1
|
Kihn K, Thomas CAD, Brelidze TI. VICR: A Novel Software for Unbiased Video and Image Analysis in Scientific Research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600811. [PMID: 38979144 PMCID: PMC11230449 DOI: 10.1101/2024.06.26.600811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
In scientific research, objectivity and unbiased data analysis is crucial for the validity and reproducibility of outcomes. This is particularly important for studies involving video or image categorization. A common approach of decreasing the bias is delegating data analysis to researchers unfamiliar with the experimental settings. However, this requires additional personnel and is prone to cognitive biases. Here we describe the Video & Image Cutter & Randomizer (VICR) software (https://github.com/kkihnphd/VICR), designed for unbiased analysis by segmenting and then randomizing videos or still images. VICR allows a single researcher to conduct and analyze studies in a blinded manner, eliminating the bias in analysis and streamlining the research process. We describe the features of the VICR software and demonstrate its capabilities using zebrafish behavior studies. To our knowledge, VICR is the only software for the randomization of video and image segments capable of eliminating bias in data analysis in a variety of research fields.
Collapse
Affiliation(s)
- Kyle Kihn
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Clementine A D Thomas
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, 20057, USA
| | - Tinatin I Brelidze
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, 20057, USA
| |
Collapse
|
2
|
Whyte-Fagundes PA, Vance A, Carroll A, Figueroa F, Manukyan C, Baraban SC. Testing of putative antiseizure medications in a preclinical Dravet syndrome zebrafish model. Brain Commun 2024; 6:fcae135. [PMID: 38707709 PMCID: PMC11069116 DOI: 10.1093/braincomms/fcae135] [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: 11/09/2023] [Revised: 03/27/2024] [Accepted: 04/12/2024] [Indexed: 05/07/2024] Open
Abstract
Dravet syndrome is a severe genetic epilepsy primarily caused by de novo mutations in a voltage-activated sodium channel gene (SCN1A). Patients face life-threatening seizures that are largely resistant to available anti-seizure medications. Preclinical Dravet syndrome animal models are a valuable tool to identify candidate anti-seizure medications for these patients. Among these, scn1lab mutant zebrafish, exhibiting spontaneous seizure-like activity, are particularly amenable to large-scale drug screening. Thus far, we have screened more than 3000 drug candidates in scn1lab zebrafish mutants, identifying valproate, stiripentol, and fenfluramine e.g. Food and Drug Administration-approved drugs, with clinical application in the Dravet syndrome population. Successful phenotypic screening in scn1lab mutant zebrafish is rigorous and consists of two stages: (i) a locomotion-based assay measuring high-velocity convulsive swim behaviour and (ii) an electrophysiology-based assay, using in vivo local field potential recordings, to quantify electrographic seizure-like events. Historically, nearly 90% of drug candidates fail during translation from preclinical models to the clinic. With such a high failure rate, it becomes necessary to address issues of replication and false positive identification. Leveraging our scn1lab zebrafish assays is one approach to address these problems. Here, we curated a list of nine anti-seizure drug candidates recently identified by other groups using preclinical Dravet syndrome models: 1-Ethyl-2-benzimidazolinone, AA43279, chlorzoxazone, donepezil, lisuride, mifepristone, pargyline, soticlestat and vorinostat. First-stage locomotion-based assays in scn1lab mutant zebrafish identified only 1-Ethyl-2-benzimidazolinone, chlorzoxazone and lisuride. However, second-stage local field potential recording assays did not show significant suppression of spontaneous electrographic seizure activity for any of the nine anti-seizure drug candidates. Surprisingly, soticlestat induced frank electrographic seizure-like discharges in wild-type control zebrafish. Taken together, our results failed to replicate clear anti-seizure efficacy for these drug candidates highlighting a necessity for strict scientific standards in preclinical identification of anti-seizure medications.
Collapse
Affiliation(s)
- Paige A Whyte-Fagundes
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Anjelica Vance
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Aloe Carroll
- Behavioral Neurosciences, Northeastern University, Boston, MA 02115, USA
| | - Francisco Figueroa
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Catherine Manukyan
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
| | - Scott C Baraban
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
3
|
Wei C, Fu M, Zhang H, Yao B. How is the P2X7 receptor signaling pathway involved in epileptogenesis? Neurochem Int 2024; 173:105675. [PMID: 38211839 DOI: 10.1016/j.neuint.2024.105675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
Epilepsy, a condition characterized by spontaneous recurrent epileptic seizures, is among the most prevalent neurological disorders. This disorder is estimated to affect approximately 70 million people worldwide. Although antiseizure medications are considered the first-line treatments for epilepsy, most of the available antiepileptic drugs are not effective in nearly one-third of patients. This calls for the development of more effective drugs. Evidence from animal models and epilepsy patients suggests that strategies that interfere with the P2X7 receptor by binding to adenosine triphosphate (ATP) are potential treatments for this patient population. This review describes the role of the P2X7 receptor signaling pathways in epileptogenesis. We highlight the genes, purinergic signaling, Pannexin1, glutamatergic signaling, adenosine kinase, calcium signaling, and inflammatory response factors involved in the process, and conclude with a synopsis of these key connections. By unraveling the intricate interplay between P2X7 receptors and epileptogenesis, this review provides ideas for designing potent clinical therapies that will revolutionize both prevention and treatment for epileptic patients.
Collapse
Affiliation(s)
- Caichuan Wei
- Department of Pediatrics, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Miaoying Fu
- Department of Pediatrics, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Haiju Zhang
- Department of Pediatrics, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuchang District, Wuhan, Hubei Province 430060, China
| | - Baozhen Yao
- Department of Pediatrics, Renmin Hospital of Wuhan University, 99 Zhang Zhidong Road, Wuchang District, Wuhan, Hubei Province 430060, China.
| |
Collapse
|
4
|
Whyte-Fagundes P, Vance A, Carroll A, Figueroa F, Manukyan C, Baraban SC. Testing of putative antiseizure drugs in a preclinical Dravet syndrome zebrafish model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566723. [PMID: 38014342 PMCID: PMC10680609 DOI: 10.1101/2023.11.11.566723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Dravet syndrome (DS) is a severe genetic epilepsy primarily caused by de novo mutations in a voltage-activated sodium channel gene (SCN1A). Patients face life-threatening seizures that are largely resistant to available anti-seizure medications (ASM). Preclinical DS animal models are a valuable tool to identify candidate ASMs for these patients. Among these, scn1lab mutant zebrafish exhibiting spontaneous seizure-like activity are particularly amenable to large-scale drug screening. Prior screening in a scn1lab mutant zebrafish line generated using N-ethyl-Nnitrosourea (ENU) identified valproate, stiripentol, and fenfluramine e.g., Federal Drug Administration (FDA) approved drugs with clinical application in the DS population. Successful phenotypic screening in scn1lab mutant zebrafish consists of two stages: (i) a locomotion-based assay measuring high-velocity convulsive swim behavior and (ii) an electrophysiology-based assay, using in vivo local field potential (LFP) recordings, to quantify electrographic seizure-like events. Using this strategy more than 3000 drug candidates have been screened in scn1lab zebrafish mutants. Here, we curated a list of nine additional anti-seizure drug candidates recently identified in preclinical models: 1-EBIO, AA43279, chlorzoxazone, donepezil, lisuride, mifepristone, pargyline, soticlestat and vorinostat. First-stage locomotion-based assays in scn1lab mutant zebrafish identified only 1-EBIO, chlorzoxazone and lisuride. However, second-stage LFP recording assays did not show significant suppression of spontaneous electrographic seizure activity for any of the nine anti-seizure drug candidates. Surprisingly, soticlestat induced frank electrographic seizure-like discharges in wild-type control zebrafish. Taken together, our results failed to replicate clear anti-seizure efficacy for these drug candidates highlighting a necessity for strict scientific standards in preclinical identification of ASMs.
Collapse
Affiliation(s)
- P Whyte-Fagundes
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - A Vance
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - A Carroll
- Behavioral Neurosciences, Northeastern University, Boston, MA, USA
| | - F Figueroa
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - C Manukyan
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| | - S C Baraban
- Epilepsy Research Laboratory and Weill Institute for Neuroscience, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
| |
Collapse
|
5
|
Wu YL, Yang AH, Chiu YH. Recent advances in the structure and activation mechanisms of metabolite-releasing Pannexin 1 channels. Biochem Soc Trans 2023; 51:1687-1699. [PMID: 37622532 DOI: 10.1042/bst20230038] [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: 06/29/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
Pannexin 1 (PANX1) is a widely expressed large-pore ion channel located in the plasma membrane of almost all vertebrate cells. It possesses a unique ability to act as a conduit for both inorganic ions (e.g. potassium or chloride) and bioactive metabolites (e.g. ATP or glutamate), thereby activating varying signaling pathways in an autocrine or paracrine manner. Given its crucial role in cell-cell interactions, the activity of PANX1 has been implicated in maintaining homeostasis of cardiovascular, immune, and nervous systems. Dysregulation of PANX1 has also been linked to numerous diseases, such as ischemic stroke, seizure, and inflammatory disorders. Therefore, the mechanisms underlying different modes of PANX1 activation and its context-specific channel properties have gathered significant attention. In this review, we summarize the roles of PANX1 in various physiological processes and diseases, and analyze the accumulated lines of evidence supporting diverse molecular mechanisms associated with different PANX1 activation modalities. We focus on examining recent discoveries regarding PANX1 regulations by reversible post-translational modifications, elevated intracellular calcium concentration, and protein-protein interactions, as well as by irreversible cleavage of its C-terminal tail. Additionally, we delve into the caveats in the proposed PANX1 gating mechanisms and channel open-closed configurations by critically analyzing the structural insights derived from cryo-EM studies and the unitary properties of PANX1 channels. By doing so, we aim to identify potential research directions for a better understanding of the functions and regulations of PANX1 channels.
Collapse
Affiliation(s)
- Yi-Ling Wu
- Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
| | - Ai-Hsing Yang
- Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
| | - Yu-Hsin Chiu
- Department of Life Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
- Institute of Biotechnology and Department of Medical Science, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd., Hsinchu 300044, Taiwan
| |
Collapse
|
6
|
Sluyter R, Adriouch S, Fuller SJ, Nicke A, Sophocleous RA, Watson D. Animal Models for the Investigation of P2X7 Receptors. Int J Mol Sci 2023; 24:ijms24098225. [PMID: 37175933 PMCID: PMC10179175 DOI: 10.3390/ijms24098225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
The P2X7 receptor is a trimeric ligand-gated cation channel activated by extracellular adenosine 5'-triphosphate. The study of animals has greatly advanced the investigation of P2X7 and helped to establish the numerous physiological and pathophysiological roles of this receptor in human health and disease. Following a short overview of the P2X7 distribution, roles and functional properties, this article discusses how animal models have contributed to the generation of P2X7-specific antibodies and nanobodies (including biologics), recombinant receptors and radioligands to study P2X7 as well as to the pharmacokinetic testing of P2X7 antagonists. This article then outlines how mouse and rat models have been used to study P2X7. These sections include discussions on preclinical disease models, polymorphic P2X7 variants, P2X7 knockout mice (including bone marrow chimeras and conditional knockouts), P2X7 reporter mice, humanized P2X7 mice and P2X7 knockout rats. Finally, this article reviews the limited number of studies involving guinea pigs, rabbits, monkeys (rhesus macaques), dogs, cats, zebrafish, and other fish species (seabream, ayu sweetfish, rainbow trout and Japanese flounder) to study P2X7.
Collapse
Affiliation(s)
- Ronald Sluyter
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Sahil Adriouch
- UniRouen, INSERM, U1234, Pathophysiology, Autoimmunity, and Immunotherapy, (PANTHER), Univ Rouen Normandie, University of Rouen, F-76000 Rouen, France
| | - Stephen J Fuller
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Nepean Hospital, Kingswood, NSW 2750, Australia
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany
| | - Reece A Sophocleous
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Debbie Watson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| |
Collapse
|
7
|
Purohit R, Bera AK. Carboxyl terminus of Pannexin-1 plays a crucial role in P2X7 receptor-mediated signaling. Biochem Biophys Res Commun 2023; 664:20-26. [PMID: 37130457 DOI: 10.1016/j.bbrc.2023.04.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/04/2023]
Abstract
The cellular implications of the interaction between Pannexin-1 (Panx1) channel and P2X7 receptor (P2X7R) have not been fully elucidated. Evidence suggests that ATP, released through Panx1, activates P2X7R, which in turn promotes further activation of Panx1. In a previous study, we reported that the C-terminus of Panx1 (Panx1-CT) attenuates P2X7R-mediated Ca2+ influx and cell death. One of the distinctive features of P2X7R is the gradual increase in current with repetitive stimulation. In the current study, we report an effect of Panx1-CT (amino acid residues 350 to 426) on P2X7R current, which differs from the effect of full-length Panx1. Panx1-CT inhibited P2X7R current, which persisted in all consecutive agonist applications. However, full-length Panx1 reduced P2X7R current at initial stimulations, followed by gradual augmentation. When P2X7R was activated for an extended period, cells expressing Panx1-CT exhibited less mitochondrial depolarization, reactive oxygen species (ROS) generation, Caspase 3 activation and cell death, whereas cells overexpressing full-length Panx1 showed the opposite effect. Taken together, these findings suggest that Panx1 can either attenuate or augment P2X7R-mediated cellular processes depending on the degree of P2X7R activation.
Collapse
Affiliation(s)
- Rutambhara Purohit
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, Tamil Nadu, India.
| | - Amal Kanti Bera
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, Tamil Nadu, India.
| |
Collapse
|
8
|
Brown-Panton CA, Sabour S, Zoidl GSO, Zoidl C, Tabatabaei N, Zoidl GR. Gap junction Delta-2b ( gjd2b/Cx35.1) depletion causes hyperopia and visual-motor deficiencies in the zebrafish. Front Cell Dev Biol 2023; 11:1150273. [PMID: 36936688 PMCID: PMC10017553 DOI: 10.3389/fcell.2023.1150273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
The zebrafish is a powerful model to investigate the developmental roles of electrical synapses because many signaling pathways that regulate the development of the nervous system are highly conserved from fish to humans. Here, we provide evidence linking the mammalian connexin-36 (Cx36) ortholog gjd2b/Cx35.1, a major component of electrical synapses in the zebrafish, with a refractive error in the context of morphological, molecular, and behavioral changes of zebrafish larvae. Two abnormalities were identified. The optical coherence tomography analysis of the adult retina confirmed changes to the refractive properties caused by eye axial length reduction, leading to hyperopic shifts. The gjd2b/Cx35.1 depletion was also correlated with morphological changes to the head and body ratios in larvae. The differential expression of Wnt/ß-catenin signaling genes, connexins, and dopamine receptors suggested a contribution to the observed phenotypic differences. The alteration of visual-motor behavioral responses to abrupt light transitions was aggravated in larvae, providing evidence that cone photoreceptor cell activity was enhanced when gjd2b/Cx35.1 was depleted. The visual disturbances were reversed under low light conditions in gjd2b -/- /Cx35.1-/- larvae. Since qRT-PCR data demonstrated that two rhodopsin genes were downregulated, we speculated that rod photoreceptor cells in gjd2b/Cx35.1-/- larvae were less sensitive to bright light transitions, thus providing additional evidence that a cone-mediated process caused the VMR light-ON hyperactivity after losing Cx35.1 expression. Together, this study provides evidence for the role of gjd2b/Cx35.1 in the development of the visual system and visually guided behaviors.
Collapse
Affiliation(s)
- Cherie A. Brown-Panton
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
- *Correspondence: Cherie A. Brown-Panton, ; Georg R. Zoidl,
| | - Shiva Sabour
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Georg S. O. Zoidl
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
| | - Christiane Zoidl
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
| | - Nima Tabatabaei
- Center for Vision Research, York University, Toronto, ON, Canada
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Georg R. Zoidl
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
- Department of Psychology, York University, Toronto, ON, Canada
- *Correspondence: Cherie A. Brown-Panton, ; Georg R. Zoidl,
| |
Collapse
|