with metabolic proteins compared with the uninjured cellular proteome, bearing relevance for post-traumatic metabolic depression. Astrocyte-specific deletion of signal transducer and activator of transcription 3 (STAT3-CKO) resulted in reduced stretch-injury tolerance, elevated necrosis and increased protein release. Consistent with more lysed cells, more protein complexes, nuclear and transport proteins were released from STAT3-CKO versus nontransgenic astrocytes. STAT3-CKO astrocytes had reduced basal expression of GFAP, lactate dehydrogenase B (LDHB), aldolase C (ALDOC), and astrocytic phosphoprotein 15 (PEA15), and elevated levels of tropomyosin (TPM4) and α actinin 4 (ACTN4). Stretching caused STAT3-dependent cellular depletion of PEA15 and GFAP, and its filament disassembly in subpopulations of injured astrocytes. PEA15 and ALDOC signals were low in injured astrocytes acutely after mouse spinal cord crush injury and were robustly expressed in reactive astrocytes 1 day postinjury. In contrast, α crystallin (CRYAB) was present in acutely injured astrocytes, and absent from uninjured and reactive astrocytes, demonstrating novel marker differences among postinjury astrocytes. These findings reveal a proteomic signature of traumatically-injured astrocytes reflecting STAT3-dependent cellular survival with potential diagnostic value.
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Affiliation(s)
- Jaclynn Levine
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Eunice Kwon
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Pablo Paez
- Department of Pharmacology and Toxicology, Hunter James Kelly Research Institute, School of Medicine and Biomedical Sciences, SUNY, University at Buffalo, NYS Center of Excellence, Buffalo, New York
| | - Weihong Yan
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California
| | - Gregg Czerwieniec
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California.,UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California
| | - Michael V Sofroniew
- Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Ina-Beate Wanner
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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10
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Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
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Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
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11
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Sundberg M, Bergquist J, Ramström M. High-abundant protein depletion strategies applied on dog cerebrospinal fluid and evaluated by high-resolution mass spectrometry. Biochem Biophys Rep 2015; 3:68-75. [PMID: 30338299 PMCID: PMC6189695 DOI: 10.1016/j.bbrep.2015.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/18/2015] [Accepted: 07/22/2015] [Indexed: 12/27/2022] Open
Abstract
As the number of fully sequenced animal genomes and the performance of advanced mass spectrometry-based proteomics techniques are continuously improving, there is now a great opportunity to increase the knowledge of various animal proteomes. This research area is further stimulated by a growing interest from veterinary medicine and the pharmaceutical industry. Cerebrospinal fluid (CSF) is a good source for better understanding of diseases related to the central nervous system, both in humans and other animals. In this study, four high-abundant protein depletion columns, developed for human or rat serum, were evaluated for dog CSF. For the analysis, a shotgun proteomics approach, based on nanoLC-LTQ Orbitrap MS/MS, was applied. All the selected approaches were shown to deplete dog CSF with different success. It was demonstrated that the columns significantly improved the coverage of the detected dog CSF proteome. An antibody-based column showed the best performance, in terms of efficiency, repeatability and the number of proteins detected in the sample. In total 983 proteins were detected. Of those, 801 proteins were stated as uncharacterized in the UniProt database. To the best of our knowledge, this is the so far largest number of proteins reported for dog CSF in one single study. We evaluated four high-abundant protein depletion kits on dog CSF. High abundant depletion kit developed for humans/rats can be used for dog CSF. Protein depletion of dog CSF gives extended coverage of the CSF proteome. In total, 983 dog proteins were identified in this study.
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Affiliation(s)
- Mårten Sundberg
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Margareta Ramström
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
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12
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Harish G, Mahadevan A, Pruthi N, Sreenivasamurthy SK, Puttamallesh VN, Keshava Prasad TS, Shankar SK, Srinivas Bharath MM. Characterization of traumatic brain injury in human brains reveals distinct cellular and molecular changes in contusion and pericontusion. J Neurochem 2015; 134:156-72. [PMID: 25712633 DOI: 10.1111/jnc.13082] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 01/07/2015] [Accepted: 02/19/2015] [Indexed: 12/22/2022]
Abstract
Traumatic brain injury (TBI) contributes to fatalities and neurological disabilities worldwide. While primary injury causes immediate damage, secondary events contribute to long-term neurological defects. Contusions (Ct) are primary injuries correlated with poor clinical prognosis, and can expand leading to delayed neurological deterioration. Pericontusion (PC) (penumbra), the region surrounding Ct, can also expand with edema, increased intracranial pressure, ischemia, and poor clinical outcome. Analysis of Ct and PC can therefore assist in understanding the pathobiology of TBI and its management. This study on human TBI brains noted extensive neuronal, astroglial and inflammatory changes, alterations in mitochondrial, synaptic and oxidative markers, and associated proteomic profile, with distinct differences in Ct and PC. While Ct displayed petechial hemorrhages, thrombosis, inflammation, neuronal pyknosis, and astrogliosis, PC revealed edema, vacuolation of neuropil, axonal loss, and dystrophic changes. Proteomic analysis demonstrated altered immune response, synaptic, and mitochondrial dysfunction, among others, in Ct, while PC displayed altered regulation of neurogenesis and cytoskeletal architecture, among others. TBI brains displayed oxidative damage, glutathione depletion, mitochondrial dysfunction, and loss of synaptic proteins, with these changes being more profound in Ct. We suggest that analysis of markers specific to Ct and PC may be valuable in the evaluation of TBI pathobiology and therapeutics. We have characterized the primary injury in human traumatic brain injury (TBI). Contusions (Ct) - the injury core displayed hemorrhages, inflammation, and astrogliosis, while the surrounding pericontusion (PC) revealed edema, vacuolation, microglial activation, axonal loss, and dystrophy. Proteomic analysis demonstrated altered immune response, synaptic and mitochondrial dysfunction in Ct, and altered regulation of neurogenesis and cytoskeletal architecture in PC. Ct displayed more oxidative damage, mitochondrial, and synaptic dysfunction compared to PC.
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Affiliation(s)
- Gangadharappa Harish
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
| | - Nupur Pruthi
- Department of Neurosurgery, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
| | | | | | | | - Susarla Krishna Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, Karnataka, India
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13
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Agoston DV. Bench-to-Bedside and Bedside Back to the Bench; Seeking a Better Understanding of the Acute Pathophysiological Process in Severe Traumatic Brain Injury. Front Neurol 2015; 6:47. [PMID: 25852631 PMCID: PMC4362297 DOI: 10.3389/fneur.2015.00047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/23/2015] [Indexed: 12/11/2022] Open
Abstract
Despite substantial investments, traumatic brain injury (TBI) remains one of the major disorders that lack specific pharmacotherapy. To a substantial degree, this situation is due to lack of understanding of the pathophysiological process of the disease. Experimental TBI research offers controlled, rapid, and cost-effective means to identify the pathophysiology but translating experimental findings into clinical practice can be further improved by using the same or similar outcome measures and clinically relevant time points. The pathophysiology during the acute phase of severe TBI is especially poorly understood. In this Mini review, I discuss some of the incongruences between current clinical practices and needs versus information provided by experimental TBI research as well as the benefits of designing animal experiments with translation into clinical practice in mind.
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Affiliation(s)
- Denes V Agoston
- Department of Anatomy, Physiology and Genetics, Uniformed Services University , Bethesda, MD , USA ; Department of Neuroscience, Experimental Neurotrauma, Karolinska Institutet , Stockholm , Sweden
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14
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Stawicki SP, Stoltzfus JC, Aggarwal P, Bhoi S, Bhatt S, Kalra OP, Bhalla A, Hoey BA, Galwankar SC, Paladino L, Papadimos TJ. Academic College of Emergency Experts in India's INDO-US Joint Working Group and OPUS12 Foundation Consensus Statement on Creating A Coordinated, Multi-Disciplinary, Patient-Centered, Global Point-of-Care Biomarker Discovery Network. Int J Crit Illn Inj Sci 2014; 4:200-8. [PMID: 25337481 PMCID: PMC4200545 DOI: 10.4103/2229-5151.141398] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Biomarker science brings great promise to clinical medicine. This is especially true in the era of technology miniaturization, rapid dissemination of knowledge, and point-of-care (POC) implementation of novel diagnostics. Despite this tremendous progress, the journey from a candidate biomarker to a scientifically validated biomarker continues to be an arduous one. In addition to substantial financial resources, biomarker research requires considerable expertise and a multidisciplinary approach. Investigational designs must also be taken into account, with the randomized controlled trial remaining the “gold standard”. The authors present a condensed overview of biomarker science and associated investigational methods, followed by specific examples from clinical areas where biomarker development and/or implementation resulted in tangible enhancements in patient care. This manuscript also serves as a call to arms for the establishment of a truly global, well-coordinated infrastructure dedicated to biomarker research and development, with focus on delivery of the latest discoveries directly to the patient via point-of-care technology.
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Affiliation(s)
- Stanislaw P Stawicki
- Department of Research and Innovation, Research Institute, Bethlehem, Pennsylvania ; Department of Research and Innovation, OPUS 12 Foundation Global, Columbus, USA
| | - Jill C Stoltzfus
- Department of Research and Innovation, Research Institute, Bethlehem, Pennsylvania ; Department of Research and Innovation, Research Institute, Bethlehem, Pennsylvania
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjeev Bhoi
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Shashi Bhatt
- Department of Anesthesiology, University of Toledo, College of Medicine, Toledo, USA
| | - O P Kalra
- Department of Medicine, University College of Medical Sciences, New Delhi, India
| | - Ashish Bhalla
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Brian A Hoey
- Department of Research and Innovation, OPUS 12 Foundation Global, Columbus, USA ; Department of Surgery, St Luke's University Health Network, Bethlehem, Pennsylvania
| | - Sagar C Galwankar
- Department of Research and Innovation, OPUS 12 Foundation Global, Columbus, USA ; Department of Emergency Medicine, University of Florida and Winter Haven Hospital, Florida, USA
| | - Lorenzo Paladino
- Department of Emergency Medicine, SUNY Downstate Medical Center, Long Island College Hospital, New York, USA
| | - Thomas J Papadimos
- Department of Research and Innovation, OPUS 12 Foundation Global, Columbus, USA ; Department of Anesthesiology, The Ohio State University College of Medicine, Columbus, Ohio, USA
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15
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Abstract
Epileptogenesis, a process leading to a reduced threshold for seizures after transient brain insults, as well as the mechanisms underlying the propensity to generate spontaneous epileptic seizures, are highly dynamic processes. Biomarkers--objective measures of biological processes--would be excellent tools for monitoring epileptogenesis and the dynamics of increased seizure propensity, as well as the potential to interfere, for example pharmacologically, with these key pathological aspects of epilepsy. Molecular biomarkers have revolutionized therapies, as well as response prediction and monitoring of therapies in other biomedical fields. However, high-impact molecular biomarkers are still not available in the context of epilepsy. Several factors, such as the large heterogeneity of epileptic syndromes and their underlying pathological patterns, as well as the limited availability of tissue samples, represent a particular challenge to the development of molecular biomarkers in epileptogenesis and epilepsy. However, substantial technical progress has been made recently with respect to biomarker characterization and monitoring by large throughput analysis on the genomic, mRNA, and proteomic levels, starting from minute amounts of brain tissue or body fluids, for example cerebrospinal fluid, blood, serum, or plasma. Given the substantial cellular- and network-level functional pathophysiology involved in epilepsy, it may be beneficial in the future to combine molecular analysis with other methods, such as imaging and electrophysiological biomarkers.
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Affiliation(s)
- Katarzyna Lukasiuk
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02 093 Warsaw, Poland
| | - Albert J. Becker
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
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16
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Shen S, Loo RRO, Wanner IB, Loo JA. Addressing the needs of traumatic brain injury with clinical proteomics. Clin Proteomics 2014; 11:11. [PMID: 24678615 PMCID: PMC3976360 DOI: 10.1186/1559-0275-11-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 02/10/2014] [Indexed: 12/15/2022] Open
Abstract
Background Neurotrauma or injuries to the central nervous system (CNS) are a serious public health problem worldwide. Approximately 75% of all traumatic brain injuries (TBIs) are concussions or other mild TBI (mTBI) forms. Evaluation of concussion injury today is limited to an assessment of behavioral symptoms, often with delay and subject to motivation. Hence, there is an urgent need for an accurate chemical measure in biofluids to serve as a diagnostic tool for invisible brain wounds, to monitor severe patient trajectories, and to predict survival chances. Although a number of neurotrauma marker candidates have been reported, the broad spectrum of TBI limits the significance of small cohort studies. Specificity and sensitivity issues compound the development of a conclusive diagnostic assay, especially for concussion patients. Thus, the neurotrauma field currently has no diagnostic biofluid test in clinical use. Content We discuss the challenges of discovering new and validating identified neurotrauma marker candidates using proteomics-based strategies, including targeting, selection strategies and the application of mass spectrometry (MS) technologies and their potential impact to the neurotrauma field. Summary Many studies use TBI marker candidates based on literature reports, yet progress in genomics and proteomics have started to provide neurotrauma protein profiles. Choosing meaningful marker candidates from such ‘long lists’ is still pending, as only few can be taken through the process of preclinical verification and large scale translational validation. Quantitative mass spectrometry targeting specific molecules rather than random sampling of the whole proteome, e.g., multiple reaction monitoring (MRM), offers an efficient and effective means to multiplex the measurement of several candidates in patient samples, thereby omitting the need for antibodies prior to clinical assay design. Sample preparation challenges specific to TBI are addressed. A tailored selection strategy combined with a multiplex screening approach is helping to arrive at diagnostically suitable candidates for clinical assay development. A surrogate marker test will be instrumental for critical decisions of TBI patient care and protection of concussion victims from repeated exposures that could result in lasting neurological deficits.
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Affiliation(s)
| | | | | | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.
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17
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Ahmed F, Gyorgy A, Kamnaksh A, Ling G, Tong L, Parks S, Agoston D. Time-dependent changes of protein biomarker levels in the cerebrospinal fluid after blast traumatic brain injury. Electrophoresis 2013; 33:3705-11. [PMID: 23161535 DOI: 10.1002/elps.201200299] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 08/30/2012] [Accepted: 09/10/2012] [Indexed: 01/01/2023]
Abstract
Time-dependent changes of protein biomarkers in the cerebrospinal fluid (CSF) can be used to identify the pathological processes in traumatic brain injury (TBI) as well as to follow the progression of the disease. We obtained CSF from a large animal model (swine) of blast-induced traumatic brain injury prior to and at 6, 24, 72 h, and 2 wk after a single exposure to blast overpressure, and determined changes in the CSF levels of neurofilament-heavy chain, neuron-specific enolase, brain-specific creatine kinase, glial fibrillary acidic protein, calcium-binding protein β (S100β), Claudin-5, vascular endothelial growth factor, and von Willebrand factor using reverse phase protein microarray. We detected biphasic temporal patterns in the CSF concentrations of all tested protein markers except S100β. The CSF levels of all markers were significantly increased 6 h after the injury compared to preinjury levels. Values were then decreased at 24 h, prior to a second increase in all markers but S100β at 72 h. At 2 wk postinjury, the CSF concentrations of all biomarkers were decreased once again; brain-specific creatine kinase, Claudin-5, von Willebrand factor, and S100β levels were no longer significantly higher than their preinjury values while neurofilament-heavy chain, neuron-specific enolase, vascular endothelial growth factor, and glial fibrillary acidic protein levels remained significantly elevated compared to baseline. Our findings implicate neuronal and glial cell damage, compromised vascular permeability, and inflammation in blast-induced traumatic brain injury, as well as demonstrate the value of determining the temporal pattern of biomarker changes that may be of diagnostic value.
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Affiliation(s)
- Farid Ahmed
- Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD 20814, USA
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18
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Gama MR, Collins CH, Bottoli CBG. Nano-Liquid Chromatography in Pharmaceutical and Biomedical Research. J Chromatogr Sci 2013; 51:694-703. [DOI: 10.1093/chromsci/bmt023] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Cunningham R, Jany P, Messing A, Li L. Protein changes in immunodepleted cerebrospinal fluid from a transgenic mouse model of Alexander disease detected using mass spectrometry. J Proteome Res 2013; 12:719-28. [PMID: 23272901 DOI: 10.1021/pr300785h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cerebrospinal fluid (CSF) is a low protein content biological fluid with a dynamic range spanning at least 9 orders of magnitude in protein content and is in direct contact with the brain. A modified IgY-14 immunodepletion treatment was performed to enhance analysis of the low volumes of CSF that are obtainable from mice. As a model system in which to test this approach, we utilized transgenic mice that overexpress the intermediate filament glial fibrillary acidic protein (GFAP). These mice are models for Alexander disease (AxD), a severe leukodystrophy in humans. From the CSF of control and transgenic mice we report the identification of 289 proteins, with relative quantification of 103 proteins. Biological and technical triplicates were performed to address animal variability as well as reproducibility in mass spectrometric analysis. Relative quantitation was performed using distributive normalized spectral abundance factor (dNSAF) spectral counting analysis. A panel of biomarker proteins with significant changes in the CSF of GFAP transgenic mice has been identified with validation from enzyme-linked immunosorbent assay (ELISA) and microarray data, demonstrating the utility of our methodology and providing interesting targets for future investigations on the molecular and pathological aspects of AxD.
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Affiliation(s)
- Robert Cunningham
- Department of Chemistry & School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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20
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Choi YS. Reaching for the deep proteome: recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome. Arch Pharm Res 2012; 35:1861-70. [PMID: 23212627 DOI: 10.1007/s12272-012-1102-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/30/2012] [Accepted: 08/21/2012] [Indexed: 11/24/2022]
Abstract
In the last decade, there has been a dramatic progress in separation techniques, mass spectrometry, and bioinformatics, and this progress has significantly improved the techniques on protein analysis. However, the analysis of low-abundance proteins is still challenging because of the limited performance in the method of choice compared to the complexity and the vast dynamic range of biological samples. Since this issue is a big obstacle in most proteomics investigations, great interest has been paid recently to various techniques, such as multi-dimensional analysis, specific peptide selection, high-abundance protein depletion, ligand library treatment, to address this challenge. Therefore, here, the author reviews recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome, mainly focusing on their methods and perspectives.
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Affiliation(s)
- Yong Seok Choi
- College of Pharmacy, Dankook University, Cheonan 330-714, Korea.
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21
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Mass Spectrometry-based Proteomics and Peptidomics for Systems Biology and Biomarker Discovery. ACTA ACUST UNITED AC 2012; 7:313-335. [PMID: 24504115 DOI: 10.1007/s11515-012-1218-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large datasets of proteins or peptides involved in various biological and disease progression processes producing testable hypothesis for complex biological questions. This review provides an introduction and insight to relevant topics in proteomics and peptidomics including biological material selection, sample preparation, separation techniques, peptide fragmentation, post-translation modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature and remaining challenges and emerging technologies for proteomics and peptidomics are presented.
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22
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Bora A, Anderson C, Bachani M, Nath A, Cotter RJ. Robust two-dimensional separation of intact proteins for bottom-up tandem mass spectrometry of the human CSF proteome. J Proteome Res 2012; 11:3143-9. [PMID: 22537003 DOI: 10.1021/pr300057v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cerebrospinal fluid (CSF) is produced in the brain by cells in the choroid plexus at a rate of 500 mL/day. It is the only body fluid in direct contact with the brain. Thus, any changes in the CSF composition will reflect pathological processes and make CSF a potential source of biomarkers for different disease states. Proteomics offers a comprehensive view of the proteins found in CSF. In this study, we use a recently developed nongel based method of sample preparation of CSF followed by liquid chromatography-high accuracy mass spectrometry (LC-MS) for MS and MS/MS analyses, allowing unambiguous identification of peptides/proteins. Gel-eluted liquid fraction entrapment electrophoresis (Gelfree) is used to separate a CSF complex protein mixture in 12 user-selectable liquid-phase molecular weight fractions. Using this high throughput workflow, we have been able to separate CSF intact proteins over a broad mass range (3.5-100 kDa) with high resolution (between 15 and 100 kDa) in 2 h and 40 min. We have completely eliminated albumin and were able to interrogate the low abundance CSF proteins in a highly reproducible manner from different CSF samples at the same time. Using LC-MS as a downstream analysis, we identified 368 proteins using MidiTrap G-10 desalting columns and 166 proteins (including 57 unique proteins) using Zeba spin columns with a 5% false discovery rate (FDR). Prostaglandin D2 synthase, Chromogranin A, Apolipoprotein E, Chromogranin B, Secretogranin III, Cystatin C, VGF nerve growth factor, and Cadherin 2 are a few of the proteins that were characterized. Gelfree-LC-MS is a robust method for the analysis of the human proteome that we will use to develop biomarkers for several neurodegenerative diseases and to quantitate these markers using multiple reaction monitoring.
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Affiliation(s)
- Adriana Bora
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine , Baltimore, Maryland, United States
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23
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Hartwig S, Lehr S. Combination of highly efficient hexapeptide ligand library-based sample preparation with 2D DIGE for the analysis of the hidden human serum/plasma proteome. Methods Mol Biol 2012; 854:169-180. [PMID: 22311760 DOI: 10.1007/978-1-61779-573-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Blood serum/plasma samples provide the major source to identify diagnostically relevant or treatment response-related proteins. But its complexity and the enormous dynamic range hinders comprehensive analysis. Therefore, more detailed analysis, in particular, of low-abundant peptides/proteins requires extensive pre-fractionation, which frequently influences the native composition and may lead to a loss of potentially important information. In order to overcome these barriers, we describe an innovative sample preparation tool utilizing combinatorial hexapeptide ligand libraries to efficiently enrich low-abundance proteins with a simple protocol. In contrast to the most common approaches based on the immuno-depletion of antibody-targeted high-abundance proteins, this technology concentrates low-abundance proteins and concurrently reduces the high-abundance species. Thus, the dynamic range is compressed, and low-abundance proteins become more easily detectable. We show how this sample preparation technique can be easily combined with 2D DIGE analysis to enable more comprehensive and quantitative profiling of complex biological samples.
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Affiliation(s)
- Sonja Hartwig
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Düsseldorf, Germany
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24
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Dahlin AP, Hjort K, Hillered L, Sjödin MOD, Bergquist J, Wetterhall M. Multiplexed quantification of proteins adsorbed to surface-modified and non-modified microdialysis membranes. Anal Bioanal Chem 2011; 402:2057-67. [PMID: 22159469 DOI: 10.1007/s00216-011-5614-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 11/16/2011] [Accepted: 11/25/2011] [Indexed: 11/28/2022]
Abstract
A simple and straightforward method for discovery and quantification of proteins adsorbed onto delicate and sensitive membrane surfaces is presented. The adsorbed proteins were enzymatically cleaved while still adsorbed onto the membranes using an on-surface enzymatic digestion (oSED). This was followed by isobaric tagging, nanoliquid chromatography, and tandem mass spectrometry. Protein adsorption on tri-block copolymer Poloxamer 407 surface-modified microdialysis (MD) membranes were compared with protein adsorption on unmodified MD membranes. Ventricular cerebrospinal fluid (vCSF) kept at 37 °C was used as sample matrix. In total, 19 proteins were quantified in two biological replicates. The surface-modified membranes adsorbed 33% less proteins than control membranes and the most abundant proteins were subunits of hemoglobin and clusterin. The adsorption of clusterin on the modified membranes was on average 36% compared to control membranes. The most common protein in vCSF, Albumin, was not identified adsorbed to the surface at all. It was also experimentally verified that oSED, in conjunction with tandem mass spectrometry can be used to quantify femtomole amounts of proteins adsorbed on limited and delicate surfaces, such as MD membranes. The method has great potential and can be used to study much more complex protein adsorption systems than previously reported.
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Affiliation(s)
- Andreas P Dahlin
- Department of Engineering Sciences, Uppsala University, Uppsala, Sweden.
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Teng PN, Bateman NW, Hood BL, Conrads TP. Advances in proximal fluid proteomics for disease biomarker discovery. J Proteome Res 2010; 9:6091-100. [PMID: 21028795 DOI: 10.1021/pr100904q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although serum/plasma has been the preferred source for identification of disease biomarkers, these efforts have been met with little success, in large part due the relatively small number of highly abundant proteins that render the reliable detection of low abundant disease-related proteins challenging due to the expansive dynamic range of concentration of proteins in this sample. Proximal fluid, the fluid derived from the extracellular milieu of tissues, contains a large repertoire of shed and secreted proteins that are likely to be present at higher concentrations relative to plasma/serum. It is hypothesized that many, if not all, proximal fluid proteins exchange with peripheral circulation, which has provided significant motivation for utilizing proximal fluids as a primary sample source for protein biomarker discovery. The present review highlights recent advances in proximal fluid proteomics, including the various protocols utilized to harvest proximal fluids along with detailing the results from mass spectrometry- and antibody-based analyses.
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Affiliation(s)
- Pang-ning Teng
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
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