1
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Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O'Connell KMS, Singh S, Murdy TJ, Merchant E, Bjerke I, Kleven H, Schlegel U, Leergaard TB, Puchades MA, Bjaalie JG, Kaczorowski CC. Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model. Commun Biol 2024; 7:605. [PMID: 38769398 PMCID: PMC11106287 DOI: 10.1038/s42003-024-06242-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Alzheimer's disease (AD) is broadly characterized by neurodegeneration, pathology accumulation, and cognitive decline. There is considerable variation in the progression of clinical symptoms and pathology in humans, highlighting the importance of genetic diversity in the study of AD. To address this, we analyze cell composition and amyloid-beta deposition of 6- and 14-month-old AD-BXD mouse brains. We utilize the analytical QUINT workflow- a suite of software designed to support atlas-based quantification, which we expand to deliver a highly effective method for registering and quantifying cell and pathology changes in diverse disease models. In applying the expanded QUINT workflow, we quantify near-global age-related increases in microglia, astrocytes, and amyloid-beta, and we identify strain-specific regional variation in neuron load. To understand how individual differences in cell composition affect the interpretation of bulk gene expression in AD, we combine hippocampal immunohistochemistry analyses with bulk RNA-sequencing data. This approach allows us to categorize genes whose expression changes in response to AD in a cell and/or pathology load-dependent manner. Ultimately, our study demonstrates the use of the QUINT workflow to standardize the quantification of immunohistochemistry data in diverse mice, - providing valuable insights into regional variation in cellular load and amyloid deposition in the AD-BXD model.
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Affiliation(s)
- Brianna Gurdon
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
| | - Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gergely Csucs
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Niran Hadad
- The Jackson Laboratory, Bar Harbor, ME, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Andrew Ouellette
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
| | - Tionna Ouellette
- The Jackson Laboratory, Bar Harbor, ME, USA
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA
| | - Kristen M S O'Connell
- The Jackson Laboratory, Bar Harbor, ME, USA
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA
| | - Surjeet Singh
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Ingvild Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ulrike Schlegel
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
| | - Catherine C Kaczorowski
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME, USA.
- Tufts University Graduate School of Biomedical Sciences, Medford, MA, USA.
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
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Yang L, Liu F, Hahm H, Okuda T, Li X, Zhang Y, Kalyanaraman V, Heitmeier MR, Samineni VK. Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590975. [PMID: 38712231 PMCID: PMC11071495 DOI: 10.1101/2024.04.24.590975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.
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Affiliation(s)
- Lite Yang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
- Neuroscience Graduate Program, Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, United States
| | - Fang Liu
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Hannah Hahm
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Takao Okuda
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Xiaoyue Li
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Yufen Zhang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vani Kalyanaraman
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Monique R. Heitmeier
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vijay K. Samineni
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
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3
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Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology. Nat Commun 2024; 15:2642. [PMID: 38531900 PMCID: PMC10966039 DOI: 10.1038/s41467-024-47027-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
A key hallmark of Parkinson's disease (PD) is Lewy pathology. Composed of α-synuclein, Lewy pathology is found both in dopaminergic neurons that modulate motor function, and cortical regions that control cognitive function. Recent work has established the molecular identity of dopaminergic neurons susceptible to death, but little is known about cortical neurons susceptible to Lewy pathology or molecular changes induced by aggregates. In the current study, we use spatial transcriptomics to capture whole transcriptome signatures from cortical neurons with α-synuclein pathology compared to neurons without pathology. We find, both in PD and related PD dementia, dementia with Lewy bodies and in the pre-formed fibril α-synucleinopathy mouse model, that specific classes of excitatory neurons are vulnerable to developing Lewy pathology. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. Neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and describe a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas M Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lisa Turner
- Van Andel Institute Pathology Core, Grand Rapids, MI, 49503, USA
| | - Katelyn Becker
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Van Andel Institute Genomics Core, Grand Rapids, MI, 49503, USA
| | | | - Michael X Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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4
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Geertsma HM, Fisk ZA, Sauline L, Prigent A, Kurgat K, Callaghan SM, Henderson MX, Rousseaux MWC. A topographical atlas of α-synuclein dosage and cell type-specific expression in adult mouse brain and peripheral organs. NPJ Parkinsons Dis 2024; 10:65. [PMID: 38504090 PMCID: PMC10951202 DOI: 10.1038/s41531-024-00672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide and presents pathologically with Lewy pathology and dopaminergic neurodegeneration. Lewy pathology contains aggregated α-synuclein (αSyn), a protein encoded by the SNCA gene which is also mutated or duplicated in a subset of familial PD cases. Due to its predominant presynaptic localization, immunostaining for the protein results in a diffuse reactivity pattern, providing little insight into the types of cells expressing αSyn. As a result, insight into αSyn expression-driven cellular vulnerability has been difficult to ascertain. Using a combination of knock-in mice that target αSyn to the nucleus (SncaNLS) and in situ hybridization of Snca in wild-type mice, we systematically mapped the topography and cell types expressing αSyn in the mouse brain, spinal cord, retina, and gut. We find a high degree of correlation between αSyn protein and RNA levels and further identify cell types with low and high αSyn content. We also find high αSyn expression in neurons, particularly those involved in PD, and to a lower extent in non-neuronal cell types, notably those of oligodendrocyte lineage, which are relevant to multiple system atrophy pathogenesis. Surprisingly, we also found that αSyn is relatively absent from select neuron types, e.g., ChAT-positive motor neurons, whereas enteric neurons universally express some degree of αSyn. Together, this integrated atlas provides insight into the cellular topography of αSyn, and provides a quantitative map to test hypotheses about the role of αSyn in network vulnerability, and thus serves investigations into PD pathogenesis and other α-synucleinopathies.
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Affiliation(s)
- Haley M Geertsma
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Zoe A Fisk
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Lillian Sauline
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Alice Prigent
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Kevin Kurgat
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Steve M Callaghan
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Michael X Henderson
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA.
| | - Maxime W C Rousseaux
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, K1H8M5, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H8M5, Canada.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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5
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Lubben N, Brynildsen JK, Webb CM, Li HL, Leyns CEG, Changolkar L, Zhang B, Meymand ES, O'Reilly M, Madaj Z, DeWeerd D, Fell MJ, Lee VMY, Bassett DS, Henderson MX. LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology progression. Transl Neurodegener 2024; 13:13. [PMID: 38438877 PMCID: PMC10910783 DOI: 10.1186/s40035-024-00403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease (PD). These mutations elevate the LRRK2 kinase activity, making LRRK2 kinase inhibitors an attractive therapeutic. LRRK2 kinase activity has been consistently linked to specific cell signaling pathways, mostly related to organelle trafficking and homeostasis, but its relationship to PD pathogenesis has been more difficult to define. LRRK2-PD patients consistently present with loss of dopaminergic neurons in the substantia nigra but show variable development of Lewy body or tau tangle pathology. Animal models carrying LRRK2 mutations do not develop robust PD-related phenotypes spontaneously, hampering the assessment of the efficacy of LRRK2 inhibitors against disease processes. We hypothesized that mutations in LRRK2 may not be directly related to a single disease pathway, but instead may elevate the susceptibility to multiple disease processes, depending on the disease trigger. To test this hypothesis, we have previously evaluated progression of α-synuclein and tau pathologies following injection of proteopathic seeds. We demonstrated that transgenic mice overexpressing mutant LRRK2 show alterations in the brain-wide progression of pathology, especially at older ages. METHODS Here, we assess tau pathology progression in relation to long-term LRRK2 kinase inhibition. Wild-type or LRRK2G2019S knock-in mice were injected with tau fibrils and treated with control diet or diet containing LRRK2 kinase inhibitor MLi-2 targeting the IC50 or IC90 of LRRK2 for 3-6 months. Mice were evaluated for tau pathology by brain-wide quantitative pathology in 844 brain regions and subsequent linear diffusion modeling of progression. RESULTS Consistent with our previous work, we found systemic alterations in the progression of tau pathology in LRRK2G2019S mice, which were most pronounced at 6 months. Importantly, LRRK2 kinase inhibition reversed these effects in LRRK2G2019S mice, but had minimal effect in wild-type mice, suggesting that LRRK2 kinase inhibition is likely to reverse specific disease processes in G2019S mutation carriers. Additional work may be necessary to determine the potential effect in non-carriers. CONCLUSIONS This work supports a protective role of LRRK2 kinase inhibition in G2019S carriers and provides a rational workflow for systematic evaluation of brain-wide phenotypes in therapeutic development.
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Affiliation(s)
- Noah Lubben
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Julia K Brynildsen
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Connor M Webb
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Institute On Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Howard L Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Institute On Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Cheryl E G Leyns
- Neuroscience Discovery, Merck & Co., Inc., Boston, MA, 02115, USA
| | - Lakshmi Changolkar
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Institute On Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Institute On Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Emily S Meymand
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Institute On Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mia O'Reilly
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zach Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, 333 Bostwick Ave., NE, Grand Rapids, MI, 49503, USA
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Matthew J Fell
- Neuroscience Discovery, Merck & Co., Inc., Boston, MA, 02115, USA
| | - Virginia M Y Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Institute On Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dani S Bassett
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Michael X Henderson
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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6
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Blixhavn CH, Reiten I, Kleven H, Øvsthus M, Yates SC, Schlegel U, Puchades MA, Schmid O, Bjaalie JG, Bjerke IE, Leergaard TB. The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases. Front Neuroinform 2024; 18:1284107. [PMID: 38421771 PMCID: PMC10884250 DOI: 10.3389/fninf.2024.1284107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Neuroscientists employ a range of methods and generate increasing amounts of data describing brain structure and function. The anatomical locations from which observations or measurements originate represent a common context for data interpretation, and a starting point for identifying data of interest. However, the multimodality and abundance of brain data pose a challenge for efforts to organize, integrate, and analyze data based on anatomical locations. While structured metadata allow faceted data queries, different types of data are not easily represented in a standardized and machine-readable way that allow comparison, analysis, and queries related to anatomical relevance. To this end, three-dimensional (3D) digital brain atlases provide frameworks in which disparate multimodal and multilevel neuroscience data can be spatially represented. We propose to represent the locations of different neuroscience data as geometric objects in 3D brain atlases. Such geometric objects can be specified in a standardized file format and stored as location metadata for use with different computational tools. We here present the Locare workflow developed for defining the anatomical location of data elements from rodent brains as geometric objects. We demonstrate how the workflow can be used to define geometric objects representing multimodal and multilevel experimental neuroscience in rat or mouse brain atlases. We further propose a collection of JSON schemas (LocareJSON) for specifying geometric objects by atlas coordinates, suitable as a starting point for co-visualization of different data in an anatomical context and for enabling spatial data queries.
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Affiliation(s)
- Camilla H. Blixhavn
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ingrid Reiten
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Martin Øvsthus
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon C. Yates
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ulrike Schlegel
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A. Puchades
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Jan G. Bjaalie
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ingvild E. Bjerke
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B. Leergaard
- Neural Systems Laboratory, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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7
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Kleven H, Bjerke IE, Clascá F, Groenewegen HJ, Bjaalie JG, Leergaard TB. Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration. Nat Methods 2023; 20:1822-1829. [PMID: 37783883 PMCID: PMC10630136 DOI: 10.1038/s41592-023-02034-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
Volumetric brain atlases are increasingly used to integrate and analyze diverse experimental neuroscience data acquired from animal models, but until recently a publicly available digital atlas with complete coverage of the rat brain has been missing. Here we present an update of the Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource. This brain atlas features annotations of 222 structures, of which 112 are new and 57 revised compared to previous versions. It provides a detailed map of the cerebral cortex, hippocampal region, striatopallidal areas, midbrain dopaminergic system, thalamic cell groups, the auditory system and main fiber tracts. We document the criteria underlying the annotations and demonstrate how the atlas with related tools and workflows can be used to support interpretation, integration, analysis and dissemination of experimental rat brain data.
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Affiliation(s)
- Heidi Kleven
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ingvild E Bjerke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Francisco Clascá
- Department of Anatomy and Neuroscience, Autónoma de Madrid University, Madrid, Spain
| | - Henk J Groenewegen
- Department of Anatomy and Neurosciences, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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8
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Reiten I, Olsen GM, Bjaalie JG, Witter MP, Leergaard TB. The efferent connections of the orbitofrontal, posterior parietal, and insular cortex of the rat brain. Sci Data 2023; 10:645. [PMID: 37735463 PMCID: PMC10514078 DOI: 10.1038/s41597-023-02527-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023] Open
Abstract
The orbitofrontal, posterior parietal, and insular cortices are sites of higher-order cognitive processing implicated in a wide range of behaviours, including working memory, attention guiding, decision making, and spatial navigation. To better understand how these regions contribute to such functions, we need detailed knowledge about the underlying structural connectivity. Several tract-tracing studies have investigated specific aspects of orbitofrontal, posterior parietal and insular connectivity, but a digital resource for studying the cortical and subcortical projections from these areas in detail is not available. We here present a comprehensive collection of brightfield and fluorescence microscopic images of serial coronal sections from 49 rat brain tract-tracing experiments, in which discrete injections of the anterograde tracers biotinylated dextran amine and/or Phaseolus vulgaris leucoagglutinin were placed in the orbitofrontal, parietal, or insular cortex. The images are spatially registered to the Waxholm Space Rat brain atlas. The image collection, with corresponding reference atlas maps, is suitable as a reference framework for investigating the brain-wide efferent connectivity of these cortical association areas.
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Affiliation(s)
- Ingrid Reiten
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Grethe M Olsen
- Kavli Institute for Systems Neuroscience, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve B Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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9
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Carey H, Pegios M, Martin L, Saleeba C, Turner AJ, Everett NA, Bjerke IE, Puchades MA, Bjaalie JG, McMullan S. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas. Nat Commun 2023; 14:5884. [PMID: 37735467 PMCID: PMC10514056 DOI: 10.1038/s41467-023-41645-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analyzed, yet accurate registration remains expertise-dependent and slow. In order to address this limitation, we have trained a neural network, DeepSlice, to register mouse brain histological images to the Allen Brain Common Coordinate Framework, retaining registration accuracy while improving speed by >1000 fold.
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Affiliation(s)
- Harry Carey
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Michael Pegios
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
| | | | - Chris Saleeba
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
| | - Anita J Turner
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
| | | | - Ingvild E Bjerke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Simon McMullan
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia.
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10
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Bjerke IE, Yates SC, Carey H, Bjaalie JG, Leergaard TB. Scaling up cell-counting efforts in neuroscience through semi-automated methods. iScience 2023; 26:107562. [PMID: 37636060 PMCID: PMC10457595 DOI: 10.1016/j.isci.2023.107562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Quantifying how the cellular composition of brain regions vary across development, aging, sex, and disease, is crucial in experimental neuroscience, and the accuracy of different counting methods is continuously debated. Due to the tedious nature of most counting procedures, studies are often restricted to one or a few brain regions. Recently, there have been considerable methodological advances in combining semi-automated feature extraction with brain atlases for cell quantification. Such methods hold great promise for scaling up cell-counting efforts. However, little focus has been paid to how these methods should be implemented and reported to support reproducibility. Here, we provide an overview of practices for conducting and reporting cell counting in mouse and rat brains, showing that critical details for interpretation are typically lacking. We go on to discuss how novel methods may increase efficiency and reproducibility of cell counting studies. Lastly, we provide practical recommendations for researchers planning cell counting.
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Affiliation(s)
- Ingvild Elise Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon Christine Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Harry Carey
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan Gunnar Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve Brauns Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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11
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Kleven H, Gillespie TH, Zehl L, Dickscheid T, Bjaalie JG, Martone ME, Leergaard TB. AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures. Sci Data 2023; 10:486. [PMID: 37495585 PMCID: PMC10372146 DOI: 10.1038/s41597-023-02389-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.
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Affiliation(s)
- Heidi Kleven
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Lyuba Zehl
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Timo Dickscheid
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Institute of Computer Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maryann E Martone
- Department of Neurosciences, University of California, San Diego, USA
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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12
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Goralski T, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse D, Henderson MX. Spatial transcriptomics reveals molecular dysfunction associated with Lewy pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541144. [PMID: 37292685 PMCID: PMC10245657 DOI: 10.1101/2023.05.17.541144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lewy pathology composed of α-synuclein is the key pathological hallmark of Parkinson's disease (PD), found both in dopaminergic neurons that control motor function, and throughout cortical regions that control cognitive function. Recent work has investigated which dopaminergic neurons are most susceptible to death, but little is known about which neurons are vulnerable to developing Lewy pathology and what molecular changes an aggregate induces. In the current study, we use spatial transcriptomics to selectively capture whole transcriptome signatures from cortical neurons with Lewy pathology compared to those without pathology in the same brains. We find, both in PD and in a mouse model of PD, that there are specific classes of excitatory neurons that are vulnerable to developing Lewy pathology in the cortex. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. This gene signature indicates that neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. However, beyond DNA repair gene upregulation, we find that neurons also activate apoptotic pathways, suggesting that if DNA repair fails, neurons undergo programmed cell death. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and identify a conserved signature of molecular dysfunction in both mice and humans.
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Affiliation(s)
- Thomas Goralski
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Lindsay Meyerdirk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Libby Breton
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Laura Brasseur
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
| | - Kevin Kurgat
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Daniella DeWeerd
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | | | | | | | | | - Michael X. Henderson
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
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13
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Blixhavn CH, Haug FMŠ, Kleven H, Puchades MA, Bjaalie JG, Leergaard TB. A Timm-Nissl multiplane microscopic atlas of rat brain zincergic terminal fields and metal-containing glia. Sci Data 2023; 10:150. [PMID: 36944675 PMCID: PMC10030855 DOI: 10.1038/s41597-023-02012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/09/2023] [Indexed: 03/23/2023] Open
Abstract
The ability of Timm's sulphide silver method to stain zincergic terminal fields has made it a useful neuromorphological marker. Beyond its roles in zinc-signalling and neuromodulation, zinc is involved in the pathophysiology of ischemic stroke, epilepsy, degenerative diseases and neuropsychiatric conditions. In addition to visualising zincergic terminal fields, the method also labels transition metals in neuronal perikarya and glial cells. To provide a benchmark reference for planning and interpretation of experimental investigations of zinc-related phenomena in rat brains, we have established a comprehensive repository of serial microscopic images from a historical collection of coronally, horizontally and sagittally oriented rat brain sections stained with Timm's method. Adjacent Nissl-stained sections showing cytoarchitecture, and customised atlas overlays from a three-dimensional rat brain reference atlas registered to each section image are included for spatial reference and guiding identification of anatomical boundaries. The Timm-Nissl atlas, available from EBRAINS, enables experimental researchers to navigate normal rat brain material in three planes and investigate the spatial distribution and density of zincergic terminal fields across the entire brain.
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Affiliation(s)
- Camilla H Blixhavn
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Finn-Mogens Š Haug
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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14
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Kleven H, Reiten I, Blixhavn CH, Schlegel U, Øvsthus M, Papp EA, Puchades MA, Bjaalie JG, Leergaard TB, Bjerke IE. A neuroscientist's guide to using murine brain atlases for efficient analysis and transparent reporting. Front Neuroinform 2023; 17:1154080. [PMID: 36970659 PMCID: PMC10033636 DOI: 10.3389/fninf.2023.1154080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
Brain atlases are widely used in neuroscience as resources for conducting experimental studies, and for integrating, analyzing, and reporting data from animal models. A variety of atlases are available, and it may be challenging to find the optimal atlas for a given purpose and to perform efficient atlas-based data analyses. Comparing findings reported using different atlases is also not trivial, and represents a barrier to reproducible science. With this perspective article, we provide a guide to how mouse and rat brain atlases can be used for analyzing and reporting data in accordance with the FAIR principles that advocate for data to be findable, accessible, interoperable, and re-usable. We first introduce how atlases can be interpreted and used for navigating to brain locations, before discussing how they can be used for different analytic purposes, including spatial registration and data visualization. We provide guidance on how neuroscientists can compare data mapped to different atlases and ensure transparent reporting of findings. Finally, we summarize key considerations when choosing an atlas and give an outlook on the relevance of increased uptake of atlas-based tools and workflows for FAIR data sharing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ingvild E. Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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15
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Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O'Connell K, Singh S, Murdy T, Merchant E, Bjerke I, Kleven H, Schlegel U, Leergaard TB, Puchades MA, Bjaalie JG, Kaczorowski CC. Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530226. [PMID: 36909528 PMCID: PMC10002670 DOI: 10.1101/2023.02.27.530226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Alzheimer's disease (AD) is characterized by neurodegeneration, pathology accumulation, and progressive cognitive decline. There is significant variation in age at onset and severity of symptoms highlighting the importance of genetic diversity in the study of AD. To address this, we analyzed cell and pathology composition of 6- and 14-month-old AD-BXD mouse brains using the semi-automated workflow (QUINT); which we expanded to allow for nonlinear refinement of brain atlas-registration, and quality control assessment of atlas-registration and brain section integrity. Near global age-related increases in microglia, astrocyte, and amyloid-beta accumulation were measured, while regional variation in neuron load existed among strains. Furthermore, hippocampal immunohistochemistry analyses were combined with bulk RNA-sequencing results to demonstrate the relationship between cell composition and gene expression. Overall, the additional functionality of the QUINT workflow delivers a highly effective method for registering and quantifying cell and pathology changes in diverse disease models.
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Affiliation(s)
- Brianna Gurdon
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
| | - Sharon C Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gergely Csucs
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nicolaas E Groeneboom
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | | | - Andrew Ouellette
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
| | - Tionna Ouellette
- The Jackson Laboratory, Bar Harbor, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
| | - Kristen O'Connell
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
| | | | - Tom Murdy
- The Jackson Laboratory, Bar Harbor, ME
| | | | - Ingvild Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Heidi Kleven
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ulrike Schlegel
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Catherine C Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME
- The University of Maine Graduate School of Biomedical Sciences and Engineering, Orono, ME
- Tufts University Graduate School of Biomedical Sciences, Medford, MA
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16
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Davoudian PA, Shao LX, Kwan AC. Shared and Distinct Brain Regions Targeted for Immediate Early Gene Expression by Ketamine and Psilocybin. ACS Chem Neurosci 2023; 14:468-480. [PMID: 36630309 PMCID: PMC9898239 DOI: 10.1021/acschemneuro.2c00637] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Psilocybin is a psychedelic with therapeutic potential. While there is growing evidence that psilocybin exerts its beneficial effects through enhancing neural plasticity, the exact brain regions involved are not completely understood. Determining the impact of psilocybin on plasticity-related gene expression throughout the brain can broaden our understanding of the neural circuits involved in psychedelic-evoked neural plasticity. In this study, whole-brain serial two-photon microscopy and light sheet microscopy were employed to map the expression of the immediate early gene, c-Fos, in male and female mice. The drug-induced c-Fos expression following psilocybin administration was compared to that of subanesthetic ketamine and saline control. Psilocybin and ketamine produced acutely comparable elevations in c-Fos expression in numerous brain regions, including anterior cingulate cortex, locus coeruleus, primary visual cortex, central and basolateral amygdala, medial and lateral habenula, and claustrum. Select regions exhibited drug-preferential differences, such as dorsal raphe and insular cortex for psilocybin and the CA1 subfield of hippocampus for ketamine. To gain insights into the contributions of receptors and cell types, the c-Fos expression maps were related to brain-wide in situ hybridization data. The transcript analyses showed that the endogenous levels of Grin2a and Grin2b predict whether a cortical region is sensitive to drug-evoked neural plasticity for both ketamine and psilocybin. Collectively, the systematic mapping approach produced an unbiased list of brain regions impacted by psilocybin and ketamine. The data are a resource that highlights previously underappreciated regions for future investigations. Furthermore, the robust relationships between drug-evoked c-Fos expression and endogenous transcript distributions suggest glutamatergic receptors as a potential convergent target for how psilocybin and ketamine produce their rapid-acting and long-lasting therapeutic effects.
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Affiliation(s)
- Pasha A. Davoudian
- Medical Scientist Training Program, Yale University School of Medicine, New Haven, Connecticut, 06511, USA
- Interdepartmental Neuroscience Program, Yale University School of Medicine, New Haven, Connecticut, 06511, USA
| | - Ling-Xiao Shao
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, 06511, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, 14853, USA
| | - Alex C. Kwan
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, 06511, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, 06511, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, 14853, USA
- Department of Psychiatry, Weill Cornell Medicine, New York, New York, 10065, USA
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17
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Yao Y, Barger Z, Saffari Doost M, Tso CF, Darmohray D, Silverman D, Liu D, Ma C, Cetin A, Yao S, Zeng H, Dan Y. Cardiovascular baroreflex circuit moonlights in sleep control. Neuron 2022; 110:3986-3999.e6. [PMID: 36170850 DOI: 10.1016/j.neuron.2022.08.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/02/2022] [Accepted: 08/29/2022] [Indexed: 01/04/2023]
Abstract
Sleep disturbances are strongly associated with cardiovascular diseases. Baroreflex, a basic cardiovascular regulation mechanism, is modulated by sleep-wake states. Here, we show that neurons at key stages of baroreflex pathways also promote sleep. Using activity-dependent genetic labeling, we tagged neurons in the nucleus of the solitary tract (NST) activated by blood pressure elevation and confirmed their barosensitivity with optrode recording and calcium imaging. Chemogenetic or optogenetic activation of these neurons promoted non-REM sleep in addition to decreasing blood pressure and heart rate. GABAergic neurons in the caudal ventrolateral medulla (CVLM)-a downstream target of the NST for vasomotor baroreflex-also promote non-REM sleep, partly by inhibiting the sympathoexcitatory and wake-promoting adrenergic neurons in the rostral ventrolateral medulla (RVLM). Cholinergic neurons in the nucleus ambiguous-a target of the NST for cardiac baroreflex-promoted non-REM sleep as well. Thus, key components of the cardiovascular baroreflex circuit are also integral to sleep-wake brain-state regulation.
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Affiliation(s)
- Yuanyuan Yao
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zeke Barger
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mohammad Saffari Doost
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chak Foon Tso
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana Darmohray
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel Silverman
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Danqian Liu
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chenyan Ma
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ali Cetin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yang Dan
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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18
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Lopes MM, Paysan J, Rino J, Lopes SM, Pereira de Almeida L, Cortes L, Nobre RJ. A new protocol for whole-brain biodistribution analysis of AAVs by tissue clearing, light-sheet microscopy and semi-automated spatial quantification. Gene Ther 2022; 29:665-679. [PMID: 36316447 DOI: 10.1038/s41434-022-00372-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 12/23/2022]
Abstract
Recombinant adeno-associated virus (rAAV) has become one of the most promising gene delivery systems for both in vitro and in vivo applications. However, a key challenge is the lack of suitable imaging technologies to evaluate delivery, biodistribution and tropism of rAAVs and efficiently monitor disease amelioration promoted by AAV-based therapies at a whole-organ level with single-cell resolution. Therefore, we aimed to establish a new pipeline for the biodistribution analysis of natural and new variants of AAVs at a whole-brain level by tissue clearing and light-sheet fluorescence microscopy (LSFM). To test this platform, neonatal C57BL/6 mice were intravenously injected with rAAV9 encoding EGFP and, after sacrifice, brains were processed by standard immunohistochemistry and a recently released aqueous-based clearing procedure. This clearing technique required no dedicated equipment and rendered highly cleared brains, while simultaneously preserving endogenous fluorescence. Moreover, three-dimensional imaging by LSFM allowed the quantitative analysis of EGFP at a whole-brain level, as well as the reconstruction of Purkinje cells for the retrieval of valuable morphological information inaccessible by standard immunohistochemistry. In conclusion, the pipeline herein described takes the AAVs to a new level when coupled to LSFM, proving its worth as a bioimaging tool in tropism and gene therapy studies.
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Affiliation(s)
- Miguel M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | | | - José Rino
- iMM - Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sara M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Luís Pereira de Almeida
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,ViraVector - Viral Vectors for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal. .,FFUC - Faculty of Pharmacy of the University of Coimbra, Coimbra, Portugal.
| | - Luísa Cortes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal. .,MICC-CNC - Microscopy Imaging Center of Coimbra - CNC, University of Coimbra, Coimbra, Portugal.
| | - Rui Jorge Nobre
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal. .,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal. .,ViraVector - Viral Vectors for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal.
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19
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Leergaard TB, Bjaalie JG. Atlas-based data integration for mapping the connections and architecture of the brain. Science 2022; 378:488-492. [DOI: 10.1126/science.abq2594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Detailed knowledge about the neural connections among regions of the brain is key for advancing our understanding of normal brain function and changes that occur with aging and disease. Researchers use a range of experimental techniques to map connections at different levels of granularity in rodent animal models, but the results are often challenging to compare and integrate. Three-dimensional reference atlases of the brain provide new opportunities for cumulating, integrating, and reinterpreting research findings across studies. Here, we review approaches for integrating data describing neural connections and other modalities in rodent brain atlases and discuss how atlas-based workflows can facilitate brainwide analyses of neural network organization in relation to other facets of neuroarchitecture.
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Affiliation(s)
- Trygve B. Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G. Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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20
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Ham GX, Augustine GJ. Topologically Organized Networks in the Claustrum Reflect Functional Modularization. Front Neuroanat 2022; 16:901807. [PMID: 35815332 PMCID: PMC9259979 DOI: 10.3389/fnana.2022.901807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/11/2022] [Indexed: 12/04/2022] Open
Abstract
Using genetic strategies and viral-based directional tracers, we investigated the topological location and output networks of claustrum (CLA) neuron populations projecting to either the retrosplenial cortex, primary motor cortex, or basolateral amygdala. We found that all three CLA neuron populations clearly reside in distinct topological locations within the CLA complex and project broadly to multiple downstream targets. Each neuron population projects to different targets, suggesting that each CLA subzone coordinates a unique set of brain-wide functions. Our findings establish that the claustrum complex encompasses at least three minimally overlapping networks that are compartmentalized into different topological subzones. Such modularity is likely to be important for CLA function.
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Affiliation(s)
| | - George J. Augustine
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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DOPAMAP, high-resolution images of dopamine 1 and 2 receptor expression in developing and adult mouse brains. Sci Data 2022; 9:175. [PMID: 35440585 PMCID: PMC9018709 DOI: 10.1038/s41597-022-01268-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/08/2022] [Indexed: 11/21/2022] Open
Abstract
The dopaminergic system undergoes major reorganization during development, a period especially vulnerable to mental disorders. Forebrain neurons expressing dopamine 1 and 2 receptors (D1R and D2R, respectively) play a key role in this system. However, neuroanatomical information about the typical development of these neurons is sparse and scattered across publications investigating one or a few brain regions. We here present a public online collection of microscopic images of immunohistochemically stained serial sections from male and female mice at five stages of development (postnatal day 17 (P17), P25, P35, P49, and adult), showing the distribution of D1R and D2R expressing neurons across the forebrain. All images from adult brains are registered to the Allen Mouse brain Common Coordinate Framework, while images from P17-P35 age groups are registered to spatially modified atlas versions matching the morphology of young brains. This online resource provides microscopic visualization of the developing dopaminergic system in mice, which is suitable as a benchmark reference for performing new experiments and building computational models of the brain. Measurement(s) | mRNA expression | Technology Type(s) | transgenic Mouse • immunohistochemistry staining method | Sample Characteristic - Organism | Mus musculus |
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22
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Whilden CM, Chevée M, An SY, Brown SP. The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse. J Comp Neurol 2021; 529:3751-3771. [PMID: 33908623 PMCID: PMC8551307 DOI: 10.1002/cne.25163] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
Although corticothalamic neurons (CThNs) represent the largest source of synaptic input to thalamic neurons, their role in regulating thalamocortical interactions remains incompletely understood. CThNs in sensory cortex have historically been divided into two types, those with cell bodies in Layer 6 (L6) that project back to primary sensory thalamic nuclei and those with cell bodies in Layer 5 (L5) that project to higher-order thalamic nuclei and subcortical structures. Recently, diversity among L6 CThNs has increasingly been appreciated. In the rodent somatosensory cortex, two major classes of L6 CThNs have been identified: one projecting to the ventral posterior medial nucleus (VPM-only L6 CThNs) and one projecting to both VPM and the posterior medial nucleus (VPM/POm L6 CThNs). Using rabies-based tracing methods in mice, we asked whether these L6 CThN populations integrate similar synaptic inputs. We found that both types of L6 CThNs received local input from somatosensory cortex and thalamic input from VPM and POm. However, VPM/POm L6 CThNs received significantly more input from a number of additional cortical areas, higher order thalamic nuclei, and subcortical structures. We also found that the two types of L6 CThNs target different functional regions within the thalamic reticular nucleus (TRN). Together, our results indicate that these two types of L6 CThNs represent distinct information streams in the somatosensory cortex and suggest that VPM-only L6 CThNs regulate, via their more restricted circuits, sensory responses related to a cortical column while VPM/POm L6 CThNs, which are integrated into more widespread POm-related circuits, relay contextual information.
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Affiliation(s)
- Courtney Michelle Whilden
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA
| | - Maxime Chevée
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Seong Yeol An
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Solange Pezon Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Localizing Microemboli within the Rodent Brain through Block-Face Imaging and Atlas Registration. eNeuro 2021; 8:ENEURO.0216-21.2021. [PMID: 34272259 PMCID: PMC8342264 DOI: 10.1523/eneuro.0216-21.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/01/2022] Open
Abstract
Brain microinfarcts are prevalent in humans, however because of the inherent difficulty of identifying and localizing individual microinfarcts, brain-wide quantification is impractical. In mice, microinfarcts have been created by surgically introducing microemboli into the brain, but a major limitation of this model is the absence of automated methods to identify and localize individual occlusions. We present a novel and semi-automated workflow to identify the anatomic location of fluorescent emboli (microspheres) within the mouse brain through histologic processing and atlas registration. By incorporating vibratome block-face imaging with the QuickNII brain registration tool, we show that the anatomic location of microspheres can be accurately registered to brain structures within the Allen mouse brain (AMB) atlas (e.g., somatomotor areas, hippocampal region, visual areas, etc.). Compared with registering images of slide mounted sections to the AMB atlas, microsphere location was more accurately determined when block-face images were used. As a proof of principle, using this workflow we compared the distribution of microspheres within the brains of mice that were either perfused or immersion fixed. No significant effect of perfusion on total microsphere number or location was detected. In general, microspheres were distributed brain-wide, with the largest density found in the thalamus. In sum, our block-face imaging workflow enables efficient characterization of the widespread distribution of fluorescent microemboli, facilitating future investigation into the impact of microinfarct load and location on brain health.
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Bjerke IE, Yates SC, Laja A, Witter MP, Puchades MA, Bjaalie JG, Leergaard TB. Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain. iScience 2021; 24:101906. [PMID: 33385111 PMCID: PMC7770605 DOI: 10.1016/j.isci.2020.101906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 01/12/2023] Open
Abstract
The calcium-binding proteins parvalbumin and calbindin are expressed in neuronal populations regulating brain networks involved in spatial navigation, memory processes, and social interactions. Information about the numbers of these neurons across brain regions is required to understand their functional roles but is scarcely available. Employing semi-automated image analysis, we performed brain-wide analysis of immunohistochemically stained parvalbumin and calbindin sections and show that these neurons distribute in complementary patterns across the mouse brain. Parvalbumin neurons dominate in areas related to sensorimotor processing and navigation, whereas calbindin neurons prevail in regions reflecting behavioral states. We also find that parvalbumin neurons distribute according to similar principles in the hippocampal region of the rat and mouse brain. We validated our results against manual counts and evaluated variability of results among researchers. Comparison of our results to previous reports showed that neuron numbers vary, whereas patterns of relative densities and numbers are consistent. Brain-wide, semi-automatic quantification of parvalbumin and calbindin neurons Largely complementary distribution of calbindin and parvalbumin neurons in mice Comparison with several previous studies shows variable numbers but similar trends Similar distribution of parvalbumin neurons in the rat and mouse hippocampal region
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Affiliation(s)
- Ingvild E Bjerke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon C Yates
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Arthur Laja
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maja A Puchades
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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