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Deng H, Jia G, Li P, Tang Y, Zhao L, Yang Q, Zhao J, Wang J, Tu Y, Yong X, Zhang S, Mo X, Billadeau DD, Su Z, Jia D. The WDR11 complex is a receptor for acidic-cluster-containing cargo proteins. Cell 2024; 187:4272-4288.e20. [PMID: 39013469 PMCID: PMC11316641 DOI: 10.1016/j.cell.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/06/2024] [Accepted: 06/18/2024] [Indexed: 07/18/2024]
Abstract
Vesicle trafficking is a fundamental process that allows for the sorting and transport of specific proteins (i.e., "cargoes") to different compartments of eukaryotic cells. Cargo recognition primarily occurs through coats and the associated proteins at the donor membrane. However, it remains unclear whether cargoes can also be selected at other stages of vesicle trafficking to further enhance the fidelity of the process. The WDR11-FAM91A1 complex functions downstream of the clathrin-associated AP-1 complex to facilitate protein transport from endosomes to the TGN. Here, we report the cryo-EM structure of human WDR11-FAM91A1 complex. WDR11 directly and specifically recognizes a subset of acidic clusters, which we term super acidic clusters (SACs). WDR11 complex assembly and its binding to SAC-containing proteins are indispensable for the trafficking of SAC-containing proteins and proper neuronal development in zebrafish. Our studies thus uncover that cargo proteins could be recognized in a sequence-specific manner downstream of a protein coat.
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Affiliation(s)
- Huaqing Deng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guowen Jia
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Ping Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yingying Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Qin Yang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jia Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jinrui Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yingfeng Tu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Xianming Mo
- Department of Pediatric Surgery and Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhaoming Su
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610044, China.
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China.
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2
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Schmidt L, Saynisch M, Hoegsbjerg C, Schmidt A, Mackey A, Lackmann JW, Müller S, Koch M, Brachvogel B, Kjaer M, Antczak P, Krüger M. Spatial proteomics of skeletal muscle using thin cryosections reveals metabolic adaptation at the muscle-tendon transition zone. Cell Rep 2024; 43:114374. [PMID: 38900641 DOI: 10.1016/j.celrep.2024.114374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/05/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Morphological studies of skeletal muscle tissue provide insights into the architecture of muscle fibers, the surrounding cells, and the extracellular matrix (ECM). However, a spatial proteomics analysis of the skeletal muscle including the muscle-tendon transition zone is lacking. Here, we prepare cryotome muscle sections of the mouse soleus muscle and measure each slice using short liquid chromatography-mass spectrometry (LC-MS) gradients. We generate 3,000 high-resolution protein profiles that serve as the basis for a network analysis to reveal the complex architecture of the muscle-tendon junction. Among the protein profiles that increase from muscle to tendon, we find proteins related to neuronal activity, fatty acid biosynthesis, and the renin-angiotensin system (RAS). Blocking the RAS in cultured mouse tenocytes using losartan reduces the ECM synthesis. Overall, our analysis of thin cryotome sections provides a spatial proteome of skeletal muscle and reveals that the RAS acts as an additional regulator of the matrix within muscle-tendon junctions.
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Affiliation(s)
- Luisa Schmidt
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Michael Saynisch
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Christian Hoegsbjerg
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Abigail Mackey
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan-Wilm Lackmann
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Stefan Müller
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Michael Kjaer
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philipp Antczak
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
| | - Marcus Krüger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
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Calì F, Di Blasi FD, Avola E, Vinci M, Musumeci A, Gloria A, Greco D, Raciti DR, Zagami A, Rizzo B, Città S, Federico C, Vetri L, Saccone S, Buono S. Specific Learning Disorders: Variation Analysis of 15 Candidate Genes in 9 Multiplex Families. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1503. [PMID: 37629793 PMCID: PMC10456226 DOI: 10.3390/medicina59081503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/13/2023] [Accepted: 08/20/2023] [Indexed: 08/27/2023]
Abstract
Background and Objectives: Specific Learning Disorder (SLD) is a complex neurobiological disorder characterized by a persistent difficult in reading (dyslexia), written expression (dysgraphia), and mathematics (dyscalculia). The hereditary and genetic component is one of the underlying causes of SLD, but the relationship between genes and the environment should be considered. Several genetic studies were performed in different populations to identify causative genes. Materials and Methods: Here, we show the analysis of 9 multiplex families with at least 2 individuals diagnosed with SLD per family, with a total of 37 persons, 21 of whom are young subjects with SLD, by means of Next-Generation Sequencing (NGS) to identify possible causative mutations in a panel of 15 candidate genes: CCPG1, CYP19A1, DCDC2, DGKI, DIP2A, DYM, GCFC2, KIAA0319, MC5R, MRPL19, NEDD4L, PCNT, PRMT2, ROBO1, and S100B. Results: We detected, in eight families out nine, SNP variants in the DGKI, DIP2A, KIAA0319, and PCNT genes, even if in silico analysis did not show any causative effect on this behavioral condition. In all cases, the mutation was transmitted by one of the two parents, thus excluding the case of de novo mutation. Moreover, the parent carrying the allelic variant transmitted to the children, in six out of seven families, reports language difficulties. Conclusions: Although the present results cannot be considered conclusive due to the limited sample size, the identification of genetic variants in the above genes can provide input for further research on the same, as well as on other genes/mutations, to better understand the genetic basis of this disorder, and from this perspective, to better understand also the neuropsychological and social aspects connected to this disorder, which affects an increasing number of young people.
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Affiliation(s)
- Francesco Calì
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | | | - Emanuela Avola
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Mirella Vinci
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Antonino Musumeci
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Angelo Gloria
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Donatella Greco
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Daniela Rita Raciti
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Alessandro Zagami
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Biagio Rizzo
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Santina Città
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Concetta Federico
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Luigi Vetri
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
| | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Serafino Buono
- Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy; (F.C.); (F.D.D.B.); (S.B.)
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Zhao J, Yang Q, Cheng C, Wang Z. Cumulative genetic score of KIAA0319 affects reading ability in Chinese children: moderation by parental education and mediation by rapid automatized naming. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2023; 19:10. [PMID: 37259151 DOI: 10.1186/s12993-023-00212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
KIAA0319, a well-studied candidate gene, has been shown to be associated with reading ability and developmental dyslexia. In the present study, we investigated whether KIAA0319 affects reading ability by interacting with the parental education level and whether rapid automatized naming (RAN), phonological awareness and morphological awareness mediate the relationship between KIAA0319 and reading ability. A total of 2284 Chinese children from primary school grades 3 and 6 participated in this study. Chinese character reading accuracy and word reading fluency were used as measures of reading abilities. The cumulative genetic risk score (CGS) of 13 SNPs in KIAA0319 was calculated. Results revealed interaction effect between CGS of KIAA0319 and parental education level on reading fluency. The interaction effect suggested that individuals with a low CGS of KIAA0319 were better at reading fluency in a positive environment (higher parental educational level) than individuals with a high CGS. Moreover, the interaction effect coincided with the differential susceptibility model. The results of the multiple mediator model revealed that RAN mediates the impact of the genetic cumulative effect of KIAA0319 on reading abilities. These findings provide evidence that KIAA0319 is a risk vulnerability gene that interacts with environmental factor to impact reading abilities and demonstrate the reliability of RAN as an endophenotype between genes and reading associations.
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Affiliation(s)
- Jingjing Zhao
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Yanta District, 199 South Chang'an Road, Xi'an, 710062, China.
| | - Qing Yang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Yanta District, 199 South Chang'an Road, Xi'an, 710062, China
| | - Chen Cheng
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Yanta District, 199 South Chang'an Road, Xi'an, 710062, China
| | - Zhengjun Wang
- School of Psychology, Shaanxi Normal University and Shaanxi Provincial Key Research Center of Child Mental and Behavioral Health, Yanta District, 199 South Chang'an Road, Xi'an, 710062, China.
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5
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How the Competition for Cysteine May Promote Infection of SARS-CoV-2 by Triggering Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12020483. [PMID: 36830041 PMCID: PMC9952211 DOI: 10.3390/antiox12020483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
SARS-CoV-2 induces a broad range of clinical manifestations. Besides the main receptor, ACE2, other putative receptors and co-receptors have been described and could become genuinely relevant to explain the different tropism manifested by new variants. In this study, we propose a biochemical model envisaging the competition for cysteine as a key mechanism promoting the infection and the selection of host receptors. The SARS-CoV-2 infection produces ROS and triggers a massive biosynthesis of proteins rich in cysteine; if this amino acid becomes limiting, glutathione levels are depleted and cannot control oxidative stress. Hence, infection succeeds. A receptor should be recognized as a marker of suitable intracellular conditions, namely the full availability of amino acids except for low cysteine. First, we carried out a comparative investigation of SARS-CoV-2 proteins and human ACE2. Then, using hierarchical cluster protein analysis, we searched for similarities between all human proteins and spike produced by the latest variant, Omicron BA.1. We found 32 human proteins very close to spike in terms of amino acid content. Most of these potential SARS-CoV-2 receptors have less cysteine than spike. We suggest that these proteins could signal an intracellular shortage of cysteine, predicting a burst of oxidative stress when used as viral entry mediators.
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6
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Zane G, Silveria M, Meyer N, White T, Duan R, Zou X, Chapman M. Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution. Acta Crystallogr D Struct Biol 2023; 79:140-153. [PMID: 36762860 PMCID: PMC9912921 DOI: 10.1107/s2059798322012190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as serotypes), each with their own transfection characteristics. Here, a high-resolution cryo-electron microscopy structure (2.2 Å) of AAV serotype 4 (AAV4) is presented. The receptor responsible for transduction of the AAV4 clade of AAV viruses (including AAV11, AAV12 and AAVrh32.33) is unknown. Other AAVs interact with the same cell receptor, adeno-associated virus receptor (AAVR), in one of two different ways. AAV5-like viruses interact exclusively with the polycystic kidney disease-like 1 (PKD1) domain of AAVR, while most other AAVs interact primarily with the PKD2 domain. A comparison of the present AAV4 structure with prior corresponding structures of AAV5, AAV2 and AAV1 in complex with AAVR provides a foundation for understanding why the AAV4-like clade is unable to interact with either PKD1 or PKD2 of AAVR. The conformation of the AAV4 capsid in variable regions I, III, IV and V on the viral surface appears to be sufficiently different from AAV2 to ablate binding with PKD2. Differences between AAV4 and AAV5 in variable region VII appear to be sufficient to exclude binding with PKD1.
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Affiliation(s)
- Grant Zane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Mark Silveria
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Nancy Meyer
- Center for Spatial Systems Biomedicine, Oregon Health Sciences University, Portland, Oregon, USA
| | - Tommi White
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Bayer Crop Science, Bayer (United States), Chesterfield, MO 63017, USA
- Electron Microscopy Core, University of Missouri, Columbia, MO 65211, USA
| | - Rui Duan
- Dalton Cardiovascular Center, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Center, University of Missouri, Columbia, MO 65211, USA
- Department of Physics, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Michael Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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Large EE, Silveria MA, Weerakoon O, White TA, Chapman MS. Cross-Species Permissivity: Structure of a Goat Adeno-Associated Virus and Its Complex with the Human Receptor AAVR. J Virol 2022; 96:e0148422. [PMID: 36453885 PMCID: PMC9769368 DOI: 10.1128/jvi.01484-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/06/2022] [Indexed: 12/05/2022] Open
Abstract
Adeno-associated virus (AAV) is a small ssDNA satellite virus of high interest (in recombinant form) as a safe and effective gene therapy vector. AAV's human cell entry receptor (AAVR) contains polycystic kidney disease (PKD) domains bound by AAV. Seeking understanding of the spectrum of interactions, goat AAVGo.1 is investigated, because its host is the species most distant from human with reciprocal cross-species cell susceptibility. The structure of AAVGo.1, solved by cryo-EM to 2.9 Å resolution, is most similar to AAV5. Through ELISA (enzyme-linked immunosorbent assay) studies, it is shown that AAVGo.1 binds to human AAVR more strongly than do AAV2 or AAV5, and that it joins AAV5 in a class that binds exclusively to PKD domain 1 (PKD1), in contrast to other AAVs that interact primarily with PKD2. The AAVGo.1 cryo-EM structure of a complex with a PKD12 fragment of AAVR at 2.4 Å resolution shows PKD1 bound with minimal change in virus structure. There are only minor conformational adaptations in AAVR, but there is a near-rigid rotation of PKD1 with maximal displacement of the receptor domain by ~1 Å compared to PKD1 bound to AAV5. AAVGo.1 joins AAV5 as the second member of an emerging class of AAVs whose mode of receptor-binding is completely different from other AAVs, typified by AAV2. IMPORTANCE Adeno-associated virus (AAV) is a small ssDNA satellite parvovirus. As a recombinant vector with a protein shell encapsidating a transgene, recombinant AAV (rAAV) is a leading delivery vehicle for gene therapy, with two FDA-approved treatments and 150 clinical trials for 30 diseases. The human entry receptor AAVR has five PKD domains. To date, all serotypes, except AAV5, have interacted primarily with the second PKD domain, PKD2. Goat is the AAV host most distant from human with cross-species cell infectivity. AAVGo.1 is similar in structure to AAV5, the two forming a class with a distinct mode of receptor-binding. Within the two classes, binding interactions are mostly conserved, giving an indication of the latitude available in modulating delivery vectors.
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Affiliation(s)
- Edward E. Large
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Mark A. Silveria
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Onellah Weerakoon
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Tommi A. White
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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8
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Galesi O, Di Blasi FD, Grillo L, Elia F, Giambirtone MC, Figura MG, Rizzo B, Buono S, Romano C. Dyslexia and Attention Deficit Hyperactivity Disorder Associated to a De Novo 1p34.3 Microdeletion. Genes (Basel) 2022; 13:genes13111926. [PMID: 36360163 PMCID: PMC9689888 DOI: 10.3390/genes13111926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/04/2022] Open
Abstract
The authors report on a boy with dyslexia and attention deficit hyperactivity disorder. A protocol of standardized tests assessed the neuroadaptive profile, allowing deep neuropsychiatric phenotyping. In addition to the diagnosis of dyslexia and attention deficit hyperactivity disorder, such methodology led to endeavor cognitive, adaptive, and academic skills. Chromosomal microarray analysis detected a 452.4 Kb de novo heterozygous microdeletion in chromosomal region 1p34.3, including seven OMIM genes. The authors took a thorough evaluation of the association to the phenotype of the deleted genes. Further reports could strengthen such association.
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Affiliation(s)
- Ornella Galesi
- Laboratory of Medical Genetics, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | | | - Lucia Grillo
- Laboratory of Medical Genetics, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Flaviana Elia
- Unit of Psychology, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | | | - Maria Grazia Figura
- Unit of Neurology and Clinical Neurophysiopathology, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Biagio Rizzo
- Unit of Otorhinolaryngology, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Serafino Buono
- Unit of Psychology, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Corrado Romano
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, 94018 Troina, Italy
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 95123 Catania, Italy
- Correspondence: ; Tel.: +39-095-4781189
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Abstract
Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.
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Affiliation(s)
- Scott
M. Stagg
- Department
of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States
- Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department
of Biomedical Engineering, Oregon Health
& Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S. Chapman
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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10
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Adeno-Associated Virus Receptor-Binding: Flexible Domains and Alternative Conformations through Cryo-Electron Tomography of Adeno-Associated Virus 2 (AAV2) and AAV5 Complexes. J Virol 2022; 96:e0010622. [PMID: 35674430 PMCID: PMC9278096 DOI: 10.1128/jvi.00106-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recombinant forms of adeno-associated virus (rAAV) are vectors of choice in the development of treatments for a number of genetic dispositions. Greater understanding of AAV’s molecular virology is needed to underpin needed improvements in efficiency and specificity. Recent advances have included identification of a near-universal entry receptor, AAVR, and structures detected by cryo-electron microscopy (EM) single particle analysis (SPA) that revealed, at high resolution, only the domains of AAVR most tightly bound to AAV. Here, cryogenic electron tomography (cryo-ET) is applied to reveal the neighboring domains of the flexible receptor. For AAV5, where the PKD1 domain is bound strongly, PKD2 is seen in three configurations extending away from the virus. AAV2 binds tightly to the PKD2 domain at a distinct site, and cryo-ET now reveals four configurations of PKD1, all different from that seen in AAV5. The AAV2 receptor complex also shows unmodeled features on the inner surface that appear to be an equilibrium alternate configuration. Other AAV structures start near the 5-fold axis, but now β-strand A is the minor conformer and, for the major conformer, partially ordered N termini near the 2-fold axis join the canonical capsid jellyroll fold at the βA-βB turn. The addition of cryo-ET is revealing unappreciated complexity that is likely relevant to viral entry and to the development of improved gene therapy vectors. IMPORTANCE With 150 clinical trials for 30 diseases under way, AAV is a leading gene therapy vector. Immunotoxicity at high doses used to overcome inefficient transduction has occasionally proven fatal and highlighted gaps in fundamental virology. AAV enters cells, interacting through distinct sites with different domains of the AAVR receptor, according to AAV clade. Single domains are resolved in structures by cryogenic electron microscopy. Here, the adjoining domains are revealed by cryo-electron tomography of AAV2 and AAV5 complexes. They are in flexible configurations interacting minimally with AAV, despite measurable dependence of AAV2 transduction on both domains.
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Meyer NL, Chapman MS. Adeno-associated virus (AAV) cell entry: structural insights. Trends Microbiol 2022; 30:432-451. [PMID: 34711462 PMCID: PMC11225776 DOI: 10.1016/j.tim.2021.09.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Adeno-associated virus (AAV) is the leading vector in emerging treatments of inherited diseases. Higher transduction efficiencies and cellular specificity are required for broader clinical application, motivating investigations of virus-host molecular interactions during cell entry. High-throughput methods are identifying host proteins more comprehensively, with subsequent molecular studies revealing unanticipated complexity and serotype specificity. Cryogenic electron microscopy (cryo-EM) provides a path towards structural details of these sometimes heterogeneous virus-host complexes, and is poised to illuminate more fully the steps in entry. Here presented, is progress in understanding the distinct steps of glycan attachment, and receptor-mediated entry/trafficking. Comparison with structures of antibody complexes provides new insights on immune neutralization with implications for the design of improved gene therapy vectors.
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Affiliation(s)
- Nancy L Meyer
- Pacific Northwest Cryo-EM Center, Oregon Health and Science University (OHSU) Center for Spatial Systems Biomedicine, Portland, OR, USA
| | - Michael S Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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12
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Tosolini AP, Sleigh JN. Intramuscular Delivery of Gene Therapy for Targeting the Nervous System. Front Mol Neurosci 2020; 13:129. [PMID: 32765219 PMCID: PMC7379875 DOI: 10.3389/fnmol.2020.00129] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Virus-mediated gene therapy has the potential to deliver exogenous genetic material into specific cell types to promote survival and counteract disease. This is particularly enticing for neuronal conditions, as the nervous system is renowned for its intransigence to therapeutic targeting. Administration of gene therapy viruses into skeletal muscle, where distal terminals of motor and sensory neurons reside, has been shown to result in extensive transduction of cells within the spinal cord, brainstem, and sensory ganglia. This route is minimally invasive and therefore clinically relevant for gene therapy targeting to peripheral nerve soma. For successful transgene expression, viruses administered into muscle must undergo a series of processes, including host cell interaction and internalization, intracellular sorting, long-range retrograde axonal transport, endosomal liberation, and nuclear import. In this review article, we outline key characteristics of major gene therapy viruses—adenovirus, adeno-associated virus (AAV), and lentivirus—and summarize the mechanisms regulating important steps in the virus journey from binding at peripheral nerve terminals to nuclear delivery. Additionally, we describe how neuropathology can negatively influence these pathways, and conclude by discussing opportunities to optimize the intramuscular administration route to maximize gene delivery and thus therapeutic potential.
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Affiliation(s)
- Andrew P Tosolini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - James N Sleigh
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.,UK Dementia Research Institute, University College London, London, United Kingdom
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13
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Price KM, Wigg KG, Feng Y, Blokland K, Wilkinson M, He G, Kerr EN, Carter TC, Guger SL, Lovett MW, Strug LJ, Barr CL. Genome-wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders. GENES BRAIN AND BEHAVIOR 2020; 19:e12648. [PMID: 32108986 DOI: 10.1111/gbb.12648] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/28/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022]
Abstract
Reading disabilities (RD) are the most common neurocognitive disorder, affecting 5% to 17% of children in North America. These children often have comorbid neurodevelopmental/psychiatric disorders, such as attention deficit/hyperactivity disorder (ADHD). The genetics of RD and their overlap with other disorders is incompletely understood. To contribute to this, we performed a genome-wide association study (GWAS) for word reading. Then, using summary statistics from neurodevelopmental/psychiatric disorders, we computed polygenic risk scores (PRS) and used them to predict reading ability in our samples. This enabled us to test the shared aetiology between RD and other disorders. The GWAS consisted of 5.3 million single nucleotide polymorphisms (SNPs) and two samples; a family-based sample recruited for reading difficulties in Toronto (n = 624) and a population-based sample recruited in Philadelphia [Philadelphia Neurodevelopmental Cohort (PNC)] (n = 4430). The Toronto sample SNP-based analysis identified suggestive SNPs (P ~ 5 × 10-7 ) in the ARHGAP23 gene, which is implicated in neuronal migration/axon pathfinding. The PNC gene-based analysis identified significant associations (P < 2.72 × 10-6 ) for LINC00935 and CCNT1, located in the region of the KANSL2/CCNT1/LINC00935/SNORA2B/SNORA34/MIR4701/ADCY6 genes on chromosome 12q, with near significant SNP-based analysis. PRS identified significant overlap between word reading and intelligence (R2 = 0.18, P = 7.25 × 10-181 ), word reading and educational attainment (R2 = 0.07, P = 4.91 × 10-48 ) and word reading and ADHD (R2 = 0.02, P = 8.70 × 10-6 ; threshold for significance = 7.14 × 10-3 ). Overlap was also found between RD and autism spectrum disorder (ASD) as top-ranked genes were previously implicated in autism by rare and copy number variant analyses. These findings support shared risk between word reading, cognitive measures, educational outcomes and neurodevelopmental disorders, including ASD.
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Affiliation(s)
- Kaitlyn M Price
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Karen G Wigg
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Yu Feng
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kirsten Blokland
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margaret Wilkinson
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gengming He
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth N Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Tasha-Cate Carter
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Holland Bloorview Rehabilitation Hospital, Toronto, Ontario, Canada
| | - Sharon L Guger
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maureen W Lovett
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Cathy L Barr
- Genetics and Development Division, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada
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14
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Criscitiello MF, Kraev I, Lange S. Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)-Novel insights into camelid immunity. Mol Immunol 2020; 117:37-53. [PMID: 31733447 PMCID: PMC7112542 DOI: 10.1016/j.molimm.2019.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/05/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Furthermore, PADs have been found to be a phylogenetically conserved regulator for extracellular vesicle (EVs) release. EVs are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins in serum and serum-EVs are described for the first time in camelids, using the llama (Lama glama L. 1758) as a model animal. We report a poly-dispersed population of llama serum EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. In serum, 60 deiminated proteins were identified that were not in EVs, and 25 deiminated proteins were found to be unique to EVs, with 43 shared deiminated protein hits between both serum and EVs. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in llama serum. PAD homologues were identified in llama serum by Western blotting, via cross reaction with human PAD antibodies, and detected at an expected 70 kDa size. This is the first report of deiminated proteins in serum and EVs of a camelid species, highlighting a hitherto unrecognized post-translational modification in key immune and metabolic proteins in camelids, which may be translatable to and inform a range of human metabolic and inflammatory pathologies.
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Affiliation(s)
- Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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15
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Zengel J, Carette JE. Structural and cellular biology of adeno-associated virus attachment and entry. Adv Virus Res 2020; 106:39-84. [PMID: 32327148 DOI: 10.1016/bs.aivir.2020.01.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adeno-associated virus (AAV) is a nonenveloped, ssDNA virus in the parvovirus family, which has become one of the leading candidate vectors for human gene therapy. AAV has been studied extensively to identify host cellular factors involved in infection, as well as to identify capsid variants that confer clinically favorable transduction profiles ex vivo and in vivo. Recent advances in technology have allowed for direct genetic approaches to be used to more comprehensively characterize host factors required for AAV infection and allowed for identification of a critical multi-serotype receptor, adeno-associated virus receptor (AAVR). In this chapter, we will discuss the interactions of AAV with its glycan and proteinaceous receptors and describe the host and viral components involved in AAV entry, which requires cellular attachment, endocytosis, trafficking to the trans-Golgi network and nuclear import. AAV serves as a paradigm for entry of nonenveloped viruses. Furthermore, we will discuss the potential of utilizing our increased understanding of virus-host interactions during AAV entry to develop better AAV-based therapeutics, with a focus on host factors and capsid interactions involved in in vivo tropism.
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16
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Landi N, Perdue M. Neuroimaging genetics studies of specific reading disability and developmental language disorder: A review. LANGUAGE AND LINGUISTICS COMPASS 2019; 13:e12349. [PMID: 31844423 PMCID: PMC6913889 DOI: 10.1111/lnc3.12349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Developmental disorders of spoken and written language are heterogeneous in nature with impairments observed across various linguistic, cognitive, and sensorimotor domains. These disorders are also associated with characteristic patterns of atypical neural structure and function that are observable early in development, often before formal schooling begins. Established patterns of heritability point toward genetic contributions, and molecular genetics approaches have identified genes that play a role in these disorders. Still, identified genes account for only a limited portion of phenotypic variance in complex developmental disorders, described as the problem of "missing heritability." The characterization of intermediate phenotypes at the neural level may fill gaps in our understanding of heritability patterns in complex disorders, and the emerging field of neuroimaging genetics offers a promising approach to accomplish this goal. The neuroimaging genetics approach is gaining prevalence in language- and reading-related research as it is well-suited to incorporate behavior, genetics, and neurobiology into coherent etiological models of complex developmental disorders. Here, we review research applying the neuroimaging genetics approach to the study of specific reading disability (SRD) and developmental language disorder (DLD), much of which links genes with known neurodevelopmental function to functional and structural abnormalities in the brain.
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Affiliation(s)
- Nicole Landi
- Department of Psychological Sciences, University of Connecticut, Storrs, Connecticut, United States; Haskins Laboratories, United States
| | - Meaghan Perdue
- Department of Psychological Sciences, University of Connecticut, Storrs, Connecticut, United States; Haskins Laboratories, United States
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17
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Using Human iPSC-Derived Neurons to Uncover Activity-Dependent Non-Coding RNAs. Genes (Basel) 2017; 8:genes8120401. [PMID: 29261115 PMCID: PMC5748719 DOI: 10.3390/genes8120401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/05/2017] [Accepted: 12/13/2017] [Indexed: 12/27/2022] Open
Abstract
Humans are arguably the most complex organisms present on Earth with their ability to imagine, create, and problem solve. As underlying mechanisms enabling these capacities reside in the brain, it is not surprising that the brain has undergone an extraordinary increase in size and complexity within the last few million years. Human induced pluripotent stem cells (hiPSCs) can be differentiated into many cell types that were virtually inaccessible historically, such as neurons. Here, we used hiPSC-derived neurons to investigate the cellular response to activation at the transcript level. Neuronal activation was performed with potassium chloride (KCl) and its effects were assessed by RNA sequencing. Our results revealed the involvement of long non-coding RNAs and human-specific genetic variants in response to neuronal activation and help validate hiPSCs as a valuable resource for the study of human neuronal networks. In summary, we find that genes affected by KCl-triggered activation are implicated in pathways that drive cell proliferation, differentiation, and the emergence of specialized morphological features. Interestingly, non-coding RNAs of various classes are amongst the most highly expressed genes in activated hiPSC-derived neurons, thus suggesting these play crucial roles in neural pathways and may significantly contribute to the unique functioning of the human brain.
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18
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Adeno-associated Virus (AAV) Serotypes Have Distinctive Interactions with Domains of the Cellular AAV Receptor. J Virol 2017; 91:JVI.00391-17. [PMID: 28679762 PMCID: PMC5571256 DOI: 10.1128/jvi.00391-17] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/27/2017] [Indexed: 12/20/2022] Open
Abstract
Adeno-associated virus (AAV) entry is determined by its interactions with specific surface glycans and a proteinaceous receptor(s). Adeno-associated virus receptor (AAVR) (also named KIAA0319L) is an essential cellular receptor required for the transduction of vectors derived from multiple AAV serotypes, including the evolutionarily distant serotypes AAV2 and AAV5. Here, we further biochemically characterize the AAV-AAVR interaction and define the domains within the ectodomain of AAVR that facilitate this interaction. By using a virus overlay assay, it was previously shown that the major AAV2 binding protein in membrane preparations of human cells corresponds to a glycoprotein with a molecular mass of 150 kDa. By establishing a purification procedure, performing further protein separation by two-dimensional electrophoresis, and utilizing mass spectrometry, we now show that this glycoprotein is identical to AAVR. While we find that AAVR is an N-linked glycosylated protein, this glycosylation is not a strict requirement for AAV2 binding or functional transduction. Using a combination of genetic complementation with deletion constructs and virus overlay assays with individual domains, we find that AAV2 functionally interacts predominantly with the second Ig-like polycystic kidney disease (PKD) repeat domain (PKD2) present in the ectodomain of AAVR. In contrast, AAV5 interacts primarily through the first, most membrane-distal, PKD domain (PKD1) of AAVR to promote transduction. Furthermore, other AAV serotypes, including AAV1 and -8, require a combination of PKD1 and PKD2 for optimal transduction. These results suggest that despite their shared dependence on AAVR as a critical entry receptor, different AAV serotypes have evolved distinctive interactions with the same receptor. IMPORTANCE Over the past decade, AAV vectors have emerged as leading gene delivery tools for therapeutic applications and biomedical research. However, fundamental aspects of the AAV life cycle, including how AAV interacts with host cellular factors to facilitate infection, are only partly understood. In particular, AAV receptors contribute significantly to AAV vector transduction efficiency and tropism. The recently identified AAV receptor (AAVR) is a key host receptor for multiple serotypes, including the most studied serotype, AAV2. AAVR binds directly to AAV2 particles and is rate limiting for viral transduction. Defining the AAV-AAVR interface in more detail is important to understand how AAV engages with its cellular receptor and how the receptor facilitates the entry process. Here, we further define AAV-AAVR interactions, genetically and biochemically, and show that different AAV serotypes have discrete interactions with the Ig-like PKD domains of AAVR. These findings reveal an unexpected divergence of AAVR engagement within these parvoviruses.
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19
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The role of READ1 and KIAA0319 genetic variations in developmental dyslexia: testing main and interactive effects. J Hum Genet 2017; 62:949-955. [DOI: 10.1038/jhg.2017.80] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 12/23/2022]
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20
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Franquinho F, Nogueira-Rodrigues J, Duarte JM, Esteves SS, Carter-Su C, Monaco AP, Molnár Z, Velayos-Baeza A, Brites P, Sousa MM. The Dyslexia-susceptibility Protein KIAA0319 Inhibits Axon Growth Through Smad2 Signaling. Cereb Cortex 2017; 27:1732-1747. [PMID: 28334068 PMCID: PMC5905272 DOI: 10.1093/cercor/bhx023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/23/2016] [Accepted: 01/18/2017] [Indexed: 01/21/2023] Open
Abstract
KIAA0319 is a transmembrane protein associated with dyslexia with a presumed role in neuronal migration. Here we show that KIAA0319 expression is not restricted to the brain but also occurs in sensory and spinal cord neurons, increasing from early postnatal stages to adulthood and being downregulated by injury. This suggested that KIAA0319 participates in functions unrelated to neuronal migration. Supporting this hypothesis, overexpression of KIAA0319 repressed axon growth in hippocampal and dorsal root ganglia neurons; the intracellular domain of KIAA0319 was sufficient to elicit this effect. A similar inhibitory effect was observed in vivo as axon regeneration was impaired after transduction of sensory neurons with KIAA0319. Conversely, the deletion of Kiaa0319 in neurons increased neurite outgrowth in vitro and improved axon regeneration in vivo. At the mechanistic level, KIAA0319 engaged the JAK2-SH2B1 pathway to activate Smad2, which played a central role in KIAA0319-mediated repression of axon growth. In summary, we establish KIAA0319 as a novel player in axon growth and regeneration with the ability to repress the intrinsic growth potential of axons. This study describes a novel regulatory mechanism operating during peripheral nervous system and central nervous system axon growth, and offers novel targets for the development of effective therapies to promote axon regeneration.
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Affiliation(s)
- Filipa Franquinho
- Nerve Regeneration group, Instituto de Biologia Molecular e Celular – IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar – ICBAS, 4050-313 Porto, Portugal
| | - Joana Nogueira-Rodrigues
- Nerve Regeneration group, Instituto de Biologia Molecular e Celular – IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Joana M. Duarte
- Nerve Regeneration group, Instituto de Biologia Molecular e Celular – IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Sofia S. Esteves
- Nerve Regeneration group, Instituto de Biologia Molecular e Celular – IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Christin Carter-Su
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109-22, USA
| | - Anthony P. Monaco
- The Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
- Office of the President, Ballou Hall, Tufts University, Medford, MA 02155, USA
| | - Zoltán Molnár
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | | | - Pedro Brites
- Nerve Regeneration group, Instituto de Biologia Molecular e Celular – IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Mónica M. Sousa
- Nerve Regeneration group, Instituto de Biologia Molecular e Celular – IBMC and Instituto de Inovação e Investigação em Saúde, University of Porto, 4200-135 Porto, Portugal
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Neurogenetics of developmental dyslexia: from genes to behavior through brain neuroimaging and cognitive and sensorial mechanisms. Transl Psychiatry 2017; 7:e987. [PMID: 28045463 PMCID: PMC5545717 DOI: 10.1038/tp.2016.240] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 01/18/2023] Open
Abstract
Developmental dyslexia (DD) is a complex neurodevelopmental deficit characterized by impaired reading acquisition, in spite of adequate neurological and sensorial conditions, educational opportunities and normal intelligence. Despite the successful characterization of DD-susceptibility genes, we are far from understanding the molecular etiological pathways underlying the development of reading (dis)ability. By focusing mainly on clinical phenotypes, the molecular genetics approach has yielded mixed results. More optimally reduced measures of functioning, that is, intermediate phenotypes (IPs), represent a target for researching disease-associated genetic variants and for elucidating the underlying mechanisms. Imaging data provide a viable IP for complex neurobehavioral disorders and have been extensively used to investigate both morphological, structural and functional brain abnormalities in DD. Performing joint genetic and neuroimaging studies in humans is an emerging strategy to link DD-candidate genes to the brain structure and function. A limited number of studies has already pursued the imaging-genetics integration in DD. However, the results are still not sufficient to unravel the complexity of the reading circuit due to heterogeneous study design and data processing. Here, we propose an interdisciplinary, multilevel, imaging-genetic approach to disentangle the pathways from genes to behavior. As the presence of putative functional genetic variants has been provided and as genetic associations with specific cognitive/sensorial mechanisms have been reported, new hypothesis-driven imaging-genetic studies must gain momentum. This approach would lead to the optimization of diagnostic criteria and to the early identification of 'biologically at-risk' children, supporting the definition of adequate and well-timed prevention strategies and the implementation of novel, specific remediation approach.
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Comparative Transcriptomics of Alternative Developmental Phenotypes in a Marine Gastropod. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:151-67. [DOI: 10.1002/jez.b.22674] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 11/07/2022]
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Affiliation(s)
| | - R. Jude Samulski
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
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The Roles of Genes in the Neuronal Migration and Neurite Outgrowth Network in Developmental Dyslexia: Single- and Multiple-Risk Genetic Variants. Mol Neurobiol 2015; 53:3967-3975. [PMID: 26184631 DOI: 10.1007/s12035-015-9334-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 07/01/2015] [Indexed: 01/21/2023]
Abstract
Abnormal regulation of neural migration and neurite growth is thought to be an important feature of developmental dyslexia (DD). We investigated 16 genetic variants, selected by bioinformatics analyses, in six key genes in the neuronal migration and neurite outgrowth network in a Chinese population. We first observed that KIAA0319L rs28366021, KIAA0319 rs4504469, and DOCK4 rs2074130 were significantly associated with DD risk after false discovery rate (FDR) adjustment for multiple comparisons (odds ratio (OR) = 0.672, 95 % confidence interval (CI) = 0.505-0.894, P = 0.006; OR = 1.608, 95 % CI = 1.174-2.203, P = 0.003; OR = 1.681, 95 % CI = 1.203-2.348, P = 0.002). The following classification and regression tree (CART) analysis revealed a prediction value of gene-gene interactions among DOCK4 rs2074130, KIAA0319 rs4504469, DCDC2 rs2274305, and KIAA0319L rs28366021 variants. Compared with the lowest risk carriers of the combination of rs2074130 CC, rs4504469 CC, and rs2274305 GG genotype, individuals carrying the combined genotypes of rs2074130 CC, rs4504469 CT or TT, and rs28366021 GG had a significantly increased risk for DD (OR = 2.492, 95 % CI = 1.447-4.290, P = 0.001); individuals with the combination of rs2074130 CT or TT and rs28366021 GG genotype exhibited the highest risk for DD (OR = 2.770, 95 % CI = 2.265-6.276, P = 0.000). A significant dose effect was observed among these four variants (P for trend = 0.000). In summary, this study supports the importance of single- and multiple-risk variants in this network in DD susceptibility in China.
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An assessment of gene-by-gene interactions as a tool to unfold missing heritability in dyslexia. Hum Genet 2015; 134:749-60. [DOI: 10.1007/s00439-015-1555-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/12/2015] [Indexed: 12/24/2022]
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Mascheretti S, Riva V, Giorda R, Beri S, Lanzoni LFE, Cellino MR, Marino C. KIAA0319 and ROBO1: evidence on association with reading and pleiotropic effects on language and mathematics abilities in developmental dyslexia. J Hum Genet 2014; 59:189-97. [PMID: 24430574 DOI: 10.1038/jhg.2013.141] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/13/2013] [Accepted: 12/22/2013] [Indexed: 01/17/2023]
Abstract
Substantial heritability has been reported for developmental dyslexia (DD), and KIAA0319 and ROBO1 appear as more than plausible candidate susceptibility genes for this developmental disorder. Converging evidence indicates that developmental difficulties in oral language and mathematics can predate or co-occur with DD, and substantial genetic correlations have been found between these abilities and reading traits. In this study, we explored the role of eight single-nucleotide polymorphisms spanning within KIAA0319 and ROBO1 genes, and DD as a dichotomic trait, related neuropsychological phenotypes and comorbid language and mathematical (dis)abilities in a large cohort of 493 Italian nuclear families ascertained through a proband with a diagnosis of DD. Marker-trait association was analyzed by implementing a general test of family-based association for quantitative traits (that is, the Quantitative Transmission Disequilibrium Test, version 2.5.1). By providing evidence for significant association with mathematics skills, our data add further result in support of ROBO1 contributing to the deficits in DD and its correlated phenotypes. Taken together, our findings shed further light into the etiologic basis and the phenotypic complexity of this developmental disorder.
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Affiliation(s)
- Sara Mascheretti
- Child Psychopathology Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Valentina Riva
- Child Psychopathology Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Roberto Giorda
- Molecular Biology Lab, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Silvana Beri
- Molecular Biology Lab, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | | | - Maria Rosaria Cellino
- Centro Regionale di Riferimento per i Disturbi dell'Apprendimento-CRRDA, ULSS 20, Verona, Italy
| | - Cecilia Marino
- 1] Centre de recherche de l'Institut universitaire en santé mentale de Québec, Québec, QC, Canada [2] Département de Psychiatrie et Neurosciences, Faculté de Médecine, Université Laval, Québec, QC, Canada
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Worthey EA, Raca G, Laffin JJ, Wilk BM, Harris JM, Jakielski KJ, Dimmock DP, Strand EA, Shriberg LD. Whole-exome sequencing supports genetic heterogeneity in childhood apraxia of speech. J Neurodev Disord 2013; 5:29. [PMID: 24083349 PMCID: PMC3851280 DOI: 10.1186/1866-1955-5-29] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/16/2013] [Indexed: 12/12/2022] Open
Abstract
Background Childhood apraxia of speech (CAS) is a rare, severe, persistent pediatric motor speech disorder with associated deficits in sensorimotor, cognitive, language, learning and affective processes. Among other neurogenetic origins, CAS is the disorder segregating with a mutation in FOXP2 in a widely studied, multigenerational London family. We report the first whole-exome sequencing (WES) findings from a cohort of 10 unrelated participants, ages 3 to 19 years, with well-characterized CAS. Methods As part of a larger study of children and youth with motor speech sound disorders, 32 participants were classified as positive for CAS on the basis of a behavioral classification marker using auditory-perceptual and acoustic methods that quantify the competence, precision and stability of a speaker’s speech, prosody and voice. WES of 10 randomly selected participants was completed using the Illumina Genome Analyzer IIx Sequencing System. Image analysis, base calling, demultiplexing, read mapping, and variant calling were performed using Illumina software. Software developed in-house was used for variant annotation, prioritization and interpretation to identify those variants likely to be deleterious to neurodevelopmental substrates of speech-language development. Results Among potentially deleterious variants, clinically reportable findings of interest occurred on a total of five chromosomes (Chr3, Chr6, Chr7, Chr9 and Chr17), which included six genes either strongly associated with CAS (FOXP1 and CNTNAP2) or associated with disorders with phenotypes overlapping CAS (ATP13A4, CNTNAP1, KIAA0319 and SETX). A total of 8 (80%) of the 10 participants had clinically reportable variants in one or two of the six genes, with variants in ATP13A4, KIAA0319 and CNTNAP2 being the most prevalent. Conclusions Similar to the results reported in emerging WES studies of other complex neurodevelopmental disorders, our findings from this first WES study of CAS are interpreted as support for heterogeneous genetic origins of this pediatric motor speech disorder with multiple genes, pathways and complex interactions. We also submit that our findings illustrate the potential use of WES for both gene identification and case-by-case clinical diagnostics in pediatric motor speech disorders.
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Affiliation(s)
- Elizabeth A Worthey
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Avenue, Madison, WI, 53705, USA.
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Platt MP, Adler WT, Mehlhorn AJ, Johnson GC, Wright KA, Choi RT, Tsang WH, Poon MW, Yeung SY, Waye MMY, Galaburda AM, Rosen GD. Embryonic disruption of the candidate dyslexia susceptibility gene homolog Kiaa0319-like results in neuronal migration disorders. Neuroscience 2013; 248:585-93. [PMID: 23831424 DOI: 10.1016/j.neuroscience.2013.06.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 02/04/2023]
Abstract
Developmental dyslexia, the most common childhood learning disorder, is highly heritable, and recent studies have identified KIAA0319-Like (KIAA0319L) as a candidate dyslexia susceptibility gene at the 1p36-34 (DYX8) locus. In this experiment, we investigated the anatomical effects of knocking down this gene during rat corticogenesis. Cortical progenitor cells were transfected using in utero electroporation on embryonic day (E) 15.5 with plasmids encoding either: (1) Kiaa0319l small hairpin RNA (shRNA), (2) an expression construct for human KIAA0319L, (3) Kiaa0319l shRNA+KIAA0319L expression construct (rescue), or (4) controls (scrambled Kiaa0319l shRNA or empty expression vector). Mothers were injected with 5-bromo-2-deoxyuridine (BrdU) at either E13.5, E15.5, or E17.5. Disruption of Kiaa0319l function (by knockdown, overexpression, or rescue) resulted in the formation of large nodular periventricular heterotopia in approximately 25% of the rats, which can be seen as early as postnatal day 1. Only a small subset of heterotopic neurons had been transfected, indicating non-cell autonomous effects of the transfection. Most heterotopic neurons were generated in mid- to late-gestation, and laminar markers suggest that they were destined for upper cortical laminae. Finally, we found that transfected neurons in the cerebral cortex were located in their expected laminae. These results indicate that KIAA0319L is the fourth of four candidate dyslexia susceptibility genes that is involved in neuronal migration, which supports the association of abnormal neuronal migration with developmental dyslexia.
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Affiliation(s)
- M P Platt
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - W T Adler
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - A J Mehlhorn
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - G C Johnson
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - K A Wright
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - R T Choi
- School of Biomedical Sciences & School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - W H Tsang
- School of Biomedical Sciences & School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - M W Poon
- School of Biomedical Sciences & School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - S Y Yeung
- School of Biomedical Sciences & School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - M M Y Waye
- School of Biomedical Sciences & School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - A M Galaburda
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - G D Rosen
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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Centanni TM, Booker AB, Sloan AM, Chen F, Maher BJ, Carraway RS, Khodaparast N, Rennaker R, LoTurco JJ, Kilgard MP. Knockdown of the dyslexia-associated gene Kiaa0319 impairs temporal responses to speech stimuli in rat primary auditory cortex. Cereb Cortex 2013; 24:1753-66. [PMID: 23395846 DOI: 10.1093/cercor/bht028] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
One in 15 school age children have dyslexia, which is characterized by phoneme-processing problems and difficulty learning to read. Dyslexia is associated with mutations in the gene KIAA0319. It is not known whether reduced expression of KIAA0319 can degrade the brain's ability to process phonemes. In the current study, we used RNA interference (RNAi) to reduce expression of Kiaa0319 (the rat homolog of the human gene KIAA0319) and evaluate the effect in a rat model of phoneme discrimination. Speech discrimination thresholds in normal rats are nearly identical to human thresholds. We recorded multiunit neural responses to isolated speech sounds in primary auditory cortex (A1) of rats that received in utero RNAi of Kiaa0319. Reduced expression of Kiaa0319 increased the trial-by-trial variability of speech responses and reduced the neural discrimination ability of speech sounds. Intracellular recordings from affected neurons revealed that reduced expression of Kiaa0319 increased neural excitability and input resistance. These results provide the first evidence that decreased expression of the dyslexia-associated gene Kiaa0319 can alter cortical responses and impair phoneme processing in auditory cortex.
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Affiliation(s)
- T M Centanni
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | | | - A M Sloan
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | - F Chen
- University of Connecticut
| | | | - R S Carraway
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | - N Khodaparast
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | - R Rennaker
- School of Behavioral and Brain Sciences, University of Texas at Dallas
| | | | - M P Kilgard
- School of Behavioral and Brain Sciences, University of Texas at Dallas
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Raskind WH, Peter B, Richards T, Eckert MM, Berninger VW. The genetics of reading disabilities: from phenotypes to candidate genes. Front Psychol 2013; 3:601. [PMID: 23308072 PMCID: PMC3538356 DOI: 10.3389/fpsyg.2012.00601] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/18/2012] [Indexed: 12/19/2022] Open
Abstract
This article provides an overview of (a) issues in definition and diagnosis of specific reading disabilities at the behavioral level that may occur in different constellations of developmental and phenotypic profiles (patterns); (b) rapidly expanding research on genetic heterogeneity and gene candidates for dyslexia and other reading disabilities; (c) emerging research on gene-brain relationships; and (d) current understanding of epigenetic mechanisms whereby environmental events may alter behavioral expression of genetic variations. A glossary of genetic terms (denoted by bold font) is provided for readers not familiar with the technical terms.
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Affiliation(s)
- Wendy H Raskind
- Department of Medicine, University of Washington Seattle, WA, USA ; Department of Psychiatry and Behavioral Sciences, University of Washington Seattle, WA, USA
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