1
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Wu M, Jiang H, Li Q, Liu Y, Zhang H, Li X, Shao Z. OGT-1 regulates synaptic assembly through the insulin signaling pathway. J Cell Biochem 2023; 124:1919-1930. [PMID: 37991448 DOI: 10.1002/jcb.30497] [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: 07/27/2023] [Revised: 10/21/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
The formation and maintenance of synapses are precisely regulated, and the misregulation often leads to neurodevelopmental or neurodegenerative disorders. Besides intrinsic genetically encoded signaling pathways, synaptic structure and function are also regulated by extrinsic factors, such as nutrients. O-GlcNAc transferase (OGT), a nutrient sensor, is abundant in the nervous system and required for synaptic plasticity, learning, and memory. However, whether OGT is involved in synaptic development and the mechanism underlying the process are largely unknown. In this study, we found that OGT-1, the OGT homolog in C. elegans, regulates the presynaptic assembly in AIY interneurons. The insulin receptor DAF-2 acts upstream of OGT-1 to promote the presynaptic assembly by positively regulating the expression of ogt-1. This insulin-OGT-1 axis functions most likely by regulating neuronal activity. In this study, we elucidated a novel mechanism for synaptic development, and provided a potential link between synaptic development and insulin-related neurological disorders.
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Affiliation(s)
- Mengting Wu
- Department of Neurosurgery, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Huihui Jiang
- Department of Neurosurgery, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qian Li
- Department of Neurosurgery, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunhe Liu
- Department of Neurosurgery, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongjun Zhang
- Department of Neurosurgery, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xuekun Li
- School of Medicine, The Children's Hospital, Zhejiang University, Hangzhou, China
- School of Medicine, The Institute of Translational Medicine, Zhejiang University, Hangzhou, China
- National Clinical Research Center for Child Health, Hangzhou, China
- Zhejiang University Cancer Center, Zhejiang University, Hangzhou, China
| | - Zhiyong Shao
- Department of Neurosurgery, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
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2
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Kepler LD, McDiarmid TA, Rankin CH. Rapid assessment of the temporal function and phenotypic reversibility of neurodevelopmental disorder risk genes in Caenorhabditis elegans. Dis Model Mech 2022; 15:dmm049359. [PMID: 35363276 PMCID: PMC9092656 DOI: 10.1242/dmm.049359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
Recent studies have indicated that some phenotypes caused by decreased function of select neurodevelopmental disorder (NDD) risk genes can be reversed by restoring gene function in adulthood. However, few of the hundreds of risk genes have been assessed for adult phenotypic reversibility. We developed a strategy to rapidly assess the temporal requirements and phenotypic reversibility of NDD risk gene orthologs using a conditional protein degradation system and machine-vision phenotypic profiling in Caenorhabditis elegans. We measured how degrading and re-expressing orthologs of EBF3, BRN3A and DYNC1H1 at multiple periods throughout development affect 30 morphological, locomotor, sensory and learning phenotypes. We found that phenotypic reversibility was possible for each gene studied. However, the temporal requirements of gene function and degree of rescue varied by gene and phenotype. This work highlights the critical need to assess multiple windows of degradation and re-expression and a large number of phenotypes to understand the many roles a gene can have across the lifespan. This work also demonstrates the benefits of using a high-throughput model system to prioritize NDD risk genes for re-expression studies in other organisms.
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Affiliation(s)
- Lexis D. Kepler
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Troy A. McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
- Department of Genome Sciences, University of Washington School of Medicine, Foege Building S-250 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Catharine H. Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
- Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, BC V6T 1Z4, Canada
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3
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Ippolito D, Thapliyal S, Glauser DA. Ca 2+/CaM binding to CaMKI promotes IMA-3 importin binding and nuclear translocation in sensory neurons to control behavioral adaptation. eLife 2021; 10:71443. [PMID: 34766550 PMCID: PMC8635976 DOI: 10.7554/elife.71443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/11/2021] [Indexed: 12/29/2022] Open
Abstract
Sensory and behavioral plasticity are essential for animals to thrive in changing environments. As key effectors of intracellular calcium signaling, Ca2+/calmodulin-dependent protein kinases (CaMKs) can bridge neural activation with the many regulatory processes needed to orchestrate sensory adaptation, including by relaying signals to the nucleus. Here, we elucidate the molecular mechanism controlling the cell activation-dependent nuclear translocation of CMK-1, the Caenorhabditis elegans ortholog of mammalian CaMKI/IV, in thermosensory neurons in vivo. We show that an intracellular Ca2+ concentration elevation is necessary and sufficient to favor CMK-1 nuclear import. The binding of Ca2+/CaM to CMK-1 increases its affinity for IMA-3 importin, causing a redistribution with a relatively slow kinetics, matching the timescale of sensory adaptation. Furthermore, we show that this mechanism enables the encoding of opposite nuclear signals in neuron types with opposite calcium-responses and that it is essential for experience-dependent behavioral plasticity and gene transcription control in vivo. Since CaMKI/IV are conserved regulators of adaptable behaviors, similar mechanisms could exist in other organisms and for other sensory modalities.
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Affiliation(s)
- Domenica Ippolito
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Saurabh Thapliyal
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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4
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Rahmani A, Chew YL. Investigating the molecular mechanisms of learning and memory using Caenorhabditis elegans. J Neurochem 2021; 159:417-451. [PMID: 34528252 DOI: 10.1111/jnc.15510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/15/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022]
Abstract
Learning is an essential biological process for survival since it facilitates behavioural plasticity in response to environmental changes. This process is mediated by a wide variety of genes, mostly expressed in the nervous system. Many studies have extensively explored the molecular and cellular mechanisms underlying learning and memory. This review will focus on the advances gained through the study of the nematode Caenorhabditis elegans. C. elegans provides an excellent system to study learning because of its genetic tractability, in addition to its invariant, compact nervous system (~300 neurons) that is well-characterised at the structural level. Importantly, despite its compact nature, the nematode nervous system possesses a high level of conservation with mammalian systems. These features allow the study of genes within specific sensory-, inter- and motor neurons, facilitating the interrogation of signalling pathways that mediate learning via defined neural circuits. This review will detail how learning and memory can be studied in C. elegans through behavioural paradigms that target distinct sensory modalities. We will also summarise recent studies describing mechanisms through which key molecular and cellular pathways are proposed to affect associative and non-associative forms of learning.
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Affiliation(s)
- Aelon Rahmani
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Yee Lian Chew
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
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5
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Reiss AP, Rankin CH. Gaining an understanding of behavioral genetics through studies of foraging in Drosophila and learning in C. elegans. J Neurogenet 2021; 35:119-131. [PMID: 34151727 DOI: 10.1080/01677063.2021.1928113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The pursuit of understanding behavior has led to investigations of how genes, the environment, and the nervous system all work together to produce and influence behavior, giving rise to a field of research known as behavioral neurogenetics. This review focuses on the research journeys of two pioneers of aspects of behavioral neurogenetic research: Dr. Marla Sokolowski and Dr. Catharine Rankin as examples of how different approaches have been used to understand relationships between genes and behavior. Marla Sokolowski's research is centered around the discovery and analysis of foraging, a gene responsible for the natural behavioral polymorphism of Drosophila melanogaster larvae foraging behavior. Catharine Rankin's work began with demonstrating the ability to learn in Caenorhabditis elegans and then setting out to investigate the mechanisms underlying the "simplest" form of learning, habituation. Using these simple invertebrate organisms both investigators were able to perform in-depth dissections of behavior at genetic and molecular levels. By exploring their research and highlighting their findings we present ways their work has furthered our understanding of behavior and contributed to the field of behavioral neurogenetics.
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Affiliation(s)
- Aaron P Reiss
- Department of Psychology, University of British Columbia, Vancouver, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Catharine H Rankin
- Department of Psychology, University of British Columbia, Vancouver, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
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6
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Rankin CH. But can they learn? My accidental discovery of learning and memory in C. elegans. J Neurogenet 2021; 34:251-254. [DOI: 10.1080/01677063.2020.1833009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Catharine H. Rankin
- Department of Psychology and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
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7
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Urso SJ, Comly M, Hanover JA, Lamitina T. The O-GlcNAc transferase OGT is a conserved and essential regulator of the cellular and organismal response to hypertonic stress. PLoS Genet 2020; 16:e1008821. [PMID: 33006972 PMCID: PMC7556452 DOI: 10.1371/journal.pgen.1008821] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/14/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
The conserved O-GlcNAc transferase OGT O-GlcNAcylates serine and threonine residues of intracellular proteins to regulate their function. OGT is required for viability in mammalian cells, but its specific roles in cellular physiology are poorly understood. Here we describe a conserved requirement for OGT in an essential aspect of cell physiology: the hypertonic stress response. Through a forward genetic screen in Caenorhabditis elegans, we discovered OGT is acutely required for osmoprotective protein expression and adaptation to hypertonic stress. Gene expression analysis shows that ogt-1 functions through a post-transcriptional mechanism. Human OGT partially rescues the C. elegans phenotypes, suggesting that the osmoregulatory functions of OGT are ancient. Intriguingly, expression of O-GlcNAcylation-deficient forms of human or worm OGT rescue the hypertonic stress response phenotype. However, expression of an OGT protein lacking the tetracopeptide repeat (TPR) domain does not rescue. Our findings are among the first to demonstrate a specific physiological role for OGT at the organismal level and demonstrate that OGT engages in important molecular functions outside of its well described roles in post-translational O-GlcNAcylation of intracellular proteins.
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Affiliation(s)
- Sarel J. Urso
- Graduate Program in Cell Biology and Molecular Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Marcella Comly
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, United States of America
| | - John A. Hanover
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, United States of America
| | - Todd Lamitina
- Graduate Program in Cell Biology and Molecular Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States of America
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8
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Lia AS, Glauser DA. A system for the high-throughput analysis of acute thermal avoidance and adaptation in C. elegans. J Biol Methods 2020; 7:e129. [PMID: 32313814 PMCID: PMC7163209 DOI: 10.14440/jbm.2020.324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 02/06/2023] Open
Abstract
Nociception and its plasticity are essential biological processes controlling adaptive behavioral responses in animals. These processes are also linked to different pain conditions in human and have received considerable attention, notably via studies in rodent models and the use of heat-evoked withdrawal behavior assays as a readout of unpleasant experience. More recently, invertebrates have also emerged as useful complementary models, with their own set of advantages, including their amenability to genetic manipulations, the accessibility and relative simplicity of their nervous system and ethical concerns linked to animal suffering. Like humans, the nematode Caenorhabditis elegans (C. elegans) can detect noxious heat and produce avoidance responses such as reversals. Here, we present a methodology suitable for the high-throughput analysis of C. elegans heat-evoked reversals and the adaptation to repeated stimuli. We introduce two platforms: the INFERNO (for infrared-evoked reversal analysis platform), allowing the quantification of the thermal sensitivity in a petri dish containing a large population (> 100 animals), and the ThermINATOR (for thermal adaptation multiplexed induction platform), allowing the mass-adaptation of up to 18 worm populations at the same time. We show that wild type animals progressively desensitize in response to repeated noxious heat pulses. Furthermore, analyzing the phenotype of mutant animals, we show that the mechanisms underlying baseline sensitivity and adaptation, respectively, are supported by genetically separable molecular pathways. In conclusion, the presented method enables the high-throughput evaluation of thermal avoidance in C. elegans and will contribute to accelerate studies in the field with this invertebrate model.
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Affiliation(s)
- Andrei-Stefan Lia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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9
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McDiarmid TA, Belmadani M, Liang J, Meili F, Mathews EA, Mullen GP, Hendi A, Wong WR, Rand JB, Mizumoto K, Haas K, Pavlidis P, Rankin CH. Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation. Proc Natl Acad Sci U S A 2020; 117:656-667. [PMID: 31754030 PMCID: PMC6968627 DOI: 10.1073/pnas.1912049116] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A major challenge facing the genetics of autism spectrum disorders (ASDs) is the large and growing number of candidate risk genes and gene variants of unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated genes in vivo. Using our custom machine vision system, we quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, and habituation learning in 135 strains each carrying a mutation in an ortholog of an ASD-associated gene. We identified hundreds of genotype-phenotype relationships ranging from severe developmental delays and uncoordinated movement to subtle deficits in sensory and learning behaviors. We clustered genes by similarity in phenomic profiles and used epistasis analysis to discover parallel networks centered on CHD8•chd-7 and NLGN3•nlg-1 that underlie mechanosensory hyperresponsivity and impaired habituation learning. We then leveraged our data for in vivo functional assays to gauge missense variant effect. Expression of wild-type NLG-1 in nlg-1 mutant C. elegans rescued their sensory and learning impairments. Testing the rescuing ability of conserved ASD-associated neuroligin variants revealed varied partial loss of function despite proper subcellular localization. Finally, we used CRISPR-Cas9 auxin-inducible degradation to determine that phenotypic abnormalities caused by developmental loss of NLG-1 can be reversed by adult expression. This work charts the phenotypic landscape of ASD-associated genes, offers in vivo variant functional assays, and potential therapeutic targets for ASD.
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Affiliation(s)
- Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Manuel Belmadani
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joseph Liang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Fabian Meili
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Eleanor A Mathews
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Gregory P Mullen
- Biology Program, Oklahoma City University, Oklahoma City, OK 73106
| | - Ardalan Hendi
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Wan-Rong Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - James B Rand
- Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Kurt Haas
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Paul Pavlidis
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 2B5, Canada;
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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10
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McDiarmid TA, Yu AJ, Rankin CH. Habituation Is More Than Learning to Ignore: Multiple Mechanisms Serve to Facilitate Shifts in Behavioral Strategy. Bioessays 2019; 41:e1900077. [DOI: 10.1002/bies.201900077] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/13/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Troy A. McDiarmid
- Djavad Mowafaghian Centre for Brain HealthUniversity of British Columbia 2211 Wesbrook Mall Vancouver BC V6T 2B5 Canada
| | - Alex J. Yu
- Djavad Mowafaghian Centre for Brain HealthUniversity of British Columbia 2211 Wesbrook Mall Vancouver BC V6T 2B5 Canada
| | - Catharine H. Rankin
- Djavad Mowafaghian Centre for Brain HealthUniversity of British Columbia 2211 Wesbrook Mall Vancouver BC V6T 2B5 Canada
- Department of PsychologyUniversity of British Columbia 2136 West Mall Vancouver BC V6T 1Z4 Canada
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11
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Randlett O, Haesemeyer M, Forkin G, Shoenhard H, Schier AF, Engert F, Granato M. Distributed Plasticity Drives Visual Habituation Learning in Larval Zebrafish. Curr Biol 2019; 29:1337-1345.e4. [PMID: 30955936 PMCID: PMC6545104 DOI: 10.1016/j.cub.2019.02.039] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/18/2019] [Accepted: 02/15/2019] [Indexed: 12/15/2022]
Abstract
Habituation is a simple form of learning where animals learn to reduce their responses to repeated innocuous stimuli [1]. Habituation is thought to occur via at least two temporally and molecularly distinct mechanisms, which lead to short-term memories that last for seconds to minutes and long-term memories that last for hours or longer [1, 2]. Here, we focus on long-term habituation, which, due to the extended time course, necessitates stable alterations to circuit properties [2-4]. In its simplest form, long-term habituation could result from a plasticity event at a single point in a circuit, and many studies have focused on identifying the site and underlying mechanism of plasticity [5-10]. However, it is possible that these individual sites are only one of many points in the circuit where plasticity is occurring. Indeed, studies of short-term habituation in C. elegans indicate that in this paradigm, multiple genetically separable mechanisms operate to adapt specific aspects of behavior [11-13]. Here, we use a visual assay in which larval zebrafish habituate their response to sudden reductions in illumination (dark flashes) [14, 15]. Through behavioral analyses, we find that multiple components of the dark-flash response habituate independently of one another using different molecular mechanisms. This is consistent with a modular model in which habituation originates from multiple independent processes, each adapting specific components of behavior. This may allow animals to more specifically or flexibly habituate based on stimulus context or internal states.
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Affiliation(s)
- Owen Randlett
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Martin Haesemeyer
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Greg Forkin
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hannah Shoenhard
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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12
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McDiarmid TA, Au V, Loewen AD, Liang J, Mizumoto K, Moerman DG, Rankin CH. CRISPR-Cas9 human gene replacement and phenomic characterization in Caenorhabditis elegans to understand the functional conservation of human genes and decipher variants of uncertain significance. Dis Model Mech 2018; 11:dmm.036517. [PMID: 30361258 PMCID: PMC6307914 DOI: 10.1242/dmm.036517] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Our ability to sequence genomes has vastly surpassed our ability to interpret the genetic variation we discover. This presents a major challenge in the clinical setting, where the recent application of whole-exome and whole-genome sequencing has uncovered thousands of genetic variants of uncertain significance. Here, we present a strategy for targeted human gene replacement and phenomic characterization, based on CRISPR-Cas9 genome engineering in the genetic model organism Caenorhabditis elegans, that will facilitate assessment of the functional conservation of human genes and structure-function analysis of disease-associated variants with unprecedented precision. We validate our strategy by demonstrating that direct single-copy replacement of the C. elegans ortholog (daf-18) with the critical human disease-associated gene phosphatase and tensin homolog (PTEN) is sufficient to rescue multiple phenotypic abnormalities caused by complete deletion of daf-18, including complex chemosensory and mechanosensory impairments. In addition, we used our strategy to generate animals harboring a single copy of the known pathogenic lipid phosphatase inactive PTEN variant (PTEN-G129E), and showed that our automated in vivo phenotypic assays could accurately and efficiently classify this missense variant as loss of function. The integrated nature of the human transgenes allows for analysis of both homozygous and heterozygous variants and greatly facilitates high-throughput precision medicine drug screens. By combining genome engineering with rapid and automated phenotypic characterization, our strategy streamlines the identification of novel conserved gene functions in complex sensory and learning phenotypes that can be used as in vivo functional assays to decipher variants of uncertain significance.
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Affiliation(s)
- Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Vinci Au
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Aaron D Loewen
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Joseph Liang
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada .,Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, BC V6T 1Z4, Canada
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13
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Ardiel EL, McDiarmid TA, Timbers TA, Lee KCY, Safaei J, Pelech SL, Rankin CH. Insights into the roles of CMK-1 and OGT-1 in interstimulus interval-dependent habituation in Caenorhabditis elegans. Proc Biol Sci 2018; 285:rspb.2018.2084. [PMID: 30429311 DOI: 10.1098/rspb.2018.2084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/25/2018] [Indexed: 12/19/2022] Open
Abstract
Habituation is a ubiquitous form of non-associative learning observed as a decrement in responding to repeated stimulation that cannot be explained by sensory adaptation or motor fatigue. One of the defining characteristics of habituation is its sensitivity to the rate at which training stimuli are presented-animals habituate faster in response to more rapid stimulation. The molecular mechanisms underlying this interstimulus interval (ISI)-dependent characteristic of habituation remain unknown. In this article, we use behavioural neurogenetic and bioinformatic analyses in the nematode Caenorhabiditis elegans to identify the first molecules that modulate habituation in an ISI-dependent manner. We show that the Caenorhabditis elegans orthologues of Ca2+/calmodulin-dependent kinases CaMK1/4, CMK-1 and O-linked N-acetylglucosamine (O-GlcNAc) transferase, OGT-1, both function in primary sensory neurons to inhibit habituation at short ISIs and promote it at long ISIs. In addition, both cmk-1 and ogt-1 mutants display a rare mechanosensory hyper-responsive phenotype (i.e. larger mechanosensory responses than wild-type). Overall, our work identifies two conserved genes that function in sensory neurons to modulate habituation in an ISI-dependent manner, providing the first insights into the molecular mechanisms underlying the universally observed phenomenon that habituation has different properties when stimuli are delivered at different rates.
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Affiliation(s)
- Evan L Ardiel
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada V6T 2B5
| | - Troy A McDiarmid
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada V6T 2B5
| | - Tiffany A Timbers
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada V6T 2B5
| | - Kirsten C Y Lee
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada V6T 2B5
| | - Javad Safaei
- Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Steven L Pelech
- Department of Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, British Columbia, Canada V5Z 1M9.,Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada V6P 6T3
| | - Catharine H Rankin
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2211 Wesbrook Mall, Vancouver, British Columbia, Canada V6T 2B5 .,Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, British Columbia, Canada V6T 1Z4
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