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 among 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.
Original language | English |
---|---|
Journal | Human Mutation |
Volume | 43 |
Issue number | 11 |
Pages (from-to) | 1609-1628 |
ISSN | 1059-7794 |
DOIs | |
Publication status | Published - 2022 |
Bibliographical note
Publisher Copyright:© 2022 Wiley Periodicals LLC.
Keywords
- clinical diagnostics
- DNA methylation
- episignatures
- neurodevelopmental syndromes
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Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders. / Levy, Michael A.; Relator, Raissa; McConkey, Haley; Pranckeviciene, Erinija; Kerkhof, Jennifer; Barat-Houari, Mouna; Bargiacchi, Sara; Biamino, Elisa; Palomares Bralo, María; Cappuccio, Gerarda; Ciolfi, Andrea; Clarke, Angus; DuPont, Barbara R.; Elting, Mariet W.; Faivre, Laurence; Fee, Timothy; Ferilli, Marco; Fletcher, Robin S.; Cherick, Florian; Foroutan, Aidin; Friez, Michael J.; Gervasini, Cristina; Haghshenas, Sadegheh; Hilton, Benjamin A.; Jenkins, Zandra; Kaur, Simranpreet; Lewis, Suzanne; Louie, Raymond J.; Maitz, Silvia; Milani, Donatella; Morgan, Angela T.; Oegema, Renske; Østergaard, Elsebet; Pallares, Nathalie R.; Piccione, Maria; Plomp, Astrid S.; Poulton, Cathryn; Reilly, Jack; Rius, Rocio; Robertson, Stephen; Rooney, Kathleen; Rousseau, Justine; Santen, Gijs W.E.; Santos-Simarro, Fernando; Schijns, Josephine; Squeo, Gabriella M.; John, Miya St; Thauvin-Robinet, Christel; Traficante, Giovanna; van der Sluijs, Pleuntje J.; Vergano, Samantha A.; Vos, Niels; Walden, Kellie K.; Azmanov, Dimitar; Balci, Tugce B.; Banka, Siddharth; Gecz, Jozef; Henneman, Peter; Lee, Jennifer A.; Mannens, Marcel M.A.M.; Roscioli, Tony; Siu, Victoria; Amor, David J.; Baynam, Gareth; Bend, Eric G.; Boycott, Kym; Brunetti-Pierri, Nicola; Campeau, Philippe M.; Campion, Dominique; Christodoulou, John; Dyment, David; Esber, Natacha; Fahrner, Jill A.; Fleming, Mark D.; Genevieve, David; Heron, Delphine; Husson, Thomas; Kernohan, Kristin D.; McNeill, Alisdair; Menke, Leonie A.; Merla, Giuseppe; Prontera, Paolo; Rockman-Greenberg, Cheryl; Schwartz, Charles; Skinner, Steven A.; Stevenson, Roger E.; Vincent, Marie; Vitobello, Antonio; Tartaglia, Marco; Alders, Marielle; Tedder, Matthew L.; Sadikovic, Bekim.
In: Human Mutation, Vol. 43, No. 11, 2022, p. 1609-1628.Research output: Contribution to journal › Journal article › Research › peer-review
}
TY - JOUR
T1 - Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders
AU - Levy, Michael A.
AU - Relator, Raissa
AU - McConkey, Haley
AU - Pranckeviciene, Erinija
AU - Kerkhof, Jennifer
AU - Barat-Houari, Mouna
AU - Bargiacchi, Sara
AU - Biamino, Elisa
AU - Palomares Bralo, María
AU - Cappuccio, Gerarda
AU - Ciolfi, Andrea
AU - Clarke, Angus
AU - DuPont, Barbara R.
AU - Elting, Mariet W.
AU - Faivre, Laurence
AU - Fee, Timothy
AU - Ferilli, Marco
AU - Fletcher, Robin S.
AU - Cherick, Florian
AU - Foroutan, Aidin
AU - Friez, Michael J.
AU - Gervasini, Cristina
AU - Haghshenas, Sadegheh
AU - Hilton, Benjamin A.
AU - Jenkins, Zandra
AU - Kaur, Simranpreet
AU - Lewis, Suzanne
AU - Louie, Raymond J.
AU - Maitz, Silvia
AU - Milani, Donatella
AU - Morgan, Angela T.
AU - Oegema, Renske
AU - Østergaard, Elsebet
AU - Pallares, Nathalie R.
AU - Piccione, Maria
AU - Plomp, Astrid S.
AU - Poulton, Cathryn
AU - Reilly, Jack
AU - Rius, Rocio
AU - Robertson, Stephen
AU - Rooney, Kathleen
AU - Rousseau, Justine
AU - Santen, Gijs W.E.
AU - Santos-Simarro, Fernando
AU - Schijns, Josephine
AU - Squeo, Gabriella M.
AU - John, Miya St
AU - Thauvin-Robinet, Christel
AU - Traficante, Giovanna
AU - van der Sluijs, Pleuntje J.
AU - Vergano, Samantha A.
AU - Vos, Niels
AU - Walden, Kellie K.
AU - Azmanov, Dimitar
AU - Balci, Tugce B.
AU - Banka, Siddharth
AU - Gecz, Jozef
AU - Henneman, Peter
AU - Lee, Jennifer A.
AU - Mannens, Marcel M.A.M.
AU - Roscioli, Tony
AU - Siu, Victoria
AU - Amor, David J.
AU - Baynam, Gareth
AU - Bend, Eric G.
AU - Boycott, Kym
AU - Brunetti-Pierri, Nicola
AU - Campeau, Philippe M.
AU - Campion, Dominique
AU - Christodoulou, John
AU - Dyment, David
AU - Esber, Natacha
AU - Fahrner, Jill A.
AU - Fleming, Mark D.
AU - Genevieve, David
AU - Heron, Delphine
AU - Husson, Thomas
AU - Kernohan, Kristin D.
AU - McNeill, Alisdair
AU - Menke, Leonie A.
AU - Merla, Giuseppe
AU - Prontera, Paolo
AU - Rockman-Greenberg, Cheryl
AU - Schwartz, Charles
AU - Skinner, Steven A.
AU - Stevenson, Roger E.
AU - Vincent, Marie
AU - Vitobello, Antonio
AU - Tartaglia, Marco
AU - Alders, Marielle
AU - Tedder, Matthew L.
AU - Sadikovic, Bekim
N1 - Publisher Copyright: © 2022 Wiley Periodicals LLC.
PY - 2022
Y1 - 2022
N2 - 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 among 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.
AB - 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 among 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.
KW - clinical diagnostics
KW - DNA methylation
KW - episignatures
KW - neurodevelopmental syndromes
U2 - 10.1002/humu.24446
DO - 10.1002/humu.24446
M3 - Journal article
C2 - 35904121
AN - SCOPUS:85136511967
VL - 43
SP - 1609
EP - 1628
JO - Human Mutation
JF - Human Mutation
SN - 1059-7794
IS - 11
ER -