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

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; Jill A Fahrner

doi:10.1038/s41525-021-00256-y

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

NPJ Genom Med. 2021 Nov 8;6(1):92. doi: 10.1038/s41525-021-00256-y.

Authors

Michael A Levy^#¹, David B Beck^#², Kay Metcalfe^{3

4}, Sofia Douzgou^{3

4}, Sivagamy Sithambaram⁴, Trudie Cottrell⁴, Muhammad Ansar⁵, Jennifer Kerkhof¹, Cyril Mignot⁶, Marie-Christine Nougues⁷, Boris Keren⁸, Hannah W Moore⁹, Renske Oegema¹⁰, Jacques C Giltay¹⁰, Marleen Simon¹⁰, Richard H van Jaarsveld¹⁰, Jessica Bos¹¹, Mieke van Haelst¹¹, M Mahdi Motazacker¹², Elles M J Boon¹³, Gijs W E Santen¹⁴, Claudia A L Ruivenkamp¹⁴, Marielle Alders¹⁵, Teresa Romeo Luperchio¹⁶, Leandros Boukas^{16

17}, Keri Ramsey¹⁸, Vinodh Narayanan¹⁸, G Bradley Schaefer¹⁹, Roberto Bonasio^{20

21}, Kimberly F Doheny^{16

22}, Roger E Stevenson⁹, Siddharth Banka^{3

4}, Bekim Sadikovic^#^{23

24}, Jill A Fahrner^{25

26}

Affiliations

¹ Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada.
² National Human Genome Research Institute, Bethesda, MD, 20892, USA.
³ Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.
⁴ Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK.
⁵ Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320, Islamabad, Pakistan.
⁶ Assistance Publique-Hopitaux de Paris, Sorbonne Université, Departement de Génétique, Groupe Hospitalier Pitie-Salpetriere et Hopital Trousseau, Paris, 75651, France.
⁷ Department of Neuropediatrics, Armand Trousseau Hospital, Assistance Publique-Hopitaux de Paris, Paris, 75012, France.
⁸ Laboratoire de génétique, Hôpital Pïtié-Salpêtrière, Assistance Publique-Hopitaux de Paris, Paris, 75013, France.
⁹ Greenwood Genetic Center, Greenwood, SC, 29646, USA.
¹⁰ Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
¹¹ Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
¹² Department of Human Genetics, Laboratory of Genome Diagnostics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands.
¹³ Department of Human Genetics, VU University Medical Center Amsterdam, Amsterdam UMC, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands.
¹⁴ Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
¹⁵ Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
¹⁶ Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
¹⁷ Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA.
¹⁸ Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA.
¹⁹ University of Arkansas for Medical Sciences, Springdale, AR, 72762, USA.
²⁰ Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
²¹ Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
²² Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
²³ Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada. Bekim.Sadikovic@lhsc.on.ca.
²⁴ Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A5W9, Canada. Bekim.Sadikovic@lhsc.on.ca.
²⁵ Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jfahrne1@jhmi.edu.
²⁶ Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. jfahrne1@jhmi.edu.

^# Contributed equally.

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.

Abstract

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