Mutations in SETD2 Cause a Novel Overgrowth Condition
Mutations in SETD2 Cause a Novel Overgrowth Condition
Background. Overgrowth conditions are a heterogeneous group of disorders characterised by increased growth and variable features, including macrocephaly, distinctive facial appearance and various degrees of learning difficulties and intellectual disability. Among them, Sotos and Weaver syndromes are clinically well defined and due to heterozygous mutations in NSD1 and EZH2, respectively. NSD1 and EZH2 are both histone-modifying enzymes. These two epigenetic writers catalyse two specific post-translational modifications of histones: methylation of histone 3 lysine 36 (H3K36) and lysine 27 (H3K27). We postulated that mutations in writers of these two chromatin marks could cause overgrowth conditions, resembling Sotos or Weaver syndromes, in patients with no NSD1 or EZH2 abnormalities.
Methods. We analysed the coding sequences of 14 H3K27 methylation-related genes and eight H3K36 methylation-related genes using a targeted next-generation sequencing approach in three Sotos, 11 'Sotos-like' and two Weaver syndrome patients.
Results. We identified two heterozygous mutations in the SETD2 gene in two patients with 'Sotos-like' syndrome: one missense p.Leu1815Trp de novo mutation in a boy and one nonsense p.Gln274* mutation in an adopted girl. SETD2 is non-redundantly responsible for H3K36 trimethylation. The two probands shared similar clinical features, including postnatal overgrowth, macrocephaly, obesity, speech delay and advanced carpal ossification.
Conclusions. Our results illustrate the power of targeted next-generation sequencing to identify rare disease-causing variants. We provide a compelling argument for Sotos and Sotos-like syndromes as epigenetic diseases caused by loss-of-function mutations of epigenetic writers of the H3K36 histone mark.
Sotos syndrome (SoS) (Mendelian Inheritance in Man (MIM) 117550), also known as cerebral gigantism, was first described by Sotos et al in 1964. Although most cases are sporadic, several reports of autosomal-dominant inheritance have been described. This overgrowth syndrome is characterised by excessive growth during childhood, macrocephaly, distinctive facial appearance and various degrees of learning difficulty. The typical craniofacial features include macro-dolichocephaly, a broad forehead with a receding hairline, a prominent chin and down-slanting of the palpebral fissures. SoS can be associated with other features like advanced bone age, neonatal jaundice, hypotonia, seizures, cardiac defects and genitourinary anomalies. Since its first description, hundreds of SoS cases have been reported in the literature. The phenotypic spectrum of these patients is usually broad, varying from a classical SoS phenotype to patients exhibiting only a few Sotos syndrome features (Sotos-like syndrome). Weaver syndrome (WS; MIM 277590) is seen less commonly than SoS and shows significant phenotypic overlap with SoS. WS comprises prenatal and postnatal overgrowth, a typical craniofacial appearance (micrognathia with a deep horizontal chin crease), deep set nails, camptodactyly and advanced carpal osseous maturation. Carpal bone development is advanced over the rest of the hand in WS, whereas in SoS carpal bone development it is at or behind that of the rest of the hand.
In 2002, the genetic origin of SoS was elucidated. In a patient with SoS, the 5q35 translocation breakpoint of a de novo balanced chromosomal translocation was shown to disrupt the NSD1 gene (nuclear receptor binding SET-domain containing gene 1) (MIM 606681). The NSD1 protein belongs to histone 'writer' proteins. NSD1 is a SET (Su(var)3–9, Enhancer of Zeste and Trithorax) domain histone methyltransferase that primarily targets nucleosomal histone H3 lysine 36 (H3K36). Histone lysine methylation signalling is a principal chromatin regulatory mechanism that influences fundamental nuclear processes linked to downstream biological functions by methyllysine-binding proteins. Lysine (K) residues can accept up to three methyl groups to form mono-, di- and trimethylated derivatives. H3K36 dimethylation (H3K36me2), mediated by NSD1, is regarded as an activating chromatin mark. Since this discovery, reports have indicated that approximately 60–80% of the clinically diagnosed patients with SoS harbour heterozygous NSD1 intragenic mutations or microdeletions. Therefore, there are a substantial number of patients suspected of SoS but without a molecular explanation.
Molecular overlap has been demonstrated between SoS and WS conditions. NSD1 mutations account for some WS cases. However, trio-based whole-exome sequencing in three NSD1-negative WS families recently identified de novo mutations in the EZH2 gene (enhancer of zeste homologue 2) (MIM 601573).EZH2 mutations were then identified in 3/29 individuals with Weaver-like phenotypes (A.S.A. Cohen et al, 2013, 63rd ASHG Annual Meeting, abstract). The EZH2 protein partners with SUZ12 and EED to form the minimal polycomb repressive complex 2 (PRC2). This complex catalyses the trimethylation of lysine 27 of histone H3 (H3K27me3), and EZH2 itself forms the catalytic subunit for this reaction. EZH2 forms a key component of molecular machinery that shuts off transcription of loci to which trimethylated H3K27 is bound.
Constitutional heterozygous mutations in NSD1 and EZH2 cause the two overlapping overgrowth syndromes SoS and WS. NSD1 and EZH2 are both epigenetic writers that catalyse two specific post-translational modifications of histones: methylation of histone 3 lysine 36 (H3K36) and lysine 27 (H3K27), respectively. We postulated that mutations in other genes coding writers of these two chromatin marks could cause overgrowth conditions resembling Sotos or Weaver syndromes in patients with no NSD1 or EZH2 abnormalities. Due to its low cost and high throughput, targeted next-generation sequencing (NGS) delivered a step change in the ability to simultaneously sequence multiple genes. We analysed the coding sequences of 14 H3K27 methylation-related genes and eight H3K36 methylation-related genes in 16 patients with SoS, Sotos-like and WS, using a targeted NGS approach.
Abstract and Introduction
Abstract
Background. Overgrowth conditions are a heterogeneous group of disorders characterised by increased growth and variable features, including macrocephaly, distinctive facial appearance and various degrees of learning difficulties and intellectual disability. Among them, Sotos and Weaver syndromes are clinically well defined and due to heterozygous mutations in NSD1 and EZH2, respectively. NSD1 and EZH2 are both histone-modifying enzymes. These two epigenetic writers catalyse two specific post-translational modifications of histones: methylation of histone 3 lysine 36 (H3K36) and lysine 27 (H3K27). We postulated that mutations in writers of these two chromatin marks could cause overgrowth conditions, resembling Sotos or Weaver syndromes, in patients with no NSD1 or EZH2 abnormalities.
Methods. We analysed the coding sequences of 14 H3K27 methylation-related genes and eight H3K36 methylation-related genes using a targeted next-generation sequencing approach in three Sotos, 11 'Sotos-like' and two Weaver syndrome patients.
Results. We identified two heterozygous mutations in the SETD2 gene in two patients with 'Sotos-like' syndrome: one missense p.Leu1815Trp de novo mutation in a boy and one nonsense p.Gln274* mutation in an adopted girl. SETD2 is non-redundantly responsible for H3K36 trimethylation. The two probands shared similar clinical features, including postnatal overgrowth, macrocephaly, obesity, speech delay and advanced carpal ossification.
Conclusions. Our results illustrate the power of targeted next-generation sequencing to identify rare disease-causing variants. We provide a compelling argument for Sotos and Sotos-like syndromes as epigenetic diseases caused by loss-of-function mutations of epigenetic writers of the H3K36 histone mark.
Introduction
Sotos syndrome (SoS) (Mendelian Inheritance in Man (MIM) 117550), also known as cerebral gigantism, was first described by Sotos et al in 1964. Although most cases are sporadic, several reports of autosomal-dominant inheritance have been described. This overgrowth syndrome is characterised by excessive growth during childhood, macrocephaly, distinctive facial appearance and various degrees of learning difficulty. The typical craniofacial features include macro-dolichocephaly, a broad forehead with a receding hairline, a prominent chin and down-slanting of the palpebral fissures. SoS can be associated with other features like advanced bone age, neonatal jaundice, hypotonia, seizures, cardiac defects and genitourinary anomalies. Since its first description, hundreds of SoS cases have been reported in the literature. The phenotypic spectrum of these patients is usually broad, varying from a classical SoS phenotype to patients exhibiting only a few Sotos syndrome features (Sotos-like syndrome). Weaver syndrome (WS; MIM 277590) is seen less commonly than SoS and shows significant phenotypic overlap with SoS. WS comprises prenatal and postnatal overgrowth, a typical craniofacial appearance (micrognathia with a deep horizontal chin crease), deep set nails, camptodactyly and advanced carpal osseous maturation. Carpal bone development is advanced over the rest of the hand in WS, whereas in SoS carpal bone development it is at or behind that of the rest of the hand.
In 2002, the genetic origin of SoS was elucidated. In a patient with SoS, the 5q35 translocation breakpoint of a de novo balanced chromosomal translocation was shown to disrupt the NSD1 gene (nuclear receptor binding SET-domain containing gene 1) (MIM 606681). The NSD1 protein belongs to histone 'writer' proteins. NSD1 is a SET (Su(var)3–9, Enhancer of Zeste and Trithorax) domain histone methyltransferase that primarily targets nucleosomal histone H3 lysine 36 (H3K36). Histone lysine methylation signalling is a principal chromatin regulatory mechanism that influences fundamental nuclear processes linked to downstream biological functions by methyllysine-binding proteins. Lysine (K) residues can accept up to three methyl groups to form mono-, di- and trimethylated derivatives. H3K36 dimethylation (H3K36me2), mediated by NSD1, is regarded as an activating chromatin mark. Since this discovery, reports have indicated that approximately 60–80% of the clinically diagnosed patients with SoS harbour heterozygous NSD1 intragenic mutations or microdeletions. Therefore, there are a substantial number of patients suspected of SoS but without a molecular explanation.
Molecular overlap has been demonstrated between SoS and WS conditions. NSD1 mutations account for some WS cases. However, trio-based whole-exome sequencing in three NSD1-negative WS families recently identified de novo mutations in the EZH2 gene (enhancer of zeste homologue 2) (MIM 601573).EZH2 mutations were then identified in 3/29 individuals with Weaver-like phenotypes (A.S.A. Cohen et al, 2013, 63rd ASHG Annual Meeting, abstract). The EZH2 protein partners with SUZ12 and EED to form the minimal polycomb repressive complex 2 (PRC2). This complex catalyses the trimethylation of lysine 27 of histone H3 (H3K27me3), and EZH2 itself forms the catalytic subunit for this reaction. EZH2 forms a key component of molecular machinery that shuts off transcription of loci to which trimethylated H3K27 is bound.
Constitutional heterozygous mutations in NSD1 and EZH2 cause the two overlapping overgrowth syndromes SoS and WS. NSD1 and EZH2 are both epigenetic writers that catalyse two specific post-translational modifications of histones: methylation of histone 3 lysine 36 (H3K36) and lysine 27 (H3K27), respectively. We postulated that mutations in other genes coding writers of these two chromatin marks could cause overgrowth conditions resembling Sotos or Weaver syndromes in patients with no NSD1 or EZH2 abnormalities. Due to its low cost and high throughput, targeted next-generation sequencing (NGS) delivered a step change in the ability to simultaneously sequence multiple genes. We analysed the coding sequences of 14 H3K27 methylation-related genes and eight H3K36 methylation-related genes in 16 patients with SoS, Sotos-like and WS, using a targeted NGS approach.
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