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Scheetz TE, Tollefson MR, Roos BR, Boese EA, Pouw AE, Stone EM, Schnieders MJ, Fingert JH. METTL23 Variants and Patients With Normal-Tension Glaucoma. JAMA Ophthalmol 2024; 142:1037-1045. [PMID: 39325437 PMCID: PMC11428026 DOI: 10.1001/jamaophthalmol.2024.3829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/27/2024] [Indexed: 09/27/2024]
Abstract
Importance This research confirms and further establishes that pathogenic variants in a fourth gene, METTL23, are associated with autosomal dominant normal-tension glaucoma (NTG). Objective To determine the frequency of glaucoma-causing pathogenic variants in the METTL23 gene in a cohort of patients with NTG from Iowa. Design, Setting, and Participants This case-control study took place at a single tertiary care center in Iowa from January 1997 to January 2024, with analysis occurring between January 2023 and January 2024. Two groups of participants were enrolled from the University of Iowa clinics: 331 patients with NTG and 362 control individuals without glaucoma. Patients with a history of trauma; steroid use; stigmata of pigment dispersion syndrome; exfoliation syndrome; or pathogenic variants in MYOC, TBK1, or OPTN were also excluded. Main Outcomes and Measures Detection of an enrichment of METTL23 pathogenic variants in individuals with NTG compared with control individuals without glaucoma. Results The study included 331 patients with NTG (mean [SD] age, 68.0 [11.7] years; 228 [68.9%] female and 103 [31.1%] male) and 362 control individuals without glaucoma (mean [SD] age, 64.5 [12.6] years; 207 [57.2%] female and 155 [42.8%] male). There were 5 detected instances of 4 unique METTL23 pathogenic variants in patients with NTG. Three METTL23 variants-p.Ala7Val, p.Pro22Arg, and p.Arg63Trp-were judged to be likely pathogenic and were detected in 3 patients (0.91%) with NTG. However, when all detected variants were evaluated with either mutation burden analysis or logistic regression, their frequency was not statistically higher in individuals with NTG than in control individuals without glaucoma (1.5% vs 2.5%; P = .27). Conclusion and Relevance This investigation provides evidence that pathogenic variants in METTL23 are associated with NTG. Within an NTG cohort at a tertiary care center, pathogenic variants were associated with approximately 1% of NTG cases, a frequency similar to that of other known normal-tension glaucoma genes, including optineurin (OPTN), TANK-binding kinase 1 (TBK1), and myocilin (MYOC). The findings suggest that METTL23 pathogenic variants are likely involved in a biologic pathway that is associated with glaucoma that occurs at lower intraocular pressures.
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Affiliation(s)
- Todd. E. Scheetz
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Mallory R. Tollefson
- Deparment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - Ben R. Roos
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Erin A. Boese
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Andrew E. Pouw
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Edwin M. Stone
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Michael J. Schnieders
- Institute for Vision Research, University of Iowa, Iowa City
- Deparment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - John H. Fingert
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
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2
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Sun J, Wang C, Wu Y, Xiang J, Zhang Y. Association Analysis of METTL23 Gene Polymorphisms with Reproductive Traits in Kele Pigs. Genes (Basel) 2024; 15:1061. [PMID: 39202421 PMCID: PMC11353829 DOI: 10.3390/genes15081061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/27/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Methyltransferase-like 23 (METTL23) is a kind of RNA methyltransferase that catalyzes the methylation transfer to the N6-adenosine of RNA, serving as one of the key mediators in this process. However, the METTL23 gene has been poorly researched in pigs. In this study, we investigated the genetic effects of METTL23 single-nucleotide polymorphism(SNPs) on reproductive traits in Kele pigs. The DNA was extracted from 228 healthy multiparous Kele sows, and Sanger sequencing revealed three SNPs, g.4804958 G > T (intron 2), g.4805082 C > T (exon 2), and g.4806821 A > G (exon 3). The polymorphism information content (PIC) for each SNP was 0.264, 0.25, and 0.354, indicating moderate polymorphism (0.25 < PIC < 0.5) and providing genetic information. Linkage disequilibrium analysis showed no strong linkage disequilibrium between the three SNPs. The association analysis revealed that in the SNP g.4804958 G > T individuals with the GG genotype had a significantly higher number of piglets born alive, litter birth weight, number of weaned piglets, and weaning litter weight compared to those with the TT genotype (p < 0.05). Individuals with the GG genotype in the SNP g.4806821 A > G group had significantly higher litter birth weight and average birth weight than those with the AA genotype (p < 0.05). The H4H4 diplotype showed significant effects on the number of piglets born alive, litter birth weight, number of weaned piglets, weaning litter weight, and weaning weight (p < 0.05). Together, the METTL23 gene could be used as a candidate gene for the selection of reproductive traits in Kele pigs.
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Affiliation(s)
- Jie Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China; (J.S.); (C.W.); (Y.W.); (J.X.)
- Institute of Xiang Pigs, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China
| | - Chunyuan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China; (J.S.); (C.W.); (Y.W.); (J.X.)
- Institute of Xiang Pigs, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China
| | - Yan Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China; (J.S.); (C.W.); (Y.W.); (J.X.)
- Institute of Xiang Pigs, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China
| | - Jin Xiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China; (J.S.); (C.W.); (Y.W.); (J.X.)
- Institute of Xiang Pigs, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China
| | - Yiyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China; (J.S.); (C.W.); (Y.W.); (J.X.)
- Institute of Xiang Pigs, Guizhou University, West Campus, Huaxi District, Guiyang 550025, China
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3
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Zha J, Chen Y, Cao F, Yu Y, Wang R, Zhong J. Identification of a novel METTL23 gene variant in a patient with an intellectual development disorder: a literature review and case report. Front Pediatr 2024; 12:1328063. [PMID: 39026940 PMCID: PMC11254747 DOI: 10.3389/fped.2024.1328063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
METTL23 belongs to a family of protein lysine methyltransferases that methylate non-histone proteins. Recently, the METTL23 gene has been reported to be related to an intellectual developmental disorder, autosomal recessive 44. Patients present with developmental delay, intellectual disability (ID), and variable dysmorphic features. Here, we report on a Chinese girl who presented with global developmental delay, abnormal brain structure, and multiple facial deformities, including a short/upturned nose with a sunken bridge, thin lips, and flat occiput. Whole-exome sequencing identified a novel variant (NM_001080510.5: c.322+1del) on the METTL23 gene. This variant was not collected on public human variants databases such as gnomAD, predicted to influence the splicing as a classical splicing variant, and classified as Pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Since patients with METTL23-related ID are rare, we summarize and compare the clinical phenotype of reported patients with METTL23 variants. Our report further expands the METTL23 variants and provides new evidence for clinical diagnosis of METTL23-related ID.
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Affiliation(s)
- Jian Zha
- Department of Neurology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Yong Chen
- Department of Neurology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Fangfang Cao
- Department of Neurology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Yanghong Yu
- Department of Radiology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Ruiyan Wang
- Department of Neurology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Jianmin Zhong
- Department of Neurology, Jiangxi Provincial Children’s Hospital, Nanchang, China
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4
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Weng Y, Zhou S, Morillo K, Kaletsky R, Lin S, Murphy CT. The neuron-specific IIS/FOXO transcriptome in aged animals reveals regulatory mechanisms of cognitive aging. eLife 2024; 13:RP95621. [PMID: 38922671 PMCID: PMC11208049 DOI: 10.7554/elife.95621] [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] [Indexed: 06/27/2024] Open
Abstract
Cognitive decline is a significant health concern in our aging society. Here, we used the model organism C. elegans to investigate the impact of the IIS/FOXO pathway on age-related cognitive decline. The daf-2 Insulin/IGF-1 receptor mutant exhibits a significant extension of learning and memory span with age compared to wild-type worms, an effect that is dependent on the DAF-16 transcription factor. To identify possible mechanisms by which aging daf-2 mutants maintain learning and memory with age while wild-type worms lose neuronal function, we carried out neuron-specific transcriptomic analysis in aged animals. We observed downregulation of neuronal genes and upregulation of transcriptional regulation genes in aging wild-type neurons. By contrast, IIS/FOXO pathway mutants exhibit distinct neuronal transcriptomic alterations in response to cognitive aging, including upregulation of stress response genes and downregulation of specific insulin signaling genes. We tested the roles of significantly transcriptionally-changed genes in regulating cognitive functions, identifying novel regulators of learning and memory. In addition to other mechanistic insights, a comparison of the aged vs young daf-2 neuronal transcriptome revealed that a new set of potentially neuroprotective genes is upregulated; instead of simply mimicking a young state, daf-2 may enhance neuronal resilience to accumulation of harm and take a more active approach to combat aging. These findings suggest a potential mechanism for regulating cognitive function with age and offer insights into novel therapeutic targets for age-related cognitive decline.
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Affiliation(s)
- Yifei Weng
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Shiyi Zhou
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Katherine Morillo
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Rachel Kaletsky
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
- Princeton UniversityPrincetonUnited States
| | - Sarah Lin
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
- Princeton UniversityPrincetonUnited States
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5
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Zhong G, Choi YA, Shen Y. VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Commun Biol 2023; 6:774. [PMID: 37491581 PMCID: PMC10368729 DOI: 10.1038/s42003-023-05155-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
Rare or de novo variants have substantial contribution to human diseases, but the statistical power to identify risk genes by rare variants is generally low due to rarity of genotype data. Previous studies have shown that risk genes usually have high expression in relevant cell types, although for many conditions the identity of these cell types are largely unknown. Recent efforts in single cell atlas in human and model organisms produced large amount of gene expression data. Here we present VBASS, a Bayesian method that integrates single-cell expression and de novo variant (DNV) data to improve power of disease risk gene discovery. VBASS models disease risk prior as a function of expression profiles, approximated by deep neural networks. It learns the weights of neural networks and parameters of Gamma-Poisson likelihood models of DNV counts jointly from expression and genetics data. On simulated data, VBASS shows proper error rate control and better power than state-of-the-art methods. We applied VBASS to published datasets and identified more candidate risk genes with supports from literature or data from independent cohorts. VBASS can be generalized to integrate other types of functional genomics data in statistical genetics analysis.
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Affiliation(s)
- Guojie Zhong
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Yoolim A Choi
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
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6
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Bizzari S, Nair P, Hana S, Deepthi A, Al-Ali MT, Al-Gazali L, El-Hayek S. Spectrum of genetic disorders and gene variants in the United Arab Emirates national population: insights from the CTGA database. Front Genet 2023; 14:1177204. [PMID: 37214420 PMCID: PMC10194840 DOI: 10.3389/fgene.2023.1177204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Like many other Arab countries, the United Arab Emirates (UAE) has a relatively high prevalence of genetic disorders. Here we present the first review and analysis of all genetic disorders and gene variants reported in Emirati nationals and hosted on the Catalogue for Transmission Genetics in Arabs (CTGA), an open-access database hosting bibliographic data on human gene variants associated with inherited or heritable phenotypes in Arabs. To date, CTGA hosts 665 distinct genetic conditions that have been described in Emiratis, 621 of which follow a clear Mendelian inheritance. Strikingly, over half of these are extremely rare according to global prevalence rates, predominantly with an autosomal recessive mode of inheritance. This is likely due to the relatively high consanguinity rates within the Emirati population. The 665 conditions include disorders that are unique to the Emirati population, as well as clearly monogenic disorders that have not yet been mapped to a causal genetic locus. We also describe 1,365 gene variants reported in Emiratis, most of which are substitutions and over half are classified as likely pathogenic or pathogenic. Of these, 235 had not been reported on the international databases dbSNP and Clinvar, as of December 2022. Further analysis of this Emirati variant dataset allows a comparison of clinical significance as reported by Clinvar and CTGA, where the latter is derived from the study cited. A total of 307 pathogenic/likely pathogenic variants from CTGA's Emirati dataset, were classified as benign, variants of uncertain significance, or were missing a clinical significance or had not been reported by Clinvar. In conclusion, we present here the spectrum of genetic disorders and gene variants reported in Emiratis. This review emphasizes the importance of ethnic databases such as CTGA in addressing the underrepresentation of Arab variant data in international databases and documenting population-specific discrepancies in variant interpretation, reiterating the value of such repositories for clinicians and researchers, especially when dealing with rare disorders.
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Affiliation(s)
- Sami Bizzari
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - Pratibha Nair
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - Sayeeda Hana
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - Asha Deepthi
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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7
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Brielle ES, Fleisher J, Wynne-Jones S, Sirak K, Broomandkhoshbacht N, Callan K, Curtis E, Iliev L, Lawson AM, Oppenheimer J, Qiu L, Stewardson K, Workman JN, Zalzala F, Ayodo G, Gidna AO, Kabiru A, Kwekason A, Mabulla AZP, Manthi FK, Ndiema E, Ogola C, Sawchuk E, Al-Gazali L, Ali BR, Ben-Salem S, Letellier T, Pierron D, Radimilahy C, Rakotoarisoa JA, Raaum RL, Culleton BJ, Mallick S, Rohland N, Patterson N, Mwenje MA, Ahmed KB, Mohamed MM, Williams SR, Monge J, Kusimba S, Prendergast ME, Reich D, Kusimba CM. Entwined African and Asian genetic roots of medieval peoples of the Swahili coast. Nature 2023; 615:866-873. [PMID: 36991187 PMCID: PMC10060156 DOI: 10.1038/s41586-023-05754-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/24/2023] [Indexed: 03/31/2023]
Abstract
The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people1,2. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast3. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia4. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.
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Affiliation(s)
- Esther S Brielle
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | | | - Stephanie Wynne-Jones
- Department of Archaeology, University of York, York, UK.
- University of South Africa, Pretoria, South Africa.
| | - Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kim Callan
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - J Noah Workman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - George Ayodo
- Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | | | - Angela Kabiru
- Department of Archaeology, National Museums of Kenya, Nairobi, Kenya
- British Institute of Eastern Africa, Nairobi, Kenya
| | | | - Audax Z P Mabulla
- Department of Archaeology and Heritage Studies, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Emmanuel Ndiema
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Christine Ogola
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Elizabeth Sawchuk
- Cleveland Museum of Natural History, Cleveland, OH, USA
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
| | - Lihadh Al-Gazali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Salma Ben-Salem
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Thierry Letellier
- Laboratoire Evolution et Santé Orale, Faculté de Chirurgie Dentaire, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Denis Pierron
- Laboratoire Evolution et Santé Orale, Faculté de Chirurgie Dentaire, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Chantal Radimilahy
- Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, Antananarivo, Madagascar
| | - Jean-Aimé Rakotoarisoa
- Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, Antananarivo, Madagascar
| | - Ryan L Raaum
- Department of Anthropology, Lehman College and The Graduate Center, The City University of New York, New York, NY, USA
- The New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | - Sloan R Williams
- Department of Anthropology, University of Illinois at Chicago, Chicago, IL, USA
| | - Janet Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA, USA
| | - Sibel Kusimba
- Department of Anthropology, University of South Florida, Tampa, FL, USA
| | - Mary E Prendergast
- Department of Anthropology, Rice University, Houston, TX, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Chapurukha M Kusimba
- Department of Archaeology, National Museums of Kenya, Nairobi, Kenya.
- Department of Anthropology, University of South Florida, Tampa, FL, USA.
- Institute of African Studies, University of Nairobi, Museum Hill, Nairobi, Kenya.
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8
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Pan Y, Suga A, Kimura I, Kimura C, Minegishi Y, Nakayama M, Yoshitake K, Iejima D, Minematsu N, Yamamoto M, Mabuchi F, Takamoto M, Shiga Y, Araie M, Kashiwagi K, Aihara M, Nakazawa T, Iwata T. METTL23 mutation alters histone H3R17 methylation in normal-tension glaucoma. J Clin Invest 2022; 132:e153589. [PMID: 36099048 PMCID: PMC9621137 DOI: 10.1172/jci153589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Normal-tension glaucoma (NTG) is a heterogeneous disease characterized by retinal ganglion cell (RGC) death leading to cupping of the optic nerve head and visual field loss at normal intraocular pressure (IOP). The pathogenesis of NTG remains unclear. Here, we describe a single nucleotide mutation in exon 2 of the methyltransferase-like 23 (METTL23) gene identified in 3 generations of a Japanese family with NTG. This mutation caused METTL23 mRNA aberrant splicing, which abolished normal protein production and altered subcellular localization. Mettl23-knock-in (Mettl23+/G and Mettl23G/G) and -knockout (Mettl23+/- and Mettl23-/-) mice developed a glaucoma phenotype without elevated IOP. METTL23 is a histone arginine methyltransferase expressed in murine and macaque RGCs. However, the novel mutation reduced METTL23 expression in RGCs of Mettl23G/G mice, which recapitulated both clinical and biological phenotypes. Moreover, our findings demonstrated that METTL23 catalyzed the dimethylation of H3R17 in the retina and was required for the transcription of pS2, an estrogen receptor α target gene that was critical for RGC homeostasis through the negative regulation of NF-κB-mediated TNF-α and IL-1β feedback. These findings suggest an etiologic role of METTL23 in NTG with tissue-specific pathology.
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Affiliation(s)
- Yang Pan
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Akiko Suga
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Itaru Kimura
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
- Department of Ophthalmology, Tokai University Hachioji Hospital, Tokyo, Japan
| | | | - Yuriko Minegishi
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mao Nakayama
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kazutoshi Yoshitake
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Daisuke Iejima
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Naoko Minematsu
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Megumi Yamamoto
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
- JAC Ltd., Tokyo, Japan
| | - Fumihiko Mabuchi
- Department of Ophthalmology, University of Yamanashi, Yamanashi, Japan
| | | | - Yukihiro Shiga
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Makoto Araie
- Department of Ophthalmology, University of Tokyo, Tokyo, Japan
- Kanto Central Hospital of the Mutual Aid Association of Public School Teachers, Tokyo, Japan
| | - Kenji Kashiwagi
- Department of Ophthalmology, University of Yamanashi, Yamanashi, Japan
| | - Makoto Aihara
- Department of Ophthalmology, University of Tokyo, Tokyo, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeshi Iwata
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
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9
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Bataglia L, Simões ZLP, Nunes FMF. Active genic machinery for epigenetic RNA modifications in bees. INSECT MOLECULAR BIOLOGY 2021; 30:566-579. [PMID: 34291855 DOI: 10.1111/imb.12726] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Epitranscriptomics is an emerging field of investigation dedicated to the study of post-transcriptional RNA modifications. RNA methylations regulate RNA metabolism and processing, including changes in response to environmental cues. Although RNA modifications are conserved from bacteria to eukaryotes, there is little evidence of an epitranscriptomic pathway in insects. Here we identified genes related to RNA m6 A (N6-methyladenine) and m5 C (5-methylcytosine) methylation machinery in seven bee genomes (Apis mellifera, Melipona quadrifasciata, Frieseomelitta varia, Eufriesea mexicana, Bombus terrestris, Megachile rotundata and Dufourea novaeangliae). In A. mellifera, we validated the expression of methyltransferase genes and found that the global levels of m6 A and m5 C measured in the fat body and brain of adult workers differ significantly. Also, m6 A levels were differed significantly mainly between the fourth larval instar of queens and workers. Moreover, we found a conserved m5 C site in the honeybee 28S rRNA. Taken together, we confirm the existence of epitranscriptomic machinery acting in bees and open avenues for future investigations on RNA epigenetics in a wide spectrum of hymenopteran species.
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Affiliation(s)
- L Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Z L P Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
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10
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Wong JM, Eirin-Lopez JM. Evolution of methyltransferase like (METTL) proteins in Metazoa: A complex gene family involved in epitranscriptomic regulation and other epigenetic processes. Mol Biol Evol 2021; 38:5309-5327. [PMID: 34480573 PMCID: PMC8662637 DOI: 10.1093/molbev/msab267] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The methyltransferase-like (METTL) proteins constitute a family of seven-beta-strand methyltransferases with S-adenosyl methionine-binding domains that modify DNA, RNA, and proteins. Methylation by METTL proteins contributes to the epigenetic, and in the case of RNA modifications, epitranscriptomic regulation of a variety of biological processes. Despite their functional importance, most investigations of the substrates and functions of METTLs within metazoans have been restricted to model vertebrate taxa. In the present work, we explore the evolutionary mechanisms driving the diversification and functional differentiation of 33 individual METTL proteins across Metazoa. Our results show that METTLs are nearly ubiquitous across the animal kingdom, with most having arisen early in metazoan evolution (i.e., occur in basal metazoan phyla). Individual METTL lineages each originated from single independent ancestors, constituting monophyletic clades, which suggests that each METTL was subject to strong selective constraints driving its structural and/or functional specialization. Interestingly, a similar process did not extend to the differentiation of nucleoside-modifying and protein-modifying METTLs (i.e., each METTL type did not form a unique monophyletic clade). The members of these two types of METTLs also exhibited differences in their rates of evolution. Overall, we provide evidence that the long-term evolution of METTL family members was driven by strong purifying selection, which in combination with adaptive selection episodes, led to the functional specialization of individual METTL lineages. This work contributes useful information regarding the evolution of a gene family that fulfills a variety of epigenetic functions, and can have profound influences on molecular processes and phenotypic traits.
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Affiliation(s)
- Juliet M Wong
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, United States
| | - Jose M Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, United States
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11
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Eslami Rasekh M, Hernández Y, Drinan SD, Fuxman Bass J, Benson G. Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. Nucleic Acids Res 2021; 49:4308-4324. [PMID: 33849068 PMCID: PMC8096271 DOI: 10.1093/nar/gkab224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/06/2021] [Accepted: 03/18/2021] [Indexed: 11/12/2022] Open
Abstract
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.
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Affiliation(s)
| | - Yözen Hernández
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | | | - Juan I Fuxman Bass
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Gary Benson
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Computer Science, Boston University, Boston, MA 02215, USA
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12
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Khan A, Miao Z, Umair M, Ullah A, Alshabeeb MA, Bilal M, Ahmad F, Rappold GA, Ansar M, Carapito R. Two Cases of Recessive Intellectual Disability Caused by NDST1 and METTL23 Variants. Genes (Basel) 2020; 11:E1021. [PMID: 32878022 PMCID: PMC7563614 DOI: 10.3390/genes11091021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/03/2022] Open
Abstract
Intellectual disability (ID) is a highly heterogeneous genetic condition with more than a thousand genes described so far. By exome sequencing of two consanguineous families presenting hallmark features of ID, we identified two homozygous variants in two genes previously associated with autosomal recessive ID: NDST1 (c.1966G>A; p.Asp656Asn) and METTL23 (c.310T>C; p.Phe104Leu). The segregation of the variants was validated by Sanger sequencing in all family members. In silico homology modeling of wild-type and mutated proteins revealed substantial changes in the secondary structure of both proteins, indicating a possible effect on function. The identification and validation of new pathogenic NDST1 and METTL23 variants in two cases of autosomal recessive ID further highlight the importance of these genes in proper brain function and development.
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Affiliation(s)
- Amjad Khan
- Laboratoire d’ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085 Strasbourg, France;
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK;
- Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, No.1878 North Sichuan Road, Hongkou District, Shanghai 200081, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi Arabia;
| | - Amir Ullah
- Nephrology and Dialysis Unit, District Head Quarter Teaching Hospital, Bannu 28100, Pakistan;
| | - Mohammad A. Alshabeeb
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia;
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.B.); (M.A.)
| | - Farooq Ahmad
- Department of Chemistry, Women University Swabi, Khyber Pakhtunkhwa 23430, Pakistan;
| | - Gudrun A. Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University, 69118 Heidelberg, Germany;
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.B.); (M.A.)
| | - Raphael Carapito
- Laboratoire d’ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085 Strasbourg, France;
- Service d’Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg, France
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13
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Exome sequencing revealed a novel homozygous METTL23 gene mutation leading to familial mild intellectual disability with dysmorphic features. Eur J Med Genet 2020; 63:103951. [PMID: 32439618 DOI: 10.1016/j.ejmg.2020.103951] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/06/2020] [Accepted: 05/09/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Genetic factors represent a considerable part of the etiologies of intellectual disability; however, the identification of causal genetic anomaly has long been complicated by the great clinical and genetic heterogeneity of this type of disease. With advances in next-generation sequencing technologies and functional studies, the identification of genes involved in intellectual development has led to more accurate diagnostics and better understanding of the underlying biological pathways. CASE REPORT We report on the case of two Moroccan siblings presenting mild intellectual disability with minimal dysmorphic features in which whole exome sequencing analysis revealed homozygous mutation in the METTL23 gene. Mutations in this gene have been reported to cause autosomal recessive mild intellectual disability but the association with dysmorphic features remains controversial. CONCLUSION Hereby, we highlight the similarity of the dysmorphic traits and the characteristic facial features in patients with METTL23-related intellectual disability, suggesting the consideration of a distinct clinical entity associating mild intellectual deficiency with specific facial dysmorphy for an efficient diagnosis orientation and a better phenotype-genotype correlation in intellectual disability disorders.
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14
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Harris CJ, Davis BA, Zweig JA, Nevonen KA, Quinn JF, Carbone L, Gray NE. Age-Associated DNA Methylation Patterns Are Shared Between the Hippocampus and Peripheral Blood Cells. Front Genet 2020; 11:111. [PMID: 32211019 PMCID: PMC7067920 DOI: 10.3389/fgene.2020.00111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/30/2020] [Indexed: 12/13/2022] Open
Abstract
As the population ages, interest in identifying biomarkers of healthy aging and developing antiaging interventions has increased. DNA methylation has emerged as a potentially powerful molecular marker of aging. Methylation changes at specific sites in the human genome that have been identified in peripheral blood have been used as robust estimators of chronological age. Similar age-related DNA methylation signatures are also seen in various tissue types in rodents. However, whether these peripheral alterations in methylation status reflect changes that also occur in the central nervous system remains unknown. This study begins to address this issue by identifying age-related methylation patterns in the hippocampus and blood of young and old mice. Reduced-representation bisulfite sequencing (RBSS) was used to identify differentially methylated regions (DMRs) in the blood and hippocampus of 2- and 20-month-old C57/Bl6 mice. Of the thousands of DMRs identified genome-wide only five were both found in gene promoters and significantly changed in the same direction with age in both tissues. We analyzed the hippocampal expression of these five hypermethylated genes and found that three were expressed at significantly lower levels in aged mice [suppressor of fused homolog (Sufu), nitric oxide synthase 1 (Nos1) and tripartite motif containing 2 (Trim2)]. We also identified several transcription factor binding motifs common to both hippocampus and blood that were enriched in the DMRs. Overall, our findings suggest that some age-related methylation changes that occur in the brain are also evident in the blood and could have significant translational relevance.
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Affiliation(s)
- Christopher J Harris
- Department of Neurology, Oregon Health and Science University, Portland, OR, United States
| | - Brett A Davis
- Department of Medicine, KCVI, Oregon Health and Science University, Portland, OR, United States
| | - Jonathan A Zweig
- Department of Neurology, Oregon Health and Science University, Portland, OR, United States
| | - Kimberly A Nevonen
- Department of Medicine, KCVI, Oregon Health and Science University, Portland, OR, United States
| | - Joseph F Quinn
- Department of Neurology, Oregon Health and Science University, Portland, OR, United States.,Parkinson's Disease Research, Education, and Clinical Center, Portland Veteran's Affairs Medical Center, Portland, OR, United States
| | - Lucia Carbone
- Department of Medicine, KCVI, Oregon Health and Science University, Portland, OR, United States.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, United States.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, United States
| | - Nora E Gray
- Department of Neurology, Oregon Health and Science University, Portland, OR, United States
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15
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Serre NBC, Sarthou M, Gigarel O, Figuet S, Corso M, Choulet J, Rofidal V, Alban C, Santoni V, Bourguignon J, Verbruggen N, Ravanel S. Protein lysine methylation contributes to modulating the response of sensitive and tolerant Arabidopsis species to cadmium stress. PLANT, CELL & ENVIRONMENT 2020; 43:760-774. [PMID: 31759334 DOI: 10.1111/pce.13692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/04/2019] [Accepted: 11/19/2019] [Indexed: 05/10/2023]
Abstract
The mechanisms underlying the response and adaptation of plants to excess of trace elements are not fully described. Here, we analysed the importance of protein lysine methylation for plants to cope with cadmium. We analysed the effect of cadmium on lysine-methylated proteins and protein lysine methyltransferases (KMTs) in two cadmium-sensitive species, Arabidopsis thaliana and A. lyrata, and in three populations of A. halleri with contrasting cadmium accumulation and tolerance traits. We showed that some proteins are differentially methylated at lysine residues in response to Cd and that a few genes coding KMTs are regulated by cadmium. Also, we showed that 9 out of 23 A. thaliana mutants disrupted in KMT genes have a tolerance to cadmium that is significantly different from that of wild-type seedlings. We further characterized two of these mutants, one was knocked out in the calmodulin lysine methyltransferase gene and displayed increased tolerance to cadmium, and the other was interrupted in a KMT gene of unknown function and showed a decreased capacity to cope with cadmium. Together, our results showed that lysine methylation of non-histone proteins is impacted by cadmium and that several methylation events are important for modulating the response of Arabidopsis plants to cadmium stress.
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Affiliation(s)
- Nelson B C Serre
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Manon Sarthou
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Océane Gigarel
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Sylvie Figuet
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Massimiliano Corso
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Justine Choulet
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Valérie Rofidal
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier, Cedex 2, France
| | - Claude Alban
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
| | - Véronique Santoni
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier, Montpellier, Cedex 2, France
| | | | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Stéphane Ravanel
- University of Grenoble Alpes, CEA, INRA, CNRS, IRIG, PCV, Grenoble, France
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16
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Almannai M, Obaid O, Faqeih E, Alasmari A, Samman MM, Pinz H, Braddock SR, Alkuraya FS. Further delineation of METTL23-associated intellectual disability. Am J Med Genet A 2020; 182:785-791. [PMID: 32067349 DOI: 10.1002/ajmg.a.61503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/08/2019] [Accepted: 01/17/2020] [Indexed: 11/07/2022]
Abstract
METTL23 belongs to a family of methyltransferase like proteins (METTL) that transfer methyl group to various substrates. Recently, pathogenic homozygous variants in METTL23 were identified in patients from three families who presented with intellectual disability (ID) and variable dysmorphic features. In this report, we present unpublished phenotypic data from the original family as well as six new subjects from four families who also presented with mild to moderate ID and dysmorphic features, and were found to harbor four previously unpublished homozygous or compound heterozygous variants in METTL23. Our report further supports the role of this gene in autosomal recessive ID and emphasizes the mild but consistent facial features.
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Affiliation(s)
- Mohammed Almannai
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Osama Obaid
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Alasmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Manar M Samman
- Pathology and Clinical Laboratory Medicine Administration, Section of Molecular Pathology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hailey Pinz
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Medical Center, St. Louis, Missouri.,Department of Pediatrics, Saint Louis University Hospital, St. Louis, Missouri
| | - Stephen R Braddock
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Medical Center, St. Louis, Missouri.,Department of Pediatrics, Saint Louis University Hospital, St. Louis, Missouri
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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17
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Bi-allelic Variants in METTL5 Cause Autosomal-Recessive Intellectual Disability and Microcephaly. Am J Hum Genet 2019; 105:869-878. [PMID: 31564433 DOI: 10.1016/j.ajhg.2019.09.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/04/2019] [Indexed: 02/01/2023] Open
Abstract
Intellectual disability (ID) is a genetically and clinically heterogeneous disorder, characterized by limited cognitive abilities and impaired adaptive behaviors. In recent years, exome sequencing (ES) has been instrumental in deciphering the genetic etiology of ID. Here, through ES of a large cohort of individuals with ID, we identified two bi-allelic frameshift variants in METTL5, c.344_345delGA (p.Arg115Asnfs∗19) and c.571_572delAA (p.Lys191Valfs∗10), in families of Pakistani and Yemenite origin. Both of these variants were segregating with moderate to severe ID, microcephaly, and various facial dysmorphisms, in an autosomal-recessive fashion. METTL5 is a member of the methyltransferase-like protein family, which encompasses proteins with a seven-beta-strand methyltransferase domain. We found METTL5 expression in various substructures of rodent and human brains and METTL5 protein to be enriched in the nucleus and synapses of the hippocampal neurons. Functional studies of these truncating variants in transiently transfected orthologous cells and cultured hippocampal rat neurons revealed no effect on the localization of METTL5 but alter its level of expression. Our in silico analysis and 3D modeling simulation predict disruption of METTL5 function by both variants. Finally, mettl5 knockdown in zebrafish resulted in microcephaly, recapitulating the human phenotype. This study provides evidence that biallelic variants in METTL5 cause ID and microcephaly in humans and highlights the essential role of METTL5 in brain development and neuronal function.
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18
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Taguchi YH, Turki T. Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Single-Cell Gene Expression Analysis. Front Genet 2019; 10:864. [PMID: 31608111 PMCID: PMC6761323 DOI: 10.3389/fgene.2019.00864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022] Open
Abstract
Although single-cell RNA sequencing (scRNA-seq) technology is newly invented and a promising one, but because of lack of enough information that labels individual cells, it is hard to interpret the obtained gene expression of each cell. Because of insufficient information available, unsupervised clustering, for example, t-distributed stochastic neighbor embedding and uniform manifold approximation and projection, is usually employed to obtain low-dimensional embedding that can help to understand cell–cell relationship. One possible drawback of this strategy is that the outcome is highly dependent upon genes selected for the usage of clustering. In order to fulfill this requirement, there are many methods that performed unsupervised gene selection. In this study, a tensor decomposition (TD)-based unsupervised feature extraction (FE) was applied to the integration of two scRNA-seq expression profiles that measure human and mouse midbrain development. TD-based unsupervised FE could select not only coincident genes between human and mouse but also biologically reliable genes. Coincidence between two species as well as biological reliability of selected genes is increased compared with that using principal component analysis (PCA)-based FE applied to the same data set in the previous study. Since PCA-based unsupervised FE outperformed the other three popular unsupervised gene selection methods, highly variable genes, bimodal genes, and dpFeature, TD-based unsupervised FE can do so as well. In addition to this, 10 transcription factors (TFs) that might regulate selected genes and might contribute to midbrain development were identified. These 10 TFs, BHLHE40, EGR1, GABPA, IRF3, PPARG, REST, RFX5, STAT3, TCF7L2, and ZBTB33, were previously reported to be related to brain functions and diseases. TD-based unsupervised FE is a promising method to integrate two scRNA-seq profiles effectively.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, Japan
| | - Turki Turki
- Department of Computer Science, King Abdulaziz University, Jeddah, Saudi Arabia
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19
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Yang G, Lu H, Wang L, Zhao J, Zeng W, Zhang T. Genome-Wide Identification and Transcriptional Expression of the METTL21C Gene Family in Chicken. Genes (Basel) 2019; 10:genes10080628. [PMID: 31434291 PMCID: PMC6723737 DOI: 10.3390/genes10080628] [Citation(s) in RCA: 5] [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: 06/26/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022] Open
Abstract
The chicken is a common type of poultry that is economically important both for its medicinal and nutritional values. Previous studies have found that free-range chickens have more skeletal muscle mass. The methyltransferase-like 21C gene (METTL21C) plays an important role in muscle development; however, there have been few reports on the role of METTL21C in chickens. In this study, we performed a genome-wide identification of chicken METTL21C genes and analyzed their phylogeny, transcriptional expression profile, and real-time quantitative polymerase chain reaction (qPCR). We identified 10 GgMETTL21C genes from chickens, 11 from mice, and 32 from humans, and these genes were divided into six groups, which showed a large amount of variation among these three species. A total of 15 motifs were detected in METTL21C genes, and the intron phase of the gene structure showed that the METTL21C gene family was conservative in evolution. Further, both the transcript data and qPCR showed that a single gene’s (GgMETTL21C3) expression level increased with the muscle development of chickens, indicating that the METTL21C genes are involved in the development of chicken muscles. Our results provide some reference value for the subsequent study of the function of METTL21C.
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Affiliation(s)
- Ge Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Jiarong Zhao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China.
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20
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Uyhelji HA, Kupfer DM, White VL, Jackson ML, Van Dongen HPA, Burian DM. Exploring gene expression biomarker candidates for neurobehavioral impairment from total sleep deprivation. BMC Genomics 2018; 19:341. [PMID: 29739334 PMCID: PMC5941663 DOI: 10.1186/s12864-018-4664-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
Abstract
Background Although sleep deprivation is associated with neurobehavioral impairment that may underlie significant risks to performance and safety, there is no reliable biomarker test to detect dangerous levels of impairment from sleep loss in humans. This study employs microarrays and bioinformatics analyses to explore candidate gene expression biomarkers associated with total sleep deprivation (TSD), and more specifically, the phenotype of neurobehavioral impairment from TSD. Healthy adult volunteers were recruited to a sleep laboratory for seven consecutive days (six nights). After two Baseline nights of 10 h time in bed, 11 subjects underwent an Experimental phase of 62 h of continuous wakefulness, followed by two Recovery nights of 10 h time in bed. Another six subjects underwent a well-rested Control condition of 10 h time in bed for all six nights. Blood was drawn for measuring gene expression on days two, four, and six at 4 h intervals from 08:00 to 20:00 h, corresponding to 12 timepoints across one Baseline, one Experimental, and one Recovery day. Results Altogether 212 genes changed expression in response to the TSD Treatment, with most genes exhibiting down-regulation during TSD. Also, 28 genes were associated with neurobehavioral impairment as measured by the Psychomotor Vigilance Test. The results support previous findings associating TSD with the immune response and ion signaling, and reveal novel candidate biomarkers such as the Speedy/RINGO family of cell cycle regulators. Conclusions This study serves as an important step toward understanding gene expression changes during sleep deprivation. In addition to exploring potential biomarkers for TSD, this report presents novel candidate biomarkers associated with lapses of attention during TSD. Although further work is required for biomarker validation, analysis of these genes may aid fundamental understanding of the impact of TSD on neurobehavioral performance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4664-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hilary A Uyhelji
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA.
| | - Doris M Kupfer
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA.
| | - Vicky L White
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA
| | - Melinda L Jackson
- Sleep and Performance Research Center & Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, 99210, USA.,Present address: School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia
| | - Hans P A Van Dongen
- Sleep and Performance Research Center & Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, 99210, USA
| | - Dennis M Burian
- Civil Aerospace Medical Institute, Federal Aviation Administration, Oklahoma City, OK, 73169, USA
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21
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Hamey JJ, Wienert B, Quinlan KGR, Wilkins MR. METTL21B Is a Novel Human Lysine Methyltransferase of Translation Elongation Factor 1A: Discovery by CRISPR/Cas9 Knockout. Mol Cell Proteomics 2017; 16:2229-2242. [PMID: 28663172 DOI: 10.1074/mcp.m116.066308] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/28/2017] [Indexed: 02/03/2023] Open
Abstract
Lysine methylation is widespread on human proteins, however the enzymes that catalyze its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we used the CRISPR/Cas9 system to knockout putative protein methyltransferases METTL21B and METTL23 in K562 cells, to determine if they methylate elongation factor eEF1A. The known eEF1A methyltransferase EEF1AKMT1 was also knocked out as a control. Targeted mass spectrometry revealed the loss of lysine 165 methylation upon knockout of METTL21B, and the expected loss of lysine 79 methylation on knockout of EEF1AKMT1 No loss of eEF1A methylation was seen in the METTL23 knockout. Recombinant METTL21B was shown in vitro to catalyze methylation on lysine 165 in eEF1A1 and eEF1A2, confirming it as the methyltransferase responsible for this methylation site. Proteomic analysis by SILAC revealed specific upregulation of large ribosomal subunit proteins in the METTL21B knockout, and changes to further processes related to eEF1A function in knockouts of both METTL21B and EEF1AKMT1 This indicates that the methylation of lysine 165 in human eEF1A has a very specific role. METTL21B exists only in vertebrates, with its target lysine showing similar evolutionary conservation. We suggest METTL21B be renamed eEF1A-KMT3. This is the first study to specifically generate CRISPR/Cas9 knockouts of putative protein methyltransferase genes, for substrate discovery and site mapping. Our approach should prove useful for the discovery of further novel methyltransferases, and more generally for the discovery of sites for other protein-modifying enzymes.
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Affiliation(s)
- Joshua J Hamey
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Beeke Wienert
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Kate G R Quinlan
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Marc R Wilkins
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
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22
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Khan MA, Khan S, Windpassinger C, Badar M, Nawaz Z, Mohammad RM. The Molecular Genetics of Autosomal Recessive Nonsyndromic Intellectual Disability: a Mutational Continuum and Future Recommendations. Ann Hum Genet 2017; 80:342-368. [PMID: 27870114 DOI: 10.1111/ahg.12176] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022]
Abstract
Intellectual disability (ID) is a clinical manifestation of the central nervous system without any major dysmorphologies of the brain. Biologically it affects learning capabilities, memory, and cognitive functioning. The basic defining features of ID are characterized by IQ<70, age of onset before 18 years, and impairment of at least two of the adaptive skills. Clinically it is classified in a syndromic (with additional abnormalities) and a nonsyndromic form (with only cognitive impairment). The study of nonsyndromic intellectual disability (NSID) can best explain the pathophysiology of cognition, intelligence and memory. Genetic analysis in autosomal recessive nonsyndrmic ID (ARNSID) has mapped 51 disease loci, 34 of which have revealed their defective genes. These genes play diverse physiological roles in various molecular processes, including methylation, proteolysis, glycosylation, signal transduction, transcription regulation, lipid metabolism, ion homeostasis, tRNA modification, ubiquitination and neuromorphogenesis. High-density SNP array and whole exome sequencing has increased the pace of gene discoveries and many new mutations are being published every month. The lack of uniform criteria has assigned multiple identifiers (or accession numbers) to the same MRT locus (e.g. MRT7 and MRT22). Here in this review we describe the molecular genetics of ARNSID, prioritize the candidate genes in uncharacterized loci, and propose a new nomenclature to reorganize the mutation data that will avoid the confusion of assigning duplicate accession numbers to the same ID locus and to make the data manageable in the future as well.
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Affiliation(s)
- Muzammil Ahmad Khan
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar.,Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan, 29050 KPK, Pakistan
| | - Saadullah Khan
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar.,Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, KPK, Pakistan
| | | | - Muhammad Badar
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan, 29050 KPK, Pakistan
| | - Zafar Nawaz
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Ramzi M Mohammad
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
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23
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GABPA predicts prognosis and inhibits metastasis of hepatocellular carcinoma. BMC Cancer 2017; 17:380. [PMID: 28549418 PMCID: PMC5446731 DOI: 10.1186/s12885-017-3373-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
Background Increasing evidence indicates that abnormal expression of GABPA is associated with tumor development and progression. However, the function and clinicopathological significance of GABPA in hepatocellular carcinoma (HCC) remain obscure. Methods The mRNA and protein expression of GABPA in HCC clinical specimens and cell lines was examined by real-time PCR and western blotting, respectively. Follow-up data were used to uncover the relationship between GABPA expression and the prognosis of HCC patients. HCC cell lines stably overexpressing or silencing GABPA were established to explore the function of GABPA in HCC cell migration and invasion by Transwell and wound healing assays in vitro and in a xenograft model in vivo. Restoration of function analysis was used to examine the underlying molecular mechanisms. Results GABPA was downregulated at the protein and mRNA levels in HCC tissues compared with adjacent normal tissues. Decreased GABPA expression was correlated with alpha-fetoprotein levels (P = 0.001), tumor grade (P = 0.017), and distant metastasis (P = 0.021). Kaplan-Meier survival analysis showed that patients with lower GABPA expression had significantly shorter survival times than those with higher GABPA (P = 0.031). In vivo and in vitro assays demonstrated that GABPA negatively regulated HCC cell migration and invasion, and the effect of GABPA on HCC cell migration was mediated at least partly by the regulation of E-cadherin. Conclusions Collectively, our data indicate that GABPA inhibits HCC cell migration by modulating E-cadherin and could serve as a novel biomarker for HCC prognosis. GABPA may act as a tumor suppressor during HCC progression and metastasis, and is a potential therapeutic target in HCC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3373-7) contains supplementary material, which is available to authorized users.
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24
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Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. BMC Genomics 2017; 18:386. [PMID: 28521758 PMCID: PMC5437562 DOI: 10.1186/s12864-017-3754-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Results Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Conclusions Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3754-y) contains supplementary material, which is available to authorized users.
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25
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Protein lysine methylation by seven-β-strand methyltransferases. Biochem J 2017; 473:1995-2009. [PMID: 27407169 DOI: 10.1042/bcj20160117] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/24/2016] [Indexed: 11/17/2022]
Abstract
Methylation of biomolecules is a frequent biochemical reaction within the cell, and a plethora of highly specific methyltransferases (MTases) catalyse the transfer of a methyl group from S-adenosylmethionine (AdoMet) to various substrates. The posttranslational methylation of lysine residues, catalysed by numerous lysine (K)-specific protein MTases (KMTs), is a very common and important protein modification, which recently has been subject to intense studies, particularly in the case of histone proteins. The majority of KMTs belong to a class of MTases that share a defining 'SET domain', and these enzymes mostly target lysines in the flexible tails of histones. However, the so-called seven-β-strand (7BS) MTases, characterized by a twisted beta-sheet structure and certain conserved sequence motifs, represent the largest MTase class, and these enzymes methylate a wide range of substrates, including small metabolites, lipids, nucleic acids and proteins. Until recently, the histone-specific Dot1/DOT1L was the only identified eukaryotic 7BS KMT. However, a number of novel 7BS KMTs have now been discovered, and, in particular, several recently characterized human and yeast members of MTase family 16 (MTF16) have been found to methylate lysines in non-histone proteins. Here, we review the status and recent progress on the 7BS KMTs, and discuss these enzymes at the levels of sequence/structure, catalytic mechanism, substrate recognition and biological significance.
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26
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Kwok J, O'Shea M, Hume DA, Lengeling A. Jmjd6, a JmjC Dioxygenase with Many Interaction Partners and Pleiotropic Functions. Front Genet 2017; 8:32. [PMID: 28360925 PMCID: PMC5352680 DOI: 10.3389/fgene.2017.00032] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
Lysyl hydroxylation and arginyl demethylation are post-translational events that are important for many cellular processes. The jumonji domain containing protein 6 (JMJD6) has been reported to catalyze both lysyl hydroxylation and arginyl demethylation on diverse protein substrates. It also interacts directly with RNA. This review summarizes knowledge of JMJD6 functions that have emerged in the last 15 years and considers how a single Jumonji C (JmjC) domain-containing enzyme can target so many different substrates. New links and synergies between the three main proposed functions of Jmjd6 in histone demethylation, promoter proximal pause release of polymerase II and RNA splicing are discussed. The physiological context of the described molecular functions is considered and recently described novel roles for JMJD6 in cancer and immune biology are reviewed. The increased knowledge of JMJD6 functions has wider implications for our general understanding of the JmjC protein family of which JMJD6 is a member.
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Affiliation(s)
- Janice Kwok
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Marie O'Shea
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Andreas Lengeling
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
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27
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Hamey JJ, Hart-Smith G, Erce MA, Wilkins MR. The activity of a yeast Family 16 methyltransferase, Efm2, is affected by a conserved tryptophan and its N-terminal region. FEBS Open Bio 2016; 6:1320-1330. [PMID: 28255539 PMCID: PMC5324768 DOI: 10.1002/2211-5463.12153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/24/2016] [Accepted: 11/01/2016] [Indexed: 12/17/2022] Open
Abstract
The Family 16 methyltransferases are a group of eukaryotic nonhistone protein methyltransferases. Sixteen of these have recently been described in yeast and human, but little is known about their sequence and structural features. Here we investigate one of these methyltransferases, Saccharomyces cerevisiae elongation factor methyltransferase 2 (Efm2), by site-directed mutagenesis and truncation. We show that an active site-associated tryptophan, invariant in Family 16 methyltransferases and at position 222 in Efm2, is important for methyltransferase activity. A second highly conserved tryptophan, at position 318 in Efm2, is likely involved in S-adenosyl methionine binding but is of lesser consequence for catalysis. By truncation analysis, we show that the N-terminal 50-200 amino acids of Efm2 are critical for its methyltransferase activity. As N-terminal regions are variable among Family 16 methyltransferases, this suggests a possible role in determining substrate specificity. This is consistent with recently solved structures that show the core of Family 16 methyltransferases to be near-identical but the N termini to be structurally quite different. Finally, we show that Efm2 can exist as an oligomer but that its N terminus is not necessary for oligomerisation to occur.
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Affiliation(s)
- Joshua J Hamey
- Systems Biology Initiative School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney Australia
| | - Gene Hart-Smith
- Systems Biology Initiative School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney Australia
| | - Melissa A Erce
- Systems Biology Initiative School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney Australia
| | - Marc R Wilkins
- Systems Biology Initiative School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney Australia
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28
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Royall DR, Palmer RF. Thrombopoietin is associated with δ's intercept, and only in Non-Hispanic Whites. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2016; 3:35-42. [PMID: 27239547 PMCID: PMC4879650 DOI: 10.1016/j.dadm.2016.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Serum thrombopoietin (THPO) is a biomarker of Alzheimer's disease (AD) and the latent dementia phenotype, "δ". Both associations may be specific to non-Hispanic whites (NHW), not Mexican-Americans (MA). In this analysis, we examine ethnicity's effect on THPO's association with change in δ scores, in the Texas Alzheimer's Research and Care Consortium (TARCC). METHODS We constructed an ethnicity equivalent δ homolog ("dEQ") among n = 1113 MA and n = 1958 NHW. dEQ was output as a composite "dEQ-score" for each of five annual TARCC waves. Those composites were used as indicators of a latent growth curve (LGC). The mean dEQ intercept (idEQ) and slope (ΔdEQ) were estimated in a random subset of N = 1528 participants and replicated in the remainder (n = 1544). THPO was regressed onto idEQ and ΔdEQ. Those associations were tested separately in MA and NHW. RESULTS dEQ correlated strongly with CDR-SB (r = 0.99, P < .001) and achieved high AUCs for AD diagnosis at each wave (range = 0.95-0.99). THPO was significantly associated with idEQ but not ΔdEQ. That effect was observed in NHW only. In MA, THPO had no associations with either idEQ or ΔdEQ. DISCUSSION We confirm THPO's ethnicity-specific association with δ in NHW. It is further clarified that this association is specific to δ's intercept and not its slope. This analysis provides a model for how dementia's specific serum biomarkers can be characterized.
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Affiliation(s)
- Donald R. Royall
- Department of Psychiatry, The University of Texas Health Science Center, San Antonio, TX, USA
- Department of Medicine, The University of Texas Health Science Center, San Antonio, TX, USA
- Department of Family and Community Medicine, The University of Texas Health Science Center, San Antonio, TX, USA
- South Texas Veterans' Health System, Audie L. Murphy Division GRECC, San Antonio, TX, USA
| | - Raymond F. Palmer
- Department of Family and Community Medicine, The University of Texas Health Science Center, San Antonio, TX, USA
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Fusser M, Kernstock S, Aileni VK, Egge-Jacobsen W, Falnes PØ, Klungland A. Lysine Methylation of the Valosin-Containing Protein (VCP) Is Dispensable for Development and Survival of Mice. PLoS One 2015; 10:e0141472. [PMID: 26544960 PMCID: PMC4636187 DOI: 10.1371/journal.pone.0141472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 10/08/2015] [Indexed: 01/02/2023] Open
Abstract
Valosin-containing protein (VCP) is a homohexameric ATPase involved in a multitude cellular processes and it was recently shown that VCP is trimethylated at lysine 315 by the VCP lysine methyltransferase (VCPKMT). Here, we generated and validated a constitutive knockout mouse by targeting exon 1-4 of the Vcpkmt gene. We show that Vcpkmt is ubiquitously expressed in all tissues examined and confirm the sub-cellular localization to the cytoplasm. We show by (I) mass spectrometric analysis, (II) VCPKMT-mediated in vitro methylation of VCP in cell extracts and (III) immunostaining with a methylation specific antibody, that in Vcpkmt-/- mice the methylation of lysine 315 in VCP is completely abolished. In contrast, VCP is almost exclusively trimethylated in wild-type mice. Furthermore, we investigated the specificity of VCPKMT with in vitro methylation assays using as source of substrate protein extracts from Vcpkmt-/- mouse organs or three human Vcpkmt-/- cell lines. The results show that VCPKMT is a highly specific enzyme, and suggest that VCP is its sole substrate. The Vcpkmt-/- mice were viable, fertile and had no obvious pathological phenotype. Their body weight, life span and acute endurance capacity were comparable to wild-type controls. Overall the results show that VCPKMT is an enzyme required for methylation of K315 of VCP in vivo, but VCPKMT is not essential for development or survival under unstressed conditions.
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Affiliation(s)
- Markus Fusser
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Stefan Kernstock
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Vinay Kumar Aileni
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Wolfgang Egge-Jacobsen
- Glyconor Mass Spectrometry, Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pål Ø. Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- * E-mail:
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Ben-Salem S, Gleeson JG, Al-Shamsi AM, Islam B, Hertecant J, Ali BR, Al-Gazali L. Asparagine synthetase deficiency detected by whole exome sequencing causes congenital microcephaly, epileptic encephalopathy and psychomotor delay. Metab Brain Dis 2015; 30:687-94. [PMID: 25227173 PMCID: PMC4915861 DOI: 10.1007/s11011-014-9618-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/08/2014] [Indexed: 02/05/2023]
Abstract
Deficiency of Asparagine Synthetase (ASNSD, MIM 615574) is a very rare autosomal recessive disorder presenting with some brain abnormalities. Affected individuals have congenital microcephaly and progressive encephalopathy associated with severe intellectual disability and intractable seizures. The loss of function of the asparagine synthetase (ASNS, EC 6.3.5.4), particularly in the brain, is the major cause of this particular congenital microcephaly. In this study, we clinically evaluated an affected child from a consanguineous Emirati family presenting with congenital microcephaly and epileptic encephalopathy. In addition, whole-exome sequencing revealed a novel homozygous substitution mutation (c.1193A > C) in the ASNS gene. This mutation resulted in the substitution of highly conserved tyrosine residue by cysteine (p.Y398C). Molecular modeling analysis predicts hypomorphic and damaging effects of this mutation on the protein structure and altering its enzymatic activity. Therefore, we conclude that the loss of ASNS function is most likely the cause of this condition in the studied family. This report brings the number of reported families with this very rare disorder to five and the number of pathogenic mutations in the ASNS gene to four. This finding extends the ASNS pathogenic mutations spectrum and highlights the utility of whole-exome sequencing in elucidation the causes of rare recessive disorders that are heterogeneous and/or overlap with other conditions.
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Joseph G. Gleeson
- Department of Neuroscience and Pediatrics, Neurogenetics Laboratory, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Aisha M. Al-Shamsi
- Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates, Al-Ain, United Arab Emirates
| | - Barira Islam
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
| | - Jozef Hertecant
- Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates, Al-Ain, United Arab Emirates
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
| | - Bassam R. Ali
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
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31
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Nakayama T, Al-Maawali A, El-Quessny M, Rajab A, Khalil S, Stoler JM, Tan WH, Nasir R, Schmitz-Abe K, Hill RS, Partlow JN, Al-Saffar M, Servattalab S, LaCoursiere CM, Tambunan DE, Coulter ME, Elhosary PC, Gorski G, Barkovich AJ, Markianos K, Poduri A, Mochida GH. Mutations in PYCR2, Encoding Pyrroline-5-Carboxylate Reductase 2, Cause Microcephaly and Hypomyelination. Am J Hum Genet 2015; 96:709-19. [PMID: 25865492 PMCID: PMC4570282 DOI: 10.1016/j.ajhg.2015.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/05/2015] [Indexed: 12/27/2022] Open
Abstract
Despite recent advances in understanding the genetic bases of microcephaly, a large number of cases of microcephaly remain unexplained, suggesting that many microcephaly syndromes and associated genes have yet to be identified. Here, we report mutations in PYCR2, which encodes an enzyme in the proline biosynthesis pathway, as the cause of a unique syndrome characterized by postnatal microcephaly, hypomyelination, and reduced cerebral white-matter volume. Linkage mapping and whole-exome sequencing identified homozygous mutations (c.355C>T [p.Arg119Cys] and c.751C>T [p.Arg251Cys]) in PYCR2 in the affected individuals of two consanguineous families. A lymphoblastoid cell line from one affected individual showed a strong reduction in the amount of PYCR2. When mutant cDNAs were transfected into HEK293FT cells, both variant proteins retained normal mitochondrial localization but had lower amounts than the wild-type protein, suggesting that the variant proteins were less stable. A PYCR2-deficient HEK293FT cell line generated by genome editing with the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system showed that PYCR2 loss of function led to decreased mitochondrial membrane potential and increased susceptibility to apoptosis under oxidative stress. Morpholino-based knockdown of a zebrafish PYCR2 ortholog, pycr1b, recapitulated the human microcephaly phenotype, which was rescued by wild-type human PYCR2 mRNA, but not by mutant mRNAs, further supporting the pathogenicity of the identified variants. Hypomyelination and the absence of lax, wrinkly skin distinguishes this condition from that caused by previously reported mutations in the gene encoding PYCR2's isozyme, PYCR1, suggesting a unique and indispensable role for PYCR2 in the human CNS during development.
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Affiliation(s)
- Tojo Nakayama
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Almundher Al-Maawali
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, College of Medicine and Health Science, Sultan Qaboos University, Muscat 123, Oman
| | - Malak El-Quessny
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Anna Rajab
- National Genetics Center, Directorate General of Health Affairs, Ministry of Health, Muscat 113, Oman
| | - Samir Khalil
- Department of Pediatrics, Al-Makassed Islamic Charitable Society Hospital, Jerusalem 91220; Faculty of Medicine, Al-Quds University, Jerusalem 90612
| | - Joan M Stoler
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ramzi Nasir
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Developmental Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Klaus Schmitz-Abe
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Muna Al-Saffar
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab Emirates
| | - Sarah Servattalab
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Dimira E Tambunan
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael E Coulter
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Princess C Elhosary
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Grzegorz Gorski
- Cellular Neuroscience Core, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - A James Barkovich
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kyriacos Markianos
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA.
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Ben-Salem S, Al-Shamsi AM, John A, Ali BR, Al-Gazali L. A novel whole exon deletion in WWOX gene causes early epilepsy, intellectual disability and optic atrophy. J Mol Neurosci 2014; 56:17-23. [PMID: 25403906 DOI: 10.1007/s12031-014-0463-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 02/05/2023]
Abstract
Recent studies have implicated the WW domain-containing oxidoreductase encoding gene (WWOX) in a severe form of autosomal recessive neurological disorder. This condition showed an overlapping spectrum of clinical features including spinocerebellar ataxia associated with generalized seizures and delayed psychomotor development to growth retardation, spasticity, and microcephaly. We evaluated a child from a consanguineous Emirati family that presented at birth with growth retardation, microcephaly, epileptic seizures, and later developed spasticity and delayed psychomotor development. Screening for deletions and duplications using whole-chromosomal microarray analysis identified a novel homozygous microdeletion encompassing exon 5 of the WWOX gene. Analysis of parental DNA indicated that this deletion was inherited from both parents and lies within a large region of homozygosity. Sanger sequencing of the cDNA showed that the deletion resulted in exon 5 skipping leading to a frame-shift and creating a premature stop codon at amino acid position 212. Quantification of mRNA revealed striking low level of WWOX expression in the child and moderate level of expression in the mother compared to a healthy control. To the best of our knowledge, this is the first homozygous germline structural variation in WWOX gene resulting in truncated transcripts that were presumably subject to NMD pathway. Our findings extend the clinical and genetic spectrum of WWOX mutations and support a crucial role of this gene in neurological development.
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates,
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Davydova E, Ho AYY, Malecki J, Moen A, Enserink JM, Jakobsson ME, Loenarz C, Falnes PØ. Identification and characterization of a novel evolutionarily conserved lysine-specific methyltransferase targeting eukaryotic translation elongation factor 2 (eEF2). J Biol Chem 2014; 289:30499-30510. [PMID: 25231979 DOI: 10.1074/jbc.m114.601658] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The components of the cellular protein translation machinery, such as ribosomal proteins and translation factors, are subject to numerous post-translational modifications. In particular, this group of proteins is frequently methylated. However, for the majority of these methylations, the responsible methyltransferases (MTases) remain unknown. The human FAM86A (family with sequence similarity 86) protein belongs to a recently identified family of protein MTases, and we here show that FAM86A catalyzes the trimethylation of eukaryotic elongation factor 2 (eEF2) on Lys-525. Moreover, we demonstrate that the Saccharomyces cerevisiae MTase Yjr129c, which displays sequence homology to FAM86A, is a functional FAM86A orthologue, modifying the corresponding residue (Lys-509) in yeast eEF2, both in vitro and in vivo. Finally, Yjr129c-deficient yeast cells displayed phenotypes related to eEF2 function (i.e. increased frameshifting during protein translation and hypersensitivity toward the eEF2-specific drug sordarin). In summary, the present study establishes the function of the previously uncharacterized MTases FAM86A and Yjr129c, demonstrating that these enzymes introduce a functionally important lysine methylation in eEF2. Based on the previous naming of similar enzymes, we have redubbed FAM86A and Yjr129c as eEF2-KMT and Efm3, respectively.
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Affiliation(s)
- Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Angela Y Y Ho
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jedrzej Malecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jorrit M Enserink
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0027 Oslo, Norway, and
| | - Magnus E Jakobsson
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Christoph Loenarz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway,.
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Alkuraya FS. Genetics and genomic medicine in Saudi Arabia. Mol Genet Genomic Med 2014; 2:369-78. [PMID: 25333061 PMCID: PMC4190871 DOI: 10.1002/mgg3.97] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 01/01/2023] Open
Affiliation(s)
- Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center Riyadh, Saudi Arabia ; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University Riyadh, Saudi Arabia
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35
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Bernkopf M, Webersinke G, Tongsook C, Koyani CN, Rafiq MA, Ayaz M, Müller D, Enzinger C, Aslam M, Naeem F, Schmidt K, Gruber K, Speicher MR, Malle E, Macheroux P, Ayub M, Vincent JB, Windpassinger C, Duba HC. Disruption of the methyltransferase-like 23 gene METTL23 causes mild autosomal recessive intellectual disability. Hum Mol Genet 2014; 23:4015-23. [PMID: 24626631 PMCID: PMC4082365 DOI: 10.1093/hmg/ddu115] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe the characterization of a gene for mild nonsyndromic autosomal recessive intellectual disability (ID) in two unrelated families, one from Austria, the other from Pakistan. Genome-wide single nucleotide polymorphism microarray analysis enabled us to define a region of homozygosity by descent on chromosome 17q25. Whole-exome sequencing and analysis of this region in an affected individual from the Austrian family identified a 5 bp frameshifting deletion in the METTL23 gene. By means of Sanger sequencing of METTL23, a nonsense mutation was detected in a consanguineous ID family from Pakistan for which homozygosity-by-descent mapping had identified a region on 17q25. Both changes lead to truncation of the putative METTL23 protein, which disrupts the predicted catalytic domain and alters the cellular localization. 3D-modelling of the protein indicates that METTL23 is strongly predicted to function as an S-adenosyl-methionine (SAM)-dependent methyltransferase. Expression analysis of METTL23 indicated a strong association with heat shock proteins, which suggests that these may act as a putative substrate for methylation by METTL23. A number of methyltransferases have been described recently in association with ID. Disruption of METTL23 presented here supports the importance of methylation processes for intact neuronal function and brain development.
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Affiliation(s)
- Marie Bernkopf
- Laboratory of Molecular Biology and Tumorcytogenetics, Department of Internal Medicine, Krankenhaus der Barmherzigen Schwestern, Linz, Austria
| | - Gerald Webersinke
- Laboratory of Molecular Biology and Tumorcytogenetics, Department of Internal Medicine, Krankenhaus der Barmherzigen Schwestern, Linz, Austria
| | - Chanakan Tongsook
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Chintan N Koyani
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Muhammad A Rafiq
- Molecular Neuropsychiatry and Development (MiND) Lab, The Campbell Family Brain Research Institute, The Centre for Addiction & Mental Health (CAMH), Toronto, ON, Canada
| | - Muhammad Ayaz
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan
| | - Doris Müller
- Department of Human Genetics, Landes-Frauen und Kinderklinik, Linz, Austria
| | | | - Muhammad Aslam
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan
| | - Farooq Naeem
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan Division of Developmental Disabilities, Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Kurt Schmidt
- Department of Pharmacology and Toxicology, Karl-Franzens University Graz, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Ernst Malle
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Muhammad Ayub
- Lahore Institute of Research and Development, Lahore, Punjab Province, Pakistan Division of Developmental Disabilities, Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, The Campbell Family Brain Research Institute, The Centre for Addiction & Mental Health (CAMH), Toronto, ON, Canada Department of Psychiatry and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
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