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Goodwin NL, Choong JJ, Hwang S, Pitts K, Bloom L, Islam A, Zhang YY, Szelenyi ER, Tong X, Newman EL, Miczek K, Wright HR, McLaughlin RJ, Norville ZC, Eshel N, Heshmati M, Nilsson SRO, Golden SA. Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience. Nat Neurosci 2024; 27:1411-1424. [PMID: 38778146 PMCID: PMC11268425 DOI: 10.1038/s41593-024-01649-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
The study of complex behaviors is often challenging when using manual annotation due to the absence of quantifiable behavioral definitions and the subjective nature of behavioral annotation. Integration of supervised machine learning approaches mitigates some of these issues through the inclusion of accessible and explainable model interpretation. To decrease barriers to access, and with an emphasis on accessible model explainability, we developed the open-source Simple Behavioral Analysis (SimBA) platform for behavioral neuroscientists. SimBA introduces several machine learning interpretability tools, including SHapley Additive exPlanation (SHAP) scores, that aid in creating explainable and transparent behavioral classifiers. Here we show how the addition of explainability metrics allows for quantifiable comparisons of aggressive social behavior across research groups and species, reconceptualizing behavior as a sharable reagent and providing an open-source framework. We provide an open-source, graphical user interface (GUI)-driven, well-documented package to facilitate the movement toward improved automation and sharing of behavioral classification tools across laboratories.
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Affiliation(s)
- Nastacia L Goodwin
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
| | - Jia J Choong
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Sophia Hwang
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Kayla Pitts
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Liana Bloom
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Aasiya Islam
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Yizhe Y Zhang
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
| | - Eric R Szelenyi
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
| | - Xiaoyu Tong
- New York University Neuroscience Institute, New York, NY, USA
| | - Emily L Newman
- Department of Psychiatry, Harvard Medical School McLean Hospital, Belmont, MA, USA
| | - Klaus Miczek
- Department of Psychology, Tufts University, Medford, MA, USA
| | - Hayden R Wright
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
- Graduate Program in Neuroscience, Washington State University, Pullman, WA, USA
| | - Ryan J McLaughlin
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
- Graduate Program in Neuroscience, Washington State University, Pullman, WA, USA
| | | | - Neir Eshel
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Mitra Heshmati
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Simon R O Nilsson
- Department of Biological Structure, University of Washington, Seattle, WA, USA.
| | - Sam A Golden
- Department of Biological Structure, University of Washington, Seattle, WA, USA.
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA.
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Haikonen J, Szrinivasan R, Ojanen S, Rhee JK, Ryazantseva M, Sulku J, Zumaraite G, Lauri SE. GluK1 kainate receptors are necessary for functional maturation of parvalbumin interneurons regulating amygdala circuit function. Mol Psychiatry 2024:10.1038/s41380-024-02641-2. [PMID: 38942774 DOI: 10.1038/s41380-024-02641-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Parvalbumin expressing interneurons (PV INs) are key players in the local inhibitory circuits and their developmental maturation coincides with the onset of adult-type network dynamics in the brain. Glutamatergic signaling regulates emergence of the unique PV IN phenotype, yet the receptor mechanisms involved are not fully understood. Here we show that GluK1 subunit containing kainate receptors (KARs) are necessary for development and maintenance of the neurochemical and functional properties of PV INs in the lateral and basal amygdala (BLA). Ablation of GluK1 expression specifically from PV INs resulted in low parvalbumin expression and loss of characteristic high firing rate throughout development. In addition, we observed reduced spontaneous excitatory synaptic activity at adult GluK1 lacking PV INs. Intriguingly, inactivation of GluK1 expression in adult PV INs was sufficient to abolish their high firing rate and to reduce PV expression levels, suggesting a role for GluK1 in dynamic regulation of PV IN maturation state. The PV IN dysfunction in the absence of GluK1 perturbed the balance between evoked excitatory vs. inhibitory synaptic inputs and long-term potentiation (LTP) in LA principal neurons, and resulted in aberrant development of the resting-state functional connectivity between mPFC and BLA. Behaviorally, the absence of GluK1 from PV INs associated with hyperactivity and increased fear of novelty. These results indicate a critical role for GluK1 KARs in regulation of PV IN function across development and suggest GluK1 as a potential therapeutic target for pathologies involving PV IN malfunction.
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Affiliation(s)
- Joni Haikonen
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Rakenduvadhana Szrinivasan
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Simo Ojanen
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Jun Kyu Rhee
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Maria Ryazantseva
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Janne Sulku
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Gabija Zumaraite
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Sari E Lauri
- HiLife Neuroscience Center and Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland.
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Iida I, Konno K, Natsume R, Abe M, Watanabe M, Sakimura K, Terunuma M. Behavioral analysis of kainate receptor KO mice and the role of GluK3 subunit in anxiety. Sci Rep 2024; 14:4521. [PMID: 38402313 PMCID: PMC10894277 DOI: 10.1038/s41598-024-55063-z] [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: 12/24/2023] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
Kainate receptors (KARs) are one of the ionotropic glutamate receptors in the central nervous system (CNS) comprised of five subunits, GluK1-GluK5. There is a growing interest in the association between KARs and psychiatric disorders, and there have been several studies investigating the behavioral phenotypes of KAR deficient mice, however, the difference in the genetic background has been found to affect phenotype in multiple mouse models of human diseases. Here, we examined GluK1-5 single KO mice in a pure C57BL/6N background and identified that GluK3 KO mice specifically express anxiolytic-like behavior with an alteration in dopamine D2 receptor (D2R)-induced anxiety, and reduced D2R expression in the striatum. Biochemical studies in the mouse cortex confirmed that GluK3 subunits do not assemble with GluK4 and GluK5 subunits, that can be activated by lower concentration of agonists. Overall, we found that GluK3-containing KARs function to express anxiety, which may represent promising anti-anxiety medication targets.
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Affiliation(s)
- Izumi Iida
- Division of Oral Biochemistry, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8514, Japan
- Research Center for Advanced Oral Science, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8514, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, 153-8902, Japan
| | - Kohtarou Konno
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Rie Natsume
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.
| | - Miho Terunuma
- Division of Oral Biochemistry, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 951-8514, Japan.
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Díaz-Rodríguez SM, Ivorra I, Espinosa J, Vegar C, Herrero-Turrión MJ, López DE, Gómez-Nieto R, Alberola-Die A. Enhanced Membrane Incorporation of H289Y Mutant GluK1 Receptors from the Audiogenic Seizure-Prone GASH/Sal Model: Functional and Morphological Impacts on Xenopus Oocytes. Int J Mol Sci 2023; 24:16852. [PMID: 38069190 PMCID: PMC10706347 DOI: 10.3390/ijms242316852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Epilepsy is a neurological disorder characterized by abnormal neuronal excitability, with glutamate playing a key role as the predominant excitatory neurotransmitter involved in seizures. Animal models of epilepsy are crucial in advancing epilepsy research by faithfully replicating the diverse symptoms of this disorder. In particular, the GASH/Sal (genetically audiogenic seizure-prone hamster from Salamanca) model exhibits seizures resembling human generalized tonic-clonic convulsions. A single nucleotide polymorphism (SNP; C9586732T, p.His289Tyr) in the Grik1 gene (which encodes the kainate receptor GluK1) has been previously identified in this strain. The H289Y mutation affects the amino-terminal domain of GluK1, which is related to the subunit assembly and trafficking. We used confocal microscopy in Xenopus oocytes to investigate how the H289Y mutation, compared to the wild type (WT), affects the expression and cell-surface trafficking of GluK1 receptors. Additionally, we employed the two-electrode voltage-clamp technique to examine the functional effects of the H289Y mutation. Our results indicate that this mutation increases the expression and incorporation of GluK1 receptors into an oocyte's membrane, enhancing kainate-evoked currents, without affecting their functional properties. Although further research is needed to fully understand the molecular mechanisms responsible for this epilepsy, the H289Y mutation in GluK1 may be part of the molecular basis underlying the seizure-prone circuitry in the GASH/Sal model.
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Affiliation(s)
- Sandra M. Díaz-Rodríguez
- Neuroscience Institute of Castilla y León (INCyL), University of Salamanca, E-37007 Salamanca, Spain; (S.M.D.-R.); (M.J.H.-T.); (R.G.-N.)
- Institute of Biomedical Research of Salamanca (IBSAL), E-37007 Salamanca, Spain
| | - Isabel Ivorra
- Department of Physiology, Genetics and Microbiology, University of Alicante, E-03690 Alicante, Spain; (I.I.); (J.E.); (C.V.); (A.A.-D.)
| | - Javier Espinosa
- Department of Physiology, Genetics and Microbiology, University of Alicante, E-03690 Alicante, Spain; (I.I.); (J.E.); (C.V.); (A.A.-D.)
| | - Celia Vegar
- Department of Physiology, Genetics and Microbiology, University of Alicante, E-03690 Alicante, Spain; (I.I.); (J.E.); (C.V.); (A.A.-D.)
| | - M. Javier Herrero-Turrión
- Neuroscience Institute of Castilla y León (INCyL), University of Salamanca, E-37007 Salamanca, Spain; (S.M.D.-R.); (M.J.H.-T.); (R.G.-N.)
- Institute of Biomedical Research of Salamanca (IBSAL), E-37007 Salamanca, Spain
- Neurological Tissue Bank INCYL (BTN-INCYL), University of Salamanca, E-37007 Salamanca, Spain
| | - Dolores E. López
- Neuroscience Institute of Castilla y León (INCyL), University of Salamanca, E-37007 Salamanca, Spain; (S.M.D.-R.); (M.J.H.-T.); (R.G.-N.)
- Institute of Biomedical Research of Salamanca (IBSAL), E-37007 Salamanca, Spain
| | - Ricardo Gómez-Nieto
- Neuroscience Institute of Castilla y León (INCyL), University of Salamanca, E-37007 Salamanca, Spain; (S.M.D.-R.); (M.J.H.-T.); (R.G.-N.)
- Institute of Biomedical Research of Salamanca (IBSAL), E-37007 Salamanca, Spain
| | - Armando Alberola-Die
- Department of Physiology, Genetics and Microbiology, University of Alicante, E-03690 Alicante, Spain; (I.I.); (J.E.); (C.V.); (A.A.-D.)
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Atanasova T, Savonlehto T, Kukko-Lukjanov TK, Kharybina Z, Chang WC, Lauri SE, Taira T. Progressive development of synchronous activity in the hippocampal neuronal network is modulated by GluK1 kainate receptors. Neuropharmacology 2023; 239:109671. [PMID: 37567438 DOI: 10.1016/j.neuropharm.2023.109671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023]
Abstract
Kainate receptors are potent modulators of circuit excitability and have been repeatedly implicated in pathophysiological synchronization of limbic networks. While the role of aberrant GluK2 subunit containing KARs in generation of epileptiform hypersynchronous activity is well described, the contribution of other KAR subtypes, including GluK1 subunit containing KARs remain less well understood. To investigate the contribution of GluK1 KARs in developmental and pathological synchronization of the hippocampal neural network, we used multielectrode array recordings on organotypic hippocampal slices that display first multi-unit activity and later spontaneous population discharges resembling ictal-like epileptiform activity (IEA). Chronic blockage of GluK1 activity using selective antagonist ACET or lentivirally delivered shRNA significantly delayed developmental synchronization of the hippocampal CA3 network and generation of IEA. GluK1 overexpression, on the other hand, had no significant effect on occurrence of IEA, but enhanced the size of the neuron population participating in the population discharges. Correlation analysis indicated that local knockdown of GluK1 locally in the CA3 neurons reduced their functional connectivity, while GluK1 overexpression increased the connectivity to both CA1 and DG. These data suggest that GluK1 KARs regulate functional connectivity between the excitatory neurons, possibly via morphological changes in glutamatergic circuit, affecting synchronization of neuronal populations. The significant effects of GluK1 manipulations on network activity call for further research on GluK1 KAR as potential targets for antiepileptic treatments, particularly during the early postnatal development when GluK1 KARs are strongly expressed in the limbic neural networks.
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Affiliation(s)
- Tsvetomira Atanasova
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Tiina Savonlehto
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | | | - Zoia Kharybina
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Wei-Chih Chang
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Sari E Lauri
- HiLife Neuroscience Center, University of Helsinki, Helsinki, Finland; Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland.
| | - Tomi Taira
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Finland.
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