1
|
Kapustina M, Zhang AA, Tsai JYJ, Bristow BN, Kraus L, Sullivan KE, Erwin SR, Wang L, Stach TR, Clements J, Lemire AL, Cembrowski MS. The cell-type-specific spatial organization of the anterior thalamic nuclei of the mouse brain. Cell Rep 2024; 43:113842. [PMID: 38427564 DOI: 10.1016/j.celrep.2024.113842] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/22/2023] [Accepted: 02/07/2024] [Indexed: 03/03/2024] Open
Abstract
Understanding the cell-type composition and spatial organization of brain regions is crucial for interpreting brain computation and function. In the thalamus, the anterior thalamic nuclei (ATN) are involved in a wide variety of functions, yet the cell-type composition of the ATN remains unmapped at a single-cell and spatial resolution. Combining single-cell RNA sequencing, spatial transcriptomics, and multiplexed fluorescent in situ hybridization, we identify three discrete excitatory cell-type clusters that correspond to the known nuclei of the ATN and uncover marker genes, molecular pathways, and putative functions of these cell types. We further illustrate graded spatial variation along the dorsomedial-ventrolateral axis for all individual nuclei of the ATN and additionally demonstrate that the anteroventral nucleus exhibits spatially covarying protein products and long-range inputs. Collectively, our study reveals discrete and continuous cell-type organizational principles of the ATN, which will help to guide and interpret experiments on ATN computation and function.
Collapse
Affiliation(s)
- Margarita Kapustina
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Angela A Zhang
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jennifer Y J Tsai
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Brianna N Bristow
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Larissa Kraus
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Kaitlin E Sullivan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sarah R Erwin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Lihua Wang
- Janelia Research Campus, HHMI, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Tara R Stach
- School of Biomedical Engineering, Biomedical Research Centre, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jody Clements
- Janelia Research Campus, HHMI, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Andrew L Lemire
- Janelia Research Campus, HHMI, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada; Janelia Research Campus, HHMI, 19700 Helix Drive, Ashburn, VA 20147, USA.
| |
Collapse
|
2
|
Abdelfattah AS, Zheng J, Singh A, Huang YC, Reep D, Tsegaye G, Tsang A, Arthur BJ, Rehorova M, Olson CVL, Shuai Y, Zhang L, Fu TM, Milkie DE, Moya MV, Weber TD, Lemire AL, Baker CA, Falco N, Zheng Q, Grimm JB, Yip MC, Walpita D, Chase M, Campagnola L, Murphy GJ, Wong AM, Forest CR, Mertz J, Economo MN, Turner GC, Koyama M, Lin BJ, Betzig E, Novak O, Lavis LD, Svoboda K, Korff W, Chen TW, Schreiter ER, Hasseman JP, Kolb I. Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator. Neuron 2023; 111:1547-1563.e9. [PMID: 37015225 PMCID: PMC10280807 DOI: 10.1016/j.neuron.2023.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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: 12/06/2022] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 04/05/2023]
Abstract
The ability to optically image cellular transmembrane voltages at millisecond-timescale resolutions can offer unprecedented insight into the function of living brains in behaving animals. Here, we present a point mutation that increases the sensitivity of Ace2 opsin-based voltage indicators. We use the mutation to develop Voltron2, an improved chemigeneic voltage indicator that has a 65% higher sensitivity to single APs and 3-fold higher sensitivity to subthreshold potentials than Voltron. Voltron2 retained the sub-millisecond kinetics and photostability of its predecessor, although with lower baseline fluorescence. In multiple in vitro and in vivo comparisons with its predecessor across multiple species, we found Voltron2 to be more sensitive to APs and subthreshold fluctuations. Finally, we used Voltron2 to study and evaluate the possible mechanisms of interneuron synchronization in the mouse hippocampus. Overall, we have discovered a generalizable mutation that significantly increases the sensitivity of Ace2 rhodopsin-based sensors, improving their voltage reporting capability.
Collapse
Affiliation(s)
| | - Jihong Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Amrita Singh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Yi-Chieh Huang
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Daniel Reep
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Getahun Tsegaye
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Arthur Tsang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Benjamin J Arthur
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Monika Rehorova
- Department of Physiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Carl V L Olson
- Department of Physiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Yichun Shuai
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Lixia Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Tian-Ming Fu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Maria V Moya
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Timothy D Weber
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Natalie Falco
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Mighten C Yip
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Deepika Walpita
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | | | - Allan M Wong
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Craig R Forest
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Michael N Economo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Glenn C Turner
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Bei-Jung Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Departments of Molecular and Cell Biology and Physics, Howard Hughes Medical Institute, Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ondrej Novak
- Department of Physiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Tsai-Wen Chen
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Jeremy P Hasseman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Ilya Kolb
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; GENIE Project Team, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| |
Collapse
|
3
|
Chen C, Niehaus JK, Dinc F, Huang KL, Barnette AL, Shuster SA, Wang L, Lemire AL, Menon V, Ritola K, Hantman A, Zeng H, Schnitzer MJ, Scherrer G. Impaired Feedforward Inhibition Of Corticopontine Neurons Drives Placebo Analgesia. The Journal of Pain 2023. [DOI: 10.1016/j.jpain.2023.02.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
|
4
|
Sullivan KE, Kraus L, Kapustina M, Wang L, Stach TR, Lemire AL, Clements J, Cembrowski MS. Sharp cell-type-identity changes differentiate the retrosplenial cortex from the neocortex. Cell Rep 2023; 42:112206. [PMID: 36881508 DOI: 10.1016/j.celrep.2023.112206] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/22/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
The laminae of the neocortex are fundamental processing layers of the mammalian brain. Notably, such laminae are believed to be relatively stereotyped across short spatial scales such that shared laminae between nearby brain regions exhibit similar constituent cells. Here, we consider a potential exception to this rule by studying the retrosplenial cortex (RSC), a brain region known for sharp cytoarchitectonic differences across its granular-dysgranular border. Using a variety of transcriptomics techniques, we identify, spatially map, and interpret the excitatory cell-type landscape of the mouse RSC. In doing so, we uncover that RSC gene expression and cell types change sharply at the granular-dysgranular border. Additionally, supposedly homologous laminae between the RSC and the neocortex are effectively wholly distinct in their cell-type composition. In collection, the RSC exhibits a variety of intrinsic cell-type specializations and embodies an organizational principle wherein cell-type identities can vary sharply within and between brain regions.
Collapse
Affiliation(s)
- Kaitlin E Sullivan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Boulevard, Vancouver, BC, Canada
| | - Larissa Kraus
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Boulevard, Vancouver, BC, Canada
| | - Margarita Kapustina
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Boulevard, Vancouver, BC, Canada
| | - Lihua Wang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC, Canada
| | - Tara R Stach
- School of Biomedical Engineering, Biomedical Research Centre, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, Canada
| | - Andrew L Lemire
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC, Canada
| | - Jody Clements
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC, Canada
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Boulevard, Vancouver, BC, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC, Canada; Janelia Research Campus, HHMI, 19700 Helix Dr, Ashburn, VA, USA.
| |
Collapse
|
5
|
Wang Y, Krabbe S, Eddison M, Henry FE, Fleishman G, Lemire AL, Wang L, Korff W, Tillberg PW, Lüthi A, Sternson SM. Multimodal mapping of cell types and projections in the central nucleus of the amygdala. eLife 2023; 12:84262. [PMID: 36661218 PMCID: PMC9977318 DOI: 10.7554/elife.84262] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-seq) to classify molecularly defined cell types in the CEA and identified marker genes to map the location of these neuronal types using expansion-assisted iterative fluorescence in situ hybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of ~30,000 molecularly defined CEA neurons. Our study revealed spatiomolecular organization of the CEA, with medial and lateral CEA associated with distinct molecularly defined cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.
Collapse
Affiliation(s)
- Yuhan Wang
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Sabine Krabbe
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Mark Eddison
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Fredrick E Henry
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Greg Fleishman
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Paul W Tillberg
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Andreas Lüthi
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Scott M Sternson
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Howard Hughes Medical Institute & Department of Neurosciences, University of California, San DiegoSan DiegoUnited States
| |
Collapse
|
6
|
O’Leary TP, Kendrick RM, Bristow BN, Sullivan KE, Wang L, Clements J, Lemire AL, Cembrowski MS. Neuronal cell types, projections, and spatial organization of the central amygdala. iScience 2022; 25:105497. [DOI: 10.1016/j.isci.2022.105497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 07/07/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
|
7
|
Wang Y, Eddison M, Fleishman G, Weigert M, Xu S, Wang T, Rokicki K, Goina C, Henry FE, Lemire AL, Schmidt U, Yang H, Svoboda K, Myers EW, Saalfeld S, Korff W, Sternson SM, Tillberg PW. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization. Cell 2021; 184:6361-6377.e24. [PMID: 34875226 DOI: 10.1016/j.cell.2021.11.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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] [Received: 02/21/2021] [Revised: 08/22/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022]
Abstract
Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.
Collapse
Affiliation(s)
- Yuhan Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Mark Eddison
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Greg Fleishman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Martin Weigert
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Institute of Bioengineering, School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Shengjin Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tim Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Konrad Rokicki
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Cristian Goina
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Fredrick E Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Uwe Schmidt
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Hui Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Scott M Sternson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Paul W Tillberg
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| |
Collapse
|
8
|
de Rus Jacquet A, Tancredi JL, Lemire AL, DeSantis MC, Li WP, O'Shea EK. The LRRK2 G2019S mutation alters astrocyte-to-neuron communication via extracellular vesicles and induces neuron atrophy in a human iPSC-derived model of Parkinson's disease. eLife 2021; 10:e73062. [PMID: 34590578 PMCID: PMC8514240 DOI: 10.7554/elife.73062] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 08/15/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022] Open
Abstract
Astrocytes are essential cells of the central nervous system, characterized by dynamic relationships with neurons that range from functional metabolic interactions and regulation of neuronal firing activities, to the release of neurotrophic and neuroprotective factors. In Parkinson's disease (PD), dopaminergic neurons are progressively lost during the course of the disease, but the effects of PD on astrocytes and astrocyte-to-neuron communication remain largely unknown. This study focuses on the effects of the PD-related mutation LRRK2 G2019S in astrocytes generated from patient-derived induced pluripotent stem cells. We report the alteration of extracellular vesicle (EV) biogenesis in astrocytes and identify the abnormal accumulation of key PD-related proteins within multivesicular bodies (MVBs). We found that dopaminergic neurons internalize astrocyte-secreted EVs and that LRRK2 G2019S EVs are abnormally enriched in neurites and fail to provide full neurotrophic support to dopaminergic neurons. Thus, dysfunctional astrocyte-to-neuron communication via altered EV biological properties may participate in the progression of PD.
Collapse
Affiliation(s)
| | - Jenna L Tancredi
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Michael C DeSantis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Wei-Ping Li
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Erin K O'Shea
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| |
Collapse
|
9
|
Brown TA, Schaefer KS, Tsang A, Yi HA, Grimm JB, Lemire AL, Jradi FM, Kim C, McGowan K, Ritola K, Armstrong DT, Mostafa HH, Korff W, Vale RD, Lavis LD. Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes. J Biomol Tech 2021; 32:121-133. [PMID: 35027870 PMCID: PMC8730524 DOI: 10.7171/jbt.21-3203-007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The worldwide coronavirus disease 2019 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce 2 pH-sensitive "LAMPshade" dyes as novel readouts in an isothermal Reverse Transcriptase Loop-mediated isothermal AMPlification amplification assay for severe acute respiratory syndrome coronavirus 2 RNA. The resulting JaneliaLAMP assay is robust, simple, inexpensive, and has low technical requirements, and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.
Collapse
Affiliation(s)
- Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | | | - Arthur Tsang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Hyun Ah Yi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Andrew L. Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Charles Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Kevin McGowan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Kimberly Ritola
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Derek T. Armstrong
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287-7093
| | - Heba H. Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287-7093
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Ronald D. Vale
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| |
Collapse
|
10
|
Erwin SR, Bristow BN, Sullivan KE, Kendrick RM, Marriott B, Wang L, Clements J, Lemire AL, Jackson J, Cembrowski MS. Spatially patterned excitatory neuron subtypes and projections of the claustrum. eLife 2021; 10:68967. [PMID: 34397382 PMCID: PMC8367382 DOI: 10.7554/elife.68967] [Citation(s) in RCA: 12] [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: 03/31/2021] [Accepted: 07/28/2021] [Indexed: 01/22/2023] Open
Abstract
The claustrum is a functionally and structurally complex brain region, whose very spatial extent remains debated. Histochemical-based approaches typically treat the claustrum as a relatively narrow anatomical region that primarily projects to the neocortex, whereas circuit-based approaches can suggest a broader claustrum region containing projections to the neocortex and other regions. Here, in the mouse, we took a bottom-up and cell-type-specific approach to complement and possibly unite these seemingly disparate conclusions. Using single-cell RNA-sequencing, we found that the claustrum comprises two excitatory neuron subtypes that are differentiable from the surrounding cortex. Multicolor retrograde tracing in conjunction with 12-channel multiplexed in situ hybridization revealed a core-shell spatial arrangement of these subtypes, as well as differential downstream targets. Thus, the claustrum comprises excitatory neuron subtypes with distinct molecular and projection properties, whose spatial patterns reflect the narrower and broader claustral extents debated in previous research. This subtype-specific heterogeneity likely shapes the functional complexity of the claustrum.
Collapse
Affiliation(s)
- Sarah R Erwin
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Brianna N Bristow
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Kaitlin E Sullivan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Rennie M Kendrick
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Brian Marriott
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jody Clements
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jesse Jackson
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada.,Department of Physiology, University of Alberta, Edmonton, Canada
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| |
Collapse
|
11
|
Korgaonkar A, Han C, Lemire AL, Siwanowicz I, Bennouna D, Kopec RE, Andolfatto P, Shigenobu S, Stern DL. A novel family of secreted insect proteins linked to plant gall development. Curr Biol 2021; 31:1836-1849.e12. [PMID: 33657407 PMCID: PMC8119383 DOI: 10.1016/j.cub.2021.01.104] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022]
Abstract
In an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here, we study the aphid Hormaphis cornu, which makes distinctive "cone" galls on leaves of witch hazel Hamamelis virginiana. We found that derived genetic variants in the aphid gene determinant of gall color (dgc) are associated with strong downregulation of dgc transcription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls and that this results in differential expression of a small number of plant genes. dgc is a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins. bicycle genes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development. bicycle genes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.
Collapse
Affiliation(s)
- Aishwarya Korgaonkar
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Clair Han
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Andrew L Lemire
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Igor Siwanowicz
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Djawed Bennouna
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, 262G Campbell Hall, 1787 Neil Avenue, Columbus, OH 43210, USA
| | - Rachel E Kopec
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, 262G Campbell Hall, 1787 Neil Avenue, Columbus, OH 43210, USA; Ohio State University's Foods for Health Discovery Theme, The Ohio State University, 262G Campbell Hall, 1787 Neil Avenue, Columbus, OH 43210, USA
| | - Peter Andolfatto
- Department of Biology, Columbia University, 600 Fairchild Center, New York, NY 10027, USA
| | - Shuji Shigenobu
- Laboratory of Evolutionary Genomics, Center for the Development of New Model Organism, National Institute for Basic Biology, Okazaki 444-8585, Japan; NIBB Research Core Facilities, National Institute for Basic Biology, Okazaki 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - David L Stern
- Janelia Research Campus of the Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| |
Collapse
|
12
|
Korgaonkar A, Han C, Lemire AL, Siwanowicz I, Bennouna D, Kopec RE, Andolfatto P, Shigenobu S, Stern DL. A novel family of secreted insect proteins linked to plant gall development. Curr Biol 2021. [PMID: 33974861 DOI: 10.1101/2020.10.28.359562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
AbstractIn an elaborate form of inter-species exploitation, many insects hijack plant development to induce novel plant organs called galls that provide the insect with a source of nutrition and a temporary home. Galls result from dramatic reprogramming of plant cell biology driven by insect molecules, but the roles of specific insect molecules in gall development have not yet been determined. Here we study the aphidHormaphis cornu, which makes distinctive “cone” galls on leaves of witch hazelHamamelis virginiana. We found that derived genetic variants in the aphid genedeterminant of gall color(dgc) are associated with strong downregulation ofdgctranscription in aphid salivary glands, upregulation in galls of seven genes involved in anthocyanin synthesis, and deposition of two red anthocyanins in galls. We hypothesize that aphids inject DGC protein into galls, and that this results in differential expression of a small number of plant genes.Dgcis a member of a large, diverse family of novel predicted secreted proteins characterized by a pair of widely spaced cysteine-tyrosine-cysteine (CYC) residues, which we named BICYCLE proteins.Bicyclegenes are most strongly expressed in the salivary glands specifically of galling aphid generations, suggesting that they may regulate many aspects of gall development.Bicyclegenes have experienced unusually frequent diversifying selection, consistent with their potential role controlling gall development in a molecular arms race between aphids and their host plants.One Sentence SummaryAphidbicyclegenes, which encode diverse secreted proteins, contribute to plant gall development.
Collapse
|
13
|
Korgaonkar A, Han C, Lemire AL, Siwanowicz I, Bennouna D, Kopec RE, Andolfatto P, Shigenobu S, Stern DL. A novel family of secreted insect proteins linked to plant gall development. Curr Biol 2021; 31:2038. [PMID: 33974861 DOI: 10.1016/j.cub.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
14
|
Asou Y, Ray RP, Long X, Bushey D, Cichewicz K, Ngo TTB, Sharp B, Christoforou C, Hu A, Lemire AL, Tillberg P, Hirsh J, Litwin-Kumar A, Rubin GM. Correction: Nitric oxide acts as a cotransmitter in a subset of dopaminergic neurons to diversify memory dynamics. eLife 2020; 9:64094. [PMID: 33090093 PMCID: PMC7581427 DOI: 10.7554/elife.64094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
15
|
Xu S, Yang H, Menon V, Lemire AL, Wang L, Henry FE, Turaga SC, Sternson SM. Behavioral state coding by molecularly defined paraventricular
hypothalamic cell type ensembles. Science 2020; 370:370/6514/eabb2494. [DOI: 10.1126/science.abb2494] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022]
Abstract
Brains encode behaviors using neurons amenable to systematic
classification by gene expression. The contribution of molecular identity to
neural coding is not understood because of the challenges involved with
measuring neural dynamics and molecular information from the same cells. We
developed CaRMA (calcium and RNA multiplexed activity) imaging based on
recording in vivo single-neuron calcium dynamics followed by gene expression
analysis. We simultaneously monitored activity in hundreds of neurons in
mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker
genes had predictive power for neuronal responses across 11 behavioral
states. The PVH uses combinatorial assemblies of molecularly defined neuron
populations for grouped-ensemble coding of survival behaviors. The
neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated
multiple cell types with similar responses. Our results show that
molecularly defined neurons are important processing units for brain
function.
Collapse
Affiliation(s)
- Shengjin Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Hui Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Vilas Menon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew L. Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Fredrick E. Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Srinivas C. Turaga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Scott M. Sternson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| |
Collapse
|
16
|
O'Leary TP, Sullivan KE, Wang L, Clements J, Lemire AL, Cembrowski MS. Extensive and spatially variable within-cell-type heterogeneity across the basolateral amygdala. eLife 2020; 9:59003. [PMID: 32869744 PMCID: PMC7486123 DOI: 10.7554/elife.59003] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 05/16/2020] [Accepted: 08/26/2020] [Indexed: 01/04/2023] Open
Abstract
The basolateral amygdala complex (BLA), extensively connected with both local amygdalar nuclei as well as long-range circuits, is involved in a diverse array of functional roles. Understanding the mechanisms of such functional diversity will be greatly informed by understanding the cell-type-specific landscape of the BLA. Here, beginning with single-cell RNA sequencing, we identified both discrete and graded continuous gene-expression differences within the mouse BLA. Via in situ hybridization, we next mapped this discrete transcriptomic heterogeneity onto a sharp spatial border between the basal and lateral amygdala nuclei, and identified continuous spatial gene-expression gradients within each of these regions. These discrete and continuous spatial transformations of transcriptomic cell-type identity were recapitulated by local morphology as well as long-range connectivity. Thus, BLA excitatory neurons are a highly heterogenous collection of neurons that spatially covary in molecular, cellular, and circuit properties. This heterogeneity likely drives pronounced spatial variation in BLA computation and function.
Collapse
Affiliation(s)
- Timothy P O'Leary
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Kaitlin E Sullivan
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jody Clements
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| |
Collapse
|
17
|
Aso Y, Ray RP, Long X, Bushey D, Cichewicz K, Ngo TT, Sharp B, Christoforou C, Hu A, Lemire AL, Tillberg P, Hirsh J, Litwin-Kumar A, Rubin GM. Nitric oxide acts as a cotransmitter in a subset of dopaminergic neurons to diversify memory dynamics. eLife 2019; 8:49257. [PMID: 31724947 PMCID: PMC6948953 DOI: 10.7554/elife.49257] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [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: 06/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022] Open
Abstract
Animals employ diverse learning rules and synaptic plasticity dynamics to record temporal and statistical information about the world. However, the molecular mechanisms underlying this diversity are poorly understood. The anatomically defined compartments of the insect mushroom body function as parallel units of associative learning, with different learning rates, memory decay dynamics and flexibility (Aso and Rubin, 2016). Here, we show that nitric oxide (NO) acts as a neurotransmitter in a subset of dopaminergic neurons in Drosophila. NO's effects develop more slowly than those of dopamine and depend on soluble guanylate cyclase in postsynaptic Kenyon cells. NO acts antagonistically to dopamine; it shortens memory retention and facilitates the rapid updating of memories. The interplay of NO and dopamine enables memories stored in local domains along Kenyon cell axons to be specialized for predicting the value of odors based only on recent events. Our results provide key mechanistic insights into how diverse memory dynamics are established in parallel memory systems.
Collapse
Affiliation(s)
- Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Robert P Ray
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Xi Long
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Daniel Bushey
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Karol Cichewicz
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Teri-Tb Ngo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Brandi Sharp
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | | | - Amy Hu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Paul Tillberg
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jay Hirsh
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Ashok Litwin-Kumar
- Department of Neuroscience, Columbia University, New York, United States
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| |
Collapse
|
18
|
Phillips JW, Schulmann A, Hara E, Winnubst J, Liu C, Valakh V, Wang L, Shields BC, Korff W, Chandrashekar J, Lemire AL, Mensh B, Dudman JT, Nelson SB, Hantman AW. Publisher Correction: A repeated molecular architecture across thalamic pathways. Nat Neurosci 2019; 22:1945. [PMID: 31576055 DOI: 10.1038/s41593-019-0521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- James W Phillips
- HHMI Janelia Research Campus, Ashburn, VA, USA. .,Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Anton Schulmann
- HHMI Janelia Research Campus, Ashburn, VA, USA.,Brandeis University, Waltham, MA, USA
| | - Erina Hara
- HHMI Janelia Research Campus, Ashburn, VA, USA.,Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | | | | | - Lihua Wang
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | - Brenda C Shields
- HHMI Janelia Research Campus, Ashburn, VA, USA.,Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Wyatt Korff
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | | | | | - Brett Mensh
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | | | - Sacha B Nelson
- HHMI Janelia Research Campus, Ashburn, VA, USA. .,Brandeis University, Waltham, MA, USA.
| | | |
Collapse
|
19
|
Sugino K, Clark E, Schulmann A, Shima Y, Wang L, Hunt DL, Hooks BM, Tränkner D, Chandrashekar J, Picard S, Lemire AL, Spruston N, Hantman AW, Nelson SB. Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain. eLife 2019; 8:38619. [PMID: 30977723 PMCID: PMC6499542 DOI: 10.7554/elife.38619] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 07/20/2018] [Accepted: 04/11/2019] [Indexed: 01/27/2023] Open
Abstract
Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here, we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases, we provide an extensive resource for further investigation of mouse neuronal cell types.
Collapse
Affiliation(s)
- Ken Sugino
- Janelia Research CampusAshburnUnited States
| | | | | | | | - Lihua Wang
- Janelia Research CampusAshburnUnited States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Cembrowski MS, Wang L, Lemire AL, Copeland M, DiLisio SF, Clements J, Spruston N. The subiculum is a patchwork of discrete subregions. eLife 2018; 7:37701. [PMID: 30375971 PMCID: PMC6226292 DOI: 10.7554/elife.37701] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [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: 04/19/2018] [Accepted: 10/27/2018] [Indexed: 11/13/2022] Open
Abstract
In the hippocampus, the classical pyramidal cell type of the subiculum acts as a primary output, conveying hippocampal signals to a diverse suite of downstream regions. Accumulating evidence suggests that the subiculum pyramidal cell population may actually be comprised of discrete subclasses. Here, we investigated the extent and organizational principles governing pyramidal cell heterogeneity throughout the mouse subiculum. Using single-cell RNA-seq, we find that the subiculum pyramidal cell population can be deconstructed into eight separable subclasses. These subclasses were mapped onto abutting spatial domains, ultimately producing a complex laminar and columnar organization with heterogeneity across classical dorsal-ventral, proximal-distal, and superficial-deep axes. We further show that these transcriptomically defined subclasses correspond to differential protein products and can be associated with specific projection targets. This work deconstructs the complex landscape of subiculum pyramidal cells into spatially segregated subclasses that may be observed, controlled, and interpreted in future experiments.
Collapse
Affiliation(s)
- Mark S Cembrowski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Andrew L Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Monique Copeland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Salvatore F DiLisio
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jody Clements
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nelson Spruston
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| |
Collapse
|
21
|
Jurata LW, Gallagher P, Lemire AL, Charles V, Brockman JA, Illingworth EL, Altar CA. Altered expression of hippocampal dentate granule neuron genes in a mouse model of human 22q11 deletion syndrome. Schizophr Res 2006; 88:251-9. [PMID: 17008057 DOI: 10.1016/j.schres.2006.07.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 07/11/2006] [Accepted: 07/20/2006] [Indexed: 11/26/2022]
Abstract
Hemizygous deletion of a 3 Mb region of 22q11.2 is found in 1/4000 humans and produces 22q11 deletion syndrome (22q11DS). Up to 35% of 22q11DS patients develop schizophrenia, making it the second highest risk factor for schizophrenia. A mouse model for 22q11DS, the Df1/+ mouse, carries a hemizygous deletion in a region syntenic with the human deletion. Df1/+ mice are mostly viable but display deficits in prepulse inhibition and learning and memory, two common traits of schizophrenia thought to result, at least in part, from defects in hippocampal neurons. We used oligonucleotide microarrays and QRT-PCR to evaluate gene expression changes in hippocampal dentate granule neurons of Df1/+ mice versus wild-type littermates (n=12/group). The expression of only 287 genes changed with p value significance below 0.05 by microarray, yet 12 of the 21 Df1 region genes represented on the array showed highly significantly reduced expression compared to wild-type controls (33% on average, p values from 10(-3) to 10(-7)). Variants in two of these genes, COMT and PRODH, have been linked with schizophrenia. Overlap of the 287 genes with the reportedly reduced expression of mitochondrial, ubiquitin/proteasome, and synaptic plasticity genes in schizophrenia dentate granule neurons, was not significant. However, modest increases in expression of mitochondrial electron transport genes were observed in the Df1/+ mice. This perhaps indicates a compensation for mitochondrial dysfunction caused by the strongly reduced expression of the Df1 region-encoded mitochondrial enzymes proline dehydrogenase (Prodh) and thioredoxin reductase 2 (Txnrd2).
Collapse
Affiliation(s)
- Linda W Jurata
- Psychiatric Genomics, Inc., 19 Firstfield Road, Gaithersburg, Maryland 20878, USA
| | | | | | | | | | | | | |
Collapse
|
22
|
Laeng P, Pitts RL, Lemire AL, Drabik CE, Weiner A, Tang H, Thyagarajan R, Mallon BS, Altar CA. The mood stabilizer valproic acid stimulates GABA neurogenesis from rat forebrain stem cells. J Neurochem 2004; 91:238-51. [PMID: 15379904 DOI: 10.1111/j.1471-4159.2004.02725.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Valproate, an anticonvulsant drug used to treat bipolar disorder, was studied for its ability to promote neurogenesis from embryonic rat cortical or striatal primordial stem cells. Six days of valproate exposure increased by up to fivefold the number and percentage of tubulin beta III-immunopositive neurons, increased neurite outgrowth, and decreased by fivefold the number of astrocytes without changing the number of cells. Valproate also promoted neuronal differentiation in human fetal forebrain stem cell cultures. The neurogenic effects of valproate on rat stem cells exceeded those obtained with the neurotrophins brain-derived growth factor (BDNF) or NT-3, and slightly exceeded the effects obtained with another mood stabilizer, lithium. No effect was observed with carbamazepine. Most of the newly formed neurons were GABAergic, as shown by 10-fold increases in neurons that immunostained for GABA and the GABA-synthesizing enzyme GAD65/67. Double immunostaining for bromodeoxyuridine and tubulin beta III showed that valproate increased by four- to fivefold the proliferation of neuronal progenitors derived from rat stem cells and increased cyclin D2 expression. Valproate also regulated the expression of survival genes, Bad and Bcl-2, at different times of treatment. The expression of prostaglandin E synthase, analyzed by quantitative RT-PCR, was increased by ninefold as early as 6 h into treatment by valproate. The enhancement of GABAergic neuron numbers, neurite outgrowth, and phenotypic expression via increases in the neuronal differentiation of neural stem cell may contribute to the therapeutic effects of valproate in the treatment of bipolar disorder.
Collapse
Affiliation(s)
- Pascal Laeng
- Gene Discovery, Psychiatric Genomics, Inc., Gaithersburg, Maryland 20878, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Jurata LW, Bukhman YV, Charles V, Capriglione F, Bullard J, Lemire AL, Mohammed A, Pham Q, Laeng P, Brockman JA, Altar CA. Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures. J Neurosci Methods 2004; 138:173-88. [PMID: 15325126 DOI: 10.1016/j.jneumeth.2004.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [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: 12/09/2003] [Revised: 03/31/2004] [Accepted: 04/01/2004] [Indexed: 11/24/2022]
Abstract
The gene expression profiles of human postmortem parietal and prefrontal cortex samples of normal controls and patients with bipolar disease, or human neuroblastoma flat (NBFL) cells treated with the mood-stabilizing drug, valproate, were used to compare the performance of Affymetrix oligonucleotide U133A GeneChips and Agilent Human 1 cDNA microarrays. Among those genes represented on both platforms, the oligo array identified 26-53% more differentially expressed genes compared to the cDNA array in the three experiments, when identical fold change and t-test criteria were applied. The increased sensitivity was primarily the result of more robust fold changes measured by the oligonucleotide system. Essentially all gene changes overlapping between the two platforms were co-directional, and ranged from 4 to 19% depending upon the amount of biological variability within and between the comparison groups. Q-PCR validation rates were virtually identical for the two platforms, with 23-24% validation in the prefrontal cortex experiment, and 56% for both platforms in the cell culture experiment. Validated genes included dopa decarboxylase, dopamine beta-hydroxylase, and dihydropyrimidinase-related protein 3, which were decreased in NBFL cells exposed to valproate, and spinocerebellar ataxia 7, which was increased in bipolar disease. The modest overlap but similar validation rates show that each microarray system identifies a unique set of differentially expressed genes, and thus the greatest information is obtained from the use of both platforms.
Collapse
Affiliation(s)
- Linda W Jurata
- Psychiatric Genomics Inc., 19 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|