1
|
Zhao G, Fu Y, Yang C, Yang X, Hu X. Identification and Validation of Endoplasmic Reticulum Stress-Related Gene in Traumatic Brain Injury. J Mol Neurosci 2024; 74:87. [PMID: 39264510 DOI: 10.1007/s12031-024-02265-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/01/2023] [Indexed: 09/13/2024]
Abstract
Endoplasmic reticulum stress (ERS) plays an essential role in the development of traumatic brain injury (TBI). We aimed to identify and validate the potential ERS-related genes of TBI through bioinformatics analysis and in vitro cell experiment. A total of 19 TBI and ERS-related genes were obtained from the GeneCards database and Comparative Toxicogenomics Database (CTD). Enrichment analysis primarily enriched in apoptosis. NFE2L2 was identified as a hub gene based on the protein-protein interactions (PPI) network that combined seven ranked methods included in cytoHubba. To further explore the effect of Nrf2, the protein encoded by NFE2L2, on ERS-induced apoptosis, we conducted cell experiments with tert-butylhydroquinone (tBHQ), the classical inducer of Nrf2. Western blot suggested tBHQ pretreatment could diminish ERS and reduce the protein expressions of apoptosis in the primary cultured neuron injury model. These data may establish some theoretical basis for the treatment of TBI and provide inspiration and innovative ideas for clinicians and pathologists to understand TBI comprehensively.
Collapse
Affiliation(s)
- Gengshui Zhao
- Department of Neurosurgery, The People's Hospital of Hengshui City, Hengshui, 053000, Hebei, China.
| | - Yongqi Fu
- Department of Endocrinology, The People's Hospital of Hengshui City, Hengshui, 053000, Hebei, China
| | - Chao Yang
- Department of Orthopedics, The People's Hospital of Hengshui City, Hengshui, 053000, Hebei, China
| | - Xuehui Yang
- Department of Neurosurgery, The People's Hospital of Hengshui City, Hengshui, 053000, Hebei, China
| | - Xiaoxiao Hu
- Department of Neurosurgery, The People's Hospital of Hengshui City, Hengshui, 053000, Hebei, China
| |
Collapse
|
2
|
Wang S, Xie Z, Jun T, Ma X, Zhang M, Rao F, Xu H, Lu J, Ding X, Li Z. Identification of potential crucial genes and therapeutic targets for epilepsy. Eur J Med Res 2024; 29:43. [PMID: 38212777 PMCID: PMC10782668 DOI: 10.1186/s40001-024-01643-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Epilepsy, a central neurological disorder, has a complex genetic architecture. There is some evidence suggesting that genetic factors play a role in both the occurrence of epilepsy and its treatment. However, the genetic determinants of epilepsy are largely unknown. This study aimed to identify potential therapeutic targets for epilepsy. METHODS Differentially expressed genes (DEGs) were extracted from the expression profiles of GSE44031 and GSE1834. Gene co-expression analysis was used to confirm the regulatory relationship between newly discovered epilepsy candidate genes and known epilepsy genes. Expression quantitative trait loci analysis was conducted to determine if epilepsy risk single-nucleotide polymorphisms regulate DEGs' expression in human brain tissue. Finally, protein-protein interaction analysis and drug-gene interaction analysis were performed to assess the role of DEGs in epilepsy treatment. RESULTS The study found that the protein tyrosine phosphatase receptor-type O gene (PTPRO) and the growth arrest and DNA damage inducible alpha gene (GADD45A) were significantly upregulated in epileptic rats compared to controls in both datasets. Gene co-expression analysis revealed that PTPRO was co-expressed with RBP4, NDN, PAK3, FOXG1, IDS, and IDS, and GADD45A was co-expressed with LRRK2 in human brain tissue. Expression quantitative trait loci analysis suggested that epilepsy risk single-nucleotide polymorphisms could be responsible for the altered PTPRO and GADD45A expression in human brain tissue. Moreover, the protein encoded by GADD45A had a direct interaction with approved antiepileptic drug targets, and GADD45A interacts with genistein and cisplatin. CONCLUSIONS The results of this study highlight PTPRO and GADD45A as potential genes for the diagnosis and treatment of epilepsy.
Collapse
Affiliation(s)
- Shitao Wang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China.
| | - Zhenrong Xie
- The Medical Biobank, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Tian Jun
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Xuelu Ma
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Mengen Zhang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Feng Rao
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Hui Xu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Jinghong Lu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Xiangqian Ding
- Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Zongyou Li
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| |
Collapse
|
3
|
Park J, Lee SH, Shin D, Kim Y, Kim YS, Seong MY, Lee JJ, Seo HG, Cho WS, Ro YS, Kim Y, Oh BM. Multiplexed Quantitative Proteomics Reveals Proteomic Alterations in Two Rodent Traumatic Brain Injury Models. J Proteome Res 2024; 23:249-263. [PMID: 38064581 DOI: 10.1021/acs.jproteome.3c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
In many cases of traumatic brain injury (TBI), conspicuous abnormalities, such as scalp wounds and intracranial hemorrhages, abate over time. However, many unnoticeable symptoms, including cognitive, emotional, and behavioral dysfunction, often last from several weeks to years after trauma, even for mild injuries. Moreover, the cause of such persistence of symptoms has not been examined extensively. Recent studies have implicated the dysregulation of the molecular system in the injured brain, necessitating an in-depth analysis of the proteome and signaling pathways that mediate the consequences of TBI. Thus, in this study, the brain proteomes of two TBI models were examined by quantitative proteomics during the recovery period to determine the molecular mechanisms of TBI. Our results show that the proteomes in both TBI models undergo distinct changes. A bioinformatics analysis demonstrated robust activation and inhibition of signaling pathways and core proteins that mediate biological processes after brain injury. These findings can help determine the molecular mechanisms that underlie the persistent effects of TBI and identify novel targets for drug interventions.
Collapse
Affiliation(s)
- Junho Park
- Department of Pharmacology, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Research Institute for Basic Medical Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Seung Hak Lee
- Department of Rehabilitation Medicine, Asan Medical Center, 88 Olympic-Ro 43-Gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Dongyoon Shin
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Yeongshin Kim
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Young Sik Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Min Yong Seong
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Jin Joo Lee
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Han Gil Seo
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Won-Sang Cho
- Department of Neurosurgery, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Young Sun Ro
- Department of Emergency Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Youngsoo Kim
- Proteomics Research Team, CHA Future Medicine Research Institute, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
- Department of Life Science, School of Medicine, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Byung-Mo Oh
- Department of Rehabilitation Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- Institute of Aging, Seoul National University College of Medicine, 71 Ihwajang-gil, Jongno-gu, Seoul 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
- National Traffic Injury Rehabilitation Hospital, 260 Jungang-ro, Yangpyeong-gun 12564, Gyeonggi-do, Republic of Korea
| |
Collapse
|
4
|
Kajevu N, Lipponen A, Andrade P, Bañuelos I, Puhakka N, Hämäläinen E, Natunen T, Hiltunen M, Pitkänen A. Treatment of Status Epilepticus after Traumatic Brain Injury Using an Antiseizure Drug Combined with a Tissue Recovery Enhancer Revealed by Systems Biology. Int J Mol Sci 2023; 24:14049. [PMID: 37762352 PMCID: PMC10531083 DOI: 10.3390/ijms241814049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
We tested a hypothesis that in silico-discovered compounds targeting traumatic brain injury (TBI)-induced transcriptomics dysregulations will mitigate TBI-induced molecular pathology and augment the effect of co-administered antiseizure treatment, thereby alleviating functional impairment. In silico bioinformatic analysis revealed five compounds substantially affecting TBI-induced transcriptomics regulation, including calpain inhibitor, chlorpromazine, geldanamycin, tranylcypromine, and trichostatin A (TSA). In vitro exposure of neuronal-BV2-microglial co-cultures to compounds revealed that TSA had the best overall neuroprotective, antioxidative, and anti-inflammatory effects. In vivo assessment in a rat TBI model revealed that TSA as a monotherapy (1 mg/kg/d) or in combination with the antiseizure drug levetiracetam (LEV 150 mg/kg/d) mildly mitigated the increase in plasma levels of the neurofilament subunit pNF-H and cortical lesion area. The percentage of rats with seizures during 0-72 h post-injury was reduced in the following order: TBI-vehicle 80%, TBI-TSA (1 mg/kg) 86%, TBI-LEV (54 mg/kg) 50%, TBI-LEV (150 mg/kg) 40% (p < 0.05 vs. TBI-vehicle), and TBI-LEV (150 mg/kg) combined with TSA (1 mg/kg) 30% (p < 0.05). Cumulative seizure duration was reduced in the following order: TBI-vehicle 727 ± 688 s, TBI-TSA 898 ± 937 s, TBI-LEV (54 mg/kg) 358 ± 715 s, TBI-LEV (150 mg/kg) 42 ± 64 (p < 0.05 vs. TBI-vehicle), and TBI-LEV (150 mg/kg) combined with TSA (1 mg/kg) 109 ± 282 s (p < 0.05). This first preclinical intervention study on post-TBI acute seizures shows that a combination therapy with the tissue recovery enhancer TSA and LEV was safe but exhibited no clear benefit over LEV monotherapy on antiseizure efficacy. A longer follow-up is needed to confirm the possible beneficial effects of LEV monotherapy and combination therapy with TSA on chronic post-TBI structural and functional outcomes, including epileptogenesis.
Collapse
Affiliation(s)
- Natallie Kajevu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Anssi Lipponen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, P.O. Box 95, 70701 Kuopio, Finland
| | - Pedro Andrade
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Ivette Bañuelos
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Noora Puhakka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Elina Hämäläinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| |
Collapse
|
5
|
Kruk PK, Nader K, Skupien-Jaroszek A, Wójtowicz T, Buszka A, Olech-Kochańczyk G, Wilczynski GM, Worch R, Kalita K, Włodarczyk J, Dzwonek J. Astrocytic CD44 Deficiency Reduces the Severity of Kainate-Induced Epilepsy. Cells 2023; 12:1483. [PMID: 37296604 PMCID: PMC10252631 DOI: 10.3390/cells12111483] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Epilepsy affects millions of people worldwide, yet we still lack a successful treatment for all epileptic patients. Most of the available drugs modulate neuronal activity. Astrocytes, the most abundant cells in the brain, may constitute alternative drug targets. A robust expansion of astrocytic cell bodies and processes occurs after seizures. Highly expressed in astrocytes, CD44 adhesion protein is upregulated during injury and is suggested to be one of the most important proteins associated with epilepsy. It connects the astrocytic cytoskeleton to hyaluronan in the extracellular matrix, influencing both structural and functional aspects of brain plasticity. METHODS Herein, we used transgenic mice with an astrocyte CD44 knockout to evaluate the impact of the hippocampal CD44 absence on the development of epileptogenesis and ultrastructural changes at the tripartite synapse. RESULTS We demonstrated that local, virally-induced CD44 deficiency in hippocampal astrocytes reduces reactive astrogliosis and decreases the progression of kainic acid-induced epileptogenesis. We also observed that CD44 deficiency resulted in structural changes evident in a higher dendritic spine number along with a lower percentage of astrocyte-synapse contacts, and decreased post-synaptic density size in the hippocampal molecular layer of the dentate gyrus. CONCLUSIONS Overall, our study indicates that CD44 signaling may be important for astrocytic coverage of synapses in the hippocampus and that alterations of astrocytes translate to functional changes in the pathology of epilepsy.
Collapse
Affiliation(s)
- Patrycja K. Kruk
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Karolina Nader
- Laboratory of Neurobiology, Nencki-EMBL Partnership for Neural Plasticity and Brain Disorders-Braincity, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Anna Skupien-Jaroszek
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Tomasz Wójtowicz
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Anna Buszka
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Gabriela Olech-Kochańczyk
- Laboratory of Molecular and Structural Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Grzegorz M. Wilczynski
- Laboratory of Molecular and Structural Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Remigiusz Worch
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Katarzyna Kalita
- Laboratory of Neurobiology, Nencki-EMBL Partnership for Neural Plasticity and Brain Disorders-Braincity, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Jakub Włodarczyk
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| | - Joanna Dzwonek
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St, 02-093 Warsaw, Poland
| |
Collapse
|
6
|
Lipponen A, Kajevu N, Natunen T, Ciszek R, Puhakka N, Hiltunen M, Pitkänen A. Gene Expression Profile as a Predictor of Seizure Liability. Int J Mol Sci 2023; 24:ijms24044116. [PMID: 36835526 PMCID: PMC9963992 DOI: 10.3390/ijms24044116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Analysis platforms to predict drug-induced seizure liability at an early phase of drug development would improve safety and reduce attrition and the high cost of drug development. We hypothesized that a drug-induced in vitro transcriptomics signature predicts its ictogenicity. We exposed rat cortical neuronal cultures to non-toxic concentrations of 34 compounds for 24 h; 11 were known to be ictogenic (tool compounds), 13 were associated with a high number of seizure-related adverse event reports in the clinical FDA Adverse Event Reporting System (FAERS) database and systematic literature search (FAERS-positive compounds), and 10 were known to be non-ictogenic (FAERS-negative compounds). The drug-induced gene expression profile was assessed from RNA-sequencing data. Transcriptomics profiles induced by the tool, FAERS-positive and FAERS-negative compounds, were compared using bioinformatics and machine learning. Of the 13 FAERS-positive compounds, 11 induced significant differential gene expression; 10 of the 11 showed an overall high similarity to the profile of at least one tool compound, correctly predicting the ictogenicity. Alikeness-% based on the number of the same differentially expressed genes correctly categorized 85%, the Gene Set Enrichment Analysis score correctly categorized 73%, and the machine-learning approach correctly categorized 91% of the FAERS-positive compounds with reported seizure liability currently in clinical use. Our data suggest that the drug-induced gene expression profile could be used as a predictive biomarker for seizure liability.
Collapse
Affiliation(s)
- Anssi Lipponen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, P.O. Box 95, FIN-70701 Kuopio, Finland
| | - Natallie Kajevu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Robert Ciszek
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Noora Puhakka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland
- Correspondence: ; Tel.: +358-50-517-2091; Fax: +358-17-16-3030
| |
Collapse
|
7
|
Xu XJ, Liu BY, Dong JQ, Ge QQ, Lu SH, Yang MS, Zhuang Y, Zhang B, Niu F. Tandem Mass Tag-based proteomics analysis reveals the vital role of inflammation in traumatic brain injury in a mouse model. Neural Regen Res 2023. [PMID: 35799536 PMCID: PMC9241417 DOI: 10.4103/1673-5374.343886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
8
|
Mahmoudi A, Heydari S, Markina YV, Barreto GE, Sahebkar A. Role of statins in regulating molecular pathways following traumatic brain injury: A system pharmacology study. Biomed Pharmacother 2022; 153:113304. [PMID: 35724514 DOI: 10.1016/j.biopha.2022.113304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/28/2022] Open
Abstract
Traumatic brain injury (TBI) is a serious disorder with debilitating physical and psychological complications. Previous studies have indicated that genetic factors have a critical role in modulating the secondary phase of injury in TBI. Statins have interesting pleiotropic properties such as antiapoptotic, antioxidative, and anti-inflammatory effects, which make them a suitable class of drugs for repurposing in TBI. In this study, we aimed to explore how statins modulate proteins and pathways involved in TBI using system pharmacology. We first explored the target associations with statins in two databases to discover critical clustering groups, candidate hub and critical hub genes in the network of TBI, and the possible connections of statins with TBI-related genes. Our results showed 1763 genes associated with TBI. Subsequently, the analysis of centralities in the PPI network displayed 55 candidate hub genes and 15 hub genes. Besides, MCODE analysis based on threshold score:10 determined four modular clusters. Intersection analysis of genes related to TBI and statins demonstrated 204 shared proteins, which suggested that statins influence 31 candidate hub and 9 hub genes. Moreover, statins had the highest interaction with MCODE1. The biological processes of the 31 shared proteins are related to gene expression, inflammation, antioxidant activity, and cell proliferation. Biological enriched pathways showed Programmed Cell Death proteins, AGE-RAGE signaling pathway, C-type lectin receptor signalling pathway, and MAPK signaling pathway as top clusters. In conclusion, statins could target several critical post-TBI genes mainly involved in inflammation and apoptosis, supporting the previous research results as a potential therapeutic agent.
Collapse
Affiliation(s)
- Ali Mahmoudi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9177899191, the Islamic Republic of Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Sahar Heydari
- Department of Physiology and Pharmacology, Faculty of Medicine, Sabzevar University of Medical Sciences, the Islamic Republic of Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Yuliya V Markina
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Avtsyn Research Institute of Human Morphology of FSBI "Petrovsky National Research Center of Surgery", 3 Tsyurupy Str., 117418, Moscow, the Russian Federation
| | - George E Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran.
| |
Collapse
|
9
|
Tang Q, Song M, Zhao R, Han X, Deng L, Xue H, Li W, Li G. Comprehensive RNA Expression Analysis Revealed Biological Functions of Key Gene Sets and Identified Disease-Associated Cell Types Involved in Rat Traumatic Brain Injury. J Clin Med 2022; 11:jcm11123437. [PMID: 35743506 PMCID: PMC9224987 DOI: 10.3390/jcm11123437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/06/2022] [Accepted: 06/11/2022] [Indexed: 12/29/2022] Open
Abstract
Traumatic brain injury (TBI) is a worldwide public health concern without major therapeutic breakthroughs over the past decades. Developing effective treatment options and improving the prognosis of TBI depends on a better understanding of the mechanisms underlying TBI. This study performed a comprehensive analysis of 15 RNA expression datasets of rat TBIs from the GEO database. By integrating the results from the various analyses, this study investigated the biological processes, pathways, and cell types associated with TBI and explored the activity of these cells during various TBI phases. The results showed the response to cytokine, inflammatory response, bacteria-associated response, metabolic and biosynthetic processes, and pathways of neurodegeneration to be involved in the pathogenesis of TBI. The cellular abundance of microglia, perivascular macrophages (PM), and neurons were found to differ after TBI and at different times postinjury. In conclusion, immune- and inflammation-related pathways, as well as pathways of neurodegeneration, are closely related to TBI. Microglia, PM, and neurons are thought to play roles in TBI with different activities that vary by phase of TBI.
Collapse
Affiliation(s)
- Qilin Tang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, China; (Q.T.); (R.Z.); (X.H.); (L.D.); (H.X.); (W.L.)
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, China
| | - Mengmeng Song
- Department of Nuclear Medicine, Qilu Hospital, Shandong University, Jinan 250012, China;
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, China; (Q.T.); (R.Z.); (X.H.); (L.D.); (H.X.); (W.L.)
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, China
| | - Xiao Han
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, China; (Q.T.); (R.Z.); (X.H.); (L.D.); (H.X.); (W.L.)
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, China
- Department of Neurosurgery, Children’s Hospital Affiliated to Shandong University, Jinan 250012, China
| | - Lin Deng
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, China; (Q.T.); (R.Z.); (X.H.); (L.D.); (H.X.); (W.L.)
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, China; (Q.T.); (R.Z.); (X.H.); (L.D.); (H.X.); (W.L.)
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, China
| | - Weiguo Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, China; (Q.T.); (R.Z.); (X.H.); (L.D.); (H.X.); (W.L.)
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, China; (Q.T.); (R.Z.); (X.H.); (L.D.); (H.X.); (W.L.)
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, China
- Correspondence:
| |
Collapse
|
10
|
Shin SS, Gottschalk AC, Mazandi VM, Kilbaugh TJ, Hefti MM. Transcriptional Profiling in a Novel Swine Model of Traumatic Brain Injury. Neurotrauma Rep 2022; 3:178-184. [PMID: 35558731 PMCID: PMC9081013 DOI: 10.1089/neur.2021.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Transcriptomic investigations of traumatic brain injury (TBI) can give us deep insights into the pathological and compensatory processes post-injury. Thus far, transcriptomic studies in TBI have mostly used microarrays and have focused on rodent models. However, a large animal model of TBI bears a much stronger resemblance to human TBI with regard to the anatomical details, mechanics of injury, genetics, and, possibly, molecular response. Because of the advantages of a large animal TBI model, we investigated the gene expression changes between injured and uninjured sides of pig cerebral cortex after TBI. Given acute inflammation that follows after TBI and the important role that immune response plays in neuroplasticity and recovery, we hypothesized that transcriptional changes involving immune function will be upregulated. Eight female 4-week-old piglets were injured on the right hemisphere with controlled cortical impact (CCI). At 5 days after TBI, pericontusional cortex tissues from the injured side and contralateral cortical tissues were collected. After RNA extraction, library preparation and sequencing as well as gene expression changes between the ipsi- and contralateral sides were compared. There were 6642 genes that were differentially expressed between the ipsi- and contralateral sides, and 1993 genes among them had at least 3-fold differences. Differentially expressed genes were enriched for biological processes related to immune system activation, regulation of immune response, and leukocyte activation. Many of the differentially expressed genes, such as CD4, CD86, IL1A, IL23R, and IL1R1, were major regulators of immune function. This study demonstrated some of the major transcriptional changes between the pericontusional and contralateral tissue at an acute time point after TBI in pigs.
Collapse
Affiliation(s)
- Samuel S. Shin
- Department of Neurology, Hospital of University of Pennsylvania, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amy C. Gottschalk
- College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Vanessa M. Mazandi
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Todd J. Kilbaugh
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marco M. Hefti
- Department of Pathology, University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
11
|
Luo W, Yang Z, Zhang W, Zhou D, Guo X, Wang S, He F, Wang Y. Quantitative Proteomics Reveals the Dynamic Pathophysiology Across Different Stages in a Rat Model of Severe Traumatic Brain Injury. Front Mol Neurosci 2022; 14:785938. [PMID: 35145378 PMCID: PMC8821658 DOI: 10.3389/fnmol.2021.785938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/30/2021] [Indexed: 11/30/2022] Open
Abstract
Background Severe traumatic brain injury (TBI) has become a global health problem and causes a vast worldwide societal burden. However, distinct mechanisms between acute and subacute stages have not been systemically revealed. The present study aimed to identify differentially expressed proteins in severe TBI from the acute to subacute phase. Methods Sixty Sprague Dawley (SD) rats were randomly divided into sham surgery and model groups. The severe TBI models were induced by the controlled cortical impact (CCI) method. We evaluated the neurological deficits through the modified neurological severity score (NSS). Meanwhile, H&E staining and immunofluorescence were performed to assess the injured brain tissues. The protein expressions of the hippocampus on the wounded side of CCI groups and the same side of Sham groups were analyzed by the tandem mass tag-based (TMT) quantitative proteomics on the third and fourteenth days. Then, using the gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and protein–protein interaction (PPI), the shared and stage-specific differentially expressed proteins (DEPs) were screened, analyzed, and visualized. Eventually, target proteins were further verified by Western blotting (WB). Results In the severe TBI, the neurological deficits always exist from the acute stage to the subacute stage, and brain parenchyma was dramatically impaired in either period. Of the significant DEPs identified, 312 were unique to the acute phase, 76 were specific to the subacute phase, and 63 were shared in both. Of the 375 DEPs between Sham-a and CCI-a, 240 and 135 proteins were up-regulated and down-regulated, respectively. Of 139 DEPs, 84 proteins were upregulated, and 55 were downregulated in the Sham-s and CCI-s. Bioinformatics analysis revealed that the differential pathophysiology across both stages. One of the most critical shared pathways is the complement and coagulation cascades. Notably, three pathways associated with gastric acid secretion, insulin secretion, and thyroid hormone synthesis were only enriched in the acute phase. Amyotrophic lateral sclerosis (ALS) was significantly enriched in the subacute stage. WB experiments confirmed the reliability of the TMT quantitative proteomics results. Conclusion Our findings highlight the same and different pathological processes in the acute and subacute phases of severe TBI at the proteomic level. The results of potential protein biomarkers might facilitate the design of novel strategies to treat TBI.
Collapse
Affiliation(s)
- Weikang Luo
- Department of Integrated Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaoyu Yang
- Department of Integrated Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhang
- The College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Dan Zhou
- Periodical Office, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaohang Guo
- Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Shunshun Wang
- Postpartum Health Care Department, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Feng He
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yang Wang
- Department of Integrated Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Yang Wang,
| |
Collapse
|
12
|
Transfer RNA-Derived Fragments and isomiRs Are Novel Components of Chronic TBI-Induced Neuropathology. Biomedicines 2022; 10:biomedicines10010136. [PMID: 35052815 PMCID: PMC8773447 DOI: 10.3390/biomedicines10010136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Neuroinflammation is a secondary injury mechanism that evolves in the brain for months after traumatic brain injury (TBI). We hypothesized that an altered small non-coding RNA (sncRNA) signature plays a key role in modulating post-TBI secondary injury and neuroinflammation. At 3threemonths post-TBI, messenger RNA sequencing (seq) and small RNAseq were performed on samples from the ipsilateral thalamus and perilesional cortex of selected rats with a chronic inflammatory endophenotype, and sham-operated controls. The small RNAseq identified dysregulation of 2 and 19 miRNAs in the thalamus and cortex, respectively. The two candidates from the thalamus and the top ten from the cortex were selected for validation. In the thalamus, miR-146a-5p and miR-155-5p levels were upregulated, and in the cortex, miR-375-3p and miR-211-5p levels were upregulated. Analysis of isomiRs of differentially expressed miRNAs identified 3′ nucleotide additions that were increased after TBI. Surprisingly, we found fragments originating from 16 and 13 tRNAs in the thalamus and cortex, respectively. We further analyzed two upregulated fragments, 3′tRF-IleAAT and 3′tRF-LysTTT. Increased expression of the full miR-146a profile, and 3′tRF-IleAAT and 3′tRF-LysTTT was associated with a worse behavioral outcome in animals with chronic neuroinflammation. Our results highlight the importance of understanding the regulatory roles of as-yet unknown sncRNAs for developing better strategies to treat TBI and neuroinflammation.
Collapse
|
13
|
TIAN Y, ZHAO R, LI X, ZHOU J, ZHAN D, WANG Y, HE Y, ZHANG J, YUAN H. Alterations of microRNAs expression profiles in small extracellular vesicle after traumatic brain injury in mice. Exp Anim 2022; 71:329-337. [PMID: 35249933 PMCID: PMC9388336 DOI: 10.1538/expanim.21-0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Traumatic brain injury (TBI) is one of the leading causes of mortality and morbidity worldwide. Tools available for diagnosis and therapy are limited. Small extracellular vesicle (sEV)
microRNAs (miRNAs) play an important role in TBI disease progression. This study aimed to investigate the alterations in sEV miRNAs expression in the mouse brain extracellular space after
TBI. Twenty-four C57BL/6J mice were randomly divided into two groups (12/group). The TBI group was subjected to all surgical procedures and fluid percussion injury (FPI). The sham group only
underwent surgery. Brain specimens were collected 3 h after TBI/sham. The brain sEV were isolated. Differentially expressed miRNAs were identified. A total of 50 miRNAs were observed to be
differentially expressed (fold change ≥1.5 and P<0.05) after TBI, including 5 upregulated and 45 downregulated. The major enriched Gene Ontology terms were metabolic
processes, cell, intracellular, organelle, cytoplasm, axon, binding, protein kinase activity, protein binding, and protein dimerization activity. The KEGG pathway analysis predicted that the
pathways affected by the variation of miRNAs in sEVs after TBI included the Wnt signaling pathway and NF-κB signaling pathway. The changes in five miRNAs were confirmed by qRT-PCR. In
conclusion, this study demonstrated the differential expression of a series of miRNAs in brain sEV after TBI, which might be correlated with post-TBI physiological and pathological
processes. The findings might also provide novel targets for further investigating the molecular mechanisms underlying TBI and potential therapeutic interventions.
Collapse
Affiliation(s)
- Ye TIAN
- Department of Neurosurgery, General Hospital, Tianjin Neurological Institute, Tianjin Medical University
| | - Ruiting ZHAO
- Department of Pharmacy, Tianjin Medical University General Hospital Airport Hospital
| | - Xiaochun LI
- Department of Pharmacy, General Hospital, Tianjin Medical University
| | - Ju ZHOU
- Department of Pharmacy, General Hospital, Tianjin Medical University
| | - Daqiang ZHAN
- Department of Pharmacy, General Hospital, Tianjin Medical University
| | - Yuanzhi WANG
- Department of Pharmacy, General Hospital, Tianjin Medical University
| | - Yifan HE
- Department of Pharmacy, General Hospital, Tianjin Medical University
| | - Jiacheng ZHANG
- Department of Pharmacy, General Hospital, Tianjin Medical University
| | - Hengjie YUAN
- Department of Neurosurgery, General Hospital, Tianjin Neurological Institute, Tianjin Medical University
| |
Collapse
|
14
|
van Alphen B, Stewart S, Iwanaszko M, Xu F, Li K, Rozenfeld S, Ramakrishnan A, Itoh TQ, Sisobhan S, Qin Z, Lear BC, Allada R. Glial immune-related pathways mediate effects of closed head traumatic brain injury on behavior and lethality in Drosophila. PLoS Biol 2022; 20:e3001456. [PMID: 35081110 PMCID: PMC8791498 DOI: 10.1371/journal.pbio.3001456] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/22/2021] [Indexed: 02/07/2023] Open
Abstract
In traumatic brain injury (TBI), the initial injury phase is followed by a secondary phase that contributes to neurodegeneration, yet the mechanisms leading to neuropathology in vivo remain to be elucidated. To address this question, we developed a Drosophila head-specific model for TBI termed Drosophila Closed Head Injury (dCHI), where well-controlled, nonpenetrating strikes are delivered to the head of unanesthetized flies. This assay recapitulates many TBI phenotypes, including increased mortality, impaired motor control, fragmented sleep, and increased neuronal cell death. TBI results in significant changes in the transcriptome, including up-regulation of genes encoding antimicrobial peptides (AMPs). To test the in vivo functional role of these changes, we examined TBI-dependent behavior and lethality in mutants of the master immune regulator NF-κB, important for AMP induction, and found that while sleep and motor function effects were reduced, lethality effects were enhanced. Similarly, loss of most AMP classes also renders flies susceptible to lethal TBI effects. These studies validate a new Drosophila TBI model and identify immune pathways as in vivo mediators of TBI effects.
Collapse
Affiliation(s)
- Bart van Alphen
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Samuel Stewart
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Marta Iwanaszko
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
- Department of Preventive Medicine—Biostatistics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Fangke Xu
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Keyin Li
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Sydney Rozenfeld
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Anujaianthi Ramakrishnan
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Taichi Q. Itoh
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Shiju Sisobhan
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Zuoheng Qin
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Bridget C. Lear
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston, Illinois, United States of America
| |
Collapse
|
15
|
Rivera AD, Pieropan F, Williams G, Calzolari F, Butt AM, Azim K. Drug connectivity mapping and functional analysis reveal therapeutic small molecules that differentially modulate myelination. Biomed Pharmacother 2022; 145:112436. [PMID: 34813998 PMCID: PMC8664715 DOI: 10.1016/j.biopha.2021.112436] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/29/2021] [Accepted: 11/12/2021] [Indexed: 12/30/2022] Open
Abstract
Disruption or loss of oligodendrocytes (OLs) and myelin has devastating effects on CNS function and integrity, which occur in diverse neurological disorders, including Multiple Sclerosis (MS), Alzheimer's disease and neuropsychiatric disorders. Hence, there is a need to develop new therapies that promote oligodendrocyte regeneration and myelin repair. A promising approach is drug repurposing, but most agents have potentially contrasting biological actions depending on the cellular context and their dose-dependent effects on intracellular pathways. Here, we have used a combined systems biology and neurobiological approach to identify compounds that exert positive and negative effects on oligodendroglia, depending on concentration. Notably, next generation pharmacogenomic analysis identified the PI3K/Akt modulator LY294002 as the most highly ranked small molecule with both pro- and anti-oligodendroglial concentration-dependent effects. We validated these in silico findings using multidisciplinary approaches to reveal a profoundly bipartite effect of LY294002 on the generation of OPCs and their differentiation into myelinating oligodendrocytes in both postnatal and adult contexts. Finally, we employed transcriptional profiling and signalling pathway activity assays to determine cell-specific mechanisms of action of LY294002 on oligodendrocytes and resolve optimal in vivo conditions required to promote myelin repair. These results demonstrate the power of multidisciplinary strategies in determining the therapeutic potential of small molecules in neurodegenerative disorders.
Collapse
Affiliation(s)
- A D Rivera
- Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, PO1 2DT Portsmouth, UK; Section of Human Anatomy, Department of Neuroscience, University of Padua, Padua, Italy.
| | - F Pieropan
- Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, PO1 2DT Portsmouth, UK
| | - G Williams
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London, UK
| | - F Calzolari
- Research Group Adult Neurogenesis & Cellular Reprogramming Institute of Physiological Chemistry, University Medical Center, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 19, 55128 Mainz, Germany
| | - A M Butt
- Institute of Biomedical and Biomolecular Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, PO1 2DT Portsmouth, UK
| | - K Azim
- Department of Neurology, Neuroregeneration, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
| |
Collapse
|
16
|
Catta-Preta R, Zdilar I, Jenner B, Doisy ET, Tercovich K, Nord AS, Gurkoff GG. Transcriptional Pathology Evolves over Time in Rat Hippocampus after Lateral Fluid Percussion Traumatic Brain Injury. Neurotrauma Rep 2021; 2:512-525. [PMID: 34909768 PMCID: PMC8667199 DOI: 10.1089/neur.2021.0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Traumatic brain injury (TBI) causes acute and lasting impacts on the brain, driving pathology along anatomical, cellular, and behavioral dimensions. Rodent models offer an opportunity to study the temporal progression of disease from injury to recovery. Transcriptomic and epigenomic analysis were applied to evaluate gene expression in ipsilateral hippocampus at 1 and 14 days after sham (n = 2 and 4, respectively per time point) and moderate lateral fluid percussion injury (n = 4 per time point). This enabled the identification of dynamic changes and differential gene expression (differentially expressed genes; DEGs) modules linked to underlying epigenetic response. We observed acute signatures associated with cell death, astrocytosis, and neurotransmission that largely recovered by 2 weeks. Inflammation and immune signatures segregated into upregulated modules with distinct expression trajectories and functions. Whereas most down-regulated genes recovered by 14 days, two modules with delayed and persistent changes were associated with cholesterol metabolism, amyloid beta clearance, and neurodegeneration. Differential expression was paralleled by changes in histone H3 lysine residue 4 trimethylation at the promoters of DEGs at 1 day post-TBI, with the strongest changes observed for inflammation and immune response genes. These results demonstrate how integrated genomics analysis in the pre-clinical setting has the potential to identify stage-specific biomarkers for injury and/or recovery. Though limited in scope here, our general strategy has the potential to capture pathological signatures over time and evaluate treatment efficacy at the systems level.
Collapse
Affiliation(s)
- Rinaldo Catta-Preta
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Iva Zdilar
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Bradley Jenner
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Emily T. Doisy
- Department of Neurological Surgery, University of California Davis, Davis, California, USA
| | - Kayleen Tercovich
- Department of Neurological Surgery, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Alex S. Nord
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| | - Gene G. Gurkoff
- Department of Neurological Surgery, University of California Davis, Davis, California, USA
- Center for Neuroscience, University of California Davis, Davis, California, USA
| |
Collapse
|
17
|
Raikwar SP, Thangavel R, Ahmed ME, Selvakumar GP, Kempuraj D, Wu K, Khan O, Bazley K, Bussinger B, Kukulka K, Zaheer S, Iyer SS, Govindarajan R, Burton C, James D, Zaheer A. Real-Time Noninvasive Bioluminescence, Ultrasound and Photoacoustic Imaging in NFκB-RE-Luc Transgenic Mice Reveal Glia Maturation Factor-Mediated Immediate and Sustained Spatio-Temporal Activation of NFκB Signaling Post-Traumatic Brain Injury in a Gender-Specific Manner. Cell Mol Neurobiol 2021; 41:1687-1706. [PMID: 32785863 PMCID: PMC8188847 DOI: 10.1007/s10571-020-00937-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022]
Abstract
Neurotrauma especially traumatic brain injury (TBI) is the leading cause of death and disability worldwide. To improve upon the early diagnosis and develop precision-targeted therapies for TBI, it is critical to understand the underlying molecular mechanisms and signaling pathways. The transcription factor, nuclear factor kappa B (NFκB), which is ubiquitously expressed, plays a crucial role in the normal cell survival, proliferation, differentiation, function, as well as in disease states like neuroinflammation and neurodegeneration. Here, we hypothesized that real-time noninvasive bioluminescence molecular imaging allows rapid and precise monitoring of TBI-induced immediate and rapid spatio-temporal activation of NFκB signaling pathway in response to Glia maturation factor (GMF) upregulation which in turn leads to neuroinflammation and neurodegeneration post-TBI. To test and validate our hypothesis and to gain novel mechanistic insights, we subjected NFκB-RE-Luc transgenic male and female mice to TBI and performed real-time noninvasive bioluminescence imaging (BLI) as well as photoacoustic and ultrasound imaging (PAI). Our BLI data revealed that TBI leads to an immediate and sustained activation of NFκB signaling. Further, our BLI data suggest that especially in male NFκB-RE-Luc transgenic mice subjected to TBI, in addition to brain, there is widespread activation of NFκB signaling in multiple organs. However, in the case of the female NFκB-RE-Luc transgenic mice, TBI induces a very specific and localized activation of NFκB signaling in the brain. Further, our microRNA data suggest that TBI induces significant upregulation of mir-9-5p, mir-21a-5p, mir-34a-5p, mir-16-3p, as well as mir-155-5p within 24 h and these microRNAs can be successfully used as TBI-specific biomarkers. To the best of our knowledge, this is one of the first and unique study of its kind to report immediate and sustained activation of NFκB signaling post-TBI in a gender-specific manner by utilizing real-time non-invasive BLI and PAI in NFκB-RE-Luc transgenic mice. Our study will prove immensely beneficial to gain novel mechanistic insights underlying TBI, unravel novel therapeutic targets, as well as enable us to monitor in real-time the response to innovative TBI-specific precision-targeted gene and stem cell-based precision medicine.
Collapse
Affiliation(s)
- Sudhanshu P Raikwar
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA.
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA.
| | - Ramasamy Thangavel
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Mohammad Ejaz Ahmed
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Govindhasamy Pushpavathi Selvakumar
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Duraisamy Kempuraj
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Kristopher Wu
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Osaid Khan
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Kieran Bazley
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Bret Bussinger
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Klaudia Kukulka
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Smita Zaheer
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Shankar S Iyer
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Raghav Govindarajan
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA
| | | | | | - Asgar Zaheer
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Center for Translational Neuroscience, School of Medicine, University of Missouri, Columbia, MO, USA.
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA.
| |
Collapse
|
18
|
Hiltunen J, Ndode-Ekane XE, Lipponen A, Drexel M, Sperk G, Puhakka N, Pitkänen A. Regulation of Parvalbumin Interactome in the Perilesional Cortex after Experimental Traumatic Brain Injury. Neuroscience 2021; 475:52-72. [PMID: 34455012 DOI: 10.1016/j.neuroscience.2021.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Traumatic brain injury (TBI) causes 10-20% of structural epilepsy, with seizures typically originating in the cortex. Alterations in the neuronal microcircuits in the cortical epileptogenic zone, however, are poorly understood. Here, we assessed TBI-induced changes in perisomatic gamma aminobutyric acid (GABA)-ergic innervation in the perilesional cortex. We hypothesized that TBI will damage parvalbumin (PV)-immunoreactive inhibitory neurons and induce regulation of the associated GABAergic molecular interactome. TBI was induced in adult male Sprague-Dawley rats by lateral fluid-percussion injury. At 1-month post-TBI, the number of PV-positive somata was plotted on unfolded cortical maps and the distribution and density of immunopositive terminals analyzed. Qualitative analysis revealed either patchy microlesions of several hundred micrometers in diameter or diffuse neuronal loss. Quantitative analysis demonstrated a reduction in the number of PV-positive interneurons in patches down to 0% of that in sham-operated controls in the perilesional cortex. In the majority of patches, the cell numbers ranged from 71% to 90% that of the controls. The loss of PV-positive somata was accompanied by decreased axonal labeling. In situ hybridization revealed downregulated PV mRNA expression in the perilesional cortex. Gene Set Enrichment Analysis indicated a robustly downregulated expression profile of PV-related genes, which was confirmed by quantitative reverse transcriptase polymerase chain reaction. Specifically, we found that genes encoding postsynaptic GABA-A receptor genes, Gabrg2 and Gabrd, were downregulated in TBI animals compared with controls. Our data suggests that patchy reduction in PV-positive perisomatic inhibitory innervation contributes to the development of focal cortical inhibitory deficit after TBI.
Collapse
Affiliation(s)
- Johanna Hiltunen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Xavier Ekolle Ndode-Ekane
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Anssi Lipponen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Meinrad Drexel
- Institute of Molecular and Cellular Pharmacology, Medical University Innsbruck, Peter-Mayr-Str. 1, 6020 Innsbruck, Austria
| | - Günther Sperk
- Department of Pharmacology, Medical University Innsbruck, Peter-Mayr-Str. 1a, 6020 Innsbruck, Austria
| | - Noora Puhakka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211 Kuopio, Finland.
| |
Collapse
|
19
|
Application of Thermodynamics and Protein–Protein Interaction Network Topology for Discovery of Potential New Treatments for Temporal Lobe Epilepsy. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11178059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this paper, we propose a bioinformatics-based method, which introduces thermodynamic measures and topological characteristics aimed to identify potential drug targets for pharmaco-resistant epileptic patients. We apply the Gibbs homology analysis to the protein–protein interaction network characteristic of temporal lobe epilepsy. With the identification of key proteins involved in the disease, particularly a number of ribosomal proteins, an assessment of their inhibitors is the next logical step. The results of our work offer a direction for future development of prospective therapeutic solutions for epilepsy patients, especially those who are not responding to the current standard of care.
Collapse
|
20
|
Inampudi C, Ciccotosto GD, Cappai R, Crack PJ. Genetic Modulators of Traumatic Brain Injury in Animal Models and the Impact of Sex-Dependent Effects. J Neurotrauma 2021; 37:706-723. [PMID: 32027210 DOI: 10.1089/neu.2019.6955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Traumatic brain injury (TBI) is a major health problem causing disability and death worldwide. There is no effective treatment, due in part to the complexity of the injury pathology and factors affecting its outcome. The extent of brain injury depends on the type of insult, age, sex, lifestyle, genetic risk factors, socioeconomic status, other co-injuries, and underlying health problems. This review discusses the genes that have been directly tested in TBI models, and whether their effects are known to be sex-dependent. Sex differences can affect the incidence, symptom onset, pathology, and clinical outcomes following injury. Adult males are more susceptible at the acute phase and females show greater injury in the chronic phase. TBI is not restricted to a single sex; despite variations in the degree of symptom onset and severity, it is important to consider both female and male animals in TBI pre-clinical research studies.
Collapse
Affiliation(s)
- Chaitanya Inampudi
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia
| | - Giuseppe D Ciccotosto
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia
| | - Roberto Cappai
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia
| | - Peter J Crack
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
21
|
S100A4 in the Physiology and Pathology of the Central and Peripheral Nervous System. Cells 2021; 10:cells10040798. [PMID: 33918416 PMCID: PMC8066633 DOI: 10.3390/cells10040798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/27/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
S100A4 is a member of the large family of S100 proteins, exerting a broad range of intracellular and extracellular functions that vary upon different cellular contexts. While S100A4 has long been implicated mainly in tumorigenesis and metastatization, mounting evidence shows that S100A4 is a key player in promoting pro-inflammatory phenotypes and organ pro-fibrotic pathways in the liver, kidney, lung, heart, tendons, and synovial tissues. Regarding the nervous system, there is still limited information concerning S100A4 presence and function. It was observed that S100A4 exerts physiological roles contributing to neurogenesis, cellular motility and chemotaxis, cell differentiation, and cell-to cell communication. Furthermore, S100A4 is likely to participate to numerous pathological processes of the nervous system by affecting the functions of astrocytes, microglia, infiltrating cells and neurons and thereby modulating inflammation and immune reactions, fibrosis as well as neuronal plasticity and survival. This review summarizes the current state of knowledge concerning the localization, deregulation, and possible functions of S100A4 in the physiology of the central and peripheral nervous system. Furthermore, we highlight S100A4 as a gene involved in the pathogenesis of neurological disorders such as brain tumors, neurodegenerative diseases, and acute injuries.
Collapse
|
22
|
"Omics" in traumatic brain injury: novel approaches to a complex disease. Acta Neurochir (Wien) 2021; 163:2581-2594. [PMID: 34273044 PMCID: PMC8357753 DOI: 10.1007/s00701-021-04928-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/23/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND To date, there is neither any pharmacological treatment with efficacy in traumatic brain injury (TBI) nor any method to halt the disease progress. This is due to an incomplete understanding of the vast complexity of the biological cascades and failure to appreciate the diversity of secondary injury mechanisms in TBI. In recent years, techniques for high-throughput characterization and quantification of biological molecules that include genomics, proteomics, and metabolomics have evolved and referred to as omics. METHODS In this narrative review, we highlight how omics technology can be applied to potentiate diagnostics and prognostication as well as to advance our understanding of injury mechanisms in TBI. RESULTS The omics platforms provide possibilities to study function, dynamics, and alterations of molecular pathways of normal and TBI disease states. Through advanced bioinformatics, large datasets of molecular information from small biological samples can be analyzed in detail and provide valuable knowledge of pathophysiological mechanisms, to include in prognostic modeling when connected to clinically relevant data. In such a complex disease as TBI, omics enables broad categories of studies from gene compositions associated with susceptibility to secondary injury or poor outcome, to potential alterations in metabolites following TBI. CONCLUSION The field of omics in TBI research is rapidly evolving. The recent data and novel methods reviewed herein may form the basis for improved precision medicine approaches, development of pharmacological approaches, and individualization of therapeutic efforts by implementing mathematical "big data" predictive modeling in the near future.
Collapse
|
23
|
Wu Y, Wu H, Guo X, Pluimer B, Zhao Z. Blood-Brain Barrier Dysfunction in Mild Traumatic Brain Injury: Evidence From Preclinical Murine Models. Front Physiol 2020; 11:1030. [PMID: 32973558 PMCID: PMC7472692 DOI: 10.3389/fphys.2020.01030] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
Mild traumatic brain injury (mTBI) represents more than 80% of total TBI cases and is a robust environmental risk factor for neurodegenerative diseases including Alzheimer’s disease (AD). Besides direct neuronal injury and neuroinflammation, blood–brain barrier (BBB) dysfunction is also a hallmark event of the pathological cascades after mTBI. However, the vascular link between BBB impairment caused by mTBI and subsequent neurodegeneration remains undefined. In this review, we focus on the preclinical evidence from murine models of BBB dysfunction in mTBI and provide potential mechanistic links between BBB disruption and the development of neurodegenerative diseases.
Collapse
Affiliation(s)
- Yingxi Wu
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Haijian Wu
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinying Guo
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Brock Pluimer
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Neuroscience Graduate Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Zhen Zhao
- Center for Neurodegeneration and Regeneration, Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Neuroscience Graduate Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
24
|
Diverse Roles for Hyaluronan and Hyaluronan Receptors in the Developing and Adult Nervous System. Int J Mol Sci 2020; 21:ijms21175988. [PMID: 32825309 PMCID: PMC7504301 DOI: 10.3390/ijms21175988] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 02/07/2023] Open
Abstract
Hyaluronic acid (HA) plays a vital role in the extracellular matrix of neural tissues. Originally thought to hydrate tissues and provide mechanical support, it is now clear that HA is also a complex signaling molecule that can regulate cell processes in the developing and adult nervous systems. Signaling properties are determined by molecular weight, bound proteins, and signal transduction through specific receptors. HA signaling regulates processes such as proliferation, differentiation, migration, and process extension in a variety of cell types including neural stem cells, neurons, astrocytes, microglia, and oligodendrocyte progenitors. The synthesis and catabolism of HA and the expression of HA receptors are altered in disease and influence neuroinflammation and disease pathogenesis. This review discusses the roles of HA, its synthesis and breakdown, as well as receptor expression in neurodevelopment, nervous system function and disease.
Collapse
|
25
|
Shah EJ, Gurdziel K, Ruden DM. Drosophila Exhibit Divergent Sex-Based Responses in Transcription and Motor Function After Traumatic Brain Injury. Front Neurol 2020; 11:511. [PMID: 32636795 PMCID: PMC7316956 DOI: 10.3389/fneur.2020.00511] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/08/2020] [Indexed: 12/31/2022] Open
Abstract
Every year, millions of people in the US suffer brain damage from mild to severe traumatic brain injuries (TBI) that result from a sudden impact to the head. Despite TBI being a leading cause of death and disability worldwide, sex differences that contribute to varied outcomes post-injury are not extensively studied and therefore, poorly understood. In this study, we aimed to explore biological sex as a variable influencing response to TBI using Drosophila melanogaster as a model, since flies have been shown to exhibit symptoms commonly seen in other mammalian models of TBI. After inflicting TBI using the high-impact trauma device, we isolated w1118 fly brains and assessed gene transcription changes in male and female flies at control and 1, 2, and 4 hr after TBI. Our results suggest that overall, Drosophila females show more gene transcript changes than males. Females also exhibit upregulated expression changes in immune response and mitochondrial genes across all time-points. In addition, we looked at the impact of injury on mitochondrial health and motor function in both sexes before and after injury. Although both sexes report similar changes in mitochondrial oxidation and negative geotaxis, locomotor activity appears to be more impaired in males than females. These data suggest that sex-differences not only influence the response to TBI but also contribute to varied outcomes post-injury.
Collapse
Affiliation(s)
- Ekta J Shah
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Katherine Gurdziel
- Office of the Vice President for Research, Wayne State University, Detroit, MI, United States
| | - Douglas M Ruden
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States.,Office of the Vice President for Research, Wayne State University, Detroit, MI, United States.,Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States
| |
Collapse
|
26
|
Abstract
Translational genomics represents a broad field of study that combines genome and transcriptome-wide studies in humans and model systems to refine our understanding of human biology and ultimately identify new ways to treat and prevent disease. The approaches to translational genomics can be broadly grouped into two methodologies, forward and reverse genomic translation. Traditional (forward) genomic translation begins with model systems and aims at using unbiased genetic associations in these models to derive insight into biological mechanisms that may also be relevant in human disease. Reverse genomic translation begins with observations made through human genomic studies and refines these observations through follow-up studies using model systems. The ultimate goal of these approaches is to clarify intervenable processes as targets for therapeutic development. In this review, we describe some of the approaches being taken to apply translational genomics to the study of diseases commonly encountered in the neurocritical care setting, including hemorrhagic and ischemic stroke, traumatic brain injury, subarachnoid hemorrhage, and status epilepticus, utilizing both forward and reverse genomic translational techniques. Further, we highlight approaches in the field that could be applied in neurocritical care to improve our ability to identify new treatment modalities as well as to provide important information to patients about risk and prognosis.
Collapse
Affiliation(s)
- Pavlos Myserlis
- Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Farid Radmanesh
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher D Anderson
- Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge Street, CPZN 6818, Boston, MA, 02114, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Henry and Allison McCance Center for Brain Health, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
27
|
Vuokila N, Aronica E, Korotkov A, van Vliet EA, Nuzhat S, Puhakka N, Pitkänen A. Chronic Regulation of miR-124-3p in the Perilesional Cortex after Experimental and Human TBI. Int J Mol Sci 2020; 21:ijms21072418. [PMID: 32244461 PMCID: PMC7177327 DOI: 10.3390/ijms21072418] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injury (TBI) dysregulates microRNAs, which are the master regulators of gene expression. Here we investigated the changes in a brain-enriched miR-124-3p, which is known to associate with major post-injury pathologies, such as neuroinflammation. RT-qPCR of the rat tissue sampled at 7 d and 3 months in the perilesional cortex adjacent to the necrotic lesion core (aPeCx) revealed downregulation of miR-124-3p at 7 d (fold-change (FC) 0.13, p < 0.05 compared with control) and 3 months (FC 0.40, p < 0.05) post-TBI. In situ hybridization confirmed the downregulation of miR-124-3p at 7 d and 3 months post-TBI in the aPeCx (both p < 0.01). RT-qPCR confirmed the upregulation of the miR-124-3p target Stat3 in the aPeCx at 7 d post-TBI (7-fold, p < 0.05). mRNA-Seq revealed 312 downregulated and 311 upregulated miR-124 targets (p < 0.05). To investigate whether experimental findings translated to humans, we performed in situ hybridization of miR-124-3p in temporal lobe autopsy samples of TBI patients. Our data revealed downregulation of miR-124-3p in individual neurons of cortical layer III. These findings indicate a persistent downregulation of miR-124-3p in the perilesional cortex that might contribute to post-injury neurodegeneration and inflammation.
Collapse
Affiliation(s)
- Niina Vuokila
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; (N.V.); (S.N.); (A.P.)
| | - Eleonora Aronica
- Department of (Neuro)pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (E.A.); (A.K.); (E.A.v.V.)
- Stichting Epilepsie Instellingen Nederland (SEIN), 0397 Heemstede, The Netherlands
| | - Anatoly Korotkov
- Department of (Neuro)pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (E.A.); (A.K.); (E.A.v.V.)
| | - Erwin Alexander van Vliet
- Department of (Neuro)pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (E.A.); (A.K.); (E.A.v.V.)
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Science Park 904, P.O. Box 94246, 1090 GE Amsterdam, The Netherlands
| | - Salma Nuzhat
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; (N.V.); (S.N.); (A.P.)
| | - Noora Puhakka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; (N.V.); (S.N.); (A.P.)
- Correspondence: ; Tel.: +358-40-861-4939
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; (N.V.); (S.N.); (A.P.)
| |
Collapse
|
28
|
Dynamics of clusterin protein expression in the brain and plasma following experimental traumatic brain injury. Sci Rep 2019; 9:20208. [PMID: 31882899 PMCID: PMC6934775 DOI: 10.1038/s41598-019-56683-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022] Open
Abstract
Progress in the preclinical and clinical development of neuroprotective and antiepileptogenic treatments for traumatic brain injury (TBI) necessitates the discovery of prognostic biomarkers for post-injury outcome. Our previous mRNA-seq data revealed a 1.8–2.5 fold increase in clusterin mRNA expression in lesioned brain areas in rats with lateral fluid-percussion injury (FPI)-induced TBI. On this basis, we hypothesized that TBI leads to increases in the brain levels of clusterin protein, and consequently, increased plasma clusterin levels. For evaluation, we induced TBI in adult male Sprague-Dawley rats (n = 80) by lateral FPI. We validated our mRNA-seq findings with RT-qPCR, confirming increased clusterin mRNA levels in the perilesional cortex (FC 3.3, p < 0.01) and ipsilateral thalamus (FC 2.4, p < 0.05) at 3 months post-TBI. Immunohistochemistry revealed a marked increase in extracellular clusterin protein expression in the perilesional cortex and ipsilateral hippocampus (7d to 1 month post-TBI), and ipsilateral thalamus (14d to 12 months post-TBI). In the thalamus, punctate immunoreactivity was most intense around activated microglia and mitochondria. Enzyme-linked immunoassays indicated that an acute 15% reduction, rather than an increase in plasma clusterin levels differentiated animals with TBI from sham-operated controls (AUC 0.851, p < 0.05). Our findings suggest that plasma clusterin is a candidate biomarker for acute TBI diagnosis.
Collapse
|
29
|
Zhao J, Xu C, Cao H, Zhang L, Wang X, Chen S. Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats. PeerJ 2019; 7:e8324. [PMID: 31875163 PMCID: PMC6925952 DOI: 10.7717/peerj.8324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/01/2019] [Indexed: 01/01/2023] Open
Abstract
Background Traumatic brain injury (TBI) is a common neurological emergency observed in hospitals. A considerable number of patients suffer from long-term disabilities after TBI. This study aimed to identify altered gene expression signatures and mechanisms related to TBI-induced chronic neuroinflammation and neurodegeneration. Methods An integrated analysis was performed using published RNA-sequencing studies to determine TBI-induced differentially expressed genes (DEGs). Based on the DEG data, functional annotation, signal-net, and transcription factor analyses were conducted to understand the mechanism of chronic neuroinflammation and neurodegeneration induced after TBI. Results Two datasets were obtained using the Gene Expression Omnibus database, of which, 6,513 DEGs were identified (6,464 upregulated and 49 downregulated). Positive regulation of biological process, positive regulation of cellular process, nucleus, and heterocyclic compound binding were Gene Ontology terms significantly enriched in post-TBI rat models. Leukocyte transendothelial migration, chemokine signaling pathway, neurotrophin signaling pathway, and longevity-regulating pathway were significantly enriched after TBI. With regard to the signal-net analysis, FOXO3, DGKZ and ILK were considered the most critical genes derived using high–betweenness centrality calculation. A total of 44 TFs, including FOXO1, SRY and KLF4, were predicted to play an important role in the upregulation of gene expression. Using integrated bioinformatics analysis, TBI was found to be associated with a significant inflammatory response and neurodegeneration. FOXO3, apolipoprotein (APOE), microtubule-associated protein tau (MAPT), and TREM2 were probably associated with the TBI pathological process. The mitochondrial electron transport chain may be associated with neurodegeneration in patients with TBI, serving as a potential therapeutic target.
Collapse
Affiliation(s)
- Jianwei Zhao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chen Xu
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Heli Cao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lin Zhang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xuyang Wang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shiwen Chen
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| |
Collapse
|
30
|
Lipponen A, Natunen T, Hujo M, Ciszek R, Hämäläinen E, Tohka J, Hiltunen M, Paananen J, Poulsen D, Kansanen E, Ekolle Ndode-Ekane X, Levonen AL, Pitkänen A. In Vitro and In Vivo Pipeline for Validation of Disease-Modifying Effects of Systems Biology-Derived Network Treatments for Traumatic Brain Injury-Lessons Learned. Int J Mol Sci 2019; 20:ijms20215395. [PMID: 31671916 PMCID: PMC6861918 DOI: 10.3390/ijms20215395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/19/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
Abstract
We developed a pipeline for the discovery of transcriptomics-derived disease-modifying therapies and used it to validate treatments in vitro and in vivo that could be repurposed for TBI treatment. Desmethylclomipramine, ionomycin, sirolimus and trimipramine, identified by in silico LINCS analysis as candidate treatments modulating the TBI-induced transcriptomics networks, were tested in neuron-BV2 microglial co-cultures, using tumour necrosis factor α as a monitoring biomarker for neuroinflammation, nitrite for nitric oxide-mediated neurotoxicity and microtubule associated protein 2-based immunostaining for neuronal survival. Based on (a) therapeutic time window in silico, (b) blood-brain barrier penetration and water solubility, (c) anti-inflammatory and neuroprotective effects in vitro (p < 0.05) and (d) target engagement of Nrf2 target genes (p < 0.05), desmethylclomipramine was validated in a lateral fluid-percussion model of TBI in rats. Despite the favourable in silico and in vitro outcomes, in vivo assessment of clomipramine, which metabolizes to desmethylclomipramine, failed to demonstrate favourable effects on motor and memory tests. In fact, clomipramine treatment worsened the composite neuroscore (p < 0.05). Weight loss (p < 0.05) and prolonged upregulation of plasma cytokines (p < 0.05) may have contributed to the worsened somatomotor outcome. Our pipeline provides a rational stepwise procedure for evaluating favourable and unfavourable effects of systems-biology discovered compounds that modulate post-TBI transcriptomics.
Collapse
Affiliation(s)
- Anssi Lipponen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Mika Hujo
- School of Computing, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Robert Ciszek
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Elina Hämäläinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Jussi Tohka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
- Bioinformatics Center, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - David Poulsen
- Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, 875 Ellicott St, 6071 CTRC, Buffalo, NY 14203, USA.
| | - Emilia Kansanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Xavier Ekolle Ndode-Ekane
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Anna-Liisa Levonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| |
Collapse
|
31
|
Saadipour K, Tiberi A, Lombardo S, Grajales E, Montroull L, Mañucat-Tan NB, LaFrancois J, Cammer M, Mathews PM, Scharfman HE, Liao FF, Friedman WJ, Zhou XF, Tesco G, Chao MV. Regulation of BACE1 expression after injury is linked to the p75 neurotrophin receptor. Mol Cell Neurosci 2019; 99:103395. [PMID: 31422108 DOI: 10.1016/j.mcn.2019.103395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/24/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
BACE1 is a transmembrane aspartic protease that cleaves various substrates and it is required for normal brain function. BACE1 expression is high during early development, but it is reduced in adulthood. Under conditions of stress and injury, BACE1 levels are increased; however, the underlying mechanisms that drive BACE1 elevation are not well understood. One mechanism associated with brain injury is the activation of injurious p75 neurotrophin receptor (p75), which can trigger pathological signals. Here we report that within 72 h after controlled cortical impact (CCI) or laser injury, BACE1 and p75 are increased and tightly co-expressed in cortical neurons of mouse brain. Additionally, BACE1 is not up-regulated in p75 null mice in response to focal cortical injury, while p75 over-expression results in BACE1 augmentation in HEK-293 and SY5Y cell lines. A luciferase assay conducted in SY5Y cell line revealed that BACE1 expression is regulated at the transcriptional level in response to p75 transfection. Interestingly, this effect does not appear to be dependent upon p75 ligands including mature and pro-neurotrophins. In addition, BACE1 activity on amyloid precursor protein (APP) is enhanced in SY5Y-APP cells transfected with a p75 construct. Lastly, we found that the activation of c-jun n-terminal kinase (JNK) by p75 contributes to BACE1 up-regulation. This study explores how two injury-induced molecules are intimately connected and suggests a potential link between p75 signaling and the expression of BACE1 after brain injury.
Collapse
Affiliation(s)
- Khalil Saadipour
- Departments of Cell Biology, Physiology & Neuroscience, and Psychiatry, Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center, New York, New York 10016, USA.
| | - Alexia Tiberi
- Departments of Cell Biology, Physiology & Neuroscience, and Psychiatry, Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center, New York, New York 10016, USA; Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, 56126, Italy
| | - Sylvia Lombardo
- Alzheimer's Disease Research Laboratory, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
| | - Elena Grajales
- Departments of Cell Biology, Physiology & Neuroscience, and Psychiatry, Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center, New York, New York 10016, USA
| | - Laura Montroull
- Department of Biological Sciences, Rutgers Life Sciences Center, Rutgers University, Newark, NJ 07102, USA
| | - Noralyn B Mañucat-Tan
- School of Pharmacy and Medical Sciences, Sansom Institute, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - John LaFrancois
- The Nathan Kline Institute of Psychiatric Research, Center for Dementia Research, Orangeburg, NY 10962, USA
| | - Michael Cammer
- DART Microscopy Laboratory, NYU Langone Medical Center, New York, NY 10016, USA
| | - Paul M Mathews
- The Nathan Kline Institute of Psychiatric Research, Center for Dementia Research, Orangeburg, NY 10962, USA
| | - Helen E Scharfman
- The Nathan Kline Institute of Psychiatric Research, Center for Dementia Research, Orangeburg, NY 10962, USA
| | - Francesca-Fang Liao
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Wilma J Friedman
- Department of Biological Sciences, Rutgers Life Sciences Center, Rutgers University, Newark, NJ 07102, USA
| | - Xin-Fu Zhou
- School of Pharmacy and Medical Sciences, Sansom Institute, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Giueseppina Tesco
- Alzheimer's Disease Research Laboratory, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
| | - Moses V Chao
- Departments of Cell Biology, Physiology & Neuroscience, and Psychiatry, Skirball Institute of Biomolecular Medicine, New York University Langone Medical Center, New York, New York 10016, USA.
| |
Collapse
|
32
|
Izzy S, Liu Q, Fang Z, Lule S, Wu L, Chung JY, Sarro-Schwartz A, Brown-Whalen A, Perner C, Hickman SE, Kaplan DL, Patsopoulos NA, El Khoury J, Whalen MJ. Time-Dependent Changes in Microglia Transcriptional Networks Following Traumatic Brain Injury. Front Cell Neurosci 2019; 13:307. [PMID: 31440141 PMCID: PMC6694299 DOI: 10.3389/fncel.2019.00307] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
The neuroinflammatory response to traumatic brain injury (TBI) is critical to both neurotoxicity and neuroprotection, and has been proposed as a potentially modifiable driver of secondary injury in animal and human studies. Attempts to broadly target immune activation have been unsuccessful in improving outcomes, in part because the precise cellular and molecular mechanisms driving injury and outcome at acute, subacute, and chronic time points after TBI remain poorly defined. Microglia play a critical role in neuroinflammation and their persistent activation may contribute to long-term functional deficits. Activated microglia are characterized by morphological transformation and transcriptomic changes associated with specific inflammatory states. We analyzed the temporal course of changes in inflammatory genes of microglia isolated from injured brains at 2, 14, and 60 days after controlled cortical impact (CCI) in mice, a well-established model of focal cerebral contusion. We identified a time dependent, injury-associated change in the microglial gene expression profile toward a reduced ability to sense tissue damage, perform housekeeping, and maintain homeostasis in the early stages following CCI, with recovery and transition to a specialized inflammatory state over time. This later state starts at 14 days post-injury and is characterized by a biphasic pattern of IFNγ, IL-4, and IL-10 gene expression changes, with concurrent proinflammatory and anti-inflammatory gene changes. Our transcriptomic data sets are an important step to understand microglial role in TBI pathogenesis at the molecular level and identify common pathways that affect outcome. More studies to evaluate gene expression at the single cell level and focusing on subacute and chronic timepoint are warranted.
Collapse
Affiliation(s)
- Saef Izzy
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Qiong Liu
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai, China
| | - Zhou Fang
- Harvard Medical School, Boston, MA, United States.,Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, United States.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sevda Lule
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Limin Wu
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Joon Yong Chung
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Aliyah Sarro-Schwartz
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Alexander Brown-Whalen
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States
| | - Caroline Perner
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Suzanne E Hickman
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Nikolaos A Patsopoulos
- Harvard Medical School, Boston, MA, United States.,Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, United States.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Joseph El Khoury
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Michael J Whalen
- Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States.,Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
33
|
Choi KY, Han HS, Lee ES, Shin JM, Almquist BD, Lee DS, Park JH. Hyaluronic Acid-Based Activatable Nanomaterials for Stimuli-Responsive Imaging and Therapeutics: Beyond CD44-Mediated Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1803549. [PMID: 30773699 DOI: 10.1002/adma.201803549] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 12/27/2018] [Indexed: 05/24/2023]
Abstract
There is a rapidly increasing interest in developing stimuli-responsive nanomaterials for treating a variety of diseases. By enabling the activation of function locally at the sites of interest, it is possible to increase therapeutic efficacy significantly while simultaneously reducing adverse side effects. While there are many sophisticated nanomaterials available, they are often highly complex and not easily transferrable to industrial scales and clinical settings. However, nanomaterials based on hyaluronic acid offer a compelling strategy for reducing their complexity while retaining several desirable benefits such as active targeting and stimuli-responsive degradation. Herein, the basic properties of hyaluronic acid, its binding partners, and natural routes for degradation by hyaluronidases-hyaluronic-acid-degrading enzymes-and oxidative stresses are discussed. Recent advances in designing hyaluronic acid-based, actively targeted, hyaluronidase- or reactive-oxygen-species-responsive nanomaterials for both diagnostic imaging and therapeutic delivery, which go beyond merely the classical targeting of CD44, are summarized.
Collapse
Affiliation(s)
- Ki Young Choi
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Hwa Seung Han
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Eun Sook Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jung Min Shin
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | | | - Doo Sung Lee
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Theranostic Macromolecules Research Center, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jae Hyung Park
- School of Chemical Engineering, College of Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| |
Collapse
|
34
|
Boone DR, Weisz HA, Willey HE, Torres KEO, Falduto MT, Sinha M, Spratt H, Bolding IJ, Johnson KM, Parsley MA, DeWitt DS, Prough DS, Hellmich HL. Traumatic brain injury induces long-lasting changes in immune and regenerative signaling. PLoS One 2019; 14:e0214741. [PMID: 30943276 PMCID: PMC6447179 DOI: 10.1371/journal.pone.0214741] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 03/19/2019] [Indexed: 12/19/2022] Open
Abstract
There are no existing treatments for the long-term degenerative effects of traumatic brain injury (TBI). This is due, in part, to our limited understanding of chronic TBI and uncertainty about which proposed mechanisms for long-term neurodegeneration are amenable to treatment with existing or novel drugs. Here, we used microarray and pathway analyses to interrogate TBI-induced gene expression in the rat hippocampus and cortex at several acute, subchronic and chronic intervals (24 hours, 2 weeks, 1, 2, 3, 6 and 12 months) after parasagittal fluid percussion injury. We used Ingenuity pathway analysis (IPA) and Gene Ontology enrichment analysis to identify significantly expressed genes and prominent cell signaling pathways that are dysregulated weeks to months after TBI and potentially amenable to therapeutic modulation. We noted long-term, coordinated changes in expression of genes belonging to canonical pathways associated with the innate immune response (i.e., NF-κB signaling, NFAT signaling, Complement System, Acute Phase Response, Toll-like receptor signaling, and Neuroinflammatory signaling). Bioinformatic analysis suggested that dysregulation of these immune mediators—many are key hub genes—would compromise multiple cell signaling pathways essential for homeostatic brain function, particularly those involved in cell survival and neuroplasticity. Importantly, the temporal profile of beneficial and maladaptive immunoregulatory genes in the weeks to months after the initial TBI suggests wider therapeutic windows than previously indicated.
Collapse
Affiliation(s)
- Deborah R. Boone
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Harris A. Weisz
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Hannah E. Willey
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Michael T. Falduto
- GenUs Biosystems, Northbrook, Illinois, United States of America
- Paradise Genomics, Inc., Northbrook, Illinois, United States of America
| | - Mala Sinha
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Heidi Spratt
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Ian J. Bolding
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kathea M. Johnson
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Margaret A. Parsley
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Douglas S. DeWitt
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Donald S. Prough
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Helen L. Hellmich
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
| |
Collapse
|
35
|
Arneson D, Zhang G, Ying Z, Zhuang Y, Byun HR, Ahn IS, Gomez-Pinilla F, Yang X. Single cell molecular alterations reveal target cells and pathways of concussive brain injury. Nat Commun 2018; 9:3894. [PMID: 30254269 PMCID: PMC6156584 DOI: 10.1038/s41467-018-06222-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 08/27/2018] [Indexed: 02/07/2023] Open
Abstract
The complex neuropathology of traumatic brain injury (TBI) is difficult to dissect, given the convoluted cytoarchitecture of affected brain regions such as the hippocampus. Hippocampal dysfunction during TBI results in cognitive decline that may escalate to other neurological disorders, the molecular basis of which is hidden in the genomic programs of individual cells. Using the unbiased single cell sequencing method Drop-seq, we report that concussive TBI affects previously undefined cell populations, in addition to classical hippocampal cell types. TBI also impacts cell type-specific genes and pathways and alters gene co-expression across cell types, suggesting hidden pathogenic mechanisms and therapeutic target pathways. Modulating the thyroid hormone pathway as informed by the T4 transporter transthyretin Ttr mitigates TBI-associated genomic and behavioral abnormalities. Thus, single cell genomics provides unique information about how TBI impacts diverse hippocampal cell types, adding new insights into the pathogenic pathways amenable to therapeutics in TBI and related disorders.
Collapse
Affiliation(s)
- Douglas Arneson
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Guanglin Zhang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhe Ying
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Yumei Zhuang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hyae Ran Byun
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| |
Collapse
|
36
|
Ferguson LB, Harris RA, Mayfield RD. From gene networks to drugs: systems pharmacology approaches for AUD. Psychopharmacology (Berl) 2018; 235:1635-1662. [PMID: 29497781 PMCID: PMC6298603 DOI: 10.1007/s00213-018-4855-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/06/2018] [Indexed: 12/29/2022]
Abstract
The alcohol research field has amassed an impressive number of gene expression datasets spanning key brain areas for addiction, species (humans as well as multiple animal models), and stages in the addiction cycle (binge/intoxication, withdrawal/negative effect, and preoccupation/anticipation). These data have improved our understanding of the molecular adaptations that eventually lead to dysregulation of brain function and the chronic, relapsing disorder of addiction. Identification of new medications to treat alcohol use disorder (AUD) will likely benefit from the integration of genetic, genomic, and behavioral information included in these important datasets. Systems pharmacology considers drug effects as the outcome of the complex network of interactions a drug has rather than a single drug-molecule interaction. Computational strategies based on this principle that integrate gene expression signatures of pharmaceuticals and disease states have shown promise for identifying treatments that ameliorate disease symptoms (called in silico gene mapping or connectivity mapping). In this review, we suggest that gene expression profiling for in silico mapping is critical to improve drug repurposing and discovery for AUD and other psychiatric illnesses. We highlight studies that successfully apply gene mapping computational approaches to identify or repurpose pharmaceutical treatments for psychiatric illnesses. Furthermore, we address important challenges that must be overcome to maximize the potential of these strategies to translate to the clinic and improve healthcare outcomes.
Collapse
Affiliation(s)
- Laura B Ferguson
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 1 University Station A4800, Austin, TX, 78712, USA
- Intitute for Neuroscience, University of Texas at Austin, Austin, TX, 78712, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 1 University Station A4800, Austin, TX, 78712, USA
| | - Roy Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 1 University Station A4800, Austin, TX, 78712, USA.
| |
Collapse
|
37
|
Ferguson LB, Ozburn AR, Ponomarev I, Metten P, Reilly M, Crabbe JC, Harris RA, Mayfield RD. Genome-Wide Expression Profiles Drive Discovery of Novel Compounds that Reduce Binge Drinking in Mice. Neuropsychopharmacology 2018; 43:1257-1266. [PMID: 29251283 PMCID: PMC5916369 DOI: 10.1038/npp.2017.301] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/06/2017] [Accepted: 11/24/2017] [Indexed: 12/18/2022]
Abstract
Transcriptome-based drug discovery has identified new treatments for some complex diseases, but has not been applied to alcohol use disorder (AUD) or other psychiatric diseases, where there is a critical need for improved pharmacotherapies. High Drinking in the Dark (HDID-1) mice are a genetic model of AUD risk that have been selectively bred (from the HS/Npt line) to achieve intoxicating blood alcohol levels (BALs) after binge-like drinking. We compared brain gene expression of HDID-1 and HS/Npt mice, to determine a molecular signature for genetic risk for high intensity, binge-like drinking. Using multiple computational methods, we queried LINCS-L1000 (Library of Integrated Network-Based Cellular Signatures), a database containing gene expression signatures of thousands of compounds, to predict candidate drugs with the greatest potential to decrease alcohol consumption. Our analyses predicted novel compounds for testing, many with anti-inflammatory properties, providing further support for a neuroimmune mechanism of excessive alcohol drinking. We validated the top 2 candidates in vivo as a proof-of-concept. Terreic acid (a Bruton's tyrosine kinase inhibitor) and pergolide (a dopamine and serotonin receptor agonist) robustly reduced alcohol intake and BALs in HDID-1 mice, providing the first evidence for transcriptome-based drug discovery to target an addiction trait. Effective drug treatments for many psychiatric diseases are lacking, and the emerging tools and approaches outlined here offer researchers studying complex diseases renewed opportunities to discover new or repurpose existing compounds and expedite treatment options.
Collapse
Affiliation(s)
- Laura B Ferguson
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - Angela R Ozburn
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - Igor Ponomarev
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - Pamela Metten
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - Matthew Reilly
- Division of Neuroscience and Behavior, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA
| | - John C Crabbe
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | - R Adron Harris
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - R Dayne Mayfield
- The Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
38
|
Dekker SE, Nikolian VC, Sillesen M, Bambakidis T, Schober P, Alam HB. Different resuscitation strategies and novel pharmacologic treatment with valproic acid in traumatic brain injury. J Neurosci Res 2018; 96:711-719. [PMID: 28742231 PMCID: PMC5785554 DOI: 10.1002/jnr.24125] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 12/28/2022]
Abstract
Traumatic brain injury (TBI) is a leading cause of death in young adults, and effective treatment strategies have the potential to save many lives. TBI results in coagulopathy, endothelial dysfunction, inflammation, cell death, and impaired epigenetic homeostasis, ultimately leading to morbidity and/or mortality. Commonly used resuscitation fluids such as crystalloids or colloids have several disadvantages and might even be harmful when administered in large quantities. There is a need for next-generation treatment strategies (especially in the prehospital setting) that minimize cellular damage, improve survival, and enhance neurological recovery. Pharmacologic treatment with histone deacetylase inhibitors, such as valproic acid, has shown promising results in animal studies of TBI and may therefore be an excellent example of next-generation therapy. This review briefly describes traditional resuscitation strategies for TBI combined with hemorrhagic shock and describes preclinical studies on valproic acid as a new pharmacologic agent in the treatment of TBI. It finally discusses limitations and future directions on the use of histone deacetylase inhibitors for the treatment of TBI.
Collapse
Affiliation(s)
- Simone E. Dekker
- Department of Surgery, University of Michigan Hospital, Ann Arbor, Michigan, USA
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Anesthesiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Vahagn C. Nikolian
- Department of Surgery, University of Michigan Hospital, Ann Arbor, Michigan, USA
| | - Martin Sillesen
- Department of Surgical Gastroenterology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark; Institute for Inflammation Research, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ted Bambakidis
- Department of Surgery, University of Michigan Hospital, Ann Arbor, Michigan, USA
| | - Patrick Schober
- Department of Anesthesiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Hasan B. Alam
- Department of Surgery, University of Michigan Hospital, Ann Arbor, Michigan, USA
| |
Collapse
|
39
|
Simonato M. Epilepsy an Update on Disease Mechanisms: The Potential Role of MicroRNAs. Front Neurol 2018; 9:176. [PMID: 29615968 PMCID: PMC5868323 DOI: 10.3389/fneur.2018.00176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/07/2018] [Indexed: 01/25/2023] Open
Abstract
So far, research on epilepsy mechanisms has been designed mainly using animal models and tracking down molecular mechanisms underlying seizures in that model. While this approach is clearly valuable, it can be questioned if it is the best possible. One attractive alternative approach may stem from the consideration of epilepsy as a complex disease of a very complex organ, the brain. This short review summarizes data from analyses of the alterations in expression of microRNAs and their target messenger RNAs in a specific brain subregion, the dentate gyrus of the hippocampus, in three experimental models of lesional epilepsy. The findings are discussed within the conceptual framework of complex systems.
Collapse
Affiliation(s)
- Michele Simonato
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy.,School of Medicine, University Vita-Salute San Raffaele, Milan, Italy
| |
Collapse
|
40
|
Lipponen A, El-Osta A, Kaspi A, Ziemann M, Khurana I, KN H, Navarro-Ferrandis V, Puhakka N, Paananen J, Pitkänen A. Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury. Acta Neuropathol Commun 2018; 6:17. [PMID: 29482641 PMCID: PMC5828078 DOI: 10.1186/s40478-018-0519-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/15/2018] [Indexed: 11/10/2022] Open
Abstract
Traumatic brain injury (TBI) induces a wide variety of cellular and molecular changes that can continue for days to weeks to months, leading to functional impairments. Currently, there are no pharmacotherapies in clinical use that favorably modify the post-TBI outcome, due in part to limited understanding of the mechanisms of TBI-induced pathologies. Our system biology analysis tested the hypothesis that chronic transcriptomics changes induced by TBI are controlled by altered DNA-methylation in gene promoter areas or by transcription factors. We performed genome-wide methyl binding domain (MBD)-sequencing (seq) and RNA-seq in perilesional, thalamic, and hippocampal tissue sampled at 3 months after TBI induced by lateral fluid percussion in adult male Sprague-Dawley rats. We investigated the regulated molecular networks and mechanisms underlying the chronic regulation, particularly DNA methylation and transcription factors. Finally, we identified compounds that modulate the transcriptomics changes and could be repurposed to improve recovery. Unexpectedly, DNA methylation was not a major regulator of chronic post-TBI transcriptomics changes. On the other hand, the transcription factors Cebpd, Pax6, Spi1, and Tp73 were upregulated at 3 months after TBI (False discovery rate < 0.05), which was validated using digital droplet polymerase chain reaction. Transcription regulatory network analysis revealed that these transcription factors regulate apoptosis, inflammation, and microglia, which are well-known contributors to secondary damage after TBI. Library of Integrated Network-based Cellular Signatures (LINCS) analysis identified 118 pharmacotherapies that regulate the expression of Cebpd, Pax6, Spi1, and Tp73. Of these, the antidepressant and/or antipsychotic compounds trimipramine, rolipramine, fluspirilene, and chlorpromazine, as well as the anti-cancer therapies pimasertib, tamoxifen, and vorinostat were strong regulators of the identified transcription factors, suggesting their potential to modulate the regulated transcriptomics networks to improve post-TBI recovery.
Collapse
Affiliation(s)
- Anssi Lipponen
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
- Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Ishant Khurana
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Harikrishnan KN
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Vicente Navarro-Ferrandis
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Noora Puhakka
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- University of Eastern Finland Bioinformatics Center, University of Eastern Finland, Kuopio, Finland
| | - Asla Pitkänen
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| |
Collapse
|
41
|
Meta-Analysis of MicroRNAs Dysregulated in the Hippocampal Dentate Gyrus of Animal Models of Epilepsy. eNeuro 2017; 4:eN-NWR-0152-17. [PMID: 29291240 PMCID: PMC5745610 DOI: 10.1523/eneuro.0152-17.2017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 12/12/2022] Open
Abstract
The identification of mechanisms transforming normal to seizure-generating tissue after brain injury is key to developing new antiepileptogenic treatments. MicroRNAs (miRNAs) may act as regulators and potential treatment targets for epileptogenesis. Here, we undertook a meta-analysis of changes in miRNA expression in the hippocampal dentate gyrus (DG) following an epileptogenic insult in three epilepsy models. We identified 26 miRNAs significantly differentially expressed during epileptogenesis, and five differentially expressed in chronic epilepsy. Of these, 13 were not identified in any of the individual studies. To assess the role of these miRNAs, we predicted their mRNA targets and then filtered the list to include only target genes expressed in DG and negatively correlated with miRNA expression. Functional enrichment analysis of mRNA targets of miRNAs dysregulated during epileptogenesis suggested a role for molecular processes related to inflammation and synaptic function. Our results identify new miRNAs associated with epileptogenesis from existing data, highlighting the utility of meta-analysis in maximizing value from preclinical data.
Collapse
|
42
|
Jones SV, Kounatidis I. Nuclear Factor-Kappa B and Alzheimer Disease, Unifying Genetic and Environmental Risk Factors from Cell to Humans. Front Immunol 2017; 8:1805. [PMID: 29312321 PMCID: PMC5732234 DOI: 10.3389/fimmu.2017.01805] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/30/2017] [Indexed: 12/26/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, an eversible, progressive disease that causes problems with memory, thinking, language, planning, and behavior. There are a number of risk factors associated with developing AD but the exact cause remains unknown. The predominant theory is that excessive build-up of amyloid protein leads to cell death, brain atrophy, and cognitive and functional decline. However, the amyloid hypothesis has not led to a single successful treatment. The recent failure of Solanezumab, a monoclonal antibody to amyloid, in a large phase III trial was emblematic of the repeated failure of anti-amyloid therapeutics. New disease targets are urgently needed. The innate immune system is increasingly being implicated in the pathology of number of chronic diseases. This focused review will summarize the role of transcription factor nuclear factor-kappa B (NF-κB), a key regulator of innate immunity, in the major genetic and environmental risk factors in cellular, invertebrate and vertebrate models of AD. The paper will also explore the relationship between NF-κB and emerging environmental risk factors in an attempt to assess the potential for this transcription factor to be targeted for disease prevention.
Collapse
Affiliation(s)
- Simon Vann Jones
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, United Kingdom
| | - Ilias Kounatidis
- Laboratory of Cell Biology, Development and Genetics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
43
|
Pierce JD, Shen Q, Peltzer J, Thimmesch A, Hiebert JB. A pilot study exploring the effects of ubiquinol on brain genomics after traumatic brain injury. Nurs Outlook 2017; 65:S44-S52. [DOI: 10.1016/j.outlook.2017.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 12/14/2022]
|
44
|
Assessment of the role of intracranial hypertension and stress on hippocampal cell apoptosis and hypothalamic-pituitary dysfunction after TBI. Sci Rep 2017. [PMID: 28630478 PMCID: PMC5476648 DOI: 10.1038/s41598-017-04008-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In recent years, hypopituitarism caused by traumatic brain injury (TBI) has been explored in many clinical studies; however, few studies have focused on intracranial hypertension and stress caused by TBI. In this study, an intracranial hypertension model, with epidural hematoma as the cause, was used to explore the physiopathological and neuroendocrine changes in the hypothalamic-pituitary axis and hippocampus. The results demonstrated that intracranial hypertension increased the apoptosis rate, caspase-3 levels and proliferating cell nuclear antigen (PCNA) in the hippocampus, hypothalamus, pituitary gland and showed a consistent rate of apoptosis within each group. The apoptosis rates of hippocampus, hypothalamus and pituitary gland were further increased when intracranial pressure (ICP) at 24 hour (h) were still increased. The change rates of apoptosis in hypothalamus and pituitary gland were significantly higher than hippocampus. Moreover, the stress caused by surgery may be a crucial factor in apoptosis. To confirm stress leads to apoptosis in the hypothalamus and pituitary gland, we used rabbits to establish a standard stress model. The results confirmed that stress leads to apoptosis of neuroendocrine cells in the hypothalamus and pituitary gland, moreover, the higher the stress intensity, the higher the apoptosis rate in the hypothalamus and pituitary gland.
Collapse
|
45
|
Braun M, Vaibhav K, Saad NM, Fatima S, Vender JR, Baban B, Hoda MN, Dhandapani KM. White matter damage after traumatic brain injury: A role for damage associated molecular patterns. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2614-2626. [PMID: 28533056 DOI: 10.1016/j.bbadis.2017.05.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/09/2017] [Accepted: 05/16/2017] [Indexed: 12/12/2022]
Abstract
Traumatic brain injury (TBI) is a leading cause of mortality and long-term morbidity worldwide. Despite decades of pre-clinical investigation, therapeutic strategies focused on acute neuroprotection failed to improve TBI outcomes. This lack of translational success has necessitated a reassessment of the optimal targets for intervention, including a heightened focus on secondary injury mechanisms. Chronic immune activation correlates with progressive neurodegeneration for decades after TBI; however, significant challenges remain in functionally and mechanistically defining immune activation after TBI. In this review, we explore the burgeoning evidence implicating the acute release of damage associated molecular patterns (DAMPs), such as adenosine 5'-triphosphate (ATP), high mobility group box protein 1 (HMGB1), S100 proteins, and hyaluronic acid in the initiation of progressive neurological injury, including white matter loss after TBI. The role that pattern recognition receptors, including toll-like receptor and purinergic receptors, play in progressive neurological injury after TBI is detailed. Finally, we provide support for the notion that resident and infiltrating macrophages are critical cellular targets linking acute DAMP release with adaptive immune responses and chronic injury after TBI. The therapeutic potential of targeting DAMPs and barriers to clinical translational, in the context of TBI patient management, are discussed.
Collapse
Affiliation(s)
- Molly Braun
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Kumar Vaibhav
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA, United States; Department of Medical Laboratory, Imaging & Radiologic Sciences, College of Allied Health Science, Augusta University, Augusta, GA, United States
| | - Nancy M Saad
- Department of Oral Biology, Dental College of Georgia, Augusta University, Augusta, GA, United States
| | - Sumbul Fatima
- Department of Medical Laboratory, Imaging & Radiologic Sciences, College of Allied Health Science, Augusta University, Augusta, GA, United States
| | - John R Vender
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Babak Baban
- Department of Oral Biology, Dental College of Georgia, Augusta University, Augusta, GA, United States; Department of Neurology, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Md Nasrul Hoda
- Department of Medical Laboratory, Imaging & Radiologic Sciences, College of Allied Health Science, Augusta University, Augusta, GA, United States; Department of Neurology, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Krishnan M Dhandapani
- Department of Neurosurgery, Medical College of Georgia, Augusta University, Augusta, GA, United States.
| |
Collapse
|
46
|
Puhakka N, Bot AM, Vuokila N, Debski KJ, Lukasiuk K, Pitkänen A. Chronically dysregulated NOTCH1 interactome in the dentate gyrus after traumatic brain injury. PLoS One 2017; 12:e0172521. [PMID: 28273100 PMCID: PMC5342204 DOI: 10.1371/journal.pone.0172521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injury (TBI) can result in several dentate gyrus-regulated disabilities. Almost nothing is known about the chronic molecular changes after TBI, and their potential as treatment targets. We hypothesized that chronic transcriptional alterations after TBI are under microRNA (miRNA) control. Expression of miRNAs and their targets in the dentate gyrus was analyzed using microarrays at 3 months after experimental TBI. Of 305 miRNAs present on the miRNA-array, 12 were downregulated (p<0.05). In parallel, 75 of their target genes were upregulated (p<0.05). A bioinformatics analysis of miRNA targets highlighted the dysregulation of the transcription factor NOTCH1 and 39 of its target genes (NOTCH1 interactome). Validation assays confirmed downregulation of miR-139-5p, upregulation of Notch1 and its activated protein, and positive enrichment of NOTCH1 target gene expression. These findings demonstrate that miRNA-based transcriptional regulation can be present at chronic time points after TBI, and highlight the NOTCH1 interactome as one of the mechanisms behind the dentate gyrus pathology-related morbidities.
Collapse
Affiliation(s)
- Noora Puhakka
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anna Maria Bot
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Niina Vuokila
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Konrad Jozef Debski
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Lukasiuk
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Asla Pitkänen
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- * E-mail:
| |
Collapse
|
47
|
Paananen J. Bioinformatics in the Identification of Novel Targets and Pathways in Neurodegenerative Diseases. CURRENT GENETIC MEDICINE REPORTS 2017. [DOI: 10.1007/s40142-017-0115-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Meng Q, Zhuang Y, Ying Z, Agrawal R, Yang X, Gomez-Pinilla F. Traumatic Brain Injury Induces Genome-Wide Transcriptomic, Methylomic, and Network Perturbations in Brain and Blood Predicting Neurological Disorders. EBioMedicine 2017; 16:184-194. [PMID: 28174132 PMCID: PMC5474519 DOI: 10.1016/j.ebiom.2017.01.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
The complexity of the traumatic brain injury (TBI) pathology, particularly concussive injury, is a serious obstacle for diagnosis, treatment, and long-term prognosis. Here we utilize modern systems biology in a rodent model of concussive injury to gain a thorough view of the impact of TBI on fundamental aspects of gene regulation, which have the potential to drive or alter the course of the TBI pathology. TBI perturbed epigenomic programming, transcriptional activities (expression level and alternative splicing), and the organization of genes in networks centered around genes such as Anax2, Ogn, and Fmod. Transcriptomic signatures in the hippocampus are involved in neuronal signaling, metabolism, inflammation, and blood function, and they overlap with those in leukocytes from peripheral blood. The homology between genomic signatures from blood and brain elicited by TBI provides proof of concept information for development of biomarkers of TBI based on composite genomic patterns. By intersecting with human genome-wide association studies, many TBI signature genes and network regulators identified in our rodent model were causally associated with brain disorders with relevant link to TBI. The overall results show that concussive brain injury reprograms genes which could lead to predisposition to neurological and psychiatric disorders, and that genomic information from peripheral leukocytes has the potential to predict TBI pathogenesis in the brain.
Collapse
Affiliation(s)
- Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yumei Zhuang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhe Ying
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rahul Agrawal
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|