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Kumar A, Schrader AW, Aggarwal B, Boroojeny AE, Asadian M, Lee J, Song YJ, Zhao SD, Han HS, Sinha S. Intracellular spatial transcriptomic analysis toolkit (InSTAnT). Nat Commun 2024; 15:7794. [PMID: 39242579 PMCID: PMC11379969 DOI: 10.1038/s41467-024-49457-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/04/2024] [Indexed: 09/09/2024] Open
Abstract
Imaging-based spatial transcriptomics technologies such as Multiplexed error-robust fluorescence in situ hybridization (MERFISH) can capture cellular processes in unparalleled detail. However, rigorous and robust analytical tools are needed to unlock their full potential for discovering subcellular biological patterns. We present Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT), a computational toolkit for extracting molecular relationships from spatial transcriptomics data at single molecule resolution. InSTAnT employs specialized statistical tests and algorithms to detect gene pairs and modules exhibiting intriguing patterns of co-localization, both within individual cells and across the cellular landscape. We showcase the toolkit on five different datasets representing two different cell lines, two brain structures, two species, and three different technologies. We perform rigorous statistical assessment of discovered co-localization patterns, find supporting evidence from databases and RNA interactions, and identify associated subcellular domains. We uncover several cell type and region-specific gene co-localizations within the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions.
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Affiliation(s)
- Anurendra Kumar
- College of Computing, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alex W Schrader
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Bhavay Aggarwal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Marisa Asadian
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - JuYeon Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sihai Dave Zhao
- Department of Statistics, University of Illinois Urbana-Champaign, Urbana, IL, 61820, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Saurabh Sinha
- H. Milton Stewart School of Industrial & Systems Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA.
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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2
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Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Maguire JA, Weidekamp MA, Hodge KM, Boehm K, Lu S, Chesi A, Bradfield JP, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SFA. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. CELL GENOMICS 2024; 4:100556. [PMID: 38697123 PMCID: PMC11099382 DOI: 10.1016/j.xgen.2024.100556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 05/04/2024]
Abstract
The ch12q13 locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via cis-regulation. We implicated rs7132908 as a putative causal variant by leveraging our in-house 3D genomic data and public domain datasets. Using a luciferase reporter assay, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. We generated isogenic human embryonic stem cell lines homozygous for either rs7132908 allele to assess changes in gene expression and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. The rs7132908 obesity risk allele influenced expression of FAIM2 and other genes and decreased the proportion of neurons produced by differentiation. We have functionally validated rs7132908 as a causal obesity variant that temporally regulates nearby effector genes and influences neurodevelopment and survival.
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Affiliation(s)
- Sheridan H Littleton
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B Trang
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M Volpe
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan P Bradfield
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Quantinuum Research LLC, San Diego, CA 92101, USA
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A Anderson
- Department of Child and Adolescent Psychiatry, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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3
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Aydin AG, Lemenze A, Bieszczad KM. Functional diversities within neurons and astrocytes in the adult rat auditory cortex revealed by single-nucleus RNA sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589831. [PMID: 38659766 PMCID: PMC11042262 DOI: 10.1101/2024.04.16.589831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The mammalian cerebral cortex is composed of a rich diversity of cell types. Cortical cells are organized into networks that rely on their functional diversity to ultimately carry out a variety of sophisticated cognitive functions. To investigate the breadth of transcriptional diverse cell types in the sensory cortex, we have used single-nucleus RNA sequencing (snRNA-seq) in the auditory cortex of the adult rat. A variety of unique excitatory and inhibitory neuron types were identified. In addition, we report for the first time a diversity of astrocytes in the auditory cortex that may represent functionally unique subtypes. Together, these results pave the way for building models of how neurons in the sensory cortex work in concert with astrocytes at synapses to fulfill high-cognitive functions like learning and memory.
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Szepanowski LP, Wruck W, Kapr J, Rossi A, Fritsche E, Krutmann J, Adjaye J. Cockayne Syndrome Patient iPSC-Derived Brain Organoids and Neurospheres Show Early Transcriptional Dysregulation of Biological Processes Associated with Brain Development and Metabolism. Cells 2024; 13:591. [PMID: 38607030 PMCID: PMC11011893 DOI: 10.3390/cells13070591] [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: 02/29/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Cockayne syndrome (CS) is a rare hereditary autosomal recessive disorder primarily caused by mutations in Cockayne syndrome protein A (CSA) or B (CSB). While many of the functions of CSB have been at least partially elucidated, little is known about the actual developmental dysregulation in this devasting disorder. Of particular interest is the regulation of cerebral development as the most debilitating symptoms are of neurological nature. We generated neurospheres and cerebral organoids utilizing Cockayne syndrome B protein (CSB)-deficient induced pluripotent stem cells derived from two patients with distinct severity levels of CS and healthy controls. The transcriptome of both developmental timepoints was explored using RNA-Seq and bioinformatic analysis to identify dysregulated biological processes common to both patients with CS in comparison to the control. CSB-deficient neurospheres displayed upregulation of the VEGFA-VEGFR2 signalling pathway, vesicle-mediated transport and head development. CSB-deficient cerebral organoids exhibited downregulation of brain development, neuron projection development and synaptic signalling. We further identified the upregulation of steroid biosynthesis as common to both timepoints, in particular the upregulation of the cholesterol biosynthesis branch. Our results provide insights into the neurodevelopmental dysregulation in patients with CS and strengthen the theory that CS is not only a neurodegenerative but also a neurodevelopmental disorder.
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Affiliation(s)
- Leon-Phillip Szepanowski
- Institute for Stem Cell Research and Regenerative Medicine, University Hospital Düsseldorf, Moorenstrasse 5, D-40225 Duesseldorf, Germany; (L.-P.S.)
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, D-40225 Duesseldorf, Germany
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, University Hospital Düsseldorf, Moorenstrasse 5, D-40225 Duesseldorf, Germany; (L.-P.S.)
| | - Julia Kapr
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, D-40225 Duesseldorf, Germany
| | - Andrea Rossi
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, D-40225 Duesseldorf, Germany
| | - Ellen Fritsche
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, D-40225 Duesseldorf, Germany
| | - Jean Krutmann
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, D-40225 Duesseldorf, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, University Hospital Düsseldorf, Moorenstrasse 5, D-40225 Duesseldorf, Germany; (L.-P.S.)
- Zayed Centre for Research into Rare Diseases in Children (ZCR), University College London (UCL)—EGA Institute for Women’s Health, 20 Guilford Street, London WC1N 1DZ, UK
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Wheeler DW, Kopsick JD, Sutton N, Tecuatl C, Komendantov AO, Nadella K, Ascoli GA. Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. eLife 2024; 12:RP90597. [PMID: 38345923 PMCID: PMC10942544 DOI: 10.7554/elife.90597] [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] [Indexed: 02/15/2024] Open
Abstract
Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Previously, Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression (Wheeler et al., 2015). Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.
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Affiliation(s)
- Diek W Wheeler
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Jeffrey D Kopsick
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason UniversityFairfaxUnited States
| | - Nate Sutton
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Carolina Tecuatl
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Alexander O Komendantov
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Kasturi Nadella
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason UniversityFairfaxUnited States
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason UniversityFairfaxUnited States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason UniversityFairfaxUnited States
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Miao S, Fourgeaud L, Burrola PG, Stern S, Zhang Y, Happonen KE, Novak SW, Gage FH, Lemke G. Tyro3 promotes the maturation of glutamatergic synapses. Front Neurosci 2024; 18:1327423. [PMID: 38410160 PMCID: PMC10894971 DOI: 10.3389/fnins.2024.1327423] [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: 10/24/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
The receptor tyrosine kinase Tyro3 is abundantly expressed in neurons of the neocortex, hippocampus, and striatum, but its role in these cells is unknown. We found that neuronal expression of this receptor was markedly up-regulated in the postnatal mouse neocortex immediately prior to the final development of glutamatergic synapses. In the absence of Tyro3, cortical and hippocampal synapses never completed end-stage differentiation and remained electrophysiologically and ultrastructurally immature. Tyro3-/- cortical neurons also exhibited diminished plasma membrane expression of the GluA2 subunits of AMPA-type glutamate receptors, which are essential to mature synaptic function. Correspondingly, GluA2 membrane insertion in wild-type neurons was stimulated by Gas6, a Tyro3 ligand widely expressed in the postnatal brain. Behaviorally, Tyro3-/- mice displayed learning enhancements in spatial recognition and fear-conditioning assays. Together, these results demonstrate that Tyro3 promotes the functional maturation of glutamatergic synapses by driving plasma membrane translocation of GluA2 AMPA receptor subunits.
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Affiliation(s)
- Sheng Miao
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Lawrence Fourgeaud
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Patrick G Burrola
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Shani Stern
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Yuhan Zhang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Kaisa E Happonen
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Sammy Weiser Novak
- Waitt Advanced Biophotonics Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Greg Lemke
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States
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7
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de Cássia Collaço R, Lammens M, Blevins C, Rodgers K, Gurau A, Yamauchi S, Kim C, Forrester J, Liu E, Ha J, Mei Y, Boehm C, Wohler E, Sobreira N, Rowe PC, Valle D, Brock MV, Bosmans F. Anxiety and dysautonomia symptoms in patients with a Na V1.7 mutation and the potential benefits of low-dose short-acting guanfacine. Clin Auton Res 2024; 34:191-201. [PMID: 38064009 DOI: 10.1007/s10286-023-01004-1] [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: 09/05/2023] [Accepted: 11/15/2023] [Indexed: 03/17/2024]
Abstract
PURPOSE Guanfacine is an α2A-adrenergic receptor agonist, FDA-approved to treat attention-deficit hyperactivity disorder and high blood pressure, typically as an extended-release formulation up to 7 mg/day. In our dysautonomia clinic, we observed that off-label use of short-acting guanfacine at 1 mg/day facilitated symptom relief in two families with multiple members presenting with severe generalized anxiety. We also noted anecdotal improvements in associated dysautonomia symptoms such as hyperhidrosis, cognitive impairment, and palpitations. We postulated that a genetic deficit existed in these patients that might augment guanfacine susceptibility. METHODS We used whole-exome sequencing to identify mutations in patients with shared generalized anxiety and dysautonomia symptoms. Guanfacine-induced changes in the function of voltage-gated Na+ channels were investigated using voltage-clamp electrophysiology. RESULTS Whole-exome sequencing uncovered the p.I739V mutation in SCN9A in the proband of two nonrelated families. Moreover, guanfacine inhibited ionic currents evoked by wild-type and mutant NaV1.7 encoded by SCN9A, as well as other NaV channel subtypes to a varying degree. CONCLUSION Our study provides further evidence for a possible pathophysiological role of NaV1.7 in anxiety and dysautonomia. Combined with off-target effects on NaV channel function, daily administration of 1 mg short-acting guanfacine may be sufficient to normalize NaV channel mutation-induced changes in sympathetic activity, perhaps aided by partial inhibition of NaV1.7 or other channel subtypes. In a broader context, expanding genetic and functional data about ion channel aberrations may enable the prospect of stratifying patients in which mutation-induced increased sympathetic tone normalization by guanfacine can support treatment strategies for anxiety and dysautonomia symptoms.
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Affiliation(s)
- Rita de Cássia Collaço
- Molecular Physiology and Neurophysics Group, Department of Basic and Applied Medical Sciences, University of Ghent, Ghent, Belgium
| | - Maxime Lammens
- Molecular Physiology and Neurophysics Group, Department of Basic and Applied Medical Sciences, University of Ghent, Ghent, Belgium
| | - Carley Blevins
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kristen Rodgers
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Andrei Gurau
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Suguru Yamauchi
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Christine Kim
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jeannine Forrester
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Edward Liu
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jinny Ha
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yuping Mei
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Corrine Boehm
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Peter C Rowe
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Malcolm V Brock
- Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Frank Bosmans
- Molecular Physiology and Neurophysics Group, Department of Basic and Applied Medical Sciences, University of Ghent, Ghent, Belgium.
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Wheeler DW, Kopsick JD, Sutton N, Tecuatl C, Komendantov AO, Nadella K, Ascoli GA. Hippocampome.org v2.0: a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.12.540597. [PMID: 37425693 PMCID: PMC10327012 DOI: 10.1101/2023.05.12.540597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression. Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.
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Affiliation(s)
- Diek W. Wheeler
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Jeffrey D. Kopsick
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Interdisciplinary Program in Neuroscience; College of Science; George Mason University, Fairfax, VA, USA
| | - Nate Sutton
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Carolina Tecuatl
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Alexander O. Komendantov
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Kasturi Nadella
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
| | - Giorgio A. Ascoli
- Center for Neural Informatics, Structures, & Plasticity; Krasnow Institute for Advanced Study; George Mason University, Fairfax, VA, USA
- Interdisciplinary Program in Neuroscience; College of Science; George Mason University, Fairfax, VA, USA
- Bioengineering Department and Center for Neural Informatics, Structures, & Plasticity; College of Engineering and Computing; George Mason University, Fairfax, VA, USA
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9
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Ogonowski N, Santamaria-Garcia H, Baez S, Lopez A, Laserna A, Garcia-Cifuentes E, Ayala-Ramirez P, Zarante I, Suarez-Obando F, Reyes P, Kauffman M, Cochran N, Schulte M, Sirkis DW, Spina S, Yokoyama JS, Miller BL, Kosik KS, Matallana D, Ibáñez A. Frontotemporal dementia presentation in patients with heterozygous p.H157Y variant of TREM2. J Med Genet 2023; 60:894-904. [PMID: 36813542 PMCID: PMC10447405 DOI: 10.1136/jmg-2022-108627] [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: 08/09/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND The triggering receptor expressed on myeloid cell 2 (TREM2) is a major regulator of neuroinflammatory processes in neurodegeneration. To date, the p.H157Y variant of TREM2 has been reported only in patients with Alzheimer's disease. Here, we report three patients with frontotemporal dementia (FTD) from three unrelated families with heterozygous p.H157Y variant of TREM2: two patients from Colombian families (study 1) and a third Mexican origin case from the USA (study 2). METHODS To determine if the p.H157Y variant might be associated with a specific FTD presentation, we compared in each study the cases with age-matched, sex-matched and education-matched groups-a healthy control group (HC) and a group with FTD with neither TREM2 mutations nor family antecedents (Ng-FTD and Ng-FTD-MND). RESULTS The two Colombian cases presented with early behavioural changes, greater impairments in general cognition and executive function compared with both HC and Ng-FTD groups. These patients also exhibited brain atrophy in areas characteristic of FTD. Furthermore, TREM2 cases showed increased atrophy compared with Ng-FTD in frontal, temporal, parietal, precuneus, basal ganglia, parahippocampal/hippocampal and cerebellar regions. The Mexican case presented with FTD and motor neuron disease (MND), showing grey matter reduction in basal ganglia and thalamus, and extensive TDP-43 type B pathology. CONCLUSION In all TREM2 cases, multiple atrophy peaks overlapped with the maximum peaks of TREM2 gene expression in crucial brain regions including frontal, temporal, thalamic and basal ganglia areas. These results provide the first report of an FTD presentation potentially associated with the p.H157Y variant with exacerbated neurocognitive impairments.
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Affiliation(s)
- Natalia Ogonowski
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Adolfo Ibanez University, Santiago, Chile, Santiago de Chile, Chile
| | - Hernando Santamaria-Garcia
- Global Brain Health Institute (GBHI), University California San Francisco (UCSF), San Francisco, California, USA
- Pontificia Universidad Javeriana. Ph.D Program of Neuroscience, Bogotá, Colombia
- Hospital Universitario San Ignacio. Centro de Memoria y Cognición Intellectus, Bogotá, Colombia
| | | | - Andrea Lopez
- Hospital Universitario de la Fundación Santa Fe de Bogotá, Bogota, Colombia
- Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Andrés Laserna
- Pontificia Universidad Javeriana, Bogota, Colombia
- University of Rochester Medical Center. Department of Anesthesiology and Perioperative Medicine. of Anesthesiology and Perioperative Medicine, Rochester, NY, New York, USA
| | - Elkin Garcia-Cifuentes
- Pontificia Universidad Javeriana, Bogota, Colombia
- Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Paola Ayala-Ramirez
- Human Genomics Institute, Pontificia Universidad Javeriana, Bogota, Colombia
| | | | | | - Pablo Reyes
- Pontificia Universidad Javeriana, Bogota, Colombia
| | - Marcelo Kauffman
- Hospital General de Agudos Jose Maria Ramos Mejia Consultorio y Laboratorio de Neurogenetica, Buenos Aires, Argentina
- Universidad Austral. IIMT-FCB. Conicet, Buenos Aires, Argentina
| | | | | | - Daniel W Sirkis
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
- Weil Institute of Neuroscience, University of California, San Francisco, San Francisco, California, USA
| | - Salvatore Spina
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Jennifer S Yokoyama
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
- Weil Institute of Neuroscience, University of California, San Francisco, San Francisco, California, USA
| | | | - Kenneth S Kosik
- University of California Santa Barbara, Santa Barbara, California, USA
| | - Diana Matallana
- Pontificia Universidad Javeriana, Bogota, Colombia
- Hospital Universitario Fundación Santa Fe, Bogotá, Colombia
| | - Agustín Ibáñez
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Adolfo Ibanez University, Santiago, Chile, Santiago de Chile, Chile
- Global Brain Health Institute (GBHI), Trinity College Dublin, Dublin, Ireland
- Cognitive Neuroscience Center (CNC), Universidad de San Andres & CONICET, Buenos Aires, Argentina
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10
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Littleton SH, Trang KB, Volpe CM, Cook K, DeBruyne N, Ann Maguire J, Ann Weidekamp M, Boehm K, Chesi A, Pippin JA, Anderson SA, Wells AD, Pahl MC, Grant SF. Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.553157. [PMID: 37662342 PMCID: PMC10473629 DOI: 10.1101/2023.08.21.553157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ch12q13 obesity locus is among the most significant childhood obesity loci identified in genome-wide association studies. This locus resides in a non-coding region within FAIM2; thus, the underlying causal variant(s) presumably influence disease susceptibility via an influence on cis-regulation within the genomic region. We implicated rs7132908 as a putative causal variant at this locus leveraging a combination of our inhouse 3D genomic data, public domain datasets, and several computational approaches. Using a luciferase reporter assay in human primary astrocytes, we observed allele-specific cis-regulatory activity of the immediate region harboring rs7132908. Motivated by this finding, we went on to generate isogenic human embryonic stem cell lines homozygous for either rs7132908 allele with CRISPR-Cas9 homology-directed repair to assess changes in gene expression due to genotype and chromatin accessibility throughout a differentiation to hypothalamic neurons, a key cell type known to regulate feeding behavior. We observed that the rs7132908 obesity risk allele influenced the expression of FAIM2 along with other genes, decreased the proportion of neurons produced during differentiation, up-regulated cell death gene sets, and conversely down-regulated neuron differentiation gene sets. We have therefore functionally validated rs7132908 as a causal obesity variant which temporally regulates nearby effector genes at the ch12q13 locus and influences neurodevelopment and survival.
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Affiliation(s)
- Sheridan H. Littleton
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Khanh B. Trang
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christina M. Volpe
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kieona Cook
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nicole DeBruyne
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Ann Maguire
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mary Ann Weidekamp
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keith Boehm
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James A. Pippin
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A. Anderson
- Department of Child and Adolescent Psychiatry, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew D. Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C. Pahl
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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11
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Nejatbakhsh A, Dey N, Venkatachalam V, Yemini E, Paninski L, Varol E. Learning Probabilistic Piecewise Rigid Atlases of Model Organisms via Generative Deep Networks. INFORMATION PROCESSING IN MEDICAL IMAGING : PROCEEDINGS OF THE ... CONFERENCE 2023; 13939:332-343. [PMID: 37476079 PMCID: PMC10358289 DOI: 10.1007/978-3-031-34048-2_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Atlases are crucial to imaging statistics as they enable the standardization of inter-subject and inter-population analyses. While existing atlas estimation methods based on fluid/elastic/diffusion registration yield high-quality results for the human brain, these deformation models do not extend to a variety of other challenging areas of neuroscience such as the anatomy of C. elegans worms and fruit flies. To this end, this work presents a general probabilistic deep network-based framework for atlas estimation and registration which can flexibly incorporate various deformation models and levels of keypoint supervision that can be applied to a wide class of model organisms. Of particular relevance, it also develops a deformable piecewise rigid atlas model which is regularized to preserve inter-observation distances between neighbors. These modeling considerations are shown to improve atlas construction and key-point alignment across a diversity of datasets with small sample sizes including neuron positions in C. elegans hermaphrodites, fluorescence microscopy of male C. elegans, and images of fruit fly wings. Code is accessible at https://github.com/amin-nejat/Deformable-Atlas.
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Affiliation(s)
- Amin Nejatbakhsh
- Departments of Neuroscience and Statistics, Columbia University, New York, USA
| | - Neel Dey
- Computer Science and Artificial Intelligence Lab, MIT, Massachusetts, USA
| | | | - Eviatar Yemini
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, USA
| | - Liam Paninski
- Departments of Neuroscience and Statistics, Columbia University, New York, USA
| | - Erdem Varol
- Department of Computer Science and Engineering, New York University, New York, USA
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12
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Rudolph HC, Stafford AM, Hwang HE, Kim CH, Prokop JW, Vogt D. Structure-Function of the Human WAC Protein in GABAergic Neurons: Towards an Understanding of Autosomal Dominant DeSanto-Shinawi Syndrome. BIOLOGY 2023; 12:589. [PMID: 37106788 PMCID: PMC10136313 DOI: 10.3390/biology12040589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/29/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023]
Abstract
Dysfunction of the WW domain-containing adaptor with coiled-coil, WAC, gene underlies a rare autosomal dominant disorder, DeSanto-Shinawi syndrome (DESSH). DESSH is associated with facial dysmorphia, hypotonia, and cognitive alterations, including attention deficit hyperactivity disorder and autism. How the WAC protein localizes and functions in neural cells is critical to understanding its role during development. To understand the genotype-phenotype role of WAC, we developed a knowledgebase of WAC expression, evolution, human genomics, and structural/motif analysis combined with human protein domain deletions to assess how conserved domains guide cellular distribution. Then, we assessed localization in a cell type implicated in DESSH, cortical GABAergic neurons. WAC contains conserved charged amino acids, phosphorylation signals, and enriched nuclear motifs, suggesting a role in cellular signaling and gene transcription. Human DESSH variants are found within these regions. We also discovered and tested a nuclear localization domain that impacts the cellular distribution of the protein. These data provide new insights into the potential roles of this critical developmental gene, establishing a platform to assess further translational studies, including the screening of missense genetic variants in WAC. Moreover, these studies are essential for understanding the role of human WAC variants in more diverse neurological phenotypes, including autism spectrum disorder.
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Affiliation(s)
- Hannah C. Rudolph
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - April M. Stafford
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
| | - Hye-Eun Hwang
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, USA
- Neuroscience Program, Michigan State University, East Lansing, MI 48824, USA
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13
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Hu Z, Yang Y, Ye D, Chen S, Gong Y, Chukwu C, Chen H. Targeted delivery of therapeutic agents to the mouse brain using a stereotactic-guided focused ultrasound device. STAR Protoc 2023; 4:102132. [PMID: 36861835 PMCID: PMC9988659 DOI: 10.1016/j.xpro.2023.102132] [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: 11/22/2022] [Revised: 12/28/2022] [Accepted: 02/06/2023] [Indexed: 03/03/2023] Open
Abstract
Existing protocols of focused ultrasound (FUS) combined with microbubble-mediated blood-brain barrier (BBB) opening (FUS-BBBO) in preclinical research require expensive ultrasound equipment and complex operating procedures. We developed a low-cost, easy-to-use, and precise FUS device for small animal models in preclinical research. Here, we provide a detailed protocol for building the FUS transducer, attaching the transducer to a stereotactic frame for precise brain targeting, applying the integrated FUS device to perform FUS-BBBO in mice, and evaluating the FUS-BBBO outcome. For complete details on the use and execution of this protocol, please refer to Hu et al. (2022).1.
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Affiliation(s)
- Zhongtao Hu
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA.
| | - Yaoheng Yang
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Dezhuang Ye
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Si Chen
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Yan Gong
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Chinwendu Chukwu
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Hong Chen
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; Department of Radiation Oncology, Washington University School of Medicine, Saint Louis, MO 63108, USA.
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14
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Grogan DP, Skelton HM, Fernandez AM, Gutekunst CANE, Gross RE. The laterodorsal tegmentum and seizure regulation: Revisiting the evidence. J Neurosci Res 2023; 101:256-262. [PMID: 36349730 DOI: 10.1002/jnr.25144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022]
Abstract
Electrical deep brain stimulation (DBS) is now a routine treatment option for patients suffering from medically refractory epilepsy. DBS of the anterior nucleus of the thalamus (ANT) has proven to be effective but, despite its success, few patients experience complete cessation of seizure activity. However, improving the therapy is challenging because the mechanism underlying its action remains largely unknown. One angle on improving the effectiveness of ANT stimulation is to better understand the various anatomic regions that send projections to and through this area. Here, the authors utilized a connectomic atlas of the mouse brain to better understand the regions projecting to the ANT and were particularly interested by the presence of robust cholinergic projections from the laterodorsal tegmentum (LDT). A subsequent review of the literature resulted in limited studies, which presented convincing evidence supporting this region's role in seizure control present in acute rodent models of epilepsy. It is thus the purpose of this paper to encourage further research into the role of the LDT on seizure mitigation, with mechanistic effects likely stemming from its cholinergic projections to the ANT. While previous studies have laid a firm foundation supporting the role of this region in modulation of seizure activity, modern scientific methodology has yet to be applied to further elucidate the mechanisms and potential benefits associated with LDT stimulation in the epileptic population.
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Affiliation(s)
- Dayton P Grogan
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Henry M Skelton
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Alejandra M Fernandez
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Robert E Gross
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Neurology, Emory University, Atlanta, Georgia, USA
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15
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Appukuttan S, Bologna LL, Schürmann F, Migliore M, Davison AP. EBRAINS Live Papers - Interactive Resource Sheets for Computational Studies in Neuroscience. Neuroinformatics 2023; 21:101-113. [PMID: 35986836 PMCID: PMC9931781 DOI: 10.1007/s12021-022-09598-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 01/23/2023]
Abstract
We present here an online platform for sharing resources underlying publications in neuroscience. It enables authors to easily upload and distribute digital resources, such as data, code, and notebooks, in a structured and systematic way. Interactivity is a prominent feature of the Live Papers, with features to download, visualise or simulate data, models and results presented in the corresponding publications. The resources are hosted on reliable data storage servers to ensure long term availability and easy accessibility. All data are managed via the EBRAINS Knowledge Graph, thereby helping maintain data provenance, and enabling tight integration with tools and services offered under the EBRAINS ecosystem.
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Affiliation(s)
- Shailesh Appukuttan
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, 91400 France
| | - Luca L. Bologna
- Institute of Biophysics, National Research Council, Palermo, 90143 Italy
| | - Felix Schürmann
- Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, 1202 Switzerland
| | - Michele Migliore
- Institute of Biophysics, National Research Council, Palermo, 90143 Italy
| | - Andrew P. Davison
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, 91400 France
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16
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Santamaría-García H, Ogonowsky N, Baez S, Palacio N, Reyes P, Schulte M, López A, Matallana D, Ibanez A. Neurocognitive patterns across genetic levels in behavioral variant frontotemporal dementia: a multiple single cases study. BMC Neurol 2022; 22:454. [PMID: 36474176 PMCID: PMC9724347 DOI: 10.1186/s12883-022-02954-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/06/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Behavioral variant frontotemporal dementia (bvFTD) has been related to different genetic factors. Identifying multimodal phenotypic heterogeneity triggered by various genetic influences is critical for improving diagnosis, prognosis, and treatments. However, the specific impact of different genetic levels (mutations vs. risk variants vs. sporadic presentations) on clinical and neurocognitive phenotypes is not entirely understood, specially in patites from underrepresented regions such as Colombia. METHODS Here, in a multiple single cases study, we provide systematic comparisons regarding cognitive, neuropsychiatric, brain atrophy, and gene expression-atrophy overlap in a novel cohort of FTD patients (n = 42) from Colombia with different genetic levels, including patients with known genetic influences (G-FTD) such as those with genetic mutations (GR1) in particular genes (MAPT, TARDBP, and TREM2); patients with risk variants (GR2) in genes associated with FTD (tau Haplotypes H1 and H2 and APOE variants including ε2, ε3, ε4); and sporadic FTD patients (S-FTD (GR3)). RESULTS We found that patients from GR1 and GR2 exhibited earlier disease onset, pervasive cognitive impairments (cognitive screening, executive functioning, ToM), and increased brain atrophy (prefrontal areas, cingulated cortices, basal ganglia, and inferior temporal gyrus) than S-FTD patients (GR3). No differences in disease duration were observed across groups. Additionally, significant neuropsychiatric symptoms were observed in the GR1. The GR1 also presented more clinical and neurocognitive compromise than GR2 patients; these groups, however, did not display differences in disease onset or duration. APOE and tau patients showed more neuropsychiatric symptoms and primary atrophy in parietal and temporal cortices than GR1 patients. The gene-atrophy overlap analysis revealed atrophy in regions with specific genetic overexpression in all G-FTD patients. A differential family presentation did not explain the results. CONCLUSIONS Our results support the existence of genetic levels affecting the clinical, neurocognitive, and, to a lesser extent, neuropsychiatric presentation of bvFTD in the present underrepresented sample. These results support tailored assessments characterization based on the parallels of genetic levels and neurocognitive profiles in bvFTD.
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Affiliation(s)
- Hernando Santamaría-García
- PhD program in Neuroscience, Pontificia Universidad Javeriana, Bogotá, Colombia.
- Memory and cognition Center, Intellectus, Hospital Universitario San Ignacio, Bogotá, Colombia.
- Department of Neurology, Global Brain Health Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Natalia Ogonowsky
- CONICET & Cognitive Neuroscience Center (CNC), Universidad de San Andrés, Buenos Aires, Argentina
| | - Sandra Baez
- Faculty of Psychology, Universidad de los Andes, Bogotá, Colombia
| | - Nicole Palacio
- Integrated Program in Neuroscience, McGill University, Montreal, Canada
| | - Pablo Reyes
- PhD program in Neuroscience, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Michael Schulte
- CONICET & Cognitive Neuroscience Center (CNC), Universidad de San Andrés, Buenos Aires, Argentina
| | - Andrea López
- Pontificia Universidad Javeriana, Bogotá, Colombia
- Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | | | - Agustín Ibanez
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago de Chile, Chile.
- Cognitive Neuroscience Center (CNC), Universidad de San Andrés, & National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina.
- Trinity Collegue of Dublin, Dublin, Irland.
- Global Brain Health Insititute, Universidad California San Francisco-Trinity College of Dublin, San Francisco, USA.
- Global Brain Health Insititute, Universidad California San Francisco-Trinity College of Dublin, Dublin, Irland.
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17
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Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data. Nat Commun 2022; 13:6912. [PMID: 36376296 PMCID: PMC9663444 DOI: 10.1038/s41467-022-34567-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
Spatially resolved transcriptomics is a relatively new technique that maps transcriptional information within a tissue. Analysis of these datasets is challenging because gene expression values are highly sparse due to dropout events, and there is a lack of tools to facilitate in silico detection and annotation of regions based on their molecular content. Therefore, we develop a computational tool for detecting molecular regions and region-based Missing value Imputation for Spatially Transcriptomics (MIST). We validate MIST-identified regions across multiple datasets produced by 10x Visium Spatial Transcriptomics, using manually annotated histological images as references. We benchmark MIST against a spatial k-nearest neighboring baseline and other imputation methods designed for single-cell RNA sequencing. We use holdout experiments to demonstrate that MIST accurately recovers spatial transcriptomics missing values. MIST facilitates identifying intra-tissue heterogeneity and recovering spatial gene-gene co-expression signals. Using MIST before downstream analysis thus provides unbiased region detections to facilitate annotations with the associated functional analyses and produces accurately denoised spatial gene expression profiles.
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18
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Machado TA, Kauvar IV, Deisseroth K. Multiregion neuronal activity: the forest and the trees. Nat Rev Neurosci 2022; 23:683-704. [PMID: 36192596 PMCID: PMC10327445 DOI: 10.1038/s41583-022-00634-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed remarkable advances in the simultaneous measurement of neuronal activity across many brain regions, enabling fundamentally new explorations of the brain-spanning cellular dynamics that underlie sensation, cognition and action. These recently developed multiregion recording techniques have provided many experimental opportunities, but thoughtful consideration of methodological trade-offs is necessary, especially regarding field of view, temporal acquisition rate and ability to guarantee cellular resolution. When applied in concert with modern optogenetic and computational tools, multiregion recording has already made possible fundamental biological discoveries - in part via the unprecedented ability to perform unbiased neural activity screens for principles of brain function, spanning dozens of brain areas and from local to global scales.
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Affiliation(s)
- Timothy A Machado
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Isaac V Kauvar
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
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19
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Biswas D, Kumari N, Lachén-Montes M, Dutta S, Agrawal I, Samanta D, Shenoy SV, Halder A, Fernández-Irigoyen J, Padhye AR, Santamaría E, Srivastava S. Deep Phosphoproteome Landscape of Interhemispheric Functionality of Neuroanatomical Regions of the Human Brain. J Proteome Res 2022; 22:1043-1055. [PMID: 36317652 DOI: 10.1021/acs.jproteome.2c00244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Post-translational modifications (PTMs) are one of the compulsive and predominant biological processes that regulate the diverse molecular mechanism, modulate the onset of disease, and are the reason behind the functional diversity of proteins. Despite the widespread research findings in neuroproteomics, one of the key drawbacks has been the lack of proteome-level knowledge of hemispheric lateralization. We have investigated the proteome level expression in different neuroanatomical regions under the Human Brain Proteome Project (HBPP) and developed the global interhemispheric brain proteome map (Brainprot) earlier. Furthermore, this study has extended to decipher the phosphoproteome map of human brain interhemispheric regions through high-resolution mass spectrometry. The phosphoproteomics examination of 12 unique interhemispheric neurological brain regions using Orbitrap fusion liquid chromatography with tandem mass spectrometry provided comprehensive coverage of 996 phosphoproteins, 2010 phosphopeptides, and 3567 phosphosites. Moreover, interhemispheric phosphoproteome profiling has been categorized according to synaptic ontologies and interhemispheric expression to understand the functionality. Finally, we have integrated the phosphosites data under the PhosphoMap section in the Inter-Hemispheric Brain Proteome Map Portal (https://www.brainprot.org/) for the advancement and support of the ongoing neuroproteomics research worldwide. Data is available via ProteomeXchange with the identifier PXD031188.
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Affiliation(s)
- Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Neha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sampurna Dutta
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata700032, India
| | - Ishita Agrawal
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi221005, India
| | - Debabrata Samanta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal721302, India
| | - Sanjyot Vinayak Shenoy
- Department of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Advait Rahul Padhye
- Department of Computer Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), 31008Pamplona, Spain
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
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20
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BRIDE v2: A Validated Collection of Genes Involved in the Mammalian Brain Response to Low-Dose Ionizing Radiation. RADIATION 2022. [DOI: 10.3390/radiation2040024] [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] Open
Abstract
There is significant interest in the response of the mammalian brain to low-dose ionizing radiation (LDIR), mainly examined by gene or protein expression, with applications in radiation safety on Earth, the atmosphere and outer space. Potential associations of molecular-level responses with sensory or cognitive defects and neurodegenerative diseases are currently under investigation. Previously, we have described a light-weight approach for the storage, analysis and distribution of relevant datasets, with the platform BRIDE. We have re-implemented the platform as BRIDE v2 on the cloud, using the bioinformatics infrastructure ELIXIR. We connected the annotated list of 3174 unique gene records with modern omics resources for downstream computational analysis. BRIDE v2 is a cloud-based platform with capabilities that enable researchers to extract, analyze, visualize as well as export the gene collection. The resource is freely available online at <http://bride-db.eu>.
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21
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Davis BT, Chen Z, Islam MB, Timken ME, Procissi D, Schwulst SJ. POSTINJURY FECAL MICROBIOME TRANSPLANT DECREASES LESION SIZE AND NEUROINFLAMMATION IN TRAUMATIC BRAIN INJURY. Shock 2022; 58:287-294. [PMID: 36256625 PMCID: PMC9586470 DOI: 10.1097/shk.0000000000001979] [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] [Indexed: 11/05/2022]
Abstract
ABSTRACT Background: Traumatic brain injury (TBI) is an underrecognized public health threat. The constitutive activation of microglia after TBI has been linked to long-term neurocognitive deficits and the progression of neurodegenerative disease. Evolving evidence indicates a critical role for the gut-brain axis in this process. Specifically, TBI has been shown to induce the depletion of commensal gut bacteria. The resulting gut dysbiosis is associated with neuroinflammation and disease. Hypothesis: We hypothesized that fecal microbiota transplantation would attenuate microglial activation and improve neuropathology after TBI. Methods: C57Bl/6 mice were subjected to severe TBI (n = 10) or sham injury (n = 10) via an open-head controlled cortical impact. The mice underwent fecal microbiota transplantation (FMT) or vehicle alone via oral gavage once weekly for 4 weeks after injury. At 59 days after TBI, mice underwent three-dimensional, contrast-enhanced magnetic resonance imaging. Following imaging, mice were killed, brains harvested at 60 DPI, and CD45+ cells isolated via florescence-activated cell sorting. cDNA libraries were prepared using the 10x Genomics Chromium Single Cell 3' Reagent kit followed by sequencing on a HiSeq4000 instrument, and computational analysis was performed. Results: Fecal microbiota transplantation resulted in a >marked reduction of ventriculomegaly (P < 0.002) and preservation of white matter connectivity at 59 days after TBI (P < 0.0001). In addition, microglia from FMT-treated mice significantly reduced inflammatory gene expression and enriched pathways involving the heat-shock response compared with mice treated with vehicle alone. Conclusions: We hypothesized that restoring gut microbial community structure via FMT would attenuate microglial activation and reduce neuropathology after TBI. Our data demonstrated significant preservation of cortical volume and white matter connectivity after an injury compared with mice treated with vehicle alone. This preservation of neuroanatomy after TBI was associated with a marked reduction in inflammatory gene expression within the microglia of FMT-treated mice. Microglia from FMT-treated mice enriched pathways in the heat-shock response, which is known to play a neuroprotective role in TBI and other neurodegenerative disease processes.
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Affiliation(s)
- Booker T Davis
- Department of Surgery, Division of Trauma and Critical Care, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Zhangying Chen
- Department of Surgery, Division of Trauma and Critical Care, Northwestern University Feinberg School of Medicine, Chicago IL
- Driskill Graduate Program in Life Science, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Mecca B.A.R. Islam
- Department of Surgery, Division of Trauma and Critical Care, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Madeline E. Timken
- Department of Surgery, Division of Trauma and Critical Care, Northwestern University Feinberg School of Medicine, Chicago IL
| | - Daniele Procissi
- Department of Radiology, Northwestern University Feinberg School of Medicine, Chicago, USA
- Center for Translational Pain Research Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Steven J. Schwulst
- Department of Surgery, Division of Trauma and Critical Care, Northwestern University Feinberg School of Medicine, Chicago IL
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22
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Aryal SP, Xia M, Ortinski PI, Richards CI. Study of Calcium Signaling in Astrocytes with a Novel Endoplasmic Reticulum-Targeted GCaMP Sensor. Curr Protoc 2022; 2:e491. [PMID: 35938843 PMCID: PMC9373517 DOI: 10.1002/cpz1.491] [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] [Indexed: 06/15/2023]
Abstract
The endoplasmic reticulum (ER), the major organelle for the storage of Ca2+ , maintains a concentration of Ca2+ much higher than in the cytosol or other subcellular organelles, such as the mitochondria. A variety of tools have been developed for measuring Ca2+ activity in neuronal and glial cells, but most of these sensors target either the plasma membrane (PM) or the cytosol. Though these sensors are important for measuring Ca2+ transients, they lack the capability to measure activity in the periphery of the ER or to measure low-amplitude events resulting from Ca2+ exchange between the ER and other organelles, such as the mitochondria. We recently developed an ER-targeted GCaMP6f anchored to the cytosolic side of the ER that can measure minute calcium exchange occurring in this region. In this article, we discuss detailed methods to characterize the ER-GCaMP6f sensor, utilize it for calcium imaging in cultured astrocytes, and assess its expression and calcium imaging in astrocytes in rodent brains. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Expression and characterization of ER-GCaMP6f Support Protocol 1: ER-GCaMP6f-expressing stable cell line generation Basic Protocol 2: In vitro calcium imaging with ER-GCaMP6f Support Protocol 2: Imaging of drug-induced calcium activity Alternate Protocol 1: Transduction of astrocytes with ER-GCaMP6f AAV Alternate Protocol 2: Calcium imaging of astrocytes with Fluo-4 AM Basic Protocol 3: In vivo ER-GCaMP6f expression and slice calcium imaging Support Protocol 3: Pharmacological studies with 2-APB in brain slices.
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Affiliation(s)
- Surya P Aryal
- Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | - Mengfan Xia
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky
| | - Pavel I Ortinski
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky
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23
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Ramezanian-Panahi M, Abrevaya G, Gagnon-Audet JC, Voleti V, Rish I, Dumas G. Generative Models of Brain Dynamics. Front Artif Intell 2022; 5:807406. [PMID: 35910192 PMCID: PMC9335006 DOI: 10.3389/frai.2022.807406] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/10/2022] [Indexed: 01/28/2023] Open
Abstract
This review article gives a high-level overview of the approaches across different scales of organization and levels of abstraction. The studies covered in this paper include fundamental models in computational neuroscience, nonlinear dynamics, data-driven methods, as well as emergent practices. While not all of these models span the intersection of neuroscience, AI, and system dynamics, all of them do or can work in tandem as generative models, which, as we argue, provide superior properties for the analysis of neuroscientific data. We discuss the limitations and unique dynamical traits of brain data and the complementary need for hypothesis- and data-driven modeling. By way of conclusion, we present several hybrid generative models from recent literature in scientific machine learning, which can be efficiently deployed to yield interpretable models of neural dynamics.
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Affiliation(s)
| | - Germán Abrevaya
- Mila-Quebec AI Institute, Montréal, QC, Canada
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Instituto de Física de Buenos Aires (IFIBA), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Vikram Voleti
- Mila-Quebec AI Institute, Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
| | - Irina Rish
- Mila-Quebec AI Institute, Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
| | - Guillaume Dumas
- Mila-Quebec AI Institute, Montréal, QC, Canada
- Université de Montréal, Montréal, QC, Canada
- Department of Psychiatry, CHU Sainte-Justine Research Center, Mila-Quebec AI Institute, Université de Montréal, Montréal, QC, Canada
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24
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Mesmoudi S, Lapina C, Rodic M, Peschanski D. Multi-Data Integration Towards a Global Understanding of the Neurological Impact of Human Brain Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Front Integr Neurosci 2022; 16:756604. [PMID: 35910337 PMCID: PMC9326261 DOI: 10.3389/fnint.2022.756604] [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: 08/10/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
As the COVID-19 pandemic continues to unfold, numerous neurological symptoms emerge. The literature reports more and more manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) related to headache, dizziness, impaired consciousness, cognitive impairment, and motor disorders. Moreover, the infection of SARS-CoV-2 may have a durable neurological impact. ACE2/TMPRSS2 is the main entry point into cells for some strains of coronaviruses (CoVs), including SARS-CoV-2, which uses it to target the central nervous system (CNS). The aim of this study was to characterize the scope of the potential complex impact of a SARS-CoV-2 infection in the brain. It concerns different scales: the topographic, cognitive, sensorimotor, and genetic one. We investigated which cognitive and sensorimotor functions are associated with the brain regions where ACE2/TMPRSS2 is overexpressed, hypothesising that they might be particularly affected by the infection. Furthermore, overexpressed genes in these regions are likely to be impacted by COVID-19. This general understanding is crucial to establish the potential neurological manifestations of the infection. Data on mRNA expression levels of genes were provided by the Allen Institute for Brain Science (AIBS), and the localisation of brain functions by the LinkRbrain platform. The latter was also used to analyze the spatial overlap between ACE2/TMPRSS2 overexpression, and either function-specific brain activations or regional overexpression of other genes. The characterisation of these overexpressed genes was based on the GeneCards platform and the gene GSE164332 from the Gene Expression Omnibus database. We analysed the cognitive and sensorimotor functions whose role might be impaired, of which 88 have been categorised into seven groups: memory and recollection, motor function, pain, lucidity, emotion, sensory, and reward. Furthermore, we categorised the genes showing a significant increase in concentration of their mRNAs in the same regions where ACE2/TMPRSS2 mRNA levels are the highest. Eleven groups emerged from a bibliographical research: neurodegenerative disease, immunity, inflammation, olfactory receptor, cancer/apoptosis, executive function, senses, ischemia, motor function, myelination, and dependence. The results of this exploration could be in relation to the neurological symptoms of COVID-19. Furthermore, some genes from peripheral blood are already considered as biomarker of COVID-19. This method could generate new hypotheses to explore the neurological manifestations of COVID-19.
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Affiliation(s)
- Salma Mesmoudi
- Paris-1-Panthéon-Sorbonne University CESSP-UMR 8209, Paris, France
- French National Centre for Scientific Research (CNRS), Paris, France
- MATRICE Equipex, Seine-Saint-Denis, France
- Complex Systems Institute Paris Île-de-France, Paris, France
| | - Colline Lapina
- French National Centre for Scientific Research (CNRS), Paris, France
- MATRICE Equipex, Seine-Saint-Denis, France
- Complex Systems Institute Paris Île-de-France, Paris, France
- Graduate School of Cognitive Engineering (ENSC), Talence, France
| | | | - Denis Peschanski
- Paris-1-Panthéon-Sorbonne University CESSP-UMR 8209, Paris, France
- French National Centre for Scientific Research (CNRS), Paris, France
- MATRICE Equipex, Seine-Saint-Denis, France
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25
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Ren W, Li L, Zhang J, Vaas M, Klohs J, Ripoll J, Wolf M, Ni R, Rudin M. Non-invasive visualization of amyloid-beta deposits in Alzheimer amyloidosis mice using magnetic resonance imaging and fluorescence molecular tomography. BIOMEDICAL OPTICS EXPRESS 2022; 13:3809-3822. [PMID: 35991935 PMCID: PMC9352276 DOI: 10.1364/boe.458290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Abnormal cerebral accumulation of amyloid-beta peptide (Aβ) is a major hallmark of Alzheimer's disease. Non-invasive monitoring of Aβ deposits enables assessing the disease burden in patients and animal models mimicking aspects of the human disease as well as evaluating the efficacy of Aβ-modulating therapies. Previous in vivo assessments of plaque load have been predominantly based on macroscopic fluorescence reflectance imaging (FRI) and confocal or two-photon microscopy using Aβ-specific imaging agents. However, the former method lacks depth resolution, whereas the latter is restricted by the limited field of view preventing a full coverage of the large brain region. Here, we utilized a fluorescence molecular tomography (FMT)-magnetic resonance imaging (MRI) pipeline with the curcumin derivative fluorescent probe CRANAD-2 to achieve full 3D brain coverage for detecting Aβ accumulation in the arcAβ mouse model of cerebral amyloidosis. A homebuilt FMT system was used for data acquisition, whereas a customized software platform enabled the integration of MRI-derived anatomical information as prior information for FMT image reconstruction. The results obtained from the FMT-MRI study were compared to those from conventional planar FRI recorded under similar physiological conditions, yielding comparable time courses of the fluorescence intensity following intravenous injection of CRANAD-2 in a region-of-interest comprising the brain. In conclusion, we have demonstrated the feasibility of visualizing Aβ deposition in 3D using a multimodal FMT-MRI strategy. This hybrid imaging method provides complementary anatomical, physiological and molecular information, thereby enabling the detailed characterization of the disease status in arcAβ mouse models, which can also facilitate monitoring the efficacy of putative treatments targeting Aβ.
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Affiliation(s)
- Wuwei Ren
- Institute for Biomedical Engineering, ETH and University of Zurich, Zurich 8006, Switzerland
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Linlin Li
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jianru Zhang
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Markus Vaas
- Institute for Biomedical Engineering, ETH and University of Zurich, Zurich 8006, Switzerland
| | - Jan Klohs
- Institute for Biomedical Engineering, ETH and University of Zurich, Zurich 8006, Switzerland
| | - Jorge Ripoll
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, Madrid 28005, Spain
| | - Martin Wolf
- Biomedical Optics Research Laboratory, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Ruiqing Ni
- Institute for Biomedical Engineering, ETH and University of Zurich, Zurich 8006, Switzerland
- Institute for Regenerative Medicine, University of Zurich, Zurich 8952, Switzerland
| | - Markus Rudin
- Institute for Biomedical Engineering, ETH and University of Zurich, Zurich 8006, Switzerland
- The LOOP Zurich, Translational Research Center, Zurich 8044, Switzerland
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26
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Delprato A, Xiao E, Manoj D. Connecting DCX, COMT and FMR1 in social behavior and cognitive impairment. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2022; 18:7. [PMID: 35590332 PMCID: PMC9121553 DOI: 10.1186/s12993-022-00191-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/14/2022] [Indexed: 11/24/2022]
Abstract
Genetic variants of DCX, COMT and FMR1 have been linked to neurodevelopmental disorders related to intellectual disability and social behavior. In this systematic review we examine the roles of the DCX, COMT and FMR1 genes in the context of hippocampal neurogenesis with respect to these disorders with the aim of identifying important hubs and signaling pathways that may bridge these conditions. Taken together our findings indicate that factors connecting DCX, COMT, and FMR1 in intellectual disability and social behavior may converge at Wnt signaling, neuron migration, and axon and dendrite morphogenesis. Data derived from genomic research has identified a multitude of genes that are linked to brain disorders and developmental differences. Information about where and how these genes function and cooperate is lagging behind. The approach used here may help to shed light on the biological underpinnings in which key genes interface and may prove useful for the testing of specific hypotheses.
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Affiliation(s)
- Anna Delprato
- Department of Research and Education, BioScience Project, Wakefield, MA, 01880, USA.
| | - Emily Xiao
- Department of Research and Education, BioScience Project, Wakefield, MA, 01880, USA.,Alexander Mackenzie High School, Richmond Hill, ON, 14519, Canada
| | - Devika Manoj
- Department of Research and Education, BioScience Project, Wakefield, MA, 01880, USA.,Lambert High School, Suwanee, GA, 30024, USA
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27
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Chen P, Lin X, Liu A, Li J. The Brain Research Hotspot Database (BRHD): A Panoramic Database of the Latest Hotspots in Brain Research. Brain Sci 2022; 12:brainsci12050638. [PMID: 35625024 PMCID: PMC9139690 DOI: 10.3390/brainsci12050638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/21/2022] [Accepted: 05/03/2022] [Indexed: 01/25/2023] Open
Abstract
Brain science, an emerging, dynamic, multidisciplinary basic research field, is generating numerous valuable data. However, there are still several obstacles for the utilization of these data, such as data fragmentation, heterogeneity, availability, and annotation divergence. Thus, to overcome these obstacles and construct an online community, we developed a panoramic database named Brain Research Hotspot Database (BRHD). As of 30 January 2022, the database had been integrated with standardized vocabularies from various resources, including 423,681 papers, 46,344 patents, 9585 transcriptomic datasets, 261 cell markers, as well as with information regarding brain initiatives that were officially launched and well-known scholars in brain research. Based on the keywords entered by users and the search options they set, data can be accessed and retrieved through exact and fuzzy search scenarios. In addition, for brain diseases, we developed three featured functions based on deep data mining: (1) a brain disease–genome network, which collects the associations between common brain diseases, genes, and mutations reported in the literature; (2) brain and gut microbiome associations, based on the literature related to this topic, with added annotations for reference; (3) 3D brain structure, containing a high-precision brain anatomy model with visual links to quickly connect to an organ-on-a-chip database. In short, the BRHD integrates data from a variety of brain science resources to provide a friendly user interface and freely accessible viewing and downloading environment. Furthermore, the original functions developed based on these data provide references and insights for brain research.
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Affiliation(s)
- Pin Chen
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing 210018, China; (P.C.); (A.L.)
| | - Xue Lin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China;
| | - Anna Liu
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing 210018, China; (P.C.); (A.L.)
| | - Jian Li
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing 210018, China; (P.C.); (A.L.)
- Correspondence: ; Tel.: +86-130-5288-1142
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28
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Therapeutic Targets for Regulating Oxidative Damage Induced by Ischemia-Reperfusion Injury: A Study from a Pharmacological Perspective. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8624318. [PMID: 35450409 PMCID: PMC9017553 DOI: 10.1155/2022/8624318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 12/22/2022]
Abstract
Ischemia-reperfusion (I-R) injury is damage caused by restoring blood flow into ischemic tissues or organs. This complex and characteristic lesion accelerates cell death induced by signaling pathways such as apoptosis, necrosis, and even ferroptosis. In addition to the direct association between I-R and the release of reactive oxygen species and reactive nitrogen species, it is involved in developing mitochondrial oxidative damage. Thus, its mechanism plays a critical role via reactive species scavenging, calcium overload modulation, electron transport chain blocking, mitochondrial permeability transition pore activation, or noncoding RNA transcription. Other receptors and molecules reduce tissue and organ damage caused by this pathology and other related diseases. These molecular targets have been gradually discovered and have essential roles in I-R resolution. Therefore, the current study is aimed at highlighting the importance of these discoveries. In this review, we inquire about the oxidative damage receptors that are relevant to reducing the damage induced by oxidative stress associated with I-R. Several complications on surgical techniques and pathology interventions do not mitigate the damage caused by I-R. Nevertheless, these therapies developed using alternative targets could work as coadjuvants in tissue transplants or I-R-related pathologies
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29
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Prokop JW, Jdanov V, Savage L, Morris M, Lamb N, VanSickle E, Stenger CL, Rajasekaran S, Bupp CP. Computational and Experimental Analysis of Genetic Variants. Compr Physiol 2022; 12:3303-3336. [PMID: 35578967 DOI: 10.1002/cphy.c210012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics has grown exponentially over the last decade. Common variants are associated with physiological changes through statistical strategies such as Genome-Wide Association Studies (GWAS) and quantitative trail loci (QTL). Rare variants are associated with diseases through extensive filtering tools, including population genomics and trio-based sequencing (parents and probands). However, the genomic associations require follow-up analyses to narrow causal variants, identify genes that are influenced, and to determine the physiological changes. Large quantities of data exist that can be used to connect variants to gene changes, cell types, protein pathways, clinical phenotypes, and animal models that establish physiological genomics. This data combined with bioinformatics including evolutionary analysis, structural insights, and gene regulation can yield testable hypotheses for mechanisms of genomic variants. Molecular biology, biochemistry, cell culture, CRISPR editing, and animal models can test the hypotheses to give molecular variant mechanisms. Variant characterizations can be a significant component of educating future professionals at the undergraduate, graduate, or medical training programs through teaching the basic concepts and terminology of genetics while learning independent research hypothesis design. This article goes through the computational and experimental analysis strategies of variant characterization and provides examples of these tools applied in publications. © 2022 American Physiological Society. Compr Physiol 12:3303-3336, 2022.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Vladislav Jdanov
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Lane Savage
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, Alabama, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, Michigan, USA.,Office of Research, Spectrum Health, Grand Rapids, Michigan, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA.,Medical Genetics, Spectrum Health, Grand Rapids, Michigan, USA
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30
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Castañeyra-Ruiz L, González-Marrero I, Hernández-Abad LG, Carmona-Calero EM, Pardo MR, Baz-Davila R, Lee S, Muhonen M, Borges R, Castañeyra-Perdomo A. AQP4 labels a subpopulation of white matter-dependent glial radial cells affected by pediatric hydrocephalus, and its expression increased in glial microvesicles released to the cerebrospinal fluid in obstructive hydrocephalus. Acta Neuropathol Commun 2022; 10:41. [PMID: 35346374 PMCID: PMC8962176 DOI: 10.1186/s40478-022-01345-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/11/2022] [Indexed: 01/16/2023] Open
Abstract
Hydrocephalus is a distension of the ventricular system associated with ventricular zone disruption, reactive astrogliosis, periventricular white matter ischemia, axonal impairment, and corpus callosum alterations. The condition's etiology is typically attributed to a malfunction in classical cerebrospinal fluid (CSF) bulk flow; however, this approach does not consider the unique physiology of CSF in fetal and perinatal patients. The parenchymal fluid contributes to the glymphatic system, and plays a fundamental role in pediatric hydrocephalus, with aquaporin 4 (AQP4) as the primary facilitator of these fluid movements. Despite the importance of AQP4 in the pathophysiology of hydrocephalus, it’s expression in human fetal life is not well-studied. This manuscript systematically defines the brain expression of AQP4 in human brain development under control (n = 13) and hydrocephalic conditions (n = 3). Brains from 8 postconceptional weeks (PCW) onward and perinatal CSF from control (n = 2), obstructive (n = 6) and communicating (n = 6) hydrocephalic samples were analyzed through immunohistochemistry, immunofluorescence, western blot, and flow cytometry. Our results indicate that AQP4 expression is observed first in the archicortex, followed by the ganglionic eminences and then the neocortex. In the neocortex, it is initially at the perisylvian regions, and lastly at the occipital and prefrontal zones. Characteristic astrocyte end-feet labeling surrounding the vascular system was not established until 25 PCW. We also found AQP4 expression in a subpopulation of glial radial cells with processes that do not progress radially but, rather, curve following white matter tracts (corpus callosum and fornix), which were considered as glial stem cells (GSC). Under hydrocephalic conditions, GSC adjacent to characteristic ventricular zone disruption showed signs of early differentiation into astrocytes which may affect normal gliogenesis and contribute to the white matter dysgenesis. Finally, we found that AQP4 is expressed in the microvesicle fraction (p < 0.01) of CSF from patients with obstructive hydrocephalus. These findings suggest the potential use of AQP4 as a diagnostic and prognostic marker of pediatric hydrocephalus and as gliogenesis biomarker.
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Chen A, Tarapore E, To AG, Catolico DM, Nguyen KC, Coleman MJ, Spence RD. Introducing immunohistochemistry to the molecular biology laboratory. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:229-236. [PMID: 35178833 PMCID: PMC9304200 DOI: 10.1002/bmb.21611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 11/01/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Widely used in research laboratories, immunohistochemistry (IHC) is a transferable skill that prepares undergraduate students for a variety of careers in the biomedical field. We have developed an inquiry-based learning IHC laboratory exercise, which introduces students to the theory, procedure, and data interpretation of antibody staining. Students are tasked with performing IHC using an "unknown" antibody and then asked to identify the cells or molecular structures within the nervous systems specific for that unknown antibody. In two lab sessions, students are exposed to handling of delicate brain slices, fluorescent microscopy, and data analysis using the Allen Brain Atlas (ABA), an online freely accessible database of mRNA transcript expression patterns in the brain. Here, we present guidelines for easy implementation in the classroom and assess learning gains achieved by the students upon completion of the IHC laboratory module. Students clearly displayed an increase in knowledge in data interpretation, procedural knowledge, and theory surrounding IHC. Thus, this module works as an inquiry-based learning based method to introduce IHC principles to undergraduate students.
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Affiliation(s)
- Audrey Chen
- Department of Neurobiology and BehaviorSchool of Biological Sciences, University of CaliforniaIrvineCaliforniaUSA
| | - Eric Tarapore
- Department of Developmental and Cell BiologySchool of Biological Sciences, University of CaliforniaIrvineCaliforniaUSA
| | - Allisen G. To
- W.M. Keck Science DepartmentClaremontCaliforniaUSA
- Scripps CollegeClaremontCaliforniaUSA
| | - Davis M. Catolico
- W.M. Keck Science DepartmentClaremontCaliforniaUSA
- Claremont McKenna CollegeClaremontCaliforniaUSA
| | - Kelly C. Nguyen
- Department of Quantitative and Computational Biology and Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | | | - Rory D. Spence
- Department of Quantitative and Computational Biology and Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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Martins S, Erichsen L, Datsi A, Wruck W, Goering W, Chatzantonaki E, de Amorim VCM, Rossi A, Chrzanowska KH, Adjaye J. Impaired p53-Mediated DNA Damage Response Contributes to Microcephaly in Nijmegen Breakage Syndrome Patient-Derived Cerebral Organoids. Cells 2022; 11:cells11050802. [PMID: 35269426 PMCID: PMC8909307 DOI: 10.3390/cells11050802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/18/2022] [Indexed: 12/11/2022] Open
Abstract
Nijmegen Breakage Syndrome (NBS) is a rare autosomal recessive genetic disorder caused by mutations within nibrin (NBN), a DNA damage repair protein. Hallmarks of NBS include chromosomal instability and clinical manifestations such as growth retardation, immunodeficiency, and progressive microcephaly. We employed induced pluripotent stem cell-derived cerebral organoids from two NBS patients to study the etiology of microcephaly. We show that NBS organoids carrying the homozygous 657del5 NBN mutation are significantly smaller with disrupted cyto-architecture. The organoids exhibit premature differentiation, and Neuronatin (NNAT) over-expression. Furthermore, pathways related to DNA damage response and cell cycle are differentially regulated compared to controls. After exposure to bleomycin, NBS organoids undergo delayed p53-mediated DNA damage response and aberrant trans-synaptic signaling, which ultimately leads to neuronal apoptosis. Our data provide insights into how mutations within NBN alters neurogenesis in NBS patients, thus providing a proof of concept that cerebral organoids are a valuable tool for studying DNA damage-related disorders.
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Affiliation(s)
- Soraia Martins
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (S.M.); (L.E.); (W.W.); (E.C.); (V.C.M.d.A.)
| | - Lars Erichsen
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (S.M.); (L.E.); (W.W.); (E.C.); (V.C.M.d.A.)
| | - Angeliki Datsi
- Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine University, 40225 Düsseldorf, Germany;
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (S.M.); (L.E.); (W.W.); (E.C.); (V.C.M.d.A.)
| | - Wolfgang Goering
- Institute for Pathology, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany;
| | - Eleftheria Chatzantonaki
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (S.M.); (L.E.); (W.W.); (E.C.); (V.C.M.d.A.)
| | - Vanessa Cristina Meira de Amorim
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (S.M.); (L.E.); (W.W.); (E.C.); (V.C.M.d.A.)
| | - Andrea Rossi
- IUF-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany;
| | - Krystyna H. Chrzanowska
- Department of Medical Genetics, Children’s Memorial Health Institute, 04-730 Warsaw, Poland;
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University, 40225 Düsseldorf, Germany; (S.M.); (L.E.); (W.W.); (E.C.); (V.C.M.d.A.)
- Correspondence:
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Basaia S, Agosta F, Diez I, Bueichekú E, d'Oleire Uquillas F, Delgado-Alvarado M, Caballero-Gaudes C, Rodriguez-Oroz M, Stojkovic T, Kostic VS, Filippi M, Sepulcre J. Neurogenetic traits outline vulnerability to cortical disruption in Parkinson's disease. Neuroimage Clin 2022; 33:102941. [PMID: 35091253 PMCID: PMC8800137 DOI: 10.1016/j.nicl.2022.102941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 01/18/2023]
Abstract
The genetic traits that underlie vulnerability to neuronal damage across specific brain circuits in Parkinson's disease (PD) remain to be elucidated. In this study, we characterized the brain topological intersection between propagating connectivity networks in controls and PD participants and gene expression patterns across the human cortex - such as the SNCA gene. We observed that brain connectivity originated from PD-related pathology epicenters in the brainstem recapitulated the anatomical distribution of alpha-synuclein histopathology in postmortem data. We also discovered that the gene set most related to cortical propagation patterns of PD-related pathology was primarily involved in microtubule cellular components. Thus, this study sheds light on new avenues for enhancing detection of PD neuronal vulnerability via an evaluation of in vivo connectivity trajectories across the human brain and successful integration of neuroimaging-genetic strategies.
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Affiliation(s)
- Silvia Basaia
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Federica Agosta
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Neurology Unit, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Ibai Diez
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elisenda Bueichekú
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Federico d'Oleire Uquillas
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Manuel Delgado-Alvarado
- Neurology Department, Sierrallana Hospital, Torrelavega, Spain; IDIVAL, Valdecilla Biomedical Research Institute, Santander, Spain; Biomedical Research Networking Center for Mental Health (CIBERSAM), Madrid, Spain
| | | | - MariCruz Rodriguez-Oroz
- Neurology Department, Clínica Universidad de Navarra, Neuroscience Unit, CIMA Universidad de Navarra, Spain
| | - Tanja Stojkovic
- Clinic of Neurology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vladimir S Kostic
- Clinic of Neurology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Massimo Filippi
- Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy; Neurology Unit, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Jorge Sepulcre
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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Untapped Neuroimaging Tools for Neuro-Oncology: Connectomics and Spatial Transcriptomics. Cancers (Basel) 2022; 14:cancers14030464. [PMID: 35158732 PMCID: PMC8833690 DOI: 10.3390/cancers14030464] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Brain imaging, specifically magnetic resonance imaging (MRI), plays a key role in the clinical and research aspects of neuro-oncology. Novel neuroimaging techniques enable the transformation of a brain MRI into a so-called average brain. This allows projects using already acquired brain MRIs to perform group analyses and draw conclusions. Once the data are in this average brain, several types of analyses can be performed. For example, determining the most vulnerable locations for certain tumor types or perhaps even the underlying circuitry and gene expression that might cause predisposition to tumor growth. This information may further our understanding of tumor behavior, leading to better patient counseling, surgery timing, and treatment monitoring. Abstract Neuro-oncology research is broad and includes several branches, one of which is neuroimaging. Magnetic resonance imaging (MRI) is instrumental for the diagnosis and treatment monitoring of patients with brain tumors. Most commonly, structural and perfusion MRI sequences are acquired to characterize tumors and understand their behaviors. Thanks to technological advances, structural brain MRI can now be transformed into a so-called average brain accounting for individual morphological differences, which enables retrospective group analysis. These normative analyses are uncommonly used in neuro-oncology research. Once the data have been normalized, voxel-wise analyses and spatial mapping can be performed. Additionally, investigations of underlying connectomics can be performed using functional and structural templates. Additionally, a recently available template of spatial transcriptomics has enabled the assessment of associated gene expression. The few published normative analyses have shown relationships between tumor characteristics and spatial localization, as well as insights into the circuitry associated with epileptogenic tumors and depression after cingulate tumor resection. The wide breadth of possibilities with normative analyses remain largely unexplored, specifically in terms of connectomics and imaging transcriptomics. We provide a framework for performing normative analyses in oncology while also highlighting their limitations. Normative analyses are an opportunity to address neuro-oncology questions from a different perspective.
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Chen W, Hepburn I, Martyushev A, De Schutter E. Modeling Neurons in 3D at the Nanoscale. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1359:3-24. [DOI: 10.1007/978-3-030-89439-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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The relationship between transcription and eccentricity in human V1. Brain Struct Funct 2021; 226:2807-2818. [PMID: 34618233 DOI: 10.1007/s00429-021-02387-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023]
Abstract
Gene expression gradients radiating from regions of primary sensory cortices have recently been described and are thought to underlie the large-scale organization of the human cerebral cortex. However, the role of transcription in the functional layout of a single region within the adult brain has yet to be clarified, likely owing to the difficulty of identifying a brain region anatomically consistent enough across individuals with dense enough tissue sampling. Overcoming these hurdles in human primary visual cortex (V1), we show a relationship between differential gene expression and the cortical layout of eccentricity in human V1. Interestingly, these genes are unique from those previously identified that contribute to the positioning of cortical areas in the visual processing hierarchy. Enrichment analyses show that a subset of the identified genes encode for structures related to inhibitory interneurons, ion channels, as well as cellular projections, and are expressed more in foveal compared to peripheral portions of human V1. These findings predict that tissue density should be higher in foveal compared to peripheral V1. Using a histological pipeline, we validate this prediction using Nissl-stained sections of postmortem occipital cortex. We discuss these findings relative to previous studies in non-human primates, as well as in the context of an organizational pattern in which the adult human brain employs transcription gradients at multiple spatial scales: across the cerebral cortex, across areas within processing hierarchies, and within single cortical areas.
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Bueichekú E, Gonzalez-de-Echavarri JM, Ortiz-Teran L, Montal V, d'Oleire Uquillas F, De Marcos L, Orwig W, Kim CM, Ortiz-Teran E, Basaia S, Diez I, Sepulcre J. Divergent connectomic organization delineates genetic evolutionary traits in the human brain. Sci Rep 2021; 11:19692. [PMID: 34608211 PMCID: PMC8490416 DOI: 10.1038/s41598-021-99082-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
The relationship between human brain connectomics and genetic evolutionary traits remains elusive due to the inherent challenges in combining complex associations within cerebral tissue. In this study, insights are provided about the relationship between connectomics, gene expression and divergent evolutionary pathways from non-human primates to humans. Using in vivo human brain resting-state data, we detected two co-existing idiosyncratic functional systems: the segregation network, in charge of module specialization, and the integration network, responsible for information flow. Their topology was approximated to whole-brain genetic expression (Allen Human Brain Atlas) and the co-localization patterns yielded that neuron communication functionalities-linked to Neuron Projection-were overrepresented cell traits. Homologue-orthologue comparisons using dN/dS-ratios bridged the gap between neurogenetic outcomes and biological data, summarizing the known evolutionary divergent pathways within the Homo Sapiens lineage. Evidence suggests that a crosstalk between functional specialization and information flow reflects putative biological qualities of brain architecture, such as neurite cellular functions like axonal or dendrite processes, hypothesized to have been selectively conserved in the species through positive selection. These findings expand our understanding of human brain function and unveil aspects of our cognitive trajectory in relation to our simian ancestors previously left unexplored.
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Affiliation(s)
- Elisenda Bueichekú
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jose M Gonzalez-de-Echavarri
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Barcelona βeta Brain Research Center, Barcelona, Spain
| | - Laura Ortiz-Teran
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Department of Radiology, Division of Nuclear Medicine and Molecular Imaging, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Victor Montal
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Memory Unit, Department of Neurology, Hospital de la Santa Creu i Sant Pau, Biomedical Research Institute Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- Centro de Investigacón Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Federico d'Oleire Uquillas
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, USA
| | - Lola De Marcos
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- University of Navarra School of Medicine, University of Navarra, Pamplona, Navarra, Spain
| | - William Orwig
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Chan-Mi Kim
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA
| | - Elena Ortiz-Teran
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Facultad de Ciencias Jurídicas y Sociales, Universidad Rey Juan Carlos, Madrid, Spain
| | - Silvia Basaia
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Neuroimaging Research Unit, San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Ibai Diez
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA
| | - Jorge Sepulcre
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA.
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Toscano E, Zampieri N. An atlas for unveiling the functional organization of spinal circuits. CELL REPORTS METHODS 2021; 1:100086. [PMID: 35474670 PMCID: PMC9017158 DOI: 10.1016/j.crmeth.2021.100086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Defining the positional organization of neurons in the spinal cord is critical for understanding their function. In this issue, Fiederling and colleagues present a method to accurately map position and connectivity of neurons in a universal three-dimensional spinal cord reference atlas.
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Affiliation(s)
- Elisa Toscano
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Niccolò Zampieri
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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Huang WK, Wong SZH, Pather SR, Nguyen PTT, Zhang F, Zhang DY, Zhang Z, Lu L, Fang W, Chen L, Fernandes A, Su Y, Song H, Ming GL. Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells. Cell Stem Cell 2021; 28:1657-1670.e10. [PMID: 33961804 PMCID: PMC8419002 DOI: 10.1016/j.stem.2021.04.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/21/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022]
Abstract
Human brain organoids represent remarkable platforms for recapitulating features of human brain development and diseases. Existing organoid models do not resolve fine brain subregions, such as different nuclei in the hypothalamus. We report the generation of arcuate organoids (ARCOs) from human induced pluripotent stem cells (iPSCs) to model the development of the human hypothalamic arcuate nucleus. Single-cell RNA sequencing of ARCOs revealed significant molecular heterogeneity underlying different arcuate cell types, and machine learning-aided analysis based on the neonatal human hypothalamus single-nucleus transcriptome further showed a human arcuate nucleus molecular signature. We also explored ARCOs generated from Prader-Willi syndrome (PWS) patient iPSCs. These organoids exhibit aberrant differentiation and transcriptomic dysregulation similar to postnatal hypothalamus of PWS patients, indicative of cellular differentiation deficits and exacerbated inflammatory responses. Thus, patient iPSC-derived ARCOs represent a promising experimental model for investigating nucleus-specific features and disease-relevant mechanisms during early human arcuate development.
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Affiliation(s)
- Wei-Kai Huang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Samuel Zheng Hao Wong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarshan R Pather
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phuong T T Nguyen
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Y Zhang
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhijian Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lu Lu
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanqi Fang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luyun Chen
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Analiese Fernandes
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yijing Su
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Wang F, Sun W, Chang L, Sun K, Hou L, Qian L, Jin C, Chen J, Pu J, Ye P, Qiu S, Luo J, Duan S, Zhang B, Gao Z, Hu X. cFos-ANAB: A cFos-based Web Tool for Exploring Activated Neurons and Associated Behaviors. Neurosci Bull 2021; 37:1441-1453. [PMID: 34302617 DOI: 10.1007/s12264-021-00744-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
cFos is one of the most widely-studied genes in the field of neuroscience. Currently, there is no systematic database focusing on cFos in neuroscience. We developed a curated database-cFos-ANAB-a cFos-based web tool for exploring activated neurons and associated behaviors in rats and mice, comprising 398 brain nuclei and sub-nuclei, and five associated behaviors: pain, fear, feeding, aggression, and sexual behavior. Direct relationships among behaviors and nuclei (even cell types) under specific stimulating conditions were constructed based on cFos expression profiles extracted from original publications. Moreover, overlapping nuclei and sub-nuclei with potentially complex functions among different associated behaviors were emphasized, leading to results serving as important clues to the development of valid hypotheses for exploring as yet unknown circuits. Using the analysis function of cFos-ANAB, multi-layered pictures of networks and their relationships can quickly be explored depending on users' purposes. These features provide a useful tool and good reference for early exploration in neuroscience. The cFos-ANAB database is available at www.cfos-db.net .
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Affiliation(s)
- Fan Wang
- Center for Neuroscience and Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wenjie Sun
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lei Chang
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Kefang Sun
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Leying Hou
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Linna Qian
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Chaoyin Jin
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiandong Chen
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiali Pu
- Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Panmeng Ye
- Hangzhou Hikvision Digital Technology Co., Ltd, Hangzhou, 310053, China
| | - Shuang Qiu
- Center for Neuroscience and Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jianhong Luo
- Center for Neuroscience and Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Shumin Duan
- Center for Neuroscience and Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Baorong Zhang
- Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
| | - Zhihua Gao
- Center for Neuroscience and Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Xiaojun Hu
- Medical Information Center, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda. Neuroinformatics 2021; 19:685-701. [PMID: 34282528 PMCID: PMC8566446 DOI: 10.1007/s12021-021-09531-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2021] [Indexed: 12/25/2022]
Abstract
Simulation of large-scale networks of neurons is an important approach to understanding and interpreting experimental data from healthy and diseased brains. Owing to the rapid development of simulation software and the accumulation of quantitative data of different neuronal types, it is possible to predict both computational and dynamical properties of local microcircuits in a ‘bottom-up’ manner. Simulated data from these models can be compared with experiments and ‘top-down’ modelling approaches, successively bridging the scales. Here we describe an open source pipeline, using the software Snudda, for predicting microcircuit connectivity and for setting up simulations using the NEURON simulation environment in a reproducible way. We also illustrate how to further ‘curate’ data on single neuron morphologies acquired from public databases. This model building pipeline was used to set up a first version of a full-scale cellular level model of mouse dorsal striatum. Model components from that work are here used to illustrate the different steps that are needed when modelling subcortical nuclei, such as the basal ganglia.
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Dong X, Liu C, Dozmorov M. Review of multi-omics data resources and integrative analysis for human brain disorders. Brief Funct Genomics 2021; 20:223-234. [PMID: 33969380 PMCID: PMC8287916 DOI: 10.1093/bfgp/elab024] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/05/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022] Open
Abstract
In the last decade, massive omics datasets have been generated for human brain research. It is evolving so fast that a timely update is urgently needed. In this review, we summarize the main multi-omics data resources for the human brains of both healthy controls and neuropsychiatric disorders, including schizophrenia, autism, bipolar disorder, Alzheimer's disease, Parkinson's disease, progressive supranuclear palsy, etc. We also review the recent development of single-cell omics in brain research, such as single-nucleus RNA-seq, single-cell ATAC-seq and spatial transcriptomics. We further investigate the integrative multi-omics analysis methods for both tissue and single-cell data. Finally, we discuss the limitations and future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Xianjun Dong
- Harvard Medical School, head of the Genomics and Bioinformatics Hub at Brigham and Women’s Hospital
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Liu H, Xin J, Cai S, Jiang X. Mendelian randomization analysis provides causality of smoking on the expression of ACE2, a putative SARS-CoV-2 receptor. eLife 2021; 10:e64188. [PMID: 34227468 PMCID: PMC8282334 DOI: 10.7554/elife.64188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/19/2021] [Indexed: 01/22/2023] Open
Abstract
Background To understand a causal role of modifiable lifestyle factors in angiotensin-converting enzyme 2 (ACE2) expression (a putative severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] receptor) across 44 human tissues/organs, and in coronavirus disease 2019 (COVID-19) susceptibility and severity, we conducted a phenome-wide two-sample Mendelian randomization (MR) study. Methods More than 500 genetic variants were used as instrumental variables to predict smoking and alcohol consumption. Inverse-variance weighted approach was adopted as the primary method to estimate a causal association, while MR-Egger regression, weighted median, and MR pleiotropy residual sum and outlier (MR-PRESSO) were performed to identify potential horizontal pleiotropy. Results We found that genetically predicted smoking intensity significantly increased ACE2 expression in thyroid (β=1.468, p=1.8×10-8), and increased ACE2 expression in adipose, brain, colon, and liver with nominal significance. Additionally, genetically predicted smoking initiation significantly increased the risk of COVID-19 onset (odds ratio=1.14, p=8.7×10-5). No statistically significant result was observed for alcohol consumption. Conclusions Our work demonstrates an important role of smoking, measured by both status and intensity, in the susceptibility to COVID-19. Funding XJ is supported by research grants from the Swedish Research Council (VR-2018-02247) and Swedish Research Council for Health, Working Life and Welfare (FORTE-2020-00884).
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Affiliation(s)
- Hui Liu
- Biomedical Research Center, Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhouChina
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang UniversityHangzhouChina
| | - Xia Jiang
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska InstituteStockholmSweden
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Conte C. Possible Link between SARS-CoV-2 Infection and Parkinson's Disease: The Role of Toll-Like Receptor 4. Int J Mol Sci 2021; 22:7135. [PMID: 34281186 PMCID: PMC8269350 DOI: 10.3390/ijms22137135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is the most common neurodegenerative motor disorder characterized by selective degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNpc) of the midbrain, depletion of dopamine (DA), and impaired nigrostriatal pathway. The pathological hallmark of PD includes the aggregation and accumulation α-synuclein (α-SYN). Although the precise mechanisms underlying the pathogenesis of PD are still unknown, the activation of toll-like receptors (TLRs), mainly TLR4 and subsequent neuroinflammatory immune response, seem to play a significant role. Mounting evidence suggests that viral infection can concur with the precipitation of PD or parkinsonism. The recently identified coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of ongoing pandemic coronavirus disease 2019 (COVID-19), responsible for 160 million cases that led to the death of more than three million individuals worldwide. Studies have reported that many patients with COVID-19 display several neurological manifestations, including acute cerebrovascular diseases, conscious disturbance, and typical motor and non-motor symptoms accompanying PD. In this review, the neurotropic potential of SARS-CoV-2 and its possible involvement in the pathogenesis of PD are discussed. Specifically, the involvement of the TLR4 signaling pathway in mediating the virus entry, as well as the massive immune and inflammatory response in COVID-19 patients is explored. The binding of SARS-CoV-2 spike (S) protein to TLR4 and the possible interaction between SARS-CoV-2 and α-SYN as contributing factors to neuronal death are also considered.
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Affiliation(s)
- Carmela Conte
- Department of Pharmaceutical Sciences, University of Perugia, via Fabretti, 06123 Perugia, Italy
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Abstract
By evaluating children with a malformed cerebral cortex, we identified an ATPase pump (ATP1A3) with an early role in brain development. The ATP1A3 pump maintains the physiological concentration of sodium and potassium ions in cells, a process critical for osmotic equilibrium and membrane potential across several developing cell populations. We employed single-cell sequencing approaches to identify key enrichments for ATP1A3 expression during human cortex development. Unravelling this early cell-type–specific pathophysiology in the developing brain offers a potential basis for the treatment of ATP1A3-related diseases affecting prenatal and early childhood development. Osmotic equilibrium and membrane potential in animal cells depend on concentration gradients of sodium (Na+) and potassium (K+) ions across the plasma membrane, a function catalyzed by the Na+,K+-ATPase α-subunit. Here, we describe ATP1A3 variants encoding dysfunctional α3-subunits in children affected by polymicrogyria, a developmental malformation of the cerebral cortex characterized by abnormal folding and laminar organization. To gain cell-biological insights into the spatiotemporal dynamics of prenatal ATP1A3 expression, we built an ATP1A3 transcriptional atlas of fetal cortical development using mRNA in situ hybridization and transcriptomic profiling of ∼125,000 individual cells with single-cell RNA sequencing (Drop-seq) from 11 areas of the midgestational human neocortex. We found that fetal expression of ATP1A3 is most abundant to a subset of excitatory neurons carrying transcriptional signatures of the developing subplate, yet also maintains expression in nonneuronal cell populations. Moving forward a year in human development, we profiled ∼52,000 nuclei from four areas of an infant neocortex and show that ATP1A3 expression persists throughout early postnatal development, most predominantly in inhibitory neurons, including parvalbumin interneurons in the frontal cortex. Finally, we discovered the heteromeric Na+,K+-ATPase pump complex may form nonredundant cell-type–specific α-β isoform combinations, including α3-β1 in excitatory neurons and α3-β2 in inhibitory neurons. Together, the developmental malformation phenotype of affected individuals and single-cell ATP1A3 expression patterns point to a key role for α3 in human cortex development, as well as a cell-type basis for pre- and postnatal ATP1A3-associated diseases.
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Rapid brain structure and tumour margin detection on whole frozen tissue sections by fast multiphotometric mid-infrared scanning. Sci Rep 2021; 11:11307. [PMID: 34050224 PMCID: PMC8163866 DOI: 10.1038/s41598-021-90777-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/17/2021] [Indexed: 01/31/2023] Open
Abstract
Frozen section analysis is a frequently used method for examination of tissue samples, especially for tumour detection. In the majority of cases, the aim is to identify characteristic tissue morphologies or tumour margins. Depending on the type of tissue, a high number of misdiagnoses are associated with this process. In this work, a fast spectroscopic measurement device and workflow was developed that significantly improves the speed of whole frozen tissue section analyses and provides sufficient information to visualize tissue structures and tumour margins, dependent on their lipid and protein molecular vibrations. That optical and non-destructive method is based on selected wavenumbers in the mid-infrared (MIR) range. We present a measuring system that substantially outperforms a commercially available Fourier Transform Infrared (FT-IR) Imaging system, since it enables acquisition of reduced spectral information at a scan field of 1 cm2 in 3 s, with a spatial resolution of 20 µm. This allows fast visualization of segmented structure areas with little computational effort. For the first time, this multiphotometric MIR system is applied to biomedical tissue sections. We are referencing our novel MIR scanner on cryopreserved murine sagittal and coronal brain sections, especially focusing on the hippocampus, and show its usability for rapid identification of primary hepatocellular carcinoma (HCC) in mouse liver.
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Regional Localization of Mouse Brain Slices Based on Unified Modal Transformation. Symmetry (Basel) 2021. [DOI: 10.3390/sym13060929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Brain science research often requires accurate localization and quantitative analysis of neuronal activity in different brain regions. The premise of related analysis is to determine the brain region of each site on the brain slice by referring to the Allen Reference Atlas (ARA), namely the regional localization of the brain slice. The image registration methodology can be used to solve the problem of regional localization. However, the conventional multi-modal image registration method is not satisfactory because of the complexity of modality between the brain slice and the ARA. Inspired by the idea that people can automatically ignore noise and establish correspondence based on key regions, we proposed a novel method known as the Joint Enhancement of Multimodal Information (JEMI) network, which is based on a symmetric encoder–decoder. In this way, the brain slice and the ARA are converted into a segmentation map with unified modality, which greatly reduces the difficulty of registration. Furthermore, combined with the diffeomorphic registration algorithm, the existing topological structure was preserved. The results indicate that, compared with the existing methods, the method proposed in this study can effectively overcome the influence of non-unified modal images and achieve accurate and rapid localization of the brain slice.
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Co-Therapy of Albendazole and Dexamethasone Reduces Pathological Changes in the Cerebral Parenchyma of Th-1 and Th-2 Dominant Mice Heavily Infected with Angiostrongylus cantonensis: Histopathological and RNA-seq Analyses. Biomolecules 2021; 11:biom11040536. [PMID: 33917604 PMCID: PMC8067505 DOI: 10.3390/biom11040536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 11/24/2022] Open
Abstract
Administration of albendazole alone was not very suitable for the treatment of cerebral angiostrongyliasis. This study was designed to evaluate the effects of the co-therapy of this drug and dexamethasone in Th-1 and Th-2 dominant mice infected with Angiostrongylus cantonensis. Each of BALB/c and C57BL/6 mice infected with 50 A. cantonensis third-stage larvae were administered albendazole (10 mg/kg/day) alone, dexamethasone (0.5 mg/kg/day) alone, or co-therapy of the two drugs from day 7 or 14 post-infection for 7 or 14 days. After sacrifice, coronal slices were prepared from five brain regions and stained with hematoxylin and eosin. Eight pathological changes were employed to determine the therapeutic effectiveness using a scoring system. RNA-seq analysis was performed to confirm the histopathological findings. The infected BALB/c and C57BL/6 mice had similar patterns in the pathological changes. Meningitis, hemorrhage, size of worms, and encephalitis in the cerebral parenchyma were slighter in the mice treated with co-therapy than the remaining groups. Mice treated from day 14 had more severe changes than those from day 7. The histopathological findings were found to be consistent to immune responses determined by RNA-seq analysis. Co-therapy was determined to reduce pathological changes after administration to mice infected with A. cantonensis.
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Small Extracellular Vesicles Control Dendritic Spine Development through Regulation of HDAC2 Signaling. J Neurosci 2021; 41:3799-3807. [PMID: 33741723 DOI: 10.1523/jneurosci.0766-20.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 01/06/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022] Open
Abstract
The release of small extracellular vesicles (sEVs) has recently been reported, but knowledge of their function in neuron development remains limited. Using LC-MS/MS, we found that sEVs released from developing cortical neurons in vitro obtained from mice of both sexes were enriched in cytoplasm, exosome, and protein-binding and DNA/RNA-binding pathways. The latter included HDAC2, which was of particular interest, because HDAC2 regulates spine development, and populations of neurons expressing different levels of HDAC2 co-exist in vivo during the period of spine growth. Here, we found that HDAC2 levels decrease in neurons as they acquire synapses and that sEVs from HDAC2-rich neurons regulate HDAC2 signaling in HDAC2-low neurons possibly through HDAC2 transfer. This regulation led to a transcriptional decrease in HDAC2 synaptic targets and the density of excitatory synapses. These data suggest that sEVs provide inductive cell-cell signaling that coordinates the development of dendritic spines via the activation of HDAC2-dependent transcriptional programs.SIGNIFICANCE STATEMENT A role of small extracellular vesicles (sEVs; also called exosomes) in neuronal development is of particular interest, because sEVs could provide a major signaling modality between developing neurons when synapses are not fully functional or immature. However, knowledge of sEVs on neuron, and more precisely spine development, is limited. We provide several lines of evidence that sEVs released from developing cortical neurons regulate the development of dendritic spines via the regulation of HDAC2 signaling. This paracrine communication is temporally restricted during development because of the age-dependent decrease in sEV release as neurons mature and acquire spines.
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Dynamic control of the dopamine transporter in neurotransmission and homeostasis. NPJ Parkinsons Dis 2021; 7:22. [PMID: 33674612 PMCID: PMC7935902 DOI: 10.1038/s41531-021-00161-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
The dopamine transporter (DAT) transports extracellular dopamine into the intracellular space contributing to the regulation of dopamine neurotransmission. A reduction of DAT density is implicated in Parkinson's disease (PD) by neuroimaging; dopamine turnover is dopamine turnover is elevated in early symptomatic PD and in presymptomatic individuals with monogenic mutations causal for parkinsonism. As an integral plasma membrane protein, DAT surface expression is dynamically regulated through endocytic trafficking, enabling flexible control of dopamine signaling in time and space, which in turn critically modulates movement, motivation and learning behavior. Yet the cellular machinery and functional implications of DAT trafficking remain enigmatic. In this review we summarize mechanisms governing DAT trafficking under normal physiological conditions and discuss how PD-linked mutations may disturb DAT homeostasis. We highlight the complexity of DAT trafficking and reveal DAT dysregulation as a common theme in genetic models of parkinsonism.
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