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Pitkänen A, Paananen T, Kyyriäinen J, Das Gupta S, Heiskanen M, Vuokila N, Bañuelos-Cabrera I, Lapinlampi N, Kajevu N, Andrade P, Ciszek R, Lara-Valderrábano L, Ekolle Ndode-Ekane X, Puhakka N. Biomarkers for posttraumatic epilepsy. Epilepsy Behav 2021; 121:107080. [PMID: 32317161 DOI: 10.1016/j.yebeh.2020.107080] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/17/2022]
Abstract
A biomarker is a characteristic that can be objectively measured as an indicator of normal biologic processes, pathogenic processes, or responses to an exposure or intervention, including therapeutic interventions. Biomarker modalities include molecular, histologic, radiographic, or physiologic characteristics. To improve the understanding and use of biomarker terminology in biomedical research, clinical practice, and medical product development, the Food and Drug Administration (FDA)-National Institutes of Health (NIH) Joint Leadership Council developed the BEST Resource (Biomarkers, EndpointS, and other Tools). The seven BEST biomarker categories include the following: (a) susceptibility/risk biomarkers, (b) diagnostic biomarkers, (c) monitoring biomarkers, (d) prognostic biomarkers, (e) predictive biomarkers, (f) pharmacodynamic/response biomarkers, and (g) safety biomarkers. We hypothesize some potential overlap between the reported biomarkers of traumatic brain injury (TBI), epilepsy, and posttraumatic epilepsy (PTE). Here, we tested this hypothesis by reviewing studies focusing on biomarker discovery for posttraumatic epileptogenesis and epilepsy. The biomarker modalities reviewed here include plasma/serum and cerebrospinal fluid molecular biomarkers, imaging biomarkers, and electrophysiologic biomarkers. Most of the reported biomarkers have an area under the receiver operating characteristic curve greater than 0.800, suggesting both high sensitivity and high specificity. Our results revealed little overlap in the biomarker candidates between TBI, epilepsy, and PTE. In addition to using single parameters as biomarkers, machine learning approaches have highlighted the potential for utilizing patterns of markers as biomarkers. Although published data suggest the possibility of identifying biomarkers for PTE, we are still in the early phase of the development curve. Many of the seven biomarker categories lack PTE-related biomarkers. Thus, further exploration using proper, statistically powered, and standardized study designs with validation cohorts, and by developing and applying novel analytical methods, is needed for PTE biomarker discovery.
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Affiliation(s)
- Asla Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
| | - Tomi Paananen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Jenni Kyyriäinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Shalini Das Gupta
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Mette Heiskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Niina Vuokila
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Ivette Bañuelos-Cabrera
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Niina Lapinlampi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Natallie Kajevu
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Pedro Andrade
- A.I. Virtanen Institute for Molecular Sciences, 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
| | - Leonardo Lara-Valderrábano
- 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
| | - Noora Puhakka
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
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Korotkov A, Puhakka N, Gupta SD, Vuokila N, Broekaart DWM, Anink JJ, Heiskanen M, Karttunen J, van Scheppingen J, Huitinga I, Mills JD, van Vliet EA, Pitkänen A, Aronica E. Increased expression of miR142 and miR155 in glial and immune cells after traumatic brain injury may contribute to neuroinflammation via astrocyte activation. Brain Pathol 2020; 30:897-912. [PMID: 32460356 PMCID: PMC7540383 DOI: 10.1111/bpa.12865] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 02/17/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury (TBI) is associated with the pathological activation of immune-competent cells in the brain, such as astrocytes, microglia and infiltrating immune blood cells, resulting in chronic inflammation and gliosis. This may contribute to the secondary injury after TBI, thus understanding of these processes is crucial for the development of effective treatments of post-traumatic pathologies. MicroRNAs (miRNAs, miRs) are small noncoding RNAs, functioning as posttranscriptional regulators of gene expression. The increased expression of inflammation-associated microRNAs miR155 and miR142 has been reported after TBI in rats. However, expression of these miRNAs in the human brain post-TBI is not studied and their functions are not well understood. Moreover, circulating miR155 and miR142 are candidate biomarkers. Therefore, we characterized miR142 and miR155 expression in the perilesional cortex and plasma of rats that underwent lateral fluid-percussion injury, a model for TBI and in the human perilesional cortex post-TBI. We demonstrated higher miR155 and miR142 expression in the perilesional cortex of rats 2 weeks post-TBI. In plasma, miR155 was associated with proteins and miR142 with extracellular vesicles, however their expression did not change. In the human perilesional cortex miR155 was most prominently expressed by activated astrocytes, whereas miR142 was expressed predominantly by microglia, macrophages and lymphocytes. Pro-inflammatory medium from macrophage-like cells stimulated miR155 expression in astrocytes and overexpression of miR142 in these cells further potentiated a pro-inflammatory state of activated astrocytes. We conclude that miR155 and miR142 promote brain inflammation via astrocyte activation and may be involved in the secondary brain injury after TBI.
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Affiliation(s)
- Anatoly Korotkov
- Department of (Neuro)Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of AmsterdamMeibergdreef 9Amsterdam1105 AZthe Netherlands
| | - Noora Puhakka
- Department of Neurology, A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFI‐70211Finland
| | - Shalini Das Gupta
- Department of Neurology, A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFI‐70211Finland
| | - Niina Vuokila
- Department of Neurology, A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFI‐70211Finland
| | - Diede W. M. Broekaart
- Department of (Neuro)Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of AmsterdamMeibergdreef 9Amsterdam1105 AZthe Netherlands
| | - Jasper J. Anink
- Department of (Neuro)Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of AmsterdamMeibergdreef 9Amsterdam1105 AZthe Netherlands
| | - Mette Heiskanen
- Department of Neurology, A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFI‐70211Finland
| | - Jenni Karttunen
- Department of Neurology, A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFI‐70211Finland
| | - Jackelien van Scheppingen
- Department of (Neuro)Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of AmsterdamMeibergdreef 9Amsterdam1105 AZthe Netherlands
- Department of NeuroimmunologyNetherlands Institute for NeuroscienceMeibergdreef 47Amsterdam1105 BAthe Netherlands
| | - Inge Huitinga
- Department of NeuroimmunologyNetherlands Institute for NeuroscienceMeibergdreef 47Amsterdam1105 BAthe Netherlands
| | - James D. Mills
- Department of (Neuro)Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of AmsterdamMeibergdreef 9Amsterdam1105 AZthe Netherlands
| | - Erwin A. van Vliet
- Department of (Neuro)Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of AmsterdamMeibergdreef 9Amsterdam1105 AZthe Netherlands
- Swammerdam Institute for Life Sciences, Center for NeuroscienceUniversity of AmsterdamScience Park 904Amsterdam1090 GEthe Netherlands
| | - Asla Pitkänen
- Department of Neurology, A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFI‐70211Finland
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of AmsterdamMeibergdreef 9Amsterdam1105 AZthe Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN)Heemstedethe Netherlands
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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: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.)
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Vuokila N, Das Gupta S, Huusko R, Tohka J, Puhakka N, Pitkänen A. Elevated Acute Plasma miR-124-3p Level Relates to Evolution of Larger Cortical Lesion Area after Traumatic Brain Injury. Neuroscience 2020; 433:21-35. [PMID: 32142864 DOI: 10.1016/j.neuroscience.2020.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022]
Abstract
Mechanisms initiated by traumatic brain injury (TBI), leading to the development of progressive secondary injury are poorly understood. MicroRNAs (miRNAs) have a proposed role in orchestrating the post-injury aftermath as a single miRNA can control the expression of several genes. We hypothesized that the post-injury level of circulating brain-enriched miR-124-3p explains the extent of post-TBI cortical lesion. Three separate cohorts of adult male Sprague-Dawley rats (total n = 57) were injured with lateral fluid-percussion-induced TBI. The miR-124-3p levels were measured in whole blood and/or plasma in cohorts 1 and 2 before TBI as well as at 2 d, 7 d, 2 months or 3 months post-TBI. The third cohort (22/57) was imaged with T2-weighted magnetic resonance imaging (MRI) at 2 months post-TBI to quantify cortical lesion area and perilesional T2-enhancement volume. Our data shows that miR-124-3p levels were elevated at 2 d post-TBI in both blood (FC 4.63, p < 0.01) and plasma (FC 1.39, p < 0.05) as compared to controls. Receiver operating curve (ROC) analysis indicated that plasma miR-124-3p level of 34 copies/µl or higher differentiated TBI animals from controls [area under curve (AUC) 0.815, p < 0.05]. The data was validated in the third cohort (FC 1.68, p < 0.05). T2-weighted MRI revealed inter-animal differences in cortical lesion area. Linear regression analysis revealed that higher the plasma miR-124-3p level at 2 d post-TBI, larger the lesion area at chronic time point (R2 = 0.327, p < 0.01). Our findings indicate that the extent of lateral fluid-percussion injury-induced chronic cortical pathology associated with the acutely elevated plasma miR-124-3p level.
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Affiliation(s)
- Niina Vuokila
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Shalini Das Gupta
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Riina Huusko
- Natural Resources Institute Finland (Luke), PO Box 413, FI-90014 Oulu, Finland
| | - Jussi Tohka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Noora Puhakka
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FI-70211 Kuopio, Finland.
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Vuokila N, Lukasiuk K, Bot AM, van Vliet EA, Aronica E, Pitkänen A, Puhakka N. miR-124-3p is a chronic regulator of gene expression after brain injury. Cell Mol Life Sci 2018; 75:4557-4581. [PMID: 30155647 DOI: 10.1007/s00018-018-2911-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023]
Abstract
Traumatic brain injury (TBI) initiates molecular and cellular pathologies that underlie post-injury morbidities, including hippocampus-related memory decline and epileptogenesis. Non-coding small RNAs are master regulators of gene expression with the potential to affect multiple molecular pathways. To evaluate whether hippocampal gene expression networks are chronically regulated by microRNAs after TBI, we sampled the dentate gyrus of rats with severe TBI induced by lateral fluid-percussion injury 3 months earlier. Ingenuity pathway analysis revealed 30 upregulated miR-124-3p targets, suggesting that miR-124-3p is downregulated post-TBI (z-score = - 5.146, p < 0.05). Droplet digital polymerase chain reaction (ddPCR) and in situ hybridization confirmed the chronic downregulation of miR-124-3p (p < 0.05). Quantitative PCR analysis of two targets, Plp2 and Stat3, indicated that their upregulation correlated with the miR-124-3p downregulation (r = - 0.647, p < 0.05; r = - 0.629, p < 0.05, respectively). Immunohistochemical staining of STAT3 confirmed the increased protein expression. STRING analysis showed that 9 of the 30 miR-124-3p targets belonged to a STAT3 network. Reactome analysis and data mining connected the targets especially to inflammation and signal transduction. L1000CDS2 software revealed drugs (e.g., importazole, trichostatin A, and IKK-16) that could reverse the observed molecular changes. The translational value of our data was emphasized by in situ hybridization showing chronic post-traumatic downregulation of miR-124-3p in the dentate gyrus of TBI patients. Analysis of another brain injury model, status epilepticus, highlighted the fact that chronic downregulation of miR-124 is a common phenomenon after brain injury. Together, our findings indicate that miR-124-3p is a chronic modulator of molecular networks relevant to post-injury hippocampal pathologies in experimental models and in humans.
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Affiliation(s)
- Niina Vuokila
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland
| | - Katarzyna Lukasiuk
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Anna Maria Bot
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Str, 02-093, Warsaw, Poland
| | - Erwin A van Vliet
- Department of (Neuro)pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)pathology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Amsterdam, The Netherlands
| | - Asla Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland.
| | - Noora Puhakka
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, 70211, Kuopio, Finland.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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:
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