1
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Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD. BEAM: A combinatorial recombinase toolbox for binary gene expression and mosaic genetic analysis. Cell Rep 2024; 43:114650. [PMID: 39159043 DOI: 10.1016/j.celrep.2024.114650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 05/25/2024] [Accepted: 08/01/2024] [Indexed: 08/21/2024] Open
Abstract
We describe a binary expression aleatory mosaic (BEAM) system, which relies on DNA delivery by transfection or viral transduction along with nested recombinase activity to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Control cells labeled with red fluorescent protein (RFP) can be directly compared with experimental cells manipulated by genetic gain or loss of function and labeled with GFP. Importantly, BEAM incorporates recombinase-dependent signal amplification and delayed reporter expression to enable sharper delineation of control and experimental cells and to improve reliability relative to existing methods. We applied BEAM to a variety of known phenotypes to illustrate its advantages for identifying temporally or spatially aberrant phenotypes, for revealing changes in cell proliferation or death, and for controlling for procedural variability. In addition, we used BEAM to test the cortical protomap hypothesis at the individual radial unit level, revealing that area identity is cell autonomously specified in adjacent radial units.
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Affiliation(s)
- Luciano C Greig
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Mollie B Woodworth
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Alexandros Poulopoulos
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Stephanie Lim
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
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2
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Hosur V, Erhardt V, Hartig E, Lorenzo K, Megathlin H, Tarchini B. Large-Scale Genome-Wide Optimization and Prediction of the Cre Recombinase System for Precise Genome Manipulation in Mice. RESEARCH SQUARE 2024:rs.3.rs-4595968. [PMID: 39011108 PMCID: PMC11247941 DOI: 10.21203/rs.3.rs-4595968/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The Cre-Lox recombination system is a powerful tool in mouse genetics, offering spatial-temporal control over gene expression and facilitating the large-scale generation of conditional knockout mice. Its versatility also extends to other research models, such as rats, pigs, and zebrafish. However, the Cre-Lox technology presents a set of challenges that includes high costs, a time-intensive process, and the occurrence of unpredictable recombination events, which can lead to unexpected phenotypic outcomes. To better understand factors affecting recombination, we embarked on a systematic and genome-wide analysis of Cre-mediated recombination in mice. To ensure uniformity and reproducibility, we generated 11 novel strains with conditional alleles at the ROSA26 locus, utilizing a single inbred mouse strain background, C57BL/6J. We examined several factors influencing Cre-recombination, including the inter-loxP distance, mutant loxP sites, the zygosity of the conditional alleles, chromosomal location, and the age of the breeders. We discovered that the selection of the Cre-driver strain profoundly impacts recombination efficiency. We also found that successful and complete recombination is best achieved when loxP sites are spaced between 1 to 4 kb apart, with mutant loxP sites facilitating recombination at distances of 1 to 3 kb. Furthermore, we demonstrate that complete recombination does not occur at an inter-loxP distance of ≥ 15 kb with wildtype loxP sites, nor at a distance of ≥ 7 kb with mutant lox71/66 sites. Interestingly, the age of the Cre-driver mouse at the time of breeding emerged as a critical factor in recombination efficiency, with best results observed between 8 and 20 weeks old. Moreover, crossing heterozygous floxed alleles with the Cre-driver strain resulted in more efficient recombination than using homozygous floxed alleles. Lastly, maintaining an inter-loxP distance of 4 kb or less ensures efficient recombination of the conditional allele, regardless of the chromosomal location. While CRISPR/Cas has revolutionized genome editing in mice, Cre-Lox technology remains a cornerstone for the generation of sophisticated alleles and for precise control of gene expression in mice. The knowledge gained here will enable investigators to select a Cre-Lox approach that is most efficient for their desired outcome in the generation of both germline and non-germline mouse models of human disease, thereby reducing time and cost of Cre-Lox technology-mediated genome modification.
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Affiliation(s)
| | | | - Elli Hartig
- The Jackson Laboratory for Mammalian Genetics
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3
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Hughes AC, Pittman BG, Xu B, Gammons JW, Webb CM, Nolen HG, Chapman P, Bikoff JB, Schwarz LA. A single-vector intersectional AAV strategy for interrogating cellular diversity and brain function. Nat Neurosci 2024; 27:1400-1410. [PMID: 38802592 DOI: 10.1038/s41593-024-01659-7] [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: 01/27/2023] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
As discovery of cellular diversity in the brain accelerates, so does the need for tools that target cells based on multiple features. Here we developed Conditional Viral Expression by Ribozyme Guided Degradation (ConVERGD), an adeno-associated virus-based, single-construct, intersectional targeting strategy that combines a self-cleaving ribozyme with traditional FLEx switches to deliver molecular cargo to specific neuronal subtypes. ConVERGD offers benefits over existing intersectional expression platforms, such as expanded intersectional targeting with up to five recombinase-based features, accommodation of larger and more complex payloads and a vector that is easy to modify for rapid toolkit expansion. In the present report we employed ConVERGD to characterize an unexplored subpopulation of norepinephrine (NE)-producing neurons within the rodent locus coeruleus that co-express the endogenous opioid gene prodynorphin (Pdyn). These studies showcase ConVERGD as a versatile tool for targeting diverse cell types and reveal Pdyn-expressing NE+ locus coeruleus neurons as a small neuronal subpopulation capable of driving anxiogenic behavioral responses in rodents.
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Affiliation(s)
- Alex C Hughes
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Human Cell Types, Allen Institute for Brain Science, Seattle, WA, USA
| | - Brittany G Pittman
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jesse W Gammons
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charis M Webb
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hunter G Nolen
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Phillip Chapman
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jay B Bikoff
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lindsay A Schwarz
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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4
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Aloway JA, Ruteshouser EC, Huff V, Behringer RR. Generation of a Wt1 conditional deletion, nuclear red fluorescent protein reporter allele in the mouse. Differentiation 2024; 138:100791. [PMID: 38941819 DOI: 10.1016/j.diff.2024.100791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024]
Abstract
A Wt1 conditional deletion, nuclear red fluorescent protein (RFP) reporter allele was generated in the mouse by gene targeting in embryonic stem cells. Upon Cre-mediated recombination, a deletion allele is generated that expresses RFP in a Wt1-specific pattern. RFP expression was detected in embryonic and adult tissues known to express Wt1, including the kidney, mesonephros, and testis. In addition, RFP expression and WT1 co-localization was detected in the adult uterine stroma and myometrium, suggesting a role in uterine function. Crosses with Wnt7a-Cre transgenic mice that express Cre in the Müllerian duct epithelium activate Wt1-directed RFP expression in the epithelium of the oviduct but not the stroma and myometrium of the uterus. This new mouse strain should be a useful resource for studies of Wt1 function and marking Wt1-expressing cells.
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Affiliation(s)
- Jace A Aloway
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Genetics and Epigenetics Program, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - E Cristy Ruteshouser
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vicki Huff
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Genetics and Epigenetics Program, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Genetics and Epigenetics Program, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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5
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Thome C, Janssen JM, Karabulut S, Acuna C, D’Este E, Soyka SJ, Baum K, Bock M, Lehmann N, Roos J, Stevens NA, Hasegawa M, Ganea DA, Benoit CM, Gründemann J, Min L, Bird KM, Schultz C, Bennett V, Jenkins PM, Engelhardt M. Live imaging of excitable axonal microdomains in ankyrin-G-GFP mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.01.525891. [PMID: 38948770 PMCID: PMC11212890 DOI: 10.1101/2023.02.01.525891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The axon initial segment (AIS) constitutes not only the site of action potential initiation, but also a hub for activity-dependent modulation of output generation. Recent studies shedding light on AIS function used predominantly post-hoc approaches since no robust murine in vivo live reporters exist. Here, we introduce a reporter line in which the AIS is intrinsically labeled by an ankyrin-G-GFP fusion protein activated by Cre recombinase, tagging the native Ank3 gene. Using confocal, superresolution, and two-photon microscopy as well as whole-cell patch-clamp recordings in vitro, ex vivo, and in vivo, we confirm that the subcellular scaffold of the AIS and electrophysiological parameters of labeled cells remain unchanged. We further uncover rapid AIS remodeling following increased network activity in this model system, as well as highly reproducible in vivo labeling of AIS over weeks. This novel reporter line allows longitudinal studies of AIS modulation and plasticity in vivo in real-time and thus provides a unique approach to study subcellular plasticity in a broad range of applications.
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Affiliation(s)
- Christian Thome
- Institute of Anatomy and Cell Biology, Johannes Kepler University, 4020 Linz, Austria
- Clinical Research Institute of Neuroscience, Johannes Kepler University, 4020 Linz, Austria
- Institute of Physiology and Pathophysiology, Heidelberg University, 69120 Heidelberg, Germany
| | - Jan Maximilian Janssen
- Institute of Anatomy and Cell Biology, Johannes Kepler University, 4020 Linz, Austria
- Clinical Research Institute of Neuroscience, Johannes Kepler University, 4020 Linz, Austria
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Seda Karabulut
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Claudio Acuna
- Chica and Heinz Schaller Research Group, Institute of Anatomy and Cell Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Elisa D’Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Stella J. Soyka
- Institute of Anatomy and Cell Biology, Dept. of Functional Neuroanatomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Konrad Baum
- Institute of Anatomy and Cell Biology, Johannes Kepler University, 4020 Linz, Austria
- Clinical Research Institute of Neuroscience, Johannes Kepler University, 4020 Linz, Austria
| | - Michael Bock
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Nadja Lehmann
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Johannes Roos
- Institute of Anatomy and Cell Biology, Johannes Kepler University, 4020 Linz, Austria
- Clinical Research Institute of Neuroscience, Johannes Kepler University, 4020 Linz, Austria
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Nikolas A. Stevens
- Institute of Physiology and Pathophysiology, Heidelberg University, 69120 Heidelberg, Germany
| | - Masashi Hasegawa
- German Center for Neurodegenerative Disease (DZNE), Neural Circuit Computations, 53127 Bonn, Germany
| | - Dan A. Ganea
- University of Basel, Department of Biomedicine, 4031 Basel, Switzerland
| | - Chloé M. Benoit
- German Center for Neurodegenerative Disease (DZNE), Neural Circuit Computations, 53127 Bonn, Germany
- University of Basel, Department of Biomedicine, 4031 Basel, Switzerland
| | - Jan Gründemann
- German Center for Neurodegenerative Disease (DZNE), Neural Circuit Computations, 53127 Bonn, Germany
- University of Basel, Department of Biomedicine, 4031 Basel, Switzerland
| | - Lia Min
- Departments of Pharmacology and Psychiatry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kalynn M. Bird
- Departments of Pharmacology and Psychiatry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christian Schultz
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Vann Bennett
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Paul M. Jenkins
- Departments of Pharmacology and Psychiatry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maren Engelhardt
- Institute of Anatomy and Cell Biology, Johannes Kepler University, 4020 Linz, Austria
- Clinical Research Institute of Neuroscience, Johannes Kepler University, 4020 Linz, Austria
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
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6
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Erhardt V, Hartig E, Lorenzo K, Megathlin HR, Tarchini B, Hosur V. Large-Scale Genome-Wide Optimization and Prediction of the Cre Recombinase System for Precise Genome Manipulation in Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599022. [PMID: 38948742 PMCID: PMC11212873 DOI: 10.1101/2024.06.14.599022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The Cre-Lox recombination system is a powerful tool in mouse genetics, offering spatial-temporal control over gene expression and facilitating the large-scale generation of conditional knockout mice. Its versatility also extends to other research models, such as rats, pigs, and zebrafish. However, the Cre-Lox technology presents a set of challenges that includes high costs, a time-intensive process, and the occurrence of unpredictable recombination events, which can lead to unexpected phenotypic outcomes. To better understand factors affecting recombination, we embarked on a systematic and genome-wide analysis of Cre-mediated recombination in mice. To ensure uniformity and reproducibility, we generated 11 novel strains with conditional alleles at the ROSA26 locus, utilizing a single inbred mouse strain background, C57BL/6J. We examined several factors influencing Cre-recombination, including the inter-loxP distance, mutant loxP sites, the zygosity of the conditional alleles, chromosomal location, and the age of the breeders. We discovered that the selection of the Cre-driver strain profoundly impacts recombination efficiency. We also found that successful and complete recombination is best achieved when loxP sites are spaced between 1 to 4 kb apart, with mutant loxP sites facilitating recombination at distances of 1 to 3 kb. Furthermore, we demonstrate that complete recombination does not occur at an inter-loxP distance of ≥ 15 kb with wildtype loxP sites, nor at a distance of ≥ 7 kb with mutant lox71/66 sites. Interestingly, the age of the Cre-driver mouse at the time of breeding emerged as a critical factor in recombination efficiency, with best results observed between 8 and 20 weeks old. Moreover, crossing heterozygous floxed alleles with the Cre-driver strain resulted in more efficient recombination than using homozygous floxed alleles. Lastly, maintaining an inter-loxP distance of 4 kb or less ensures efficient recombination of the conditional allele, regardless of the chromosomal location. While CRISPR/Cas has revolutionized genome editing in mice, Cre-Lox technology remains a cornerstone for the generation of sophisticated alleles and for precise control of gene expression in mice. The knowledge gained here will enable investigators to select a Cre-Lox approach that is most efficient for their desired outcome in the generation of both germline and non-germline mouse models of human disease, thereby reducing time and cost of Cre-Lox technology-mediated genome modification.
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Affiliation(s)
- Valerie Erhardt
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
| | - Elli Hartig
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- Tufts University School of Medicine, Boston, MA
| | - Kristian Lorenzo
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- The Roux Institute at Northeastern University, Portland, ME
| | - Hannah R Megathlin
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- Graduate School of Biomedical Sciences and Engineering, UMaine, Orono, ME
| | - Basile Tarchini
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
- Tufts University School of Medicine, Boston, MA
| | - Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME
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7
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Bossini L, Sessa A. Need of orthogonal approaches in neurological disease modeling in mouse. Front Mol Neurosci 2024; 17:1399953. [PMID: 38756706 PMCID: PMC11096479 DOI: 10.3389/fnmol.2024.1399953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Over the years, advancements in modeling neurological diseases have revealed innovative strategies aimed at gaining deeper insights and developing more effective treatments for these complex conditions. However, these progresses have recently been overshadowed by an increasing number of failures in clinical trials, raising doubts about the reliability and translatability of this type of disease modeling. This mini-review does not aim to provide a comprehensive overview of the current state-of-the-art in disease mouse modeling. Instead, it offers a brief excursus over some recent approaches in modeling neurological diseases to pinpoint a few intriguing strategies applied in the field that may serve as sources of inspiration for improving currently available animal models. In particular, we aim to guide the reader toward the potential success of adopting a more orthogonal approach in the study of human diseases.
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Affiliation(s)
- Linda Bossini
- Neuroepigenetics Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- “Vita e Salute” San Raffaele University, Milan, Italy
| | - Alessandro Sessa
- Neuroepigenetics Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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8
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Jarysta A, Tadenev ALD, Day M, Krawchuk B, Low BE, Wiles MV, Tarchini B. Inhibitory G proteins play multiple roles to polarize sensory hair cell morphogenesis. eLife 2024; 12:RP88186. [PMID: 38651641 PMCID: PMC11037916 DOI: 10.7554/elife.88186] [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: 04/25/2024] Open
Abstract
Inhibitory G alpha (GNAI or Gαi) proteins are critical for the polarized morphogenesis of sensory hair cells and for hearing. The extent and nature of their actual contributions remains unclear, however, as previous studies did not investigate all GNAI proteins and included non-physiological approaches. Pertussis toxin can downregulate functionally redundant GNAI1, GNAI2, GNAI3, and GNAO proteins, but may also induce unrelated defects. Here, we directly and systematically determine the role(s) of each individual GNAI protein in mouse auditory hair cells. GNAI2 and GNAI3 are similarly polarized at the hair cell apex with their binding partner G protein signaling modulator 2 (GPSM2), whereas GNAI1 and GNAO are not detected. In Gnai3 mutants, GNAI2 progressively fails to fully occupy the sub-cellular compartments where GNAI3 is missing. In contrast, GNAI3 can fully compensate for the loss of GNAI2 and is essential for hair bundle morphogenesis and auditory function. Simultaneous inactivation of Gnai2 and Gnai3 recapitulates for the first time two distinct types of defects only observed so far with pertussis toxin: (1) a delay or failure of the basal body to migrate off-center in prospective hair cells, and (2) a reversal in the orientation of some hair cell types. We conclude that GNAI proteins are critical for hair cells to break planar symmetry and to orient properly before GNAI2/3 regulate hair bundle morphogenesis with GPSM2.
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Affiliation(s)
| | | | - Matthew Day
- The Jackson LaboratoryBar HarborUnited States
| | | | | | | | - Basile Tarchini
- The Jackson LaboratoryBar HarborUnited States
- Tufts University School of MedicineBostonUnited States
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9
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Yu L, Marchisio MA. Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2024; 52:1483-1497. [PMID: 38142459 PMCID: PMC10853767 DOI: 10.1093/nar/gkad1216] [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: 07/18/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
New, orthogonal transcription factors in eukaryotic cells have been realized by engineering nuclease-deficient CRISPR-associated proteins and/or their guide RNAs. In this work, we present a new kind of orthogonal transcriptional activators, in Saccharomyces cerevisiae, made by turning type V CRISPR RNA into a scaffold RNA (ScRNA) able to recruit a variable number of VP64 activation domains. The activator arises from the complex between the synthetic ScRNA and DNase-deficient type V Cas proteins: dCas12e and denAsCas12a. The transcription activation achieved via the newly engineered dCas:ScRNA system is up to 4.7-fold higher than that obtained with the direct fusion of VP64 to Cas proteins. The new transcription factors have been proven to be functional in circuits such as Boolean gates, converters, multiplex-gene and metabolic-pathway activation. Our results extend the CRISPR-Cas-based technology with a new effective tool that only demands RNA engineering and improves the current design of transcription factors based on type V Cas proteins.
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Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
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10
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Srinivasan D, Arostegui M, Goebel EJ, Hart KN, Aykul S, Lees-Shepard JB, Idone V, Hatsell SJ, Economides AN. How Activin A Became a Therapeutic Target in Fibrodysplasia Ossificans Progressiva. Biomolecules 2024; 14:101. [PMID: 38254701 PMCID: PMC10813747 DOI: 10.3390/biom14010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disorder characterized by episodic yet cumulative heterotopic ossification (HO) of skeletal muscles, tendons, ligaments, and fascia. FOP arises from missense mutations in Activin Receptor type I (ACVR1), a type I bone morphogenetic protein (BMP) receptor. Although initial findings implicated constitutive activity of FOP-variant ACVR1 (ACVR1FOP) and/or hyperactivation by BMPs, it was later shown that HO in FOP requires activation of ACVR1FOP by Activin A. Inhibition of Activin A completely prevents HO in FOP mice, indicating that Activin A is an obligate driver of HO in FOP, and excluding a key role for BMPs in this process. This discovery led to the clinical development of garetosmab, an investigational antibody that blocks Activin A. In a phase 2 trial, garetosmab inhibited new heterotopic bone lesion formation in FOP patients. In contrast, antibodies to ACVR1 activate ACVR1FOP and promote HO in FOP mice. Beyond their potential clinical relevance, these findings have enhanced our understanding of FOP's pathophysiology, leading to the identification of fibroadipogenic progenitors as the cells that form HO, and the discovery of non-signaling complexes between Activin A and wild type ACVR1 and their role in tempering HO, and are also starting to inform biological processes beyond FOP.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Aris N. Economides
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA; (D.S.); (M.A.); (E.J.G.); (K.N.H.); (S.A.); (J.B.L.-S.); (V.I.); (S.J.H.)
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11
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Jarysta A, Tadenev ALD, Day M, Krawchuk B, Low BE, Wiles MV, Tarchini B. Inhibitory G proteins play multiple roles to polarize sensory hair cell morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.25.542257. [PMID: 37292807 PMCID: PMC10245865 DOI: 10.1101/2023.05.25.542257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inhibitory G alpha (GNAI or Gαi) proteins are critical for the polarized morphogenesis of sensory hair cells and for hearing. The extent and nature of their actual contributions remains unclear, however, as previous studies did not investigate all GNAI proteins and included non-physiological approaches. Pertussis toxin can downregulate functionally redundant GNAI1, GNAI2, GNAI3 and GNAO proteins, but may also induce unrelated defects. Here we directly and systematically determine the role(s) of each individual GNAI protein in mouse auditory hair cells. GNAI2 and GNAI3 are similarly polarized at the hair cell apex with their binding partner GPSM2, whereas GNAI1 and GNAO are not detected. In Gnai3 mutants, GNAI2 progressively fails to fully occupy the subcellular compartments where GNAI3 is missing. In contrast, GNAI3 can fully compensate for the loss of GNAI2 and is essential for hair bundle morphogenesis and auditory function. Simultaneous inactivation of Gnai2 and Gnai3 recapitulates for the first time two distinct types of defects only observed so far with pertussis toxin: 1) a delay or failure of the basal body to migrate off-center in prospective hair cells, and 2) a reversal in the orientation of some hair cell types. We conclude that GNAI proteins are critical for hair cells to break planar symmetry and to orient properly before GNAI2/3 regulate hair bundle morphogenesis with GPSM2.
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12
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Jeong M, Choi JH, Jang H, Sohn DH, Wang Q, Lee J, Yao L, Lee EJ, Fan J, Pratelli M, Wang EH, Snyder CN, Wang XY, Shin S, Gittis AH, Sung TC, Spitzer NC, Lim BK. Viral vector-mediated transgene delivery with novel recombinase systems for targeting neuronal populations defined by multiple features. Neuron 2024; 112:56-72.e4. [PMID: 37909037 PMCID: PMC10916502 DOI: 10.1016/j.neuron.2023.09.038] [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: 07/18/2022] [Revised: 05/21/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023]
Abstract
A comprehensive understanding of neuronal diversity and connectivity is essential for understanding the anatomical and cellular mechanisms that underlie functional contributions. With the advent of single-cell analysis, growing information regarding molecular profiles leads to the identification of more heterogeneous cell types. Therefore, the need for additional orthogonal recombinase systems is increasingly apparent, as heterogeneous tissues can be further partitioned into increasing numbers of specific cell types defined by multiple features. Critically, new recombinase systems should work together with pre-existing systems without cross-reactivity in vivo. Here, we introduce novel site-specific recombinase systems based on ΦC31 bacteriophage recombinase for labeling multiple cell types simultaneously and a novel viral strategy for versatile and robust intersectional expression of any transgene. Together, our system will help researchers specifically target different cell types with multiple features in the same animal.
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Affiliation(s)
- Minju Jeong
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hyeonseok Jang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Qingdi Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joann Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Li Yao
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eun Ji Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiachen Fan
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marta Pratelli
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric H Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christen N Snyder
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xiao-Yun Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sora Shin
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA, USA; Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - Aryn H Gittis
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tsung-Chang Sung
- Transgenic Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicholas C Spitzer
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Kook Lim
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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13
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Ogawa M, Kikuchi K. Generation of Conditional Knockout Zebrafish Using an Invertible Gene-Trap Cassette. Methods Mol Biol 2024; 2707:205-214. [PMID: 37668914 DOI: 10.1007/978-1-0716-3401-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Conditional knockout (cKO) is a genetic technique to inactivate gene expression in specific tissues or cell types in a temporally regulated manner. cKO analysis is essential to investigate gene function while avoiding the confounding effects of global gene deletion. Genetic techniques enabling cKO analysis were developed in mice based on culturable embryonic stem cells that were not generally available in zebrafish, which hampered precise analysis of genetic mechanisms of organ development and regeneration. However, recent advances in genome editing technologies have resolved this limitation, providing a platform for the generation of cKO models in any organism. Here we describe a detailed protocol for the generation of cKO zebrafish using a Cre-dependent genetic switch.
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Affiliation(s)
- Masahito Ogawa
- Department of Cardiac Regeneration Biology , National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Kazu Kikuchi
- Department of Cardiac Regeneration Biology , National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan.
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14
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Chu WS, Ng J, Waddington SN, Kurian MA. Gene therapy for neurotransmitter-related disorders. J Inherit Metab Dis 2024; 47:176-191. [PMID: 38221762 PMCID: PMC11108624 DOI: 10.1002/jimd.12697] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024]
Abstract
Inborn errors of neurotransmitter (NT) metabolism are a group of rare, heterogenous diseases with predominant neurological features, such as movement disorders, autonomic dysfunction, and developmental delay. Clinical overlap with other disorders has led to delayed diagnosis and treatment, and some conditions are refractory to oral pharmacotherapies. Gene therapies have been developed and translated to clinics for paediatric inborn errors of metabolism, with 38 interventional clinical trials ongoing to date. Furthermore, efforts in restoring dopamine synthesis and neurotransmission through viral gene therapy have been developed for Parkinson's disease. Along with the recent European Medicines Agency (EMA) and Medicines and Healthcare Products Regulatory Agency (MHRA) approval of an AAV2 gene supplementation therapy for AADC deficiency, promising efficacy and safety profiles can be achieved in this group of diseases. In this review, we present preclinical and clinical advances to address NT-related diseases, and summarise potential challenges that require careful considerations for NT gene therapy studies.
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Affiliation(s)
- Wing Sum Chu
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Genetic Therapy Accelerator Centre, Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Joanne Ng
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Genetic Therapy Accelerator Centre, Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Simon N. Waddington
- Gene Transfer Technology Group, EGA Institute for Women's HealthUniversity College LondonLondonUK
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Manju A. Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- Department of NeurologyGreat Ormond Street Hospital for ChildrenLondonUK
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15
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Matsushita N, Kato S, Nishizawa K, Sugawara M, Takeuchi K, Miyasaka Y, Mashimo T, Kobayashi K. Protocol for highly selective transgene expression through the flip-excision switch system by using a unilateral spacer sequence in rodents. STAR Protoc 2023; 4:102667. [PMID: 37906596 PMCID: PMC10622305 DOI: 10.1016/j.xpro.2023.102667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/29/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
We present a protocol to induce Cre-dependent transgene expression in specific cell types in the rat brain, suppressing a leak expression in off-target cells, by using a flip-excision switch system with a unilateral spacer sequence. We describe steps for construction of transfer plasmids, preparation of adeno-associated viral vectors, intracranial injection, and detection of transgene expression. Our protocol provides a useful strategy for a better understanding of the structure and function of specific cell types in the complex neural circuit. For complete details on the use and execution of this protocol, please refer to Matsushita et al.1.
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Affiliation(s)
- Natsuki Matsushita
- Division of Laboratory Animal Research, Aichi Medical University School of Medicine, Aichi 480-1195, Japan.
| | - Shigeki Kato
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kayo Nishizawa
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Masateru Sugawara
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kosei Takeuchi
- Department of Medical Cell Biology, Aichi Medical University School of Medicine, Aichi 480-1195, Japan
| | - Yoshiki Miyasaka
- Laboratory of Reproductive Engineering, Institute of Experimental Animal Sciences, Osaka University Medical School, Suita 565-0871, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuto Kobayashi
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan.
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16
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Middleton SJ, Hu H, Perez-Sanchez J, Zuberi S, McGrath Williams J, Weir GA, Bennett DL. GluCl.Cre ON enables selective inhibition of molecularly defined pain circuits. Pain 2023; 164:2780-2791. [PMID: 37366588 PMCID: PMC10652717 DOI: 10.1097/j.pain.0000000000002976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/17/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023]
Abstract
ABSTRACT Insight into nociceptive circuits will ultimately build our understanding of pain processing and aid the development of analgesic strategies. Neural circuit analysis has been advanced greatly by the development of optogenetic and chemogenetic tools, which have allowed function to be ascribed to discrete neuronal populations. Neurons of the dorsal root ganglion, which include nociceptors, have proved challenging targets for chemogenetic manipulation given specific confounds with commonly used DREADD technology. We have developed a cre/lox dependant version of the engineered glutamate-gated chloride channel (GluCl) to restrict and direct its expression to molecularly defined neuronal populations. We have generated GluCl.Cre ON that selectively renders neurons expressing cre-recombinase susceptible to agonist-induced silencing. We have functionally validated our tool in multiple systems in vitro, and subsequently generated viral vectors and tested its applicability in vivo. Using Nav1.8 Cre mice to restrict AAV-GluCl.Cre ON to nociceptors, we demonstrate effective silencing of electrical activity in vivo and concomitant hyposensitivity to noxious thermal and noxious mechanical pain, whereas light touch and motor function remained intact. We also demonstrated that our strategy can effectively silence inflammatory-like pain in a chemical pain model. Collectively, we have generated a novel tool that can be used to selectively silence defined neuronal circuits in vitro and in vivo. We believe that this addition to the chemogenetic tool box will facilitate further understanding of pain circuits and guide future therapeutic development.
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Affiliation(s)
- Steven J. Middleton
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Huimin Hu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Jimena Perez-Sanchez
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Sana Zuberi
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | | | - Greg A. Weir
- School of Psychology and Neuroscience, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David L. Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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17
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Wang J, Lin J, Chen Y, Liu J, Zheng Q, Deng M, Wang R, Zhang Y, Feng S, Xu Z, Ye W, Hu Y, Duan J, Lin Y, Dai J, Chen Y, Li Y, Luo T, Chen Q, Lu Z. An ultra-compact promoter drives widespread neuronal expression in mouse and monkey brains. Cell Rep 2023; 42:113348. [PMID: 37910509 DOI: 10.1016/j.celrep.2023.113348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Promoters are essential tools for basic and translational neuroscience research. An ideal promoter should possess the shortest possible DNA sequence with cell-type selectivity. However, whether ultra-compact promoters can offer neuron-specific expression is unclear. Here, we report the development of an extremely short promoter that enables selective gene expression in neurons, but not glial cells, in the brain. The promoter sequence originates from the human CALM1 gene and is only 120 bp in size. The CALM1 promoter (pCALM1) embedded in an adeno-associated virus (AAV) genome directed broad reporter expression in excitatory and inhibitory neurons in mouse and monkey brains. Moreover, pCALM1, when inserted into an all-in-one AAV vector expressing SpCas9 and sgRNA, drives constitutive and conditional in vivo gene editing in neurons and elicits functional alterations. These data demonstrate the ability of pCALM1 to conduct restricted neuronal gene expression, illustrating the feasibility of ultra-miniature promoters for targeting brain-cell subtypes.
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Affiliation(s)
- Jingyi Wang
- Department of Anesthesiology, Peking University Shenzhen Hospital, Shenzhen 518034, China; Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbang Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yefei Chen
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jing Liu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Department of Anesthesiology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518027, China
| | - Qiongping Zheng
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mao Deng
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Ruiqi Wang
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yujing Zhang
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shijing Feng
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhenyan Xu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weiyi Ye
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Yu Hu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiamei Duan
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yunping Lin
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Dai
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yu Chen
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuantao Li
- Department of Anesthesiology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518027, China; Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China
| | - Tao Luo
- Department of Anesthesiology, Peking University Shenzhen Hospital, Shenzhen 518034, China
| | - Qian Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Zhonghua Lu
- Shenzhen Technological Research Center for Primate Translational Medicine, Shenzhen Key Laboratory for Molecular Biology of Neural Development, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Biomedical Imaging Science and System Key Laboratory, Chinese Academy of Sciences, Shenzhen 518055, China.
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18
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Lagunas T, Plassmeyer SP, Fischer AD, Friedman RZ, Rieger MA, Selmanovic D, Sarafinovska S, Sol YK, Kasper MJ, Fass SB, Aguilar Lucero AF, An JY, Sanders SJ, Cohen BA, Dougherty JD. A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo. Commun Biol 2023; 6:1151. [PMID: 37953348 PMCID: PMC10641075 DOI: 10.1038/s42003-023-05483-w] [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: 02/15/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
The function of regulatory elements is highly dependent on the cellular context, and thus for understanding the function of elements associated with psychiatric diseases these would ideally be studied in neurons in a living brain. Massively Parallel Reporter Assays (MPRAs) are molecular genetic tools that enable functional screening of hundreds of predefined sequences in a single experiment. These assays have not yet been adapted to query specific cell types in vivo in a complex tissue like the mouse brain. Here, using a test-case 3'UTR MPRA library with genomic elements containing variants from autism patients, we developed a method to achieve reproducible measurements of element effects in vivo in a cell type-specific manner, using excitatory cortical neurons and striatal medium spiny neurons as test cases. This targeted technique should enable robust, functional annotation of genetic elements in the cellular contexts most relevant to psychiatric disease.
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Affiliation(s)
- Tomas Lagunas
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Stephen P Plassmeyer
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Anthony D Fischer
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Ryan Z Friedman
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Michael A Rieger
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Din Selmanovic
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Simona Sarafinovska
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Yvette K Sol
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Michael J Kasper
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Stuart B Fass
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Alessandra F Aguilar Lucero
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neuroscience, University of California San Francisco, San Francisco, CA, 94518, USA
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neuroscience, University of California San Francisco, San Francisco, CA, 94518, USA
| | - Barak A Cohen
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63108, USA.
- Department of Psychiatry, Washington University School of Medicine., 660 S. Euclid Ave, Saint Louis, MO, 63108, USA.
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19
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Badr ME, Zhang Z, Tai X, Singer A. CD8 T cell tolerance results from eviction of immature autoreactive cells from the thymus. Science 2023; 382:534-541. [PMID: 37917689 PMCID: PMC11302524 DOI: 10.1126/science.adh4124] [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: 03/01/2023] [Accepted: 09/22/2023] [Indexed: 11/04/2023]
Abstract
CD8 T cell tolerance is thought to result from clonal deletion of autoreactive thymocytes before they differentiate into mature CD8 T cells in the thymus. However, we report that, in mice, CD8 T cell tolerance instead results from premature thymic eviction of immature autoreactive CD8 thymocytes into the periphery, where they differentiate into self-tolerant mature CD8 T cells. Premature thymic eviction is triggered by T cell receptor (TCR)-driven down-regulation of the transcriptional repressor Gfi1, which induces expression of sphingosine-1-phosphate receptor-1 (S1P1) on negatively selected immature CD8 thymocytes. Thus, premature thymic eviction is the basis for CD8 T cell tolerance and is the mechanism responsible for the appearance in the periphery of mature CD8 T cells bearing autoreactive TCRs that are absent from the thymus.
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Affiliation(s)
- Mohamed Elsherif Badr
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhongmei Zhang
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuguang Tai
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alfred Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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20
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Mirabella PN, Fenselau H. Advanced neurobiological tools to interrogate metabolism. Nat Rev Endocrinol 2023; 19:639-654. [PMID: 37674015 DOI: 10.1038/s41574-023-00885-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2023] [Indexed: 09/08/2023]
Abstract
Engineered neurobiological tools for the manipulation of cellular activity, such as chemogenetics and optogenetics, have become a cornerstone of modern neuroscience research. These tools are invaluable for the interrogation of the central control of metabolism as they provide a direct means to establish a causal relationship between brain activity and biological processes at the cellular, tissue and organismal levels. The utility of these methods has grown substantially due to advances in cellular-targeting strategies, alongside improvements in the resolution and potency of such tools. Furthermore, the potential to recapitulate endogenous cellular signalling has been enriched by insights into the molecular signatures and activity dynamics of discrete brain cell types. However, each modulatory tool has a specific set of advantages and limitations; therefore, tool selection and suitability are of paramount importance to optimally interrogate the cellular and circuit-based underpinnings of metabolic outcomes within the organism. Here, we describe the key principles and uses of engineered neurobiological tools. We also highlight inspiring applications and outline critical considerations to be made when using these tools within the field of metabolism research. We contend that the appropriate application of these biotechnological advances will enable the delineation of the central circuitry regulating systemic metabolism with unprecedented potential.
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Affiliation(s)
- Paul Nicholas Mirabella
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Cologne, Germany
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Cologne, Germany
| | - Henning Fenselau
- Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Cologne, Germany.
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Cologne, Germany.
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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21
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Zhang Y, Zeng J, Xu B. Phenotypic analysis with trans-recombination-based genetic mosaic models. J Biol Chem 2023; 299:105265. [PMID: 37734556 PMCID: PMC10587715 DOI: 10.1016/j.jbc.2023.105265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Mosaicism refers to the presence of genetically distinct cell populations in an individual derived from a single zygote, which occurs during the process of development, aging, and genetic diseases. To date, a variety of genetically engineered mosaic analysis models have been established and widely used in studying gene function at exceptional cellular and spatiotemporal resolution, leading to many ground-breaking discoveries. Mosaic analysis with a repressible cellular marker and mosaic analysis with double markers are genetic mosaic analysis models based on trans-recombination. These models can generate sibling cells of distinct genotypes in the same animal and simultaneously label them with different colors. As a result, they offer a powerful approach for lineage tracing and studying the behavior of individual mutant cells in a wildtype environment, which is particularly useful for determining whether gene function is cell autonomous or nonautonomous. Here, we present a comprehensive review on the establishment and applications of mosaic analysis with a repressible cellular marker and mosaic analysis with double marker systems. Leveraging the capabilities of these mosaic models for phenotypic analysis will facilitate new discoveries on the cellular and molecular mechanisms of development and disease.
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Affiliation(s)
- Yu Zhang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Jianhao Zeng
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Bing Xu
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China.
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22
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Prigge CL, Dembla M, Sharma A, El-Quessny M, Kozlowski C, Paisley CE, Miltner AM, Johnson TM, Della Santina L, Feller MB, Kay JN. Rejection of inappropriate synaptic partners in mouse retina mediated by transcellular FLRT2-UNC5 signaling. Dev Cell 2023; 58:2080-2096.e7. [PMID: 37557174 PMCID: PMC10615732 DOI: 10.1016/j.devcel.2023.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023]
Abstract
During nervous system development, neurons choose synaptic partners with remarkable specificity; however, the cell-cell recognition mechanisms governing rejection of inappropriate partners remain enigmatic. Here, we show that mouse retinal neurons avoid inappropriate partners by using the FLRT2-uncoordinated-5 (UNC5) receptor-ligand system. Within the inner plexiform layer (IPL), FLRT2 is expressed by direction-selective (DS) circuit neurons, whereas UNC5C/D are expressed by non-DS neurons projecting to adjacent IPL sublayers. In vivo gain- and loss-of-function experiments demonstrate that FLRT2-UNC5 binding eliminates growing DS dendrites that have strayed from the DS circuit IPL sublayers. Abrogation of FLRT2-UNC5 binding allows mistargeted arbors to persist, elaborate, and acquire synapses from inappropriate partners. Conversely, UNC5C misexpression within DS circuit sublayers inhibits dendrite growth and drives arbors into adjacent sublayers. Mechanistically, UNC5s promote dendrite elimination by interfering with FLRT2-mediated adhesion. Based on their broad expression, FLRT-UNC5 recognition is poised to exert widespread effects upon synaptic partner choices across the nervous system.
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Affiliation(s)
- Cameron L Prigge
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA
| | - Mayur Dembla
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA
| | - Arsha Sharma
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA
| | - Malak El-Quessny
- Helen Wills Neuroscience Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Kozlowski
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA
| | - Caitlin E Paisley
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA
| | - Adam M Miltner
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA
| | - Tyler M Johnson
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA
| | - Luca Della Santina
- Department of Vision Sciences, University of Houston College of Optometry, Houston, TX 77204, USA
| | - Marla B Feller
- Helen Wills Neuroscience Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeremy N Kay
- Departments of Neurobiology, Ophthalmology, and Cell Biology, Duke University School of Medicine, Box 3802, Durham, NC 27710, USA.
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23
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Ahn SJ, Anfray A, Anrather J, Iadecola C. Calcium transients in nNOS neurons underlie distinct phases of the neurovascular response to barrel cortex activation in awake mice. J Cereb Blood Flow Metab 2023; 43:1633-1647. [PMID: 37149758 PMCID: PMC10581240 DOI: 10.1177/0271678x231173175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/14/2023] [Accepted: 04/02/2023] [Indexed: 05/08/2023]
Abstract
Neuronal nitric oxide (NO) synthase (nNOS), a Ca2+ dependent enzyme, is expressed by distinct populations of neocortical neurons. Although neuronal NO is well known to contribute to the blood flow increase evoked by neural activity, the relationships between nNOS neurons activity and vascular responses in the awake state remain unclear. We imaged the barrel cortex in awake, head-fixed mice through a chronically implanted cranial window. The Ca2+ indicator GCaMP7f was expressed selectively in nNOS neurons using adenoviral gene transfer in nNOScre mice. Air-puffs directed at the contralateral whiskers or spontaneous motion induced Ca2+ transients in 30.2 ± 2.2% or 51.6 ± 3.3% of nNOS neurons, respectively, and evoked local arteriolar dilation. The greatest dilatation (14.8 ± 1.1%) occurred when whisking and motion occurred simultaneously. Ca2+ transients in individual nNOS neurons and local arteriolar dilation showed various degrees of correlation, which was strongest when the activity of whole nNOS neuron ensemble was examined. We also found that some nNOS neurons became active immediately prior to arteriolar dilation, while others were activated gradually after arteriolar dilatation. Discrete nNOS neuron subsets may contribute either to the initiation or to the maintenance of the vascular response, suggesting a previously unappreciated temporal specificity to the role of NO in neurovascular coupling.
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Affiliation(s)
- Sung Ji Ahn
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Antoine Anfray
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Josef Anrather
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Costantino Iadecola
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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24
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David NA, Lee RD, LaRue RS, Joo S, Farrar MA. Nuclear corepressors NCOR1 and NCOR2 entrain thymocyte signaling, selection, and emigration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559810. [PMID: 37808728 PMCID: PMC10557688 DOI: 10.1101/2023.09.27.559810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
T cell development proceeds via discrete stages that require both gene induction and gene repression. Transcription factors direct gene repression by associating with corepressor complexes containing chromatin-remodeling enzymes; the corepressors NCOR1 and NCOR2 recruit histone deacetylases to these complexes to silence transcription of target genes. Earlier work identified the importance of NCOR1 in promoting the survival of positively-selected thymocytes. Here, we used flow cytometry and single-cell RNA sequencing to identify a broader role for NCOR1 and NCOR2 in regulating thymocyte development. Using Cd4-cre mice, we found that conditional deletion of NCOR2 had no effect on thymocyte development, whereas conditional deletion of NCOR1 had a modest effect. In contrast, Cd4-cre x Ncor1f/f x Ncor2f/f mice exhibited a significant block in thymocyte development at the DP to SP transition. Combined NCOR1/2 deletion resulted in increased signaling through the T cell receptor, ultimately resulting in elevated BIM expression and increased negative selection. The NF-κB, NUR77, and MAPK signaling pathways were also upregulated in the absence of NCOR1/2, contributing to altered CD4/CD8 lineage commitment, TCR rearrangement, and thymocyte emigration. Taken together, our data identify multiple critical roles for the combined action of NCOR1 and NCOR2 over the course of thymocyte development.
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Affiliation(s)
- Natalie A David
- Center for Immunology, Masonic Cancer Center, Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Robin D Lee
- Center for Immunology, Masonic Cancer Center, Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Rebecca S LaRue
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Sookyong Joo
- Center for Immunology, Masonic Cancer Center, Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, MN 55455
| | - Michael A Farrar
- Center for Immunology, Masonic Cancer Center, Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, MN 55455
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25
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Fréchard A, Faux C, Hexnerova R, Crucifix C, Papai G, Smirnova E, McKeon C, Ping FLY, Helmlinger D, Schultz P, Ben-Shem A. The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification. Nat Struct Mol Biol 2023; 30:1337-1345. [PMID: 37550452 DOI: 10.1038/s41594-023-01056-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained.
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Affiliation(s)
- Alexander Fréchard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Céline Faux
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Rozalie Hexnerova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Corinne Crucifix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Gabor Papai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Ekaterina Smirnova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Conor McKeon
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Florie Lo Ying Ping
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Dominique Helmlinger
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France.
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France.
| | - Adam Ben-Shem
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France.
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26
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Park J, Berthoux C, Hoyos-Ramirez E, Shan L, Morimoto-Tomita M, Wang Y, Castillo PE, Tomita S. Chemogenetic regulation of the TARP-lipid interaction mimics LTP and reversibly modifies behavior. Cell Rep 2023; 42:112826. [PMID: 37471228 PMCID: PMC10528344 DOI: 10.1016/j.celrep.2023.112826] [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: 12/03/2019] [Revised: 04/10/2023] [Accepted: 07/02/2023] [Indexed: 07/22/2023] Open
Abstract
Long-term potentiation (LTP), a well-characterized form of synaptic plasticity, is believed to underlie memory formation. Hebbian, postsynaptically expressed LTP requires TARPγ-8 phosphorylation for synaptic insertion of AMPA receptors (AMPARs). However, it is unknown whether TARP-mediated AMPAR insertion alone is sufficient to modify behavior. Here, we report the development of a chemogenetic tool, ExSYTE (Excitatory SYnaptic Transmission modulator by Engineered TARPγ-8), to mimic the cytoplasmic interaction of TARP with the plasma membrane in a doxycycline-dependent manner. We use this tool to examine the specific role of synaptic AMPAR potentiation in amygdala neurons that are activated by fear conditioning. Selective expression of active ExSYTE in these neurons potentiates AMPAR-mediated synaptic transmission in a doxycycline-dependent manner, occludes synaptically induced LTP, and mimics freezing triggered by cued fear conditioning. Thus, chemogenetic controlling of the TARP-membrane interaction is sufficient for LTP-like synaptic AMPAR insertion, which mimics fear conditioning.
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Affiliation(s)
- Joongkyu Park
- Department of Cellular and Molecular Physiology, Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pharmacology, Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Coralie Berthoux
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Hoyos-Ramirez
- Department of Cellular and Molecular Physiology, Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lili Shan
- Department of Cellular and Molecular Physiology, Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Megumi Morimoto-Tomita
- Department of Cellular and Molecular Physiology, Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yixiang Wang
- Department of Cellular and Molecular Physiology, Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susumu Tomita
- Department of Cellular and Molecular Physiology, Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA.
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27
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Gaspari S, Labouèbe G, Picard A, Berney X, Rodriguez Sanchez‐Archidona A, Thorens B. Tmem117 in AVP neurons regulates the counterregulatory response to hypoglycemia. EMBO Rep 2023; 24:e57344. [PMID: 37314252 PMCID: PMC10398655 DOI: 10.15252/embr.202357344] [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: 04/14/2023] [Revised: 05/21/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023] Open
Abstract
The counterregulatory response to hypoglycemia (CRR), which ensures a sufficient glucose supply to the brain, is an essential survival function. It is orchestrated by incompletely characterized glucose-sensing neurons, which trigger a coordinated autonomous and hormonal response that restores normoglycemia. Here, we investigate the role of hypothalamic Tmem117, identified in a genetic screen as a regulator of CRR. We show that Tmem117 is expressed in vasopressin magnocellular neurons of the hypothalamus. Tmem117 inactivation in these neurons increases hypoglycemia-induced vasopressin secretion leading to higher glucagon secretion in male mice, and this effect is estrus cycle phase dependent in female mice. Ex vivo electrophysiological analysis, in situ hybridization, and in vivo calcium imaging reveal that Tmem117 inactivation does not affect the glucose-sensing properties of vasopressin neurons but increases ER stress, ROS production, and intracellular calcium levels accompanied by increased vasopressin production and secretion. Thus, Tmem117 in vasopressin neurons is a physiological regulator of glucagon secretion, which highlights the role of these neurons in the coordinated response to hypoglycemia.
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Affiliation(s)
- Sevasti Gaspari
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Gwenaël Labouèbe
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Alexandre Picard
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Xavier Berney
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | | | - Bernard Thorens
- Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
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28
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Katagiri T, Tsukamoto S, Kuratani M, Tsuji S, Nakamura K, Ohte S, Kawaguchi Y, Takaishi K. A blocking monoclonal antibody reveals dimerization of intracellular domains of ALK2 associated with genetic disorders. Nat Commun 2023; 14:2960. [PMID: 37231012 PMCID: PMC10212922 DOI: 10.1038/s41467-023-38746-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Mutations in activin receptor-like kinase 2 (ALK2) can cause the pathological osteogenic signaling seen in some patients with fibrodysplasia ossificans progressiva and other conditions such as diffuse intrinsic pontine glioma. Here, we report that intracellular domain of wild-type ALK2 readily dimerizes in response to BMP7 binding to drive osteogenic signaling. This osteogenic signaling is pathologically triggered by heterotetramers of type II receptor kinases and ALK2 mutant forms, which form intracellular domain dimers in response to activin A binding. We develop a blocking monoclonal antibody, Rm0443, that can suppress ALK2 signaling. We solve the crystal structure of the ALK2 extracellular domain complex with a Fab fragment of Rm0443 and show that Rm0443 induces dimerization of ALK2 extracellular domains in a back-to-back orientation on the cell membrane by binding the residues H64 and F63 on opposite faces of the ligand-binding site. Rm0443 could prevent heterotopic ossification in a mouse model of fibrodysplasia ossificans progressiva that carries the human R206H pathogenic mutant.
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Affiliation(s)
- Takenobu Katagiri
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan.
- Project of Clinical and Basic Research for FOP, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan.
| | - Sho Tsukamoto
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan
- Project of Clinical and Basic Research for FOP, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan
| | - Mai Kuratani
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan
| | - Shinnosuke Tsuji
- Specialty Medicine Research Laboratories I, R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Kensuke Nakamura
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Satoshi Ohte
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yoshiro Kawaguchi
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Kiyosumi Takaishi
- Specialty Medicine Research Laboratories I, R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
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29
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Takahashi M, Kobayashi T, Mizuma H, Yamauchi K, Okamoto S, Okamoto K, Ishida Y, Koike M, Watanabe M, Isa T, Hioki H. Preferential arborization of dendrites and axons of parvalbumin- and somatostatin-positive GABAergic neurons within subregions of the mouse claustrum. Neurosci Res 2023; 190:92-106. [PMID: 36574563 DOI: 10.1016/j.neures.2022.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/06/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
Abstract
The claustrum coordinates the activities of individual cortical areas through abundant reciprocal connections with the cerebral cortex. Although these excitatory connections have been extensively investigated in three subregions of the claustrum-core region and dorsal and ventral shell regions-the contribution of GABAergic neurons to the circuitry in each subregion remains unclear. Here, we examined the distribution of GABAergic neurons and their dendritic and axonal arborizations in each subregion. Combining in situ hybridization with immunofluorescence histochemistry showed that approximately 10% of neuronal nuclei-positive cells expressed glutamic acid decarboxylase 67 mRNA across the claustral subregions. Approximately 20%, 30%, and 10% of GABAergic neurons were immunoreactive for parvalbumin (PV), somatostatin (SOM), and vasoactive intestinal polypeptide, respectively, in each subregion, and these neurochemical markers showed little overlap with each other. We then reconstructed PV and SOM neurons labeled with adeno-associated virus vectors. The dendrites and axons of PV and SOM neurons were preferentially localized to their respective subregions where their cell bodies were located. Furthermore, the axons were preferentially extended in a rostrocaudal direction, whereas the dendrites were relatively isotropic. The present findings suggest that claustral PV and SOM neurons might execute information processing separately within the core and shell regions.
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Affiliation(s)
- Megumu Takahashi
- Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Research Fellow of Japan Society for the Promotion of Science (JSPS), Chiyoda-ku, Tokyo 102-0083, Japan
| | - Tomoyo Kobayashi
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Haruhi Mizuma
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Kenta Yamauchi
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Shinichiro Okamoto
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Advanced Research Institute for Health Sciences, Juntendo University, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Kazuki Okamoto
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Yoko Ishida
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Advanced Research Institute for Health Sciences, Juntendo University, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Advanced Research Institute for Health Sciences, Juntendo University, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido 060-8638, Japan
| | - Tadashi Isa
- Department of Neuroscience, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Hiroyuki Hioki
- Department of Neuroanatomy, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan; Department of Multi-Scale Brain Structure Imaging, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Tokyo 113-8421, Japan.
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30
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Landini L, Marini M, Souza Monteiro de Araujo D, Romitelli A, Montini M, Albanese V, Titiz M, Innocenti A, Bianchini F, Geppetti P, Nassini R, De Logu F. Schwann Cell Insulin-like Growth Factor Receptor Type-1 Mediates Metastatic Bone Cancer Pain in Mice. Brain Behav Immun 2023; 110:348-364. [PMID: 36940752 DOI: 10.1016/j.bbi.2023.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/27/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023] Open
Abstract
Insulin growth factor-1 (IGF-1), an osteoclast-dependent osteolysis biomarker, contributes to metastatic bone cancer pain (MBCP), but the underlying mechanism is poorly understood. In mice, the femur metastasis caused by intramammary inoculation of breast cancer cells resulted in IGF-1 increase in femur and sciatic nerve, and IGF-1-dependent stimulus/non-stimulus-evoked pain-like behaviors. Adeno-associated virus-based shRNA selective silencing of IGF-1 receptor (IGF-1R) in Schwann cells, but not in dorsal root ganglion (DRG) neurons, attenuated pain-like behaviors. Intraplantar IGF-1 evoked acute nociception and mechanical/cold allodynia, which were reduced by selective IGF-1R silencing in DRG neurons and Schwann cells, respectively. Schwann cell IGF-1R signaling promoted an endothelial nitric oxide synthase-mediated transient receptor potential ankyrin 1 (TRPA1) activation and release of reactive oxygen species that, via macrophage-colony stimulating factor-dependent endoneurial macrophage expansion, sustained pain-like behaviors. Osteoclast derived IGF-1 initiates a Schwann cell-dependent neuroinflammatory response that sustains a proalgesic pathway that provides new options for MBCP treatment.
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Affiliation(s)
- Lorenzo Landini
- Department of Health Sciences, Clinical Pharmacology and Oncology Section, University of Florence, Florence, 50139, Italy
| | - Matilde Marini
- Department of Health Sciences, Clinical Pharmacology and Oncology Section, University of Florence, Florence, 50139, Italy
| | | | - Antonia Romitelli
- Department of Health Sciences, Clinical Pharmacology and Oncology Section, University of Florence, Florence, 50139, Italy
| | - Marco Montini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Medical Genetics Unit, University of Florence, 50141, Florence, Italy
| | - Valentina Albanese
- Department of Environmental and Prevention Sciences - DEPS, University of Ferrara, Ferrara, 44121, Italy
| | - Mustafa Titiz
- Department of Health Sciences, Clinical Pharmacology and Oncology Section, University of Florence, Florence, 50139, Italy
| | - Alessandro Innocenti
- Plastic and Reconstructive Microsurgery - Careggi University Hospital, Florence, 50139, Italy
| | - Francesca Bianchini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Section of Experimental Pathology and Oncology, University of Florence, 50141, Florence, Italy
| | - Pierangelo Geppetti
- Department of Health Sciences, Clinical Pharmacology and Oncology Section, University of Florence, Florence, 50139, Italy
| | - Romina Nassini
- Department of Health Sciences, Clinical Pharmacology and Oncology Section, University of Florence, Florence, 50139, Italy.
| | - Francesco De Logu
- Department of Health Sciences, Clinical Pharmacology and Oncology Section, University of Florence, Florence, 50139, Italy
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31
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LaFosse PK, Zhou Z, Friedman NG, Deng Y, Li AJ, Akitake B, Histed MH. Bicistronic Expression of a High-Performance Calcium Indicator and Opsin for All-Optical Stimulation and Imaging at Cellular Resolution. eNeuro 2023; 10:ENEURO.0378-22.2023. [PMID: 36858826 PMCID: PMC10062490 DOI: 10.1523/eneuro.0378-22.2023] [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: 09/12/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
State-of-the-art all-optical systems promise unprecedented access to neural activity in vivo, using multiphoton optogenetics to allow simultaneous imaging and control of activity in selected neurons at cellular resolution. However, to achieve wide use of all-optical stimulation and imaging, simple strategies are needed to robustly and stably express opsins and indicators in the same cells. Here, we describe a bicistronic adeno-associated virus (AAV) that expresses both the fast and bright calcium indicator jGCaMP8s, and a soma-targeted (st) and two-photon-activatable opsin, ChrimsonR. With this method, stChrimsonR stimulation with two-photon holography in the visual cortex of mice drives robust spiking in targeted cells, and neural responses to visual sensory stimuli and spontaneous activity are strong and stable. Cells expressing this bicistronic construct show responses to both photostimulation and visual stimulation that are similar to responses measured from cells expressing the same opsin and indicator via separate viruses. This approach is a simple and robust way to prepare neurons in vivo for two-photon holography and imaging.
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Affiliation(s)
- Paul K LaFosse
- Intramural Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
- National Institutes of Health-University of Maryland Graduate Partnerships Program, Bethesda, MD 20892
- Neuroscience and Cognitive Science Program, University of Maryland College Park, College Park, MD 20742
| | - Zhishang Zhou
- Intramural Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Nina G Friedman
- Intramural Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
- National Institutes of Health-University of Maryland Graduate Partnerships Program, Bethesda, MD 20892
- Neuroscience and Cognitive Science Program, University of Maryland College Park, College Park, MD 20742
| | - Yanting Deng
- Intramural Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Anna J Li
- Intramural Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
- Department of Biological Structure, University of Washington, Seattle, WA 98195
| | - Bradley Akitake
- Intramural Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Mark H Histed
- Intramural Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
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32
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Matsushita N, Kato S, Nishizawa K, Sugawara M, Takeuchi K, Miyasaka Y, Mashimo T, Kobayashi K. Highly selective transgene expression through the flip-excision switch system by using a unilateral spacer sequence. CELL REPORTS METHODS 2023; 3:100393. [PMID: 36936079 PMCID: PMC10014282 DOI: 10.1016/j.crmeth.2022.100393] [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: 04/12/2022] [Revised: 11/09/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023]
Abstract
The flip-excision switch (FLEX) system with an adeno-associated viral (AAV) vector allows expression of transgenes in specific cell populations having Cre recombinase. A significant issue with this system is non-specific expression of transgenes in tissues after vector injection. We show here that Cre-independent recombination events in the AAV genome carrying the FLEX sequence occur mainly during the production of viral vectors in packaging cells, which results in transgene expression in off-target populations. Introduction of a relatively longer nucleotide sequence between two recognition sites at the unilateral side of the transgene cassette, termed a unilateral spacer sequence (USS), is useful to suppress the recombination in the viral genome, leading to the protection of non-specific transgene expression with enhanced gene expression selectivity. Our FLEX/USS system offers a powerful strategy for highly specific Cre-dependent transgene expression, aiming at various applications for structural and functional analyses of target cell populations.
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Affiliation(s)
- Natsuki Matsushita
- Division of Laboratory Animal Research, Aichi Medical University School of Medicine, Nagakute, Aichi 480-1195, Japan
| | - Shigeki Kato
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kayo Nishizawa
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Masateru Sugawara
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kosei Takeuchi
- Department of Medical Cell Biology, Aichi Medical University School of Medicine, Nagakute, Aichi 480-1195, Japan
| | - Yoshiki Miyasaka
- Laboratory of Reproductive Engineering, Institute of Experimental Animal Sciences, Osaka University Medical School, Suita 565-0871, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuto Kobayashi
- Department of Molecular Genetics, Institute of Biomedical Sciences, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
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33
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Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD. BEAM: a combinatorial recombinase toolbox for binary gene expression and mosaic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528875. [PMID: 36824714 PMCID: PMC9949094 DOI: 10.1101/2023.02.16.528875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Genetic mosaic analysis, in which mutant cells reside intermingled with wild-type cells, is a powerful experimental approach, but has not been widely used in mice because existing genome-based strategies require complicated and protracted breeding schemes. We have developed an alternative approach termed BEAM (for Binary Expression Aleatory Mosaic) that relies on sparse recombinase activation to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Following delivery of DNA constructs by transfection or viral transduction, combinatorial recombinase activity generates two distinct populations of cells labeled with either green or red fluorescent protein. Any gene of interest can be mis-expressed or deleted in one population for comparison with intermingled control cells. We have extensively optimized and characterized this system both in vitro and in vivo , and demonstrate its power for investigating cell autonomy, identifying temporally or spatially aberrant phenotypes, revealing changes in cell proliferation or death, and controlling for procedural variability.
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34
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Qi H, Luo L, Lu C, Chen R, Zhou X, Zhang X, Jia Y. TCF7L2 acts as a molecular switch in midbrain to control mammal vocalization through its DNA binding domain but not transcription activation domain. Mol Psychiatry 2023; 28:1703-1717. [PMID: 36782064 DOI: 10.1038/s41380-023-01993-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 01/15/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Vocalization is an essential medium for social signaling in birds and mammals. Periaqueductal gray (PAG) a conserved midbrain structure is believed to be responsible for innate vocalizations, but its molecular regulation remains largely unknown. Here, through a mouse forward genetic screening we identified one of the key Wnt/β-catenin effectors TCF7L2/TCF4 controls ultrasonic vocalization (USV) production and syllable complexity during maternal deprivation and sexual encounter. Early developmental expression of TCF7L2 in PAG excitatory neurons is necessary for the complex trait, while TCF7L2 loss reduces neuronal gene expressions and synaptic transmission in PAG. TCF7L2-mediated vocal control is independent of its β-catenin-binding domain but dependent of its DNA binding ability. Patient mutations associated with developmental disorders, including autism spectrum disorders, disrupt the transcriptional repression effect of TCF7L2, while mice carrying those mutations display severe USV impairments. Therefore, we conclude that TCF7L2 orchestrates gene expression in midbrain to control vocal production through its DNA binding but not transcription activation domain.
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Affiliation(s)
- Huihui Qi
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,School of Medicine, Tsinghua University, Beijing, 100084, China.,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Li Luo
- Tsinghua Laboratory of Brain and Intelligence (THBI), Tsinghua University, Beijing, 100084, China
| | - Caijing Lu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runze Chen
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China
| | - Xianyao Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, China
| | - Xiaohui Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Science, Beijing Normal University, Beijing, 100875, China
| | - Yichang Jia
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. .,School of Medicine, Tsinghua University, Beijing, 100084, China. .,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China. .,Tsinghua Laboratory of Brain and Intelligence (THBI), Tsinghua University, Beijing, 100084, China.
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35
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Hughes AC, Pollard BG, Xu B, Gammons JW, Chapman P, Bikoff JB, Schwarz LA. A Novel Single Vector Intersectional AAV Strategy for Interrogating Cellular Diversity and Brain Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527312. [PMID: 36798174 PMCID: PMC9934562 DOI: 10.1101/2023.02.07.527312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
As the discovery of cellular diversity in the brain accelerates, so does the need for functional tools that target cells based on multiple features, such as gene expression and projection target. By selectively driving recombinase expression in a feature-specific manner, one can utilize intersectional strategies to conditionally promote payload expression only where multiple features overlap. We developed Conditional Viral Expression by Ribozyme Guided Degradation (ConVERGD), a single-construct intersectional targeting strategy that combines a self-cleaving ribozyme with traditional FLEx switches. ConVERGD offers benefits over existing platforms, such as expanded intersectionality, the ability to accommodate larger and more complex payloads, and a vector design that is easily modified to better facilitate rapid toolkit expansion. To demonstrate its utility for interrogating neural circuitry, we employed ConVERGD to target an unexplored subpopulation of norepinephrine (NE)-producing neurons within the rodent locus coeruleus (LC) identified via single-cell transcriptomic profiling to co-express the stress-related endogenous opioid gene prodynorphin (Pdyn). These studies showcase ConVERGD as a versatile tool for targeting diverse cell types and reveal Pdyn-expressing NE+ LC neurons as a small neuronal subpopulation capable of driving anxiogenic behavioral responses in rodents.
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Affiliation(s)
- Alex C. Hughes
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, 38105
| | - Brittany G. Pollard
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, 38105
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, 38105
| | - Jesse W. Gammons
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, 38105
- Present address: Department of Pediatrics, Stanford University, Stanford, CA, 94305
| | - Phillip Chapman
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, 38105
| | - Jay B. Bikoff
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, 38105
| | - Lindsay A. Schwarz
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, 38105
- Lead contact
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36
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Lekk I, Cabrera-Cabrera F, Turconi G, Tuvikene J, Esvald EE, Rähni A, Casserly L, Garton DR, Andressoo JO, Timmusk T, Koppel I. Untranslated regions of brain-derived neurotrophic factor mRNA control its translatability and subcellular localization. J Biol Chem 2023; 299:102897. [PMID: 36639028 PMCID: PMC9943900 DOI: 10.1016/j.jbc.2023.102897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) promotes neuronal survival and growth during development. In the adult nervous system, BDNF is important for synaptic function in several biological processes such as memory formation and food intake. In addition, BDNF has been implicated in development and maintenance of the cardiovascular system. The Bdnf gene comprises several alternative untranslated 5' exons and two variants of 3' UTRs. The effects of these entire alternative UTRs on translatability have not been established. Using reporter and translating ribosome affinity purification analyses, we show that prevalent Bdnf 5' UTRs, but not 3' UTRs, exert a repressive effect on translation. However, contrary to previous reports, we do not detect a significant effect of neuronal activity on BDNF translation. In vivo analysis via knock-in conditional replacement of Bdnf 3' UTR by bovine growth hormone 3' UTR reveals that Bdnf 3' UTR is required for efficient Bdnf mRNA and BDNF protein production in the brain, but acts in an inhibitory manner in lung and heart. Finally, we show that Bdnf mRNA is enriched in rat brain synaptoneurosomes, with higher enrichment detected for exon I-containing transcripts. In conclusion, these results uncover two novel aspects in understanding the function of Bdnf UTRs. First, the long Bdnf 3' UTR does not repress BDNF expression in the brain. Second, exon I-derived 5' UTR has a distinct role in subcellular targeting of Bdnf mRNA.
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Affiliation(s)
- Ingrid Lekk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | - Giorgio Turconi
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland,Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jürgen Tuvikene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia,Protobios Llc, Tallinn, Estonia
| | - Eli-Eelika Esvald
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia,Protobios Llc, Tallinn, Estonia
| | - Annika Rähni
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia,Protobios Llc, Tallinn, Estonia
| | - Laoise Casserly
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland,Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Daniel R. Garton
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland,Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaan-Olle Andressoo
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden.
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia; Protobios Llc, Tallinn, Estonia.
| | - Indrek Koppel
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.
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37
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Nakayama M. VCre/VloxP and SCre/SloxP as Reliable Site-Specific Recombination Systems for Genome Engineering. Methods Mol Biol 2023; 2637:161-180. [PMID: 36773146 DOI: 10.1007/978-1-0716-3016-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The Cre/loxP system is a versatile and powerful tool that has been used to develop many kinds of genetically modified mice, such as conditional knockout mice and mutant protein-expressing mice through the excision of a STOP cassette. However, while numerous in vivo and in vitro applications of the Cre/loxP system have been reported, it remains difficult to target at one time more than one set of recognition sites in an identical single cell in mice using the Cre/loxP system. To overcome this barrier, we developed two novel site-specific recombination systems called VCre/VloxP and SCre/SloxP. These systems allow multiple independent site-specific recombination, for example, multiple targeted deletions in the same cell at different times. In this chapter, I describe the features of VCre/VloxP and SCre/SloxP, practical protocols and tips on how to use them in genomic engineering applications, potential problems in their use, and how problems can be identified and solved.
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Affiliation(s)
- Manabu Nakayama
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.
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38
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Tong XK, Li H, Yang L, Xie SZ, Xie S, Gong Y, Peng C, Gao XX, Shi ZL, Yang XL, Zuo JP. Multiplication of defective Ebola virus in a complementary permissive cell line. Antiviral Res 2023; 209:105491. [PMID: 36526073 DOI: 10.1016/j.antiviral.2022.105491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
In an effort to develop safe and innovative in vitro models for Ebola virus (EBOV) research, we generated a recombinant Ebola virus where the glycoprotein (GP) gene was substituted with the Cre recombinase (Cre) gene by reverse genetics. This defective virus could multiply itself in a complementary permissive cell line, which could express GP and reporter protein upon exogenous Cre existence. The main features of this novel model for Ebola virus are intact viral life cycle, robust virus multiplication and normal virions morphology. The design of this model ensures its safety, excellent stability and maneuverability as a tool for virology research as well as for antiviral agent screening and drug discovery, and such a design could be further adapted to other viruses.
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Affiliation(s)
- Xian-Kun Tong
- State Key Laboratory of Drug Research, Immunological Disease Research Center, BSL-3 Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Heng Li
- State Key Laboratory of Drug Research, Immunological Disease Research Center, BSL-3 Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Yang
- State Key Laboratory of Drug Research, Immunological Disease Research Center, BSL-3 Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shi-Zhe Xie
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sha Xie
- State Key Laboratory of Drug Research, Immunological Disease Research Center, BSL-3 Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ying Gong
- State Key Laboratory of Drug Research, Immunological Disease Research Center, BSL-3 Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Peng
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiao-Xiao Gao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Hubei Jiangxia Lab, Wuhan, 430071, China.
| | - Jian-Ping Zuo
- State Key Laboratory of Drug Research, Immunological Disease Research Center, BSL-3 Laboratory, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
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39
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Nuclear corepressors NCOR1/NCOR2 regulate B cell development, maintain genomic integrity and prevent transformation. Nat Immunol 2022; 23:1763-1776. [PMID: 36316474 PMCID: PMC9772092 DOI: 10.1038/s41590-022-01343-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/16/2022] [Indexed: 12/15/2022]
Abstract
The nuclear corepressors NCOR1 and NCOR2 interact with transcription factors involved in B cell development and potentially link these factors to alterations in chromatin structure and gene expression. Herein, we demonstrate that Ncor1/2 deletion limits B cell differentiation via impaired recombination, attenuates pre-BCR signaling and enhances STAT5-dependent transcription. Furthermore, NCOR1/2-deficient B cells exhibited derepression of EZH2-repressed gene modules, including the p53 pathway. These alterations resulted in aberrant Rag1 and Rag2 expression and accessibility. Whole-genome sequencing of Ncor1/2 DKO B cells identified increased number of structural variants with cryptic recombination signal sequences. Finally, deletion of Ncor1 alleles in mice facilitated leukemic transformation, whereas human leukemias with less NCOR1 correlated with worse survival. NCOR1/2 mutations in human leukemia correlated with increased RAG expression and number of structural variants. These studies illuminate how the corepressors NCOR1/2 regulate B cell differentiation and provide insights into how NCOR1/2 mutations may promote B cell transformation.
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40
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Le N, Appel H, Pannullo N, Hoang T, Blackshaw S. Ectopic insert-dependent neuronal expression of GFAP promoter-driven AAV constructs in adult mouse retina. Front Cell Dev Biol 2022; 10:914386. [PMID: 36200040 PMCID: PMC9527291 DOI: 10.3389/fcell.2022.914386] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Direct reprogramming of retinal Müller glia is a promising avenue for replacing photoreceptors and retinal ganglion cells lost to retinal dystrophies. However, questions have recently been raised about the accuracy of studies claiming efficient glia-to-neuron reprogramming in retina that were conducted using GFAP mini promoter-driven adeno-associated virus (AAV) vectors. In this study, we have addressed these questions using GFAP mini promoter-driven AAV constructs to simultaneously overexpress the mCherry reporter and candidate transcription factors predicted to induce glia-to-neuron conversion, in combination with prospective genetic labeling of retinal Müller glia using inducible Cre-dependent GFP reporters. We find that, while control GFAP-mCherry constructs express faithfully in Müller glia, 5 out of 7 transcription factor overexpression constructs tested are predominantly expressed in amacrine and retinal ganglion cells. These findings demonstrate strong insert-dependent effects on AAV-based GFAP mini promoter specificity that preclude its use in inferring cell lineage relationships when studying glia-to-neuron conversion in retina.
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Affiliation(s)
- Nguyet Le
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Haley Appel
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Nicole Pannullo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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41
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Wang J, Beecher K, Chehrehasa F, Moody H. The limitations of investigating appetite through circuit manipulations: are we biting off more than we can chew? Rev Neurosci 2022; 34:295-311. [PMID: 36054842 DOI: 10.1515/revneuro-2022-0072] [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: 06/14/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Disordered eating can underpin a number of debilitating and prevalent chronic diseases, such as obesity. Broader advances in psychopharmacology and biology have motivated some neuroscientists to address diet-induced obesity through reductionist, pre-clinical eating investigations on the rodent brain. Specifically, chemogenetic and optogenetic methods developed in the 21st century allow neuroscientists to perform in vivo, region-specific/projection-specific/promoter-specific circuit manipulations and immediately assess the impact of these manipulations on rodent feeding. These studies are able to rigorously conclude whether a specific neuronal population regulates feeding behaviour in the hope of eventually developing a mechanistic neuroanatomical map of appetite regulation. However, an artificially stimulated/inhibited rodent neuronal population that changes feeding behaviour does not necessarily represent a pharmacological target for treating eating disorders in humans. Chemogenetic/optogenetic findings must therefore be triangulated with the array of theories that contribute to our understanding of appetite. The objective of this review is to provide a wide-ranging discussion of the limitations of chemogenetic/optogenetic circuit manipulation experiments in rodents that are used to investigate appetite. Stepping into and outside of medical science epistemologies, this paper draws on philosophy of science, nutrition, addiction biology and neurophilosophy to prompt more integrative, transdisciplinary interpretations of chemogenetic/optogenetic appetite data. Through discussing the various technical and epistemological limitations of these data, we provide both an overview of chemogenetics and optogenetics accessible to non-neuroscientist obesity researchers, as well as a resource for neuroscientists to expand the number of lenses through which they interpret their circuit manipulation findings.
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Affiliation(s)
- Joshua Wang
- School of Clinical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia
| | - Kate Beecher
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston 4029, QLD, Australia
| | - Fatemeh Chehrehasa
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia
| | - Hayley Moody
- Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia
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42
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Agnew-Svoboda W, Ubina T, Figueroa Z, Wong YC, Vizcarra EA, Roebini B, Wilson EH, Fiacco TA, Riccomagno MM. A genetic tool for the longitudinal study of a subset of post-inflammatory reactive astrocytes. CELL REPORTS METHODS 2022; 2:100276. [PMID: 36046623 PMCID: PMC9421582 DOI: 10.1016/j.crmeth.2022.100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 06/01/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022]
Abstract
Astrocytes are vital support cells that ensure proper brain function. In brain disease, astrocytes reprogram into a reactive state that alters many of their cellular roles. A long-standing question in the field is whether downregulation of reactive astrocyte (RA) markers during resolution of inflammation is because these astrocytes revert back to a non-reactive state or die and are replaced. This has proven difficult to answer mainly because existing genetic tools cannot distinguish between healthy versus RAs. Here we describe the generation of an inducible genetic tool that can be used to specifically target and label a subset of RAs. Longitudinal analysis of an acute inflammation model using this tool revealed that the previously observed downregulation of RA markers after inflammation is likely due to changes in gene expression and not because of cell death. Our findings suggest that cellular changes associated with astrogliosis after acute inflammation are largely reversible.
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Affiliation(s)
- William Agnew-Svoboda
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Teresa Ubina
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Zoe Figueroa
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Yiu-Cheung Wong
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Edward A. Vizcarra
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521, USA
- Biomedical Sciences Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Bryan Roebini
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Emma H. Wilson
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA 92521, USA
- Biomedical Sciences Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Todd A. Fiacco
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Biomedical Sciences Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Martin M. Riccomagno
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Biomedical Sciences Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
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43
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Liang W, Hou Y, Huang W, Wang Y, Jiang T, Huang X, Wang Z, Wu F, Zheng J, Zhang J, Ou H, Li S, Ping J, Zhang Y, Ye J, Li Z, Yang Q, Zhang J, Zheng X, Li S, Zhu XH, Chen R, Zhao C. Loss of schizophrenia-related miR-501-3p in mice impairs sociability and memory by enhancing mGluR5-mediated glutamatergic transmission. SCIENCE ADVANCES 2022; 8:eabn7357. [PMID: 35984881 PMCID: PMC9390987 DOI: 10.1126/sciadv.abn7357] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/07/2022] [Indexed: 05/16/2023]
Abstract
Schizophrenia is a polygenetic disease, the heterogeneity of which is likely complicated by epigenetic modifications yet to be elucidated. Here, we performed transcriptomic analysis of peripheral blood RNA from monozygotic twins discordant for schizophrenia and identified a schizophrenia-associated down-regulated microRNA, miR-501-3p. We showed that the loss of miR-501-3p in germline knockout (KO) male mice resulted in dendritic structure defects, glutamatergic transmission enhancement, and sociability, memory, and sensorimotor gating disruptions, which were attenuated when miR-501 expression was conditionally restored in the nervous system. Combining the results of proteomic analyses with the known genes linked to schizophrenia revealed that metabotropic glutamate receptor 5 (mGluR5) was one of the miR-501-3p targets and was elevated in vivo upon loss of miR-501. Treatment with the mGluR5 negative allosteric modulator 3-2((-methyl-4-thiazolyl) ethynyl) pyridine or the N-methyl-d-aspartate receptor antagonist 2-amino-5-phosphonopentanoic acid ameliorated the deficits observed in Mir501-KO mice. The epigenetic and pathophysiological mechanism that links miR-501-3p to the modulation of glutamatergic transmission provides etiological implications for schizophrenia.
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Affiliation(s)
- Wenquan Liang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu Hou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
- Senior Department of Pediatrics, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Weiyuan Huang
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, China
| | - Yunqian Wang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Tingyun Jiang
- The Third People’s Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Xingbing Huang
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Fengchun Wu
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China
| | - Jiawei Zheng
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, China
- The National Key Clinic Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Zhang
- The Third People’s Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Haiyan Ou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuyun Li
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China
| | - Junjiao Ping
- The Third People’s Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Yuan Zhang
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, China
| | - Junping Ye
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhongwei Li
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Yang
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, China
| | - Jian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Xianzhen Zheng
- Guangdong General Hospital, Guangdong Academy of Medical Science and Guangdong Mental Health Center, Guangzhou, China
| | - Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Xin-Hong Zhu
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, China
| | - Rongqing Chen
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, China
- The National Key Clinic Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, China
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, China
- Department of Rehabilitation, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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44
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Sciolino NR, Hsiang M, Mazzone CM, Wilson LR, Plummer NW, Amin J, Smith KG, McGee CA, Fry SA, Yang CX, Powell JM, Bruchas MR, Kravitz AV, Cushman JD, Krashes MJ, Cui G, Jensen P. Natural locus coeruleus dynamics during feeding. SCIENCE ADVANCES 2022; 8:eabn9134. [PMID: 35984878 PMCID: PMC9390985 DOI: 10.1126/sciadv.abn9134] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Recent data demonstrate that noradrenergic neurons of the locus coeruleus (LC-NE) are required for fear-induced suppression of feeding, but the role of endogenous LC-NE activity in natural, homeostatic feeding remains unclear. Here, we found that LC-NE activity was suppressed during food consumption, and the magnitude of this neural response was attenuated as mice consumed more pellets throughout the session, suggesting that LC responses to food are modulated by satiety state. Visual-evoked LC-NE activity was also attenuated in sated mice, suggesting that satiety state modulates LC-NE encoding of multiple behavioral states. We also found that food intake could be attenuated by brief or longer durations of LC-NE activation. Last, we found that activation of the LC to the lateral hypothalamus pathway suppresses feeding and enhances avoidance and anxiety-like responding. Our findings suggest that LC-NE neurons modulate feeding by integrating both external cues (e.g., anxiogenic environmental cues) and internal drives (e.g., satiety).
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Affiliation(s)
- Natale R. Sciolino
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Madeline Hsiang
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Christopher M. Mazzone
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Leslie R. Wilson
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Nicholas W. Plummer
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Jaisal Amin
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Kathleen G. Smith
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Christopher A. McGee
- Comparative Medicine, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Sydney A. Fry
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Cindy X. Yang
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Jeanne M. Powell
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Michael R. Bruchas
- Departments of Anesthesiology and Pharmacology, Center for the Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA, USA
| | | | - Jesse D. Cushman
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Michael J. Krashes
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Guohong Cui
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Patricia Jensen
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
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Benedetti V, Banfi F, Zaghi M, Moll-Diaz R, Massimino L, Argelich L, Bellini E, Bido S, Muggeo S, Ordazzo G, Mastrototaro G, Moneta M, Sessa A, Broccoli V. A SOX2-engineered epigenetic silencer factor represses the glioblastoma genetic program and restrains tumor development. SCIENCE ADVANCES 2022; 8:eabn3986. [PMID: 35921410 PMCID: PMC9348799 DOI: 10.1126/sciadv.abn3986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Current therapies remain unsatisfactory in preventing the recurrence of glioblastoma multiforme (GBM), which leads to poor patient survival. By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, together with the Kruppel-associated box and DNA methyltransferase3A/L catalytic domains, we generated a synthetic repressor named SOX2 epigenetic silencer (SES), which induces the transcriptional silencing of its original targets. By doing so, SES kills both glioma cell lines and patient-derived cancer stem cells in vitro and in vivo. SES expression, through local viral delivery in mouse xenografts, induces strong regression of human tumors and survival rescue. Conversely, SES is not harmful to neurons and glia, also thanks to a minimal promoter that restricts its expression in mitotically active cells, rarely present in the brain parenchyma. Collectively, SES produces a significant silencing of a large fraction of the SOX2 transcriptional network, achieving high levels of efficacy in repressing aggressive brain tumors.
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Affiliation(s)
- Valerio Benedetti
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- CNR Institute of Neuroscience, 20129 Milan, Italy
| | - Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Raquel Moll-Diaz
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Luca Massimino
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Laura Argelich
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Simone Bido
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sharon Muggeo
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gabriele Ordazzo
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Giuseppina Mastrototaro
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Matteo Moneta
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- CNR Institute of Neuroscience, 20129 Milan, Italy
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Ansai S, Kitano J. Speciation and adaptation research meets genome editing. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200516. [PMID: 35634923 PMCID: PMC9149800 DOI: 10.1098/rstb.2020.0516] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/07/2022] [Indexed: 07/20/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation and adaptive traits in natural populations is one of the fundamental goals in evolutionary biology. Genome editing technologies based on CRISPR-Cas systems and site-specific recombinases have enabled us to modify a targeted genomic region as desired and thus to conduct functional analyses of target loci, genes and mutations even in non-conventional model organisms. Here, we review the technical properties of genome editing techniques by classifying them into the following applications: targeted gene knock-out for investigating causative gene functions, targeted gene knock-in of marker genes for visualizing expression patterns and protein functions, precise gene replacement for identifying causative alleles and mutations, and targeted chromosomal rearrangement for investigating the functional roles of chromosomal structural variations. We describe examples of their application to demonstrate functional analysis of naturally occurring genetic variations and discuss how these technologies can be applied to speciation and adaptation research. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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47
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Martínez P, Sánchez-Vázquez R, Ferrara-Romeo I, Serrano R, Flores JM, Blasco MA. A mouse model for Li-Fraumeni-Like Syndrome with cardiac angiosarcomas associated to POT1 mutations. PLoS Genet 2022; 18:e1010260. [PMID: 35727838 PMCID: PMC9212151 DOI: 10.1371/journal.pgen.1010260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
The shelterin protein POT1 has been found mutated in many different familial and sporadic cancers, however, no mouse models to understand the pathobiology of these mutations have been developed so far. To address the molecular mechanisms underlying the tumorigenic effects of POT1 mutant proteins in humans, we have generated a mouse model for the human POT1R117C mutation found in Li-Fraumeni-Like families with cases of cardiac angiosarcoma by introducing this mutation in the Pot1a endogenous locus, knock-in for Pot1aR117C. We find here that both mouse embryonic fibroblasts (MEFs) and tissues from Pot1a+/ki mice show longer telomeres than wild-type controls. Longer telomeres in Pot1a+/ki MEFs are dependent on telomerase activity as they are not found in double mutant Pot1a+/kiTert-/- telomerase-deficient MEFs. By using complementation assays we further show that POT1a pR117C exerts dominant-negative effects at telomeres. As in human Li-Fraumeni patients, heterozygous Pot1a+/ki mice spontaneously develop a high incidence of angiosarcomas, including cardiac angiosarcomas, and this is associated to the presence of abnormally long telomeres in endothelial cells as well as in the tumors. The Pot1a+/R117C mouse model constitutes a useful tool to understand human cancers initiated by POT1 mutations. We have generated a mouse model for the human POT1R117C mutation found in Li-Fraumeni-Like (LFL) families with cases of cardiac angiosarcoma by introducing this mutation in the Pot1a endogenous locus, knock-in for Pot1aR117C. The Pot1a+/ki mice show longer telomeres than wild-type controls. Longer telomeres in mutant mice are dependent on telomerase activity as they are not found in a telomerase deficient background. As in human Li-Fraumeni patients, heterozygous Pot1a+/ki mice spontaneously develop a high incidence of angiosarcomas, including cardiac angiosarcomas, and this is associated to the presence of abnormally long telomeres in endothelial cells as well as in the tumors. The ki-Pot1aR117C mouse constitutes a potential pre-clinical mouse model for LFL syndrome presenting with high angiosarcoma incidence that could provide in the future a very useful tool for the study of treatments for these tumors.
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Affiliation(s)
- Paula Martínez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Raúl Sánchez-Vázquez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Iole Ferrara-Romeo
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Rosa Serrano
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Juana M. Flores
- Animal Surgery and Medicine Department, Faculty of Veterinary Science, Complutense University of Madrid, Madrid, Spain
| | - Maria A. Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
- * E-mail:
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48
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Liu F, Kambakam S, Almeida MP, Ming Z, Welker JM, Wierson WA, Schultz-Rogers LE, Ekker SC, Clark KJ, Essner JJ, McGrail M. Cre/ lox regulated conditional rescue and inactivation with zebrafish UFlip alleles generated by CRISPR-Cas9 targeted integration. eLife 2022; 11:71478. [PMID: 35713402 PMCID: PMC9270027 DOI: 10.7554/elife.71478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The ability to regulate gene activity spatially and temporally is essential to investigate cell type-specific gene function during development and in postembryonic processes and disease models. The Cre/lox system has been widely used for performing cell and tissue-specific conditional analysis of gene function in zebrafish. However, simple and efficient methods for isolation of stable, Cre/lox regulated zebrafish alleles are lacking. Here we applied our GeneWeld CRISPR-Cas9 targeted integration strategy to generate floxed alleles that provide robust conditional inactivation and rescue. A universal targeting vector, UFlip, with sites for cloning short homology arms flanking a floxed 2A-mRFP gene trap, was integrated into an intron in rbbp4 and rb1. rbbp4off and rb1off integration alleles resulted in strong mRFP expression, >99% reduction of endogenous gene expression, and recapitulated known indel loss of function phenotypes. Introduction of Cre led to stable inversion of the floxed cassette, loss of mRFP expression, and phenotypic rescue. rbbp4on and rb1on integration alleles did not cause phenotypes in combination with a loss of function mutation. Addition of Cre led to conditional inactivation by stable inversion of the cassette, gene trapping and mRFP expression, and the expected mutant phenotype. Neural progenitor Cre drivers were used for conditional inactivation and phenotypic rescue to showcase how this approach can be used in specific cell populations. Together these results validate a simplified approach for efficient isolation of Cre/lox responsive conditional alleles in zebrafish. Our strategy provides a new toolkit for generating genetic mosaics and represents a significant advance in zebrafish genetics.
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Affiliation(s)
- Fang Liu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Sekhar Kambakam
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Maira P Almeida
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Zhitao Ming
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Jordan M Welker
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Wesley A Wierson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Laura E Schultz-Rogers
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
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Baleisyte A, Schneggenburger R, Kochubey O. Stimulation of medial amygdala GABA neurons with kinetically different channelrhodopsins yields opposite behavioral outcomes. Cell Rep 2022; 39:110850. [PMID: 35613578 DOI: 10.1016/j.celrep.2022.110850] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/20/2021] [Accepted: 04/30/2022] [Indexed: 12/11/2022] Open
Abstract
The medial amygdala (MeA) receives pheromone information about conspecifics and has crucial functions in social behaviors. A previous study showed that activation of GABA neurons in the postero-dorsal MeA (MeApd) with channelrhodopsin-2H134R (ChR2) stimulates inter-male aggression. When performing these experiments using the faster channelrhodopsinH134R,E123T (ChETA), we find the opposite behavioral outcome. A systematic comparison between the two channelrhodopsin variants reveals that optogenetic activation of MeApd GABA neurons with ChETA suppresses aggression, whereas activation under ChR2 increases aggression. Although the mechanism for this paradoxical difference is not understood, we observe that activation of MeApd GABA neurons with ChR2 causes larger plateau depolarizations, smaller action potentials, and larger local inhibition than with ChETA. Thus, the channelrhodopsin variant used for in vivo optogenetic experiments can radically influence the behavioral outcome. Future work should continue to study the role of specific sub-populations of MeApd GABA neurons in aggression control.
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Affiliation(s)
- Aiste Baleisyte
- Laboratory of Synaptic Mechanisms, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ralf Schneggenburger
- Laboratory of Synaptic Mechanisms, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Olexiy Kochubey
- Laboratory of Synaptic Mechanisms, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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50
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Tadokoro T, Bravo-Hernandez M, Agashkov K, Kobayashi Y, Platoshyn O, Navarro M, Marsala S, Miyanohara A, Yoshizumi T, Shigyo M, Krotov V, Juhas S, Juhasova J, Nguyen D, Kupcova Skalnikova H, Motlik J, Studenovska H, Proks V, Reddy R, Driscoll SP, Glenn TD, Kemthong T, Malaivijitnond S, Tomori Z, Vanicky I, Kakinohana M, Pfaff SL, Ciacci J, Belan P, Marsala M. Precision spinal gene delivery-induced functional switch in nociceptive neurons reverses neuropathic pain. Mol Ther 2022; 30:2722-2745. [PMID: 35524407 PMCID: PMC9372322 DOI: 10.1016/j.ymthe.2022.04.023] [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: 01/12/2022] [Revised: 03/31/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
Second-order spinal cord excitatory neurons play a key role in spinal processing and transmission of pain signals to the brain. Exogenously-induced change in developmentally-imprinted excitatory neurotransmitter phenotype of these neurons to inhibitory has not yet been achieved. Here we use a subpial dorsal horn-targeted delivery of AAV (adeno-associated virus) vector(s) encoding GABA (gamma-Aminobutyric acid,) synthesizing-releasing inhibitory machinery in mice with neuropathic pain. Treated animals showed a progressive and complete reversal of neuropathic pain (tactile and brush-evoked pain behavior) which persisted for minimum 2.5 months post-treatment. The mechanism of this treatment effect results from the switch of excitatory to preferential inhibitory neurotransmitter phenotype in dorsal horn nociceptive neurons and a resulting increase in inhibitory activity in regional spinal circuitry after peripheral nociceptive stimulation. No detectable side effects (such as sedation, motor weakness or loss of normal sensation) were seen between 2-13 months post-treatment in naive adult mice, pigs and non-human primates. The use of this treatment approach may represent a potent and safe treatment modality in patients suffering from spinal cord- or peripheral nerve-injury induced neuropathic pain.
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Affiliation(s)
- Takahiro Tadokoro
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Department of Anesthesiology, University of Ryukyus, Okinawa, Japan; Neurgain Technologies, 9620 Towne Centre Drive, Suite 100, San Diego, CA 92121, USA
| | - Mariana Bravo-Hernandez
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Kirill Agashkov
- Departments of Sensory Signaling and Molecular Biophysics, Bogomoletz Institute of Physiology, Kyiv, Ukraine
| | - Yoshiomi Kobayashi
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Oleksandr Platoshyn
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Michael Navarro
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Silvia Marsala
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Neurgain Technologies, 9620 Towne Centre Drive, Suite 100, San Diego, CA 92121, USA
| | - Atsushi Miyanohara
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Vector Core Laboratory, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Tetsuya Yoshizumi
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Michiko Shigyo
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Volodymyr Krotov
- Departments of Sensory Signaling and Molecular Biophysics, Bogomoletz Institute of Physiology, Kyiv, Ukraine
| | - Stefan Juhas
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jana Juhasova
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Duong Nguyen
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Helena Kupcova Skalnikova
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jan Motlik
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Hana Studenovska
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Department of Biomaterials and Bioanalogous Systems, Heyrovsky Square 2,162 06 Prague 6, Czech Republic
| | - Vladimir Proks
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Department of Biomaterials and Bioanalogous Systems, Heyrovsky Square 2,162 06 Prague 6, Czech Republic
| | - Rajiv Reddy
- Department of Anesthesiology, Pain Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shawn P Driscoll
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Thomas D Glenn
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Kaengkhoi District, Saraburi 18110, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Kaengkhoi District, Saraburi 18110, Thailand
| | - Zoltan Tomori
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Ivo Vanicky
- Institute of Neurobiology, Biomedical Research Center, Slovak Academy of Sciences, Kosice, Slovakia
| | | | - Samuel L Pfaff
- Gene Expression Laboratory and the Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph Ciacci
- Department of Neurosurgery, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Pavel Belan
- Departments of Sensory Signaling and Molecular Biophysics, Bogomoletz Institute of Physiology, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Martin Marsala
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA; Institute of Neurobiology, Biomedical Research Center, Slovak Academy of Sciences, Kosice, Slovakia.
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