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Amgalan A, Maher AS, Ghosh S, Chui HC, Bogdan P, Irimia A. Brain age estimation reveals older adults' accelerated senescence after traumatic brain injury. GeroScience 2022; 44:2509-2525. [PMID: 35792961 PMCID: PMC9768106 DOI: 10.1007/s11357-022-00597-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/23/2022] [Indexed: 01/06/2023] Open
Abstract
Adults aged 60 and over are most vulnerable to mild traumatic brain injury (mTBI). Nevertheless, the extent to which chronological age (CA) at injury affects TBI-related brain aging is unknown. This study applies Gaussian process regression to T1-weighted magnetic resonance images (MRIs) acquired within [Formula: see text]7 days and again [Formula: see text]6 months after a single mTBI sustained by 133 participants aged 20-83 (CA [Formula: see text] = 42.6 ± 17 years; 51 females). Brain BAs are estimated, modeled, and compared as a function of sex and CA at injury using a statistical model selection procedure. On average, the brains of older adults age by 15.3 ± 6.9 years after mTBI, whereas those of younger adults age only by 1.8 ± 5.6 years, a significant difference (Welch's t32 = - 9.17, p ≃ 9.47 × 10-11). For an adult aged [Formula: see text]30 to [Formula: see text]60, the expected amount of TBI-related brain aging is [Formula: see text]3 years greater than in an individual younger by a decade. For an individual over [Formula: see text]60, the respective amount is [Formula: see text]7 years. Despite no significant sex differences in brain aging (Welch's t108 = 0.78, p > 0.78), the statistical test is underpowered. BAs estimated at acute baseline versus chronic follow-up do not differ significantly (t264 = 0.41, p > 0.66, power = 80%), suggesting negligible TBI-related brain aging during the chronic stage of TBI despite accelerated aging during the acute stage. Our results indicate that a single mTBI sustained after age [Formula: see text]60 involves approximately [Formula: see text]10 years of premature and lasting brain aging, which is MRI detectable as early as [Formula: see text]7 days post-injury.
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Affiliation(s)
- Anar Amgalan
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Alexander S Maher
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Satyaki Ghosh
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Electronics and Electrical Engineering, Indian Institute of Technology, Guwahati, Assam, India
| | - Helena C Chui
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Paul Bogdan
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Andrei Irimia
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
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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: 22] [Impact Index Per Article: 3.7] [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.
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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
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Lipponen A, Paananen J, Puhakka N, Pitkänen A. Analysis of Post-Traumatic Brain Injury Gene Expression Signature Reveals Tubulins, Nfe2l2, Nfkb, Cd44, and S100a4 as Treatment Targets. Sci Rep 2016; 6:31570. [PMID: 27530814 PMCID: PMC4987651 DOI: 10.1038/srep31570] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022] Open
Abstract
We aimed to define the chronically altered gene expression signature of traumatic brain injury (TBI-sig) to discover novel treatments to reverse pathologic gene expression or reinforce the expression of recovery-related genes. Genome-wide RNA-sequencing was performed at 3 months post-TBI induced by lateral fluid-percussion injury in rats. We found 4964 regulated genes in the perilesional cortex and 1966 in the thalamus (FDR < 0.05). TBI-sig was used for a LINCS analysis which identified 11 compounds that showed a strong connectivity with the TBI-sig in neuronal cell lines. Of these, celecoxib and sirolimus were recently reported to have a disease-modifying effect in in vivo animal models of epilepsy. Other compounds revealed by the analysis were BRD-K91844626, BRD-A11009626, NO-ASA, BRD-K55260239, SDZ-NKT-343, STK-661558, BRD-K75971499, ionomycin, and desmethylclomipramine. Network analysis of overlapping genes revealed the effects on tubulins (Tubb2a, Tubb3, Tubb4b), Nfe2l2, S100a4, Cd44, and Nfkb2, all of which are linked to TBI-relevant outcomes, including epileptogenesis and tissue repair. Desmethylclomipramine modulated most of the gene targets considered favorable for TBI outcome. Our data demonstrate long-lasting transcriptomics changes after TBI. LINCS analysis predicted that these changes could be modulated by various compounds, some of which are already in clinical use but never tested in TBI.
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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
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Finland.,University of Eastern Finland Bioinformatics Center, University of Eastern Finland, Finland
| | - Noora Puhakka
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 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
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Lamprecht MR, Elkin BS, Kesavabhotla K, Crary JF, Hammers JL, Huh JW, Raghupathi R, Morrison B. Strong Correlation of Genome-Wide Expression after Traumatic Brain Injury In Vitro and In Vivo Implicates a Role for SORLA. J Neurotrauma 2016; 34:97-108. [PMID: 26919808 DOI: 10.1089/neu.2015.4306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The utility of in vitro models of traumatic brain injury (TBI) depends on their ability to recapitulate the in vivo TBI cascade. In this study, we used a genome-wide approach to compare changes in gene expression at several time points post-injury in both an in vitro model and an in vivo model of TBI. We found a total of 2073 differentially expressed genes in our in vitro model and 877 differentially expressed genes in our in vivo model when compared to noninjured controls. We found a strong correlation in gene expression changes between the two models (r = 0.69), providing confidence that the in vitro model represented at least part of the in vivo injury cascade. From these data, we searched for genes with significant changes in expression over time (analysis of covariance) and identified sorting protein-related receptor with A-type repeats (SORLA). SORLA directs amyloid precursor protein to the recycling pathway by direct binding and away from amyloid-beta producing enzymes. Mutations of SORLA have been linked to Alzheimer's disease (AD). We confirmed downregulation of SORLA expression in organotypic hippocampal slice cultures by immunohistochemistry and Western blotting and present preliminary data from human tissue that is consistent with these experimental results. Together, these data suggest that the in vitro model of TBI used in this study strongly recapitulates the in vivo TBI pathobiology and is well suited for future mechanistic or therapeutic studies. The data also suggest the possible involvement of SORLA in the post-traumatic cascade linking TBI to AD.
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Affiliation(s)
- Michael R Lamprecht
- 1 Department of Biomedical Engineering, Columbia University , New York, New York
| | - Benjamin S Elkin
- 1 Department of Biomedical Engineering, Columbia University , New York, New York.,2 MEA Forensic Engineers & Scientists , Mississauga, Ontario, Canada
| | - Kartik Kesavabhotla
- 1 Department of Biomedical Engineering, Columbia University , New York, New York
| | - John F Crary
- 3 Department of Pathology, Fishberg Department of Neuroscience, Friedman Brain Institute , and the Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jennifer L Hammers
- 4 Office of Chief Medical Examiner , City of New York, New York, New York
| | - Jimmy W Huh
- 5 Department of Anesthesia and Critical Care, Children's Hospital of Philadelphia , Philadelphia, Pennsylvania
| | - Ramesh Raghupathi
- 6 Department of Neurobiology and Anatomy, Drexel University College of Medicine , Philadelphia, Pennsylvania
| | - Barclay Morrison
- 1 Department of Biomedical Engineering, Columbia University , New York, New York
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Feng JF, Zhang KM, Jiang JY, Gao GY, Fu X, Liang YM. Effect of therapeutic mild hypothermia on the genomics of the hippocampus after moderate traumatic brain injury in rats. Neurosurgery 2011; 67:730-42. [PMID: 20651628 DOI: 10.1227/01.neu.0000378023.81727.6e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Traumatic brain injury (TBI), a major cause of morbidity and mortality, is a serious public health concern. OBJECTIVE To evaluate the effect of mild hypothermia on gene expression in the hippocampus and to try to elucidate molecular mechanisms of hypothermic neuroprotection after TBI. METHODS Rats were subjected to mild hypothermia (group 1: n = 3, 33 degrees C, 3H) or normothermia (group 2: n = 3; 37 degrees C, 3H) after TBI. Six genome arrays were applied to detect the gene expression profiles of ipsilateral hippocampus. Functional clustering and gene ontology analysis were then carried out. Another 20 rats were randomly assigned to 4 groups (n = 5 per group): group 3, sham-normothermia; group 4, sham-hypothermia; group 5, TBI-normothermia; and group 6, TBI-hypothermia. Real-time fluorescent quantitative reverse-transcription polymerase chain reaction was used to detect specific selected genes. RESULTS We found that 133 transcripts in the hypothermia group were statistically different from those in the normothermia group, including 57 transcripts that were upregulated and 76 that were downregulated after TBI (P < .01). Most of these genes were involved in various pathophysiological processes, and some were critical to cell survival. Analysis showed that 9 gene ontology categories were significantly affected by hypothermia, including the most affected categories: synapse organization and biogenesis (upregulated) and regulation of inflammatory response (downregulated). The mRNA expression of Ank3, Cmbp, Nrxn3, Tgm2, and Fcgr3 was regulated by hypothermia, TBI, or a combination of TBI and hypothermia compared with the sham-normothermia group. Their mRNA expression was significantly regulated by hypothermia in TBI groups. CONCLUSION Posttraumatic mild hypothermia has a significant effect on the gene expression profiles of the hippocampus, especially those genes belonging to the 9 gene ontology categories. Differential expression of those genes may be involved in the most fundamental molecular mechanisms of cerebral protection by mild hypothermia after TBI.
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Affiliation(s)
- Jun-feng Feng
- Department of Neurosurgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Tawfeeq NA, Halawani MM, Al-Faridi K, Aal-Shaya WA, Taha WS. Traumatic brain injury: neuroprotective anaesthetic techniques, an update. Injury 2009; 40 Suppl 4:S75-81. [PMID: 19895957 DOI: 10.1016/j.injury.2009.10.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Traumatic brain injuries remain an area of great challenge to both neurosurgeons and neuroanaesthesiologists. The management of these injuries starts at the scene of the accident. However, strategies for preventing secondary brain injury and its sequelae are continuing to evolve. These strategies include the use of pharmacological and nonpharmacological techniques. Preventing hypoxia and the use of hypertonic saline have been shown to have favourable results on the outcome of these injuries. The use of isoflurane has been shown to have a neuronprotective effect. Propofol is thought to be the future drug of choice because of its neuroprotective properties, although these still need to be further proven through research. In this review an understanding of the pathophysiology of traumatic brain injury will be outlined in order to understand the effects of pharmacological and nonpharmacological agents on secondary brain injury.
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Affiliation(s)
- Nasser A Tawfeeq
- Department of Anaesthesia, King Abdulaziz Medical City, Riyadh, Saudi Arabia
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Neuroprotection in traumatic brain injury. Drug Discov Today 2008; 13:1082-9. [PMID: 18848641 DOI: 10.1016/j.drudis.2008.09.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/09/2008] [Accepted: 09/11/2008] [Indexed: 12/21/2022]
Abstract
The management of traumatic brain injury (TBI) is challenging and there is a need for neuroprotective therapies. A better understanding of the pathomechanism of TBI, particularly of the evolution of secondary damage, is providing targets for new approaches and selected ones in clinical development are described. Clinical trials that have been discontinued in the past for lack of efficacy or other reasons are also listed. One of the problems has been the translation of promising animal experimental results into clinically successful therapies. The complexity of sequelae of TBI requires a multifaceted approach. In addition to the investigation of drugs for neuroprotective effect in TBI, new technologies based on cell/gene therapies, biomarkers and nanobiotechnology are being employed for the integration of neuroprotection with neuroregeneration and are promising.
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