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Mouradian GC, Liu P, Nakagawa P, Duffy E, Gomez Vargas J, Balapattabi K, Grobe JL, Sigmund CD, Hodges MR. Patch-to-Seq and Transcriptomic Analyses Yield Molecular Markers of Functionally Distinct Brainstem Serotonin Neurons. Front Synaptic Neurosci 2022; 14:910820. [PMID: 35844900 PMCID: PMC9280690 DOI: 10.3389/fnsyn.2022.910820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/10/2022] [Indexed: 01/22/2023] Open
Abstract
Acute regulation of CO2 and pH homeostasis requires sensory feedback from peripheral (carotid body) and central (central) CO2/pH sensitive cells - so called respiratory chemoreceptors. Subsets of brainstem serotonin (5-HT) neurons in the medullary raphe are CO2 sensitive or insensitive based on differences in embryonic origin, suggesting these functionally distinct subpopulations may have unique transcriptional profiles. Here, we used Patch-to-Seq to determine if the CO2 responses in brainstem 5-HT neurons could be correlated to unique transcriptional profiles and/or unique molecular markers and pathways. First, firing rate changes with hypercapnic acidosis were measured in fluorescently labeled 5-HT neurons in acute brainstem slices from transgenic, Dahl SS (SSMcwi) rats expressing T2/ePet-eGFP transgene in Pet-1 expressing (serotonin) neurons (SS ePet1-eGFP rats). Subsequently, the transcriptomic and pathway profiles of CO2 sensitive and insensitive 5-HT neurons were determined and compared by single cell RNA (scRNAseq) and bioinformatic analyses. Low baseline firing rates were a distinguishing feature of CO2 sensitive 5-HT neurons. scRNAseq of these recorded neurons revealed 166 differentially expressed genes among CO2 sensitive and insensitive 5-HT neurons. Pathway analyses yielded novel predicted upstream regulators, including the transcription factor Egr2 and Leptin. Additional bioinformatic analyses identified 6 candidate gene markers of CO2 sensitive 5-HT neurons, and 2 selected candidate genes (CD46 and Iba57) were both expressed in 5-HT neurons determined via in situ mRNA hybridization. Together, these data provide novel insights into the transcriptional control of cellular chemoreception and provide unbiased candidate gene markers of CO2 sensitive 5-HT neurons. Methodologically, these data highlight the utility of the patch-to-seq technique in enabling the linkage of gene expression to specific functions, like CO2 chemoreception, in a single cell to identify potential mechanisms underlying functional differences in otherwise similar cell types.
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Affiliation(s)
- Gary C. Mouradian
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Gary C. Mouradian Jr.,
| | - Pengyuan Liu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Pablo Nakagawa
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Erin Duffy
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Javier Gomez Vargas
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Kirthikaa Balapattabi
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Justin L. Grobe
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI, United States,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States,Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, United States,Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Curt D. Sigmund
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI, United States,Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Matthew R. Hodges
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, WI, United States
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Huang W, Xu Q, Liu F, Su J, Xiao D, Tang L, Hao ZZ, Liu R, Xiang K, Bi Y, Miao Z, Liu X, Liu Y, Liu S. Identification of TPBG-Expressing Amacrine Cells in DAT-tdTomato Mouse. Invest Ophthalmol Vis Sci 2022; 63:13. [PMID: 35551574 PMCID: PMC9123489 DOI: 10.1167/iovs.63.5.13] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
Purpose Neurons are the bricks of the neuronal system and experimental access to certain neuron subtypes will be of great help to decipher neuronal circuits. Here, we identified trophoblast glycoprotein (TPBG)-expressing GABAergic amacrine cells (ACs) that were selectively labeled in DAT-tdTomato transgenic mice. Methods Retina and brain sections were prepared for immunostaining with antibodies against various biomarkers. Patch-sequencing was performed to obtain the transcriptomes of tdTomato-positive cells in DAT-tdTomato mice. Whole-cell recordings were conducted to identify responses to light stimulation. Results Tyrosine hydroxylase immunoreactive cells were colocalized with tdTomato-positive cells in substantia nigra pars compacta, but not in the retina. Transcriptomes collected from tdTomato-positive cells in retinas via Patch-sequencing exhibited the expression of marker genes of ACs (Pax6 and Slc32a1) and marker genes of GABAergic neurons (Gad1, Gad2, and Slc6a1). Immunostaining with antibodies against relevant proteins (GAD67, GAD65, and GABA) also confirmed transcriptomic results. Furthermore, tdTomato-positive cells in retinas selectively expressed Tpbg, a marker gene for distinct clusters molecularly defined, which was proved with TPBG immunoreactivity in fluorescently labeled cells. Finally, tdTomato-positive cells recorded showed ON-OFF responses to light stimulation. Conclusions Ectopic expression occurs in the retina but not in the substantia nigra pars compacta in the DAT-tdTomato mouse, and fluorescently labeled cells in the retina are TPBG-expressing GABAergic ACs. This type of transgenic mice has been proved as an ideal tool to achieve efficient labeling of a distinct subset of ACs that selectively express Tpbg.
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Affiliation(s)
- Wanjing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qiang Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Feng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jing Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Dongchang Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Lei Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Ruifeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Kangjian Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yalan Bi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Xialin Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, China
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Dai XQ, Camunas-Soler J, Briant LJB, Dos Santos T, Spigelman AF, Walker EM, Arrojo E Drigo R, Bautista A, Jones RC, Avrahami D, Lyon J, Nie A, Smith N, Zhang Y, Johnson J, Manning Fox JE, Michelakis ED, Light PE, Kaestner KH, Kim SK, Rorsman P, Stein RW, Quake SR, MacDonald PE. Heterogenous impairment of α cell function in type 2 diabetes is linked to cell maturation state. Cell Metab 2022; 34:256-268.e5. [PMID: 35108513 PMCID: PMC8852281 DOI: 10.1016/j.cmet.2021.12.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 10/08/2021] [Accepted: 12/22/2021] [Indexed: 02/03/2023]
Abstract
In diabetes, glucagon secretion from pancreatic α cells is dysregulated. The underlying mechanisms, and whether dysfunction occurs uniformly among cells, remain unclear. We examined α cells from human donors and mice using electrophysiological, transcriptomic, and computational approaches. Rising glucose suppresses α cell exocytosis by reducing P/Q-type Ca2+ channel activity, and this is disrupted in type 2 diabetes (T2D). Upon high-fat feeding of mice, α cells shift toward a "β cell-like" electrophysiological profile in concert with indications of impaired identity. In human α cells we identified links between cell membrane properties and cell surface signaling receptors, mitochondrial respiratory chain complex assembly, and cell maturation. Cell-type classification using machine learning of electrophysiology data demonstrated a heterogenous loss of "electrophysiologic identity" in α cells from donors with type 2 diabetes. Indeed, a subset of α cells with impaired exocytosis is defined by an enrichment in progenitor and lineage markers and upregulation of an immature transcriptomic phenotype, suggesting important links between α cell maturation state and dysfunction.
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Affiliation(s)
- Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Joan Camunas-Soler
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94518, USA
| | - Linford J B Briant
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, Churchill Hospital, Oxford OX3 7LE, UK
| | - Theodore Dos Santos
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Aliya F Spigelman
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Emily M Walker
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48105, USA
| | - Rafael Arrojo E Drigo
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Austin Bautista
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Robert C Jones
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dana Avrahami
- Endocrinology and Metabolism Department, Hadassah-Hebrew University Medical Centre, Jerusalem, Israel
| | - James Lyon
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Aifang Nie
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Nancy Smith
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Yongneng Zhang
- Department of Medicine, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Janyne Johnson
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Jocelyn E Manning Fox
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | | | - Peter E Light
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, Churchill Hospital, Oxford OX3 7LE, UK
| | - Roland W Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94518, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G2R3, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G2R3, Canada.
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Kalmbach BE, Hodge RD, Jorstad NL, Owen S, de Frates R, Yanny AM, Dalley R, Mallory M, Graybuck LT, Radaelli C, Keene CD, Gwinn RP, Silbergeld DL, Cobbs C, Ojemann JG, Ko AL, Patel AP, Ellenbogen RG, Bakken TE, Daigle TL, Dee N, Lee BR, McGraw M, Nicovich PR, Smith K, Sorensen SA, Tasic B, Zeng H, Koch C, Lein ES, Ting JT. Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons. Neuron 2021; 109:2914-2927.e5. [PMID: 34534454 PMCID: PMC8570452 DOI: 10.1016/j.neuron.2021.08.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 06/22/2020] [Revised: 01/20/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022]
Abstract
In the neocortex, subcerebral axonal projections originate largely from layer 5 (L5) extratelencephalic-projecting (ET) neurons. The unique morpho-electric properties of these neurons have been mainly described in rodents, where retrograde tracers or transgenic lines can label them. Similar labeling strategies are infeasible in the human neocortex, rendering the translational relevance of findings in rodents unclear. We leveraged the recent discovery of a transcriptomically defined L5 ET neuron type to study the properties of human L5 ET neurons in neocortical brain slices derived from neurosurgeries. Patch-seq recordings, where transcriptome, physiology, and morphology were assayed from the same cell, revealed many conserved morpho-electric properties of human and rodent L5 ET neurons. Divergent properties were often subtler than differences between L5 cell types within these two species. These data suggest a conserved function of L5 ET neurons in the neocortical hierarchy but also highlight phenotypic divergence possibly related to functional specialization of human neocortex.
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Affiliation(s)
- Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA 98109, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA.
| | | | | | - Scott Owen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Matt Mallory
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Ryder P Gwinn
- Epilepsy Surgery and Functional Neurosurgery, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA 98195, USA
| | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA 98104, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA; Regional Epilepsy Center, Harborview Medical Center, Seattle, WA 98104, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA; Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA 98109, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA; The Washington National Primate Research Center, University of Washington, Seattle, WA 98195, USA.
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5
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Lee BR, Budzillo A, Hadley K, Miller JA, Jarsky T, Baker K, Hill D, Kim L, Mann R, Ng L, Oldre A, Rajanbabu R, Trinh J, Vargas S, Braun T, Dalley RA, Gouwens NW, Kalmbach BE, Kim TK, Smith KA, Soler-Llavina G, Sorensen S, Tasic B, Ting JT, Lein E, Zeng H, Murphy GJ, Berg J. Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization. eLife 2021; 10:e65482. [PMID: 34387544 PMCID: PMC8428855 DOI: 10.7554/elife.65482] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 12/06/2020] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
The Patch-seq approach is a powerful variation of the patch-clamp technique that allows for the combined electrophysiological, morphological, and transcriptomic characterization of individual neurons. To generate Patch-seq datasets at scale, we identified and refined key factors that contribute to the efficient collection of high-quality data. We developed patch-clamp electrophysiology software with analysis functions specifically designed to automate acquisition with online quality control. We recognized the importance of extracting the nucleus for transcriptomic success and maximizing membrane integrity during nucleus extraction for morphology success. The protocol is generalizable to different species and brain regions, as demonstrated by capturing multimodal data from human and macaque brain slices. The protocol, analysis and acquisition software are compiled at https://githubcom/AllenInstitute/patchseqtools. This resource can be used by individual labs to generate data across diverse mammalian species and that is compatible with large publicly available Patch-seq datasets.
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Affiliation(s)
- Brian R Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| | | | - DiJon Hill
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lisa Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | - Rusty Mann
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lindsay Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Aaron Oldre
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ram Rajanbabu
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jessica Trinh
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sara Vargas
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Brian E Kalmbach
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Tae Kyung Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | | | - Jonathan T Ting
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Gabe J Murphy
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology and Biophysics, University of WashingtonSeattleUnited States
| | - Jim Berg
- Allen Institute for Brain ScienceSeattleUnited States
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Kempf J, Knelles K, Hersbach BA, Petrik D, Riedemann T, Bednarova V, Janjic A, Simon-Ebert T, Enard W, Smialowski P, Götz M, Masserdotti G. Heterogeneity of neurons reprogrammed from spinal cord astrocytes by the proneural factors Ascl1 and Neurogenin2. Cell Rep 2021; 36:109409. [PMID: 34289357 PMCID: PMC8316252 DOI: 10.1016/j.celrep.2021.109409] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/14/2021] [Accepted: 06/24/2021] [Indexed: 01/21/2023] Open
Abstract
Astrocytes are a viable source for generating new neurons via direct conversion. However, little is known about the neurogenic cascades triggered in astrocytes from different regions of the CNS. Here, we examine the transcriptome induced by the proneural factors Ascl1 and Neurog2 in spinal cord-derived astrocytes in vitro. Each factor initially elicits different neurogenic programs that later converge to a V2 interneuron-like state. Intriguingly, patch sequencing (patch-seq) shows no overall correlation between functional properties and the transcriptome of the heterogenous induced neurons, except for K-channels. For example, some neurons with fully mature electrophysiological properties still express astrocyte genes, thus calling for careful molecular and functional analysis. Comparing the transcriptomes of spinal cord- and cerebral-cortex-derived astrocytes reveals profound differences, including developmental patterning cues maintained in vitro. These relate to the distinct neuronal identity elicited by Ascl1 and Neurog2 reflecting their developmental functions in subtype specification of the respective CNS region.
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Affiliation(s)
- J Kempf
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany
| | - K Knelles
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany
| | - B A Hersbach
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Graduate School of Systemic Neurosciences, LMU Munich, Planegg-Martinsried 82152, Germany
| | - D Petrik
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; School of Biosciences, The Sir Martin Evans Building, Cardiff University, CF10 3AX Cardiff, UK
| | - T Riedemann
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany
| | - V Bednarova
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany
| | - A Janjic
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Planegg-Martinsried 82152, Germany
| | - T Simon-Ebert
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany
| | - W Enard
- Biomedical Center Munich, Bioinformatic Core Facility, LMU Munich, Planegg-Martinsried 82152, Germany
| | - P Smialowski
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; School of Biosciences, The Sir Martin Evans Building, Cardiff University, CF10 3AX Cardiff, UK
| | - M Götz
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany; Excellence Cluster of Systems Neurology (SYNERGY), Munich, Germany.
| | - G Masserdotti
- Biomedical Center Munich, Physiological Genomics, LMU Munich, Planegg-Martinsried 82152, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, Neuherberg 85764, Germany.
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7
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Michel N, Narayanan P, Shomroni O, Schmidt M. Maturational Changes in Mouse Cutaneous Touch and Piezo2-Mediated Mechanotransduction. Cell Rep 2020; 32:107912. [PMID: 32697985 DOI: 10.1016/j.celrep.2020.107912] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 01/31/2020] [Revised: 04/22/2020] [Accepted: 06/25/2020] [Indexed: 01/28/2023] Open
Abstract
The age of studied animals has a profound impact on experimental outcomes in animal-based research. In mice, age influences molecular, morphological, physiological, and behavioral parameters, particularly during rapid postnatal growth and maturation until adulthood (at 12 weeks of age). Despite this knowledge, most biomedical studies use a wide-spanning age range from 4 to 12 weeks, raising concerns about reproducibility and potential masking of relevant age differences. Here, using mouse behavior and electrophysiology in cultured dorsal root ganglia (DRG), we reveal a decline in behavioral cutaneous touch sensitivity and Piezo2-mediated mechanotransduction in vitro during mouse maturation but not thereafter. In addition, we identify distinct transcript changes in individual Piezo2-expressing mechanosensitive DRG neurons by combining electrophysiology with single-cell RNA sequencing (patch-seq). Taken together, our study emphasizes the need for accurate age matching and uncovers hitherto unknown maturational plasticity in cutaneous touch at the level of behavior, mechanotransduction, and transcripts.
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Affiliation(s)
- Niklas Michel
- Max-Planck Institute of Experimental Medicine and University of Goettingen, Somatosensory Signaling and Systems Biology Group, 37075 Goettingen, Germany
| | - Pratibha Narayanan
- Max-Planck Institute of Experimental Medicine and University of Goettingen, Somatosensory Signaling and Systems Biology Group, 37075 Goettingen, Germany
| | - Orr Shomroni
- NGS Integrative Genomics, Department of Human Genetics at the University Medical Center Goettingen (UMG), 37075 Goettingen, Germany
| | - Manuela Schmidt
- Max-Planck Institute of Experimental Medicine and University of Goettingen, Somatosensory Signaling and Systems Biology Group, 37075 Goettingen, Germany.
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Camunas-Soler J, Dai XQ, Hang Y, Bautista A, Lyon J, Suzuki K, Kim SK, Quake SR, MacDonald PE. Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes. Cell Metab 2020; 31:1017-1031.e4. [PMID: 32302527 PMCID: PMC7398125 DOI: 10.1016/j.cmet.2020.04.005] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [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: 11/12/2019] [Revised: 01/23/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022]
Abstract
Impaired function of pancreatic islet cells is a major cause of metabolic dysregulation and disease in humans. Despite this, it remains challenging to directly link physiological dysfunction in islet cells to precise changes in gene expression. Here we show that single-cell RNA sequencing combined with electrophysiological measurements of exocytosis and channel activity (patch-seq) can be used to link endocrine physiology and transcriptomes at the single-cell level. We collected 1,369 patch-seq cells from the pancreata of 34 human donors with and without diabetes. An analysis of function and gene expression networks identified a gene set associated with functional heterogeneity in β cells that can be used to predict electrophysiology. We also report transcriptional programs underlying dysfunction in type 2 diabetes and extend this approach to cryopreserved cells from donors with type 1 diabetes, generating a valuable resource for understanding islet cell heterogeneity in health and disease.
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Affiliation(s)
- Joan Camunas-Soler
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94518, USA
| | - Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G 2E1, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Austin Bautista
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G 2E1, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - James Lyon
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Kunimasa Suzuki
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA.
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94518, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB T6G 2E1, Canada; Alberta Diabetes Institute, University of Alberta, Edmonton, AB T6G 2E1, Canada.
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Liu J, Wang M, Sun L, Pan NC, Zhang C, Zhang J, Zuo Z, He S, Wu Q, Wang X. Integrative analysis of in vivo recording with single-cell RNA-seq data reveals molecular properties of light-sensitive neurons in mouse V1. Protein Cell 2020; 11:417-432. [PMID: 32350740 PMCID: PMC7251024 DOI: 10.1007/s13238-020-00720-y] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/09/2020] [Indexed: 01/09/2023] Open
Abstract
Vision formation is classically based on projections from retinal ganglion cells (RGC) to the lateral geniculate nucleus (LGN) and the primary visual cortex (V1). Neurons in the mouse V1 are tuned to light stimuli. Although the cellular information of the retina and the LGN has been widely studied, the transcriptome profiles of single light-stimulated neuron in V1 remain unknown. In our study, in vivo calcium imaging and whole-cell electrophysiological patch-clamp recording were utilized to identify 53 individual cells from layer 2/3 of V1 as light-sensitive (LS) or non-light-sensitive (NS) by single-cell light-evoked calcium evaluation and action potential spiking. The contents of each cell after functional tests were aspirated in vivo through a patch-clamp pipette for mRNA sequencing. Moreover, the three-dimensional (3-D) morphological characterizations of the neurons were reconstructed in a live mouse after the whole-cell recordings. Our sequencing results indicated that V1 neurons with a high expression of genes related to transmission regulation, such as Rtn4r and Rgs7, and genes involved in membrane transport, such as Na+/K+ ATPase and NMDA-type glutamatergic receptors, preferentially responded to light stimulation. Furthermore, an antagonist that blocks Rtn4r signals could inactivate the neuronal responses to light stimulation in live mice. In conclusion, our findings of the vivo-seq analysis indicate the key role of the strength of synaptic transmission possesses neurons in V1 of light sensory.
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Affiliation(s)
- Jianwei Liu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Sun
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Clara Pan
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changjiang Zhang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junjing Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
| | - Zhentao Zuo
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sheng He
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, Beijing Institute for Brain Disorders, Capital Medical University, Beijing, 100069, China.
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10
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van den Hurk M, Erwin JA, Yeo GW, Gage FH, Bardy C. Corrigendum: Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. Front Mol Neurosci 2019; 12:150. [PMID: 31244603 PMCID: PMC6580186 DOI: 10.3389/fnmol.2019.00150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/24/2019] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fnmol.2018.00261.].
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Affiliation(s)
- Mark van den Hurk
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia
| | - Jennifer A Erwin
- The Lieber Institute for Brain Development, Baltimore, MD, United States.,Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
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11
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van den Hurk M, Erwin JA, Yeo GW, Gage FH, Bardy C. Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. Front Mol Neurosci 2018; 11:261. [PMID: 30147644 PMCID: PMC6096303 DOI: 10.3389/fnmol.2018.00261] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/12/2018] [Indexed: 11/13/2022] Open
Abstract
The human brain is composed of a complex assembly of about 171 billion heterogeneous cellular units (86 billion neurons and 85 billion non-neuronal glia cells). A comprehensive description of brain cells is necessary to understand the nervous system in health and disease. Recently, advances in genomics have permitted the accurate analysis of the full transcriptome of single cells (scRNA-seq). We have built upon such technical progress to combine scRNA-seq with patch-clamping electrophysiological recording and morphological analysis of single human neurons in vitro. This new powerful method, referred to as Patch-seq, enables a thorough, multimodal profiling of neurons and permits us to expose the links between functional properties, morphology, and gene expression. Here, we present a detailed Patch-seq protocol for isolating single neurons from in vitro neuronal cultures. We have validated the Patch-seq whole-transcriptome profiling method with human neurons generated from embryonic and induced pluripotent stem cells (ESCs/iPSCs) derived from healthy subjects, but the procedure may be applied to any kind of cell type in vitro. Patch-seq may be used on neurons in vitro to profile cell types and states in depth to unravel the human molecular basis of neuronal diversity and investigate the cellular mechanisms underlying brain disorders.
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Affiliation(s)
- Mark van den Hurk
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia
| | - Jennifer A Erwin
- The Lieber Institute for Brain Development, Baltimore, MD, United States.,Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI) Mind and Brain, Adelaide, SA, Australia.,Flinders University College of Medicine and Public Health, Adelaide, SA, Australia
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12
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Cadwell CR, Scala F, Li S, Livrizzi G, Shen S, Sandberg R, Jiang X, Tolias AS. Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq. Nat Protoc 2017; 12:2531-2553. [PMID: 29189773 PMCID: PMC6422019 DOI: 10.1038/nprot.2017.120] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [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] [Indexed: 11/09/2022]
Abstract
Neurons exhibit a rich diversity of morphological phenotypes, electrophysiological properties, and gene-expression patterns. Understanding how these different characteristics are interrelated at the single-cell level has been difficult because of the lack of techniques for multimodal profiling of individual cells. We recently developed Patch-seq, a technique that combines whole-cell patch-clamp recording, immunohistochemistry, and single-cell RNA-sequencing (scRNA-seq) to comprehensively profile single neurons from mouse brain slices. Here, we present a detailed step-by-step protocol, including modifications to the patching mechanics and recording procedure, reagents and recipes, procedures for immunohistochemistry, and other tips to assist researchers in obtaining high-quality morphological, electrophysiological, and transcriptomic data from single neurons. Successful implementation of Patch-seq allows researchers to explore the multidimensional phenotypic variability among neurons and to correlate gene expression with phenotype at the level of single cells. The entire procedure can be completed in ∼2 weeks through the combined efforts of a skilled electrophysiologist, molecular biologist, and biostatistician.
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Affiliation(s)
- Cathryn R. Cadwell
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Federico Scala
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Shuang Li
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Giulia Livrizzi
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Shan Shen
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xiaolong Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, Texas, USA
| | - Andreas S. Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, Texas, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas, USA
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