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Cartas-Cejudo P, Cortés A, Lachén-Montes M, Anaya-Cubero E, Peral E, Ausín K, Díaz-Peña R, Fernández-Irigoyen J, Santamaría E. Mapping the human brain proteome: opportunities, challenges, and clinical potential. Expert Rev Proteomics 2024; 21:55-63. [PMID: 38299555 DOI: 10.1080/14789450.2024.2313073] [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: 09/25/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Due to the segmented functions and complexity of the human brain, the characterization of molecular profiles within specific areas such as brain structures and biofluids is essential to unveil the molecular basis for structure specialization as well as the molecular imbalance associated with neurodegenerative and psychiatric diseases. AREAS COVERED Much of our knowledge about brain functionality derives from neurophysiological, anatomical, and transcriptomic approaches. More recently, laser capture and imaging proteomics, technological and computational developments in LC-MS/MS, as well as antibody/aptamer-based platforms have allowed the generation of novel cellular, spatial, and posttranslational dimensions as well as innovative facets in biomarker validation and druggable target identification. EXPERT OPINION Proteomics is a powerful toolbox to functionally characterize, quantify, and localize the extensive protein catalog of the human brain across physiological and pathological states. Brain function depends on multi-dimensional protein homeostasis, and its elucidation will help us to characterize biological pathways that are essential to properly maintain cognitive functions. In addition, comprehensive human brain pathological proteomes may be the basis in computational drug-repositioning methods as a strategy for unveiling potential new therapies in neurodegenerative and psychiatric disorders.
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Affiliation(s)
- Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Adriana Cortés
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Elena Anaya-Cubero
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Erika Peral
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Karina Ausín
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Ramón Díaz-Peña
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Mitra S, Harvey-Jones K, Kraev I, Verma V, Meehan C, Mintoft A, Norris G, Campbell E, Tucker K, Robertson NJ, Hristova M, Lange S. The Extracellular Vesicle Citrullinome and Signature in a Piglet Model of Neonatal Seizures. Int J Mol Sci 2023; 24:11529. [PMID: 37511288 PMCID: PMC10380774 DOI: 10.3390/ijms241411529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Neonatal seizures are commonly associated with acute perinatal brain injury, while understanding regarding the downstream molecular pathways related to seizures remains unclear. Furthermore, effective treatment and reliable biomarkers are still lacking. Post-translational modifications can contribute to changes in protein function, and post-translational citrullination, which is caused by modification of arginine to citrulline via the calcium-mediated activation of the peptidylarginine deiminase (PAD) enzyme family, is being increasingly linked to neurological injury. Extracellular vesicles (EVs) are lipid-bilayer structures released from cells; they can be isolated from most body fluids and act as potential liquid biomarkers for disease conditions and response to treatment. As EVs carry a range of genetic and protein cargo that can be characteristic of pathological processes, the current study assessed modified citrullinated protein cargo in EVs isolated from plasma and CSF in a piglet neonatal seizure model, also following phenobarbitone treatment. Our findings provide novel insights into roles for PAD-mediated changes on EV signatures in neonatal seizures and highlight the potential of plasma- and CSF-EVs to monitor responses to treatment.
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Affiliation(s)
- Subhabrata Mitra
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Kelly Harvey-Jones
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK
| | - Vinita Verma
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Christopher Meehan
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Alison Mintoft
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Georgina Norris
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Ellie Campbell
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Katie Tucker
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Nicola J Robertson
- Department of Neonatology, Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Mariya Hristova
- Perinatal Brain Repair Group, Department of Neonatology, UCL Institute for Women's Health, London WC1E 6HU, UK
| | - Sigrun Lange
- Perinatal Brain Repair Group, Department of Neonatology, UCL Institute for Women's Health, London WC1E 6HU, UK
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
- Pathobiology and Extracellular Vesicle Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
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Mercer A, Jaunmuktane Z, Hristova M, Lange S. Differential, Stage Dependent Detection of Peptidylarginine Deiminases and Protein Deimination in Lewy Body Diseases-Findings from a Pilot Study. Int J Mol Sci 2022; 23:13117. [PMID: 36361903 PMCID: PMC9658624 DOI: 10.3390/ijms232113117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 07/30/2023] Open
Abstract
Over 10 million people worldwide live with Parkinson's disease (PD) and 4% of affected people are diagnosed before the age of 50. Research on early PD-related pathways is therefore of considerable importance. Peptidylarginine deiminases (PADs) are a family of calcium-activated enzymes that, through post-translational deimination of arginine to citrulline, contribute to changes in protein function, including in pathological processes. Recent studies have highlighted roles for PADs in a range of neurological disorders including PD, but overall, investigations on PADs in Lewy body disease (LBD), including PD, are still scarce. Hence, the current pilot study aimed at performing an immunohistochemistry screen of post-mortem human brain sections from Braak stages 4-6 from PD patients, as well as patients with incidental LBD (ILBD). We assessed differences in PAD isozyme detection (assessing all five PADs), in total protein deimination/citrullination and histone H3 deimination-which is an indicator of epigenetic changes and extracellular trap formation (ETosis), which can elicit immune responses and has involvement in pathogenic conditions. The findings of our pilot study indicate that PADs and deimination are increased in cingulate cortex and hippocampus, particularly in earlier stages of the disease. PAD2 and PAD3 were the most strongly upregulated PAD isozymes, with some elevation also observed for PAD1, while PAD4 and PAD6 increase was less marked in PD brains. Total protein deimination and histone H3 deimination were furthermore increased in PD brains, with a considerable increase at earlier Braak stages, compared with controls. Our findings point to a significant contribution of PADs, which may further aid early disease biomarker discovery, in PD and other LBDs.
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Affiliation(s)
- Audrey Mercer
- Department of Pharmacology, UCL School of Pharmacy, London WC1N 1AX, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Mariya Hristova
- Perinatal Brain Repair Group, Department of Neonatology, UCL Institute for Women’s Health, London WC1E 6HU, UK
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6XH, UK
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Sarnik J, Makowska J. Citrullination good or bad guy? Immunobiology 2022; 227:152233. [DOI: 10.1016/j.imbio.2022.152233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/11/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022]
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D’Alessio S, Cheng H, Eaton L, Kraev I, Pamenter ME, Lange S. Acute Hypoxia Alters Extracellular Vesicle Signatures and the Brain Citrullinome of Naked Mole-Rats (Heterocephalus glaber). Int J Mol Sci 2022; 23:ijms23094683. [PMID: 35563075 PMCID: PMC9100269 DOI: 10.3390/ijms23094683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
Peptidylarginine deiminases (PADs) and extracellular vesicles (EVs) may be indicative biomarkers of physiological and pathological status and adaptive responses, including to diseases and disorders of the central nervous system (CNS) and related to hypoxia. While these markers have been studied in hypoxia-intolerant mammals, in vivo investigations in hypoxia-tolerant species are lacking. Naked mole-rats (NMR) are among the most hypoxia-tolerant mammals and are thus a good model organism for understanding natural and beneficial adaptations to hypoxia. Thus, we aimed to reveal CNS related roles for PADs in hypoxia tolerance and identify whether circulating EV signatures may reveal a fingerprint for adaptive whole-body hypoxia responses in this species. We found that following in vivo acute hypoxia, NMR: (1) plasma-EVs were remodelled, (2) whole proteome EV cargo contained more protein hits (including citrullinated proteins) and a higher number of associated KEGG pathways relating to the total proteome of plasma-EVs Also, (3) brains had a trend for elevation in PAD1, PAD3 and PAD6 protein expression, while PAD2 and PAD4 were reduced, while (4) the brain citrullinome had a considerable increase in deiminated protein hits with hypoxia (1222 vs. 852 hits in normoxia). Our findings indicate that circulating EV signatures are modified and proteomic content is reduced in hypoxic conditions in naked mole-rats, including the circulating EV citrullinome, while the brain citrullinome is elevated and modulated in response to hypoxia. This was further reflected in elevation of some PADs in the brain tissue following acute hypoxia treatment. These findings indicate a possible selective role for PAD-isozymes in hypoxia response and tolerance.
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Affiliation(s)
- Stefania D’Alessio
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6 UW, UK;
| | - Hang Cheng
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (H.C.); (L.E.); (M.E.P.)
| | - Liam Eaton
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (H.C.); (L.E.); (M.E.P.)
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Walton Hall, Milton Keynes MK7 6AA, UK;
| | - Matthew E. Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (H.C.); (L.E.); (M.E.P.)
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6 UW, UK;
- Correspondence: ; Tel.: +44-(0)-20-7911-5000 (ext. 64832)
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Agoston DV. COVID-19 and Traumatic Brain Injury (TBI); What We Can Learn From the Viral Pandemic to Better Understand the Biology of TBI, Improve Diagnostics and Develop Evidence-Based Treatments. Front Neurol 2021; 12:752937. [PMID: 34987462 PMCID: PMC8720751 DOI: 10.3389/fneur.2021.752937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Denes V. Agoston
- Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, United States
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McDonald SJ, Shultz SR, Agoston DV. The Known Unknowns: An Overview of the State of Blood-Based Protein Biomarkers of Mild Traumatic Brain Injury. J Neurotrauma 2021; 38:2652-2666. [PMID: 33906422 DOI: 10.1089/neu.2021.0011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Blood-based protein biomarkers have revolutionized several fields of medicine by enabling molecular level diagnosis, as well as monitoring disease progression and treatment efficacy. Traumatic brain injury (TBI) so far has benefitted only moderately from using protein biomarkers to improve injury outcome. Because of its complexity and dynamic nature, TBI, especially its most prevalent mild form (mild TBI; mTBI), presents unique challenges toward protein biomarker discovery and validation given that blood is frequently obtained and processed outside of the clinical laboratory (e.g., athletic fields, battlefield) under variable conditions. As it stands, the field of mTBI blood biomarkers faces a number of outstanding questions. Do elevated blood levels of currently used biomarkers-ubiquitin carboxy-terminal hydrolase L1, glial fibrillary acidic protein, neurofilament light chain, and tau/p-tau-truly mirror the extent of parenchymal damage? Do these different proteins represent distinct injury mechanisms? Is the blood-brain barrier a "brick wall"? What is the relationship between intra- versus extracranial values? Does prolonged elevation of blood levels reflect de novo release or extended protein half-lives? Does biological sex affect the pathobiological responses after mTBI and thus blood levels of protein biomarkers? At the practical level, it is unknown how pre-analytical variables-sample collection, preparation, handling, and stability-affect the quality and reliability of biomarker data. The ever-increasing sensitivity of assay systems and lack of quality control of samples, combined with the almost complete reliance on antibody-based assay platforms, represent important unsolved issues given that false-negative results can lead to false clinical decision making and adverse outcomes. This article serves as a commentary on the state of mTBI biomarkers and the landscape of significant challenges. We highlight and discusses several biological and methodological "known unknowns" and close with some practical recommendations.
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Affiliation(s)
- Stuart J McDonald
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Sandy R Shultz
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Denes V Agoston
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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Tate DF, Dennis EL, Adams JT, Adamson MM, Belanger HG, Bigler ED, Bouchard HC, Clark AL, Delano-Wood LM, Disner SG, Eapen BC, Franz CE, Geuze E, Goodrich-Hunsaker NJ, Han K, Hayes JP, Hinds SR, Hodges CB, Hovenden ES, Irimia A, Kenney K, Koerte IK, Kremen WS, Levin HS, Lindsey HM, Morey RA, Newsome MR, Ollinger J, Pugh MJ, Scheibel RS, Shenton ME, Sullivan DR, Taylor BA, Troyanskaya M, Velez C, Wade BS, Wang X, Ware AL, Zafonte R, Thompson PM, Wilde EA. Coordinating Global Multi-Site Studies of Military-Relevant Traumatic Brain Injury: Opportunities, Challenges, and Harmonization Guidelines. Brain Imaging Behav 2021; 15:585-613. [PMID: 33409819 PMCID: PMC8035292 DOI: 10.1007/s11682-020-00423-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
Traumatic brain injury (TBI) is common among military personnel and the civilian population and is often followed by a heterogeneous array of clinical, cognitive, behavioral, mood, and neuroimaging changes. Unlike many neurological disorders that have a characteristic abnormal central neurologic area(s) of abnormality pathognomonic to the disorder, a sufficient head impact may cause focal, multifocal, diffuse or combination of injury to the brain. This inconsistent presentation makes it difficult to establish or validate biological and imaging markers that could help improve diagnostic and prognostic accuracy in this patient population. The purpose of this manuscript is to describe both the challenges and opportunities when conducting military-relevant TBI research and introduce the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Military Brain Injury working group. ENIGMA is a worldwide consortium focused on improving replicability and analytical power through data sharing and collaboration. In this paper, we discuss challenges affecting efforts to aggregate data in this patient group. In addition, we highlight how "big data" approaches might be used to understand better the role that each of these variables might play in the imaging and functional phenotypes of TBI in Service member and Veteran populations, and how data may be used to examine important military specific issues such as return to duty, the late effects of combat-related injury, and alteration of the natural aging processes.
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Affiliation(s)
- David F Tate
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA.
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA.
| | - Emily L Dennis
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, Los Angeles, CA, USA
| | - John T Adams
- Western University of Health Sciences, Pomona, CA, USA
| | - Maheen M Adamson
- Defense and Veterans Brain Injury Center, VA Palo Alto, Palo Alto, CA, USA
- Neurosurgery, Stanford School of Medicine, Stanford, CA, USA
| | - Heather G Belanger
- United States Special Operations Command (USSOCOM), Tampa, FL, USA
- Department of Psychology, University of South Florida, Tampa, FL, USA
- Department of Psychiatry and Behavioral Neurosciences, University of South Florida, Tampa, FL, USA
- St Michaels Inc, Tampa, FL, USA
| | - Erin D Bigler
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Psychology, Brigham Young University, Provo, UT, USA
- Neuroscience Center, Brigham Young University, Provo, UT, USA
| | - Heather C Bouchard
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
| | - Alexandra L Clark
- VA San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Lisa M Delano-Wood
- VA San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla, CA, USA
| | - Seth G Disner
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, USA
- Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Blessen C Eapen
- Department of Physical Medicine and Rehabilitation, VA Greater Los Angeles Health Care System, Los Angeles, CA, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Carol E Franz
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Elbert Geuze
- University Medical Center Utrecht, Utrecht, Netherlands
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | - Naomi J Goodrich-Hunsaker
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA
- Department of Psychology, Brigham Young University, Provo, UT, USA
| | - Kihwan Han
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Jasmeet P Hayes
- Psychology Department, The Ohio State University, Columbus, OH, USA
- Chronic Brain Injury Program, The Ohio State University, Columbus, OH, USA
| | - Sidney R Hinds
- Department of Defense/United States Army Medical Research and Materiel Command, Fort Detrick, Frederick, MD, USA
- Department of Neurology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Cooper B Hodges
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA
- Department of Psychology, Brigham Young University, Provo, UT, USA
| | - Elizabeth S Hovenden
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrei Irimia
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Kimbra Kenney
- Department of Neurology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Inga K Koerte
- Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Boston, MA, USA
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany
| | - William S Kremen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Harvey S Levin
- H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Hannah M Lindsey
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA
- Department of Psychology, Brigham Young University, Provo, UT, USA
| | - Rajendra A Morey
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Mary R Newsome
- H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - John Ollinger
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Mary Jo Pugh
- Information Decision-Enhancement and Analytic Sciences Center, VA Salt Lake City, Salt Lake City, UT, USA
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Randall S Scheibel
- H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Martha E Shenton
- Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Boston, MA, USA
- Brockton Division, VA Boston Healthcare System, Brockton, MA, USA
| | - Danielle R Sullivan
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Brian A Taylor
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA, USA
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Maya Troyanskaya
- H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Carmen Velez
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Benjamin Sc Wade
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xin Wang
- Department of Psychiatry, University of Toledo, Toledo, OH, USA
| | - Ashley L Ware
- Department of Psychology, University of Calgary, Calgary, Alberta, Canada
| | - Ross Zafonte
- Department of Physical Medicine and Rehabilitation, Massachusetts General Hospital/Brigham & Women's Hospital, Boston, MA, USA
- Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, Los Angeles, CA, USA
- Department of Neurology, USC, Los Angeles, CA, USA
- Department of Pediatrics, USC, Los Angeles, CA, USA
- Department of Psychiatry, USC, Los Angeles, CA, USA
- Department of Radiology, USC, Los Angeles, CA, USA
- Department of Engineering, USC, Los Angeles, CA, USA
- Department of Ophthalmology, USC, Los Angeles, CA, USA
| | - Elisabeth A Wilde
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA
- H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, USA
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10
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Lange S. Peptidylarginine deiminases and extracellular vesicles: prospective drug targets and biomarkers in central nervous system diseases and repair. Neural Regen Res 2021; 16:934-938. [PMID: 33229732 PMCID: PMC8178795 DOI: 10.4103/1673-5374.297058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptidylarginine deiminases are a family of calcium-activated enzymes with multifaceted roles in physiological and pathological processes, including in the central nervous system. Peptidylarginine deiminases cause post-translational deimination/citrullination, leading to changes in structure and function of a wide range of target proteins. Deimination can facilitate protein moonlighting, modify protein-protein interaction, cause protein dysfunction and induce inflammatory responses. Peptidylarginine deiminases also regulate the biogenesis of extracellular vesicles, which play important roles in cellular communication through transfer of extracellular vesicle-cargo, e.g., proteins and genetic material. Both peptidylarginine deiminases and extracellular vesicles are linked to a number of pathologies, including in the central nervous system, and their modulation with pharmacological peptidylarginine deiminase inhibitors have shown great promise in several in vitro and in vivo central nervous system disease models. Furthermore, extracellular vesicles derived from mesenchymal stem cells have been assessed for their therapeutic application in central nervous system injury. As circulating extracellular vesicles can be used as non-invasive liquid biopsies, their specific cargo-signatures (including deiminated proteins and microRNAs) may allow for disease “fingerprinting” and aid early central nervous system disease diagnosis, inform disease progression and response to therapy. This mini-review discusses recent advances in the field of peptidylarginine deiminase and extracellular vesicle research in the central nervous system, focusing on several central nervous system acute injury, degeneration and cancer models.
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Affiliation(s)
- Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, UK
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11
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Arisan ED, Uysal-Onganer P, Lange S. Putative Roles for Peptidylarginine Deiminases in COVID-19. Int J Mol Sci 2020; 21:E4662. [PMID: 32629995 PMCID: PMC7370447 DOI: 10.3390/ijms21134662] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 02/06/2023] Open
Abstract
Peptidylarginine deiminases (PADs) are a family of calcium-regulated enzymes that are phylogenetically conserved and cause post-translational deimination/citrullination, contributing to protein moonlighting in health and disease. PADs are implicated in a range of inflammatory and autoimmune conditions, in the regulation of extracellular vesicle (EV) release, and their roles in infection and immunomodulation are known to some extent, including in viral infections. In the current study we describe putative roles for PADs in COVID-19, based on in silico analysis of BioProject transcriptome data (PRJNA615032 BioProject), including lung biopsies from healthy volunteers and SARS-CoV-2-infected patients, as well as SARS-CoV-2-infected, and mock human bronchial epithelial NHBE and adenocarcinoma alveolar basal epithelial A549 cell lines. In addition, BioProject Data PRJNA631753, analysing patients tissue biopsy data (n = 5), was utilised. We report a high individual variation observed for all PADI isozymes in the patients' tissue biopsies, including lung, in response to SARS-CoV-2 infection, while PADI2 and PADI4 mRNA showed most variability in lung tissue specifically. The other tissues assessed were heart, kidney, marrow, bowel, jejunum, skin and fat, which all varied with respect to mRNA levels for the different PADI isozymes. In vitro lung epithelial and adenocarcinoma alveolar cell models revealed that PADI1, PADI2 and PADI4 mRNA levels were elevated, but PADI3 and PADI6 mRNA levels were reduced in SARS-CoV-2-infected NHBE cells. In A549 cells, PADI2 mRNA was elevated, PADI3 and PADI6 mRNA was downregulated, and no effect was observed on the PADI4 or PADI6 mRNA levels in infected cells, compared with control mock cells. Our findings indicate a link between PADI expression changes, including modulation of PADI2 and PADI4, particularly in lung tissue, in response to SARS-CoV-2 infection. PADI isozyme 1-6 expression in other organ biopsies also reveals putative links to COVID-19 symptoms, including vascular, cardiac and cutaneous responses, kidney injury and stroke. KEGG and GO pathway analysis furthermore identified links between PADs and inflammatory pathways, in particular between PAD4 and viral infections, as well as identifying links for PADs with a range of comorbidities. The analysis presented here highlights roles for PADs in-host responses to SARS-CoV-2, and their potential as therapeutic targets in COVID-19.
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Affiliation(s)
- Elif Damla Arisan
- Gebze Technical University, Institute of Biotechnology, Gebze, 41400 Kocaeli, Turkey;
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
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12
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Fernández-Irigoyen J, Corrales F, Santamaría E. The Human Brain Proteome Project: Biological and Technological Challenges. Methods Mol Biol 2019; 2044:3-23. [PMID: 31432403 DOI: 10.1007/978-1-4939-9706-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Brain proteomics has become a method of choice that allows zooming-in where neuropathophysiological alterations are taking place, detecting protein mediators that might eventually be measured in cerebrospinal fluid (CSF) as potential neuropathologically derived biomarkers. Following this hypothesis, mass spectrometry-based neuroproteomics has emerged as a powerful approach to profile neural proteomes derived from brain structures and CSF in order to map the extensive protein catalog of the human brain. This chapter provides a historical perspective on the Human Brain Proteome Project (HBPP), some recommendation to the experimental design in neuroproteomic projects, and a brief description of relevant technological and computational innovations that are emerging in the neurobiology field thanks to the proteomics community. Importantly, this chapter highlights recent discoveries from the biology- and disease-oriented branch of the HBPP (B/D-HBPP) focused on spatiotemporal proteomic characterizations of mouse models of neurodegenerative diseases, elucidation of proteostatic networks in different types of dementia, the characterization of unresolved clinical phenotypes, and the discovery of novel biomarker candidates in CSF.
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Affiliation(s)
- Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory,, Proteored-ISCIII, CIBERehd, Madrid, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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Vuokila N, Lukasiuk K, Bot AM, van Vliet EA, Aronica E, Pitkänen A, Puhakka N. miR-124-3p is a chronic regulator of gene expression after brain injury. Cell Mol Life Sci 2018; 75:4557-4581. [PMID: 30155647 PMCID: PMC11105702 DOI: 10.1007/s00018-018-2911-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023]
Abstract
Traumatic brain injury (TBI) initiates molecular and cellular pathologies that underlie post-injury morbidities, including hippocampus-related memory decline and epileptogenesis. Non-coding small RNAs are master regulators of gene expression with the potential to affect multiple molecular pathways. To evaluate whether hippocampal gene expression networks are chronically regulated by microRNAs after TBI, we sampled the dentate gyrus of rats with severe TBI induced by lateral fluid-percussion injury 3 months earlier. Ingenuity pathway analysis revealed 30 upregulated miR-124-3p targets, suggesting that miR-124-3p is downregulated post-TBI (z-score = - 5.146, p < 0.05). Droplet digital polymerase chain reaction (ddPCR) and in situ hybridization confirmed the chronic downregulation of miR-124-3p (p < 0.05). Quantitative PCR analysis of two targets, Plp2 and Stat3, indicated that their upregulation correlated with the miR-124-3p downregulation (r = - 0.647, p < 0.05; r = - 0.629, p < 0.05, respectively). Immunohistochemical staining of STAT3 confirmed the increased protein expression. STRING analysis showed that 9 of the 30 miR-124-3p targets belonged to a STAT3 network. Reactome analysis and data mining connected the targets especially to inflammation and signal transduction. L1000CDS2 software revealed drugs (e.g., importazole, trichostatin A, and IKK-16) that could reverse the observed molecular changes. The translational value of our data was emphasized by in situ hybridization showing chronic post-traumatic downregulation of miR-124-3p in the dentate gyrus of TBI patients. Analysis of another brain injury model, status epilepticus, highlighted the fact that chronic downregulation of miR-124 is a common phenomenon after brain injury. Together, our findings indicate that miR-124-3p is a chronic modulator of molecular networks relevant to post-injury hippocampal pathologies in experimental models and in humans.
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Affiliation(s)
- Niina Vuokila
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland
| | - Katarzyna Lukasiuk
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Anna Maria Bot
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Erwin A van Vliet
- Department of (Neuro)pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Amsterdam, The Netherlands
| | - Asla Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland.
| | - Noora Puhakka
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland.
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Protein biomarkers of epileptogenicity after traumatic brain injury. Neurobiol Dis 2018; 123:59-68. [PMID: 30030023 DOI: 10.1016/j.nbd.2018.07.017] [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] [Received: 06/10/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 12/15/2022] Open
Abstract
Traumatic brain injury (TBI) is a major risk factor for acquired epilepsy. Post-traumatic epilepsy (PTE) develops over time in up to 50% of patients with severe TBI. PTE is mostly unresponsive to traditional anti-seizure treatments suggesting distinct, injury-induced pathomechanisms in the development of this condition. Moderate and severe TBIs cause significant tissue damage, bleeding, neuron and glia death, as well as axonal, vascular, and metabolic abnormalities. These changes trigger a complex biological response aimed at curtailing the physical damage and restoring homeostasis and functionality. Although a positive correlation exists between the type and severity of TBI and PTE, there is only an incomplete understanding of the time-dependent sequelae of TBI pathobiologies and their role in epileptogenesis. Determining the temporal profile of protein biomarkers in the blood (serum or plasma) and cerebrospinal fluid (CSF) can help to identify pathobiologies underlying the development of PTE, high-risk individuals, and disease modifying therapies. Here we review the pathobiological sequelae of TBI in the context of blood- and CSF-based protein biomarkers, their potential role in epileptogenesis, and discuss future directions aimed at improving the diagnosis and treatment of PTE.
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