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Ng R, Bjornsson HT, Fahrner JA, Harris J. Associations Between Executive Functioning, Behavioral Functioning, and Adaptive Functioning Difficulties in Wiedemann-Steiner Syndrome. Arch Clin Neuropsychol 2024; 39:186-195. [PMID: 37565480 PMCID: PMC10879922 DOI: 10.1093/arclin/acad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 08/12/2023] Open
Abstract
OBJECTIVES Wiedemann-Steiner syndrome (WSS) is a neurogenetic disorder caused by heterozygous variants in KMT2A. Recent investigations suggest increased anxiety and behavior regulation challenges among those with WSS although the neurobehavioral phenotype remains largely unknown. This study aims to examine the pattern of and associations between executive functioning (EF) and behavior functioning among those with WSS. METHOD This study involved utilizing caregiver-report inventories (Behavior Rating Inventory of Executive Function 2nd Edition, BRIEF-2; Adaptive Behavior Assessment 3rd Edition, ABAS-3; Strengths and Difficulties Questionnaire, SDQ) to assess day-to-day behavior functioning among those with WSS (N = 24; mean age = 10.68 years, SD = 3.19). Frequency of clinical elevations in daily difficulties in EF, adaptive behaviors, and behavior regulation were reported. Correlations and hierarchical linear regressions were used to determine the relationships between EF with behavior and adaptive functioning. RESULTS Out of our sample, 63% met clinical levels of executive functioning difficulties on the BRIEF-2, and 75% with Hyperactivity and 54% with Emotional Problems on the SDQ. In addition, 33% were rated >2 SD below the normative mean in overall adaptive functioning on the ABAS-3. Elevated ratings in BRIEF-2 Shift, reflective of challenges with mental flexibility, predicted more Emotional Problems and accounted for 33.5% of its variance. More difficulties in Emotional Control were related to greater adaptive deficits, accounting for 33.3% of its variance. CONCLUSIONS Those with WSS are at risk for EF deficits, hyperactivity, and emotional dysregulation. EF correlates with adaptive and affective behaviors, highlighting the promise of behavioral interventions to target cognitive flexibility, emotional awareness, and reactivity in this population.
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Affiliation(s)
- Rowena Ng
- Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans Tomas Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacqueline Harris
- Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Gao CW, Lin W, Riddle RC, Kushwaha P, Boukas L, Björnsson HT, Hansen KD, Fahrner JA. A mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition. JCI Insight 2024; 9:e173392. [PMID: 38015625 PMCID: PMC10906465 DOI: 10.1172/jci.insight.173392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Weaver syndrome is a Mendelian disorder of the epigenetic machinery (MDEM) caused by germline pathogenic variants in EZH2, which encodes the predominant H3K27 methyltransferase and key enzymatic component of Polycomb repressive complex 2 (PRC2). Weaver syndrome is characterized by striking overgrowth and advanced bone age, intellectual disability, and distinctive facies. We generated a mouse model for the most common Weaver syndrome missense variant, EZH2 p.R684C. Ezh2R684C/R684C mouse embryonic fibroblasts (MEFs) showed global depletion of H3K27me3. Ezh2R684C/+ mice had abnormal bone parameters, indicative of skeletal overgrowth, and Ezh2R684C/+ osteoblasts showed increased osteogenic activity. RNA-Seq comparing osteoblasts differentiated from Ezh2R684C/+, and Ezh2+/+ BM-mesenchymal stem cells (BM-MSCs) indicated collective dysregulation of the BMP pathway and osteoblast differentiation. Inhibition of the opposing H3K27 demethylases KDM6A and KDM6B substantially reversed the excessive osteogenesis in Ezh2R684C/+ cells both at the transcriptional and phenotypic levels. This supports both the ideas that writers and erasers of histone marks exist in a fine balance to maintain epigenome state and that epigenetic modulating agents have therapeutic potential for the treatment of MDEMs.
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Affiliation(s)
- Christine W. Gao
- Department of Genetic Medicine
- Department of Molecular Biology and Genetics, and
| | | | - Ryan C. Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research and Development Service, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
| | - Priyanka Kushwaha
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leandros Boukas
- Department of Genetic Medicine
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
| | - Hans T. Björnsson
- Department of Genetic Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Landspítali University Hospital, Reykjavík, Iceland
| | - Kasper D. Hansen
- Department of Genetic Medicine
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A. Fahrner
- Department of Genetic Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Kalinousky AJ, Luperchio TR, Schrode KM, Harris JR, Zhang L, DeLeon VB, Fahrner JA, Lauer AM, Bjornsson HT. KMT2D Deficiency Causes Sensorineural Hearing Loss in Mice and Humans. Genes (Basel) 2023; 15:48. [PMID: 38254937 PMCID: PMC10815913 DOI: 10.3390/genes15010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Individuals with Kabuki syndrome type 1 (KS1) often have hearing loss recognized in middle childhood. Current clinical dogma suggests that this phenotype is caused by frequent infections due to the immune deficiency in KS1 and/or secondary to structural abnormalities of the ear. To clarify some aspects of hearing loss, we collected information on hearing status from 21 individuals with KS1 and found that individuals have both sensorineural and conductive hearing loss, with the average age of presentation being 7 years. Our data suggest that while ear infections and structural abnormalities contribute to the observed hearing loss, these factors do not explain all loss. Using a KS1 mouse model, we found hearing abnormalities from hearing onset, as indicated by auditory brainstem response measurements. In contrast to mouse and human data for CHARGE syndrome, a disorder possessing overlapping clinical features with KS and a well-known cause of hearing loss and structural inner ear abnormalities, there are no apparent structural abnormalities of the cochlea in KS1 mice. The KS1 mice also display diminished distortion product otoacoustic emission levels, which suggests outer hair cell dysfunction. Combining these findings, our data suggests that KMT2D dysfunction causes sensorineural hearing loss compounded with external factors, such as infection.
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Affiliation(s)
- Allison J. Kalinousky
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (A.J.K.); (T.R.L.); (J.R.H.); (L.Z.); (J.A.F.)
| | - Teresa R. Luperchio
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (A.J.K.); (T.R.L.); (J.R.H.); (L.Z.); (J.A.F.)
| | - Katrina M. Schrode
- Department of Otolaryngology-Head and Neck Surgery and Center for Hearing and Balance, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (K.M.S.); (A.M.L.)
| | - Jacqueline R. Harris
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (A.J.K.); (T.R.L.); (J.R.H.); (L.Z.); (J.A.F.)
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Li Zhang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (A.J.K.); (T.R.L.); (J.R.H.); (L.Z.); (J.A.F.)
| | - Valerie B. DeLeon
- Department of Anthropology, University of Florida, Gainesville, FL 32610, USA;
| | - Jill A. Fahrner
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (A.J.K.); (T.R.L.); (J.R.H.); (L.Z.); (J.A.F.)
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Amanda M. Lauer
- Department of Otolaryngology-Head and Neck Surgery and Center for Hearing and Balance, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (K.M.S.); (A.M.L.)
| | - Hans T. Bjornsson
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; (A.J.K.); (T.R.L.); (J.R.H.); (L.Z.); (J.A.F.)
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Landspitali University Hospital, 102 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
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Ng R, Kalinousky A, Fahrner JA, Bjornsson HT, Harris J. The social phenotype associated with Wiedemann-Steiner syndrome: Autistic traits juxtaposed with high social drive and prosociality. Am J Med Genet A 2023; 191:2591-2601. [PMID: 37470210 DOI: 10.1002/ajmg.a.63351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/21/2023]
Abstract
The aim of this study was to provide a descriptive overview of the social characteristics associated with Wiedemann-Steiner syndrome (WSS). A total of 24 parents of children/adults with WSS (11F, mean age = 12.94 years, SD = 8.00) completed the Social Responsiveness Scale 2nd Edition (SRS-2); Colorado Learning Difficulties Questionnaire (CLDQ) and Strengths and Difficulties Questionnaire (SDQ). Almost half our sample reported a diagnosis of autism spectrum disorder (ASD) and 70% had intellectual disability. On the SDQ, over 90% of participants were rated in borderline/clinical ranges in Peer Problems, yet the majority fell within normal limits in Prosocial Behaviors. Most fell in the moderate/severe difficulties ranges across SRS-2 Social Cognition, Communication, and Restricted/Repetitive Behaviors scales (all >70%); whereas substantially less participants met these ranges for deficits in Social Awareness (50%) and Social Motivation (33.33%). A pattern of relatively strong prosocial skills and social drive in the context of difficulties with inflexible behaviors, social cognition, and communication was observed, regardless of gender, ASD or intellectual disability diagnosis. The social phenotype associated with WSS is characterized by some autistic features paired with unusually high social motivation and prosocial tendencies.
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Affiliation(s)
- Rowena Ng
- Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Allison Kalinousky
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hans Tomas Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Jacqueline Harris
- Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Gao CW, Lin W, Riddle RC, Kushwaha P, Boukas L, Björnsson HT, Hansen KD, Fahrner JA. Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition. bioRxiv 2023:2023.06.23.546270. [PMID: 37425751 PMCID: PMC10327066 DOI: 10.1101/2023.06.23.546270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Weaver syndrome is a Mendelian disorder of the epigenetic machinery (MDEM) caused by germline pathogenic variants in EZH2, which encodes the predominant H3K27 methyltransferase and key enzymatic component of Polycomb repressive complex 2 (PRC2). Weaver syndrome is characterized by striking overgrowth and advanced bone age, intellectual disability, and distinctive facies. We generated a mouse model for the most common Weaver syndrome missense variant, EZH2 p.R684C. Ezh2R684C/R684C mouse embryonic fibroblasts (MEFs) showed global depletion of H3K27me3. Ezh2R684C/+ mice had abnormal bone parameters indicative of skeletal overgrowth, and Ezh2R684C/+ osteoblasts showed increased osteogenic activity. RNA-seq comparing osteoblasts differentiated from Ezh2R684C/+ and Ezh2+/+ bone marrow mesenchymal stem cells (BM-MSCs) indicated collective dysregulation of the BMP pathway and osteoblast differentiation. Inhibition of the opposing H3K27 demethylases Kdm6a/6b substantially reversed the excessive osteogenesis in Ezh2R684C/+ cells both at the transcriptional and phenotypic levels. This supports both the ideas that writers and erasers of histone marks exist in a fine balance to maintain epigenome state, and that epigenetic modulating agents have therapeutic potential for the treatment of MDEMs.
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Affiliation(s)
- Christine W Gao
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - WanYing Lin
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ryan C Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, MD
- Research and Development Service, Baltimore Veterans Administration Medical Center, Baltimore, MD
| | - Priyanka Kushwaha
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD
| | - Hans T Björnsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Landspítali University Hospital, Reykjavík, Iceland
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
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Harris JR, Gao CW, Britton JF, Applegate CD, Bjornsson HT, Fahrner JA. Five years of experience in the Epigenetics and Chromatin Clinic: what have we learned and where do we go from here? Hum Genet 2023:10.1007/s00439-023-02537-1. [PMID: 36952035 PMCID: PMC10034257 DOI: 10.1007/s00439-023-02537-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/20/2023] [Indexed: 03/24/2023]
Abstract
The multidisciplinary Epigenetics and Chromatin Clinic at Johns Hopkins provides comprehensive medical care for individuals with rare disorders that involve disrupted epigenetics. Initially centered on classical imprinting disorders, the focus shifted to the rapidly emerging group of genetic disorders resulting from pathogenic germline variants in epigenetic machinery genes. These are collectively called the Mendelian disorders of the epigenetic machinery (MDEMs), or more broadly, Chromatinopathies. In five years, 741 clinic visits have been completed for 432 individual patients, with 153 having confirmed epigenetic diagnoses. Of these, 115 individuals have one of 26 MDEMs with every single one exhibiting global developmental delay and/or intellectual disability. This supports prior observations that intellectual disability is the most common phenotypic feature of MDEMs. Additional common phenotypes in our clinic include growth abnormalities and neurodevelopmental issues, particularly hypotonia, attention-deficit/hyperactivity disorder (ADHD), and anxiety, with seizures and autism being less common. Overall, our patient population is representative of the broader group of MDEMs and includes mostly autosomal dominant disorders impacting writers more so than erasers, readers, and remodelers of chromatin marks. There is an increased representation of dual function components with a reader and an enzymatic domain. As expected, diagnoses were made mostly by sequencing but were aided in some cases by DNA methylation profiling. Our clinic has helped to facilitate the discovery of two new disorders, and our providers are actively developing and implementing novel therapeutic strategies for MDEMs. These data and our high follow-up rate of over 60% suggest that we are achieving our mission to diagnose, learn from, and provide optimal care for our patients with disrupted epigenetics.
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Affiliation(s)
- Jacqueline R. Harris
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Kennedy Krieger Institute, Baltimore, MD USA
| | - Christine W. Gao
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Johns Hopkins Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jacquelyn F. Britton
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Carolyn D. Applegate
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Hans T. Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Jill A. Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD USA
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Ng R, Bjornsson HT, Fahrner JA, Harris J. Unique profile of academic learning difficulties in Wiedemann-Steiner syndrome. J Intellect Disabil Res 2023; 67:101-111. [PMID: 36437529 PMCID: PMC9839653 DOI: 10.1111/jir.12993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/06/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Wiedemann-Steiner syndrome (WSS) is a rare genetic disorder caused by heterozygous variants in KMT2A. To date, the cognitive profile associated with WSS remains largely unknown, although emergent case series implicate increased risk of non-verbal reasoning and visual processing deficits. This study examines the academic and learning concerns associated with WSS based on a parent-report screening measure. PARTICIPANTS AND METHODS A total of 25 parents of children/adults with a molecularly-confirmed diagnosis of WSS (mean age = 12.85 years, SD = 7.82) completed the Colorado Learning Difficulties Questionnaire (CLDQ), a parent-screening measure of learning and academic difficulties. Parent ratings were compared to those from a normative community sample to determine focal areas in Math, Reading and Spatial skills that may be weaker within this clinical population. RESULTS On average, parent ratings on the Math (mean Z = -3.08, SD = 0.87) and Spatial scales (mean Z = -2.52, SD = 0.85) were significantly more elevated than that of Reading (mean Z = -1.31, SD = 1.46) (Wilcoxon sign rank test Z < -3.83, P < 0.001), reflecting relatively more challenges observed in these areas. Distribution of parent ratings in Math items largely reflect a positively skewed distribution with most endorsing over three standard deviations below a community sample. In contrast, distributions of parent ratings in Reading and Spatial domains were more symmetric but flat. Ratings for Reading items yielded much larger variance than the other two domains, reflecting a wider range of performance variability. CONCLUSIONS Parent ratings on the CLDQ suggest more difficulties with Math and Spatial skills among those with WSS within group and relative to a community sample. Study results are consistent with recent case reports on the neuropsychological profile associated with WSS and with Kabuki syndrome, which is caused by variants in the related gene KMT2D. Findings lend support for overlapping cognitive patterns across syndromes, implicating potential common disease pathogenesis.
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Affiliation(s)
- Rowena Ng
- Kennedy Krieger Institute
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine
| | - Hans Tomas Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine
- Faculty of Medicine, University of Iceland, Reykjavik
- Landspitali University Hospital
| | - Jill A. Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine
| | - Jacqueline Harris
- Kennedy Krieger Institute
- Department of Genetic Medicine, Johns Hopkins University School of Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine
- Department of Neurology, Johns Hopkins University School of Medicine
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Ng R, Bjornsson HT, Fahrner JA, Harris J. Anxiety in Wiedemann-Steiner syndrome. Am J Med Genet A 2023; 191:437-444. [PMID: 36373844 PMCID: PMC9907226 DOI: 10.1002/ajmg.a.63040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
Abstract
This study examined anxiety in Wiedemann-Steiner syndrome (WSS). Eighteen caregivers and participants with WSS completed the parent- and self-report versions of the Screen for Child Anxiety Related Disorder or the adapted version of the Screen for Adult Anxiety Related Disorder. Approximately 33.33% of parents and 65% of participants with WSS rated in the clinical range for overall anxiety. Across anxiety subtypes, parents primarily indicated concerns with Separation Anxiety (72%), which was also endorsed by the majority of participants with WSS (82%). The emergent trend showed Total Anxiety increased with age based on parent-informant ratings. The behavioral phenotype of WSS includes elevated anxiety. Clinical management should include incorporating early behavioral interventions to bolster emotion regulation given the observed risk of anxiety with age.
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Affiliation(s)
- Rowena Ng
- Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hans Tomas Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Jill A. Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline Harris
- Kennedy Krieger Institute, Baltimore, Maryland, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Levy MA, Relator R, McConkey H, Pranckeviciene E, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Ferilli M, Fletcher RS, Cherick F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Plomp AS, Poulton C, Reilly J, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, John MS, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci TB, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Campion D, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Heron D, Husson T, Kernohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vincent M, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. Hum Mutat 2022; 43:1609-1628. [PMID: 35904121 DOI: 10.1002/humu.24446] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022]
Abstract
An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Erinija Pranckeviciene
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Mariet W Elting
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Marco Ferilli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | | | - Florian Cherick
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, The Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000, Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce B Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON, N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON, N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | | | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | | | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Delphine Heron
- AP-HP, Département de Génétique Médicale, Groupe Hospitalier Pitié Salpétrière, Paris, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, UK, and Sheffield Children's Hospital NHS Foundation Trust
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Dept of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Marie Vincent
- Service de génétique Médicale, CHU Nantes, France.,Institut du thorax, INSERM, CNRS, UNIV Nantes, 44007, Nantes, France
| | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne,, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
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10
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Brennan K, Zheng H, Fahrner JA, Shin JH, Gentles AJ, Schaefer B, Sunwoo JB, Bernstein JA, Gevaert O. NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Hum Mol Genet 2022; 31:2164-2184. [PMID: 35094088 PMCID: PMC9262396 DOI: 10.1093/hmg/ddac026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/04/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sotos syndrome (SS), the most common overgrowth with intellectual disability (OGID) disorder, is caused by inactivating germline mutations of NSD1, which encodes a histone H3 lysine 36 methyltransferase. To understand how NSD1 inactivation deregulates transcription and DNA methylation (DNAm), and to explore how these abnormalities affect human development, we profiled transcription and DNAm in SS patients and healthy control individuals. We identified a transcriptional signature that distinguishes individuals with SS from controls and was also deregulated in NSD1-mutated cancers. Most abnormally expressed genes displayed reduced expression in SS; these downregulated genes consisted mostly of bivalent genes and were enriched for regulators of development and neural synapse function. DNA hypomethylation was strongly enriched within promoters of transcriptionally deregulated genes: overexpressed genes displayed hypomethylation at their transcription start sites while underexpressed genes featured hypomethylation at polycomb binding sites within their promoter CpG island shores. SS patients featured accelerated molecular aging at the levels of both transcription and DNAm. Overall, these findings indicate that NSD1-deposited H3K36 methylation regulates transcription by directing promoter DNA methylation, partially by repressing polycomb repressive complex 2 (PRC2) activity. These findings could explain the phenotypic similarity of SS to OGID disorders that are caused by mutations in PRC2 complex-encoding genes.
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Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - June Ho Shin
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - John B Sunwoo
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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11
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Montano C, Britton JF, Harris JR, Kerkhof J, Barnes BT, Lee JA, Sadikovic B, Sobreira N, Fahrner JA. Genome-wide DNA methylation profiling confirms a case of low-level mosaic Kabuki syndrome 1. Am J Med Genet A 2022; 188:2217-2225. [PMID: 35384273 PMCID: PMC9321966 DOI: 10.1002/ajmg.a.62754] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/22/2022] [Accepted: 03/18/2022] [Indexed: 12/27/2022]
Abstract
Kabuki syndrome is a Mendelian disorder of the epigenetic machinery characterized by typical dysmorphic features, intellectual disability, and postnatal growth deficiency. Pathogenic variants in the genes encoding the chromatin modifiers KMT2D and KDM6A are responsible for Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), respectively. In addition, 11 cases of KS1 caused by mosaic variants in KMT2D have been reported in the literature. Some of these individuals display milder craniofacial and growth phenotypes, and most do not have congenital heart defects. We report the case of an infant with severe hypoplastic left heart syndrome with mitral atresia and aortic atresia (HLHS MA-AA), pulmonary vein stenosis, and atypical facies with a somatic mosaic de novo nonsense variant in KMT2D (c.8200C>T, p.R2734*) identified on trio exome sequencing of peripheral blood and present in 11.2% of sequencing reads. KS was confirmed with EpiSign, a diagnostic genome-wide DNA methylation platform used to identify epigenetic signatures. This case suggests that use of this newly available clinical test can guide the interpretation of low-level mosaic variants identified through sequencing and suggests a new lower limit of mosaicism in whole blood required for a diagnosis of KS.
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Affiliation(s)
- Carolina Montano
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jacquelyn F Britton
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Benjamin T Barnes
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A Lee
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Nara Sobreira
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG Adv 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
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Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
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13
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Ng R, Bjornsson HT, Fahrner JA, Harris J. Sleep disturbances correlate with behavioral problems among individuals with Wiedemann-Steiner syndrome. Front Genet 2022; 13:950082. [PMID: 36313433 PMCID: PMC9608624 DOI: 10.3389/fgene.2022.950082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Wiedemann-Steiner syndrome (WSS) is a rare genetic disorder caused by mutation in KMT2A and characterized by neurodevelopmental delay. This study is the first prospective investigation to examine the sleep and behavioral phenotypes among those with WSS through parent-informant screening inventories. A total of 24 parents of children/adults with WSS (11F, Mean age = 12.71 years, SD = 8.17) completed the Strengths and Difficulties Questionnaire (SDQ) and 22 of these caregivers also completed the Modified Simonds and Parraga Sleep Questionnaire (MSPSQ). On average, the majority of those with WSS (83%) were rated to show borderline to clinical level of behavioral difficulties on the SDQ. Approximately 83% were rated in these ranges for hyperactivity, 63% for emotional problems, and 50% for conduct problems. When applying prior published clinical cut-off for risk of sleep disturbance among those with neurodevelopmental disorders, over 80% of our sample exceeded this limit on the MSPSQ. Largely, caregivers' ratings suggested restless sleep, rigid bedtime rituals, sleep reluctance and breathing through the mouth in sleep were most consistent problems observed. Partial correlations between sleep and behavioral domains showed elevated emotional problems were associated with parasomnia characteristics after controlling for age. Daytime drowsiness and activity were associated with more hyperactivity. Those with more night waking problems and delayed sleep onset were rated to show more severe conduct problems. Overall, these findings suggest dysfunctional sleep behaviors, hyperactivity, and affective problems are part of the neurobehavioral phenotype of WSS. Routine clinical care for those affected by WSS should include close monitoring of sleep and overactive behaviors.
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Affiliation(s)
- Rowena Ng
- Kennedy Krieger Institute, Baltimore, MD, United States.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hans Tomas Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Reykjavik, Iceland
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jacqueline Harris
- Kennedy Krieger Institute, Baltimore, MD, United States.,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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14
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Levy MA, Beck DB, Metcalfe K, Douzgou S, Sithambaram S, Cottrell T, Ansar M, Kerkhof J, Mignot C, Nougues MC, Keren B, Moore HW, Oegema R, Giltay JC, Simon M, van Jaarsveld RH, Bos J, van Haelst M, Motazacker MM, Boon EMJ, Santen GWE, Ruivenkamp CAL, Alders M, Luperchio TR, Boukas L, Ramsey K, Narayanan V, Schaefer GB, Bonasio R, Doheny KF, Stevenson RE, Banka S, Sadikovic B, Fahrner JA. Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood. NPJ Genom Med 2021; 6:92. [PMID: 34750377 PMCID: PMC8576018 DOI: 10.1038/s41525-021-00256-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 09/23/2021] [Indexed: 11/08/2022] Open
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.
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Affiliation(s)
- Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - David B Beck
- National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Kay Metcalfe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sofia Douzgou
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320, Islamabad, Pakistan
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada
| | - Cyril Mignot
- Assistance Publique-Hopitaux de Paris, Sorbonne Université, Departement de Génétique, Groupe Hospitalier Pitie-Salpetriere et Hopital Trousseau, Paris, 75651, France
| | - Marie-Christine Nougues
- Department of Neuropediatrics, Armand Trousseau Hospital, Assistance Publique-Hopitaux de Paris, Paris, 75012, France
| | - Boris Keren
- Laboratoire de génétique, Hôpital Pïtié-Salpêtrière, Assistance Publique-Hopitaux de Paris, Paris, 75013, France
| | | | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jacques C Giltay
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marleen Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Richard H van Jaarsveld
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jessica Bos
- Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Mieke van Haelst
- Section Clinical Genetics, Department Human Genetics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - M Mahdi Motazacker
- Department of Human Genetics, Laboratory of Genome Diagnostics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Elles M J Boon
- Department of Human Genetics, VU University Medical Center Amsterdam, Amsterdam UMC, van der Boechorststraat 7, 1081 BT, Amsterdam, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kimberly F Doheny
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Health Innovation Manchester, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A5W9, Canada.
- Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A5W9, Canada.
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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15
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Solipuram V, Baretti M, Kim AY, Chen LX, Fahrner JA, Gunay-Aygun M, Peng XP, Hardenbergh D, Ferguson A, Griffith P, Wang Y, Brancati M, Gopalakrishna H, Kato T, Shubert C, Laheru D, Yarchoan M. Surgical Debulking for Refractory Hyperammonemic Encephalopathy in Fibrolamellar Hepatocellular Carcinoma. Hepatology 2021; 74:2899-2901. [PMID: 34105830 PMCID: PMC9472764 DOI: 10.1002/hep.31998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/03/2021] [Accepted: 06/04/2021] [Indexed: 01/25/2023]
Affiliation(s)
- Vinod Solipuram
- Department of Internal Medicine, Saint Agnes Hospital, Baltimore, MD
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Marina Baretti
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Alexander Y. Kim
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lucy X. Chen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jill A. Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Meral Gunay-Aygun
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Xiao P. Peng
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Dylan Hardenbergh
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Anna Ferguson
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Paige Griffith
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Yuxuan Wang
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Madelena Brancati
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Harish Gopalakrishna
- Department of Internal Medicine, Saint Agnes Hospital, Baltimore, MD
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Tomoaki Kato
- Department of Surgery, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Chris Shubert
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Daniel Laheru
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
| | - Mark Yarchoan
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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16
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Sheppard SE, Campbell IM, Harr MH, Gold N, Li D, Bjornsson HT, Cohen JS, Fahrner JA, Fatemi A, Harris JR, Nowak C, Stevens CA, Grand K, Au M, Graham JM, Sanchez-Lara PA, Campo MD, Jones MC, Abdul-Rahman O, Alkuraya FS, Bassetti JA, Bergstrom K, Bhoj E, Dugan S, Kaplan JD, Derar N, Gripp KW, Hauser N, Innes AM, Keena B, Kodra N, Miller R, Nelson B, Nowaczyk MJ, Rahbeeni Z, Ben-Shachar S, Shieh JT, Slavotinek A, Sobering AK, Abbott MA, Allain DC, Amlie-Wolf L, Au PYB, Bedoukian E, Beek G, Barry J, Berg J, Bernstein JA, Cytrynbaum C, Chung BHY, Donoghue S, Dorrani N, Eaton A, Flores-Daboub JA, Dubbs H, Felix CA, Fong CT, Fung JLF, Gangaram B, Goldstein A, Greenberg R, Ha TK, Hersh J, Izumi K, Kallish S, Kravets E, Kwok PY, Jobling RK, Knight Johnson AE, Kushner J, Lee BH, Levin B, Lindstrom K, Manickam K, Mardach R, McCormick E, McLeod DR, Mentch FD, Minks K, Muraresku C, Nelson SF, Porazzi P, Pichurin PN, Powell-Hamilton NN, Powis Z, Ritter A, Rogers C, Rohena L, Ronspies C, Schroeder A, Stark Z, Starr L, Stoler J, Suwannarat P, Velinov M, Weksberg R, Wilnai Y, Zadeh N, Zand DJ, Falk MJ, Hakonarson H, Zackai EH, Quintero-Rivera F. Expanding the genotypic and phenotypic spectrum in a diverse cohort of 104 individuals with Wiedemann-Steiner syndrome. Am J Med Genet A 2021; 185:1649-1665. [PMID: 33783954 DOI: 10.1002/ajmg.a.62124] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/19/2022]
Abstract
Wiedemann-Steiner syndrome (WSS) is an autosomal dominant disorder caused by monoallelic variants in KMT2A and characterized by intellectual disability and hypertrichosis. We performed a retrospective, multicenter, observational study of 104 individuals with WSS from five continents to characterize the clinical and molecular spectrum of WSS in diverse populations, to identify physical features that may be more prevalent in White versus Black Indigenous People of Color individuals, to delineate genotype-phenotype correlations, to define developmental milestones, to describe the syndrome through adulthood, and to examine clinicians' differential diagnoses. Sixty-nine of the 82 variants (84%) observed in the study were not previously reported in the literature. Common clinical features identified in the cohort included: developmental delay or intellectual disability (97%), constipation (63.8%), failure to thrive (67.7%), feeding difficulties (66.3%), hypertrichosis cubiti (57%), short stature (57.8%), and vertebral anomalies (46.9%). The median ages at walking and first words were 20 months and 18 months, respectively. Hypotonia was associated with loss of function (LoF) variants, and seizures were associated with non-LoF variants. This study identifies genotype-phenotype correlations as well as race-facial feature associations in an ethnically diverse cohort, and accurately defines developmental trajectories, medical comorbidities, and long-term outcomes in individuals with WSS.
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Affiliation(s)
- Sarah E Sheppard
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian M Campbell
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Margaret H Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina Gold
- Mass General Hospital for Children, Division of Medical Genetics and Metabolism and Harvard Medical School, Boston, Massachusetts, USA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Iceland
| | - Julie S Cohen
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ali Fatemi
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jacqueline R Harris
- Division of Neurogenetics and Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Catherine Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, The Feingold Center for Children, Boston, Massachusetts, USA
| | - Cathy A Stevens
- Department of Pediatrics, University of Tennessee College of Medicine, Chattanooga, Tennessee, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, and David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, California, USA
| | - Miguel Del Campo
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Marilyn C Jones
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Omar Abdul-Rahman
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jennifer A Bassetti
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Elizabeth Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah Dugan
- Division of Medical Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Julie D Kaplan
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nada Derar
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Karen W Gripp
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Natalie Hauser
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Beth Keena
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Neslida Kodra
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Rebecca Miller
- Division of Medical Genomics, Inova Translational Medicine Institute, Inova Fairfax Hospital, Falls Church, Virginia, USA
| | - Beverly Nelson
- Department of Clinical Skills, St. George's University, True Blue, Grenada
| | | | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shay Ben-Shachar
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joseph T Shieh
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Andrew K Sobering
- Department of Biochemistry, St. George's University, True Blue, Grenada
| | - Mary-Alice Abbott
- Medical Genetics, Department of Pediatrics, University of Massachusetts Medical School - Baystate, Springfield, Massachusetts, USA
| | - Dawn C Allain
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Ping Yee Billie Au
- Department of Medical Genetics, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Emma Bedoukian
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Geoffrey Beek
- Children's Hospital of Minnesota, Minneapolis, Minnesota, USA
| | - James Barry
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Janet Berg
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Sarah Donoghue
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, University of California Los Angeles, California, Los Angeles, USA.,UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA
| | - Alison Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | | | - Holly Dubbs
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carolyn A Felix
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Chin-To Fong
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jasmine Lee Fong Fung
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR
| | - Balram Gangaram
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Amy Goldstein
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rotem Greenberg
- Genetic Institute, Tel-Aviv Medical Center, affiliated to Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thoa K Ha
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Joseph Hersh
- Weisskopf Child Evaluation Center, Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Staci Kallish
- Division of Translational Medicine and Human Genetics Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elijah Kravets
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Pui-Yan Kwok
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Rebekah K Jobling
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | - Jessica Kushner
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Bo Hoon Lee
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Brooke Levin
- MD Anderson Cancer Center at Cooper, Cooper University Health Care, Camden, New Jersey, USA
| | | | - Kandamurugu Manickam
- Division of Human Genetics, Department of Internal Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Rebecca Mardach
- Division of Medical Genetics, Department of Pediatrics, University of California, and Rady Children's Hospital, San Diego, California, USA
| | - Elizabeth McCormick
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - D Ross McLeod
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly Minks
- Department of Neurology, Division of Child Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Colleen Muraresku
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stanley F Nelson
- UCLA Clinical Genomics Center, University of California Los Angeles, California, Los Angeles, USA.,Department of Human Genetics, Center for Duchenne Muscular Dystrophy University of California Los Angeles, California, Los Angeles, USA
| | - Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Pavel N Pichurin
- Clinical Genomics Center, University of California Los Angeles, Los Angeles, California, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I duPont Hospital for Children, Wilmington, Delaware, USA
| | - Zoe Powis
- Quest Diagnostics Kalamzoo, Kalamzoo, Michigan, USA
| | - Alyssa Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Caleb Rogers
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, Texas, USA.,Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, Texas, USA
| | - Carey Ronspies
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Audrey Schroeder
- Department of Pediatrics, Division of Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lois Starr
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, USA
| | - Milen Velinov
- NYS Institute for Basic Research in developmental Disabilities, Staten Island, New York, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics and Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Yael Wilnai
- Genetic Institute, Sourasky Medical Center, Te-Aviv, Tel Aviv, Israel
| | - Neda Zadeh
- Genetics Center and CHOC Children's Hospital, Orange, California, USA
| | - Dina J Zand
- Rare Disease Institute, Children's National Medical Center, Washington, District of Columbia, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elaine H Zackai
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Fabiola Quintero-Rivera
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR.,Department of Pathology and Laboratory Medicine, University of California Los Angeles, California, Los Angeles, USA
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17
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Dyment DA, O'Donnell-Luria A, Agrawal PB, Coban Akdemir Z, Aleck KA, Antaki D, Al Sharhan H, Au PYB, Aydin H, Beggs AH, Bilguvar K, Boerwinkle E, Brand H, Brownstein CA, Buyske S, Chodirker B, Choi J, Chudley AE, Clericuzio CL, Cox GF, Curry C, de Boer E, de Vries BBA, Dunn K, Dutmer CM, England EM, Fahrner JA, Geckinli BB, Genetti CA, Gezdirici A, Gibson WT, Gleeson JG, Greenberg CR, Hall A, Hamosh A, Hartley T, Jhangiani SN, Karaca E, Kernohan K, Lauzon JL, Lewis MES, Lowry RB, López-Giráldez F, Matise TC, McEvoy-Venneri J, McInnes B, Mhanni A, Garcia Minaur S, Moilanen J, Nguyen A, Nowaczyk MJM, Posey JE, Õunap K, Pehlivan D, Pajusalu S, Penney LS, Poterba T, Prontera P, Doriqui MJR, Sawyer SL, Sobreira N, Stanley V, Torun D, Wargowski D, Witmer PD, Wong I, Xing J, Zaki MS, Zhang Y, Boycott KM, Bamshad MJ, Nickerson DA, Blue EE, Innes AM. Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome. Am J Med Genet A 2021; 185:119-133. [PMID: 33098347 PMCID: PMC8197629 DOI: 10.1002/ajmg.a.61926] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/09/2020] [Accepted: 09/19/2020] [Indexed: 01/19/2023]
Abstract
Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a "Dubowitz-like" condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.
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Affiliation(s)
- David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Anne O'Donnell-Luria
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kyrieckos A Aleck
- Department of Genetics and Metabolism, Phoenix Children's Medical Group, Phoenix, Arizona, USA
| | - Danny Antaki
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Hind Al Sharhan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Ping-Yee B Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Waco, Texas, USA
| | - Harrison Brand
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Steve Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, USA
| | - Bernard Chodirker
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Albert E Chudley
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carol L Clericuzio
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Gerald F Cox
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Cynthia Curry
- University of California, San Francisco, California, USA
- Genetic Medicine, University Pediatric Specialists, Fresno, California, USA
| | - Elke de Boer
- Department of Human Genetics, Raboud University Medical Centre, Nijmegen, Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Raboud University Medical Centre, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Raboud University Medical Centre, Nijmegen, Netherlands
| | - Kathryn Dunn
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Cullen M Dutmer
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eleina M England
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
| | - Jill A Fahrner
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bilgen B Geckinli
- Department of Medical Genetics, School of Medicine, Marmara University, Istanbul, Turkey
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - William T Gibson
- Department of Medical Genetics and British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Cheryl R Greenberg
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - April Hall
- Waisman Center Clinical Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Julie L Lauzon
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics and British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - R Brian Lowry
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Francesc López-Giráldez
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Tara C Matise
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Jennifer McEvoy-Venneri
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Brenda McInnes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Aziz Mhanni
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sixto Garcia Minaur
- Sección de Genética Clínica, INGEMM (Instituto de Genética Médica y Molecular), Madrid, Spain
| | - Jukka Moilanen
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - An Nguyen
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Malgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Katrin Õunap
- United Laboratories, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Sander Pajusalu
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- United Laboratories, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Lynette S Penney
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Timothy Poterba
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia and University of Perugia, Perugia, Italy
| | | | - Sarah L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Valentina Stanley
- Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, University of California, San Diego, California, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Deniz Torun
- Department of Medical Genetics, Gulhane Military Medical Academy, Ankara, Turkey
| | - David Wargowski
- Division of Genetics, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Isaac Wong
- Broad Institute of MIT and Harvard, Broad Center for Mendelian Genomics, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Yeting Zhang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman-Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman-Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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18
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Mulder PA, van Balkom IDC, Landlust AM, Priolo M, Menke LA, Acero IH, Alkuraya FS, Arias P, Bernardini L, Bijlsma EK, Cole T, Coubes C, Dapia I, Davies S, Di Donato N, Elcioglu NH, Fahrner JA, Foster A, González NG, Huber I, Iascone M, Kaiser AS, Kamath A, Kooblall K, Lapunzina P, Liebelt J, Lynch SA, Maas SM, Mammì C, Mathijssen IB, McKee S, Mirzaa GM, Montgomery T, Neubauer D, Neumann TE, Pintomalli L, Pisanti MA, Plomp AS, Price S, Salter C, Santos-Simarro F, Sarda P, Schanze D, Segovia M, Shaw-Smith C, Smithson S, Suri M, Tatton-Brown K, Tenorio J, Thakker RV, Valdez RM, Van Haeringen A, Van Hagen JM, Zenker M, Zollino M, Dunn WW, Piening S, Hennekam RC. Development, behaviour and sensory processing in Marshall-Smith syndrome and Malan syndrome: phenotype comparison in two related syndromes. J Intellect Disabil Res 2020; 64:956-969. [PMID: 33034087 PMCID: PMC8957705 DOI: 10.1111/jir.12787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 08/19/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Ultrarare Marshall-Smith and Malan syndromes, caused by changes of the gene nuclear factor I X (NFIX), are characterised by intellectual disability (ID) and behavioural problems, although questions remain. Here, development and behaviour are studied and compared in a cross-sectional study, and results are presented with genetic findings. METHODS Behavioural phenotypes are compared of eight individuals with Marshall-Smith syndrome (three male individuals) and seven with Malan syndrome (four male individuals). Long-term follow-up assessment of cognition and adaptive behaviour was possible in three individuals with Marshall-Smith syndrome. RESULTS Marshall-Smith syndrome individuals have more severe ID, less adaptive behaviour, more impaired speech and less reciprocal interaction compared with individuals with Malan syndrome. Sensory processing difficulties occur in both syndromes. Follow-up measurement of cognition and adaptive behaviour in Marshall-Smith syndrome shows different individual learning curves over time. CONCLUSIONS Results show significant between and within syndrome variability. Different NFIX variants underlie distinct clinical phenotypes leading to separate entities. Cognitive, adaptive and sensory impairments are common in both syndromes and increase the risk of challenging behaviour. This study highlights the value of considering behaviour within developmental and environmental context. To improve quality of life, adaptations to environment and treatment are suggested to create a better person-environment fit.
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Affiliation(s)
- P A Mulder
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - I D C van Balkom
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, Netherlands
| | - A M Landlust
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - M Priolo
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - L A Menke
- Department of Paediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - I H Acero
- Genetics Unit, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - F S Alkuraya
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology, and Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - P Arias
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - L Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - E K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - T Cole
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - C Coubes
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - I Dapia
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - S Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - N Di Donato
- Institute for Clinical Genetics, TU Dresden, Dresden, Germany
| | - N H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul and Eastern Mediterranean University, Mersin, Turkey
| | - J A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Foster
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - N G González
- Unit Hospital Universitario Central de Asturias, Oviedo, Spain
| | - I Huber
- Sørland Hospital, Kristiansand, Norway
| | - M Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - A-S Kaiser
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - A Kamath
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - K Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - P Lapunzina
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - J Liebelt
- South Australian Clinical Genetics Services, Women's and Children's Hospital, North Adelaide, Australia
| | - S A Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin, Ireland
| | - S M Maas
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - C Mammì
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - I B Mathijssen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - S McKee
- Northern Ireland Regional Genetics Service, Belfast Health and Social Care Trust, Belfast, UK
| | - G M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, and Division of Genetic Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - T Montgomery
- Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - D Neubauer
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - T E Neumann
- Mitteldeutscher Praxisverbund Humangenetik, Halle, Germany
| | - L Pintomalli
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - M A Pisanti
- Medical Genetic and Laboratory Unit, "Antonio Cardarelli" Hospital, Naples, Italy
| | - A S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - S Price
- Department of Clinical Genetics, Northampton General Hospital NHS Trust, Northampton, UK
| | - C Salter
- Wessex Clinical Genetics Service, Princess Ann Hospital, Southampton, UK
| | - F Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - P Sarda
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - D Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - M Segovia
- CENAGEM, Centro Nacional de Genética, Buenos Aires, Argentina
| | - C Shaw-Smith
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - S Smithson
- University Hospitals Bristol NHS Trust, Bristol, UK
| | - M Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - K Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, London and South West Thames Regional Genetics Service, St. George's University Hospitals NHS Foundation Trust, London, UK
| | - J Tenorio
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - R V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - R M Valdez
- Genetics Unit, Hospital Militar Central "Cirujano Mayor Dr. Cosme Argerich", Buenos Aires, Argentina
| | - A Van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - J M Van Hagen
- Department of Clinical Genetics, VU University Medical Centre, Amsterdam, Netherlands
| | - M Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - M Zollino
- Department of Laboratory Medicine, Institute of Medical Genetics, Catholic University, Rome, Italy
| | - W W Dunn
- Department of Occupational Therapy Education, School of Health Professions, University of Missouri, Columbia, MO, USA
| | - S Piening
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, Netherlands
| | - R C Hennekam
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Department of Paediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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19
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Fahrner JA, Bjornsson HT. Mendelian disorders of the epigenetic machinery: postnatal malleability and therapeutic prospects. Hum Mol Genet 2020; 28:R254-R264. [PMID: 31595951 DOI: 10.1093/hmg/ddz174] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
The epigenetic machinery in conjunction with the transcriptional machinery is responsible for maintaining genome-wide chromatin states and dynamically regulating gene expression. Mendelian disorders of the epigenetic machinery (MDEMs) are genetic disorders resulting from mutations in components of the epigenetic apparatus. Though individually rare, MDEMs have emerged as a collectively common etiology for intellectual disability (ID) and growth disruption. Studies in model organisms and humans have demonstrated dosage sensitivity of this gene group with haploinsufficiency as a predominant disease mechanism. The epigenetic machinery consists of three enzymatic components (writers, erasers and chromatin remodelers) as well as one non-enzymatic group (readers). A tally of the entire census of such factors revealed that although multiple enzymatic activities never coexist within a single component, individual enzymatic activities often coexist with a reader domain. This group of disorders disrupts both the chromatin and transcription states of target genes downstream of the given component but also DNA methylation on a global scale. Elucidation of these global epigenetic changes may inform our understanding of disease pathogenesis and have diagnostic utility. Moreover, many therapies targeting epigenetic marks already exist, and some have proven successful in treating cancer. This, along with the recent observation that neurological dysfunction in these disorders may in fact be treatable in postnatal life, suggests that the scientific community should prioritize this group as a potentially treatable cause of ID. Here we summarize the recent expansion and major characteristics of MDEMs, as well as the unique therapeutic prospects for this group of disorders.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, 21205.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, 21205.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Landspitali University Hospital, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
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20
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Abstract
PURPOSE Tatton-Brown-Rahman syndrome (TBRS) is a newly defined genetic entity characterized by overgrowth and intellectual disability, resulting from germline mutations in the gene encoding DNA methyltransferase 3 alpha (DNMT3A). Affected individuals with benign and malignant tumors have been reported; to our knowledge pituitary adenomas (and other tumors identified in our patient) have not yet been described in this syndrome. CASE We report the case of a 34-year-old woman with TBRS who developed a GH-secreting pituitary macroadenoma and other benign tumors and cystic lesions involving diverse organ systems. Whole-exome sequencing revealed a heterozygous, likely pathogenic variant (c.700_709 del10, p. Gly234ArgfsX79) in exon7 of DNMT3A, and a heterozygous variant of uncertain significance (c.25 C>T, p.Arg9Trp) in exon 1 of the gene encoding aryl hydrocarbon receptor-interacting protein (AIP). The patient failed somatostatin analog treatment, and underwent surgery. The tumor retained AIP expression, and analysis of tumor DNA indicated the presence of both AIP alleles, consistent with no loss of heterozygosity. These findings suggest that the AIP variant was not the primary driver of pituitary adenoma development. CONCLUSION Our case suggests that TBRS might be associated with pituitary adenoma and a broader spectrum of tumors than previously thought, making long-term follow up of these patients crucial to identify tumors early, and to elucidate the clinical spectrum of the disorder for optimization of management.
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Affiliation(s)
- C Hage
- Division of Endocrinology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - E Sabini
- Deparment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - H Alsharhan
- McKusick-Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - J A Fahrner
- McKusick-Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Beckers
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - A Daly
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - R Salvatori
- Division of Endocrinology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University, 1830 East Monument Street #333, Baltimore, MD, 21287, USA.
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21
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Fahrner JA, Bjornsson HT. Corrigendum to: Mendelian disorders of the epigenetic machinery: postnatal malleability and therapeutic prospects. Hum Mol Genet 2020; 29:876. [PMID: 31989177 PMCID: PMC7104669 DOI: 10.1093/hmg/ddz289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 08/30/2023] Open
Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, 21205
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, 21205
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Landspitali University Hospital, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
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22
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Beck DB, Petracovici A, He C, Moore HW, Louie RJ, Ansar M, Douzgou S, Sithambaram S, Cottrell T, Santos-Cortez RLP, Prijoles EJ, Bend R, Keren B, Mignot C, Nougues MC, Õunap K, Reimand T, Pajusalu S, Zahid M, Saqib MAN, Buratti J, Seaby EG, McWalter K, Telegrafi A, Baldridge D, Shinawi M, Leal SM, Schaefer GB, Stevenson RE, Banka S, Bonasio R, Fahrner JA. Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency. Am J Hum Genet 2020; 106:234-245. [PMID: 31928709 DOI: 10.1016/j.ajhg.2019.12.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.
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Affiliation(s)
- David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Petracovici
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chongsheng He
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current address: Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082 Hunan, P.R. China
| | | | | | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Sofia Douzgou
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Boris Keren
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Cyril Mignot
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France
| | - Marie-Christine Nougues
- Assistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Department of Neuropediatrics, Paris 75012, France
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50406, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Yale University School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | | | - Julien Buratti
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Dustin Baldridge
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's D disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY 10032, USA
| | | | | | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jill A Fahrner
- Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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23
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Fahrner JA, Lin WY, Riddle RC, Boukas L, DeLeon VB, Chopra S, Lad SE, Luperchio TR, Hansen KD, Bjornsson HT. Precocious chondrocyte differentiation disrupts skeletal growth in Kabuki syndrome mice. JCI Insight 2019; 4:129380. [PMID: 31557133 DOI: 10.1172/jci.insight.129380] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
Kabuki syndrome 1 (KS1) is a Mendelian disorder of the epigenetic machinery caused by mutations in the gene encoding KMT2D, which methylates lysine 4 on histone H3 (H3K4). KS1 is characterized by intellectual disability, postnatal growth retardation, and distinct craniofacial dysmorphisms. A mouse model (Kmt2d+/βGeo) exhibits features of the human disorder and has provided insight into other phenotypes; however, the mechanistic basis of skeletal abnormalities and growth retardation remains elusive. Using high-resolution micro-CT, we show that Kmt2d+/βGeo mice have shortened long bones and ventral bowing of skulls. In vivo expansion of growth plates within skulls and long bones suggests disrupted endochondral ossification as a common disease mechanism. Stable chondrocyte cell lines harboring inactivating mutations in Kmt2d exhibit precocious differentiation, further supporting this mechanism. A known inducer of chondrogenesis, SOX9, and its targets show markedly increased expression in Kmt2d-/- chondrocytes. By transcriptome profiling, we identify Shox2 as a putative KMT2D target. We propose that decreased KMT2D-mediated H3K4me3 at Shox2 releases Sox9 inhibition and thereby leads to enhanced chondrogenesis, providing a potentially novel and plausible explanation for precocious chondrocyte differentiation. Our findings provide insight into the pathogenesis of growth retardation in KS1 and suggest therapeutic approaches for this and related disorders.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine.,Department of Pediatrics
| | | | | | - Leandros Boukas
- McKusick-Nathans Institute of Genetic Medicine.,Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Valerie B DeLeon
- Department of Anthropology, University of Florida, Gainesville, Florida, USA
| | | | - Susan E Lad
- Department of Anthropology, University of Florida, Gainesville, Florida, USA
| | | | - Kasper D Hansen
- McKusick-Nathans Institute of Genetic Medicine.,Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine.,Department of Pediatrics.,Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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24
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Priolo M, Schanze D, Tatton-Brown K, Mulder PA, Tenorio J, Kooblall K, Acero IH, Alkuraya FS, Arias P, Bernardini L, Bijlsma EK, Cole T, Coubes C, Dapia I, Davies S, Di Donato N, Elcioglu NH, Fahrner JA, Foster A, González NG, Huber I, Iascone M, Kaiser AS, Kamath A, Liebelt J, Lynch SA, Maas SM, Mammì C, Mathijssen IB, McKee S, Menke LA, Mirzaa GM, Montgomery T, Neubauer D, Neumann TE, Pintomalli L, Pisanti MA, Plomp AS, Price S, Salter C, Santos-Simarro F, Sarda P, Segovia M, Shaw-Smith C, Smithson S, Suri M, Valdez RM, Van Haeringen A, Van Hagen JM, Zollino M, Lapunzina P, Thakker RV, Zenker M, Hennekam RC. Further delineation of Malan syndrome. Hum Mutat 2018; 39:1226-1237. [PMID: 29897170 PMCID: PMC6175110 DOI: 10.1002/humu.23563] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 01/02/2023]
Abstract
Malan syndrome is an overgrowth disorder described in a limited number of individuals. We aim to delineate the entity by studying a large group of affected individuals. We gathered data on 45 affected individuals with a molecularly confirmed diagnosis through an international collaboration and compared data to the 35 previously reported individuals. Results indicate that height is > 2 SDS in infancy and childhood but in only half of affected adults. Cardinal facial characteristics include long, triangular face, macrocephaly, prominent forehead, everted lower lip, and prominent chin. Intellectual disability is universally present, behaviorally anxiety is characteristic. Malan syndrome is caused by deletions or point mutations of NFIX clustered mostly in exon 2. There is no genotype‐phenotype correlation except for an increased risk for epilepsy with 19p13.2 microdeletions. Variants arose de novo, except in one family in which mother was mosaic. Variants causing Malan and Marshall‐Smith syndrome can be discerned by differences in the site of stop codon formation. We conclude that Malan syndrome has a well recognizable phenotype that usually can be discerned easily from Marshall–Smith syndrome but rarely there is some overlap. Differentiation from Sotos and Weaver syndrome can be made by clinical evaluation only.
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Affiliation(s)
- Manuela Priolo
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Katrin Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, London and South West Thames Regional Genetics Service, St. George's University Hospitals NHS Foundation Trust, London, UK
| | - Paul A Mulder
- Autism Team Northern-Netherlands, Jonx Department of Youth Mental Health, Lentis Psychiatric Institute, Groningen, The Netherlands
| | - Jair Tenorio
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Kreepa Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Fowzan S Alkuraya
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology, and Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Pedro Arias
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Laura Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Trevor Cole
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Christine Coubes
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - Irene Dapia
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Sally Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | | | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul, and Eastern Mediterranean University, Mersin, Turkey
| | - Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alison Foster
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | | | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Ann-Sophie Kaiser
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Arveen Kamath
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Jan Liebelt
- South Australian Clinical Genetics Services, SA Pathology, North Adelaide, Australia
| | - Sally Ann Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin, Ireland
| | - Saskia M Maas
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Corrado Mammì
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - Inge B Mathijssen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Shane McKee
- Belfast HSC Trust, Northern Ireland Regional Genetics Service, Belfast, Northern Ireland
| | - Leonie A Menke
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, and Department of Human Genetics, University of Washington, Seattle, Washington
| | - Tara Montgomery
- Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Dorothee Neubauer
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | | | - Letizia Pintomalli
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | | | - Astrid S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Sue Price
- Department of Clinical Genetics, Northampton General Hospital NHS Trust, Northampton, UK
| | - Claire Salter
- Wessex Clinical Genetics Service, Princess Ann Hospital, Southampton, UK
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Pierre Sarda
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - Mabel Segovia
- CENAGEM, Centro Nacional de Genética, Buenos Aires, Argentina
| | | | | | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rita Maria Valdez
- Genetics Unit, Hospital Militar Central "Cirujano Mayor Dr. Cosme Argerich,", Buenos Aires, Argentina
| | - Arie Van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Johanna M Van Hagen
- Department of Clinical Genetics, VU University Medical Centre, Amsterdam, The Netherlands
| | - Marcela Zollino
- Department of Laboratory Medicine, Institute of Medical Genetics, Catholic University, Rome, Italy
| | - Pablo Lapunzina
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Rajesh V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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25
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Fahrner JA, Liu R, Perry MS, Klein J, Chan DC. A novel de novo dominant negative mutation in DNM1L impairs mitochondrial fission and presents as childhood epileptic encephalopathy. Am J Med Genet A 2016; 170:2002-11. [PMID: 27145208 DOI: 10.1002/ajmg.a.37721] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/17/2016] [Indexed: 11/07/2022]
Abstract
DNM1L encodes dynamin-related protein 1 (DRP1/DLP1), a key component of the mitochondrial fission machinery that is essential for proper functioning of the mammalian brain. Previously reported probands with de novo missense mutations in DNM1L presented in the first year of life with severe encephalopathy and refractory epilepsy, with several dying within the first several weeks after birth. In contrast, we report identical novel missense mutations in DNM1L in two unrelated probands who experienced normal development for several years before presenting with refractory focal status epilepticus and subsequent rapid neurological decline. We expand the phenotype of DNM1L-related mitochondrial fission defects, reveal common unique clinical characteristics and imaging findings, and compare the cellular impact of this novel mutation to the previously reported A395D lethal variant. We demonstrate that our R403C mutation, which resides in the assembly region of DRP1, acts by a dominant-negative mechanism and reduces oligomerization, mitochondrial fission activity, and mitochondrial recruitment of DRP1, but to a lesser extent compared to the A395D mutation. In contrast to the initial report of neonatal lethality resulting from DNM1L mutation and DRP1 dysfunction, our results show that milder DRP1 impairment is compatible with normal early development and subsequently results in a distinct set of neurological findings. In addition, we identify a common pathogenic mechanism whereby DNM1L mutations impair mitochondrial fission. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jill A Fahrner
- Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Raymond Liu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Michael Scott Perry
- Comprehensive Epilepsy Program, Jane and John Justin Neuroscience Center, Cook Children's Medical Center, Fort Worth, Texas
| | - Jessica Klein
- Division of Pediatric Neurology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
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Abstract
Mendelian disorders of the epigenetic machinery are a newly delineated group of multiple congenital anomaly and intellectual disability syndromes resulting from mutations in genes encoding components of the epigenetic machinery. The gene products affected in these inherited conditions act in trans and are expected to have widespread epigenetic consequences. Many of these syndromes demonstrate phenotypic overlap with classical imprinting disorders and with one another. The various writer and eraser systems involve opposing players, which we propose must maintain a balance between open and closed chromatin states in any given cell. An imbalance might lead to disrupted expression of disease-relevant target genes. We suggest that classifying disorders based on predicted effects on this balance would be informative regarding pathogenesis. Furthermore, strategies targeted at restoring this balance might offer novel therapeutic avenues, taking advantage of available agents such as histone deacetylase inhibitors and histone acetylation antagonists.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ,
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27
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Abstract
DNA sequencing has become a powerful method to discover the genetic basis of disease. Standard, widely used protocols for analysis usually begin by comparing each individual to the human reference genome. When applied to a set of related individuals, this approach reveals millions of differences, most of which are shared among the individuals and unrelated to the disease being investigated. We have developed a novel algorithm for variant detection, one that compares DNA sequences directly to one another, without aligning them to the reference genome. When used to find de novo mutations in exome sequences from family trios, or to compare normal and diseased samples from the same individual, the new method, direct alignment for mutation discovery (DIAMUND), produces a dramatically smaller list of candidate mutations than previous methods, without losing sensitivity to detect the true cause of a genetic disease. We demonstrate our results on several example cases, including two family trios in which it correctly found the disease-causing variant while excluding thousands of harmless variants that standard methods had identified.
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Affiliation(s)
- Steven L Salzberg
- Center for Computational Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205
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Fahrner JA, Murphy AM, Gunay-Aygun M. Hypertrophic cardiomyopathy: how far should we go with genetic testing? Am J Med Genet A 2012; 161A:232-3. [PMID: 23239515 DOI: 10.1002/ajmg.a.35666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 08/24/2012] [Indexed: 11/10/2022]
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Zulfiqar M, Lin DDM, Van der Graaf M, Barker PB, Fahrner JA, Marie S, Morava E, De Boer L, Willemsen MAAP, Vining E, Horská A, Engelke U, Wevers RA, Maegawa GHB. Novel proton MR spectroscopy findings in adenylosuccinate lyase deficiency. J Magn Reson Imaging 2012; 37:974-80. [PMID: 23055421 DOI: 10.1002/jmri.23852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 09/04/2012] [Indexed: 11/08/2022] Open
Abstract
Adenylosuccinate lyase (ADSL) deficiency is a rare inborn error of metabolism resulting in accumulation of metabolites including succinylaminoimidazole carboxamide riboside (SAICAr) and succinyladenosine (S-Ado) in the brain and other tissues. Patients with ADSL have progressive psychomotor retardation, neonatal seizures, global developmental delay, hypotonia, and autistic features, although variable clinical manifestations may make the initial diagnosis challenging. Two cases of the severe form of the disease are reported here: an 18-month-old boy with global developmental delay, intractable neonatal seizures, progressive cerebral atrophy, and marked hypomyelination, and a 3-month-old girl presenting with microcephaly, neonatal seizures, and marked psychomotor retardation. In both patients in vivo proton magnetic resonance spectroscopy (MRS) showed the presence of S-Ado signal at 8.3 ppm, consistent with a prior report. Interestingly, SAICAr signal was also detectable at 7.5 ppm in affected white matter, which has not been reported in vivo before. A novel splice-site mutation, c.IVS12 + 1/G > C, in the ADSL gene was identified in the second patient. Our findings confirm the utility of in vivo proton MRS in suggesting a specific diagnosis of ADSL deficiency, and also demonstrate an additional in vivo resonance (7.5 ppm) of SAICAr in the cases of severe disease.
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Affiliation(s)
- Maria Zulfiqar
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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Fahrner JA, Frazier A, Bachir S, Walsh MF, Applegate CD, Thompson R, Halushka MK, Murphy AM, Gunay-Aygun M. A rasopathy phenotype with severe congenital hypertrophic obstructive cardiomyopathy associated with a PTPN11 mutation and a novel variant in SOS1. Am J Med Genet A 2012; 158A:1414-21. [PMID: 22585553 DOI: 10.1002/ajmg.a.35363] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 03/03/2012] [Indexed: 01/26/2023]
Abstract
The RAS-MAPK pathway is critical for human growth and development. Abnormalities at different steps of this signaling cascade result in neuro-cardio-facial-cutaneous syndromes, or the RASopathies, a group of disorders with overlapping yet distinct phenotypes. RASopathy patients have variable degrees of intellectual disability, poor growth, relative macrocephaly, ectodermal abnormalities, dysmorphic features, and increased risk for certain malignancies. Congenital heart disease, particularly hypertrophic cardiomyopathy (HCM) and pulmonic stenosis, are prominent features in these disorders. Significant locus heterogeneity exists for many of the RASopathies. Traditionally, these diseases were thought to be inherited in an autosomal dominant manner. However, recently patients with defects in two components of this pathway and overlapping features of various forms of Noonan syndrome and neurofibromatosis 1 and have been reported. Here we present a patient with severe, progressive neonatal HCM, elevated urinary catecholamine metabolites, and dysmorphic features in whom we identified a known LEOPARD syndrome-associated PTPN11 mutation (c.1403 C > T; p.T468M) and a novel, potentially pathogenic missense SOS1 variant (c.1018 C > T; p.P340S) replacing a rigid nonpolar imino acid with a polar amino acid at a highly conserved position. We describe detailed clinical manifestations, cardiac histopathology, and the molecular genetic findings. Oligogenic models of inheritance with potential synergistic effects should be considered in the RASopathies.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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McGarvey KM, Greene E, Fahrner JA, Jenuwein T, Baylin SB. DNA Methylation and Complete Transcriptional Silencing of Cancer Genes Persist after Depletion of EZH2. Cancer Res 2007; 67:5097-102. [PMID: 17545586 DOI: 10.1158/0008-5472.can-06-2029] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent work suggests a link between the polycomb group protein EZH2 and mediation of gene silencing in association with maintenance of DNA methylation. However, we show that whereas basally expressed target cancer genes with minimal DNA methylation have increased transcription during EZH2 knockdown, densely DNA hypermethylated and silenced genes retain their methylation and remain transcriptionally silent. These results suggest that EZH2 can modulate transcription of basally expressed genes but not silent genes that are densely DNA methylated.
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Affiliation(s)
- Kelly M McGarvey
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University, Baltimore, MD 21231, USA
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McGarvey KM, Fahrner JA, Greene E, Martens J, Jenuwein T, Baylin SB. Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res 2006; 66:3541-9. [PMID: 16585178 DOI: 10.1158/0008-5472.can-05-2481] [Citation(s) in RCA: 239] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Histone H3 lysine 9 (H3K9) and lysine 27 (H3K27) trimethylation are properties of stably silenced heterochromatin whereas H3K9 dimethylation (H3K9me2) is important for euchromatic gene repression. In colorectal cancer cells, all of these marks, as well as the key enzymes which establish them, surround the hMLH1 promoter when it is DNA hypermethylated and aberrantly silenced, but are absent when the gene is unmethylated and fully expressed in a euchromatic state. When the aberrantly silenced gene is DNA demethylated and reexpressed following 5-aza-2'-deoxycytidine treatment, H3K9me1 and H3K9me2 are the only silencing marks that are lost. A series of other silenced and DNA hypermethylated gene promoters behave identically even when the genes are chronically DNA demethylated and reexpressed after genetic knockout of DNA methyltransferases. Our data indicate that when transcription of DNA hypermethylated genes is activated in cancer cells, their promoters remain in an environment with certain heterochromatic characteristics. This finding has important implications for the translational goal of reactivating aberrantly silenced cancer genes as a therapeutic maneuver.
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Affiliation(s)
- Kelly M McGarvey
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University, 1650 Orleans Street, Baltimore, MD 21231, USA
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Affiliation(s)
- Jill A Fahrner
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland 21231-1000, USA
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Fahrner JA, Eguchi S, Herman JG, Baylin SB. Dependence of histone modifications and gene expression on DNA hypermethylation in cancer. Cancer Res 2002; 62:7213-8. [PMID: 12499261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
We examined the relationship between aberrant DNA hypermethylation and key histone code components at a hypermethylated, silenced tumor suppressor gene promoter in human cancer. In lower eukaryotes, methylated H3-lysine 9 (methyl-H3-K9) determines DNA methylation and correlates with repressed gene transcription. Here we show that a zone of deacetylated histone H3 plus methyl-H3-K9 surrounds a hypermethylated, silenced hMLH1 promoter, which, when unmethylated and active, is embedded in methyl-H3-K4 and acetylated H3. Inhibiting DNA methyltransferases, but not histone deacetylases, leads first to promoter demethylation, second to gene reexpression, and finally to complete histone code reversal. Our findings suggest a new paradigm-DNA methylation may directly, or indirectly by inhibiting transcription, maintain key repressive elements of the histone code at a hypermethylated gene promoter in cancer.
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Affiliation(s)
- Jill A Fahrner
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland 21231-1000, USA
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Pickles RJ, Fahrner JA, Petrella JM, Boucher RC, Bergelson JM. Retargeting the coxsackievirus and adenovirus receptor to the apical surface of polarized epithelial cells reveals the glycocalyx as a barrier to adenovirus-mediated gene transfer. J Virol 2000; 74:6050-7. [PMID: 10846088 PMCID: PMC112103 DOI: 10.1128/jvi.74.13.6050-6057.2000] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Lumenal delivery of adenovirus vectors (AdV) results in inefficient gene transfer to human airway epithelium. The human coxsackievirus and adenovirus receptor (hCAR) was detected by immunofluorescence selectively at the basolateral surfaces of freshly excised human airway epithelial cells, suggesting that the absence of apical hCAR constitutes a barrier to adenovirus-mediated gene delivery in vivo. In transfected polarized Madin-Darby canine kidney cells, wild-type hCAR was expressed selectively at the basolateral membrane, whereas hCAR lacking the transmembrane and/or cytoplasmic domains was expressed on both the basolateral and apical membranes. Cells expressing apical hCAR still were not efficiently transduced by AdV applied to the apical surface. However, after the cells were treated with agents that remove components of the apical surface glycocalyx, AdV transduction occurred. These results indicate that adenovirus can infect via receptors located at the apical cell membrane but that the glycocalyx impedes interaction of AdV with apical receptors.
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Affiliation(s)
- R J Pickles
- CF/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, 27599-7248, USA.
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