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Scott EY, Safarian N, Casasbuenas DL, Dryden M, Tockovska T, Ali S, Peng J, Daniele E, Nie Xin Lim I, Bang KWA, Tripathy S, Yuzwa SA, Wheeler AR, Faiz M. Integrating single-cell and spatially resolved transcriptomic strategies to survey the astrocyte response to stroke in male mice. Nat Commun 2024; 15:1584. [PMID: 38383565 PMCID: PMC10882052 DOI: 10.1038/s41467-024-45821-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Astrocytes, a type of glial cell in the central nervous system (CNS), adopt diverse states in response to injury that are influenced by their location relative to the insult. Here, we describe a platform for spatially resolved, single-cell transcriptomics and proteomics, called tDISCO (tissue-digital microfluidic isolation of single cells for -Omics). We use tDISCO alongside two high-throughput platforms for spatial (Visium) and single-cell transcriptomics (10X Chromium) to examine the heterogeneity of the astrocyte response to a cortical ischemic stroke in male mice. We show that integration of Visium and 10X Chromium datasets infers two astrocyte populations, proximal or distal to the injury site, while tDISCO determines the spatial boundaries and molecular profiles that define these populations. We find that proximal astrocytes show differences in lipid shuttling, with enriched expression of Apoe and Fabp5. Our datasets provide a resource for understanding the roles of astrocytes in stroke and showcase the utility of tDISCO for hypothesis-driven, spatially resolved single-cell experiments.
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Affiliation(s)
- Erica Y Scott
- Department of Surgery, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Nickie Safarian
- Department of Psychiatry, University of Toronto, 250 College St., Toronto, Ontario, M5T 1R8, Canada
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, CA, 250 College St., Toronto, Ontario, M5T 1R8, Canada
| | - Daniela Lozano Casasbuenas
- Department of Surgery, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Michael Dryden
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Teodora Tockovska
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Shawar Ali
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Emerson Daniele
- Department of Surgery, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Institute of Medical Sciences, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Isabel Nie Xin Lim
- Department of Surgery, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - K W Annie Bang
- Lunenfeld-Tanenbaum Research Institute, Flow Cytometry Core, Sinai Health, Toronto, Ontario, M5G 1X5, Canada
| | - Shreejoy Tripathy
- Department of Psychiatry, University of Toronto, 250 College St., Toronto, Ontario, M5T 1R8, Canada
- The Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, CA, 250 College St., Toronto, Ontario, M5T 1R8, Canada
| | - Scott A Yuzwa
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College St., Toronto, ON, M5S 3G9, Canada
| | - Maryam Faiz
- Department of Surgery, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
- Institute of Medical Sciences, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
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Khalili A, Safarian N, van Wijngaarden E, Zoidl GS, Zoidl GR, Rezai P. Loss of Panx1 function in zebrafish alters motor behavior in a lab-on-chip model of Parkinson's disease. J Neurosci Res 2023; 101:1814-1825. [PMID: 37688406 DOI: 10.1002/jnr.25241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023]
Abstract
Pannexin 1 (Panx1) forms ATP-permeable membrane channels that play roles in purinergic signaling in the nervous system. A link between Panx1 activity and neurodegenerative disorders including Parkinson's disease (PD) has been suggested, but experimental evidence is limited. Here, a zebrafish model of PD was produced by exposing panx1a+/+ and panx1a-/- zebrafish larvae to 6-hydroxydopamine (6-OHDA). Electrical stimulation in a microfluidic chip and quantitative real-time-qPCR of zebrafish larvae tested the role of Panx1 in both pathological and normal conditions. After 72-h treatment with 6-OHDA, the electric-induced locomotor activity of 5 days post fertilization (5dpf) panx1a+/+ larvae were reduced, while the stimulus did not affect locomotor activity of age-matched panx1a-/- larvae. A RT-qPCR analysis showed an increase in the expression of genes that are functionally related to dopaminergic signaling, like the tyrosine hydroxylase (th2) and the leucine-rich repeat kinase 2 (lrrk2). Extending the 6-OHDA treatment duration to 120 h caused a significant reduction in the locomotor response of 7dpf panx1a-/- larvae compared to the untreated panx1a-/- group. The RT-qPCR data showed a reduced expression of dopaminergic signaling genes in both genotypes. It was concluded that the absence of Panx1a channels compromised dopaminergic signaling in 6-OHDA-treated zebrafish larvae and that the increase in the expression of dopaminergic genes was transient, most likely due to a compensatory upregulation. We propose that zebrafish Panx1a models offer opportunities to shed light on PD's physiological and molecular basis. Panx1a might play a role on the progression of PD, and therefore deserves further investigation.
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Affiliation(s)
- Arezoo Khalili
- Department of Mechanical Engineering, York University, Toronto, Ontario, Canada
| | - Nickie Safarian
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Georg S Zoidl
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Georg R Zoidl
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, Ontario, Canada
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Whyte-Fagundes P, Taskina D, Safarian N, Zoidl C, Carlen PL, Donaldson LW, Zoidl GR. Panx1 channels promote both anti- and pro-seizure-like activities in the zebrafish via p2rx7 receptors and ATP signaling. Commun Biol 2022; 5:472. [PMID: 35585187 PMCID: PMC9117279 DOI: 10.1038/s42003-022-03356-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/07/2021] [Accepted: 04/12/2022] [Indexed: 11/08/2022] Open
Abstract
The molecular mechanisms of excitation/inhibition imbalances promoting seizure generation in epilepsy patients are not fully understood. Evidence suggests that Pannexin1 (Panx1), an ATP release channel, modulates the excitability of the brain. In this report, we performed electrophysiological, behavioral, and molecular phenotyping experiments on zebrafish larvae bearing genetic or pharmacological knockouts of Panx1a and Panx1b channels, each homologous to human PANX1. When Panx1a function is lost, or both channels are under pharmacological blockade, seizures with ictal-like events and seizure-like locomotion are reduced in the presence of pentylenetetrazol. Transcriptome profiling by RNA-seq demonstrates a spectrum of distinct metabolic and cell signaling states which correlate with the loss of Panx1a. Furthermore, the pro- and anticonvulsant activities of both Panx1 channels affect ATP release and involve the purinergic receptor P2rx7. Our findings suggest a subfunctionalization of Panx1 enabling dual roles in seizures, providing a unique and comprehensive perspective to understanding seizure mechanisms in the context of this channel.
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Affiliation(s)
- Paige Whyte-Fagundes
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada.
- Center of Vision Research (CVR), York University, Toronto, ON, M3J1P3, Canada.
- Krembil Research Institute, University Health Network, 60 Leonard Ave, Toronto, ON, M5T 1M8, Canada.
| | - Daria Taskina
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada
- Center of Vision Research (CVR), York University, Toronto, ON, M3J1P3, Canada
| | - Nickie Safarian
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada
- Center of Vision Research (CVR), York University, Toronto, ON, M3J1P3, Canada
| | - Christiane Zoidl
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada
- Center of Vision Research (CVR), York University, Toronto, ON, M3J1P3, Canada
| | - Peter L Carlen
- Krembil Research Institute, University Health Network, 60 Leonard Ave, Toronto, ON, M5T 1M8, Canada
- Department of Medicine, Physiology and BME, University of Toronto, 399 Bathurst St., 5w442, Toronto, ON, M5T 2S8, Canada
| | | | - Georg R Zoidl
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada.
- Center of Vision Research (CVR), York University, Toronto, ON, M3J1P3, Canada.
- Krembil Research Institute, University Health Network, 60 Leonard Ave, Toronto, ON, M5T 1M8, Canada.
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Safarian N, Houshangi-Tabrizi S, Zoidl C, Zoidl GR. Panx1b Modulates the Luminance Response and Direction of Locomotion in the Zebrafish. Int J Mol Sci 2021; 22:ijms222111750. [PMID: 34769181 PMCID: PMC8584175 DOI: 10.3390/ijms222111750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/29/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 12/29/2022] Open
Abstract
Pannexin1 (Panx1) can form ATP-permeable channels that play roles in the physiology of the visual system. In the zebrafish two ohnologs of Panx1, Panx1a and Panx1b, have unique and shared channel properties and tissue expression patterns. Panx1a channels are located in horizontal cells of the outer retina and modulate light decrement detection through an ATP/pH-dependent mechanisms and adenosine/dopamine signaling. Here, we decipher how the strategic localization of Panx1b channels in the inner retina and ganglion cell layer modulates visually evoked motor behavior. We describe a panx1b knockout model generated by TALEN technology. The RNA-seq analysis of 6 days post-fertilization larvae is confirmed by real-time PCR and paired with testing of locomotion behaviors by visual motor and optomotor response tests. We show that the loss of Panx1b channels disrupts the retinal response to an abrupt loss of illumination and it decreases the larval ability to follow leftward direction of locomotion in low light conditions. We concluded that the loss of Panx1b channels compromises the final output of luminance as well as motion detection. The Panx1b protein also emerges as a modulator of the circadian clock system. The disruption of the circadian clock system in mutants suggests that Panx1b could participate in non-image forming processes in the inner retina.
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Affiliation(s)
- Nickie Safarian
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada; (N.S.); (S.H.-T.); (C.Z.)
- Center of Vision Research, York University, Toronto, ON M3J 1P3, Canada
| | - Sarah Houshangi-Tabrizi
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada; (N.S.); (S.H.-T.); (C.Z.)
| | - Christiane Zoidl
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada; (N.S.); (S.H.-T.); (C.Z.)
- Center of Vision Research, York University, Toronto, ON M3J 1P3, Canada
| | - Georg R. Zoidl
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada; (N.S.); (S.H.-T.); (C.Z.)
- Center of Vision Research, York University, Toronto, ON M3J 1P3, Canada
- Correspondence:
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Khalili A, Peimani AR, Safarian N, Youssef K, Zoidl G, Rezai P. Phenotypic chemical and mutant screening of zebrafish larvae using an on-demand response to electric stimulation. Integr Biol (Camb) 2020; 11:373-383. [PMID: 31851358 DOI: 10.1093/intbio/zyz031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 06/08/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
Behavioral responses of zebrafish larvae to environmental cues are important functional readouts that should be evoked on-demand and studied phenotypically in behavioral, genetical and developmental investigations. Very recently, it was shown that zebrafish larvae execute a voluntary and oriented movement toward the positive electrode of an electric field along a microchannel. Phenotypic characterization of this response was not feasible due to larva's rapid movement along the channel. To overcome this challenge, a microfluidic device was introduced to partially immobilize the larva's head while leaving its mid-body and tail unrestrained in a chamber to image motor behaviors in response to electric stimulation, hence achieving quantitative phenotyping of the electrically evoked movement in zebrafish larvae. The effect of electric current on the tail-beat frequency and response duration of 5-7 days postfertilization zebrafish larvae was studied. Investigations were also performed on zebrafish exposed to neurotoxin 6-hydroxydopamine and larvae carrying a pannexin1a (panx1a) gene knockout, as a proof of principle applications to demonstrate on-demand movement behavior screening in chemical and mutant assays. We demonstrated for the first time that 6-hydroxydopamine leads to electric response impairment, levodopa treatment rescues the response and panx1a is involved in the electrically evoked movement of zebrafish larvae. We envision that our technique is broadly applicable as a screening tool to quantitatively examine zebrafish larvae's movements in response to physical and chemical stimulations in investigations of Parkinson's and other neurodegenerative diseases, and as a tool to combine recent advances in genome engineering of model organisms to uncover the biology of electric response.
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Affiliation(s)
- Arezoo Khalili
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Amir Reza Peimani
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | | | - Khaled Youssef
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Georg Zoidl
- Department of Biology, York University, Toronto, ON, Canada
| | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
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