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1. Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Michael A. Levy, David B. Beck, Kay Metcalfe, Sofia Douzgou, Sivagamy Sithambaram, Trudie Cottrell, Muhammad Ansar, Jennifer Kerkhof, Cyril Mignot, Marie-Christine Nougues, Boris Keren, Hannah W. Moore, Renske Oegema, Jacques C. Giltay, Marleen Simon, Richard H. van Jaarsveld, Jessica Bos, Mieke van Haelst, M. Mahdi Motazacker, Elles M. J. Boon, Gijs W. E. Santen, Claudia A. L. Ruivenkamp, Marielle Alders, Teresa Romeo Luperchio, Leandros Boukas, Keri Ramsey, Vinodh Narayanan, G. Bradley Schaefer, Roberto Bonasio, Kimberly F. Doheny, Roger E. Stevenson, Sidharth Banka, Bekim Sadikovic, and Jill A. Fahrner

Subjects
Medicine, Genetics, QH426-470
Abstract

Abstract TET3 encodes an essential dioxygenase involved in epigenetic regulation through DNA demethylation. TET3 deficiency, or Beck-Fahrner syndrome (BEFAHRS; MIM: 618798), is a recently described neurodevelopmental disorder of the DNA demethylation machinery with a nonspecific phenotype resembling other chromatin-modifying disorders, but inconsistent variant types and inheritance patterns pose diagnostic challenges. Given TET3’s direct role in regulating 5-methylcytosine and recent identification of syndrome-specific DNA methylation profiles, we analyzed genome-wide DNA methylation in whole blood of TET3-deficient individuals and identified an episignature that distinguishes affected and unaffected individuals and those with mono-allelic and bi-allelic pathogenic variants. Validation and testing of the episignature correctly categorized known TET3 variants and determined pathogenicity of variants of uncertain significance. Clinical utility was demonstrated when the episignature alone identified an affected individual from over 1000 undiagnosed cases and was confirmed upon distinguishing TET3-deficient individuals from those with 46 other disorders. The TET3-deficient signature - and the signature resulting from activating mutations in DNMT1 which normally opposes TET3 - are characterized by hypermethylation, which for BEFAHRS involves CpG sites that may be biologically relevant. This work expands the role of epi-phenotyping in molecular diagnosis and reveals genome-wide DNA methylation profiling as a quantitative, functional readout for characterization of this new biochemical category of disease.

Published
2021
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2. Intellectual disability-associated UNC80 mutations reveal inter-subunit interaction and dendritic function of the NALCN channel complex

Author

Jinhong Wie, Apoorva Bharthur, Morgan Wolfgang, Vinodh Narayanan, Keri Ramsey, C4RCD Research Group, Kimberly Aranda, Qi Zhang, Yandong Zhou, and Dejian Ren

Subjects
Science
Abstract

The sodium-leak channel NALCN controls the resting membrane potentials of neurons. Here, the authors identified two subunits of NALCN, UNC80 and UNC79. Domains in UNC80, which are mutated in individuals with intellectual disability, interact to achieve the dendritic localization of NALCN complex.

Published
2020
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3. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy

Author

Yu-Ri Lee, Kamal Khan, Kim Armfield-Uhas, Sujata Srikanth, Nicola A. Thompson, Mercedes Pardo, Lu Yu, Joy W. Norris, Yunhui Peng, Karen W. Gripp, Kirk A. Aleck, Chumei Li, Ed Spence, Tae-Ik Choi, Soo Jeong Kwon, Hee-Moon Park, Daseuli Yu, Won Do Heo, Marie R. Mooney, Shahid M. Baig, Ingrid M. Wentzensen, Aida Telegrafi, Kirsty McWalter, Trevor Moreland, Chelsea Roadhouse, Keri Ramsey, Michael J. Lyons, Cindy Skinner, Emil Alexov, Nicholas Katsanis, Roger E. Stevenson, Jyoti S. Choudhary, David J. Adams, Cheol-Hee Kim, Erica E. Davis, and Charles E. Schwartz

Subjects
Science
Abstract

Armfield X-linked disability (XLID) disorder has previously been linked to a locus in Xq28. Here, the authors report rare missense variants in FAM50A at Xq28, show that FAM50A interacts with the spliceosome, and that mis-splicing is enriched in knockout zebrafish suggesting it is a spliceosomopathy.

Published
2020
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4. Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish

Author

Aleksandra Siekierska, Hannah Stamberger, Tine Deconinck, Stephanie N. Oprescu, Michèle Partoens, Yifan Zhang, Jo Sourbron, Elias Adriaenssens, Patrick Mullen, Patrick Wiencek, Katia Hardies, Jeong-Soo Lee, Hoi-Khoanh Giong, Felix Distelmaier, Orly Elpeleg, Katherine L. Helbig, Joseph Hersh, Sedat Isikay, Elizabeth Jordan, Ender Karaca, Angela Kecskes, James R. Lupski, Reka Kovacs-Nagy, Patrick May, Vinodh Narayanan, Manuela Pendziwiat, Keri Ramsey, Sampathkumar Rangasamy, Deepali N. Shinde, Ronen Spiegel, Vincent Timmerman, Sarah von Spiczak, Ingo Helbig, C4RCD Research Group, AR working group of the EuroEPINOMICS RES Consortium, Sarah Weckhuysen, Christopher Francklyn, Anthony Antonellis, Peter de Witte, and Peter De Jonghe

Subjects
Science
Abstract

tRNAs are linked with their cognate amino acid by aminoacyl tRNA synthetases (ARS). Here, the authors report a developmental encephalopathy associated with biallelic VARS variants (valyl-tRNA synthetase) that lead to loss of function, as determined by several in vitro assays and a vars knockout zebrafish model.

Published
2019
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5. Author Correction: Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood

Author

Michael A. Levy, David B. Beck, Kay Metcalfe, Sofia Douzgou, Sivagamy Sithambaram, Trudie Cottrell, Muhammad Ansar, Jennifer Kerkhof, Cyril Mignot, Marie-Christine Nougues, Boris Keren, Hannah W. Moore, Renske Oegema, Jacques C. Giltay, Marleen Simon, Richard H. van Jaarsveld, Jessica Bos, Mieke van Haelst, M. Mahdi Motazacker, Elles M. J. Boon, Gijs W. E. Santen, Claudia A. L. Ruivenkamp, Marielle Alders, Teresa Romeo Luperchio, Leandros Boukas, Keri Ramsey, Vinodh Narayanan, G. Bradley Schaefer, Roberto Bonasio, Kimberly F. Doheny, Roger E. Stevenson, Siddharth Banka, Bekim Sadikovic, and Jill A. Fahrner

Subjects
Medicine, Genetics, QH426-470
Published
2021
Full Text
View/download PDF

6. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy

Author

Charles E. Schwartz, Emil Alexov, Jyoti S. Choudhary, Sujata Srikanth, Joy Norris, Keri Ramsey, Lu Yu, David J. Adams, Yu-Ri Lee, Karen W. Gripp, Ed Spence, Cheol-Hee Kim, Aida Telegrafi, Roger E. Stevenson, Chelsea Roadhouse, Trevor Moreland, Tae Ik Choi, Soo Jeong Kwon, Hee Moon Park, Erica E. Davis, Ingrid M. Wentzensen, Won Do Heo, Kim Armfield-Uhas, Cindy Skinner, Nicholas Katsanis, Yunhui Peng, Kamal Khan, Mercedes Pardo, Kirsty McWalter, Shahid Mahmood Baig, Marie R. Mooney, Nicola A. Thompson, Michael J. Lyons, Chumei Li, Daseuli Yu, and Kirk Aleck

Subjects
0301 basic medicine, Male, Molecular biology, General Physics and Astronomy, 030105 genetics & heredity, medicine.disease_cause, Transcriptome, Mice, RNA, Small Nuclear, Missense mutation, lcsh:Science, Child, Zebrafish, Genetics, Mutation, Multidisciplinary, Gene Expression Regulation, Developmental, RNA-Binding Proteins, Syndrome, Phenotype, Pedigree, DNA-Binding Proteins, Protein Transport, Child, Preschool, Female, Adult, Spliceosome, congenital, hereditary, and neonatal diseases and abnormalities, RNA Splicing, Science, Mutation, Missense, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Intellectual Disability, Developmental biology, medicine, Animals, Humans, Family, RNA, Messenger, Cell Nucleus, Alternative splicing, General Chemistry, Zebrafish Proteins, biology.organism_classification, Xq28, nervous system diseases, 030104 developmental biology, Mental Retardation, X-Linked, NIH 3T3 Cells, Spliceosomes, lcsh:Q, Neuroscience
Abstract

Intellectual disability (ID) is a heterogeneous clinical entity and includes an excess of males who harbor variants on the X-chromosome (XLID). We report rare FAM50A missense variants in the original Armfield XLID syndrome family localized in Xq28 and four additional unrelated males with overlapping features. Our fam50a knockout (KO) zebrafish model exhibits abnormal neurogenesis and craniofacial patterning, and in vivo complementation assays indicate that the patient-derived variants are hypomorphic. RNA sequencing analysis from fam50a KO zebrafish show dysregulation of the transcriptome, with augmented spliceosome mRNAs and depletion of transcripts involved in neurodevelopment. Zebrafish RNA-seq datasets show a preponderance of 3′ alternative splicing events in fam50a KO, suggesting a role in the spliceosome C complex. These data are supported with transcriptomic signatures from cell lines derived from affected individuals and FAM50A protein-protein interaction data. In sum, Armfield XLID syndrome is a spliceosomopathy associated with aberrant mRNA processing during development., Armfield X-linked disability (XLID) disorder has previously been linked to a locus in Xq28. Here, the authors report rare missense variants in FAM50A at Xq28, show that FAM50A interacts with the spliceosome, and that mis-splicing is enriched in knockout zebrafish suggesting it is a spliceosomopathy.

Published
2020

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