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Akinsola OM, Musa AA, Muansangi L, Singh SP, Mukherjee S, Mukherjee A. Genomic insights into adaptation and inbreeding among Sub-Saharan African cattle from pastoral and agropastoral systems. Front Genet 2024; 15:1430291. [PMID: 39119582 PMCID: PMC11306176 DOI: 10.3389/fgene.2024.1430291] [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: 05/09/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Background In Sub-Saharan Africa (SSA), cattle are crucial for socioeconomic stability yet face numerous environmental stressors such as diseases, parasites, and extreme heat within pastoral and agropastoral systems. Despite their significance, gaps remain in understanding how genetic diversity and inbreeding influence traits essential for disease resistance and environmental adaptability. This study examines the genomic adaptations that enable SSA cattle to thrive under these conditions and assesses the impact of inbreeding on such adaptive traits. Methods We analyzed genomic data from 113 cattle across four breeds-Kuri, N'dama, Zebu-Fulani, and Zebu-Bororo-employing Runs of Homozygosity (ROH) and Integrated Haplotype Score (iHS) analyses to identify historical and recent genetic selections. Strict quality controls using PLINK software ensured accurate genomic pattern identification related to adaptation and inbreeding. Results ROH analysis revealed islands with genes such as RSAD2, CMPK2, and NOTCH1, which are involved in immune response and cellular stress management, highlighting regions of historical selection that have likely provided adaptive advantages in overcoming environmental and pathogenic stresses. In contrast, iHS analysis identified genes under recent selection like HIPK1, involved in stress response regulation, and EPHA5, which plays a crucial role in neural development and synaptic functions, potentially equipping these breeds with novel adaptations to ongoing and emergent environmental challenges. Conclusion This research confirms that selective pressures inherent in pastoral and agropastoral systems profoundly influence the genetic structure of SSA cattle. By delineating the genetic bases of key adaptive traits, our study offers crucial insights for targeted breeding programs to enhance cattle resilience and productivity. These findings provide a valuable framework for future genetic improvements and conservation strategies, crucial for sustainable livestock management and economic stability in SSA.
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Affiliation(s)
- Oludayo M. Akinsola
- Department of Theriogenology and Production, Faculty of Veterinary Medicine, University of Jos, Jos, Nigeria
| | | | - Lal Muansangi
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Sanchit P. Singh
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Sabyasachi Mukherjee
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Anupama Mukherjee
- Animal Genetics and Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana, India
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Wright GA, Rodriguez-Martinez AC, Conn H, Matarin M, Thompson P, Moore AT, Ba-Abbad R, Webster AR, Moosajee M. Enhanced Learning and Memory in Patients with CRB1 Retinopathy. Genes (Basel) 2024; 15:660. [PMID: 38927596 PMCID: PMC11203261 DOI: 10.3390/genes15060660] [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: 05/04/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations in the CRB1 gene are associated with a diverse spectrum of retinopathies with phenotypic variability causing severe visual impairment. The CRB1 gene has a role in retinal development and is expressed in the cerebral cortex and hippocampus, but its role in cognition has not been described before. This study compares cognitive function in CRB1 retinopathy individuals with subjects with other retinopathies and the normal population. METHODS Neuropsychological tests of cognitive function were used to test individuals with CRB1 and non-CRB1 retinopathies and compare results with a standardised normative dataset. RESULTS CRB1 retinopathy subjects significantly outperformed those with non-CRB1 retinopathy in list learning tasks of immediate (p = 0.001) and delayed memory (p = 0.007), tests of semantic verbal fluency (p = 0.017), verbal IQ digit span subtest (p = 0.037), and estimation test of higher execution function (p = 0.020) but not in the remaining tests of cognitive function (p > 0.05). CRB1 retinopathy subjects scored significantly higher than the normal population in all areas of memory testing (p < 0.05) and overall verbal IQ tests (p = 0.0012). Non-CRB1 retinopathy subjects scored significantly higher than the normal population in story recall, verbal fluency, and overall verbal IQ tests (p = 0.0016). CONCLUSIONS Subjects with CRB1 retinopathy may have enhanced cognitive function in areas of memory and learning. Further work is required to understand the role of CRB1 in cognition.
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Affiliation(s)
- Genevieve A. Wright
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Ana Catalina Rodriguez-Martinez
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Hanne Conn
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London Hospitals (UCLH), National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK; (H.C.); (M.M.); (P.T.)
| | - Mar Matarin
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London Hospitals (UCLH), National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK; (H.C.); (M.M.); (P.T.)
| | - Pamela Thompson
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London Hospitals (UCLH), National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK; (H.C.); (M.M.); (P.T.)
| | - Anthony T. Moore
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Rola Ba-Abbad
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Andrew R. Webster
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
| | - Mariya Moosajee
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (G.A.W.); (A.C.R.-M.); (A.T.M.); (R.B.-A.); (A.R.W.)
- Institute of Ophthalmology, University College London (UCL), London EC1V 9EL, UK
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3
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Frederick CE, Zenisek D. Ribbon Synapses and Retinal Disease: Review. Int J Mol Sci 2023; 24:5090. [PMID: 36982165 PMCID: PMC10049380 DOI: 10.3390/ijms24065090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Synaptic ribbons are presynaptic protein complexes that are believed to be important for the transmission of sensory information in the visual system. Ribbons are selectively associated with those synapses where graded changes in membrane potential drive continuous neurotransmitter release. Defective synaptic transmission can arise as a result of the mutagenesis of a single ribbon component. Visual diseases that stem from malfunctions in the presynaptic molecular machinery of ribbon synapses in the retina are rare. In this review, we provide an overview of synaptopathies that give rise to retinal malfunction and our present understanding of the mechanisms that underlie their pathogenesis and discuss muscular dystrophies that exhibit ribbon synapse involvement in the pathology.
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Affiliation(s)
| | - David Zenisek
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208026, New Haven, CT 06510, USA
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4
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Martin-Gutierrez MP, Schiff ER, Wright G, Waseem N, Mahroo OA, Michaelides M, Moore AT, Webster AR, Arno G. Dominant Cone Rod Dystrophy, Previously Assigned to a Missense Variant in RIMS1, Is Fully Explained by Co-Inheritance of a Dominant Allele of PROM1. Invest Ophthalmol Vis Sci 2022; 63:14. [PMID: 35947379 PMCID: PMC9381847 DOI: 10.1167/iovs.63.9.14] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose Autosomal dominant cone rod dystrophy 7 (CORD7) was initially linked to the gene RIMS1 and reported in a 4-generation British family in 1998. The purpose of this study was to investigate the legitimacy of this association, and to correctly characterize the genetic cause of this condition. Methods The allele frequency of RIMS1 c.2459G>A, p.Arg820His, was investigated in the Genomes Aggregation Dataset (gnomAD) datasets and whole genome sequencing (WGS) was performed for 4 members of the CORD7 family with filtering of rare pathogenic variants in a virtual gene panel comprising all genes known to be associated with inherited retinal dystrophy (IRD). Cytogenetic analysis was performed to rule out interchromosomal translocation. Results RIMS1 p.Arg820His has a maximal carrier frequency of >1:5000 in Europeans. A previously well-characterized PROM1 variant: c.1118C>T, p.Arg373Cys, was detected in 9 affected members of the CORD7 family who underwent WGS or direct sequencing. One affected family member is now known to have macular dystrophy in the absence of RIMS1 p.Arg820His. Clinical analysis of affected family members and 27 individuals with retinopathy associated with the same - PROM1 - variant showed consistent phenotypes. Conclusions The case for pathogenicity of RIMS1 p.Arg820His is not strong based on its presence on 10 alleles in the gnomAD dataset and absence from additional CORD affected individuals. The finding of a known pathogenic variant in PROM1 correlates well with the phenotypic characteristics of the affected individuals, and is likely to account for the condition. Clear evidence of association between RIMS1 and a retinal dystrophy is yet to be described.
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Affiliation(s)
| | - Elena R. Schiff
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
| | - Genevieve Wright
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
| | | | - Omar A. Mahroo
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
| | - Anthony T. Moore
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Andrew R. Webster
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
| | - Gavin Arno
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - for the Genomics England Research Consortium
- Moorfields Eye Hospital, London, United Kingdom
- UCL Institute of Ophthalmology, London, United Kingdom
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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5
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Ng TK, Cao Y, Yuan XL, Chen S, Xu Y, Chen SL, Zheng Y, Chen H. Whole exome sequencing analysis identifies novel Stargardt disease-related gene mutations in Chinese Stargardt disease and retinitis pigmentosa patients. Eye (Lond) 2022; 36:749-759. [PMID: 33846575 PMCID: PMC8956586 DOI: 10.1038/s41433-021-01525-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/17/2021] [Accepted: 03/29/2021] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES To delineate the disease-causing mutations of the Stargardt disease-related genes in Chinese patients diagnosed with Stargardt disease or retinitis pigmentosa (RP) by whole exome sequencing analysis. METHODS A total of 123 sporadic RP or Stargardt disease patients and 2 Stargardt disease families were recruited. All sporadic patients and the probands of the families were subjected to whole exome sequencing analysis. The candidate mutations were verified by direct sequencing based on the cosegregation pattern and in 200 control subjects and by the bioinformatics analyses. RESULTS A total of three reported ABCA4 mutations were identified in the probands of the two Stargardt disease families. The probands and the affected family members with either homozygous or compound heterozygous mutations showed typical Stargardt disease features, which was absent in their unaffected family members. The cosegregation pattern confirmed the mode of recessive inheritance. Moreover, two sporadic Stargardt disease patients were identified to carry two novel ABCA4 and one PROM1 mutations. In addition, 13 novel variants were found in 119 sporadic RP patients in 7 Stargardt disease-related genes, and 8 novel missense variants were conserved across different species and predicted to be damaging to the protein. All 15 novel variants were absent in our 200 control subjects. CONCLUSIONS This study revealed 22.4% study subjects carrying Stargardt disease-related gene mutations with total 15 novel variants in seven Stargardt disease-related genes, assuring that targeted next-generation sequencing analysis is a high throughput strategy to facilitate the clinical diagnosis from suspicious patients and recommended as a routine examination for inherited retinal dystrophies.
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Affiliation(s)
- Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yingjie Cao
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Xiang-Ling Yuan
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | - Shaowan Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yanxuan Xu
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Shao-Lang Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yuqian Zheng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Haoyu Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
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6
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Paul MM, Dannhäuser S, Morris L, Mrestani A, Hübsch M, Gehring J, Hatzopoulos GN, Pauli M, Auger GM, Bornschein G, Scholz N, Ljaschenko D, Müller M, Sauer M, Schmidt H, Kittel RJ, DiAntonio A, Vakonakis I, Heckmann M, Langenhan T. The human cognition-enhancing CORD7 mutation increases active zone number and synaptic release. Brain 2022; 145:3787-3802. [DOI: 10.1093/brain/awac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/29/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
Humans carrying the CORD7 (cone-rod dystrophy 7) mutation possess increased verbal IQ and working memory. This autosomal dominant syndrome is caused by the single-amino acid R844H exchange (human numbering) located in the 310 helix of the C2A domain of RIMS1/RIM1 (Rab3-interacting molecule 1). RIM is an evolutionarily conserved multi-domain protein and essential component of presynaptic active zones, which is centrally involved in fast, Ca2+-triggered neurotransmitter release. How the CORD7 mutation affects synaptic function has remained unclear thus far. Here, we established Drosophila melanogaster as a disease model for clarifying the effects of the CORD7 mutation on RIM function and synaptic vesicle release.
To this end, using protein expression and X-ray crystallography, we solved the molecular structure of the Drosophila C2A domain at 1.92 Å resolution and by comparison to its mammalian homolog ascertained that the location of the CORD7 mutation is structurally conserved in fly RIM. Further, CRISPR/Cas9-assisted genomic engineering was employed for the generation of rim alleles encoding the R915H CORD7 exchange or R915E,R916E substitutions (fly numbering) to effect local charge reversal at the 310 helix. Through electrophysiological characterization by two-electrode voltage clamp and focal recordings we determined that the CORD7 mutation exerts a semi-dominant rather than a dominant effect on synaptic transmission resulting in faster, more efficient synaptic release and increased size of the readily releasable pool but decreased sensitivity for the fast calcium chelator BAPTA. In addition, the rim CORD7 allele increased the number of presynaptic active zones but left their nanoscopic organization unperturbed as revealed by super-resolution microscopy of the presynaptic scaffold protein Bruchpilot/ELKS/CAST.
We conclude that the CORD7 mutation leads to tighter release coupling, an increased readily releasable pool size and more release sites thereby promoting more efficient synaptic transmitter release. These results strongly suggest that similar mechanisms may underlie the CORD7 disease phenotype in patients and that enhanced synaptic transmission may contribute to their increased cognitive abilities.
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Affiliation(s)
- Mila M. Paul
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
- Department of Orthopaedic Trauma, Hand, Plastic and Reconstructive Surgery, University Hospital of Würzburg, 97080 Würzburg, Germany
| | - Sven Dannhäuser
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Lydia Morris
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Achmed Mrestani
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
- Department of Neurology, Leipzig University Medical Center, 04103 Leipzig, Germany
| | - Martha Hübsch
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Jennifer Gehring
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | | | - Martin Pauli
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Genevieve M. Auger
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Grit Bornschein
- Carl Ludwig Institute of Physiology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Nicole Scholz
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Dmitrij Ljaschenko
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Martin Müller
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, 97074 Würzburg, Germany
| | - Hartmut Schmidt
- Carl Ludwig Institute of Physiology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Robert J. Kittel
- Carl Ludwig Institute of Physiology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
- Department of Animal Physiology, Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Aaron DiAntonio
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - Manfred Heckmann
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Tobias Langenhan
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
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7
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Li JX, He JJ, Elsheikha HM, Ma J, Xu XP, Zhu XQ. ROP18-Mediated Transcriptional Reprogramming of HEK293T Cell Reveals New Roles of ROP18 in the Interplay Between Toxoplasma gondii and the Host Cell. Front Cell Infect Microbiol 2020; 10:586946. [PMID: 33330132 PMCID: PMC7734210 DOI: 10.3389/fcimb.2020.586946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/30/2020] [Indexed: 12/02/2022] Open
Abstract
Toxoplasma gondii secretes a number of virulence-related effector proteins, such as the rhoptry protein 18 (ROP18). To further broaden our understanding of the molecular functions of ROP18, we examined the transcriptional response of human embryonic kidney cells (HEK293T) to ROP18 of type I T. gondii RH strain. Using RNA-sequencing, we compared the transcriptome of ROP18-expressing HEK293T cells to control HEK293T cells. Our analysis revealed that ROP18 altered the expression of 750 genes (467 upregulated genes and 283 downregulated genes) in HEK293T cells. Gene ontology (GO) and pathway enrichment analyses showed that differentially expressed genes (DEGs) were significantly enriched in extracellular matrix– and immune–related GO terms and pathways. KEGG pathway enrichment analysis revealed that DEGs were involved in several disease-related pathways, such as nervous system diseases and eye disease. ROP18 significantly increased the alternative splicing pattern “retained intron” and altered the expression of 144 transcription factors (TFs). These results provide new insight into how ROP18 may influence biological processes in the host cells via altering the expression of genes, TFs, and pathways. More in vitro and in vivo studies are required to substantiate these findings.
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Affiliation(s)
- Jie-Xi Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jun-Jun He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiao-Pei Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
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8
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Fujinami K, Oishi A, Yang L, Arno G, Pontikos N, Yoshitake K, Fujinami-Yokokawa Y, Liu X, Hayashi T, Katagiri S, Mizobuchi K, Mizota A, Shinoda K, Nakamura N, Kurihara T, Tsubota K, Miyake Y, Iwata T, Tsujikawa A, Tsunoda K. Clinical and genetic characteristics of 10 Japanese patients with PROM1-associated retinal disorder: A report of the phenotype spectrum and a literature review in the Japanese population. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:656-674. [PMID: 32820593 DOI: 10.1002/ajmg.c.31826] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 01/14/2023]
Abstract
Variants in the PROM1 gene are associated with cone (-rod) dystrophy, macular dystrophy, and other phenotypes. We describe the clinical and genetic characteristics of 10 patients from eight Japanese families with PROM1-associated retinal disorder (PROM1-RD) in a nationwide cohort. A literature review of PROM1-RD in the Japanese population was also performed. The median age at onset/examination of 10 patients was 31.0 (range, 10-45)/44.5 (22-73) years. All 10 patients showed atrophic macular changes. Seven patients (70.0%) had spared fovea to various degrees, approximately half of whom had maintained visual acuity. Generalized cone (-rod) dysfunction was demonstrated in all nine subjects with available electrophysiological data. Three PROM1 variants were identified in this study: one recurrent disease-causing variant (p.Arg373Cys), one novel putative disease-causing variant (p.Cys112Arg), and one novel variant of uncertain significance (VUS; p.Gly53Asp). Characteristic features of macular atrophy with generalized cone-dominated retinal dysfunction were shared among all 10 subjects with PROM1-RD, and the presence of foveal sparing was crucial in maintaining visual acuity. Together with the three previously reported variants [p.R373C, c.1551+1G>A (pathogenic), p.Asn580His (likely benign)] in the literature of Japanese patients, one prevalent missense variant (p.Arg373Cys, 6/9 families, 66.7%) detected in multiple studies was determined in the Japanese population, which was also frequently detected in the European population.
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Affiliation(s)
- Kaoru Fujinami
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan.,UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital, London, UK
| | - Akio Oishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Lizhu Yang
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Gavin Arno
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital, London, UK.,North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London, UK
| | - Nikolas Pontikos
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital, London, UK
| | - Kazutoshi Yoshitake
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Yu Fujinami-Yokokawa
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,UCL Institute of Ophthalmology, London, UK.,Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan.,Division of Public Health, Yokokawa Clinic, Suita, Japan
| | - Xiao Liu
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan.,Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Satoshi Katagiri
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Atsushi Mizota
- Department of Ophthalmology, Teikyo University, Tokyo, Japan
| | - Kei Shinoda
- Department of Ophthalmology, Teikyo University, Tokyo, Japan.,Department of Ophthalmology, Saitama Medical University, Saitama, Japan
| | - Natsuko Nakamura
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Department of Ophthalmology, Teikyo University, Tokyo, Japan.,Department of Ophthalmology, The University of Tokyo, Tokyo, Japan
| | - Toshihide Kurihara
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Kazuo Tsubota
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yozo Miyake
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Aichi Medical University, Nagakute, Japan.,Next vision, Kobe Eye Center, Hyogo, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Akitaka Tsujikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
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9
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Verhage M, Sørensen JB. SNAREopathies: Diversity in Mechanisms and Symptoms. Neuron 2020; 107:22-37. [PMID: 32559416 DOI: 10.1016/j.neuron.2020.05.036] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/29/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022]
Abstract
Neuronal SNAREs and their key regulators together drive synaptic vesicle exocytosis and synaptic transmission as a single integrated membrane fusion machine. Human pathogenic mutations have now been reported for all eight core components, but patients are diagnosed with very different neurodevelopmental syndromes. We propose to unify these syndromes, based on etiology and mechanism, as "SNAREopathies." Here, we review the strikingly diverse clinical phenomenology and disease severity and the also remarkably diverse genetic mechanisms. We argue that disease severity generally scales with functional redundancy and, conversely, that the large effect of mutations in some SNARE genes is the price paid for extensive integration and exceptional specialization. Finally, we discuss how subtle differences in components being rate limiting in different types of neurons helps to explain the main symptoms.
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Affiliation(s)
- Matthijs Verhage
- Department of Functional Genomics, Vrije Universiteit (VU) Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, the Netherlands; Department of Clinical Genetics, UMC Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, the Netherlands.
| | - Jakob B Sørensen
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark.
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10
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Cui H, Srinivasan S, Korkin D. Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases. Genes (Basel) 2019; 10:E933. [PMID: 31731769 PMCID: PMC6895925 DOI: 10.3390/genes10110933] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 11/16/2022] Open
Abstract
Rapid progress in high-throughput -omics technologies moves us one step closer to the datacalypse in life sciences. In spite of the already generated volumes of data, our knowledge of the molecular mechanisms underlying complex genetic diseases remains limited. Increasing evidence shows that biological networks are essential, albeit not sufficient, for the better understanding of these mechanisms. The identification of disease-specific functional modules in the human interactome can provide a more focused insight into the mechanistic nature of the disease. However, carving a disease network module from the whole interactome is a difficult task. In this paper, we propose a computational framework, Discovering most IMpacted SUbnetworks in interactoMe (DIMSUM), which enables the integration of genome-wide association studies (GWAS) and functional effects of mutations into the protein-protein interaction (PPI) network to improve disease module detection. Specifically, our approach incorporates and propagates the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on PPIs to implicate the genes that are most likely influenced by the disruptive mutations, and to identify the module with the greatest functional impact. Comparison against state-of-the-art seed-based module detection methods shows that our approach could yield modules that are biologically more relevant and have stronger association with the studied disease. We expect for our method to become a part of the common toolbox for the disease module analysis, facilitating the discovery of new disease markers.
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Affiliation(s)
- Hongzhu Cui
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Suhas Srinivasan
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA
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11
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Plassais J, Kim J, Davis BW, Karyadi DM, Hogan AN, Harris AC, Decker B, Parker HG, Ostrander EA. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. Nat Commun 2019; 10:1489. [PMID: 30940804 PMCID: PMC6445083 DOI: 10.1038/s41467-019-09373-w] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/06/2019] [Indexed: 01/14/2023] Open
Abstract
Domestic dog breeds are characterized by an unrivaled diversity of morphologic traits and breed-associated behaviors resulting from human selective pressures. To identify the genetic underpinnings of such traits, we analyze 722 canine whole genome sequences (WGS), documenting over 91 million single nucleotide and small indels, creating a large catalog of genomic variation for a companion animal species. We undertake both selective sweep analyses and genome wide association studies (GWAS) inclusive of over 144 modern breeds, 54 wild canids and a hundred village dogs. Our results identify variants of strong impact associated with 16 phenotypes, including body weight variation which, when combined with existing data, explain greater than 90% of body size variation in dogs. We thus demonstrate that GWAS and selection scans performed with WGS are powerful complementary methods for expanding the utility of companion animal systems for the study of mammalian growth and biology.
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Affiliation(s)
- Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jaemin Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Texas A&M University, College Station, TX, 77840, USA
| | - Danielle M Karyadi
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Laboratory of Genetic Susceptibility, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Andrew N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alex C Harris
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brennan Decker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Heidi G Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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12
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Sanglard LP, Nascimento M, Moriel P, Sommer J, Ashwell M, Poore MH, Duarte MDS, Serão NVL. Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning. BMC Genomics 2018; 19:702. [PMID: 30253751 PMCID: PMC6156876 DOI: 10.1186/s12864-018-5089-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023] Open
Abstract
Background Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response. Methods Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation. Results A total of 160, 164, and 346 DEG (q-value< 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in muscle metabolism. In muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 5 genes associated with muscle metabolism and development: SLCO3A1, ATP6V0D1, SLC2A1, GPC4, and RASD2. In blood, among the 10 most DEG, we found genes related to response to stress up-regulated in the REST after weaning, such as SOD3 and INO80D, and to immune response down-regulated in the REST after vaccination, such as OASL, KLRF1, and LOC104968634. Conclusion In conclusion, maternal energy restriction during late gestation may limit the expression of genes in the muscle and increase expression in the blood of calves. In addition, enrichment analysis showed that a short-term maternal energy restriction during pregnancy affects the expression of genes related to energy metabolism and muscle contraction, and immunity and stress response in the blood. Therefore, alterations in the intra-uterine environment can modify prenatal development with lasting consequences to adult life. Electronic supplementary material The online version of this article (10.1186/s12864-018-5089-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leticia P Sanglard
- Department of Animal Science, Iowa State University, Ames, 50011, USA.,Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Moysés Nascimento
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA.,Department of Statistics, Universidade Federal de Viçosa, Viçosa, 36570-000, Brazil
| | - Philipe Moriel
- Range Cattle Research and Education Center, University of Florida, Ona, Florida, 33865, USA
| | - Jeffrey Sommer
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Melissa Ashwell
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Matthew H Poore
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Márcio de S Duarte
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, 36570-000, Brazil.,Instituto Nacional de Ciência e Tecnologia - Ciência Animal, Viçosa, 36570-000, Brazil
| | - Nick V L Serão
- Department of Animal Science, Iowa State University, Ames, 50011, USA. .,Department of Animal Science, North Carolina State University, Raleigh, 27695, USA.
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13
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Chen BJ, Huang S, Janitz M. Changes in circular RNA expression patterns during human foetal brain development. Genomics 2018; 111:753-758. [PMID: 29709512 DOI: 10.1016/j.ygeno.2018.04.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 01/28/2023]
Abstract
Circular RNAs (circRNAs) are a recently identified class of long non-coding RNAs and their expression is regulated in a tissue- and developmental stage-specific manner. Recent studies indicate the potential regulatory role that circRNAs may have, particularly in the brain, where they are most abundant. This study aims to elucidate changes in circRNA patterns during human embryonic brain development. We detected a number of differentially expressed genes that showed distinct expression profiles for circular and linear transcripts despite having originated from the same genes, implicating a dichotomy in the regulation of these two RNA species. Altogether our study showed that circular and linear RNAs have independent expression patterns, and that circular transcriptomes from different developing stages have distinct characteristics in terms of transcript abundance and isoform diversity.
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Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Suleigh Huang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany.
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14
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Francescatto M, Lizio M, Philippens I, Pardo LM, Bontrop R, Sakai M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Carninci P, Hayashizaki Y, Forrest ARR, Kawaji H, Rizzu P, Heutink P. Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. Sci Data 2017; 4:170163. [PMID: 29087374 PMCID: PMC5663209 DOI: 10.1038/sdata.2017.163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 08/29/2017] [Indexed: 01/10/2023] Open
Abstract
Rhesus macaque was the second non-human primate whose genome has been fully
sequenced and is one of the most used model organisms to study human biology and
disease, thanks to the close evolutionary relationship between the two species.
But compared to human, where several previously unknown RNAs have been
uncovered, the macaque transcriptome is less studied. Publicly available RNA
expression resources for macaque are limited, even for brain, which is highly
relevant to study human cognitive abilities. In an effort to complement those
resources, FANTOM5 profiled 15 distinct anatomical regions of the aged macaque
central nervous system using Cap Analysis of Gene Expression, a high-resolution,
annotation-independent technology that allows monitoring of transcription
initiation events with high accuracy. We identified 25,869 CAGE peaks,
representing bona fide promoters. For each peak we provide detailed annotation,
expanding the landscape of ‘known’ macaque genes, and we show
concrete examples on how to use the resulting data. We believe this data
represents a useful resource to understand the central nervous system in
macaque.
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Affiliation(s)
- Margherita Francescatto
- Italian Institute of Technology, Department of Neuroscience and Brain Technologies, Via Morego 30, Genova 16163, Italy
| | - Marina Lizio
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ingrid Philippens
- Biomedical Primate Research Centre, Postbox 3306, Rijswijk 2280 GH, The Netherlands
| | | | - Ronald Bontrop
- Biomedical Primate Research Centre, Postbox 3306, Rijswijk 2280 GH, The Netherlands
| | - Mizuho Sakai
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Shoko Watanabe
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Timo Lassmann
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Western Australia 6008, Australia
| | - Jessica Severin
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, Western Australia 6009, Australia
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Advanced Center for Computing and Communication, Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases, Otfried-Müller Straße 23, Tübingen 72076, Germany
| | - Peter Heutink
- German Center for Neurodegenerative Diseases, Otfried-Müller Straße 23, Tübingen 72076, Germany
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15
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Nash BM, Wright DC, Grigg JR, Bennetts B, Jamieson RV. Retinal dystrophies, genomic applications in diagnosis and prospects for therapy. Transl Pediatr 2015; 4:139-63. [PMID: 26835369 PMCID: PMC4729094 DOI: 10.3978/j.issn.2224-4336.2015.04.03] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Retinal dystrophies (RDs) are degenerative diseases of the retina which have marked clinical and genetic heterogeneity. Common presentations among these disorders include night or colour blindness, tunnel vision and subsequent progression to complete blindness. The known causative disease genes have a variety of developmental and functional roles with mutations in more than 120 genes shown to be responsible for the phenotypes. In addition, mutations within the same gene have been shown to cause different disease phenotypes, even amongst affected individuals within the same family highlighting further levels of complexity. The known disease genes encode proteins involved in retinal cellular structures, phototransduction, the visual cycle, and photoreceptor structure or gene regulation. This review aims to demonstrate the high degree of genetic complexity in both the causative disease genes and their associated phenotypes, highlighting the more common clinical manifestation of retinitis pigmentosa (RP). The review also provides insight to recent advances in genomic molecular diagnosis and gene and cell-based therapies for the RDs.
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Affiliation(s)
- Benjamin M Nash
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Dale C Wright
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - John R Grigg
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Bruce Bennetts
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Robyn V Jamieson
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
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16
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Abstract
This review considers pharmacogenetics of the so called 'second-generation' antipsychotics. Findings for polymorphisms replicating in more than one study are emphasized and compared and contrasted with larger-scale candidate gene studies and genome-wide association study analyses. Variants in three types of genes are discussed: pharmacokinetic genes associated with drug metabolism and disposition, pharmacodynamic genes encoding drug targets, and pharmacotypic genes impacting disease presentation and subtype. Among pharmacokinetic markers, CYP2D6 metabolizer phenotype has clear clinical significance, as it impacts dosing considerations for aripiprazole, iloperidone and risperidone, and variants of the ABCB1 gene hold promise as biomarkers for dosing for olanzapine and clozapine. Among pharmacodynamic variants, the TaqIA1 allele of the DRD2 gene, the DRD3 (Ser9Gly) polymorphism, and the HTR2C -759C/T polymorphism have emerged as potential biomarkers for response and/or side effects. However, large-scale candidate gene studies and genome-wide association studies indicate that pharmacotypic genes may ultimately prove to be the richest source of biomarkers for response and side effect profiles for second-generation antipsychotics.
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Affiliation(s)
- Mark D Brennan
- Department of Biochemistry & Molecular Biology, School of Medicine, University of Louisville, Louisville, KY 40292, USA.
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17
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Bentley RA, O’Brien MJ. Cultural evolutionary tipping points in the storage and transmission of information. Front Psychol 2012; 3:569. [PMID: 23267338 PMCID: PMC3525879 DOI: 10.3389/fpsyg.2012.00569] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/01/2012] [Indexed: 12/02/2022] Open
Abstract
Human culture has evolved through a series of major tipping points in information storage and communication. The first was the appearance of language, which enabled communication between brains and allowed humans to specialize in what they do and to participate in complex mating games. The second was information storage outside the brain, most obviously expressed in the "Upper Paleolithic Revolution" - the sudden proliferation of cave art, personal adornment, and ritual in Europe some 35,000-45,000 years ago. More recently, this storage has taken the form of writing, mass media, and now the Internet, which is arguably overwhelming humans' ability to discern relevant information. The third tipping point was the appearance of technology capable of accumulating and manipulating vast amounts of information outside humans, thus removing them as bottlenecks to a seemingly self-perpetuating process of knowledge explosion. Important components of any discussion of cultural evolutionary tipping points are tempo and mode, given that the rate of change, as well as the kind of change, in information storage and transmission has not been constant over the previous million years.
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18
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Webb TR, Matarin M, Gardner JC, Kelberman D, Hassan H, Ang W, Michaelides M, Ruddle JB, Pennell CE, Yazar S, Khor CC, Aung T, Yogarajah M, Robson AG, Holder GE, Cheetham ME, Traboulsi EI, Moore AT, Sowden JC, Sisodiya SM, Mackey DA, Tuft SJ, Hardcastle AJ. X-linked megalocornea caused by mutations in CHRDL1 identifies an essential role for ventroptin in anterior segment development. Am J Hum Genet 2012; 90:247-59. [PMID: 22284829 DOI: 10.1016/j.ajhg.2011.12.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/07/2011] [Accepted: 12/26/2011] [Indexed: 01/30/2023] Open
Abstract
X-linked megalocornea (MGC1) is an ocular anterior segment disorder characterized by an increased cornea diameter and deep anterior chamber evident at birth and later onset of mosaic corneal degeneration (shagreen), arcus juvenilis, and presenile cataracts. We identified copy-number variation, frameshift, missense, splice-site and nonsense mutations in the Chordin-like 1 gene (CHRDL1) on Xq23 as the cause of the condition in seven MGC1 families. CHRDL1 encodes ventroptin, a bone morphogenic protein antagonist with a proposed role in specification of topographic retinotectal projections. Electrophysiological evaluation revealed mild generalized cone system dysfunction and, in one patient, an interhemispheric asymmetry in visual evoked potentials. We show that CHRDL1 is expressed in the developing human cornea and anterior segment in addition to the retina. We explored the impact of loss of ventroptin function on brain function and morphology in vivo. CHRDL1 is differentially expressed in the human fetal brain, and there is high expression in cerebellum and neocortex. We show that MGC1 patients have a superior cognitive ability despite a striking focal loss of myelination of white matter. Our findings reveal an unexpected requirement for ventroptin during anterior segment development and the consequences of a lack of function in the retina and brain.
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Affiliation(s)
- Tom R Webb
- Institute of Ophthalmology, University College London, UK
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Loss-of-function mutations in RAB18 cause Warburg micro syndrome. Am J Hum Genet 2011; 88:499-507. [PMID: 21473985 DOI: 10.1016/j.ajhg.2011.03.012] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/08/2011] [Accepted: 03/16/2011] [Indexed: 12/24/2022] Open
Abstract
Warburg Micro syndrome and Martsolf syndrome are heterogenous autosomal-recessive developmental disorders characterized by brain, eye, and endocrine abnormalities. Previously, identification of mutations in RAB3GAP1 and RAB3GAP2 in both these syndromes implicated dysregulation of the RAB3 cycle (which controls calcium-mediated exocytosis of neurotransmitters and hormones) in disease pathogenesis. RAB3GAP1 and RAB3GAP2 encode the catalytic and noncatalytic subunits of the hetrodimeric enzyme RAB3GAP (RAB3GTPase-activating protein), a key regulator of the RAB3 cycle. We performed autozygosity mapping in five consanguineous families without RAB3GAP1/2 mutations and identified loss-of-function mutations in RAB18. A c.71T > A (p.Leu24Gln) founder mutation was identified in four Pakistani families, and a homozygous exon 2 deletion (predicted to result in a frameshift) was found in the fifth family. A single family whose members were compound heterozygotes for an anti-termination mutation of the stop codon c.619T > C (p.X207QextX20) and an inframe arginine deletion c.277_279 del (p.Arg93 del) were identified after direct gene sequencing and multiplex ligation-dependent probe amplification (MLPA) of a further 58 families. Nucleotide binding assays for RAB18(Leu24Gln) and RAB18(Arg93del) showed that these mutant proteins were functionally null in that they were unable to bind guanine. The clinical features of Warburg Micro syndrome patients with RAB3GAP1 or RAB3GAP2 mutations and RAB18 mutations are indistinguishable, although the role of RAB18 in trafficking is still emerging, and it has not been linked previously to the RAB3 pathway. Knockdown of rab18 in zebrafish suggests that it might have a conserved developmental role. Our findings imply that RAB18 has a critical role in human brain and eye development and neurodegeneration.
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Arrigoni FI, Matarin M, Thompson PJ, Michaelides M, McClements ME, Redmond E, Clarke L, Ellins E, Mohamed S, Pavord I, Klein N, Hunt DM, Moore AT, Halcox J, Sisodiya SM. Extended extraocular phenotype of PROM1 mutation in kindreds with known autosomal dominant macular dystrophy. Eur J Hum Genet 2010; 19:131-7. [PMID: 20859302 DOI: 10.1038/ejhg.2010.147] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutations in prominin 1 (PROM1) have been shown to result in retinitis pigmentosa, macular degeneration and cone-rod dystrophy. Because of the putative role of PROM1 in hippocampal neurogenesis, we examined two kindreds with the same R373C PROM1 missense mutation using our established paradigm to study brain structure and function. As the protein encoded by PROM1, known as CD133, is used to identify stem/progenitor cells that can be found in peripheral blood and reflect endothelial reparatory mechanisms, other parameters were subsequently examined that included measures of vascular function, endothelial function and angiogenic capacity. We found that aspects of endothelial function assayed ex vivo were abnormal in patients with the R373C PROM1 mutation, with impaired adhesion capacity and higher levels of cellular damage. We also noted renal infections, haematuria and recurrent miscarriages possibly reflecting consequences of abnormal tubular modelling. Further studies are needed to confirm these findings.
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Sisodiya S. Brain structure, function, and genetics revealed by studies of the eye and face. Curr Opin Neurol 2008; 21:404-9. [DOI: 10.1097/wco.0b013e3283052d0c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Montana CL, Corbo JC. Inherited diseases of photoreceptors and prospects for gene therapy. Pharmacogenomics 2008; 9:335-47. [PMID: 18303969 DOI: 10.2217/14622416.9.3.335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The photoreceptor cells of the retina are subject to a wide range of genetic diseases. This review summarizes current knowledge regarding an important group of retinal diseases caused by mutations in photoreceptor-enriched genes. In addition, progress toward treatment of a variety of these diseases in animal models via adeno-associated virus gene therapy is described. Although no human trials have yet been initiated to treat diseases caused by mutations in photoreceptor-enriched genes, there is a great deal of optimism regarding the prospects of treating these diseases using adeno-associated virus gene therapy.
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Affiliation(s)
- Cynthia L Montana
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118; 660 South Euclid Ave. St. Louis, MO 63110, USA
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Miki T, Kiyonaka S, Uriu Y, De Waard M, Wakamori M, Beedle AM, Campbell KP, Mori Y. Mutation associated with an autosomal dominant cone-rod dystrophy CORD7 modifies RIM1-mediated modulation of voltage-dependent Ca2+ channels. Channels (Austin) 2007; 1:144-7. [PMID: 18690027 DOI: 10.4161/chan.4660] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Genetic analyses have revealed an association between the gene encoding the Rab3A-interacting molecule (RIM1) and the autosomal dominant cone-rod dystrophy CORD7. However, the pathogenesis of CORD7 remains unclear. We recently revealed that RIM1 regulates voltage-dependent Ca(2+) channel (VDCC) currents and anchors neurotransmitter-containing vesicles to VDCCs, thereby controlling neurotransmitter release. We demonstrate here that the mouse RIM1 arginine-to-histidine substitution (R655H), which corresponds to the human CORD7 mutation, modifies RIM1 function in regulating VDCC currents elicited by the P/Q-type Ca(v)2.1 and L-type Ca(v)1.4 channels. Thus, our data can raise an interesting possibility that CORD7 phenotypes including retinal deficits and enhanced cognition are at least partly due to altered regulation of presynaptic VDCC currents.
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Affiliation(s)
- Takafumi Miki
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
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