151
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Syed A, Lukacsovich T, Pomeroy M, Bardwell AJ, Decker GT, Waymire KG, Purcell J, Huang W, Gui J, Padilla EM, Park C, Paul A, Pham TBT, Rodriguez Y, Wei S, Worthge S, Zebarjedi R, Zhang B, Bardwell L, Marsh JL, MacGregor GR. Miles to go (mtgo) encodes FNDC3 proteins that interact with the chaperonin subunit CCT3 and are required for NMJ branching and growth in Drosophila. Dev Biol 2018; 445:37-53. [PMID: 30539716 DOI: 10.1016/j.ydbio.2018.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/01/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022]
Abstract
Analysis of mutants that affect formation and function of the Drosophila larval neuromuscular junction (NMJ) has provided valuable insight into genes required for neuronal branching and synaptic growth. We report that NMJ development in Drosophila requires both the Drosophila ortholog of FNDC3 genes; CG42389 (herein referred to as miles to go; mtgo), and CCT3, which encodes a chaperonin complex subunit. Loss of mtgo function causes late pupal lethality with most animals unable to escape the pupal case, while rare escapers exhibit an ataxic gait and reduced lifespan. NMJs in mtgo mutant larvae have dramatically reduced branching and growth and fewer synaptic boutons compared with control animals. Mutant larvae show normal locomotion but display an abnormal self-righting response and chemosensory deficits that suggest additional functions of mtgo within the nervous system. The pharate lethality in mtgo mutants can be rescued by both low-level pan- and neuronal-, but not muscle-specific expression of a mtgo transgene, supporting a neuronal-intrinsic requirement for mtgo in NMJ development. Mtgo encodes three similar proteins whose domain structure is most closely related to the vertebrate intracellular cytosolic membrane-anchored fibronectin type-III domain-containing protein 3 (FNDC3) protein family. Mtgo physically and genetically interacts with Drosophila CCT3, which encodes a subunit of the TRiC/CCT chaperonin complex required for maturation of actin, tubulin and other substrates. Drosophila larvae heterozygous for a mutation in CCT3 that reduces binding between CCT3 and MTGO also show abnormal NMJ development similar to that observed in mtgo null mutants. Hence, the intracellular FNDC3-ortholog MTGO and CCT3 can form a macromolecular complex, and are both required for NMJ development in Drosophila.
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Affiliation(s)
- Adeela Syed
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Tamás Lukacsovich
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Miles Pomeroy
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - A Jane Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Gentry Thomas Decker
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Katrina G Waymire
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Judith Purcell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Weijian Huang
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - James Gui
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Emily M Padilla
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Cindy Park
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Antor Paul
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Thai Bin T Pham
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Yanete Rodriguez
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Stephen Wei
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Shane Worthge
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Ronak Zebarjedi
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Bing Zhang
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Lee Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - J Lawrence Marsh
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA.
| | - Grant R MacGregor
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA.
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152
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Calhoun JD, Carvill GL. Unravelling the genetic architecture of autosomal recessive epilepsy in the genomic era. J Neurogenet 2018; 32:295-312. [PMID: 30247086 DOI: 10.1080/01677063.2018.1513509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The technological advancement of next-generation sequencing has greatly accelerated the pace of variant discovery in epilepsy. Despite an initial focus on autosomal dominant epilepsy due to the tractable nature of variant discovery with trios under a de novo model, more and more variants are being reported in families with epilepsies consistent with autosomal recessive (AR) inheritance. In this review, we touch on the classical AR epilepsy variants such as the inborn errors of metabolism and malformations of cortical development. However, we also highlight recently reported genes that are being identified by next-generation sequencing approaches and online 'matchmaking' platforms. Syndromes mainly characterized by seizures and complex neurodevelopmental disorders comorbid with epilepsy are discussed as an example of the wide phenotypic spectrum associated with the AR epilepsies. We conclude with a foray into the future, from the application of whole-genome sequencing to identify elusive epilepsy variants, to the promise of precision medicine initiatives to provide novel targeted therapeutics specific to the individual based on their clinical genetic testing.
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Affiliation(s)
- Jeffrey D Calhoun
- a Department of Neurology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
| | - Gemma L Carvill
- a Department of Neurology , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
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153
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Sarkar A, Gogia N, Glenn N, Singh A, Jones G, Powers N, Srivastava A, Kango-Singh M, Singh A. A soy protein Lunasin can ameliorate amyloid-beta 42 mediated neurodegeneration in Drosophila eye. Sci Rep 2018; 8:13545. [PMID: 30202077 PMCID: PMC6131139 DOI: 10.1038/s41598-018-31787-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 08/24/2018] [Indexed: 01/30/2023] Open
Abstract
Alzheimer's disease (AD), a fatal progressive neurodegenerative disorder, also results from accumulation of amyloid-beta 42 (Aβ42) plaques. These Aβ42 plaques trigger oxidative stress, abnormal signaling, which results in neuronal death by unknown mechanism(s). We misexpress high levels of human Aβ42 in the differentiating retinal neurons of the Drosophila eye, which results in the Alzheimer's like neuropathology. Using our transgenic model, we tested a soy-derived protein Lunasin (Lun) for a possible role in rescuing neurodegeneration in retinal neurons. Lunasin is known to have anti-cancer effect and reduces stress and inflammation. We show that misexpression of Lunasin by transgenic approach can rescue Aβ42 mediated neurodegeneration by blocking cell death in retinal neurons, and results in restoration of axonal targeting from retina to brain. Misexpression of Lunasin downregulates the highly conserved cJun-N-terminal Kinase (JNK) signaling pathway. Activation of JNK signaling can prevent neuroprotective role of Lunasin in Aβ42 mediated neurodegeneration. This neuroprotective function of Lunasin is not dependent on retinal determination gene cascade in the Drosophila eye, and is independent of Wingless (Wg) and Decapentaplegic (Dpp) signaling pathways. Furthermore, Lunasin can significantly reduce mortality rate caused by misexpression of human Aβ42 in flies. Our studies identified the novel neuroprotective role of Lunasin peptide, a potential therapeutic agent that can ameliorate Aβ42 mediated neurodegeneration by downregulating JNK signaling.
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Affiliation(s)
- Ankita Sarkar
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Neha Gogia
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Neil Glenn
- Premedical Program, University of Dayton, Dayton, OH, 45469, USA
| | - Aditi Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Gillian Jones
- Department of Biology and Biotechnology Center, Western Kentucky University, 1906 College Heights Boulevard, TCCW 351, Bowling Green, KY, 42101, USA
| | - Nathan Powers
- Department of Biology and Biotechnology Center, Western Kentucky University, 1906 College Heights Boulevard, TCCW 351, Bowling Green, KY, 42101, USA
| | - Ajay Srivastava
- Department of Biology and Biotechnology Center, Western Kentucky University, 1906 College Heights Boulevard, TCCW 351, Bowling Green, KY, 42101, USA
| | - Madhuri Kango-Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
- Premedical Program, University of Dayton, Dayton, OH, 45469, USA
- Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, 45469, USA
- The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA.
- Premedical Program, University of Dayton, Dayton, OH, 45469, USA.
- Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, 45469, USA.
- The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA.
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
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154
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Albrecht NE, Alevy J, Jiang D, Burger CA, Liu BI, Li F, Wang J, Kim SY, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gaspero A, Justice MJ, Westenskow PD, Yamamoto S, Seavitt JR, Beaudet AL, Dickinson ME, Samuel MA. Rapid and Integrative Discovery of Retina Regulatory Molecules. Cell Rep 2018; 24:2506-2519. [PMID: 30157441 PMCID: PMC6170014 DOI: 10.1016/j.celrep.2018.07.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/15/2018] [Accepted: 07/27/2018] [Indexed: 12/26/2022] Open
Abstract
Retinal function relies on precisely organized neurons and synapses and a properly patterned vasculature to support them. Alterations in these features can result in vision loss. However, our understanding of retinal organization pathways remains incomplete because of a lack of methods to rapidly identify neuron and vasculature regulators in mammals. Here we developed a pipeline for the identification of neural and synaptic integrity genes by high-throughput retinal screening (INSiGHT) that analyzes candidate expression, vascular patterning, cellular organization, and synaptic arrangement. Using this system, we examined 102 mutant mouse lines and identified 16 unique retinal regulatory genes. Fifteen of these candidates are identified as novel retina regulators, and many (9 of 16) are associated with human neural diseases. These results expand the genetic landscape involved in retinal circuit organization and provide a road map for continued discovery of mammalian retinal regulators and disease-causing alleles.
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Affiliation(s)
- Nicholas E Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan Alevy
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney A Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian I Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fenge Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julia Wang
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angelina Gaspero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica J Justice
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Peter D Westenskow
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary E Dickinson
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie A Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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155
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Comprehensive review on the molecular genetics of autosomal recessive primary microcephaly (MCPH). Genet Res (Camb) 2018; 100:e7. [PMID: 30086807 DOI: 10.1017/s0016672318000046] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Primary microcephaly (MCPH) is an autosomal recessive sporadic neurodevelopmental ailment with a trivial head size characteristic that is below 3-4 standard deviations. MCPH is the smaller upshot of an architecturally normal brain; a significant decrease in size is seen in the cerebral cortex. At birth MCPH presents with non-progressive mental retardation, while secondary microcephaly (onset after birth) presents with and without other syndromic features. MCPH is a neurogenic mitotic syndrome nevertheless pretentious patients demonstrate normal neuronal migration, neuronal apoptosis and neural function. Eighteen MCPH loci (MCPH1-MCPH18) have been mapped to date from various populations around the world and contain the following genes: Microcephalin, WDR62, CDK5RAP2, CASC5, ASPM, CENPJ, STIL, CEP135, CEP152, ZNF335, PHC1, CDK6, CENPE, SASS6, MFSD2A, ANKLE2, CIT and WDFY3, clarifying our understanding about the molecular basis of microcephaly genetic disorder. It has previously been reported that phenotype disease is caused by MCB gene mutations and the causes of this phenotype are disarrangement of positions and organization of chromosomes during the cell cycle as a result of mutated DNA, centriole duplication, neurogenesis, neuronal migration, microtubule dynamics, transcriptional control and the cell cycle checkpoint having some invisible centrosomal process that can manage the number of neurons that are produced by neuronal precursor cells. Furthermore, researchers inform us about the clinical management of families that are suffering from MCPH. Establishment of both molecular understanding and genetic advocating may help to decrease the rate of this ailment. This current review study examines newly identified genes along with previously identified genes involved in autosomal recessive MCPH.
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156
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Balakrishnan SS, Basu U, Shinde D, Thakur R, Jaiswal M, Raghu P. Regulation of PI4P levels by PI4KIIIα during G-protein-coupled PLC signaling in Drosophila photoreceptors. J Cell Sci 2018; 131:jcs.217257. [PMID: 29980590 DOI: 10.1242/jcs.217257] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/27/2018] [Indexed: 12/27/2022] Open
Abstract
The activation of phospholipase C (PLC) is a conserved mechanism of receptor-activated cell signaling at the plasma membrane. PLC hydrolyzes the minor membrane lipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2], and continued signaling requires the resynthesis and availability of PI(4,5)P2 at the plasma membrane. PI(4,5)P2 is synthesized by the phosphorylation of phosphatidylinositol 4-phosphate (PI4P). Thus, a continuous supply of PI4P is essential to support ongoing PLC signaling. While the enzyme PI4KA has been identified as performing this function in cultured mammalian cells, its function in the context of an in vivo physiological model has not been established. In this study, we show that, in Drosophila photoreceptors, PI4KIIIα activity is required to support signaling during G-protein-coupled PLC activation. Depletion of PI4KIIIα results in impaired electrical responses to light, and reduced plasma membrane levels of PI4P and PI(4,5)P2 Depletion of the conserved proteins Efr3 and TTC7 [also known as StmA and L(2)k14710, respectively, in flies], which assemble PI4KIIIα at the plasma membrane, also results in an impaired light response and reduced plasma membrane PI4P and PI(4,5)P2 levels. Thus, PI4KIIIα activity at the plasma membrane generates PI4P and supports PI(4,5)P2 levels during receptor activated PLC signaling.
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Affiliation(s)
- Sruthi S Balakrishnan
- National Centre for Biological Sciences-TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Urbashi Basu
- National Centre for Biological Sciences-TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Dhananjay Shinde
- National Centre for Biological Sciences-TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Rajan Thakur
- National Centre for Biological Sciences-TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Manish Jaiswal
- TIFR Center for Interdisciplinary Science, Hyderabad 500107, India
| | - Padinjat Raghu
- National Centre for Biological Sciences-TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India
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157
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Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LDM. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:245-260. [PMID: 30057031 PMCID: PMC6081494 DOI: 10.1016/j.ajhg.2018.07.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/02/2018] [Indexed: 12/23/2022] Open
Abstract
Interferon regulatory factor 2 binding protein-like (IRF2BPL) encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals who carry damaging heterozygous variants in IRF2BPL and are affected with neurological symptoms. Five individuals who carry IRF2BPL nonsense variants resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The IRF2BPL bioinformatics signature based on population genomics is consistent with a gene that is intolerant to variation. We show that the fruit-fly IRF2BPL ortholog, called pits (protein interacting with Ttk69 and Sin3A), is broadly detected, including in the nervous system. Complete loss of pits is lethal early in development, whereas partial knockdown with RNA interference in neurons leads to neurodegeneration, revealing a requirement for this gene in proper neuronal function and maintenance. The identified IRF2BPL nonsense variants behave as severe loss-of-function alleles in this model organism, and ectopic expression of the missense variants leads to a range of phenotypes. Taken together, our results show that IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.
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Affiliation(s)
- Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary Kay Koenig
- Division of Child & Adolescent Neurology, Department of Pediatrics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Julián A Martínez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Child and Adolescent Psychiatry, Resnick Neuropsychiatric Hospital, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew Herzog
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Agnes H Chen
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Patricia I Dickson
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Henry J Lin
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Moin U Vera
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Noriko Salamon
- Department of Radiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John M Graham
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Damara Ortiz
- Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Elena Infante
- Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Wouter Steyaert
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bart Dermaut
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bruce Poppe
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edward C Smith
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gail Spiridigliozzi
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mays El-Dairi
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Lark
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kacie Riley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dwight D Koeberl
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Loren D M Pena
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA.
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Zernant J, Lee W, Nagasaki T, Collison FT, Fishman GA, Bertelsen M, Rosenberg T, Gouras P, Tsang SH, Allikmets R. Extremely hypomorphic and severe deep intronic variants in the ABCA4 locus result in varying Stargardt disease phenotypes. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002733. [PMID: 29848554 PMCID: PMC6071568 DOI: 10.1101/mcs.a002733] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
Autosomal recessive Stargardt disease (STGD1, MIM 248200) is caused by mutations in the ABCA4 gene. Complete sequencing of the ABCA4 locus in STGD1 patients identifies two expected disease-causing alleles in ∼75% of patients and only one mutation in ∼15% of patients. Recently, many possibly pathogenic variants in deep intronic sequences of ABCA4 have been identified in the latter group. We extended our analyses of deep intronic ABCA4 variants and determined that one of these, c.4253+43G>A (rs61754045), is present in 29/1155 (2.6%) of STGD1 patients. The variant is found at statistically significantly higher frequency in patients with only one pathogenic ABCA4 allele, 23/160 (14.38%), MAF = 0.072, compared to MAF = 0.013 in all STGD1 cases and MAF = 0.006 in the matching general population (P < 1 × 10−7). The variant, which is not predicted to have any effect on splicing, is the first reported intronic “extremely hypomorphic allele” in the ABCA4 locus; that is, it is pathogenic only when in trans with a loss-of-function ABCA4 allele. It results in a distinct clinical phenotype characterized by late onset of symptoms and foveal sparing. In ∼70% of cases the variant was allelic with the c.6006-609T>A (rs575968112) variant, which was deemed nonpathogenic. Another rare deep intronic variant, c.5196+1056A>G (rs886044749), found in 5/834 (0.6%) of STGD1 cases is, conversely, a severe allele. This study determines pathogenicity for three noncoding variants in STGD1 patients of European descent accounting for ∼3% of the disease. Defining disease-associated alleles in the noncoding sequences of the ABCA4 locus can be accomplished by integrated clinical and genetic analyses.
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Affiliation(s)
- Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA
| | - Takayuki Nagasaki
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA
| | - Frederick T Collison
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago 60608, Illinois, USA
| | - Gerald A Fishman
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago 60608, Illinois, USA
| | - Mette Bertelsen
- Department of Clinical Genetics, Kennedy Center, Rigshospitalet, Glostrup 2600, Denmark
| | - Thomas Rosenberg
- Department of Ophthalmology, Rigshospitalet, Glostrup 2600, Denmark
| | - Peter Gouras
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
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159
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Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell 2018; 174:505-520. [PMID: 30053424 PMCID: PMC6247911 DOI: 10.1016/j.cell.2018.06.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/11/2022]
Abstract
Although gene discovery in neuropsychiatric disorders, including autism spectrum disorder, intellectual disability, epilepsy, schizophrenia, and Tourette disorder, has accelerated, resulting in a large number of molecular clues, it has proven difficult to generate specific hypotheses without the corresponding datasets at the protein complex and functional pathway level. Here, we describe one path forward-an initiative aimed at mapping the physical and genetic interaction networks of these conditions and then using these maps to connect the genomic data to neurobiology and, ultimately, the clinic. These efforts will include a team of geneticists, structural biologists, neurobiologists, systems biologists, and clinicians, leveraging a wide array of experimental approaches and creating a collaborative infrastructure necessary for long-term investigation. This initiative will ultimately intersect with parallel studies that focus on other diseases, as there is a significant overlap with genes implicated in cancer, infectious disease, and congenital heart defects.
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Affiliation(s)
- A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Montana T Morris
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sheng Wang
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Helen R Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nia Teerikorpi
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tierney B Baum
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kevin J Bender
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tejal A Desai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Graeme W Davis
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward Chang
- Department of Neurological Surgery, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vikaas Sohal
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel H Lowenstein
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hao Li
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Agard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael J Keiser
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian Shoichet
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark von Zastrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lennart Mucke
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Steven Finkbeiner
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Li Gan
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Ruth Huttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hugo J Bellen
- Departments of Molecular and Human Genetics and Neuroscience, Neurological Research Institute at TCH, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Loren M Frank
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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160
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Liu W, Duan X, Fang X, Shang W, Tong C. Mitochondrial protein import regulates cytosolic protein homeostasis and neuronal integrity. Autophagy 2018; 14:1293-1309. [PMID: 29909722 DOI: 10.1080/15548627.2018.1474991] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Neurodegeneration is characterized by protein aggregate deposits and mitochondrial malfunction. Reduction in Tom40 (translocase of outer membrane 40) expression, a key subunit of the translocase of the outer mitochondrial membrane complex, led to accumulation of ubiquitin (Ub)-positive protein aggregates engulfed by Atg8a-positive membranes. Other macroautophagy markers were also abnormally accumulated. Autophagy was induced but the majority of autophagosomes failed to fuse with lysosomes when Tom40 was downregulated. In Tom40 RNAi tissues, autophagosome-like (AL) structures, often not sealed, were 10 times larger than starvation induced autophagosomes. Atg5 downregulation abolished Tom40 RNAi induced AL structure formation, but the Ub-positive aggregates remained, whereas knock down of Syx17, a gene required for autophagosome-lysosome fusion, led to the disappearance of giant AL structures and accumulation of small autophagosomes and phagophores near the Ub-positive aggregates. The protein aggregates contained many mitochondrial preproteins, cytosolic proteins, and proteasome subunits. Proteasome activity and ATP levels were reduced and the ROS levels was increased in Tom40 RNAi tissues. The simultaneous inhibition of proteasome activity, reduction in ATP production, and increase in ROS, but none of these conditions alone, can mimic the imbalanced proteostasis phenotypes observed in Tom40 RNAi cells. Knockdown of ref(2)P or ectopic expression of Pink1 and park greatly reduced aggregate formation in Tom40 RNAi tissues. In nerve tissues, reduction in Tom40 activity leads to aggregate formation and neurodegeneration. Rather than diminishing the neurodegenerative phenotypes, overexpression of Pink1 enhanced them. We proposed that defects in mitochondrial protein import may be the key to linking imbalanced proteostasis and mitochondrial defects. ABBREVIATIONS AL: autophagosome-like; Atg12: Autophagy-related 12; Atg14: Autophagy-related 14; Atg16: Autophagy-related 16; Atg5: Autophagy-related 5; Atg6: Autophagy-related 6; Atg8a: Autophagy-related 8a; Atg9: Autophagy-related 9; ATP: adenosine triphosphate; Cas9: CRISPR associated protein 9; cDNA: complementary DNA; COX4: Cytochrome c oxidase subunit 4; CRISPR: clustered regularly interspaced short palindromic repeats; Cyt-c1: Cytochrome c1; DAPI: 4,6-diamidino-2-phenylindole dihydrochloride; Dcr-2: Dicer-2; FLP: Flippase recombination enzyme; FRT: FLP recombination target; GFP: green fluorescent protein; GO: gene ontology; gRNA: guide RNA; Hsp60: Heat shock protein 60A; HDAC6: Histone deacetylase 6; htt: huntingtin; Idh: Isocitrate dehydrogenase; IFA: immunofluorescence assay; Irp-1A: Iron regulatory protein 1A; kdn: knockdown; Marf: Mitochondrial assembly regulatory factor; MitoGFP: Mitochondrial-GFP; MS: mass spectrometry; MTPAP: mitochondrial poly(A) polymerase; Nmnat: Nicotinamide mononucleotide adenylyltransferase; OE: overexpression; Pink1/PINK1: PTEN-induced putative kinase 1; polyQ: polyglutamine; PRKN: parkin RBR E3 ubiquitin protein ligase; Prosα4: proteasome α4 subunit; Prosβ1: proteasome β1 subunit; Prosβ5: proteasome β5 subunit; Prosβ7: proteasome β7 subunit; ref(2)P: refractory to sigma P; RFP: red fluorescent protein; RNAi: RNA interference; ROS: reactive oxygen species; Rpn11: Regulatory particle non-ATPase 11; Rpt2: Regulatory particle triple-A ATPase 2; scu: scully; sicily: severe impairment of CI with lengthened youth; sesB: stress-sensitive B; Syx17: Syntaxin17; TEM: transmission electron microscopy; ttm50: tiny tim 50; Tom: translocase of the outer membrane; Tom20: translocase of outer membrane 20; Tom40: translocase of outer membrane 40; Tom70: translocase of outer membrane 70; UAS: upstream active sequence; Ub: ubiquitin; VNC: ventral nerve cord; ZFYVE1: zinc finger FYVE-type containing 1.
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Affiliation(s)
- Wei Liu
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Xiuying Duan
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Xuefei Fang
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Weina Shang
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
| | - Chao Tong
- a Life Sciences Institute and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , China
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161
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162
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Ono M, Lai KKY, Wu K, Nguyen C, Lin DP, Murali R, Kahn M. Nuclear receptor/Wnt beta-catenin interactions are regulated via differential CBP/p300 coactivator usage. PLoS One 2018; 13:e0200714. [PMID: 30020971 PMCID: PMC6051640 DOI: 10.1371/journal.pone.0200714] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/02/2018] [Indexed: 12/26/2022] Open
Abstract
Over 400 million years ago, the evolution of vertebrates gave rise to a life cycle in which the organism began to live longer particularly as an adult. To accommodate such a longer lifespan, the organism underwent adaptation, developing a mechanism for long-lived cellular homeostasis. This adaptation required a population of long-lived relatively quiescent somatic stem cells (SSCs) along with a more proliferative differentiated daughter cell population, and was necessary to safeguard the genetic attributes with which SSCs were endowed. Intriguingly, cAMP response element binding protein (CREB)-binding protein (CBP) and E1A-binding protein, 300 kDa (p300), the highly homologous Kat3 coactivators had diverged, through duplication of ancestral Kat3, immediately preceding the evolution of vertebrates, given that both CBP and p300 have been detected in nearly all vertebrates versus non-vertebrates. We now demonstrate that a relatively small, highly evolutionarily conserved, amino terminal 9 amino acid deletion in CBP versus p300, plays a critical role in allowing for both robust maintenance of genomic integrity in stem cells and the initiation of a feed-forward differentiation mechanism by tightly controlling the interaction of the nuclear receptor family with the Wnt signaling cascade in either an antagonistic or synergistic manner.
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Affiliation(s)
- Masaya Ono
- Department of Clinical Proteomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Keane K. Y. Lai
- Department of Pathology, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
- Department of Pathology and Southern California Research Center for ALPD and Cirrhosis, University of Southern California, Los Angeles, CA, United States of America
| | - Kaijin Wu
- Center for Molecular Pathways and Drug Discovery, University of Southern California, Los Angeles, CA, United States of America
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Cu Nguyen
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
- Center for Molecular Pathways and Drug Discovery, University of Southern California, Los Angeles, CA, United States of America
| | - David P. Lin
- Department of Pathology and Southern California Research Center for ALPD and Cirrhosis, University of Southern California, Los Angeles, CA, United States of America
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Michael Kahn
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA, United States of America
- Center for Molecular Pathways and Drug Discovery, University of Southern California, Los Angeles, CA, United States of America
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, United States of America
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, United States of America
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States of America
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163
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Tan Q, Zoghbi HY. Mouse models as a tool for discovering new neurological diseases. Neurobiol Learn Mem 2018; 165:106902. [PMID: 30030131 DOI: 10.1016/j.nlm.2018.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/11/2018] [Accepted: 07/17/2018] [Indexed: 02/08/2023]
Abstract
Animal models have been the mainstay of biological and medical research. Although there are drawbacks to any research tool, we argue that mice have been under-utilized as a tool for predicting human diseases. Here we review four examples from our research group where studying the consequences of altered gene dosage in a mouse led to the discovery of previously unrecognized human syndromes: MECP2 duplication syndrome, SHANK3 duplication syndrome, CIC haploinsufficiency syndrome, and PUM1-related disorders. We also describe the clinical phenotypes of two individuals with CIC haploinsufficiency syndrome who have not been reported previously. To help bring biological insights gained from model systems a step closer to disease gene discovery, we discuss tools and resources that will facilitate this process. Moving back and forth between the lab and the clinic, between studies of mouse models and human patients, will continue to drive disease gene discovery and lead to better understanding of gene functions and disease mechanisms, laying the groundwork for future therapeutic interventions.
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Affiliation(s)
- Qiumin Tan
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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164
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Liu J, Zhou Y, Liu S, Song X, Yang XZ, Fan Y, Chen W, Akdemir ZC, Yan Z, Zuo Y, Du R, Liu Z, Yuan B, Zhao S, Liu G, Chen Y, Zhao Y, Lin M, Zhu Q, Niu Y, Liu P, Ikegawa S, Song YQ, Posey JE, Qiu G, Zhang F, Wu Z, Lupski JR, Wu N. The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease. Hum Genet 2018; 137:553-567. [PMID: 30019117 DOI: 10.1007/s00439-018-1910-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 07/07/2018] [Indexed: 01/25/2023]
Abstract
With the recent advance in genome-wide association studies (GWAS), disease-associated single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) have been extensively reported. Accordingly, the issue of incorrect identification of recombination events that can induce the distortion of multi-allelic or hemizygous variants has received more attention. However, the potential distorted calculation bias or significance of a detected association in a GWAS due to the coexistence of CNVs and SNPs in the same genomic region may remain under-recognized. Here we performed the association study within a congenital scoliosis (CS) cohort whose genetic etiology was recently elucidated as a compound inheritance model, including mostly one rare variant deletion CNV null allele and one common variant non-coding hypomorphic haplotype of the TBX6 gene. We demonstrated that the existence of a deletion in TBX6 led to an overestimation of the contribution of the SNPs on the hypomorphic allele. Furthermore, we generalized a model to explain the calculation bias, or distorted significance calculation for an association study, that can be 'induced' by CNVs at a locus. Meanwhile, overlapping between the disease-associated SNPs from published GWAS and common CNVs (overlap 10%) and pathogenic/likely pathogenic CNVs (overlap 99.69%) was significantly higher than the random distribution (p < 1 × 10-6 and p = 0.034, respectively), indicating that such co-existence of CNV and SNV alleles might generally influence data interpretation and potential outcomes of a GWAS. We also verified and assessed the influence of colocalizing CNVs to the detection sensitivity of disease-associated SNP variant alleles in another adolescent idiopathic scoliosis (AIS) genome-wide association study. We proposed that detecting co-existent CNVs when evaluating the association signals between SNPs and disease traits could improve genetic model analyses and better integrate GWAS with robust Mendelian principles.
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Affiliation(s)
- Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Sen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xin-Zhuang Yang
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanhui Fan
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zihui Yan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuzhi Zuo
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhenlei Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yixin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanxue Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Mao Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Qiankun Zhu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, 108-8639, Japan
| | - You-Qiang Song
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, 200433, China.,Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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165
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Oriel C, Lasko P. Recent Developments in Using Drosophila as a Model for Human Genetic Disease. Int J Mol Sci 2018; 19:E2041. [PMID: 30011838 PMCID: PMC6073706 DOI: 10.3390/ijms19072041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/11/2022] Open
Abstract
Many insights into human disease have been built on experimental results in Drosophila, and research in fruit flies is often justified on the basis of its predictive value for questions related to human health. Additionally, there is now a growing recognition of the value of Drosophila for the study of rare human genetic diseases, either as a means of validating the causative nature of a candidate genetic variant found in patients, or as a means of obtaining functional information about a novel disease-linked gene when there is little known about it. For these reasons, funders in the US, Europe, and Canada have launched targeted programs to link human geneticists working on discovering new rare disease loci with researchers who work on the counterpart genes in Drosophila and other model organisms. Several of these initiatives are described here, as are a number of output publications that validate this new approach.
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Affiliation(s)
- Christine Oriel
- Maternal Infant Child Youth and Research Network, V2-230, 950 West 28th Ave, Vancouver, BC V5Z 4H4, Canada.
| | - Paul Lasko
- Department of Biology, McGill University, 3649 Promenade Sir-William-Osler, Montreal, QC H3G 0B1, Canada.
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166
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Monnier V, Llorens JV, Navarro JA. Impact of Drosophila Models in the Study and Treatment of Friedreich's Ataxia. Int J Mol Sci 2018; 19:E1989. [PMID: 29986523 PMCID: PMC6073496 DOI: 10.3390/ijms19071989] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/26/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023] Open
Abstract
Drosophila melanogaster has been for over a century the model of choice of several neurobiologists to decipher the formation and development of the nervous system as well as to mirror the pathophysiological conditions of many human neurodegenerative diseases. The rare disease Friedreich’s ataxia (FRDA) is not an exception. Since the isolation of the responsible gene more than two decades ago, the analysis of the fly orthologue has proven to be an excellent avenue to understand the development and progression of the disease, to unravel pivotal mechanisms underpinning the pathology and to identify genes and molecules that might well be either disease biomarkers or promising targets for therapeutic interventions. In this review, we aim to summarize the collection of findings provided by the Drosophila models but also to go one step beyond and propose the implications of these discoveries for the study and cure of this disorder. We will present the physiological, cellular and molecular phenotypes described in the fly, highlighting those that have given insight into the pathology and we will show how the ability of Drosophila to perform genetic and pharmacological screens has provided valuable information that is not easily within reach of other cellular or mammalian models.
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Affiliation(s)
- Véronique Monnier
- Unité de Biologie Fonctionnelle et Adaptative (BFA), Sorbonne Paris Cité, Université Paris Diderot, UMR8251 CNRS, 75013 Paris, France.
| | - Jose Vicente Llorens
- Department of Genetics, University of Valencia, Campus of Burjassot, 96100 Valencia, Spain.
| | - Juan Antonio Navarro
- Lehrstuhl für Entwicklungsbiologie, Universität Regensburg, 93040 Regensburg, Germany.
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167
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Singhal N, Jaiswal M. Pathways to neurodegeneration: lessons learnt from unbiased genetic screens in Drosophila. J Genet 2018; 97:773-781. [PMID: 30027908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Neurodegenerative diseases are a complex set of disorders that are known to be caused by environmental as well as genetic factors. In the recent past, mutations in a large number of genes have been identified that are linked to several neurodegenerative diseases. The pathogenic mechanisms in most of these disorders are unknown. Recently, studies of genes that are linked to neurodegeneration in Drosophila, the fruit flies, have contributed significantly to our understanding of mechanisms of neuroprotection and degeneration. In this review, we focus on forward genetic screens in Drosophila that helped in identification of novel genes and pathogenic mechanisms linked to neurodegeneration. We also discuss identification of four novel pathways that contribute to neurodegeneration upon mitochondrial dysfunction.
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Affiliation(s)
- Neha Singhal
- Tata Institute of Fundamental Research Hyderabad, Hyderabad 500 107, India.
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168
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Big Lessons from Tiny Flies: Drosophila melanogaster as a Model to Explore Dysfunction of Dopaminergic and Serotonergic Neurotransmitter Systems. Int J Mol Sci 2018; 19:ijms19061788. [PMID: 29914172 PMCID: PMC6032372 DOI: 10.3390/ijms19061788] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
The brain of Drosophila melanogaster is comprised of some 100,000 neurons, 127 and 80 of which are dopaminergic and serotonergic, respectively. Their activity regulates behavioral functions equivalent to those in mammals, e.g., motor activity, reward and aversion, memory formation, feeding, sexual appetite, etc. Mammalian dopaminergic and serotonergic neurons are known to be heterogeneous. They differ in their projections and in their gene expression profile. A sophisticated genetic tool box is available, which allows for targeting virtually any gene with amazing precision in Drosophila melanogaster. Similarly, Drosophila genes can be replaced by their human orthologs including disease-associated alleles. Finally, genetic manipulation can be restricted to single fly neurons. This has allowed for addressing the role of individual neurons in circuits, which determine attraction and aversion, sleep and arousal, odor preference, etc. Flies harboring mutated human orthologs provide models which can be interrogated to understand the effect of the mutant protein on cell fate and neuronal connectivity. These models are also useful for proof-of-concept studies to examine the corrective action of therapeutic strategies. Finally, experiments in Drosophila can be readily scaled up to an extent, which allows for drug screening with reasonably high throughput.
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169
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Lai YT, Maeda C, Matsuno K. Drosophila flies high over the Asia-Pacific: Report on the Fourth Asia-Pacific Drosophila Research Conference. Genes Cells 2018; 23:512-516. [PMID: 29900631 DOI: 10.1111/gtc.12601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/08/2018] [Indexed: 10/14/2022]
Abstract
The Fourth Asia-Pacific Drosophila Research Conference (APDRC4) was held at the convention center of Osaka University, Osaka, Japan, on May 8-11, 2017. Derived from the Japanese Drosophila Research Conference, the APDRC visited its home for the first time since its launch in 2011 with APDRC1 in Taipei, followed by APDRC2 in Seoul and APDRC3 in Beijing. There were 344 participants from 18 countries, more than half of whom were from abroad (Data S1). Two keynote speakers, Drs. Henry Sun and Daisuke Yamamoto, who have had rich science careers, gave overviews of their research. In addition, 14 invited speakers who are highly regarded in their fields introduced their new findings. Thirty-four oral presenters, many of them young investigators and students, were selected from the general participants to report their exciting results. During the conference, many stimulating questions and discussions were shared. Furthermore, 176 posters were presented, which also inspired enthusiastic discussions. In addition to the scientific presentations, a mixer and banquet enabled further intercommunion among the researchers (Figure b, e). During the conference, it was decided that the next Asia-Pacific Drosophila Research Conference (APDRC5) would be in Pune, India, in 2020. Thus, APDRC4 successfully achieved its mission to facilitate Drosophila research in the Asia-Pacific region.
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Affiliation(s)
- Yi-Ting Lai
- Department of Biological Sciences, Osaka University, Toyonaka, Osaka, Japan
| | - Chinami Maeda
- Department of Biological Sciences, Osaka University, Toyonaka, Osaka, Japan
| | - Kenji Matsuno
- Department of Biological Sciences, Osaka University, Toyonaka, Osaka, Japan
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170
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Morris M, Shaw A, Lambert M, Perry HH, Lowenstein E, Valenzuela D, Velazquez-Ulloa NA. Developmental nicotine exposure affects larval brain size and the adult dopaminergic system of Drosophila melanogaster. BMC DEVELOPMENTAL BIOLOGY 2018; 18:13. [PMID: 29898654 PMCID: PMC6001141 DOI: 10.1186/s12861-018-0172-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
Abstract
BACKGROUND Pregnant women may be exposed to nicotine if they smoke or use tobacco products, nicotine replacement therapy, or via e-cigarettes. Prenatal nicotine exposure has been shown to have deleterious effects on the nervous system in mammals including changes in brain size and in the dopaminergic system. The genetic and molecular mechanisms for these changes are not well understood. A Drosophila melanogaster model for these effects of nicotine exposure could contribute to faster identification of genes and molecular pathways underlying these effects. The purpose of this study was to determine if developmental nicotine exposure affects the nervous system of Drosophila melanogaster, focusing on changes to brain size and the dopaminergic system at two developmental stages. RESULTS We reared flies on control or nicotine food from egg to 3rd instar larvae or from egg to adult and determined effectiveness of the nicotine treatment. We used immunohistochemistry to visualize the whole brain and dopaminergic neurons, using tyrosine hydroxylase as the marker. We measured brain area, tyrosine hydroxylase fluorescence, and counted the number of dopaminergic neurons in brain clusters. We detected an increase in larval brain hemisphere area, a decrease in tyrosine hydroxylase fluorescence in adult central brains, and a decrease in the number of neurons in the PPM3 adult dopaminergic cluster. We tested involvement of Dα7, one of the nicotinic acetylcholine receptor subunits, and found it was involved in eclosion, as previously described, but not involved in brain size. CONCLUSIONS We conclude that developmental nicotine exposure in Drosophila melanogaster affects brain size and the dopaminergic system. Prenatal nicotine exposure in mammals has also been shown to have effects on brain size and in the dopaminergic system. This study further establishes Drosophila melanogaster as model organism to study the effects of developmental nicotine exposure. The genetic and molecular tools available for Drosophila research will allow elucidation of the mechanisms underlying the effects of nicotine exposure during development.
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Affiliation(s)
- Melanie Morris
- School of Medicine, University of Washington, Seattle, USA
| | - Ariel Shaw
- Biochemistry, Cell and Molecular Biology Program, Lewis & Clark College, Portland, USA
| | | | | | - Eve Lowenstein
- Biology Department, Lewis & Clark College, Portland, USA
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171
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Şentürk M, Bellen HJ. Genetic strategies to tackle neurological diseases in fruit flies. Curr Opin Neurobiol 2018; 50:24-32. [PMID: 29128849 PMCID: PMC5940587 DOI: 10.1016/j.conb.2017.10.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
Abstract
Drosophila melanogaster is a genetic model organism that has contributed to the discovery of numerous genes whose human homologues are associated with diseases. The development of sophisticated genetic tools to manipulate its genome accelerates the discovery of the genetic basis of undiagnosed human diseases and the elucidation of molecular pathogenic events of known and novel diseases. Here, we discuss various approaches used in flies to assess the function of the fly homologues of disease-associated genes. We highlight how systematic and combinatorial approaches based on recently established methods provide us with integrated tool sets that can be applied to the study of neurodevelopmental and neurodegenerative disorders.
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Affiliation(s)
- Mümine Şentürk
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston TX 77030, USA; Department of Neuroscience, BCM, Houston TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston TX 77030, USA; Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA.
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172
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Li T, Bellen HJ, Groves AK. Using Drosophila to study mechanisms of hereditary hearing loss. Dis Model Mech 2018; 11:11/6/dmm031492. [PMID: 29853544 PMCID: PMC6031363 DOI: 10.1242/dmm.031492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Johnston's organ - the hearing organ of Drosophila - has a very different structure and morphology to that of the hearing organs of vertebrates. Nevertheless, it is becoming clear that vertebrate and invertebrate auditory organs share many physiological, molecular and genetic similarities. Here, we compare the molecular and cellular features of hearing organs in Drosophila with those of vertebrates, and discuss recent evidence concerning the functional conservation of Usher proteins between flies and mammals. Mutations in Usher genes cause Usher syndrome, the leading cause of human deafness and blindness. In Drosophila, some Usher syndrome proteins appear to physically interact in protein complexes that are similar to those described in mammals. This functional conservation highlights a rational role for Drosophila as a model for studying hearing, and for investigating the evolution of auditory organs, with the aim of advancing our understanding of the genes that regulate human hearing and the pathogenic mechanisms that lead to deafness.
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Affiliation(s)
- Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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173
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Abstract
Primary microcephaly (MCPH, for "microcephaly primary hereditary") is a disorder of brain development that results in a head circumference more than 3 standard deviations below the mean for age and gender. It has a wide variety of causes, including toxic exposures, in utero infections, and metabolic conditions. While the genetic microcephaly syndromes are relatively rare, studying these syndromes can reveal molecular mechanisms that are critical in the regulation of neural progenitor cells, brain size, and human brain evolution. Many of the causative genes for MCPH encode centrosomal proteins involved in centriole biogenesis. However, other MCPH genes fall under different mechanistic categories, notably DNA replication and repair. Recent gene discoveries and functional studies have implicated novel cellular processes, such as cytokinesis, centromere and kinetochore function, transmembrane or intracellular transport, Wnt signaling, and autophagy, as well as the apical polarity complex. Thus, MCPH genes implicate a wide variety of molecular and cellular mechanisms in the regulation of cerebral cortical size during development.
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Affiliation(s)
- Divya Jayaraman
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard-MIT MD-PhD Program, Harvard Medical School, Boston, Massachusetts 02115, USA.,Current affiliation: Boston Combined Residency Program (Child Neurology), Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| | - Byoung-Il Bae
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut 06510, USA;
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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174
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Zhang K, Coyne AN, Lloyd TE. Drosophila models of amyotrophic lateral sclerosis with defects in RNA metabolism. Brain Res 2018; 1693:109-120. [PMID: 29752901 DOI: 10.1016/j.brainres.2018.04.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022]
Abstract
The fruit fly Drosophila Melanogaster has been widely used to study neurodegenerative diseases. The conservation of nervous system biology coupled with the rapid life cycle and powerful genetic tools in the fly have enabled the identification of novel therapeutic targets that have been validated in vertebrate model systems and human patients. A recent example is in the study of the devastating motor neuron degenerative disease amyotrophic lateral sclerosis (ALS). Mutations in genes that regulate RNA metabolism are a major cause of inherited ALS, and functional analysis of these genes in the fly nervous system has shed light on how mutations cause disease. Importantly, unbiased genetic screens have identified key pathways that contribute to ALS pathogenesis such as nucleocytoplasmic transport and stress granule assembly. In this review, we will discuss the utilization of Drosophila models of ALS with defects in RNA metabolism.
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Affiliation(s)
- Ke Zhang
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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175
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Takáts S, Glatz G, Szenci G, Boda A, Horváth GV, Hegedűs K, Kovács AL, Juhász G. Non-canonical role of the SNARE protein Ykt6 in autophagosome-lysosome fusion. PLoS Genet 2018; 14:e1007359. [PMID: 29694367 PMCID: PMC5937789 DOI: 10.1371/journal.pgen.1007359] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/07/2018] [Accepted: 04/11/2018] [Indexed: 11/25/2022] Open
Abstract
The autophagosomal SNARE Syntaxin17 (Syx17) forms a complex with Snap29 and Vamp7/8 to promote autophagosome-lysosome fusion via multiple interactions with the tethering complex HOPS. Here we demonstrate that, unexpectedly, one more SNARE (Ykt6) is also required for autophagosome clearance in Drosophila. We find that loss of Ykt6 leads to large-scale accumulation of autophagosomes that are unable to fuse with lysosomes to form autolysosomes. Of note, loss of Syx5, the partner of Ykt6 in ER-Golgi trafficking does not prevent autolysosome formation, pointing to a more direct role of Ykt6 in fusion. Indeed, Ykt6 localizes to lysosomes and autolysosomes, and forms a SNARE complex with Syx17 and Snap29. Interestingly, Ykt6 can be outcompeted from this SNARE complex by Vamp7, and we demonstrate that overexpression of Vamp7 rescues the fusion defect of ykt6 loss of function cells. Finally, a point mutant form with an RQ amino acid change in the zero ionic layer of Ykt6 protein that is thought to be important for fusion-competent SNARE complex assembly retains normal autophagic activity and restores full viability in mutant animals, unlike palmitoylation or farnesylation site mutant Ykt6 forms. As Ykt6 and Vamp7 are both required for autophagosome-lysosome fusion and are mutually exclusive subunits in a Syx17-Snap29 complex, these data suggest that Vamp7 is directly involved in membrane fusion and Ykt6 acts as a non-conventional, regulatory SNARE in this process. SNARE proteins are critical executors of most vesicle fusion events in eukaryotic cells. 4 SNARE domains assemble into a bundle to promote fusion. We have previously shown that Syntaxin 17, Snap29 (contributing 2 SNARE domains) and Vamp7 form the SNARE complex executing autophagosome-lysosome fusion in Drosophila. Surprisingly, one more SNARE protein (Ykt6) is also required in vivo for autophagosome-lysosome fusion. We find that Ykt6 can form a less stable complex with Syntaxin 17 and Snap29 than Vamp7, because Vamp7 outcompetes Ykt6. Ykt6, Vamp7 and Syntaxin 17 all bind to the tethering complex HOPS to promote vesicle fusion. Ykt6 likely plays a non-canonical role in autophagosome-lysosome fusion, because its mutant form (which is thought to be unable to assemble into a fusion-competent SNARE complex) still rescues the fusion defect of ykt6 mutant cells, and it restores viability in mutant animals.
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Affiliation(s)
- Szabolcs Takáts
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
- Hungarian Academy of Sciences, Premium Postdoctoral Research Program, Budapest, Hungary
- * E-mail: (ST); (GJ)
| | - Gábor Glatz
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Győző Szenci
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Attila Boda
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor V. Horváth
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Krisztina Hegedűs
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Attila L. Kovács
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail: (ST); (GJ)
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176
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Ueda A, Woods S, McElree I, O'Harrow TCDG, Inman C, Thenuwara S, Aftab M, Iyengar A. Two novel forms of ERG oscillation in Drosophila: age and activity dependence. J Neurogenet 2018; 32:118-126. [PMID: 29688104 DOI: 10.1080/01677063.2018.1461866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Over an animal's lifespan, neuronal circuits and systems often decline in an inherently heterogeneous fashion. To compare the age-dependent progression of changes in visual behavior with alterations in retinal physiology, we examined phototaxis and electroretinograms (ERGs) in a wild-type D. melanogaster strain (Canton-S) across their lifespan. In aged flies (beyond 50% median lifespan), we found a marked decline in phototaxis, while motor coordination was less disrupted, as indicated by relatively stronger negative geotaxis. These aged flies displayed substantially reduced ERG transient amplitudes while the receptor potentials (RP) remained largely intact. Using a repetitive light flash protocol, we serendipitously discovered two forms of activity-dependent oscillation in the ERG waveforms of young flies: 'light-off' and 'light-on' oscillations. After repeated 500 ms light flashes, light-off oscillations appeared during the ERG off-transients (frequency: 50-120 Hz, amplitude: ∼1 mV). Light-on oscillations (100-200 Hz, ∼0.3 mV) were induced by a series of 50 ms flashes, and were evident during the ERG on-transients. Both forms of oscillation were observed in other strains of D. melanogaster (Oregon-R, Berlin), additional Drosophila species (D. funerbris, D. euronotus, D. hydei, D. americana), and were evoked by a variety of light sources. Both light-off and light-on oscillations were distinct from previously described ERG oscillations in the visual mutant rosA in terms of location within the waveform and frequency. However, within rosA mutants, light-off oscillations, but not light-on oscillations could be recruited by the repetitive light flash protocol. Importantly though, we found that both forms of oscillation were rarely observed in aged flies. Although the physiological bases of these oscillations remain to be elucidated, they may provide important clues to age-related changes in neuronal excitability and synaptic transmission.
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Affiliation(s)
- Atsushi Ueda
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Scott Woods
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Ian McElree
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | | | - Casey Inman
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | | | - Muhammad Aftab
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Atulya Iyengar
- a Department of Biology , University of Iowa , Iowa City , IA , USA
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177
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Tan KL, Haelterman NA, Kwartler CS, Regalado ES, Lee PT, Nagarkar-Jaiswal S, Guo DC, Duraine L, Wangler MF, Bamshad MJ, Nickerson DA, Lin G, Milewicz DM, Bellen HJ. Ari-1 Regulates Myonuclear Organization Together with Parkin and Is Associated with Aortic Aneurysms. Dev Cell 2018; 45:226-244.e8. [PMID: 29689197 PMCID: PMC5920516 DOI: 10.1016/j.devcel.2018.03.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/15/2018] [Accepted: 03/26/2018] [Indexed: 12/25/2022]
Abstract
Nuclei are actively positioned and anchored to the cytoskeleton via the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex. We identified mutations in the Parkin-like E3 ubiquitin ligase Ariadne-1 (Ari-1) that affect the localization and distribution of LINC complex members in Drosophila. ari-1 mutants exhibit nuclear clustering and morphology defects in larval muscles. We show that Ari-1 mono-ubiquitinates the core LINC complex member Koi. Surprisingly, we discovered functional redundancy between Parkin and Ari-1: increasing Parkin expression rescues ari-1 mutant phenotypes and vice versa. We further show that rare variants in the human homolog of ari-1 (ARIH1) are associated with thoracic aortic aneurysms and dissections, conditions resulting from smooth muscle cell (SMC) dysfunction. Human ARIH1 rescues fly ari-1 mutant phenotypes, whereas human variants found in patients fail to do so. In addition, SMCs obtained from patients display aberrant nuclear morphology. Hence, ARIH1 is critical in anchoring myonuclei to the cytoskeleton.
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Affiliation(s)
- Kai Li Tan
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Callie S Kwartler
- Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Ellen S Regalado
- Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Sonal Nagarkar-Jaiswal
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
| | - Dong-Chuan Guo
- Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Lita Duraine
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
| | - Michael F Wangler
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Guang Lin
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Dianna M Milewicz
- Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA.
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178
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Lowenstein EG, Velazquez-Ulloa NA. A Fly's Eye View of Natural and Drug Reward. Front Physiol 2018; 9:407. [PMID: 29720947 PMCID: PMC5915475 DOI: 10.3389/fphys.2018.00407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Animals encounter multiple stimuli each day. Some of these stimuli are innately appetitive or aversive, while others are assigned valence based on experience. Drugs like ethanol can elicit aversion in the short term and attraction in the long term. The reward system encodes the predictive value for different stimuli, mediating anticipation for attractive or punishing stimuli and driving animal behavior to approach or avoid conditioned stimuli. The neurochemistry and neurocircuitry of the reward system is partly evolutionarily conserved. In both vertebrates and invertebrates, including Drosophila melanogaster, dopamine is at the center of a network of neurotransmitters and neuromodulators acting in concert to encode rewards. Behavioral assays in D. melanogaster have become increasingly sophisticated, allowing more direct comparison with mammalian research. Moreover, recent evidence has established the functional modularity of the reward neural circuits in Drosophila. This functional modularity resembles the organization of reward circuits in mammals. The powerful genetic and molecular tools for D. melanogaster allow characterization and manipulation at the single-cell level. These tools are being used to construct a detailed map of the neural circuits mediating specific rewarding stimuli and have allowed for the identification of multiple genes and molecular pathways that mediate the effects of reinforcing stimuli, including their rewarding effects. This report provides an overview of the research on natural and drug reward in D. melanogaster, including natural rewards such as sugar and other food nutrients, and drug rewards including ethanol, cocaine, amphetamine, methamphetamine, and nicotine. We focused mainly on the known genetic and neural mechanisms underlying appetitive reward for sugar and reward for ethanol. We also include genes, molecular pathways, and neural circuits that have been identified using assays that test the palatability of the rewarding stimulus, the preference for the rewarding stimulus, or other effects of the stimulus that indicate how it can modify behavior. Commonalities between mechanisms of natural and drug reward are highlighted and future directions are presented, putting forward questions best suited for research using D. melanogaster as a model organism.
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Affiliation(s)
- Eve G Lowenstein
- Department of Biology, Lewis & Clark College, Portland, OR, United States
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179
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Lee PT, Zirin J, Kanca O, Lin WW, Schulze KL, Li-Kroeger D, Tao R, Devereaux C, Hu Y, Chung V, Fang Y, He Y, Pan H, Ge M, Zuo Z, Housden BE, Mohr SE, Yamamoto S, Levis RW, Spradling AC, Perrimon N, Bellen HJ. A gene-specific T2A-GAL4 library for Drosophila. eLife 2018; 7:35574. [PMID: 29565247 PMCID: PMC5898912 DOI: 10.7554/elife.35574] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/16/2018] [Indexed: 12/18/2022] Open
Abstract
We generated a library of ~1000 Drosophila stocks in which we inserted a construct in the intron of genes allowing expression of GAL4 under control of endogenous promoters while arresting transcription with a polyadenylation signal 3’ of the GAL4. This allows numerous applications. First, ~90% of insertions in essential genes cause a severe loss-of-function phenotype, an effective way to mutagenize genes. Interestingly, 12/14 chromosomes engineered through CRISPR do not carry second-site lethal mutations. Second, 26/36 (70%) of lethal insertions tested are rescued with a single UAS-cDNA construct. Third, loss-of-function phenotypes associated with many GAL4 insertions can be reverted by excision with UAS-flippase. Fourth, GAL4 driven UAS-GFP/RFP reports tissue and cell-type specificity of gene expression with high sensitivity. We report the expression of hundreds of genes not previously reported. Finally, inserted cassettes can be replaced with GFP or any DNA. These stocks comprise a powerful resource for assessing gene function. Determining what role newly discovered genes play in the body is an important part of genetics. This task requires a lot of extra information about each gene, such as the specific cells where the gene is active, or what happens when the gene is deleted. To answer these questions, researchers need tools and methods to manipulate genes within a living organism. The fruit fly Drosophila is useful for such experiments because a toolbox of genetic techniques is already available. Gene editing in fruit flies allows small pieces of genetic information to be removed from or added to anywhere in the animal’s DNA. Another tool, known as GAL4-UAS, is a two-part system used to study gene activity. The GAL4 component is a protein that switches on genes. GAL4 alone does very little in Drosophila cells because it only recognizes a DNA sequence called UAS. However, if a GAL4-producing cell is also engineered to contain a UAS-controlled gene, GAL4 will switch the gene on. Lee et al. used gene editing to insert a small piece of DNA, containing the GAL4 sequence followed by a ‘stop’ signal, into many different fly genes. The insertion made the cells where each gene was normally active produce GAL4, but – thanks to the stop signal – rendered the rest of the original gene non-functional. This effectively deleted the proteins encoded by each gene, giving information about the biological processes they normally control. Lee et al. went on to use their insertion approach to make a Drosophila genetic library. This is a collection of around 1,000 different strains of fly, each carrying the GAL4/stop combination in a single gene. The library allows any gene in the collection to be studied in detail simply by combining the GAL4 with different UAS-controlled genetic tools. For example, introducing a UAS-controlled marker would pinpoint where in the body the original gene was active. Alternatively, adding UAS-controlled human versions of the gene would create humanized flies, which are a valuable tool to study potential disease-causing genes in humans. This Drosophila library is a resource that contributes new experimental tools to fly genetics. Insights gained from flies can also be applied to more complex animals like humans, especially since around 65% of genes are similar across humans and Drosophila. As such, Lee et al. hope that this resource will help other researchers shed new light on the role of many different genes in health and disease.
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Affiliation(s)
- Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Jonathan Zirin
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Wen-Wen Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Karen L Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - David Li-Kroeger
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Rong Tao
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Colby Devereaux
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Verena Chung
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Ying Fang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Yuchun He
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - Ming Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States
| | | | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Program in Developmental Biology, Baylor College of Medicine, Houston, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, United States
| | - Robert W Levis
- Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, United States
| | - Allan C Spradling
- Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, United States
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Program in Developmental Biology, Baylor College of Medicine, Houston, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, United States
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180
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Xio is a component of the Drosophila sex determination pathway and RNA N6-methyladenosine methyltransferase complex. Proc Natl Acad Sci U S A 2018; 115:3674-3679. [PMID: 29555755 DOI: 10.1073/pnas.1720945115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant chemical modification in eukaryotic mRNA, has been implicated in Drosophila sex determination by modifying Sex-lethal (Sxl) pre-mRNA and facilitating its alternative splicing. Here, we identify a sex determination gene, CG7358, and rename it xio according to its loss-of-function female-to-male transformation phenotype. xio encodes a conserved ubiquitous nuclear protein of unknown function. We show that Xio colocalizes and interacts with all previously known m6A writer complex subunits (METTL3, METTL14, Fl(2)d/WTAP, Vir/KIAA1429, and Nito/Rbm15) and that loss of xio is associated with phenotypes that resemble other m6A factors, such as sexual transformations, Sxl splicing defect, held-out wings, flightless flies, and reduction of m6A levels. Thus, Xio encodes a member of the m6A methyltransferase complex involved in mRNA modification. Since its ortholog ZC3H13 (or KIAA0853) also associates with several m6A writer factors, the function of Xio in the m6A pathway is likely evolutionarily conserved.
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181
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Koe CT, Tan YS, Lönnfors M, Hur SK, Low CSL, Zhang Y, Kanchanawong P, Bankaitis VA, Wang H. Vibrator and PI4KIIIα govern neuroblast polarity by anchoring non-muscle myosin II. eLife 2018; 7:33555. [PMID: 29482721 PMCID: PMC5828666 DOI: 10.7554/elife.33555] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/26/2018] [Indexed: 12/19/2022] Open
Abstract
A central feature of most stem cells is the ability to self-renew and undergo differentiation via asymmetric division. However, during asymmetric division the role of phosphatidylinositol (PI) lipids and their regulators is not well established. Here, we show that the sole type I PI transfer protein, Vibrator, controls asymmetric division of Drosophilaneural stem cells (NSCs) by physically anchoring myosin II regulatory light chain, Sqh, to the NSC cortex. Depletion of vib or disruption of its lipid binding and transfer activities disrupts NSC polarity. We propose that Vib stimulates PI4KIIIα to promote synthesis of a plasma membrane pool of phosphatidylinositol 4-phosphate [PI(4)P] that, in turn, binds and anchors myosin to the NSC cortex. Remarkably, Sqh also binds to PI(4)P in vitro and both Vib and Sqh mediate plasma membrane localization of PI(4)P in NSCs. Thus, reciprocal regulation between Myosin and PI(4)P likely governs asymmetric division of NSCs. Stem cells are cells that can both make copies of themselves and make new cells of various types. They can either divide symmetrically to produce two identical new cells, or they can divide asymmetrically to produce two different cells. Asymmetric division happens because the two new cells contain different molecules. Stem cells drive asymmetric division by moving key molecules to one end of the cell before they divide. Asymmetric division is key to how neural stem cells produce new brain cells. Many studies have used the developing brain of the fruit fly Drosophila melanogaster to understand this process. Errors in asymmetric division can lead to too many stem cells or not enough brain cells. This can contribute to brain tumors and other neurological disorders. Fat molecules called phosphatidylinositol lipids are some of chemicals that cause asymmetry in neural stem cells. Yet, it is not clear how these lipid molecules affect cell behavior to turn stem cells into brain cells. The production of phosphatidylinositol lipids involves proteins called Vibrator and PI4KIIIα. Koe et al. examined the role of these two proteins in asymmetric cell division of neural stem cells in fruit flies. The results show that Vibrator activates PI4KIIIα, which leads to high levels of a phosphatidylinositol lipid called PI(4)P within the cell. These lipids act as an anchor for a group of proteins called myosin, part of the machinery that physically divides the cell. Hence, myosin and phosphatidylinositol lipids together control asymmetric division of neural stem cells. Further experiments used mouse proteins to compensate for defects in the equivalent fly proteins. The results suggest that the same mechanisms are likely to hold true in mammalian brains, although this still needs to be proven. Nevertheless, given that human equivalents of Vibrator and PI4KIIIα are associated with neurodegenerative disorders, schizophrenia or cancers, these new findings are likely to help scientists better to understand several human diseases.
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Affiliation(s)
- Chwee Tat Koe
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Ye Sing Tan
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Max Lönnfors
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, United States
| | - Seong Kwon Hur
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, United States
| | | | - Yingjie Zhang
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Vytas A Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, United States
| | - Hongyan Wang
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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182
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Paspaliaris V, Vrachnis N, Iliodromiti Z, Antonakopoulos N, Papaioannou G, Vlachadis N, Anastasiadou F, Sotiriou S, Garas A, Thomaidis L, Manolakos E. 7q Deletion/12q Duplication Is the Possible Cause of an Alobar Holoprosencephaly Case. Mol Syndromol 2018; 9:52-57. [PMID: 29456484 DOI: 10.1159/000481972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
Holoprosencephaly (HPE) spectrum disorder is the most common congenital malformation of the human brain with absence of or incomplete midline cleavage. Its cause is heterogenic, making genetic counseling a challenge. In this case report, a pregnancy affected by alobar HPE is described. Using aCGH, an 8.9-Mb deletion at 7q36.1q36.3 together with a 4.9-Mb duplication at 12q24.32q24.33 is assumed to be the possible reason for this alobar HPE case. It is discussed that disruption of key elements of the developing brain, taking environmental factors into account, contributes to the HPE spectrum. The use of aCGH for invasive prenatal testing is starting to become the standard technique, providing accurate information about the cause of congenital diseases for couples receiving genetic counseling.
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Affiliation(s)
- Vassilis Paspaliaris
- Access to genome (ATG P.C.), Clinical Laboratory Genetics, University of Athens, Athens, Greece
| | | | | | | | - Giorgos Papaioannou
- Department of Gynecology, Attikon Hospital, University of Athens, Athens, Greece
| | | | - Foteini Anastasiadou
- Department of Clinical Embryology, Larissa Medical School, University of Thessaly, Larissa, Greece
| | - Sotirios Sotiriou
- Department of Clinical Embryology, Larissa Medical School, University of Thessaly, Larissa, Greece
| | - Antonios Garas
- Department of Gynecology, Larissa Medical School, University of Thessaly, Larissa, Greece
| | - Lorreta Thomaidis
- Developmental Assessment Unit, 2nd Department of Pediatrics, P&A Kyriakou Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Emmanouil Manolakos
- Access to genome (ATG P.C.), Clinical Laboratory Genetics, University of Athens, Athens, Greece.,Developmental Assessment Unit, 2nd Department of Pediatrics, P&A Kyriakou Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Department of Medical Genetics, University of Cagliari, Binaghi Hospital, Cagliari, Italy
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183
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Tang HM, Fung MC, Tang HL. Detecting Anastasis In Vivo by CaspaseTracker Biosensor. J Vis Exp 2018. [PMID: 29443051 DOI: 10.3791/54107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Anastasis (Greek for "rising to life") is a recently discovered cell recovery phenomenon whereby dying cells can reverse late-stage cell death processes that are generally assumed to be intrinsically irreversible. Promoting anastasis could in principle rescue or preserve injured cells that are difficult to replace such as cardiomyocytes or neurons, thereby facilitating tissue recovery. Conversely, suppressing anastasis in cancer cells, undergoing apoptosis after anti-cancer therapies, may ensure cancer cell death and reduce the chances of recurrence. However, these studies have been hampered by the lack of tools for tracking the fate of cells that undergo anastasis in live animals. The challenge is to identify the cells that have reversed the cell death process despite their morphologically normal appearance after recovery. To overcome this difficulty, we have developed Drosophila and mammalian CaspaseTracker biosensor systems that can identify and permanently track the anastatic cells in vitro or in vivo. Here, we present in vivo protocols for the generation and use of the CaspaseTracker dual biosensor system to detect and track anastasis in Drosophila melanogaster after transient exposure to cell death stimuli. While conventional biosensors and protocols can label cells actively undergoing apoptotic cell death, the CaspaseTracker biosensor can permanently label cells that have recovered after caspase activation - a hallmark of late-stage apoptosis, and simultaneously identify active apoptotic processes. This biosensor can also track the recovery of the cells that attempted other forms of cell death that directly or indirectly involved caspase activity. Therefore, this protocol enables us to continuously track the fate of these cells and their progeny, facilitating future studies of the biological functions, molecular mechanisms, physiological and pathological consequences, and therapeutic implications of anastasis. We also discuss the appropriate controls to distinguish cells that undergo anastasis from those that display non-apoptotic caspase activity in vivo.
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Affiliation(s)
- Ho Man Tang
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine; School of Life Sciences, Chinese University of Hong Kong;
| | - Ming Chiu Fung
- School of Life Sciences, Chinese University of Hong Kong;
| | - Ho Lam Tang
- Department of Neurosurgery, Johns Hopkins University School of Medicine;
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184
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White JJ, Mazzeu JF, Coban-Akdemir Z, Bayram Y, Bahrambeigi V, Hoischen A, van Bon BWM, Gezdirici A, Gulec EY, Ramond F, Touraine R, Thevenon J, Shinawi M, Beaver E, Heeley J, Hoover-Fong J, Durmaz CD, Karabulut HG, Marzioglu-Ozdemir E, Cayir A, Duz MB, Seven M, Price S, Ferreira BM, Vianna-Morgante AM, Ellard S, Parrish A, Stals K, Flores-Daboub J, Jhangiani SN, Gibbs RA, Brunner HG, Sutton VR, Lupski JR, Carvalho CMB. WNT Signaling Perturbations Underlie the Genetic Heterogeneity of Robinow Syndrome. Am J Hum Genet 2018; 102:27-43. [PMID: 29276006 DOI: 10.1016/j.ajhg.2017.10.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/06/2017] [Indexed: 12/12/2022] Open
Abstract
Locus heterogeneity characterizes a variety of skeletal dysplasias often due to interacting or overlapping signaling pathways. Robinow syndrome is a skeletal disorder historically refractory to molecular diagnosis, potentially stemming from substantial genetic heterogeneity. All current known pathogenic variants reside in genes within the noncanonical Wnt signaling pathway including ROR2, WNT5A, and more recently, DVL1 and DVL3. However, ∼70% of autosomal-dominant Robinow syndrome cases remain molecularly unsolved. To investigate this missing heritability, we recruited 21 families with at least one family member clinically diagnosed with Robinow or Robinow-like phenotypes and performed genetic and genomic studies. In total, four families with variants in FZD2 were identified as well as three individuals from two families with biallelic variants in NXN that co-segregate with the phenotype. Importantly, both FZD2 and NXN are relevant protein partners in the WNT5A interactome, supporting their role in skeletal development. In addition to confirming that clustered -1 frameshifting variants in DVL1 and DVL3 are the main contributors to dominant Robinow syndrome, we also found likely pathogenic variants in candidate genes GPC4 and RAC3, both linked to the Wnt signaling pathway. These data support an initial hypothesis that Robinow syndrome results from perturbation of the Wnt/PCP pathway, suggest specific relevant domains of the proteins involved, and reveal key contributors in this signaling cascade during human embryonic development. Contrary to the view that non-allelic genetic heterogeneity hampers gene discovery, this study demonstrates the utility of rare disease genomic studies to parse gene function in human developmental pathways.
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Affiliation(s)
- Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Juliana F Mazzeu
- University of Brasilia, Brasilia 70910, Brazil; Robinow Syndrome Foundation, Anoka, MN 55303, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
| | - Vahid Bahrambeigi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Bregje W M van Bon
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul 34303, Turkey
| | - Francis Ramond
- Service de Génétique, CHU-Hôpital Nord, 42000 Saint-Etienne, France
| | - Renaud Touraine
- Service de Génétique, CHU-Hôpital Nord, 42000 Saint-Etienne, France
| | - Julien Thevenon
- Inserm UMR 1231 GAD team, Genetics of Developmental Anomalies, Université de Bourgogne-Franche Comté, 21000 Dijon, France; FHU-TRANSLAD, Université de Bourgogne, 21000 CHU Dijon, France; Centre de génétique, Hôpital Couple-Enfant, CHU de Grenoble-Alpes, 38700 La Tronche, France
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erin Beaver
- Mercy Clinic-Kids Genetics, Mercy Children's Hospital St. Louis, St. Louis, MO 63141, USA
| | - Jennifer Heeley
- Mercy Clinic-Kids Genetics, Mercy Children's Hospital St. Louis, St. Louis, MO 63141, USA
| | - Julie Hoover-Fong
- Greenberg Center for Skeletal Dysplasias, McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Ceren D Durmaz
- Department of Medical Genetics, Ankara University School of Medicine, 06100 Ankara, Turkey
| | - Halil Gurhan Karabulut
- Department of Medical Genetics, Ankara University School of Medicine, 06100 Ankara, Turkey
| | - Ebru Marzioglu-Ozdemir
- Department of Medical Genetics, Erzurum Regional and Training Hospital, 25070 Erzurum, Turkey
| | - Atilla Cayir
- Erzurum Training and Research Hospital, Department of Pediatric Endocrinology, 25070 Erzurum, Turkey
| | - Mehmet B Duz
- Department of Medical Genetics, Cerrahpasa Medical School, Istanbul University, 34452 Istanbul, Turkey
| | - Mehmet Seven
- Department of Medical Genetics, Cerrahpasa Medical School, Istanbul University, 34452 Istanbul, Turkey
| | - Susan Price
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford OX3 7LD, UK
| | | | - Angela M Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, Sao Paulo - SP 05508-090, Brazil
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK; Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX1 2LU, UK
| | - Andrew Parrish
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Karen Stals
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Josue Flores-Daboub
- Department of Pediatric Genetics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA.
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185
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Humanized Flies and Resources for Cross-Species Study. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1076:277-288. [DOI: 10.1007/978-981-13-0529-0_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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186
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Salazar JL, Yamamoto S. Integration of Drosophila and Human Genetics to Understand Notch Signaling Related Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:141-185. [PMID: 30030826 PMCID: PMC6233323 DOI: 10.1007/978-3-319-89512-3_8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Notch signaling research dates back to more than one hundred years, beginning with the identification of the Notch mutant in the fruit fly Drosophila melanogaster. Since then, research on Notch and related genes in flies has laid the foundation of what we now know as the Notch signaling pathway. In the 1990s, basic biological and biochemical studies of Notch signaling components in mammalian systems, as well as identification of rare mutations in Notch signaling pathway genes in human patients with rare Mendelian diseases or cancer, increased the significance of this pathway in human biology and medicine. In the 21st century, Drosophila and other genetic model organisms continue to play a leading role in understanding basic Notch biology. Furthermore, these model organisms can be used in a translational manner to study underlying mechanisms of Notch-related human diseases and to investigate the function of novel disease associated genes and variants. In this chapter, we first briefly review the major contributions of Drosophila to Notch signaling research, discussing the similarities and differences between the fly and human pathways. Next, we introduce several biological contexts in Drosophila in which Notch signaling has been extensively characterized. Finally, we discuss a number of genetic diseases caused by mutations in genes in the Notch signaling pathway in humans and we expand on how Drosophila can be used to study rare genetic variants associated with these and novel disorders. By combining modern genomics and state-of-the art technologies, Drosophila research is continuing to reveal exciting biology that sheds light onto mechanisms of disease.
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Affiliation(s)
- Jose L Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA.
- Program in Developmental Biology, BCM, Houston, TX, USA.
- Department of Neuroscience, BCM, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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187
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188
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Bhargav DS, Sreedevi N, Swapna N, Vivek S, Kovvali S. Whole exome sequencing identifies a novel homozygous frameshift mutation in the ASPM gene, which causes microcephaly 5, primary, autosomal recessive. F1000Res 2017; 6:2163. [PMID: 29375817 PMCID: PMC5770997 DOI: 10.12688/f1000research.12102.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/15/2017] [Indexed: 12/20/2022] Open
Abstract
Microcephaly is a genetically heterogeneous disorder and is one of the frequently notable conditions in paediatric neuropathology which exists either as a single entity or in association with other co-morbidities. More than a single gene is implicated in true microcephaly and the list is growing with the recent advancements in sequencing technologies. Using massive parallel sequencing, we identified a novel frame shift insertion in the abnormal spindle-like microcephaly-associated protein gene in a client with true autosomal recessive primary microcephaly. Exome sequencing in the present case helped in identifying the true cause behind the disease, which helps in the premarital counselling for the sibling to avoid future recurrence of the disorder in the family.
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Affiliation(s)
| | - N Sreedevi
- Department of Clinical Services, All India Institute of Speech and Hearing, Manasagangothri, India
| | - N Swapna
- Department of Speech Language Pathology, All India Institute of Speech and Hearing, Manasagangothri, India
| | - Soumya Vivek
- Unit for Human Genetics, All India Institute of Speech and Hearing, Manasagangothri, India
| | - Srinivas Kovvali
- Unit for Human Genetics, All India Institute of Speech and Hearing, Manasagangothri, India
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189
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De Nobrega AK, Lyons LC. Drosophila: An Emergent Model for Delineating Interactions between the Circadian Clock and Drugs of Abuse. Neural Plast 2017; 2017:4723836. [PMID: 29391952 PMCID: PMC5748135 DOI: 10.1155/2017/4723836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/13/2017] [Indexed: 01/12/2023] Open
Abstract
Endogenous circadian oscillators orchestrate rhythms at the cellular, physiological, and behavioral levels across species to coordinate activity, for example, sleep/wake cycles, metabolism, and learning and memory, with predictable environmental cycles. The 21st century has seen a dramatic rise in the incidence of circadian and sleep disorders with globalization, technological advances, and the use of personal electronics. The circadian clock modulates alcohol- and drug-induced behaviors with circadian misalignment contributing to increased substance use and abuse. Invertebrate models, such as Drosophila melanogaster, have proven invaluable for the identification of genetic and molecular mechanisms underlying highly conserved processes including the circadian clock, drug tolerance, and reward systems. In this review, we highlight the contributions of Drosophila as a model system for understanding the bidirectional interactions between the circadian system and the drugs of abuse, alcohol and cocaine, and illustrate the highly conserved nature of these interactions between Drosophila and mammalian systems. Research in Drosophila provides mechanistic insights into the corresponding behaviors in higher organisms and can be used as a guide for targeted inquiries in mammals.
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Affiliation(s)
- Aliza K. De Nobrega
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Lisa C. Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
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190
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Goffinet AM. The evolution of cortical development: the synapsid-diapsid divergence. Development 2017; 144:4061-4077. [PMID: 29138289 DOI: 10.1242/dev.153908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cerebral cortex covers the rostral part of the brain and, in higher mammals and particularly humans, plays a key role in cognition and consciousness. It is populated with neuronal cell bodies distributed in radially organized layers. Understanding the common and lineage-specific molecular mechanisms that orchestrate cortical development and evolution are key issues in neurobiology. During evolution, the cortex appeared in stem amniotes and evolved divergently in two main branches of the phylogenetic tree: the synapsids (which led to present day mammals) and the diapsids (reptiles and birds). Comparative studies in organisms that belong to those two branches have identified some common principles of cortical development and organization that are possibly inherited from stem amniotes and regulated by similar molecular mechanisms. These comparisons have also highlighted certain essential features of mammalian cortices that are absent or different in diapsids and that probably evolved after the synapsid-diapsid divergence. Chief among these is the size and multi-laminar organization of the mammalian cortex, and the propensity to increase its area by folding. Here, I review recent data on cortical neurogenesis, neuronal migration and cortical layer formation and folding in this evolutionary perspective, and highlight important unanswered questions for future investigation.
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Affiliation(s)
- Andre M Goffinet
- University of Louvain, Avenue Mounier, 73 Box B1.73.16, B1200 Brussels, Belgium
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191
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Liu L, MacKenzie KR, Putluri N, Maletić-Savatić M, Bellen HJ. The Glia-Neuron Lactate Shuttle and Elevated ROS Promote Lipid Synthesis in Neurons and Lipid Droplet Accumulation in Glia via APOE/D. Cell Metab 2017; 26:719-737.e6. [PMID: 28965825 PMCID: PMC5677551 DOI: 10.1016/j.cmet.2017.08.024] [Citation(s) in RCA: 306] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/21/2017] [Accepted: 08/30/2017] [Indexed: 01/04/2023]
Abstract
Elevated reactive oxygen species (ROS) induce the formation of lipids in neurons that are transferred to glia, where they form lipid droplets (LDs). We show that glial and neuronal monocarboxylate transporters (MCTs), fatty acid transport proteins (FATPs), and apolipoproteins are critical for glial LD formation. MCTs enable glia to secrete and neurons to absorb lactate, which is converted to pyruvate and acetyl-CoA in neurons. Lactate metabolites provide a substrate for synthesis of fatty acids, which are processed and transferred to glia by FATP and apolipoproteins. In the presence of high ROS, inhibiting lactate transfer or lowering FATP or apolipoprotein levels decreases glial LD accumulation in flies and in primary mouse glial-neuronal cultures. We show that human APOE can substitute for a fly glial apolipoprotein and that APOE4, an Alzheimer's disease susceptibility allele, is impaired in lipid transport and promotes neurodegeneration, providing insights into disease mechanisms.
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Affiliation(s)
- Lucy Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin R MacKenzie
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology and Advanced Technology Cor, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mirjana Maletić-Savatić
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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192
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Joris M, Schloesser M, Baurain D, Hanikenne M, Muller M, Motte P. Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors. Nucleic Acids Res 2017; 45:9547-9557. [PMID: 28934490 PMCID: PMC5766196 DOI: 10.1093/nar/gkx638] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022] Open
Abstract
Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the programmable site-specific nucleases. Consistent with previous research, we revealed discrepancies between the mutant and morphant phenotypes and we show that these inconsistencies may result from a large number of unsuspected inadvertent morpholino RNA targets. While microinjection of MOs directed against srsf5a (sMOsrsf5a) led to developmental defects, the corresponding homozygous mutants did not display any phenotypic traits. Furthermore, microinjection of sMOsrsf5a into srsf5a−/− led to the previously observed morphant phenotype. Similar findings were observed for other SR genes. sMOsrsf5a alternative target genes were identified using deep mRNA sequencing. We uncovered that only 11 consecutive bases complementary to sMOsrsf5a are sufficient for binding and subsequent blocking of splice sites. In addition, we observed that sMOsrsf5a secondary targets can be reduced by increasing embryos growth temperature after microinjection. Our data contribute to the debate about MO specificity, efficacy and the number of unknown targeted sequences.
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Affiliation(s)
- Marine Joris
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
| | - Marie Schloesser
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, 4000 Liège, Belgium
| | - Marc Hanikenne
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
| | - Marc Muller
- Laboratory for Organogenesis and Regeneration, GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Patrick Motte
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
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193
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Lin JJ, Chin TY, Chen CP, Chan HL, Wu TY. Zika virus: An emerging challenge for obstetrics and gynecology. Taiwan J Obstet Gynecol 2017; 56:585-592. [PMID: 29037541 DOI: 10.1016/j.tjog.2017.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2017] [Indexed: 10/18/2022] Open
Abstract
Microcephaly is a rare birth defect, however, the re-emerging mosquito and sexual transmitted flavivirus, Zika virus (ZIKV), had changed the situation and caused an urgent challenge for the obstetrics and gynecology. This review will brief summarize the epidemiology and virology of ZIKV. And compared the animal models that had developed for the ZIKV infections. These animal models will be benefit for the development of vaccines and anti-ZIKV drugs. Furthermore, the genes that are involved in the causation of microcephaly were also summarized. Finally, the Wnt signal is critical for the brain development as well as innate immune response. Based on previous literatures, we proposed that ZIKV-induced microcephaly might result from the influence of Wnt/β-catenin signaling pathway through the regulation of miRNA-34.
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Affiliation(s)
- Jhe-Jhih Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ting-Yu Chin
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli, Taiwan
| | - Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
| | - Tzong-Yuan Wu
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.
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194
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Cavallin M, Rujano MA, Bednarek N, Medina-Cano D, Bernabe Gelot A, Drunat S, Maillard C, Garfa-Traore M, Bole C, Nitschké P, Beneteau C, Besnard T, Cogné B, Eveillard M, Kuster A, Poirier K, Verloes A, Martinovic J, Bidat L, Rio M, Lyonnet S, Reilly ML, Boddaert N, Jenneson-Liver M, Motte J, Doco-Fenzy M, Chelly J, Attie-Bitach T, Simons M, Cantagrel V, Passemard S, Baffet A, Thomas S, Bahi-Buisson N. WDR81 mutations cause extreme microcephaly and impair mitotic progression in human fibroblasts and Drosophila neural stem cells. Brain 2017; 140:2597-2609. [PMID: 28969387 DOI: 10.1093/brain/awx218] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/06/2017] [Indexed: 12/16/2022] Open
Abstract
Microlissencephaly is a rare brain malformation characterized by congenital microcephaly and lissencephaly. Microlissencephaly is suspected to result from abnormalities in the proliferation or survival of neural progenitors. Despite the recent identification of six genes involved in microlissencephaly, the pathophysiological basis of this condition remains poorly understood. We performed trio-based whole exome sequencing in seven subjects from five non-consanguineous families who presented with either microcephaly or microlissencephaly. This led to the identification of compound heterozygous mutations in WDR81, a gene previously associated with cerebellar ataxia, intellectual disability and quadrupedal locomotion. Patient phenotypes ranged from severe microcephaly with extremely reduced gyration with pontocerebellar hypoplasia to moderate microcephaly with cerebellar atrophy. In patient fibroblast cells, WDR81 mutations were associated with increased mitotic index and delayed prometaphase/metaphase transition. Similarly, in vivo, we showed that knockdown of the WDR81 orthologue in Drosophila led to increased mitotic index of neural stem cells with delayed mitotic progression. In summary, we highlight the broad phenotypic spectrum of WDR81-related brain malformations, which include microcephaly with moderate to extremely reduced gyration and cerebellar anomalies. Our results suggest that WDR81 might have a role in mitosis that is conserved between Drosophila and humans.
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Affiliation(s)
- Mara Cavallin
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Pediatric Neurology APHP- Necker Enfants Malades University Hospital, Paris, France
| | - Maria A Rujano
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Laboratory of Epithelial biology and disease, INSERM UMR 1163, Imagine Institute, Paris, France
| | | | - Daniel Medina-Cano
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Antoinette Bernabe Gelot
- AP-HP, Hôpital Armand Trousseau, Laboratoire d'Anatomie Pathologique, Neuropathologie, Paris, France.,INMED, INSERM U 901 Campus de Luminy, Marseille, France
| | - Severine Drunat
- Department of Medical Genetics and INSERM UMR1141, APHP-Robert DEBRE Universitary Hospital, Paris, France
| | - Camille Maillard
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | | | - Christine Bole
- Genomic Core Facility, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Patrick Nitschké
- Bioinformatics Core Facility, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Claire Beneteau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
| | - Marion Eveillard
- CHU Nantes, Service d'Hématologie Biologique, 9 quai Moncousu, 44093 Nantes CEDEX 1, France
| | - Alice Kuster
- CHU Nantes, Service de réanimation Pédiatrique, Centre de compétence des maladies héréditaires du métabolisme, 38 boulevard Jean Monet, 44093 Nantes, France
| | - Karine Poirier
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France
| | - Alain Verloes
- Department of Medical Genetics and INSERM UMR1141, APHP-Robert DEBRE Universitary Hospital, Paris, France.,Sorbonne-Paris Cité University, Denis Diderot School of Medicine, Paris, France
| | - Jelena Martinovic
- Unit of Fetal Pathology Hospital Antoine Béclère, AP-HP, Clamart, France
| | - Laurent Bidat
- Department of Prenatal Diagnosis, Department of Obstetrics and Gynecology, René Dubos Hospital, Pontoise, France
| | - Marlene Rio
- Service de Génétique, Necker Enfants Malades University Hospital, AP-HP, Paris, France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - M Louise Reilly
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Laboratory of Inherited Kidney Disease, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Diderot University, 75013 Paris, France
| | - Nathalie Boddaert
- Pediatric Radiology, Necker Enfants Malades University Hospital, APHP, Paris, France.,Image - Institut Imagine, INSERM UMR1163, Université Paris Descartes, Hôpital Necker Enfants Malades, Paris, France
| | | | - Jacques Motte
- University of Reims Champagne Ardennes, UFR médecine, Reims, France
| | | | - Jamel Chelly
- IGBMC, INSERM U964, CNRS UMR 7104, Université de Strasbourg. 67404 Illkirch Cedex, France.,Pôle de biologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Tania Attie-Bitach
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Service de Génétique, Necker Enfants Malades University Hospital, AP-HP, Paris, France
| | - Matias Simons
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Laboratory of Epithelial biology and disease, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Vincent Cantagrel
- Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Sandrine Passemard
- Department of Medical Genetics and INSERM UMR1141, APHP-Robert DEBRE Universitary Hospital, Paris, France.,Sorbonne-Paris Cité University, Denis Diderot School of Medicine, Paris, France
| | - Alexandre Baffet
- Institut Curie. CNRS UMR144, PSL Research University, Paris, France
| | - Sophie Thomas
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Nadia Bahi-Buisson
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute, Paris, France.,Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Pediatric Neurology APHP- Necker Enfants Malades University Hospital, Paris, France
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195
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Chao HT, Liu L, Bellen HJ. Building dialogues between clinical and biomedical research through cross-species collaborations. Semin Cell Dev Biol 2017; 70:49-57. [PMID: 28579453 PMCID: PMC5623622 DOI: 10.1016/j.semcdb.2017.05.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/16/2017] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
Today, biomedical science is equipped with an impressive array of technologies and genetic resources that bolster our basic understanding of fundamental biology and enhance the practice of modern medicine by providing clinicians with a diverse toolkit to diagnose, prognosticate, and treat a plethora of conditions. Many significant advances in our understanding of disease mechanisms and therapeutic interventions have arisen from fruitful dialogues between clinicians and biomedical research scientists. However, the increasingly specialized scientific and medical disciplines, globalization of science and technology, and complex datasets often hinder the development of effective interdisciplinary collaborations between clinical medicine and biomedical research. The goal of this review is to provide examples of diverse strategies to enhance communication and collaboration across diverse disciplines. First, we discuss examples of efforts to foster interdisciplinary collaborations at institutional and multi-institutional levels. Second, we explore resources and tools for clinicians and research scientists to facilitate effective bi-directional dialogues. Third, we use our experiences in neurobiology and human genetics to highlight how communication between clinical medicine and biomedical research lead to effective implementation of cross-species model organism approaches to uncover the biological underpinnings of health and disease.
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Affiliation(s)
- Hsiao-Tuan Chao
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine, Houston, TX 77030, United States; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, United States.
| | - Lucy Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, United States; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, United States
| | - Hugo J Bellen
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, United States; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, United States; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, United States; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, United States; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, United States.
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196
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Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SHL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 2017; 9:83. [PMID: 28934986 PMCID: PMC5607840 DOI: 10.1186/s13073-017-0472-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. RESULTS In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. CONCLUSIONS Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Amber N Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sailaja Golla
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lauren Dengle
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Reuben Matalon
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Lisa Emrick
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica B Proud
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Treadwell-Deering
- Department of Psychiatry and Behavioral Sciences, Child and Adolescent Psychiatry Division, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hannele Koillinen
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Chester Brown
- Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38105, USA.,Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | - Nora Urraca
- Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | | | | | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Patricia I Bader
- Northeast Indiana Genetic Counseling Center, Wayne, IN, 46804, USA
| | - Gary Bellus
- Section of Clinical Genetics & Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael Cummings
- Department of Psychiatry Erie County Medical Center, Buffalo, NY, 14215, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Myla Ashfaq
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | | | - Robert Wildin
- St. Luke's Children's Hospital, Boise, ID, 83702, USA.,The National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Anita E Beck
- Seattle Children's Hospital, Seattle, WA, 98105, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Lindsay Elton
- Child Neurology Consultants of Austin, Austin, TX, 78731, USA
| | - Shaun Varghese
- THINK Neurology for Kids/Children's Memorial Hermann Hospital, The Woodlands, TX, 77380, USA
| | - Edward Buchanan
- Division of Plastic Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Mathilde Lefebvre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sung-Hae L Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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197
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Duerinckx S, Abramowicz M. The genetics of congenitally small brains. Semin Cell Dev Biol 2017; 76:76-85. [PMID: 28912110 DOI: 10.1016/j.semcdb.2017.09.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 12/14/2022]
Abstract
Primary microcephaly (PM) refers to a congenitally small brain, resulting from insufficient prenatal production of neurons, and serves as a model disease for brain volumic development. Known PM genes delineate several cellular pathways, among which the centriole duplication pathway, which provide interesting clues about the cellular mechanisms involved. The general interest of the genetic dissection of PM is illustrated by the convergence of Zika virus infection and PM gene mutations on congenital microcephaly, with CENPJ/CPAP emerging as a key target. Physical (protein-protein) and genetic (digenic inheritance) interactions of Wdr62 and Aspm have been demonstrated in mice, and should now be sought in humans using high throughput parallel sequencing of multiple PM genes in PM patients and control subjects, in order to categorize mutually interacting genes, hence delineating functional pathways in vivo in humans.
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Affiliation(s)
- Sarah Duerinckx
- IRIBHM, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Marc Abramowicz
- IRIBHM, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium; Department of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
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198
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Ultrastructural features of aberrant glial cells isolated from the spinal cord of paralytic rats expressing the amyotrophic lateral sclerosis-linked SOD1G93A mutation. Cell Tissue Res 2017; 370:391-401. [PMID: 28864831 DOI: 10.1007/s00441-017-2681-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/07/2017] [Indexed: 12/24/2022]
Abstract
In the rat model of amyotrophic lateral sclerosis expressing the G93A superoxide dismutase-1 mutation, motor neuron death and rapid paralysis progression are associated with the emergence of a population of aberrant glial cells (AbAs) that proliferate in the degenerating spinal cord. Targeting of AbAs with anti-neoplasic drugs reduced paralysis progression, suggesting a pathogenic potential contribution of these cells accelerating paralysis progression. In the present study, analyze the cellular and ultrastructural features of AbAs following their isolation and establishment in culture during several passages. We found that AbAs exhibit permanent loss of contact inhibition, absence of intermediate filaments and abundance of microtubules, together with an important production of extracellular matrix components. Remarkably, AbAs also exhibited exacerbated ER stress together with a significant abundance of lipid droplets, as well as autophagic and secretory vesicles, all characteristic features of cellular stress and inflammatory activation. Taken together, the present data show AbA cells as a unique aberrant phenotype for a glial cell that might explain their pathogenic and neurotoxic effects.
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199
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Wangler MF, Yamamoto S, Chao HT, Posey JE, Westerfield M, Postlethwait J, Hieter P, Boycott KM, Campeau PM, Bellen HJ. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research. Genetics 2017; 207:9-27. [PMID: 28874452 PMCID: PMC5586389 DOI: 10.1534/genetics.117.203067] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions. Here, we review the current state of research into undiagnosed diseases, highlighting large efforts in North America and internationally, including the Undiagnosed Diseases Network (UDN) (Supplemental Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM). We discuss how merging human genetics with model organism research guides experimental studies to solve these medical mysteries, gain new insights into disease pathogenesis, and uncover new therapeutic strategies.
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Affiliation(s)
- Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Hsiao-Tuan Chao
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4C, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario K1H 8L1, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Quebec H3T 1C5, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
- Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, Texas 77030
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200
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Abstract
Several recent studies in a number of model systems including zebrafish, Arabidopsis, and mouse have revealed phenotypic differences between knockouts (i.e., mutants) and knockdowns (e.g., antisense-treated animals). These differences have been attributed to a number of reasons including off-target effects of the antisense reagents. An alternative explanation was recently proposed based on a zebrafish study reporting that genetic compensation was observed in egfl7 mutant but not knockdown animals. Dosage compensation was first reported in Drosophila in 1932, and genetic compensation in response to a gene knockout was first reported in yeast in 1969. Since then, genetic compensation has been documented many times in a number of model organisms; however, our understanding of the underlying molecular mechanisms remains limited. In this review, we revisit studies reporting genetic compensation in higher eukaryotes and outline possible molecular mechanisms, which may include both transcriptional and posttranscriptional processes.
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Affiliation(s)
- Mohamed A. El-Brolosy
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail:
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