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Lanza DG, Mao J, Lorenzo I, Liao L, Seavitt JR, Ljungberg MC, Simpson EM, DeMayo FJ, Heaney JD. An oocyte-specific Cas9-expressing mouse for germline CRISPR/Cas9-mediated genome editing. Genesis 2024; 62:e23589. [PMID: 38523431 PMCID: PMC10987075 DOI: 10.1002/dvg.23589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
Cas9 transgenes can be employed for genome editing in mouse zygotes. However, using transgenic instead of exogenous Cas9 to produce gene-edited animals creates unique issues including ill-defined transgene integration sites, the potential for prolonged Cas9 expression in transgenic embryos, and increased genotyping burden. To overcome these issues, we generated mice harboring an oocyte-specific, Gdf9 promoter driven, Cas9 transgene (Gdf9-Cas9) targeted as a single copy into the Hprt1 locus. The X-linked Hprt1 locus was selected because it is a defined integration site that does not influence transgene expression, and breeding of transgenic males generates obligate transgenic females to serve as embryo donors. Using microinjections and electroporation to introduce sgRNAs into zygotes derived from transgenic dams, we demonstrate that Gdf9-Cas9 mediates genome editing as efficiently as exogenous Cas9 at several loci. We show that genome editing efficiency is independent of transgene inheritance, verifying that maternally derived Cas9 facilitates genome editing. We also show that paternal inheritance of Gdf9-Cas9 does not mediate genome editing, confirming that Gdf9-Cas9 is not expressed in embryos. Finally, we demonstrate that off-target mutagenesis is equally rare when using transgenic or exogenous Cas9. Together, these results show that the Gdf9-Cas9 transgene is a viable alternative to exogenous Cas9.
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Affiliation(s)
- Denise G. Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
| | - Jianqiang Mao
- Department of Molecular & Cellular Biology, Baylor College of Medicine Houston, TX, USA 77030
| | - Isabel Lorenzo
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
| | - Lan Liao
- Department of Molecular & Cellular Biology, Baylor College of Medicine Houston, TX, USA 77030
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
- Present address: The Jackson Laboratory 600 Main St., Bar Harbor, Maine, ME, USA 04609
| | - M. Cecilia Ljungberg
- Department of Pediatrics – Neurology, Baylor College of Medicine Houston, TX, USA 77030
- Duncan Neurological Research Institute, Texas Children’s Hospital Houston, TX, USA 77030
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital Department of Medical Genetics, The University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada
| | - Francesco J. DeMayo
- Reproductive and Developmental Biology Laboratory National Institute of Environmental Health Sciences Research Triangle Park, NC, USA 27709
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, TX, USA 77030
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Kofoed RH, Simpson EM, Hynynen K, Aubert I. Sonoselective delivery using ultrasound and microbubbles combined with intravenous rAAV9 CLDN5-GFP does not increase endothelial gene expression. Gene Ther 2023; 30:807-811. [PMID: 36781945 DOI: 10.1038/s41434-023-00389-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023]
Abstract
Transcranial ultrasound combined with intravenous microbubbles can be used to increase blood-brain barrier permeability or, at lower pressures, to mediate sonoselective gene delivery to endothelial cells. Previously, sonoselective gene delivery with plasmid-coated microbubbles as gene carriers resulted in transient transgene expression in the brain endothelium. We investigated the potential of recombinant adeno-associated virus 9 (rAAV9), a serotype known for its efficient transduction and long-term transgene expression, for sonoselective gene delivery to endothelial cells of the brain. We found that rAAV9 led to gene delivery to brain endothelial cells following intravenous administration at a dosage of 1 × 1011 GC/g. However, the sonoselective gene delivery approach with intravenous rAAV9, using the same parameters as previously used for plasmid delivery, did not increase transgene expression in brain endothelial cells targeted. These results suggest that intravenous rAAV9 are using mechanisms of entry into the cerebrovasculature that are not significantly influenced by sonoselective treatments known to facilitate endothelial cell entry of plasmids coated onto microbubbles.
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Affiliation(s)
- Rikke Hahn Kofoed
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, Department of Medical Genetics, The University of British Columbia, Vancouver, Canada
| | - Kullervo Hynynen
- Physical Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Isabelle Aubert
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Toronto, ON, Canada.
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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3
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Mirjalili Mohanna SZ, Korecki AJ, Simpson EM. rAAV-PHP.B escapes the mouse eye and causes lethality whereas rAAV9 can transduce aniridic corneal limbal stem cells without lethality. Gene Ther 2023; 30:670-684. [PMID: 37072572 PMCID: PMC10506911 DOI: 10.1038/s41434-023-00400-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 04/20/2023]
Abstract
Recently safety concerns have been raised in connection with high doses of recombinant adeno-associated viruses (rAAV). Therefore, we undertook a series of experiments to test viral capsid (rAAV9 and rAAV-PHP.B), dose, and route of administration (intrastromal, intravitreal, and intravenous) focused on aniridia, a congenital blindness that currently has no cure. The success of gene therapy for aniridia may depend on the presence of functional limbal stem cells (LSCs) in the damaged aniridic corneas and whether rAAV can transduce them. Both these concerns were unknown, and thus were also addressed by our studies. For the first time, we report ataxia and lethality after intravitreal or intrastromal rAAV-PHP.B virus injections. We demonstrated virus escape from the eye and transduction of non-ocular tissues by rAAV9 and rAAV-PHP.B capsids. We have also shown that intrastromal and intravitreal delivery of rAAV9 can transduce functional LSCs, as well as all four PAX6-expressing retinal cell types in aniridic eye, respectively. Overall, lack of adverse events and successful transduction of LSCs and retinal cells makes it clear that rAAV9 is the capsid of choice for future aniridia gene therapy. Our finding of rAAV lethality after intraocular injections will be impactful for other researchers developing rAAV-based gene therapies.
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Affiliation(s)
- Seyedeh Zeinab Mirjalili Mohanna
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada.
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Simpson EM, Clarke IJ, Scott CJ, Stephen CP, Rao A, Gunn AJ. The GLP-1 agonist, exendin-4, stimulates LH secretion in female sheep. J Endocrinol 2023; 259:e230105. [PMID: 37466202 PMCID: PMC10448581 DOI: 10.1530/joe-23-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/18/2023] [Indexed: 07/20/2023]
Abstract
Our previous studies showed that microinjection into the median eminence of the sheep of glucagon-like peptide- 1 (GLP-1) or its receptor agonist exendin-4 stimulates luteinising hormone (LH) secretion, but it is unknown whether the same effect may be obtained by systemic administration of the same. The present study measured the response in terms of plasma LH concentrations to intravenous (iv) infusion of exendin-4. A preliminary study showed that infusion of 2 mg exendin-4 into ewes produced a greater LH response in the follicular phase of the oestrous cycle than the luteal phase. Accordingly, the main study monitored plasma LH levels in response to either 0.5 mg or 2 mg exendin-4 or vehicle (normal saline) delivered by jugular infusion for 1 h in the follicular phase of the oestrous cycle. Blood samples were collected at 10 min intervals before, during and after infusion. Both doses of exendin-4 increased mean plasma LH concentrations and increased LH peripheral pulse amplitude. There was no effect on inter-pulse interval or timing of the preovulatory LH surge. These doses of exendin-4 did not alter plasma insulin or glucose concentrations. Quantitative PCR of the gastrointestinal tract samples from a population of ewes confirmed the expression of the preproglucagon gene (GCG). Expression increased aborally and was greatest in the rectum. It is concluded that endogenous GLP-1, most likely derived from the hindgut, may act systemically to stimulate LH secretion. The present data suggest that this effect may be obtained with levels of agonist that are lower than those functioning as an incretin.
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Affiliation(s)
- Elizabeth M Simpson
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Iain J Clarke
- School of Agriculture Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Christopher J Scott
- School of Dentistry and Medical Science, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Cyril P Stephen
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Alexandra Rao
- School of Agriculture Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Allan J Gunn
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia
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Adair BA, Korecki AJ, Djaksigulova D, Wagner PK, Chiu NY, Lam SL, Lengyell TC, Leavitt BR, Simpson EM. ABE8e Corrects Pax6-Aniridic Variant in Humanized Mouse ESCs and via LNPs in Ex Vivo Cortical Neurons. Ophthalmol Ther 2023; 12:2049-2068. [PMID: 37210469 PMCID: PMC10287867 DOI: 10.1007/s40123-023-00729-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023] Open
Abstract
INTRODUCTION Aniridia is a rare congenital vision-loss disease caused by heterozygous variants in the PAX6 gene. There is no vision-saving therapy, but one exciting approach is to use CRISPR/Cas9 to permanently correct the causal genomic variants. Preclinical studies to develop such a therapy in animal models face the challenge of showing efficacy when binding human DNA. Thus, we hypothesized that a CRISPR gene therapy can be developed and optimized in humanized mouse embryonic stem cells (ESCs) that will be able to distinguish between an aniridia patient variant and nonvariant chromosome and lay the foundation for human therapy. METHODS To answer the challenge of binding human DNA, we proposed the "CRISPR Humanized Minimally Mouse Models" (CHuMMMs) strategy. Thus, we minimally humanized Pax6 exon 9, the location of the most common aniridia variant c.718C > T. We generated and characterized a nonvariant CHuMMMs mouse, and a CHuMMMs cell-based disease model, in which we tested five CRISPR enzymes for therapeutic efficacy. We then delivered the therapy via lipid nanoparticles (LNPs) to alter a second variant in ex vivo cortical primary neurons. RESULTS We successfully established a nonvariant CHuMMMs mouse and three novel CHuMMMs aniridia cell lines. We showed that humanization did not disrupt Pax6 function in vivo, as the mouse showed no ocular phenotype. We developed and optimized a CRISPR therapeutic strategy for aniridia in the in vitro system, and found that the base editor, ABE8e, had the highest correction of the patient variant at 76.8%. In the ex vivo system, the LNP-encapsulated ABE8e ribonucleoprotein (RNP) complex altered the second patient variant and rescued 24.8% Pax6 protein expression. CONCLUSION We demonstrated the usefulness of the CHuMMMs approach, and showed the first genomic editing by ABE8e encapsulated as an LNP-RNP. Furthermore, we laid the foundation for translation of the proposed CRISPR therapy to preclinical mouse studies and eventually patients with aniridia.
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Affiliation(s)
- Bethany A Adair
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Diana Djaksigulova
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | | | - Nina Y Chiu
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
- Incisive Genetics Inc., Vancouver, BC, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
- Department of Medical Genetics, The University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
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Fornes O, Av-Shalom TV, Korecki AJ, Farkas RA, Arenillas DJ, Mathelier A, Simpson EM, Wasserman WW. OnTarget: in silico design of MiniPromoters for targeted delivery of expression. Nucleic Acids Res 2023:7160204. [PMID: 37166953 DOI: 10.1093/nar/gkad375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/12/2023] Open
Abstract
MiniPromoters, or compact promoters, are short DNA sequences that can drive expression in specific cells and tissues. While broadly useful, they are of high relevance to gene therapy due to their role in enabling precise control of where a therapeutic gene will be expressed. Here, we present OnTarget (http://ontarget.cmmt.ubc.ca), a webserver that streamlines the MiniPromoter design process. Users only need to specify a gene of interest or custom genomic coordinates on which to focus the identification of promoters and enhancers, and can also provide relevant cell-type-specific genomic evidence (e.g. accessible chromatin regions, histone modifications, etc.). OnTarget combines the provided data with internal data to identify candidate promoters and enhancers and design MiniPromoters. To illustrate the utility of OnTarget, we designed and characterized two MiniPromoters targeting different cell populations relevant to Parkinson Disease.
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Affiliation(s)
- Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Tamar V Av-Shalom
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Rachelle A Farkas
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - David J Arenillas
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
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Golla K, Paul M, Lengyell TC, Simpson EM, Falet H, Kim H. A novel association between platelet filamin A and soluble N-ethylmaleimide sensitive factor attachment proteins regulates granule secretion. Res Pract Thromb Haemost 2023; 7:100019. [PMID: 37538498 PMCID: PMC10394388 DOI: 10.1016/j.rpth.2022.100019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 11/04/2022] [Accepted: 11/17/2022] [Indexed: 08/05/2023] Open
Abstract
Background and Objective The molecular mechanisms that underpin platelet granule secretion remain poorly defined. Filamin A (FLNA) is an actin-crosslinking and signaling scaffold protein whose role in granule exocytosis has not been explored despite evidence that FLNA gene mutations confer platelet defects in humans. Methods and Results Using platelets from platelet-specific conditional Flna-knockout mice, we showed that the loss of FLNA confers a severe defect in alpha (α)- and dense (δ)-granule exocytosis, as measured based on the release of platelet factor 4 (aka CXCL4) and adenosine triphosphate (ATP), respectively. This defect was observed following activation of both immunoreceptor tyrosine-based activation motif (ITAM) signaling by collagen-related peptide (CRP) and G protein-coupled receptor (GPCR) signaling by thrombin and the thromboxane mimetic U46619. CRP-induced spikes in intracellular calcium [Ca2+]i were impaired in FLNA-null platelets relative to controls, confirming that FLNA regulates ITAM-driven proximal signaling. In contrast, GPCR-mediated spikes in [Ca2+]i in response to thrombin and U46619 were unaffected by FLNA. Normal platelet secretion requires complexing of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins synaptosomal-associated protein 23 (SNAP23) and syntaxin-11 (STX11). We determined that FLNA coimmunoprecipitates with both SNAP23 and STX11 upon platelet stimulation. Conclusion FLNA regulates GPCR-driven platelet granule secretion and associates with SNAP23 and STX11 in an activation-dependent manner.
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Affiliation(s)
- Kalyan Golla
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Manoj Paul
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tess C. Lengyell
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Hervé Falet
- Versiti Blood Research Institute, Milwaukee, Wisconsin, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Hugh Kim
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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Vijayasarathy C, Zeng Y, Marangoni D, Dong L, Pan ZH, Simpson EM, Fariss RN, Sieving PA. Targeted Expression of Retinoschisin by Retinal Bipolar Cells in XLRS Promotes Resolution of Retinoschisis Cysts Sans RS1 From Photoreceptors. Invest Ophthalmol Vis Sci 2022; 63:8. [PMID: 36227606 PMCID: PMC9583743 DOI: 10.1167/iovs.63.11.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Purpose Loss of retinoschisin (RS1) function underlies X-linked retinoschisis (XLRS) pathology. In the retina, both photoreceptor inner segments and bipolar cells express RS1. However, the loss of RS1 function causes schisis primarily in the inner retina. To understand these cell type-specific phenotypes, we decoupled RS1 effects in bipolar cells from that in photoreceptors. Methods Bipolar cell transgene RS1 expression was achieved using two inner retina-specific promoters: (1) a minimal promoter engineered from glutamate receptor, metabotropic glutamate receptor 6 gene (mini-mGluR6/ Grm6) and (2) MiniPromoter (Ple155). Adeno-associated virus vectors encoding RS1 gene under either the mini-mGluR6 or Ple-155 promoter were delivered to the XLRS mouse retina through intravitreal or subretinal injection on postnatal day 14. Retinal structure and function were assessed 5 weeks later: immunohistochemistry for morphological characterization, optical coherence tomography and electroretinography (ERG) for structural and functional evaluation. Results Immunohistochemical analysis of RS1expression showed that expression with the MiniPromoter (Ple155) was heavily enriched in bipolar cells. Despite variations in vector penetrance and gene transfer efficiency across the injected retinas, those retinal areas with robust bipolar cell RS1 expression showed tightly packed bipolar cells with fewer cavities and marked improvement in inner retinal structure and synaptic function as judged by optical coherence tomography and electroretinography, respectively. Conclusions These results demonstrate that RS1 gene expression primarily in bipolar cells of the XLRS mouse retina, independent of photoreceptor expression, can ameliorate retinoschisis structural pathology and provide further evidence of RS1 role in cell adhesion.
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Affiliation(s)
- Camasamudram Vijayasarathy
- Section for Translational Research in Retinal and Macular Degeneration, National Institutes of Health, Bethesda, Maryland, United States
| | - Yong Zeng
- Section for Translational Research in Retinal and Macular Degeneration, National Institutes of Health, Bethesda, Maryland, United States
| | - Dario Marangoni
- Section for Translational Research in Retinal and Macular Degeneration, National Institutes of Health, Bethesda, Maryland, United States
| | - Lijin Dong
- Genetic Engineering Facility, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Zhuo-Hua Pan
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, Michigan, United States
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert N. Fariss
- Biological Imaging Core, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Paul A. Sieving
- Section for Translational Research in Retinal and Macular Degeneration, National Institutes of Health, Bethesda, Maryland, United States,Center for Ocular Regenerative Therapy, Department of Ophthalmology, University of California Davis, United States
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9
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Mirjalili Mohanna SZ, Djaksigulova D, Hill AM, Wagner PK, Simpson EM, Leavitt BR. LNP-mediated delivery of CRISPR RNP for wide-spread in vivo genome editing in mouse cornea. J Control Release 2022; 350:401-413. [PMID: 36029893 DOI: 10.1016/j.jconrel.2022.08.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 01/02/2023]
Abstract
CRISPR/Cas9-based genome-editing therapies are poised to change the clinical outcome for many diseases with validated therapeutic targets awaiting an appropriate delivery system. Recent advances in lipid nanoparticle (LNP) technology make them an attractive platform for the delivery of various forms of CRISPR/Cas9, including the efficient and transient Cas9/gRNA ribonucleoprotein (RNP) complexes. In this study, we initially tested our novel LNP platform by delivering pre-complexed RNPs and template DNA to cultured mouse cortical neurons, and obtained successful ex vivo genome editing. We then directly injected LNP-packaged RNPs and DNA template into the mouse cornea to evaluate in vivo delivery. For the first time, we demonstrated wide-spread genome editing in the cornea using our LNP-RNPs. The ability of our LNPs to transfect the cornea highlights the potential of our novel delivery platform to be used in CRISPR/Cas9-based genome editing therapies of corneal diseases.
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Affiliation(s)
- Seyedeh Zeinab Mirjalili Mohanna
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Diana Djaksigulova
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada
| | | | | | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada.
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada; Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada; Incisive Genetics Inc., Vancouver, BC, Canada
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10
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Kofoed RH, Heinen S, Silburt J, Dubey S, Dibia CL, Maes M, Simpson EM, Hynynen K, Aubert I. Transgene distribution and immune response after ultrasound delivery of rAAV9 and PHP.B to the brain in a mouse model of amyloidosis. Mol Ther Methods Clin Dev 2021; 23:390-405. [PMID: 34761053 PMCID: PMC8560718 DOI: 10.1016/j.omtm.2021.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 01/01/2023]
Abstract
Efficient disease-modifying treatments for Alzheimer disease, the most common form of dementia, have yet to be established. Gene therapy has the potential to provide the long-term production of therapeutic in the brain following a single administration. However, the blood-brain barrier poses a challenge for gene delivery to the adult brain. We investigated the transduction efficiency and immunological response following non-invasive gene-delivery strategies to the brain of a mouse model of amyloidosis. Two emerging technologies enabling gene delivery across the blood-brain barrier were used to establish the minimal vector dosage required to reach the brain: (1) focused ultrasound combined with intravenous microbubbles, which increases the permeability of the blood-brain barrier at targeted sites and (2) the recombinant adeno-associated virus (rAAV)-based capsid named rAAV-PHP.B. We found that equal intravenous dosages of rAAV9 combined with focused ultrasound, or rAAV-PHP.B, were required for brain gene delivery. In contrast to rAAV9, focused ultrasound did not decrease the rAAV-PHP.B dosage required to transduce brain cells in a mouse model of amyloidosis. The non-invasive rAAV delivery to the brain using rAAV-PHP.B or rAAV9 with focused ultrasound triggered an immune reaction including major histocompatibility complex class II expression, complement system and microglial activation, and T cell infiltration.
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Affiliation(s)
- Rikke Hahn Kofoed
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stefan Heinen
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Joseph Silburt
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sonam Dubey
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chinaza Lilian Dibia
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Miriam Maes
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children’s Hospital, Department of Medical Genetics, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Kullervo Hynynen
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Isabelle Aubert
- Biological Sciences, Hurvitz Brain Sciences Research Program, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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11
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Al-Shekaili HH, Petkau TL, Pena I, Lengyell TC, Verhoeven-Duif NM, Ciapaite J, Bosma M, van Faassen M, Kema IP, Horvath G, Ross C, Simpson EM, Friedman JM, van Karnebeek C, Leavitt BR. A novel mouse model for pyridoxine-dependent epilepsy due to antiquitin deficiency. Hum Mol Genet 2021; 29:3266-3284. [PMID: 32969477 DOI: 10.1093/hmg/ddaa202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Pyridoxine-dependent epilepsy (PDE) is a rare autosomal recessive disease caused by mutations in the ALDH7A1 gene leading to blockade of the lysine catabolism pathway. PDE is characterized by recurrent seizures that are resistant to conventional anticonvulsant treatment but are well-controlled by pyridoxine (PN). Most PDE patients also suffer from neurodevelopmental deficits despite adequate seizure control with PN. To investigate potential pathophysiological mechanisms associated with ALDH7A1 deficiency, we generated a transgenic mouse strain with constitutive genetic ablation of Aldh7a1. We undertook extensive biochemical characterization of Aldh7a1-KO mice consuming a low lysine/high PN diet. Results showed that KO mice accumulated high concentrations of upstream lysine metabolites including ∆1-piperideine-6-carboxylic acid (P6C), α-aminoadipic semialdehyde (α-AASA) and pipecolic acid both in brain and liver tissues, similar to the biochemical picture in ALDH7A1-deficient patients. We also observed preliminary evidence of a widely deranged amino acid profile and increased levels of methionine sulfoxide, an oxidative stress biomarker, in the brains of KO mice, suggesting that increased oxidative stress may be a novel pathobiochemical mechanism in ALDH7A1 deficiency. KO mice lacked epileptic seizures when fed a low lysine/high PN diet. Switching mice to a high lysine/low PN diet led to vigorous seizures and a quick death in KO mice. Treatment with PN controlled seizures and improved survival of high-lysine/low PN fed KO mice. This study expands the spectrum of biochemical abnormalities that may be associated with ALDH7A1 deficiency and provides a proof-of-concept for the utility of the model to study PDE pathophysiology and to test new therapeutics.
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Affiliation(s)
- Hilal H Al-Shekaili
- British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Terri L Petkau
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Izabella Pena
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | - Jolita Ciapaite
- Department of Genetics, University Medical Center, Utrecht, The Netherlands
| | - Marjolein Bosma
- Department of Genetics, University Medical Center, Utrecht, The Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gabriella Horvath
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Colin Ross
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth M Simpson
- British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jan M Friedman
- British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, BC Children's Research Institute, University of British Columbia, Vancouver, BC, Canada.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Centres, Amsterdam, The Netherlands.,Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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12
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Galvan A, Petkau TL, Hill AM, Korecki AJ, Lu G, Choi D, Rahman K, Simpson EM, Leavitt BR, Smith Y. Intracerebroventricular Administration of AAV9-PHP.B SYN1-EmGFP Induces Widespread Transgene Expression in the Mouse and Monkey Central Nervous System. Hum Gene Ther 2021; 32:599-615. [PMID: 33860682 PMCID: PMC8236560 DOI: 10.1089/hum.2020.301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
Viral vectors made from adeno-associated virus (AAV) have emerged as preferred tools in basic and translational neuroscience research to introduce or modify genetic material in cells of interest. The use of viral vectors is particularly attractive in nontransgenic species, such as nonhuman primates. Injection of AAV solutions into the cerebrospinal fluid is an effective method to achieve a broad distribution of a transgene in the central nervous system. In this study, we conducted injections of AAV9-PHP.B, a recently described AAV capsid mutant, in the lateral ventricle of mice and rhesus macaques. To enhance the expression of the transgene (the tag protein emerald green fluorescent protein [EmGFP]), we used a gene promoter that confers high neuron-specific expression of the transgene, the human synapsin 1 (SYN1) promoter. The efficacy of the viral vector was first tested in mice. Our results show that intracerebroventricular injections of AAV9-PHP.B SYN1-EmGFP-woodchuck hepatitis virus posttranscriptional regulatory element resulted in neuronal EmGFP expression throughout the mice and monkey brains. We have provided a thorough characterization of the brain regions expressing EmGFP in both species. EmGFP was observed in neuronal cell bodies over the whole cerebral cortex and in the cerebellum, as well as in some subcortical regions, including the striatum and hippocampus. We also observed densely labeled neuropil in areas known to receive projections from these regions. Double fluorescence studies demonstrated that EmGFP was expressed by several types of neurons throughout the mouse and monkey brain. Our results demonstrate that a single injection in the lateral ventricle is an efficient method to obtain transgene expression in many cortical and subcortical regions, obviating the need of multiple intraparenchymal injections to cover large brain areas. The use of intraventricular injections of AAV9-PHP.B SYN1-EmGFP could provide a powerful approach to transduce widespread areas of the brain and may contribute to further development of methods to genetically target-specific populations of neurons.
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Affiliation(s)
- Adriana Galvan
- Department of Neurology, Yerkes National Primate Research Center, Udall Center of Excellence for Parkinson's Disease, Emory University, Atlanta, Georgia, USA
| | - Terri L. Petkau
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Austin M. Hill
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea J. Korecki
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ge Lu
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Diane Choi
- Department of Neurology, Yerkes National Primate Research Center, Udall Center of Excellence for Parkinson's Disease, Emory University, Atlanta, Georgia, USA
- Molecular Systems and Pharmacology Graduate Program, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Kazi Rahman
- Department of Neurology, Yerkes National Primate Research Center, Udall Center of Excellence for Parkinson's Disease, Emory University, Atlanta, Georgia, USA
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair R. Leavitt
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
- Division of Neurology, Department of Medicine, University of British Columbia Hospital, Vancouver, British Columbia, Canada
- Center for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yoland Smith
- Department of Neurology, Yerkes National Primate Research Center, Udall Center of Excellence for Parkinson's Disease, Emory University, Atlanta, Georgia, USA
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13
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Korecki AJ, Cueva-Vargas JL, Fornes O, Agostinone J, Farkas RA, Hickmott JW, Lam SL, Mathelier A, Zhou M, Wasserman WW, Di Polo A, Simpson EM. Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. Gene Ther 2021; 28:351-372. [PMID: 33531684 PMCID: PMC8222000 DOI: 10.1038/s41434-021-00227-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Small and cell-type restricted promoters are important tools for basic and preclinical research, and clinical delivery of gene therapies. In clinical gene therapy, ophthalmic trials have been leading the field, with over 50% of ocular clinical trials using promoters that restrict expression based on cell type. Here, 19 human DNA MiniPromoters were bioinformatically designed for rAAV, tested by neonatal intravenous delivery in mouse, and successful MiniPromoters went on to be tested by intravitreal, subretinal, intrastromal, and/or intravenous delivery in adult mouse. We present promoter development as an overview for each cell type, but only show results in detail for the recommended MiniPromoters: Ple265 and Ple341 (PCP2) ON bipolar, Ple349 (PDE6H) cone, Ple253 (PITX3) corneal stroma, Ple32 (CLDN5) endothelial cells of the blood-retina barrier, Ple316 (NR2E1) Müller glia, and Ple331 (PAX6) PAX6 positive. Overall, we present a resource of new, redesigned, and improved MiniPromoters for ocular gene therapy that range in size from 784 to 2484 bp, and from weaker, equal, or stronger in strength relative to the ubiquitous control promoter smCBA. All MiniPromoters will be useful for therapies involving small regulatory RNA and DNA, and proteins ranging from 517 to 1084 amino acids, representing 62.9-90.2% of human proteins.
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Affiliation(s)
- Andrea J. Korecki
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada
| | - Jorge L. Cueva-Vargas
- grid.14848.310000 0001 2292 3357Department of Neuroscience, University of Montreal Hospital Research Centre, University of Montreal, Montreal, QC Canada
| | - Oriol Fornes
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada
| | - Jessica Agostinone
- grid.14848.310000 0001 2292 3357Department of Neuroscience, University of Montreal Hospital Research Centre, University of Montreal, Montreal, QC Canada
| | - Rachelle A. Farkas
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Jack W. Hickmott
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Siu Ling Lam
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada
| | - Anthony Mathelier
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada
| | - Michelle Zhou
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada
| | - Wyeth W. Wasserman
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Adriana Di Polo
- grid.14848.310000 0001 2292 3357Department of Neuroscience, University of Montreal Hospital Research Centre, University of Montreal, Montreal, QC Canada
| | - Elizabeth M. Simpson
- grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital, University of British Columbia, Vancouver, BC Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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14
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Mirjalili Mohanna SZ, Hickmott JW, Lam SL, Chiu NY, Lengyell TC, Tam BM, Moritz OL, Simpson EM. Germline CRISPR/Cas9-Mediated Gene Editing Prevents Vision Loss in a Novel Mouse Model of Aniridia. Mol Ther Methods Clin Dev 2020; 17:478-490. [PMID: 32258211 PMCID: PMC7114625 DOI: 10.1016/j.omtm.2020.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022]
Abstract
Aniridia is a rare eye disorder, which is caused by mutations in the paired box 6 (PAX6) gene and results in vision loss due to the lack of a long-term vision-saving therapy. One potential approach to treating aniridia is targeted CRISPR-based genome editing. To enable the Pax6 small eye (Sey) mouse model of aniridia, which carries the same mutation found in patients, for preclinical testing of CRISPR-based therapeutic approaches, we endogenously tagged the Sey allele, allowing for the differential detection of protein from each allele. We optimized a correction strategy in vitro then tested it in vivo in the germline of our new mouse to validate the causality of the Sey mutation. The genomic manipulations were analyzed by PCR, as well as by Sanger and next-generation sequencing. The mice were studied by slit lamp imaging, immunohistochemistry, and western blot analyses. We successfully achieved both in vitro and in vivo germline correction of the Sey mutation, with the former resulting in an average 34.8% ± 4.6% SD correction, and the latter in restoration of 3xFLAG-tagged PAX6 expression and normal eyes. Hence, in this study we have created a novel mouse model for aniridia, demonstrated that germline correction of the Sey mutation alone rescues the mutant phenotype, and developed an allele-distinguishing CRISPR-based strategy for aniridia.
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Affiliation(s)
- Seyedeh Zeinab Mirjalili Mohanna
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Jack W Hickmott
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nina Y Chiu
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Beatrice M Tam
- Department of Ophthalmology and Visual Sciences and Centre for Macular Research, The University of British Columbia, Vancouver, BC, Canada
| | - Orson L Moritz
- Department of Ophthalmology and Visual Sciences and Centre for Macular Research, The University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
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15
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Baumann BH, Shu W, Song Y, Simpson EM, Lakhal-Littleton S, Dunaief JL. Ferroportin-mediated iron export from vascular endothelial cells in retina and brain. Exp Eye Res 2019; 187:107728. [PMID: 31323276 PMCID: PMC6759385 DOI: 10.1016/j.exer.2019.107728] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/05/2019] [Accepted: 07/15/2019] [Indexed: 12/29/2022]
Abstract
Retinal iron accumulation has been implicated in the pathogenesis of age-related macular degeneration (AMD) and other neurodegenerative diseases. The retina and the brain are protected from the systemic circulation by the blood retinal barrier (BRB) and blood brain barrier (BBB), respectively. Iron levels within the retina and brain need to be tightly regulated to prevent oxidative injury. The method of iron entry through the retina and brain vascular endothelial cells (r&bVECs), an essential component of the BRB and BBB, is not fully understood. However, localization of the cellular iron exporter, ferroportin (Fpn), to the abluminal membrane of these cells, leads to the hypothesis that Fpn may play an important role in the import of iron across the BRB and BBB. To test this hypothesis, a mouse model with deletion of Fpn within the VECs in both the retina and the brain was developed through tail vein injection of AAV9-Ple261(CLDN5)-icre to both experimental Fpnf/f, and control Fpn+/+ mice at P21. Mice were aged to 9 mo and changes in retinal and brain iron distribution were observed. In vivo fundus imaging and quantitative serum iron detection were used for model validation. Eyes and brains were collected for immunofluorescence. Deletion of Fpn from the retinal and brain VECs leads to ferritin-L accumulation, an indicator of elevated iron levels, in the retinal and brain VECs. This occurred despite lower serum iron levels in the experimental mice. This result suggests that Fpn normally transfers iron from retinal and brain VECs into the retina and brain. These results help to better define the method of retina and brain iron import and will increase understanding of neurodegenerative diseases involving iron accumulation.
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Affiliation(s)
- Bailey H Baumann
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine at the University of Pennsylvania, 305 Stellar-Chance Laboratory, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
| | - Wanting Shu
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine at the University of Pennsylvania, 305 Stellar-Chance Laboratory, 422 Curie Blvd, Philadelphia, PA, 19104, USA; Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, No. 100 Haining Road, Shanghai, 200080, China.
| | - Ying Song
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine at the University of Pennsylvania, 305 Stellar-Chance Laboratory, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.
| | - Samira Lakhal-Littleton
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
| | - Joshua L Dunaief
- F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine at the University of Pennsylvania, 305 Stellar-Chance Laboratory, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
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16
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Peeters SB, Korecki AJ, Baldry SEL, Yang C, Tosefsky K, Balaton BP, Simpson EM, Brown CJ. How do genes that escape from X-chromosome inactivation contribute to Turner syndrome? Am J Med Genet C Semin Med Genet 2019; 181:28-35. [PMID: 30779428 DOI: 10.1002/ajmg.c.31672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/09/2018] [Indexed: 12/30/2022]
Abstract
X-chromosome inactivation generally results in dosage equivalence for expression of X-linked genes between 46,XY males and 46,XX females. The 20-30% of genes that escape silencing are thus candidates for having a role in the phenotype of Turner syndrome. Understanding which genes escape from silencing, and how they avoid this chromosome-wide inactivation is therefore an important step toward understanding Turner Syndrome. We have examined the mechanism of escape using a previously reported knock-in of a BAC containing the human escape gene RPS4X in mouse. We now demonstrate that escape from inactivation for RPS4X is already established by embryonic Day 9.5, and that both silencing and escape are faithfully maintained across the lifespan. No overt abnormalities were observed for transgenic mice up to 1 year of age despite robust transcription of the human RPS4X gene with no detectable downregulation of the mouse homolog. However, there was no significant increase in protein levels, suggesting translational compensation in the mouse. Finally, while many of the protein-coding genes have been assessed for their inactivation status, less is known about the X-linked RNA genes, and we propose that for many microRNA genes their inactivation status can be predicted as they are intronic to genes for which the inactivation status is known.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Sarah E L Baldry
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Christine Yang
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Kira Tosefsky
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Bradley P Balaton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
| | - Elizabeth M Simpson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Molecular Epigenetics Group, Life Sciences Institute, Vancouver, British Columbia, Canada
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17
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Peeters SB, Korecki AJ, Simpson EM, Brown CJ. Human cis-acting elements regulating escape from X-chromosome inactivation function in mouse. Hum Mol Genet 2019; 27:1252-1262. [PMID: 29401310 PMCID: PMC6159535 DOI: 10.1093/hmg/ddy039] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/29/2018] [Indexed: 12/18/2022] Open
Abstract
A long-standing question concerning X-chromosome inactivation (XCI) has been how some genes avoid the otherwise stable chromosome-wide heterochromatinization of the inactive X chromosome. As 20% or more of human X-linked genes escape from inactivation, such genes are an important contributor to sex differences in gene expression. Although both human and mouse have genes that escape from XCI, more genes escape in humans than mice, with human escape genes often clustering in larger domains than the single escape genes of mouse. Mouse models offer a well-characterized and readily manipulated system in which to study XCI, but given the differences in genes that escape it is unclear whether the mechanism of escape gene regulation is conserved. To address conservation of the process and the potential to identify elements by modelling human escape gene regulation using mouse, we integrated a human and a mouse BAC each containing an escape gene and flanking subject genes at the mouse X-linked Hprt gene. Escape-level expression and corresponding low promoter DNA methylation of human genes RPS4X and CITED1 demonstrated that the mouse system is capable of recognizing human elements and therefore can be used as a model for further refinement of critical elements necessary for escape from XCI in humans.
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Affiliation(s)
- Samantha B Peeters
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at British Columbia Children's Hospital, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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18
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Simpson EM, Korecki AJ, Fornes O, McGill TJ, Cueva-Vargas JL, Agostinone J, Farkas RA, Hickmott JW, Lam SL, Mathelier A, Renner LM, Stoddard J, Zhou M, Di Polo A, Neuringer M, Wasserman WW. New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina. Hum Gene Ther 2018; 30:257-272. [PMID: 30062914 PMCID: PMC6437624 DOI: 10.1089/hum.2018.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Retinal gene therapy is leading the neurological gene therapy field, with 32 ongoing clinical trials of recombinant adeno-associated virus (rAAV)–based therapies. Importantly, over 50% of those trials are using restricted promoters from human genes. Promoters that restrict expression have demonstrated increased efficacy and can limit the therapeutic to the target cells thereby reducing unwanted off-target effects. Retinal ganglion cells are a critical target in ocular gene therapy; they are involved in common diseases such as glaucoma, rare diseases such as Leber's hereditary optic neuropathy, and in revolutionary optogenetic treatments. Here, we used computational biology and mined the human genome for the best genes from which to develop a novel minimal promoter element(s) designed for expression in restricted cell types (MiniPromoter) to improve the safety and efficacy of retinal ganglion cell gene therapy. Gene selection included the use of the first available droplet-based single-cell RNA sequencing (Drop-seq) dataset, and promoter design was bioinformatically driven and informed by a wide range of genomics datasets. We tested seven promoter designs from four genes in rAAV for specificity and quantified expression strength in retinal ganglion cells in mouse, and then the single best in nonhuman primate retina. Thus, we developed a new human-DNA MiniPromoter, Ple345 (NEFL), which in combination with intravitreal delivery in rAAV9 showed specific and robust expression in the retinal ganglion cells of the nonhuman-primate rhesus macaque retina. In mouse, we also developed MiniPromoters expressing in retinal ganglion cells, the hippocampus of the brain, a pan neuronal pattern in the brain, and peripheral nerves. As single-cell transcriptomics such as Drop-seq become available for other cell types, many new opportunities for additional novel restricted MiniPromoters will present.
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Affiliation(s)
- Elizabeth M Simpson
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.,2 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,3 Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,4 Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea J Korecki
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Oriol Fornes
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.,2 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Trevor J McGill
- 5 Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon.,6 Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Jorge Luis Cueva-Vargas
- 7 Department of Neuroscience and Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, Québec, Canada
| | - Jessica Agostinone
- 7 Department of Neuroscience and Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, Québec, Canada
| | - Rachelle A Farkas
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jack W Hickmott
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.,2 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siu Ling Lam
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Mathelier
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.,2 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lauren M Renner
- 5 Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon
| | - Jonathan Stoddard
- 5 Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon
| | - Michelle Zhou
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adriana Di Polo
- 7 Department of Neuroscience and Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Université de Montréal, Montréal, Québec, Canada
| | - Martha Neuringer
- 5 Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Portland, Oregon.,6 Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon
| | - Wyeth W Wasserman
- 1 Centre for Molecular Medicine and Therapeutics at BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.,2 Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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19
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Connell M, Chen H, Jiang J, Kuan CW, Fotovati A, Chu TLH, He Z, Lengyell TC, Li H, Kroll T, Li AM, Goldowitz D, Frappart L, Ploubidou A, Patel MS, Pilarski LM, Simpson EM, Lange PF, Allan DW, Maxwell CA. HMMR acts in the PLK1-dependent spindle positioning pathway and supports neural development. eLife 2017; 6:e28672. [PMID: 28994651 PMCID: PMC5681225 DOI: 10.7554/elife.28672] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023] Open
Abstract
Oriented cell division is one mechanism progenitor cells use during development and to maintain tissue homeostasis. Common to most cell types is the asymmetric establishment and regulation of cortical NuMA-dynein complexes that position the mitotic spindle. Here, we discover that HMMR acts at centrosomes in a PLK1-dependent pathway that locates active Ran and modulates the cortical localization of NuMA-dynein complexes to correct mispositioned spindles. This pathway was discovered through the creation and analysis of Hmmr-knockout mice, which suffer neonatal lethality with defective neural development and pleiotropic phenotypes in multiple tissues. HMMR over-expression in immortalized cancer cells induces phenotypes consistent with an increase in active Ran including defects in spindle orientation. These data identify an essential role for HMMR in the PLK1-dependent regulatory pathway that orients progenitor cell division and supports neural development.
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Affiliation(s)
- Marisa Connell
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
| | - Helen Chen
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
| | - Jihong Jiang
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
| | - Chia-Wei Kuan
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - Abbas Fotovati
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
| | - Tony LH Chu
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
| | - Zhengcheng He
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
| | - Tess C Lengyell
- Centre for Molecular Medicine and TherapeuticsUniversity of British ColumbiaVancouverCanada
| | - Huaibiao Li
- Leibniz Institute on Aging—Fritz Lipmann InstituteBeutenbergstrasseGermany
| | - Torsten Kroll
- Leibniz Institute on Aging—Fritz Lipmann InstituteBeutenbergstrasseGermany
| | - Amanda M Li
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and TherapeuticsUniversity of British ColumbiaVancouverCanada
- Department of Medical GeneticsUniversity of British ColumbiaVancouverCanada
| | - Lucien Frappart
- Leibniz Institute on Aging—Fritz Lipmann InstituteBeutenbergstrasseGermany
| | - Aspasia Ploubidou
- Leibniz Institute on Aging—Fritz Lipmann InstituteBeutenbergstrasseGermany
| | - Millan S Patel
- Department of Medical GeneticsUniversity of British ColumbiaVancouverCanada
| | - Linda M Pilarski
- Cross Cancer Institute, Department of OncologyUniversity of AlbertaEdmontonCanada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and TherapeuticsUniversity of British ColumbiaVancouverCanada
- Department of Medical GeneticsUniversity of British ColumbiaVancouverCanada
| | - Philipp F Lange
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
- Michael Cuccione Childhood Cancer Research ProgramBC Children’s HospitalVancouverCanada
| | - Douglas W Allan
- Department of Cellular and Physiological SciencesLife Sciences Centre, University of British ColumbiaVancouverCanada
| | - Christopher A Maxwell
- Department of PaediatricsUniversity of British ColumbiaVancouverCanada
- Michael Cuccione Childhood Cancer Research ProgramBC Children’s HospitalVancouverCanada
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20
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Corso-Díaz X, de Leeuw CN, Alonso V, Melchers D, Wong BKY, Houtman R, Simpson EM. Co-activator candidate interactions for orphan nuclear receptor NR2E1. BMC Genomics 2016; 17:832. [PMID: 27782803 PMCID: PMC5080790 DOI: 10.1186/s12864-016-3173-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 10/18/2016] [Indexed: 12/21/2022] Open
Abstract
Background NR2E1 (Tlx) is an orphan nuclear receptor that regulates the maintenance and self-renewal of neural stem cells, and promotes tumourigenesis. Nr2e1-null mice exhibit reduced cortical and limbic structures and pronounced retinal dystrophy. NR2E1 functions mainly as a repressor of gene transcription in association with the co-repressors atrophin-1, LSD1, HDAC and BCL11A. Recent evidence suggests that NR2E1 also acts as an activator of gene transcription. However, co-activator complexes that interact with NR2E1 have not yet been identified. In order to find potential novel co-regulators for NR2E1, we used a microarray assay for real-time analysis of co-regulator–nuclear receptor interaction (MARCoNI) that contains peptides representing interaction motifs from potential co-regulatory proteins, including known co-activator nuclear receptor box sequences (LxxLL motif). Results We found that NR2E1 binds strongly to an atrophin-1 peptide (Atro box) used as positive control and to 19 other peptides that constitute candidate NR2E1 partners. Two of these proteins, p300 and androgen receptor (AR), were further validated by reciprocal pull-down assays. The specificity of NR2E1 binding to peptides in the array was evaluated using two single amino acid variants, R274G and R276Q, which disrupted the majority of the binding interactions observed with wild-type NR2E1. The decreased binding affinity of these variants to co-regulators was further validated by pull-down assays using atrophin1 as bait. Despite the high conservation of arginine 274 in vertebrates, its reduced interactions with co-regulators were not significant in vivo as determined by retinal phenotype analysis in single-copy Nr2e1-null mice carrying the variant R274G. Conclusions We showed that MARCoNI is a specific assay to test interactions of NR2E1 with candidate co-regulators. In this way, we unveiled 19 potential co-regulator partners for NR2E1, including eight co-activators. All the candidates here identified need to be further validated using in vitro and in vivo models. This assay was sensitive to point mutations in NR2E1 ligand binding domain making it useful to identify mutations and/or small molecules that alter binding of NR2E1 to protein partners. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3173-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ximena Corso-Díaz
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Genetics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada
| | - Charles N de Leeuw
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Vivian Alonso
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | | | - Bibiana K Y Wong
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - René Houtman
- PamGene International B.V., Den Bosch, The Netherlands
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada. .,Genetics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada. .,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada. .,Department of Ophthalmology and Visual Science, University of British Columbia, Vancouver, BC, V5Z 3N9, Canada.
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21
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Hickmott JW, Chen CY, Arenillas DJ, Korecki AJ, Lam SL, Molday LL, Bonaguro RJ, Zhou M, Chou AY, Mathelier A, Boye SL, Hauswirth WW, Molday RS, Wasserman WW, Simpson EM. PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina. Mol Ther Methods Clin Dev 2016; 3:16051. [PMID: 27556059 PMCID: PMC4980111 DOI: 10.1038/mtm.2016.51] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/25/2016] [Accepted: 06/13/2016] [Indexed: 12/15/2022]
Abstract
Current gene therapies predominantly use small, strong, and readily available ubiquitous promoters. However, as the field matures, the availability of small, cell-specific promoters would be greatly beneficial. Here we design seven small promoters from the human paired box 6 (PAX6) gene and test them in the adult mouse retina using recombinant adeno-associated virus. We chose the retina due to previous successes in gene therapy for blindness, and the PAX6 gene since it is: well studied; known to be driven by discrete regulatory regions; expressed in therapeutically interesting retinal cell types; and mutated in the vision-loss disorder aniridia, which is in need of improved therapy. At the PAX6 locus, 31 regulatory regions were bioinformatically predicted, and nine regulatory regions were constructed into seven MiniPromoters. Driving Emerald GFP, these MiniPromoters were packaged into recombinant adeno-associated virus, and injected intravitreally into postnatal day 14 mice. Four MiniPromoters drove consistent retinal expression in the adult mouse, driving expression in combinations of cell-types that endogenously express Pax6: ganglion, amacrine, horizontal, and Müller glia. Two PAX6-MiniPromoters drive expression in three of the four cell types that express PAX6 in the adult mouse retina. Combined, they capture all four cell types, making them potential tools for research, and PAX6-gene therapy for aniridia.
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Affiliation(s)
- Jack W Hickmott
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chih-yu Chen
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David J Arenillas
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Russell J Bonaguro
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Zhou
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice Y Chou
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sanford L Boye
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - William W Hauswirth
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
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22
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de Leeuw CN, Korecki AJ, Berry GE, Hickmott JW, Lam SL, Lengyell TC, Bonaguro RJ, Borretta LJ, Chopra V, Chou AY, D'Souza CA, Kaspieva O, Laprise S, McInerny SC, Portales-Casamar E, Swanson-Newman MI, Wong K, Yang GS, Zhou M, Jones SJM, Holt RA, Asokan A, Goldowitz D, Wasserman WW, Simpson EM. rAAV-compatible MiniPromoters for restricted expression in the brain and eye. Mol Brain 2016; 9:52. [PMID: 27164903 PMCID: PMC4862195 DOI: 10.1186/s13041-016-0232-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/30/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Small promoters that recapitulate endogenous gene expression patterns are important for basic, preclinical, and now clinical research. Recently, there has been a promising revival of gene therapy for diseases with unmet therapeutic needs. To date, most gene therapies have used viral-based ubiquitous promoters-however, promoters that restrict expression to target cells will minimize off-target side effects, broaden the palette of deliverable therapeutics, and thereby improve safety and efficacy. Here, we take steps towards filling the need for such promoters by developing a high-throughput pipeline that goes from genome-based bioinformatic design to rapid testing in vivo. METHODS For much of this work, therapeutically interesting Pleiades MiniPromoters (MiniPs; ~4 kb human DNA regulatory elements), previously tested in knock-in mice, were "cut down" to ~2.5 kb and tested in recombinant adeno-associated virus (rAAV), the virus of choice for gene therapy of the central nervous system. To evaluate our methods, we generated 29 experimental rAAV2/9 viruses carrying 19 different MiniPs, which were injected intravenously into neonatal mice to allow broad unbiased distribution, and characterized in neural tissues by X-gal immunohistochemistry for icre, or immunofluorescent detection of GFP. RESULTS The data showed that 16 of the 19 (84 %) MiniPs recapitulated the expression pattern of their design source. This included expression of: Ple67 in brain raphe nuclei; Ple155 in Purkinje cells of the cerebellum, and retinal bipolar ON cells; Ple261 in endothelial cells of brain blood vessels; and Ple264 in retinal Müller glia. CONCLUSIONS Overall, the methodology and MiniPs presented here represent important advances for basic and preclinical research, and may enable a paradigm shift in gene therapy.
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Affiliation(s)
- Charles N de Leeuw
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Garrett E Berry
- Gene Therapy Centre, University of North Carolina, Chapel Hill, NC, 27599, U.S.A
| | - Jack W Hickmott
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Siu Ling Lam
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Tess C Lengyell
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Russell J Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Lisa J Borretta
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Vikramjit Chopra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Alice Y Chou
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Cletus A D'Souza
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Olga Kaspieva
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Stéphanie Laprise
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Simone C McInerny
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Elodie Portales-Casamar
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Magdalena I Swanson-Newman
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Kaelan Wong
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - George S Yang
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Michelle Zhou
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Robert A Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada
| | - Aravind Asokan
- Gene Therapy Centre, University of North Carolina, Chapel Hill, NC, 27599, U.S.A
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, BC, V5Z 4H4, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada. .,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada.
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23
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Scalabrino ML, Boye SL, Fransen KMH, Noel JM, Dyka FM, Min SH, Ruan Q, De Leeuw CN, Simpson EM, Gregg RG, McCall MA, Peachey NS, Boye SE. Intravitreal delivery of a novel AAV vector targets ON bipolar cells and restores visual function in a mouse model of complete congenital stationary night blindness. Hum Mol Genet 2015; 24:6229-39. [PMID: 26310623 DOI: 10.1093/hmg/ddv341] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Adeno-associated virus (AAV) effectively targets therapeutic genes to photoreceptors, pigment epithelia, Müller glia and ganglion cells of the retina. To date, no one has shown the ability to correct, with gene replacement, an inherent defect in bipolar cells (BCs), the excitatory interneurons of the retina. Targeting BCs with gene replacement has been difficult primarily due to the relative inaccessibility of BCs to standard AAV vectors. This approach would be useful for restoration of vision in patients with complete congenital stationary night blindness (CSNB1), where signaling through the ON BCs is eliminated due to mutations in their G-protein-coupled cascade genes. For example, the majority of CSNB1 patients carry a mutation in nyctalopin (NYX), which encodes a protein essential for proper localization of the TRPM1 cation channel required for ON BC light-evoked depolarization. As a group, CSNB1 patients have a normal electroretinogram (ERG) a-wave, indicative of photoreceptor function, but lack a b-wave due to defects in ON BC signaling. Despite retinal dysfunction, the retinas of CSNB1 patients do not degenerate. The Nyx(nob) mouse model of CSNB1 faithfully mimics this phenotype. Here, we show that intravitreally injected, rationally designed AAV2(quadY-F+T-V) containing a novel 'Ple155' promoter drives either GFP or YFP_Nyx in postnatal Nyx(nob) mice. In treated Nyx(nob) retina, robust and targeted Nyx transgene expression in ON BCs partially restored the ERG b-wave and, at the cellular level, signaling in ON BCs. Our results support the potential for gene delivery to BCs and gene replacement therapy in human CSNB1.
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Affiliation(s)
| | | | | | | | | | | | | | - Charles N De Leeuw
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Ronald G Gregg
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA
| | - Maureen A McCall
- Department of Ophthalmology and Visual Sciences, Department of Anatomical Sciences and Neurobiology and
| | - Neal S Peachey
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA and Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
| | - Shannon E Boye
- Department of Ophthalmology and, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA,
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Schmouth JF, Arenillas D, Corso-Díaz X, Xie YY, Bohacec S, Banks KG, Bonaguro RJ, Wong SH, Jones SJM, Marra MA, Simpson EM, Wasserman WW. Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development. BMC Genomics 2015. [PMID: 26204903 PMCID: PMC4512088 DOI: 10.1186/s12864-015-1770-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Nr2e1 (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundreds of target genes, and bind more than 300 co-interacting proteins. However, recognition of the critical role of Nr2e1 in neural stem cells and neocortex development is relatively recent, thus the molecular mechanisms involved for this nuclear receptor are only beginning to be understood. Serial analysis of gene expression (SAGE), has given researchers both qualitative and quantitative information pertaining to biological processes. Thus, in this work, six LongSAGE mouse libraries were generated from laser microdissected tissue samples of dorsal VZ/SVZ (ventricular zone and subventricular zone) from the telencephalon of wild-type (Wt) and Nr2e1-null embryos at the critical development ages E13.5, E15.5, and E17.5. We then used a novel approach, implementing multiple computational methods followed by biological validation to further our understanding of Nr2e1 in neocortex development. Results In this work, we have generated a list of 1279 genes that are differentially expressed in response to altered Nr2e1 expression during in vivo neocortex development. We have refined this list to 64 candidate direct-targets of NR2E1. Our data suggested distinct roles for Nr2e1 during different neocortex developmental stages. Most importantly, our results suggest a possible novel pathway by which Nr2e1 regulates neurogenesis, which includes Lhx2 as one of the candidate direct-target genes, and SOX9 as a co-interactor. Conclusions In conclusion, we have provided new candidate interacting partners and numerous well-developed testable hypotheses for understanding the pathways by which Nr2e1 functions to regulate neocortex development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1770-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean-François Schmouth
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada. .,Genetics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada. .,Current address: Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, H3A 2B4, Canada.
| | - David Arenillas
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Ximena Corso-Díaz
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada. .,Genetics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada.
| | - Yuan-Yun Xie
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Slavita Bohacec
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Kathleen G Banks
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Russell J Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Siaw H Wong
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Steven J M Jones
- Genetics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada. .,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada. .,Genetics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada. .,Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2A1, Canada.
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada. .,Genetics Graduate Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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Corso-Díaz X, Simpson EM. Nr2e1 regulates retinal lamination and the development of Müller glia, S-cones, and glycineric amacrine cells during retinogenesis. Mol Brain 2015; 8:37. [PMID: 26092486 PMCID: PMC4475312 DOI: 10.1186/s13041-015-0126-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 05/23/2015] [Indexed: 12/25/2022] Open
Abstract
Background Nr2e1 is a nuclear receptor crucial for neural stem cell proliferation and maintenance. In the retina, lack of Nr2e1 results in premature neurogenesis, aberrant blood vessel formation and dystrophy. However, the specific role of Nr2e1 in the development of different retinal cell types and its cell-autonomous and non-cell autonomous function(s) during eye development are poorly understood. Results Here, we studied the retinas of P7 and P21 Nr2e1frc/frc mice and Nr2e1+/+ ↔ Nr2e1frc/frc chimeras. We hypothesized that Nr2e1 differentially regulates the development of various retinal cell types, and thus the cellular composition of Nr2e1frc/frc retinas does not simply reflect an overrepresentation of cells born early and underrepresentation of cells born later as a consequence of premature neurogenesis. In agreement with our hypothesis, lack of Nr2e1 resulted in increased numbers of glycinergic amacrine cells with no apparent increase in other amacrine sub-types, normal numbers of Müller glia, the last cell-type to be generated, and increased numbers of Nr2e1frc/frc S-cones in chimeras. Furthermore, Nr2e1frc/frc Müller glia were mispositioned in the retina and misexpressed the ganglion cell-specific transcription factor Brn3a. Nr2e1frc/frc retinas also displayed lamination defects including an ectopic neuropil forming an additional inner plexiform layer. In chimeric mice, retinal thickness was rescued by 34 % of wild-type cells and Nr2e1frc/frc dystrophy-related phenotypes were no longer evident. However, the formation of an ectopic neuropil, misexpression of Brn3a in Müller glia, and abnormal cell numbers in the inner and outer nuclear layers at P7 were not rescued by wild-type cells. Conclusions Together, these results show that Nr2e1, in addition to having a role in preventing premature cell cycle exit, participates in several other developmental processes during retinogenesis including neurite organization in the inner retina and development of glycinergic amacrine cells, S-cones, and Müller glia. Nr2e1 also regulates various aspects of Müller glia differentiation cell-autonomously. However, Nr2e1 does not have a cell-autonomous role in preventing retinal dystrophy. Thus, Nr2e1 regulates processes involved in neurite development and terminal retinal cell differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s13041-015-0126-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ximena Corso-Díaz
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, V5Z 4H4, BC, Canada.,Genetics Graduate Program, University of British Columbia, Vancouver, V6T 1Z2, BC, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, 950 W 28 Ave, Vancouver, V5Z 4H4, BC, Canada. .,Genetics Graduate Program, University of British Columbia, Vancouver, V6T 1Z2, BC, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada. .,Department of Psychiatry, University of British Columbia, Vancouver, V6T 2A1, BC, Canada.
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White ML, Boye SL, Dyka FM, Fransen KM, de Leeuw CN, Simpson EM, Gregg RG, McCall MA, Peachey NS, Boye SE. 498. Optimization of rAAV Targets ON Bipolar Cells and Rescues the nobnyx Mouse Model of X-Linked Congenital Stationary Night Blindness. Mol Ther 2015. [DOI: 10.1016/s1525-0016(16)34107-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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27
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Hickmott JW, Chen CY, Arenillas DJ, Li Y, Molday LL, Korecki AJ, Ling Lam S, Ling Lam S, Bonaguro RJ, Zhou M, Chan AY, Boye SL, Hauswirth WW, Molday RS, Wasserman WW, Simpson EM. 599. Deep Informatics Utilized to Design MiniPromoters for Driving PAX6-Like Retinal Expression with AAV. Mol Ther 2015. [DOI: 10.1016/s1525-0016(16)34208-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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28
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de Leeuw CN, Dyka FM, Boye SL, Laprise S, Zhou M, Chou AY, Borretta L, McInerny SC, Banks KG, Portales-Casamar E, Swanson MI, D’Souza CA, Boye SE, Jones SJM, Holt RA, Goldowitz D, Hauswirth WW, Wasserman WW, Simpson EM. Targeted CNS Delivery Using Human MiniPromoters and Demonstrated Compatibility with Adeno-Associated Viral Vectors. Mol Ther Methods Clin Dev 2014; 1:5. [PMID: 24761428 PMCID: PMC3992516 DOI: 10.1038/mtm.2013.5] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/05/2013] [Indexed: 01/21/2023]
Abstract
Critical for human gene therapy is the availability of small promoter tools to drive gene expression in a highly specific and reproducible manner. We tackled this challenge by developing human DNA MiniPromoters using computational biology and phylogenetic conservation. MiniPromoters were tested in mouse as single-copy knock-ins at the Hprt locus on the X Chromosome, and evaluated for lacZ reporter expression in CNS and non-CNS tissue. Eighteen novel MiniPromoters driving expression in mouse brain were identified, two MiniPromoters for driving pan-neuronal expression, and 17 MiniPromoters for the mouse eye. Key areas of therapeutic interest were represented in this set: the cerebral cortex, embryonic hypothalamus, spinal cord, bipolar and ganglion cells of the retina, and skeletal muscle. We also demonstrated that three retinal ganglion cell MiniPromoters exhibit similar cell-type specificity when delivered via adeno-associated virus (AAV) vectors intravitreally. We conclude that our methodology and characterization has resulted in desirable expression characteristics that are intrinsic to the MiniPromoter, not dictated by copy number effects or genomic location, and results in constructs predisposed to success in AAV. These MiniPromoters are immediately applicable for pre-clinical studies towards gene therapy in humans, and are publicly available to facilitate basic and clinical research, and human gene therapy.
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Affiliation(s)
- Charles N de Leeuw
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Frank M Dyka
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Sanford L Boye
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Stéphanie Laprise
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Zhou
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alice Y Chou
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa Borretta
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simone C McInerny
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathleen G Banks
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elodie Portales-Casamar
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Magdalena I Swanson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cletus A D’Souza
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Shannon E Boye
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Steven JM Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Robert A Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - William W Hauswirth
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
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Schmouth JF, Castellarin M, Laprise S, Banks KG, Bonaguro RJ, McInerny SC, Borretta L, Amirabbasi M, Korecki AJ, Portales-Casamar E, Wilson G, Dreolini L, Jones SJM, Wasserman WW, Goldowitz D, Holt RA, Simpson EM. Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice. BMC Biol 2013; 11:106. [PMID: 24124870 PMCID: PMC4015596 DOI: 10.1186/1741-7007-11-106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/30/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In this study, we build upon our HuGX ('high-throughput human genes on the X chromosome') strategy to expand our understanding of human gene regulation in vivo. RESULTS In all, ten human genes known to express in therapeutically important brain regions were chosen for study. For eight of these genes, human bacterial artificial chromosome clones were identified, retrofitted with a reporter, knocked single-copy into the Hprt locus in mouse embryonic stem cells, and mouse strains derived. Five of these human genes expressed in mouse, and all expressed in the adult brain region for which they were chosen. This defined the boundaries of the genomic DNA sufficient for brain expression, and refined our knowledge regarding the complexity of gene regulation. We also characterized for the first time the expression of human MAOA and NR2F2, two genes for which the mouse homologs have been extensively studied in the central nervous system (CNS), and AMOTL1 and NOV, for which roles in CNS have been unclear. CONCLUSIONS We have demonstrated the use of the HuGX strategy to functionally delineate non-coding-regulatory regions of therapeutically important human brain genes. Our results also show that a careful investigation, using publicly available resources and bioinformatics, can lead to accurate predictions of gene expression.
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Affiliation(s)
- Jean-François Schmouth
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
| | - Mauro Castellarin
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Stéphanie Laprise
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Kathleen G Banks
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Russell J Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Simone C McInerny
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Lisa Borretta
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Mahsa Amirabbasi
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Andrea J Korecki
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Elodie Portales-Casamar
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Gary Wilson
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Lisa Dreolini
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
| | - Steven JM Jones
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Robert A Holt
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2A1, Canada
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2A1, Canada
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Yang C, McLeod AJ, Cotton AM, de Leeuw CN, Laprise S, Banks KG, Simpson EM, Brown CJ. Targeting of >1.5 Mb of human DNA into the mouse X chromosome reveals presence of cis-acting regulators of epigenetic silencing. Genetics 2012; 192:1281-93. [PMID: 23023002 PMCID: PMC3512139 DOI: 10.1534/genetics.112.143743] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/17/2012] [Indexed: 12/18/2022] Open
Abstract
Regulatory sequences can influence the expression of flanking genes over long distances, and X chromosome inactivation is a classic example of cis-acting epigenetic gene regulation. Knock-ins directed to the Mus musculus Hprt locus offer a unique opportunity to analyze the spread of silencing into different human DNA sequences in the identical genomic environment. X chromosome inactivation of four knock-in constructs, including bacterial artificial chromosome (BAC) integrations of over 195 kb, was demonstrated by both the lack of expression from the inactive X chromosome in females with nonrandom X chromosome inactivation and promoter DNA methylation of the human transgene in females. We further utilized promoter DNA methylation to assess the inactivation status of 74 human reporter constructs comprising >1.5 Mb of DNA. Of the 47 genes examined, only the PHB gene showed female DNA hypomethylation approaching the level seen in males, and escape from X chromosome inactivation was verified by demonstration of expression from the inactive X chromosome. Integration of PHB resulted in lower DNA methylation of the flanking HPRT promoter in females, suggesting the action of a dominant cis-acting escape element. Female-specific DNA hypermethylation of CpG islands not associated with promoters implies a widespread imposition of DNA methylation during X chromosome inactivation; yet transgenes demonstrated differential capacities to accumulate DNA methylation when integrated into the identical location on the inactive X chromosome, suggesting additional cis-acting sequence effects. As only one of the human transgenes analyzed escaped X chromosome inactivation, we conclude that elements permitting ongoing expression from the inactive X are rare in the human genome.
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Affiliation(s)
- Christine Yang
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Andrea J. McLeod
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Allison M. Cotton
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Charles N. de Leeuw
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Stéphanie Laprise
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kathleen G. Banks
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Department of Medical Genetics, Department of Psychiatry, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Carolyn J. Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
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Corso-Díaz X, Borrie AE, Bonaguro R, Schuetz JM, Rosenberg T, Jensen H, Brooks BP, MacDonald IM, Pasutto F, Walter MA, Grønskov K, Brooks-Wilson A, Simpson EM. Absence of NR2E1 mutations in patients with aniridia. Mol Vis 2012; 18:2770-82. [PMID: 23213277 PMCID: PMC3513187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 11/20/2012] [Indexed: 11/12/2022] Open
Abstract
PURPOSE Nuclear receptor 2E1 (NR2E1) is a transcription factor with many roles during eye development and thus may be responsible for the occurrence of certain congenital eye disorders in humans. To test this hypothesis, we screened NR2E1 for candidate mutations in patients with aniridia and other congenital ocular malformations (anterior segment dysgenesis, congenital optic nerve malformation, and microphthalmia). METHODS The NR2E1 coding region, 5' and 3' untranslated regions (UTRs), exon flanking regions including consensus splice sites, and six evolutionarily conserved non-coding candidate regulatory regions were analyzed by sequencing 58 probands with aniridia of whom 42 were negative for PAX6 mutations. Nineteen probands with anterior segment dysgenesis, one proband with optic nerve malformation, and two probands with microphthalmia were also sequenced. The control population comprised 376 healthy individuals. All sequences were analyzed against the GenBank sequence AL078596.8 for NR2E1. In addition, the coding region and flanking intronic sequences of FOXE3, FOXC1, PITX2, CYP1B1, PAX6, and B3GALTL were sequenced in one patient and his relatives. RESULTS Sequencing analysis showed 17 NR2E1 variants including two novel rare non-coding variants (g.-1507G>A, g.14258C>T), and one novel rare coding variant (p.Arg274Gly). The latter was present in a male diagnosed with Peters' anomaly who subsequently was found to have a known causative mutation for Peters' plus syndrome in B3GALTL (c.660+1G>A). In addition, the NR2E1 novel rare variant Arg274Gly was present in the unaffected mother of the patient but absent in 746 control chromosomes. CONCLUSIONS We eliminated a major role for NR2E1 regulatory and coding mutations in aniridia and found a novel rare coding variant in NR2E1. In addition, we found no coding region variation in the control population for NR2E1, which further supports its previously reported high level of conservation and low genetic diversity. Future NR2E1 studies in ocular disease groups such as those involving retinal and optic nerve abnormalities should be undertaken to determine whether NR2E1 plays a role in these conditions.
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Affiliation(s)
- Ximena Corso-Díaz
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada,Genetics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Adrienne E. Borrie
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Russell Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Johanna M. Schuetz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Canada’s Michael Smith’s Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Thomas Rosenberg
- National Eye Clinic for the Visually Impaired, The Kennedy Center, Glostrup, Denmark
| | - Hanne Jensen
- National Eye Clinic for the Visually Impaired, The Kennedy Center, Glostrup, Denmark,Department of Ophthalmology, Glostrup Hospital, University of Copenhagen, Glostrup, Denmark
| | - Brian P. Brooks
- National Eye Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - Ian M. MacDonald
- Department of Ophthalmology, University of Alberta, Edmonton, AB, Canada
| | - Francesca Pasutto
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Michael A. Walter
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Karen Grønskov
- Center for Applied Human Molecular Genetics, The Kennedy Center, Rigshospitalet, Glostrup, Denmark,Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Angela Brooks-Wilson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Canada’s Michael Smith’s Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada,Genetics Graduate Program, University of British Columbia, Vancouver, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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32
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Murray SA, Eppig JT, Smedley D, Simpson EM, Rosenthal N. Erratum to: Beyond knockouts: cre resources for conditional mutagenesis. Mamm Genome 2012. [DOI: 10.1007/s00335-012-9434-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Kent Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Francis Stewart A, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura KI, Yoshinaga Y, Wurst W. The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome 2012; 23:580-6. [PMID: 22968824 PMCID: PMC3463800 DOI: 10.1007/s00335-012-9422-2] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 07/20/2012] [Indexed: 11/16/2022]
Abstract
In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more than 17,400 mutant murine embryonic stem (ES) cell clones and more than 1,700 mutant mouse strains, most of them conditional. A common IKMC web portal (www.knockoutmouse.org) has been established, allowing easy access to this unparalleled biological resource. The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research.
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Affiliation(s)
- Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Abdelkader Ayadi
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - James F. Battey
- National Institute on Deafness and Other Communication Disorders (NIH), Bethesda, MD 20892 USA
| | - Cindy Bell
- Genome Canada, Ottawa, ON K2P 1P1 Canada
| | - Marie-Christine Birling
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Joanna Bottomley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Steve D. Brown
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - Antje Bürger
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | | | - Wendy Bushell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Christian Desaintes
- Infectious Diseases and Public Health, European Commission, DG Research & Innovation, 1049 Brussels, Belgium
| | - Brendan Doe
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, 00015 Rome, Italy
| | - Aris Economides
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | | | - Richard H. Finnell
- The Texas A&M Institute for Genomic Medicine, College Station, TX 77843-4485 USA
- University of Texas at Austin, Austin, TX 78712 USA
| | | | - Martin Fray
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - David Frendewey
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Roland H. Friedel
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
- Icahn Medical Institute, The Mount Sinai Hospital, New York, NY 10029 USA
| | - Frank G. Grosveld
- Department of Cell Biology, Center of Biomedical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Jens Hansen
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Yann Hérault
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Geoffrey Hicks
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E OV9 Canada
| | - Andreas Hörlein
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Richard Houghton
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Danny Huylebroeck
- Department of Development and Regeneration, Faculty of Medicine, University of Leuven (KU Leuven), 3000 Leuven, Belgium
| | - Vivek Iyer
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | | | - Cornelia Kaloff
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Karen Kennedy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Manousos Koutsourakis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - K. C. Kent Lloyd
- Mouse Biology Program, School of Veterinary Medicine, University of California, Davis, CA 95616 USA
| | - Susan Marschall
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jeremy Mason
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Colin McKerlie
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Michael P. McLeod
- The Texas A&M Institute for Genomic Medicine, College Station, TX 77843-4485 USA
| | - Harald von Melchner
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - Mark Moore
- National Institutes of Health, Bethesda, MD 20205 USA
| | - Alejandro O. Mujica
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Andras Nagy
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON M5G 1X5 Canada
| | - Mikhail Nefedov
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | - Lauryl M. Nutter
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Guillaume Pavlovic
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | | | - Jonathan Pollock
- Division of Basic Neuroscience and Research, National Institute of Drug Abuse (NIDA), Bethesda, MD 20892-0001 USA
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Derrick E. Rancourt
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Marcello Raspa
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, 00015 Rome, Italy
| | - Jacques E. Remacle
- Infectious Diseases and Public Health, European Commission, DG Research & Innovation, 1049 Brussels, Belgium
| | | | - Barry Rosen
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Nadia Rosenthal
- European Molecular Biology Laboratory (EMBL), Monterotondo, 00015 Rome, Italy
| | - Janet Rossant
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Patricia Ruiz Noppinger
- Centre for Cardiovascular Research, Department of Vertebrate Genomics, Charité, 10115 Berlin, Germany
| | - Ed Ryder
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Joel Zupicich Schick
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Frank Schnütgen
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - Paul Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG UK
| | - Claudia Seisenberger
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Mohammed Selloum
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Elizabeth M. Simpson
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Damian Smedley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
- European Bioinformatics Institute (EBI), Hinxton, Cambridge, CB10 1ST UK
| | | | - A. Francis Stewart
- Biotechnology Center (BIOTEC) of the Technische Universität Dresden, 01307 Dresden, Germany
| | - Kevin Stone
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Kate Swan
- Genome Canada, Ottawa, ON K2P 1P1 Canada
| | | | - Lydia Teboul
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | | | - David Valenzuela
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Anthony P. West
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Ken-ichi Yamamura
- Division of Developmental Genetics, Center for Animal Resources and Development, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, 860-0811 Japan
| | - Yuko Yoshinaga
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
- Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- Deutsches Zentrum fuer Neurodegenerative Erkrankungen e.V. (DZNE) Site Munich, 80336 Munich, Germany
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Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XYC, Dickman CTD, Fulton DL, Lim JS, Schnabl JM, Ramos OHP, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EWF, Kist R, Wilson MSC, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HDC, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SWZ, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW. The transcription factor encyclopedia. Genome Biol 2012; 13:R24. [PMID: 22458515 PMCID: PMC3439975 DOI: 10.1186/gb-2012-13-3-r24] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/19/2012] [Accepted: 03/29/2012] [Indexed: 12/20/2022] Open
Abstract
Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.
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Affiliation(s)
- Dimas Yusuf
- Department of Medical Genetics, Faculty of Medicine, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
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Schmouth JF, Bonaguro RJ, Corso-Diaz X, Simpson EM. Modelling human regulatory variation in mouse: finding the function in genome-wide association studies and whole-genome sequencing. PLoS Genet 2012; 8:e1002544. [PMID: 22396661 PMCID: PMC3291530 DOI: 10.1371/journal.pgen.1002544] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
An increasing body of literature from genome-wide association studies and human whole-genome sequencing highlights the identification of large numbers of candidate regulatory variants of potential therapeutic interest in numerous diseases. Our relatively poor understanding of the functions of non-coding genomic sequence, and the slow and laborious process of experimental validation of the functional significance of human regulatory variants, limits our ability to fully benefit from this information in our efforts to comprehend human disease. Humanized mouse models (HuMMs), in which human genes are introduced into the mouse, suggest an approach to this problem. In the past, HuMMs have been used successfully to study human disease variants; e.g., the complex genetic condition arising from Down syndrome, common monogenic disorders such as Huntington disease and β-thalassemia, and cancer susceptibility genes such as BRCA1. In this commentary, we highlight a novel method for high-throughput single-copy site-specific generation of HuMMs entitled High-throughput Human Genes on the X Chromosome (HuGX). This method can be applied to most human genes for which a bacterial artificial chromosome (BAC) construct can be derived and a mouse-null allele exists. This strategy comprises (1) the use of recombineering technology to create a human variant-harbouring BAC, (2) knock-in of this BAC into the mouse genome using Hprt docking technology, and (3) allele comparison by interspecies complementation. We demonstrate the throughput of the HuGX method by generating a series of seven different alleles for the human NR2E1 gene at Hprt. In future challenges, we consider the current limitations of experimental approaches and call for a concerted effort by the genetics community, for both human and mouse, to solve the challenge of the functional analysis of human regulatory variation.
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Affiliation(s)
- Jean-François Schmouth
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, Canada
| | - Russell J. Bonaguro
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Ximena Corso-Diaz
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, Canada
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Genetics Graduate Program, University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, Canada
- * E-mail:
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Aubrecht J, Goad MEP, Czopik AK, Lerner CP, Johnson KA, Simpson EM, Schiestl RH. A high G418-resistant neo(R) transgenic mouse and mouse embryonic fibroblast (MEF) feeder layers for cytotoxicity and gene targeting in vivo and in vitro. Drug Chem Toxicol 2011; 34:433-9. [PMID: 21740348 DOI: 10.3109/01480545.2010.544316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Aminoglycoside antibiotics have been in use since 1944 with the discovery of streptomycin. The aim of this study was to derive a new, highly resistant multicopy neo(R) transgenic mouse strain, named TgN3Ems, by random insertion of the plasmid, pPGKneobpA, and compare the level of drug resistance of wild-type and transgenic mice in vivo and corresponding primary mouse embryonic fibroblasts (MEFs) in vitro to a model neomycin analog, G418. The expression neoR in transgenic animals caused a 5-fold increase in the approximate lethal dose of G418, compared to wild type. No adverse pathological changes were found for the transgenic mice treated with G418, as they all died within minutes after injection. In contrast, the G418 treatment of wild-type mice resulted in a marked liver and kidney toxicity detected microscopically and via increases of serum biomarkers for liver and kidney damage. In addition, there was a mild bone marrow and lymphoid depletion. In in vitro studies, the transgenic MEFs survived 20-fold higher G418 levels, compared to the wild-type MEF cells. Therefore, TgN3Ems transgenic mice could be used as a source of G418-resistant feeder cells for gene targeting. Since the expression of drug-resistance genes in transgenic animals confers resistance to toxicity, the TgN3Ems mice might serve as a tool applicable in drug design.
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Affiliation(s)
- Jiri Aubrecht
- Harvard School of Public Health, Boston, Massachusetts, USA
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Wong BKY, Hossain SM, Trinh E, Ottmann GA, Budaghzadeh S, Zheng QY, Simpson EM. Hyperactivity, startle reactivity and cell-proliferation deficits are resistant to chronic lithium treatment in adult Nr2e1(frc/frc) mice. Genes Brain Behav 2010; 9:681-94. [PMID: 20497236 DOI: 10.1111/j.1601-183x.2010.00602.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The NR2E1 region on Chromosome 6q21-22 has been repeatedly linked to bipolar disorder (BP) and NR2E1 has been associated with BP, and more specifically bipolar I disorder (BPI). In addition, patient sequencing has shown an enrichment of rare candidate-regulatory variants. Interestingly, mice carrying either spontaneous (Nr2e1(frc) ) or targeted (Tlx(-) ) deletions of Nr2e1 (here collectively known as Nr2e1-null) show similar neurological and behavioral anomalies, including hypoplasia of the cerebrum, reduced neural stem cell proliferation, extreme aggression and deficits in fear conditioning; these are the traits that have been observed in some patients with BP. Thus, NR2E1 is a positional and functional candidate for a role in BP. However, no Nr2e1-null mice have been fully evaluated for behaviors used to model BP in rodents or pharmacological responses to drugs effective in treating BP symptoms. In this study we examine Nr2e1(frc/frc) mice, homozygous for the spontaneous deletion, for abnormalities in activity, learning and information processing, and cell proliferation; these are the phenotypes that are either affected in patients with BP or commonly assessed in rodent models of BP. The effect of lithium, a drug used to treat BP, was also evaluated for its ability to attenuate Nr2e1(frc/frc) behavioral and neural stem cell-proliferation phenotypes. We show for the first time that Nr2e1-null mice exhibit extreme hyperactivity in the open field as early as postnatal day 18 and in the home cage, deficits in open-field habituation and passive avoidance, and surprisingly, an absence of acoustic startle. We observed a reduction in neural stem/progenitor cell proliferation in Nr2e1(frc/frc) mice, similar to that seen in other Nr2e1-null strains. These behavioral and cell-proliferation phenotypes were resistant to chronic-adult-lithium treatment. Thus, Nr2e1(frc/frc) mice exhibit behavioral traits used to model BP in rodents, but our results do not support Nr2e1(frc/frc) mice as pharmacological models for BP.
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Affiliation(s)
- B K Y Wong
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Milisavljevic M, Hearty T, Wong TYT, Portales-Casamar E, Simpson EM, Wasserman WW. Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies. Mamm Genome 2010; 21:224-30. [PMID: 20411264 DOI: 10.1007/s00335-010-9258-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 03/31/2010] [Indexed: 11/27/2022]
Abstract
Laboratory Animal Management Assistant (LAMA) is an internet-based system for tracking large laboratory mouse colonies. It has a user-friendly interface with powerful search capabilities that ease day-to-day tasks such as tracking breeding cages and weaning litters. LAMA was originally developed to manage hundreds of new mouse strains generated by a large functional genomics program, the Pleiades Promoter Project ( http://www.pleiades.org ). The software system has proven to be highly flexible, suitable for diverse management approaches to mouse colonies. It allows custom tagging and grouping of animals, simplifying project-specific handling and access to data. Finally, LAMA was developed in close collaboration with mouse technicians to ease the transition from paper- or Excel-based management systems to computerized tracking, allowing data export in a popular spreadsheet format and automatic printing of cage cards. LAMA is an open-access software tool, freely available to the research community at http://launchpad.net/mousedb .
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Affiliation(s)
- Marko Milisavljevic
- Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada
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Mazarei G, Neal SJ, Becanovic K, Luthi-Carter R, Simpson EM, Leavitt BR. Expression analysis of novel striatal-enriched genes in Huntington disease. Hum Mol Genet 2009; 19:609-22. [PMID: 19934114 DOI: 10.1093/hmg/ddp527] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Selective degeneration of striatal neurons is a pathologic hallmark of Huntington disease (HD). The exact mechanism(s) behind this specific neurodegeneration is still unknown. Expression studies of diseased human post-mortem brain, as well as different mouse models exhibiting striatal degeneration, have demonstrated changes in the expression of many important genes with a large proportion of changes being observed in the striatal-enriched genes. These investigations have raised questions about how enrichment of particular transcripts in the striatum can lead to its selective vulnerability to neurodegeneration. Monitoring the expression changes of striatal-enriched genes during the course of the disease may be informative about their potential involvement in selective degeneration. In this study, we analyzed a Serial Analysis of Gene Expression (SAGE) database (www.mouseatlas.org) and compared the mouse striatum to 18 other brain regions to generate a novel list of striatal-enriched transcripts. These novel striatal-enriched transcripts were subsequently evaluated for expression changes in the YAC128 mouse model of HD, and differentially expressed transcripts were further examined in human post-mortem caudate samples. We identified transcripts with altered expression in YAC128 mice, which also showed consistent expression changes in human post-mortem tissue. The identification of novel striatal-enriched genes with altered expression in HD offers new avenues of study, leading towards a better understanding of specific pathways involved in the selective degeneration of striatal neurons in HD.
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Affiliation(s)
- Gelareh Mazarei
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
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Affiliation(s)
- Elizabeth M Simpson
- Department of Medicine, Section of Rheumatology, Medical College of Georgia, Augusta, Georgia 30912, USA
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Kumar RA, McGhee KA, Leach S, Bonaguro R, Maclean A, Aguirre-Hernandez R, Abrahams BS, Coccaro EF, Hodgins S, Turecki G, Condon A, Muir WJ, Brooks-Wilson AR, Blackwood DH, Simpson EM. Initial association of NR2E1 with bipolar disorder and identification of candidate mutations in bipolar disorder, schizophrenia, and aggression through resequencing. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:880-9. [PMID: 18205168 DOI: 10.1002/ajmg.b.30696] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nuclear receptor 2E1 gene (NR2E1) resides within a 6q21-22 locus for bipolar disorder and schizophrenia. Mice deleted for Nr2e1 show altered neurogenesis, cortical and limbic abnormalities, aggression, hyperexcitability, and cognitive impairment. NR2E1 is therefore a positional and functional candidate for involvement in mental illness. We performed association analyses in 394 patients with bipolar disorder, 396 with schizophrenia, and 479 controls using six common markers and haplotypes. We also performed a comprehensive mutation screen of NR2E1, resequencing its entire coding region, complete 5' and 3' untranslated regions, consensus splice-sites, and evolutionarily conserved regions in 126 humans with bipolar disorder, schizophrenia, or aggressive disorders. NR2E1 was associated with bipolar disorder I and II [odds ratio (OR = 0.77, P = 0.013), bipolar disorder I (OR = 0.77, P = 0.015), bipolar disorder in females (OR = 0.72, P = 0.009), and with age at onset < or = 25 years (OR = 0.67, P = 0.006)], all of which remained significant after correcting for multiple comparisons. We identified eight novel candidate mutations that were absent in 325 controls; four of these were predicted to alter known neural transcription factor binding sites. Analyses of NR2E1 mRNA in human brain revealed forebrain-specific transcription. The data presented support the hypothesis that genetic variation at NR2E1 may be associated with susceptibility to brain-behavior disorders.
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Affiliation(s)
- Ravinesh A Kumar
- Centre for Molecular Medicine & Therapeutics and Child & Family Research Institute, Vancouver, British Columbia, Canada
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D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LLC, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJM. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci 2008; 9:66. [PMID: 18625066 PMCID: PMC2483290 DOI: 10.1186/1471-2202-9-66] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Accepted: 07/14/2008] [Indexed: 11/24/2022] Open
Abstract
Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain. Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.
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Affiliation(s)
- Cletus A D'Souza
- Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave - Suite 100, Vancouver, BC, V5Z 4E6, Canada.
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Oberlander TF, Bonaguro RJ, Misri S, Papsdorf M, Ross CJD, Simpson EM. Infant serotonin transporter (SLC6A4) promoter genotype is associated with adverse neonatal outcomes after prenatal exposure to serotonin reuptake inhibitor medications. Mol Psychiatry 2008; 13:65-73. [PMID: 17519929 DOI: 10.1038/sj.mp.4002007] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reduced Apgar scores and birth weight, increased risk of respiratory distress, jitteriness and increased tone have been reported in up to 30% of neonates with prenatal exposure to serotonin reuptake inhibitor (SRI) antidepressant medications. In adults, effects of these medications may be related to the genotype for the serotonin transporter (SLC6A4) promoter. In this study we investigated whether SLC6A4 genotype influences the risk for adverse outcomes in neonates with prenatal SRI exposure. Neonatal outcomes including Apgar scores, birth weight, gestational age at birth, symptoms of poor neonatal adaptation and genotype for SLC6A4 were determined in 37 prenatally SRI exposed neonates and compared with 47 non-exposed neonates. Reduced 5 min Apgar scores were observed in exposed neonates and this was moderated by the ss genotype (P<0.001). Birth weight was lower in exposed ls neonates (P=0.008). Risk for respiratory symptoms (respiratory distress and rapid breathing) was higher in exposed neonates with the ll genotype compared to non-exposed neonates (P<0.05) and risk for neuromotor symptoms increased in exposed ss neonates (P<0.026). These relationships remained when controlling for maternal mood during pregnancy, length of gestational medication exposure and gestational age at birth and cesarean section rate. Prenatal SRI exposure was associated with adverse neonatal outcomes and these effects were moderated by infant SLC6A4 genotype. Relationships between polymorphisms and specific outcomes varied during the neonatal period, suggesting that beyond apparent gene-medication interactions, multiple mechanisms contribute to adverse neonatal outcomes following prenatal SRI exposure.
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Affiliation(s)
- T F Oberlander
- Early Human Experience Unit, Department of Pediatrics, Centre for Community Child Health Research, University of British Columbia, Vancouver, BC, Canada.
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Kumar RA, Everman DB, Morgan CT, Slavotinek A, Schwartz CE, Simpson EM. Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes. BMC Med Genet 2007; 8:48. [PMID: 17655765 PMCID: PMC1950490 DOI: 10.1186/1471-2350-8-48] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 07/26/2007] [Indexed: 11/15/2022]
Abstract
Background A disruption of sorting nexin 3 (SNX3) on 6q21 was previously reported in a patient with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and t(6;13)(q21;q12) but no SNX3 mutations were identified in another sporadic case of MMEP, suggesting involvement of another gene. In this work, SNX3 was sequenced in three patients not previously studied for this gene. In addition, we test the hypothesis that mutations in the neighbouring gene NR2E1 may underlie MMEP and related phenotypes. Methods Mutation screening was performed in five patients: the t(6;13)(q21;q12) MMEP patient, three additional patients with possible MMEP or a related phenotype, and one patient with oligodactyly, ulnar aplasia, and a t(6;7)(q21;q31.2) translocation. We used sequencing to exclude SNX3 coding mutations in three patients not previously studied for this gene. To test the hypothesis that mutations in NR2E1 may contribute to MMEP or related phenotypes, we sequenced the entire coding region, complete 5' and 3' untranslated regions, consensus splice-sites, and evolutionarily conserved regions including core and proximal promoter in all five patients. Two-hundred and fifty control subjects were genotyped for any candidate mutation. Results We did not detect any synonymous nor nonsynonymous coding mutations of NR2E1 or SNX3. In one patient with possible MMEP, we identified a candidate regulatory mutation that has been reported previously in a patient with microcephaly but was not found in 250 control subjects examined here. Conclusion Our results do not support involvement of coding mutations in NR2E1 or SNX3 in MMEP or related phenotypes; however, we cannot exclude the possibility that regulatory NR2E1 or SNX3 mutations or deletions at this locus may underlie abnormal human cortical development in some patients.
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Affiliation(s)
- Ravinesh A Kumar
- Centre for Molecular Medicine and Therapeutics, Child & Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28Ave, Vancouver, V5Z 4H4, Canada
| | - David B Everman
- Center for Molecular Studies, J.C. Self Research Institute, Greenwood Genetic Center. One Gregor Mendel Circle, Greenwood, South Carolina, 29646, USA
| | - Chad T Morgan
- Center for Molecular Studies, J.C. Self Research Institute, Greenwood Genetic Center. One Gregor Mendel Circle, Greenwood, South Carolina, 29646, USA
| | - Anne Slavotinek
- Department of Pediatrics, Division of Medical Genetics, University of California, Box 0748, 533 Parnassus St., San Francisco, California, 94143-0748, USA
| | - Charles E Schwartz
- Center for Molecular Studies, J.C. Self Research Institute, Greenwood Genetic Center. One Gregor Mendel Circle, Greenwood, South Carolina, 29646, USA
| | - Elizabeth M Simpson
- Centre for Molecular Medicine and Therapeutics, Child & Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28Ave, Vancouver, V5Z 4H4, Canada
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Kumar RA, Leach S, Bonaguro R, Chen J, Yokom DW, Abrahams BS, Seaver L, Schwartz CE, Dobyns W, Brooks-Wilson A, Simpson EM. Mutation and evolutionary analyses identify NR2E1-candidate-regulatory mutations in humans with severe cortical malformations. Genes Brain Behav 2006; 6:503-16. [PMID: 17054721 PMCID: PMC2040186 DOI: 10.1111/j.1601-183x.2006.00277.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear receptor 2E1 (NR2E1) is expressed in human fetal and adult brains; however, its role in human brain–behavior development is unknown. Previously, we have corrected the cortical hypoplasia and behavioral abnormalities in Nr2e1−/− mice using a genomic clone spanning human NR2E1, which bolsters the hypothesis that NR2E1 may similarly play a role in human cortical and behavioral development. To test the hypothesis that humans with abnormal brain–behavior development may have null or hypomorphic NR2E1 mutations, we undertook the first candidate mutation screen of NR2E1 by sequencing its entire coding region, untranslated, splice site, proximal promoter and evolutionarily conserved non-coding regions in 56 unrelated patients with cortical disorders, namely microcephaly. We then genotyped the candidate mutations in 325 unrelated control subjects and 15 relatives. We did not detect any coding region changes in NR2E1; however, we identified seven novel candidate regulatory mutations that were absent from control subjects. We used in silico tools to predict the effects of these candidate mutations on neural transcription factor binding sites (TFBS). Four candidate mutations were predicted to alter TFBS. To facilitate the present and future studies of NR2E1, we also elucidated its molecular evolution, genetic diversity, haplotype structure and linkage disequilibrium by sequencing an additional 94 unaffected humans representing Africa, the Americas, Asia, Europe, the Middle East and Oceania, as well as great apes and monkeys. We detected strong purifying selection, low genetic diversity, 21 novel polymorphisms and five common haplotypes at NR2E1. We conclude that protein-coding changes in NR2E1 do not contribute to cortical and behavioral abnormalities in the patients examined here, but that regulatory mutations may play a role.
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Affiliation(s)
- R A Kumar
- Centre for Molecular Medicine and Therapeutics and Child & Family Research InstituteVancouver, Canada
- Department of Medical Genetics, University of British ColumbiaVancouver, Canada
| | - S Leach
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer AgencyVancouver, Canada
| | - R Bonaguro
- Centre for Molecular Medicine and Therapeutics and Child & Family Research InstituteVancouver, Canada
| | - J Chen
- Centre for Molecular Medicine and Therapeutics and Child & Family Research InstituteVancouver, Canada
| | - D W Yokom
- Centre for Molecular Medicine and Therapeutics and Child & Family Research InstituteVancouver, Canada
| | - B S Abrahams
- Centre for Molecular Medicine and Therapeutics and Child & Family Research InstituteVancouver, Canada
| | - L Seaver
- Center for Molecular Studies, J.C. Self Research Institute, Greenwood Genetic CenterGreenwood, SC, USA
| | - C E Schwartz
- Center for Molecular Studies, J.C. Self Research Institute, Greenwood Genetic CenterGreenwood, SC, USA
| | - W Dobyns
- University of ChicagoChicago, IL, USA
| | - A Brooks-Wilson
- Department of Medical Genetics, University of British ColumbiaVancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer AgencyVancouver, Canada
| | - E M Simpson
- Centre for Molecular Medicine and Therapeutics and Child & Family Research InstituteVancouver, Canada
- Department of Medical Genetics, University of British ColumbiaVancouver, Canada
- Corresponding author: Elizabeth M. Simpson, 3020 980 West 28 Ave, Vancouver, BC, Canada V5Z 4H4. E-mail:
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Houde C, Dickinson RJ, Houtzager VM, Cullum R, Montpetit R, Metzler M, Simpson EM, Roy S, Hayden MR, Hoodless PA, Nicholson DW. Hippi is essential for node cilia assembly and Sonic hedgehog signaling. Dev Biol 2006; 300:523-33. [PMID: 17027958 PMCID: PMC5053816 DOI: 10.1016/j.ydbio.2006.09.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 08/30/2006] [Accepted: 09/05/2006] [Indexed: 11/28/2022]
Abstract
Hippi functions as an adapter protein that mediates pro-apoptotic signaling from poly-glutamine-expanded huntingtin, an established cause of Huntington disease, to the extrinsic cell death pathway. To explore other functions of Hippi we generated Hippi knock-out mice. This deletion causes randomization of the embryo turning process and heart looping, which are hallmarks of defective left-right (LR) axis patterning. We report that motile monocilia normally present at the surface of the embryonic node, and proposed to initiate the break in LR symmetry, are absent on Hippi-/- embryos. Furthermore, defects in central nervous system development are observed. The Sonic hedgehog (Shh) pathway is downregulated in the neural tube in the absence of Hippi, which results in failure to establish ventral neural cell fate. Together, these findings demonstrate a dual role for Hippi in cilia assembly and Shh signaling during development, in addition to its proposed role in apoptosis signal transduction in the adult brain under pathogenically stressful conditions.
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Affiliation(s)
- Caroline Houde
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
| | - Robin J. Dickinson
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | | | - Rebecca Cullum
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Rachel Montpetit
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Martina Metzler
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Sophie Roy
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
- Merck Research Laboratories, Rahway, New Jersey 07065, USA
| | - Michael R. Hayden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada V5Z 4H4
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Pamela A. Hoodless
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada V5Z 1L3
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V5Z 4H4
| | - Donald W. Nicholson
- Biochemistry Department, McGill University, Montreal, Canada H3G 1Y6
- Merck Research Laboratories, Rahway, New Jersey 07065, USA
- Corresponding author. D.N. Merck Research Laboratories, Merck and Co. Inc., RY80Y-370, 126 East Lincoln Avenue, P.O. Box 2000, Rahway, NJ 07065-0900, USA. Fax: +1 732 594 3910. (D.W. Nicholson)
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Kuo BYL, Chen Y, Bohacec S, Johansson Ö, Wasserman WW, Simpson EM. SAGE2Splice: unmapped SAGE tags reveal novel splice junctions. PLoS Comput Biol 2006; 2:e34. [PMID: 16683015 PMCID: PMC1447652 DOI: 10.1371/journal.pcbi.0020034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 03/08/2006] [Indexed: 11/18/2022] Open
Abstract
Serial analysis of gene expression (SAGE) not only is a method for profiling the global expression of genes, but also offers the opportunity for the discovery of novel transcripts. SAGE tags are mapped to known transcripts to determine the gene of origin. Tags that map neither to a known transcript nor to the genome were hypothesized to span a splice junction, for which the exon combination or exon(s) are unknown. To test this hypothesis, we have developed an algorithm, SAGE2Splice, to efficiently map SAGE tags to potential splice junctions in a genome. The algorithm consists of three search levels. A scoring scheme was designed based on position weight matrices to assess the quality of candidates. Using optimized parameters for SAGE2Splice analysis and two sets of SAGE data, candidate junctions were discovered for 5%-6% of unmapped tags. Candidates were classified into three categories, reflecting the previous annotations of the putative splice junctions. Analysis of predicted tags extracted from EST sequences demonstrated that candidate junctions having the splice junction located closer to the center of the tags are more reliable. Nine of these 12 candidates were validated by RT-PCR and sequencing, and among these, four revealed previously uncharacterized exons. Thus, SAGE2Splice provides a new functionality for the identification of novel transcripts and exons. SAGE2Splice is available online at http://www.cisreg.ca.
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Affiliation(s)
- Byron Yu-Lin Kuo
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ying Chen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Slavita Bohacec
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Öjvind Johansson
- Stockholm Bioinformatics Center, Kunliga Tekniska Högskolan, Albanova, Stockholm, Sweden
| | - Wyeth W Wasserman
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elizabeth M Simpson
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * To whom correspondence should be addressed. E-mail:
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Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BYL, Lee LLC, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJM, Helgason CD, Simpson EM, Hoodless PA, Marra MA. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A 2005; 102:18485-90. [PMID: 16352711 PMCID: PMC1311911 DOI: 10.1073/pnas.0509455102] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of approximately 24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.
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Affiliation(s)
- Asim S Siddiqui
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4S6
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Christie BR, Li AM, Redila VA, Booth H, Wong BKY, Eadie BD, Ernst C, Simpson EM. Deletion of the nuclear receptor Nr2e1 impairs synaptic plasticity and dendritic structure in the mouse dentate gyrus. Neuroscience 2005; 137:1031-7. [PMID: 16289828 DOI: 10.1016/j.neuroscience.2005.08.091] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 07/14/2005] [Accepted: 08/15/2005] [Indexed: 11/17/2022]
Abstract
The spontaneous or targeted deletion of the nuclear receptor transcription factor Nr2e1 produces a mouse that shows hypoplasia of the hippocampal formation and reduced neurogenesis in adult mice. In these studies we show that hippocampal synaptic transmission appears normal in the dentate gyrus and cornu ammonis 1 subfields of adult mice that lack Nr2e1 (Nr2e1-/-), and that fEPSP shape, paired-pulse responses, and short-term plasticity are not substantially altered in either subfield. In contrast, the expression of long-term potentiation is selectively impaired in the dentate gyrus, and not in the cornu ammonis 1 subfield. Golgi analysis revealed that there was a significant reduction in both dendritic branching and dendritic length that was specific to dentate gyrus granule cells in the Nr2e1-/- mice. These results indicate that Nr2e1 deletion can significantly alter both synaptic plasticity and dendritic structure in the dentate gyrus.
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Affiliation(s)
- B R Christie
- Department of Psychology, University of British Columbia, 2136 West Mall, Vancouver, British Columbia, Canada V6T 1Z4.
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Abrahams BS, Kwok MCH, Trinh E, Budaghzadeh S, Hossain SM, Simpson EM. Pathological aggression in "fierce" mice corrected by human nuclear receptor 2E1. J Neurosci 2005; 25:6263-70. [PMID: 16000615 PMCID: PMC6725287 DOI: 10.1523/jneurosci.4757-04.2005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Revised: 05/20/2005] [Accepted: 05/22/2005] [Indexed: 11/21/2022] Open
Abstract
"Fierce" mice, homozygous for the deletion of nuclear receptor 2E1 (NR2E1), show abnormal brain-eye development and pathological aggression. To evaluate functional equivalency between mouse and human NR2E1, we generated mice transgenic for a genomic clone spanning the human NR2E1 locus and bred these animals to fierce mice deleted for the corresponding mouse gene. In fierce mutants carrying human NR2E1, structural brain defects were eliminated and eye abnormalities ameliorated. Excitingly, behavior in these "rescue" mice was indistinguishable from controls. Because no artificial promoter was used to drive transgene expression, promoter and regulatory elements within the human NR2E1 clone are functional in mouse. Normal behavior in rescue animals suggests that mechanisms underlying the behavioral abnormalities in fierce mice may also be conserved in humans. Our data support the hypothesis that variation at NR2E1 may contribute to human behavioral disorders. Use of this rescue paradigm with other genes will permit the direct evaluation of human genes hypothesized to play a causal role in psychiatric disease but for which evidence is lacking or equivocal.
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MESH Headings
- Aggression/physiology
- Agonistic Behavior/physiology
- Animals
- Brain/abnormalities
- Brain/embryology
- Cerebral Cortex/abnormalities
- Congenital Abnormalities/embryology
- Congenital Abnormalities/genetics
- Congenital Abnormalities/therapy
- Crosses, Genetic
- Exploratory Behavior/physiology
- Eye Abnormalities/embryology
- Eye Abnormalities/genetics
- Eye Abnormalities/therapy
- Female
- Genotype
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Olfactory Bulb/abnormalities
- Orphan Nuclear Receptors
- Phenotype
- Promoter Regions, Genetic
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/deficiency
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/physiology
- Regulatory Sequences, Nucleic Acid
- Retina/abnormalities
- Reverse Transcriptase Polymerase Chain Reaction
- Species Specificity
- Territoriality
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Affiliation(s)
- Brett S Abrahams
- Graduate Program in Neuroscience, British Columbia Research Institute for Children's and Women's Health, University of British Columbia, Vancouver, British Columbia, V5Z 4H4, Canada
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