Mutations in SETD2 Cause a Novel Overgrowth Condition
Mutations in SETD2 Cause a Novel Overgrowth Condition
We report here heterozygous loss-of-function mutations in the SETD2 gene in two patients with a consistent overgrowth phenotype characterised by postnatal overgrowth (+2.5 SD), macrocephaly (+4 SD) and obesity (>+4 SD) in the course of the disease, minor facial features (long face and pointed chin) and advanced carpal ossification. Both presented with speech delay, slowness and low sociability, leading to difficulties in their professional integration.
SETD2 was discovered in 1998 and was shown to function as a histone methyltransferase via the conserved SET domain. The SET domain was first recognised as a conserved feature in chromatin-associated proteins and a number of SET domain-containing proteins have since been characterised as histone methyltransferases. SETD2 is non-redundantly responsible for all trimethylation of lysine 36 of histone H3. Homozygous disruption of Setd2 in mice resulted in embryonic lethality with severe defects in blood vessel development. One of the two SETD2 mutations introduces a premature stop codon in SETD2 mRNA (proband 1, c.820C>T, p.Gln274*), and in the other case (proband 2), the mutation could result in a loss-of-function allele (c.5444T>G, p.Leu1815Trp). The affected Leu1815 codon is evolutionarily conserved according to phyloP (score=0.998). A positive phyloP score is interpreted as a signature of evolutionary conservation, which is consistent with functional importance. The in silico analysis of the p.Leu1815Trp variant using PolyPhen-2 classified it as probably damaging (score=0.98), and the Sorting Intolerant From Tolerant (SIFT) software classified it as damaging (score=0).
Our results illustrate the power of targeted NGS to identify rare disease-causing variants. Remaining mutation-negative patients (14 cases) could present mosaic mutations undetectable in blood. Unfortunately, no additional tissues other than blood could be collected from the affected cases in our study. The remaining 14 negative index cases should now be analysed with a whole exome NGS approach to search for causal mutations in other loci in the genome. This exome sequencing approach has proven to be a useful and relevant method for the identification of disease-causing genes.
Our data identify heterozygous mutations in SETD2 (located at 3p21.31) in two patients with Sotos-like syndrome. Interestingly, involvement of region 3p21 in the development of a Sotos-like syndrome was suggested nearly 15 years ago. An apparently balanced translocation t(3;6)(p21;p21) was found in a 6-year-old boy with mental retardation, postnatal overgrowth and facial dysmorphism. Another report published in 1992 described a non-smoking female with Sotos-like syndrome (including excessive growth during childhood, accelerated osseous maturation, developmental delay, incoordination) who died of small cell lung cancer at the unusually young age of 22. Tumour cells showed a loss of heterozygosity of markers at region 3p2l.
Our data provide a compelling argument for Sotos and Sotos-like syndromes as epigenetic diseases caused by loss-of-function mutations of epigenetic writers (methylase) of the H3K36 histone mark. Recently, mutations in the DNA methyltransferase gene DNMT3A (encoding DNA (cytosine-5)-methyltransferase 3A) have also been shown to cause an overgrowth syndrome with intellectual disability. Interestingly, DNMT3A has been described to be a H3K36 epigenetic mark reader. Emerging technologies to interrogate the epigenome may demonstrate how H3K36 methylation dysregulation contributes to overgrowth phenotypes. Post-translational modification of histones by methylation is an important and widespread type of chromatin modification that is known to influence biological processes in the context of development and cellular responses. Widely described to be associated with active chromatin and continuing transcription, H3K36 methylation has also been implicated in alternative splicing, DNA replication and repair, and DNA methylation. The causality of each of these processes in the SoS phenotype remains to be explored. Further functional and mutational analyses will be of interest to extend and illuminate these observations.
The phenotypic similarities between the two syndromes caused by NSD1 and SETD2 alterations may be explained by the common H3K36 writer properties of these two proteins. Several factors probably contribute to how mutations in SETD2 or NSD1 cause different symptoms. In particular, NSD1 has been described to catalyse H3K36 dimethylation, whereas SETD2 is non-redundantly responsible for H3K36 trimethylation. However, the specific phenotype caused by SETD2 alterations remains to be further characterised in larger cohorts in order to document a well-defined nosologic entity.
Defects in the genes that maintain the levels of H3K36 methylation have also been identified at the somatic level in several cancer types. Each NSD family member behaves as an oncogene in multiple cancers, and translocations in NSD1 can lead to the development of acute leukaemia. Inactivation of SETD2 was found to be a common event in clear cell renal cell carcinoma with loss or decrease of H3K36me3 mark.SETD2 mutations were also described in high-grade gliomas and synovial sarcomas. Moreover, downregulation of SETD2 at transcriptional and protein levels was observed in breast cancer. A somatic variant p.Leu1815Phe in SETD2 has recently been described in lung adenocarcinoma and affects the same codon than the constitutional variant p.Leu1815Trp found in probant 2 in the present study. Data from long-term follow-up of individuals with Sotos syndrome (including SETD2 mutated patients) will precise the potential neoplastic complications of this rare disorder. The accumulating data on epigenetic abnormalities in cancer have led to the emerging realisation that many of the mediators of acetyl and methyl histone are susceptible to inhibition by small molecules. The hope is that these advances in oncology could benefit to a rare disease like SoS.
Discussion
We report here heterozygous loss-of-function mutations in the SETD2 gene in two patients with a consistent overgrowth phenotype characterised by postnatal overgrowth (+2.5 SD), macrocephaly (+4 SD) and obesity (>+4 SD) in the course of the disease, minor facial features (long face and pointed chin) and advanced carpal ossification. Both presented with speech delay, slowness and low sociability, leading to difficulties in their professional integration.
SETD2 was discovered in 1998 and was shown to function as a histone methyltransferase via the conserved SET domain. The SET domain was first recognised as a conserved feature in chromatin-associated proteins and a number of SET domain-containing proteins have since been characterised as histone methyltransferases. SETD2 is non-redundantly responsible for all trimethylation of lysine 36 of histone H3. Homozygous disruption of Setd2 in mice resulted in embryonic lethality with severe defects in blood vessel development. One of the two SETD2 mutations introduces a premature stop codon in SETD2 mRNA (proband 1, c.820C>T, p.Gln274*), and in the other case (proband 2), the mutation could result in a loss-of-function allele (c.5444T>G, p.Leu1815Trp). The affected Leu1815 codon is evolutionarily conserved according to phyloP (score=0.998). A positive phyloP score is interpreted as a signature of evolutionary conservation, which is consistent with functional importance. The in silico analysis of the p.Leu1815Trp variant using PolyPhen-2 classified it as probably damaging (score=0.98), and the Sorting Intolerant From Tolerant (SIFT) software classified it as damaging (score=0).
Our results illustrate the power of targeted NGS to identify rare disease-causing variants. Remaining mutation-negative patients (14 cases) could present mosaic mutations undetectable in blood. Unfortunately, no additional tissues other than blood could be collected from the affected cases in our study. The remaining 14 negative index cases should now be analysed with a whole exome NGS approach to search for causal mutations in other loci in the genome. This exome sequencing approach has proven to be a useful and relevant method for the identification of disease-causing genes.
Our data identify heterozygous mutations in SETD2 (located at 3p21.31) in two patients with Sotos-like syndrome. Interestingly, involvement of region 3p21 in the development of a Sotos-like syndrome was suggested nearly 15 years ago. An apparently balanced translocation t(3;6)(p21;p21) was found in a 6-year-old boy with mental retardation, postnatal overgrowth and facial dysmorphism. Another report published in 1992 described a non-smoking female with Sotos-like syndrome (including excessive growth during childhood, accelerated osseous maturation, developmental delay, incoordination) who died of small cell lung cancer at the unusually young age of 22. Tumour cells showed a loss of heterozygosity of markers at region 3p2l.
Our data provide a compelling argument for Sotos and Sotos-like syndromes as epigenetic diseases caused by loss-of-function mutations of epigenetic writers (methylase) of the H3K36 histone mark. Recently, mutations in the DNA methyltransferase gene DNMT3A (encoding DNA (cytosine-5)-methyltransferase 3A) have also been shown to cause an overgrowth syndrome with intellectual disability. Interestingly, DNMT3A has been described to be a H3K36 epigenetic mark reader. Emerging technologies to interrogate the epigenome may demonstrate how H3K36 methylation dysregulation contributes to overgrowth phenotypes. Post-translational modification of histones by methylation is an important and widespread type of chromatin modification that is known to influence biological processes in the context of development and cellular responses. Widely described to be associated with active chromatin and continuing transcription, H3K36 methylation has also been implicated in alternative splicing, DNA replication and repair, and DNA methylation. The causality of each of these processes in the SoS phenotype remains to be explored. Further functional and mutational analyses will be of interest to extend and illuminate these observations.
The phenotypic similarities between the two syndromes caused by NSD1 and SETD2 alterations may be explained by the common H3K36 writer properties of these two proteins. Several factors probably contribute to how mutations in SETD2 or NSD1 cause different symptoms. In particular, NSD1 has been described to catalyse H3K36 dimethylation, whereas SETD2 is non-redundantly responsible for H3K36 trimethylation. However, the specific phenotype caused by SETD2 alterations remains to be further characterised in larger cohorts in order to document a well-defined nosologic entity.
Defects in the genes that maintain the levels of H3K36 methylation have also been identified at the somatic level in several cancer types. Each NSD family member behaves as an oncogene in multiple cancers, and translocations in NSD1 can lead to the development of acute leukaemia. Inactivation of SETD2 was found to be a common event in clear cell renal cell carcinoma with loss or decrease of H3K36me3 mark.SETD2 mutations were also described in high-grade gliomas and synovial sarcomas. Moreover, downregulation of SETD2 at transcriptional and protein levels was observed in breast cancer. A somatic variant p.Leu1815Phe in SETD2 has recently been described in lung adenocarcinoma and affects the same codon than the constitutional variant p.Leu1815Trp found in probant 2 in the present study. Data from long-term follow-up of individuals with Sotos syndrome (including SETD2 mutated patients) will precise the potential neoplastic complications of this rare disorder. The accumulating data on epigenetic abnormalities in cancer have led to the emerging realisation that many of the mediators of acetyl and methyl histone are susceptible to inhibition by small molecules. The hope is that these advances in oncology could benefit to a rare disease like SoS.
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