Hypomethylation of the H19 gene causes not only Silver-Russell syndrome (SRS) but also isolated asymmetry or an SRS-like phenotype

Broad clinical spectrum in Silver-Russell syndrome and consequences for genetic testing in growth retardation

OBJECTIVE

Silver-Russell syndrome is a heterogenous disorder characterized by severe intrauterine growth restriction, lack of catch-up after birth, and specific dysmorphisms. In approximately 10% of patients, maternal uniparental disomy of chromosome 7 is detectable, but hypomethylation of the imprinting in 11p15 is the major epigenetic disturbance in Silver-Russell syndrome. The use of strict clinical criteria, indeed, results in relatively high detection rates for the 11p15 epimutation, but we feel that the application of a strict clinical scoring system is not useful in clinical workaday life because of the broad clinical spectrum in 11p15 epimutation and maternal uniparental disomy of chromosome 7 carriers.

PATIENTS AND METHODS

We report on our experience of molecular testing in 188 patients referred for routine diagnostics of Silver-Russell syndrome and in a group of 20 patients with isolated intrauterine growth restriction/postnatal growth retardation.

RESULTS

The molecular genetic results in both groups of data showed that 11p15 epimutation and maternal uniparental disomy of chromosome 7 carriers did not always show the unambiguous Silver-Russell syndrome phenotype.

CONCLUSIONS

In addition to patients with the classical Silver-Russell syndrome phenotype fulfilling the Silver-Russell syndrome-specific scores, genetic testing for the 11p15 epimutation and/or maternal uniparental disomy of chromosome 7 should also be considered in case of "Silver-Russell syndrome-like" phenotypes, for example, mild intrauterine growth restriction and postnatal growth retardation associated with a prominent forehead and triangular face or asymmetry as the only clinical signs. In particular, the lack of intrauterine growth restriction in patients with a Silver-Russell syndrome-like phenotype should not automatically result in exclusion from molecular testing.

Methylation defects of imprinted genes in human testicular spermatozoa

OBJECTIVE

To study the methylation imprinting marks of two oppositely imprinted genes, H19 and MEST/PEG1, in human testicular spermatozoa from azoospermic patients with different etiologies. Testicular spermatozoa are often used in intracytoplasmic sperm injection for treatment of male factor infertility, but the imprinting status of these cells is currently unknown.

DESIGN

Experimental prospective study.

SETTING

University research laboratory and private in vitro fertilization (IVF) clinic.

PATIENT(S)

A total of 24 men, five with anejaculation, five with secondary obstructive azoospermia, five with primary obstructive azoospermia, and nine with secretory azoospermia due to hypospermatogenesis.

INTERVENTION(S)

Spermatozoa were isolated by micromanipulation from testicular biopsies.

MAIN OUTCOME MEASURE(S)

DNA methylation patterns were analyzed using bisulfite genomic sequencing with cloning analysis.

RESULT(S)

We found H19 complete methylation was statistically significantly reduced in secretory azoospermic patients with hypospermatogenesis, with one patient presenting complete unmethylation. Hypomethylation also affected the CTCF-binding site 6, involved in regulation of IGF2 expression. Regarding the MEST gene, all patients presented complete unmethylation although this was statistically significantly reduced in the anejaculation group.

CONCLUSION(S)

Testicular spermatozoa from men with abnormal spermatogenesis carry methylation defects in the H19 imprinted gene which also affect the CTCF-binding site, further supporting an association between the occurrence of imprinting errors and disruptive spermatogenesis.

Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer

Background

Epigenetic alterations have been implicated in the pathogenesis of solid tumors, however, proto-oncogenes activated by promoter demethylation have been sporadically reported. We used an integrative method to analyze expression in primary head and neck squamous cell carcinoma (HNSCC) and pharmacologically demethylated cell lines to identify aberrantly demethylated and expressed candidate proto-oncogenes and cancer testes antigens in HNSCC.

Methodology/Principal Findings

We noted coordinated promoter demethylation and simultaneous transcriptional upregulation of proto-oncogene candidates with promoter homology, and phylogenetic footprinting of these promoters demonstrated potential recognition sites for the transcription factor BORIS. Aberrant BORIS expression correlated with upregulation of candidate proto-oncogenes in multiple human malignancies including primary non-small cell lung cancers and HNSCC, induced coordinated proto-oncogene specific promoter demethylation and expression in non-tumorigenic cells, and transformed NIH3T3 cells.

Conclusions/Significance

Coordinated, epigenetic unmasking of multiple genes with growth promoting activity occurs in aerodigestive cancers, and BORIS is implicated in the coordinated promoter demethylation and reactivation of epigenetically silenced genes in human cancers.

Exposure of mouse embryos to ethanol during preimplantation development: effect on DNA methylation in the h19 imprinting control region

In the present study, it was hypothesized that disruption of imprinting control in the H19/Igf2 domain may be a mechanism of ethanol-induced growth retardation-a key clinical feature of the fetal alcohol spectrum disorders (FASD). To test this prediction, genomic bisulphite sequencing was carried out on 473 bp of the H19 imprinting control region in DNA obtained from midgestation F(1) hybrid mouse embryos (C57BL/6 x Mus musculus castaneus) exposed to ethanol during preimplantation development. Although ethanol-exposed placentae and embryos were severely growth retarded in comparison with saline-treated controls, DNA methylation at paternal and maternal alleles was unaffected in embryos. However, paternal alleles were significantly less methylated in ethanol-treated placentae in comparison with saline-treated controls. Partial correlations suggested that the relationship between ethanol and placental weight partly depended on DNA methylation at a CCCTC-binding factor site on the paternal allele in placentae, suggesting a novel mechanism of ethanol-induced growth retardation. In contrast, partial correlations suggested that embryo growth retardation was independent of placental growth retardation. Relaxation of allele-specific DNA methylation in control placentae in comparison with control embryos was also observed, consistent with a model of imprinting in which 1) regulation of allele-specific DNA methylation in the placenta depends on a stochastic interplay between silencer and enhancer chromatin assembly factors and 2) imprinting control mechanisms in the embryo are more robust to environmental perturbations.

Clinically distinct epigenetic subgroups in Silver-Russell syndrome: the degree of H19 hypomethylation associates with phenotype severity and genital and skeletal anomalies

CONTEXT

The H19 imprinting control region (ICR), located on chromosome 11p15.5, has been reported hypomethylated in 20-65% of Silver-Russell syndrome (SRS) patients.

OBJECTIVE

We investigated the methylation status of 11p15.5 ICRs in SRS patients and children born small for gestational age (SGA) to clarify the relationship between phenotype and H19 methylation status.

METHODS

We performed methylation screens of the H19 and KCNQ1OT1 ICRs in 42 SRS patients, including seven maternal uniparental disomy of chromosome 7 patients, and 90 SGA children without SRS. Clinical data were evaluated from patient records, and seven hypomethylated patients were clinically and radiologically reexamined.

RESULTS

H19 ICR hypomethylation was found in 62% of SRS patients but in no SGA children. A clinical severity score demonstrated strong correlation between hypomethylation level and phenotype severity. Hypomethylation related to a more severe SRS phenotype, in which especially asymmetry and micrognathia were significantly more common. Extremely hypomethylated patients had abnormally high lumbar vertebrae, lumbar hypomobility, elbow subluxations, and distinct hand and foot anomalies. They also presented with congenital aplasia of the uterus and upper vagina, equivalent to the Mayer-Rokitansky-Küster-Hauser syndrome in females, and cryptorchidism and testicular agenesis in males.

CONCLUSIONS

We found a dose-response relationship between the degree of H19 hypomethylation and phenotype severity in SRS. We report for the first time the association of specific anomalies of the spine, elbows, hands and feet, and genital defects in SRS with severe H19 hypomethylation. Classical SRS features were found in H19 hypomethylation and milder symptoms in maternal uniparental disomy of chromosome 7, thus distinguishing two separate clinical and etiological subgroups.

Paternal deletion of Meg1/Grb10 DMR causes maternalization of the Meg1/Grb10 cluster in mouse proximal Chromosome 11 leading to severe pre- and postnatal growth retardation

Mice with maternal duplication of proximal Chromosome 11 (MatDp(prox11)), where Meg1/Grb10 is located, exhibit pre- and postnatal growth retardation. To elucidate the responsible imprinted gene for the growth abnormality, we examined the precise structure and regulatory mechanism of this imprinted region and generated novel model mice mimicking the pattern of imprinted gene expression observed in the MatDp(prox11) by deleting differentially methylated region of Meg1/Grb10 (Meg1-DMR). It was found that Cobl and Ddc, the neighboring genes of Meg1/Grb10, also comprise the imprinted region. We also found that the mouse-specific repeat sequence consisting of several CTCF-binding motifs in the Meg1-DMR functions as a silencer, suggesting that the Meg1/Grb10 imprinted region adopted a different regulatory mechanism from the H19/Igf2 region. Paternal deletion of the Meg1-DMR (+/DeltaDMR) caused both upregulation of the maternally expressed Meg1/Grb10 Type I in the whole body and Cobl in the yolk sac and loss of paternally expressed Meg1/Grb10 Type II and Ddc in the neonatal brain and heart, respectively, demonstrating maternalization of the entire Meg1/Grb10 imprinted region. We confirmed that the +/DeltaDMR mice exhibited the same growth abnormalities as the MatDp(prox11) mice. Fetal and neonatal growth was very sensitive to the expression level of Meg1/Grb10 Type I, indicating that the 2-fold increment of the Meg1/Grb10 Type I is one of the major causes of the growth retardation observed in the MatDp(prox11) and +/DeltaDMR mice. This suggests that the corresponding human GRB10 Type I plays an important role in the etiology of Silver-Russell syndrome caused by partial trisomy of 7p11-p13.

Determination of KCNQ1OT1 and H19 methylation levels in BWS and SRS patients using methylation-sensitive high-resolution melting analysis

Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are caused by imprinting defects on chromosome 11p15.5. Standard diagnostic tests for these syndromes include methylation analysis of the differential methylated regions of the H19 and KCNQ1OT1 genes. Traditionally this has been conducted by Southern blot analysis. PCR-based methods greatly improve the turn around time of the test and require less DNA. One of the newly emerging techniques for SNP genotyping and mutation scanning, high-resolution melting (HRM) analysis, has been shown to be also applicable for methylation analysis. We tested methylation-sensitive HRM analysis as a method for the detection of methylation defects in a group of 16 BWS and SRS patients with known methylation status (determined previously by Southern blotting), as well as 45 normal controls. HRM analysis was able to detect all methylation aberrations in the patients and appeared to be more sensitive than Southern blotting. Variation in normal controls is minimal and the presence of SNPs in the amplified fragment does not influence the outcome of the test. We conclude that methylation-sensitive HRM analysis is a robust, fast, sensitive and cost effective method for methylation analysis in BWS and SRS.

Are H19 variants associated with Silver-Russell syndrome?

Opposite (epi)mutations affecting the imprinted region 11p15 are associated with Silver-Russell (SRS) and Beckwith-Wiedemann syndrome (BWS). Apart from other disturbances more than 35% of patients with SRS show hypomethylation at the imprinting control region 1 (ICR1) in 11p15. ICR1 is paternally methylated and regulates the expression of the paternally expressed growth factor IGF2 and the maternally expressed gene H19. The exact function of the non-coding RNA H19 is still unknown. However, the finding that this gene is highly conserved in mammals indicates profound functional relevance. Due to the supposed function of H19 in the regulation of the imprinted region 11p15 we searched for mutations in the transcribed sequence and the CTCF binding sites of H19 in 44 patients with SRS. In two cases different 3 base-pair (bp) deletions in exon 1 could be identified. A third patient carried a 39 bp duplication affecting exon 2 and intron 2. These three variants were not detected in 100 controls and 42 patients with isolated growth retardation. One of the patients carrying a mutation also showed hypomethylation at the ICR1 in 11p15. Splicing studies in HEK cells transfected with constructs carrying the three different variants revealed a deviation from the normal H19 splicing pattern in two of these individuals. However, analysis of lymphocytes of one of these two patients did not verify an altered expression pattern of H19. Nevertheless, our results indicate a relevant role of H19 in the aetiology of SRS: functional effects of these variants on chromatin restructuring of the ICR1, or altered function of H19 as a posttranslational modifying factor (microRNA/antisense RNA) are conceivable.

Genomic imprinting mechanisms in mammals

Genomic imprinting is a form of epigenetic gene regulation that results in expression from a single allele in a parent-of-origin-dependent manner. This form of monoallelic expression affects a small but growing number of genes and is essential to normal mammalian development. Despite extensive studies and some major breakthroughs regarding this intriguing phenomenon, we have not yet fully characterized the underlying molecular mechanisms of genomic imprinting. This is in part due to the complexity of the system in that the epigenetic markings required for proper imprinting must be established in the germline, maintained throughout development, and then erased before being re-established in the next generation's germline. Furthermore, imprinted gene expression is often tissue or stage-specific. It has also become clear that while imprinted loci across the genome seem to rely consistently on epigenetic markings of DNA methylation and/or histone modifications to discern parental alleles, the regulatory activities underlying these markings vary among loci. Here, we discuss different modes of imprinting regulation in mammals and how perturbations of these systems result in human disease. We focus on the mechanism of genomic imprinting mediated by insulators as is present at the H19/Igf2 locus, and by non-coding RNA present at the Igf2r and Kcnq1 loci. In addition to imprinting mechanisms at autosomal loci, what is known about imprinted X-chromosome inactivation and how it compares to autosomal imprinting is also discussed. Overall, this review summarizes many years of imprinting research, while pointing out exciting new discoveries that further elucidate the mechanism of genomic imprinting, and speculating on areas that require further investigation.

Monozygotic female twins discordant for Silver-Russell syndrome and hypomethylation of the H19-DMR

Silver-Russell syndrome (SRS) is characterized by growth failure and dysmorphic features, and is frequently caused by hypomethylation of the paternally derived H19-DMR (epimutation). We observed 5 8/12-year-old female twins discordant for SRS. One twin exhibited SRS-compatible features, such as pre- and postnatal growth failure, relative macrocephaly, triangular face, left hemihypotrophy, and bilateral fifth finger clinodactyly, whereas the other twin showed apparently normal phenotype. Microsatellite analysis for 26 loci on multiple chromosomes showed monozygosity. Methylation analysis for the H19-DMR indicated epimutation in roughly half of cells in the affected twin and normal patterns in the unaffected twin and the parents. X-inactivation analysis revealed random X-inactivation with a nearly identical pattern between the twins. The discordant methylation pattern of the H19-DMR may primarily be due to a failure to maintain the DNA methyltransferase-1-dependent methylation imprint around the pre-implantation S phase, because such failure would result in the production of two different cell clones, one with normally methylated DMR and the other with demethylated DMR, leading to the separation of cells with different characters and resultant twinning.

A review of known imprinting syndromes and their association with assisted reproduction technologies

An association between assisted reproduction technologies (ART) and abnormal genomic imprinting in humans has been recognized for several years; however, the magnitude of this risk and the spectrum of imprinting syndromes to which the risk applies remains unknown. Nine human imprinting syndromes have been identified but current evidence links ART with only three: Beckwith-Wiedemann syndrome, Angelman syndrome and the newly described maternal hypomethylation syndrome. There is currently a lack of evidence linking ART with the remaining six imprinting syndromes: Prader-Willi syndrome, Russell-Silver syndrome, maternal and paternal uniparental disomy of chromosome 14, pseudohypoparathyroidism type 1b and transient neonatal diabetes. Evidence from clinical reports suggests that the association between imprinting syndromes and ART may be restricted to syndromes where the imprinting change takes the form of hypomethylation on the maternal allele. In contrast, studies of gametes and early embryos suggest that ART can be associated with hypermethylation as well as hypomethylation, with imprinting changes occurring on paternal as well as maternal alleles. The health effects of ART-associated imprinting changes may also extend beyond the nine recognized imprinting syndromes.

PCR-based analysis of differentially methylated regions of GNAS enables convenient diagnostic testing of pseudohypoparathyroidism type Ib

BACKGROUND

Pseudohypoparathyroidism type Ib (PHPIb) is characterized by parathyroid hormone (PTH) resistance, which can lead to hypocalcemia, hyperphosphatemia, and increased serum PTH. The disorder is caused by mutations in regulatory regions of the GNAS gene (GNAS complex locus) that lead to interferences in the methylation status of alternative GNAS promoters, such as exon A/B, NESP55, and XL alpha-s. PHPIb comprises disorders that show distinctive changes in methylation status but share the same clinical phenotype: (a) loss of methylation only at exon A/B of the GNAS gene and involving no other obvious epigenetic abnormalities [e.g., those caused by heterozygous microdeletions in the STX16 (syntaxin 16) region and found in many patients with autosomal dominant (AD) PHPIb]; (b) methylation abnormalities at several differentially methylated regions (DMRs), which are observed in most patients with sporadic PHPIb and some families with AD PHPIb.

METHODS

To permit early and reliable diagnosis of suspected PHPIb, we designed methylation-sensitive restriction enzyme-based and bisulfite deamination-based PCR tests for exon A/B and NESP55 DMRs.

RESULTS

Both PCR strategies permit proper methylation testing of GNAS and NESP55 DMRs and elucidate different disease subtypes. We have identified a novel microsatellite repeat polymorphism within GNAS exon A/B, and pedigree analyses have shown its presence to be conclusive evidence for familial disease.

CONCLUSIONS

We provide a simple diagnostic test for PHPIb, an imprinting disorder caused by different molecular changes within the GNAS complex locus. PHPIb, a complex and diagnostically challenging clinical phenotype, can be treated successfully by taking steps before the manifestation of symptoms to avoid clinical complications in affected patients or asymptomatic members of affected families who show positive results in genetic tests.

Maternal uniparental disomy 7 and Silver-Russell syndrome - clinical update and comparison with other subgroups

Maternal uniparental disomy (UPD) 7 is found in approximately 5% of patients with Silver-Russell syndrome. By a descriptive and comparative clinical analysis of all published cases (more than 60 to date) their phenotype is updated and compared with the clinical findings in patients with Sliver-Russell syndrome (SRS) of either unexplained etiology or epimutations of the imprinting center region 1 (ICR1) on 11p15. The higher frequency of relative macrocephaly and high forehead/frontal bossing makes the face of patients with epimutations of the ICR1 on 11p15 more distinctive than the face of cases with SRS of unexplained etiology or maternal UPD 7. Because of the distinct micrognathia in the latter, their triangular facial gestalt is more pronounced than in the other groups. However, solely by clinical findings patients with maternal UPD 7 cannot be discriminated unambiguously from patients with epimutations of the ICR1 on 11p15 or SRS of unexplained etiology. Therefore, both loss of methylation of the ICR1 on 11p15 and maternal UPD 7 should be investigated for if SRS is suspected.

Epigenotype, phenotype, and tumors in patients with isolated hemihyperplasia

OBJECTIVE

To investigate whether epigenotyping of patients with isolated hemihyperplasia (IH) can, analogous to genetic screening of patients with Beckwith-Wiedemann syndrome, be used for the prediction of tumor risk and tumor type of individual patients.

STUDY DESIGN

Methylation analysis of H19 and KCNQ1OT1 of 73 patients. Questionnaires were sent to referring clinicians.

RESULTS

In 75% of the clinically confirmed patients with IH no epigenetic defect was detected. Paternal uniparental disomy was found in 15%, demethylation of KCNQ1OT1 in only 6%, and hypermethylation of H19 in 3% of isolated hemihyperplasia cases. Ten percent of the patients with IH had development of a childhood tumor associated with paternal uniparental disomy (2/8) or no methylation defect (2/30). No genetic defect was detected in 10 of 14 additional patients with cancer with IH. In these latter patients, a methylation defect of H19 was seen 3 times and a paternal uniparental disomy once. The female-to-male ratio was 6:1.

CONCLUSIONS

Aberrant methylation of the 11p15 region is not common in patients with IH and can at present not be used for tumor risk determination.

Epigenetics in Silver-Russell syndrome

Silver-Russell syndrome (SRS) is a clinically heterogeneous syndrome characterized by intra-uterine and postnatal growth retardation with spared cranial growth, dysmorphic features and frequent body asymmetry. Various cytogenetic abnormalities have been described in a small number of SRS or SRS-like cases involving chromosomes 7, 8, 11, 15, 17 and 18. However, until recent data became available involving imprinted genes on chromosome 7 and chromosome 11p15, the molecular cause of the syndrome was unknown in most cases. Genomic imprinting is the best example of transcriptional control of genes by epigenetic modifications. Many imprinted genes play key roles in fetal and placental growth and behaviour. This is illustrated in SRS, which can now be considered as a new imprinting disease model. These new findings in the pathophysiology of SRS allow long-term follow-up studies to be performed based on molecular diagnosis. This could help to define appropriate clinical guidelines regarding growth and feeding difficulties.

The endocrine phenotype in silver-russell syndrome is defined by the underlying epigenetic alteration

CONTEXT

Around 50% of children with Silver-Russell syndrome (SRS) carry a hypomethylation of the imprinting control region 1 at the IGF2/H19 locus on 11p15, the functional significance of which is unknown.

OBJECTIVE

We aimed to compare the genotype in SRS with the endocrine phenotype.

DESIGN

The retrospective study included all SRS children who were treated during the last 18 yr at our hospital and for comparison a cohort of GH treated nonsyndromic short children born small for gestational age (SGA).

PATIENTS

The 61 patients with SRS included were defined by the presence of intrauterine growth retardation, lack of catch-up growth, and at least two of the criteria: typical face, relative macrocephaly, and skeletal asymmetry. Routine karyotype and GH secretion was normal in all children studied. A subgroup of 53 patients was treated with GH.

MATERIALS AND METHODS

Genomic DNA was available from 44 children. Multiplex ligation probe-dependent amplification analysis was performed to detect hypomethylation at the imprinting control region 1 on 11p15. Uniparental disomy of chromosome 7 (UPD7) was analyzed by short tandem repeats typing. Serum levels of GH, IGF-I, and IGF-binding protein (IGFBP)-3 were measured by RIA.

RESULTS

Epimutations at 11p15 were found in 19 of 44, UPD7 in five of 44, and small structural aberrations of the short arm of chromosome 11 in two of 44 children. Of 44 cases, 18 were negative for any genetic defect known (41%). The most severe phenotype was found in children with 11p15-SRS. Children with UPD7-SRS had a significantly higher birth length (P < 0.004) but lost height sd score (SDS) postpartum, whereas children with 11p15-SRS showed no change in height SDS. IGF-I and IGFBP-3 serum levels were inadequately high in 11p15-SRS at -0.02 SDS (1.07, sd) and +1.38 SDS (1.01), compared with the low levels in UPD7-SRS and in the cohort of 58 nonsyndromic SGA children (P < 0.0009). During GH therapy, IGFBP-3 serum levels increased above normal values in 11p15-SRS (P < 10(-4)), whereas IGF-I increase was moderate. There was a trend toward more height gain in children with UPD7 than in those with 11p15 epimutation under GH therapy (+2.5 vs. +1.9 height SDS after 3 yr) (P = 0.08).

CONCLUSIONS

Children with SRS and an 11p15 epimutation have IGFBP-3 excess and show endocrine characteristics suggesting IGF-I insensitivity, whereas children with SRS and UPD7 were not different from nonsyndromic short children born SGA. This phenotype-genotype correlation implicates divergent endocrine mechanisms of growth failure in SRS.

Distinct methylation changes at the IGF2-H19 locus in congenital growth disorders and cancer

Background

Differentially methylated regions (DMRs) are associated with many imprinted genes. In mice methylation at a DMR upstream of the H19 gene known as the Imprint Control region (IC1) is acquired in the male germline and influences the methylation status of DMRs 100 kb away in the adjacent Insulin-like growth factor 2 (Igf2) gene through long-range interactions. In humans, germline-derived or post-zygotically acquired imprinting defects at IC1 are associated with aberrant activation or repression of IGF2, resulting in the congenital growth disorders Beckwith-Wiedemann (BWS) and Silver-Russell (SRS) syndromes, respectively. In Wilms tumour and colorectal cancer, biallelic expression of IGF2 has been observed in association with loss of methylation at a DMR in IGF2. This DMR, known as DMR0, has been shown to be methylated on the silent maternal IGF2 allele presumably with a role in repression. The effect of IGF2 DMR0 methylation changes in the aetiology of BWS or SRS is unknown.

Methodology/Principal Findings

We analysed the methylation status of the DMR0 in BWS, SRS and Wilms tumour patients by conventional bisulphite sequencing and pyrosequencing. We show here that, contrary to previous reports, the IGF2 DMR0 is actually methylated on the active paternal allele in peripheral blood and kidney. This is similar to the IC1 methylation status and is inconsistent with the proposed silencing function of the maternal IGF2 allele. Beckwith-Wiedemann and Silver-Russell patients with IC1 methylation defects have similar methylation defects at the IGF2 DMR0, consistent with IC1 regulating methylation at IGF2 in cis. In Wilms tumour, however, methylation profiles of IC1 and IGF2 DMR0 are indicative of methylation changes occurring on both parental alleles rather than in cis.

Conclusions/Significance

These results support a model in which DMR0 and IC1 have opposite susceptibilities to global hyper and hypomethylation during tumorigenesis independent of the parent of origin imprint. In contrast, during embryogenesis DMR0 is methylated or demethylated according to the germline methylation imprint at the IC1, indicating different mechanisms of imprinting loss in neoplastic and non-neoplastic cells.

Growth retardation versus overgrowth: Silver-Russell syndrome is genetically opposite to Beckwith-Wiedemann syndrome

Human growth is a complex process that requires the appropriate interaction of many players. Central members in the growth pathways are regulated epigenetically and thereby reflect the profound significance of imprinting for correct mammalian ontogenesis. In this review, we show that the growth retardation disorder Silver-Russell syndrome (SRS) is a suitable model to decipher the role of imprinting in growth. As we will show, SRS should not only be regarded as the genetically (and clinically) opposite disease to Beckwith-Wiedemann syndrome, but it also represents the first human disorder with imprinting disturbances that affect two different chromosomes (i.e. chromosomes 7 and 11). Thus, a functional interaction between factors encoded by chromosomes 7 and 11 is likely.

MS-MLPA is a specific and sensitive technique for detecting all chromosome 11p15.5 imprinting defects of BWS and SRS in a single-tube experiment

Human chromosome 11p15.5 harbours a large cluster of imprinted genes. Different epigenetic defects at this locus have been associated with both Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). Multiple techniques (Southern blotting, COBRA and microsatellite analysis) have been used so far to detect various DNA methylation abnormalities, uniparental disomies and copy number variations, which are characteristics of these two diseases. We have now evaluated a methylation-specific multiplex-ligation-dependent probe amplification assay (MS-MLPA) for the molecular diagnosis of BWS and SRS. Seventy-three samples derived from BWS- and SRS-affected individuals and 20 controls were analysed by conventional tests and MS-MLPA in blind. All cases that were found positive with conventional methods were also identified by MS-MLPA. These included cases with paternal UPD11, hyper- or hypo-methylation at the Imprinting Centre 1 or Imprinting Centre 2 and rare 11p15.5 duplications. In summary, this MS-MLPA assay can detect both copy number variations and methylation defects of the 11p15.5 critical region within one single experiment and represents an easy, low cost and reliable system for the molecular diagnostics of BWS and SRS.

IGF2/H19 hypomethylation in Silver-Russell syndrome and isolated hemihypoplasia

Silver-Russell syndrome (SRS) is a clinically and genetically heterogeneous syndrome characterized by severe pre and postnatal growth retardation, body asymmetry and a typical facial phenotype with a triangular face and relative macrocephaly. In 30% of patients, the differentially methylated IGF2/H19 imprinting center region (ICR1) on chromosome 11p15 was found to be hypomethylated, as determined by Southern blot analysis of an HpaII restriction site close to the third CTCF-binding site (CTS3) within ICR1. Using bisulfite treatment and a real-time PCR-based methylation assay (QAMA), we analyzed the third and sixth CTCF-binding sites (CTS3, CTS6) in 5 patients with CTS3 hypomethylation, in 14 patients who were suspected to have SRS but were normal by Southern blot analysis, and in 1 patient with body asymmetry without any other features of SRS or Beckwith-Wiedemann syndrome (BWS). In all 5 patients with CTS3 hypomethylation, in 5 of 14 patients who were judged to be normal at CTS3 by Southern blot analysis and in the patient with isolated body asymmetry, we found CTS3 and CTS6 hypomethylation by QAMA. Using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), we obtained similar results at four additional ICR1 sites in the CTS6 region. These results show that ICR1 hypomethylation occurs more often in SRS patients than as previously thought as well as in isolated hemihypoplasia. Furthermore, we show that methylation analysis by QAMA and MLPA is more sensitive in detecting ICR1 hypomethylation than Southern blot analysis of CTS3.

Abnormal methylation of imprinted genes in human sperm is associated with oligozoospermia

Genomic imprinting marks in the male germ line are already established in the adult germinal stem cell population. We studied the methylation patterns of H19 and MEST imprinted genes in sperm of control and oligozoospermic patients, by bisulphite genomic sequencing. We here report that 7 out of 15 (46.7%) patients with a sperm count below 10 x 10(6)/ml display defective methylation of H19 and/or MEST imprinted genes. In these cases, hypomethylation was observed in 5.54% (1.2-8.3%) and complete unmethylation in 2.95% (0-5.9%) of H19 clones. Similarly, for the CTCF-binding site 6, hypomethylation occurred in 4.8% (1.2-8.9%) and complete unmethylation in 3.7% (0-6.9%) of the clones. Conversely, hypermethylation occurred in 8.3% (3.8-12.2%) and complete methylation in 6.1% (3.8-7.6%) of MEST clones. Of the seven patients presenting imprinting errors, two had both H19 hypomethylation and MEST hypermethylation, whereas five displayed only one imprinted gene affected. The frequency of patients with MEST hypermethylation was highest in the severe oligozoospermia group (2/5 patients), whereas H19 hypomethylation was more frequent in the moderate oligozoospermia (2/5 patients). In all cases, global sperm genome methylation analysis (LINE1 transposon) suggested that defects were specific for imprinted genes. These findings could contribute to an explanation of the cause of Silver-Russell syndrome in children born with H19 hypomethylation after assisted reproductive technologies (ART). Additionally, unmethylation of the CTCF-binding site could lead to inactivation of the paternal IGF2 gene, and be linked to decreased embryo quality and birth weight, often associated with ART.

Genomic imprinting of Dopa decarboxylase in heart and reciprocal allelic expression with neighboring Grb10

By combining a tissue-specific microarray screen with mouse uniparental duplications, we have identified a novel imprinted gene, Dopa decarboxylase (Ddc), on chromosome 11. Ddc_exon1a is a 2-kb transcript variant that initiates from an alternative first exon in intron 1 of the canonical Ddc transcript and is paternally expressed in trabecular cardiomyocytes of the embryonic and neonatal heart. Ddc displays tight conserved linkage with the maternally expressed and methylated Grb10 gene, suggesting that these reciprocally imprinted genes may be coordinately regulated. In Dnmt3L mutant embryos that lack maternal germ line methylation imprints, we show that Ddc is overexpressed and Grb10 is silenced. Their imprinting is therefore dependent on maternal germ line methylation, but the mechanism at Ddc does not appear to involve differential methylation of the Ddc_exon1a promoter region and may instead be provided by the oocyte mark at Grb10. Our analysis of Ddc redefines the imprinted Grb10 domain on mouse proximal chromosome 11 and identifies Ddc_exon1a as the first example of a heart-specific imprinted gene.

Use of multiplex ligation-dependent probe amplification increases the detection rate for 11p15 epigenetic alterations in Silver-Russell syndrome

Silver-Russell syndrome (SRS) describes a malformation syndrome with severe intrauterine and postnatal growth retardation. Currently, two major (epi)mutations have been described: while approximately 10% of patients carry a maternal uniparental disomy of chromosome 7 (UPD7), 35-60% show a hypomethylation at the H19 differentially methylated regions (DMRs) in 11p15. Until recently, a Southern-blot based test was routinely used to identify epimutation carriers. Nevertheless, this test was time consuming and hampered by the huge amount of genomic DNA needed. With the methylation-specific multiplex ligation-dependent probe amplification assay (MLPA) for SRS, a PCR-based test is now available, allowing the analysis also of small amounts of DNA. Probes in this assay hybridize to the H19 DMRs but do not cover the genomic target of the Southern-blot probe. We now screened 72 patients with SRS by MLPA. Hypomethylation of the H19 DMRs was confirmed in all patients analyzed by Southern blot. In addition, we identified six individuals with hypomethylation of the H19 DMR who had previously normal blot results. This discrepancy can be explained by the observed generally lower degree of demethylation in this group, possibly not detectable by the less sensitive Southern-blot method but also with a varying degree of methylation at different DMRs in the same individual. Apart from hypomethylation in the H19 DMR, we observed a slight demethylation for one of the IGF2 probes. The total detection rate of 11p15 hypomethylation is now increased to >38%. Considering maternal UPD7 and chromosomal aberrations, (epi)genetic alterations now account for more than 50% of SRS patients. In summary, MLPA represents an easy, low cost and reliable system in the molecular diagnostics of SRS.

Association between paternally inherited haplotypes upstream of the insulin gene and umbilical cord IGF-II levels

The insulin (INS) and IGF 2 (IGF2) genes are in close proximity to each other and undergo maternal imprinting during fetal growth. We investigated the association between maternal and umbilical cord IGF 2 protein (IGF-II) levels and single nucleotide polymorphisms (SNPs) in the INS and IGF2 genes in 207 healthy African-American mother-newborn pairs. No association was found between maternal IGF-II levels and polymorphism in the INS-IGF2 locus. A significant association was found between newborn IGF-II levels and two SNPs (rs3842738 and rs689) at the 5' end of the INS-IGF2 locus. Analyses of haplotypes inferred from these two SNPs demonstrate a significant relationship between paternally transmitted haplotypes and newborn IGF-II levels, but no association with maternally transmitted haplotypes.

Maternally inherited duplication of chromosome 7, dup(7)(p11.2p12), associated with mild cognitive deficit without features of Silver-Russell syndrome

We report on a familial duplication in the short arm of chromosome 7, dup(7)(p11.2p12), present in three generations. The duplication was identified by GTG-banding and fluorescence in situ hybridization (FISH) with a whole chromosome 7 DNA painting probe that verified that the duplicated material originated from chromosome 7. The multicolor banding (mBAND) was used to refine the breakpoint assignment. The duplication identified in the proband was also present in her son and mother. All three carriers have mild cognitive deficiencies. Interstitial duplications of the short arm of chromosome 7, although relatively uncommon, have been described in association with a variety of clinical features, including mental retardation of varying severity. Duplication of the p11.2p13 region on chromosome 7 was reported in association with Silver-Russell syndrome (SRS), and an overlapping dup(7)(p11.2p14.1)dn was described in an individual with autistic disorder. Furthermore, a potentially overlapping maternally transmitted inverted duplication, dup(7)(p13p12.2), was reported in patients with cognitive delay. These observations and the phenotype of our duplication carriers suggest that partial trisomy of the proximal 7p region causes cognitive deficiency. The maternal origin of the duplication is of special interest in light of genomic imprinting and implication of the 7p11-p13 region in the SRS etiology. Locus-specific FISH targeting a growth factor receptor binding protein 10 (GRB10), the strong candidate for SRS residing at 7p12.2, showed that it is not duplicated in our patients. Our study helps refine the SRS critical region on 7p and extends our understanding of the clinical manifestations associated with 7p duplications.

11p15 imprinting center region 1 loss of methylation is a common and specific cause of typical Russell-Silver syndrome: clinical scoring system and epigenetic-phenotypic correlations

CONTEXT

Russell-Silver syndrome (RSS), characterized by intrauterine and postnatal growth retardation, dysmorphic features, and frequent body asymmetry, spares cranial growth. Maternal uniparental disomy for chromosome 7 (mUPD7) is found in 5-10% of cases. We identified loss of methylation (LOM) of 11p15 Imprinting Center Region 1 (ICR1) domain (including IGF-II) as a mechanism leading to RSS.

OBJECTIVE

The aim was to screen for 11p15 epimutation and mUPD7 in RSS and non-RSS small-for-gestational-age (SGA) patients and identify epigenetic-phenotypic correlations. STUDIED POPULATION AND METHODS: A total of 127 SGA patients were analyzed. Clinical diagnosis of RSS was established when the criterion of being SGA was associated with at least three of five criteria: postnatal growth retardation, relative macrocephaly, prominent forehead, body asymmetry, and feeding difficulties. Serum IGF-II was evaluated for 82 patients.

RESULTS

Of the 127 SGA patients, 58 were diagnosed with RSS; 37 of these (63.8%) displayed partial LOM of the 11p15 ICR1 domain, and three (5.2%) had mUPD7. No molecular abnormalities were found in the non-RSS SGA group (n = 69). Birth weight, birth length, and postnatal body mass index (BMI) were lower in the abnormal 11p15 RSS group (ab-ICR1-RSS) than in the normal 11p15 RSS group [-3.4 vs.-2.6 SD score (SDS), -4.4 vs.-3.4 SDS, and -2.5 vs.-1.6 SDS, respectively; P < 0.05]. Among RSS patients, prominent forehead, relative macrocephaly, body asymmetry, and low BMI were significantly associated with ICR1 LOM. All ab-ICR1-RSS patients had at least four of five criteria of the scoring system. Postnatal IGF-II levels were within normal values.

CONCLUSION

The 11p15 ICR1 epimutation is a major, specific cause of RSS exhibiting failure to thrive. We propose a clinical scoring system (including a BMI < -2 SDS), highly predictive of 11p15 ICR1 LOM, for the diagnosis of RSS.

Growth regulation, imprinted genes, and chromosome 11p15.5

Genomic imprinting refers to parent-of-origin-specific gene expression. Human chromosome band 11p15.5 houses a large cluster of genes that are imprinted. Dysregulation of this gene cluster is associated with the overgrowth and tumor predisposition syndrome, Beckwith-Wiedemann syndrome. Several genes in this imprinted cluster encode proteins involved in growth regulation, e.g. the paternally expressed IGF2 and the maternally expressed cell-cycle regulator cyclin dependent kinase inhibitor, CDKN1C. Disruption of imprinted gene expression can result from genetic or epigenetic alterations. Genetic alterations such as duplication, deletion, translocation, inversion, and mutation in imprinted regions have been shown to cause disease. In addition, epimutations that are extrinsic to the primary DNA sequence have also been shown to cause disease. These epimutations usually involve gain or loss of methylation at regulatory differentially methylated regions. Recently, several human diseases in addition to Beckwith-Wiedemann syndrome have been reported to have molecular alterations at chromosome 11p15.5. These include isolated hemihyperplasia, Russell-Silver syndrome, and transient neonatal diabetes mellitus. These molecular alterations and their phenotypic effects on growth are discussed.

Assessment and disease comparisons of hybrid developmental defects

Rodents of the genus Peromyscus are among the most common North American mammals. Crosses between natural populations of two of these species, P. maniculatus (BW) and P. polionotus (PO), produce parent-of-origin effects on growth and development. BW females mated to PO males produce growth-retarded offspring. In contrast, PO females mated to BW males produce overgrown but dysmorphic conceptuses. Variation in imprinted loci and control of genomic imprinting appear to underlie the hybrid effects. Prior morphological and genetic analyses have focused on placental and post-natal growth. Here, we assess the frequency and scope of embryonic defects. The most frequent outcome of the PO x BW cross is death prior to embryonic day 13. Conceptuses lacking an embryo proper are also observed as in gestational trophoblast disease. Among the common embryonic phenotypes described and tabulated are edema, blood vessel enlargement/hemorrhaging, macroglossia, retention of nucleated erythrocytes, placentomegaly. We investigate expression of loci known to be mis-regulated in human growth/placental disorders and/or mouse knockouts with similar phenotypes. These loci are Igf2, Cdkn1c, Grb10, Gpc3, Phlda2 and Rb1. All exhibited significant differences in either placental or embryonic expression levels at one or more of the three timepoints examined. The data underscore the importance of placental gene expression on embryonic defects. We suggest that the hybrid defects offer a novel system to understand how natural allelic combinations interact to produce disease phenotypes. We propose that such interactions and their resulting epimutations may similarly underlie the phenotypic and causal heterogeneity seen in many human diseases.

Atypical patterns of inheritance

The incomplete prediction of clinical phenotype from genotype in monogenic disorders assumes other complex mechanisms are responsible. Recent examples derived from well-known human diseases will be discussed in this review in the context of the roles of modifier genes, digenic and triallelic inheritance, and the consequence of imprinting and opposite transcripts in known human genetic disorders. Specifically, this review will focus on cystic fibrosis, Huntington's disease, sensory neural deafness due to Connexin gene mutations, Bardet-Biedl syndrome, and the Beckwith-Wiedemann syndrome as there is evidence that complex inheritance is responsible for at least part of the phenotypic variability that is not explainable by the genotype alone. This review is meant to extend and complement the other topics in this issue as the concept of atypical inheritance is explored in more detail.

Silver-Russell syndrome in a girl born after in vitro fertilization: partial hypermethylation at the differentially methylated region of PEG1/MEST

PURPOSE

The prevalence of low birth weight (LBW) is increased in subjects born after assisted reproduction technology (ART), and defective imprinting has frequently been identified in patients with Beckwith-Wiedermann and Angelman syndromes conceived by ART. Thus, we examined methylation pattern in a girl born after ART who had Silver-Russell syndrome (SRS) which can be caused by maternal uniparental disomy for chromosome 7 and by hypomethylation of the differentially methylated region (DMR) of H19.

METHODS

We examined methylation status of 31 cytosines at the CpG dinucleotides in the DMR of PEG1/MEST on 7q32.2 and 23 cytosines at the CpG dinucleotides in the DMR of H19 on 11p15, using leukocyte genomic DNA.

RESULTS

Eight of the 31 cytosines in the patient and four of the 31 cytosines in the father were hypermethylated in the PEG1/MEST-DMR. In the H19-DMR, no abnormal methylation pattern was identified in the patient.

CONCLUSION

The results suggest that hypermethylation of paternally expressed genes including PEG1/MEST, which usually have growth-promoting effects, may be relevant to LBW in subjects conceived by ART.

Mechanisms causing imprinting defects in familial Beckwith-Wiedemann syndrome with Wilms' tumour

The imprinted expression of the IGF2 and H19 genes is controlled by the Imprinting Centre 1 (IC1) at chromosome 11p15.5. This is a methylation-sensitive chromatin insulator that works by binding the zinc-finger protein CTCF in a parent-specific manner. Microdeletions abolishing some of the CTCF target sites (CTSs) of IC1 have been associated with the Beckwith-Wiedemann syndrome (BWS). However, the link between these mutations and the molecular and clinical phenotypes was debated. We have identified two novel families with IC1 deletions, in which individuals with the clinical features of the BWS are present in multiple generations. By analysing the methylation pattern at the IGF2-H19 locus together with the clinical phenotypes in the individuals with maternal and those with paternal transmission of five different deletions, we demonstrate that maternal transmission of 1.4-1.8 kb deletions in the IC1 region co-segregates with the hypermethylation of the residual CTSs and BWS phenotype with complete penetrance, whereas normal phenotype is observed upon paternal transmission. Although gene expression could not be assayed in all cases, the methylation detected at the IGF2 DMR2 and H19 promoter suggests that IC1 hypermethylation is consistently associated with biallelic activation of IGF2 and biallelic silencing of H19. Comparison of these deletions with a 2.2 kb one previously reported by another group indicates that the spacing of the CTSs on the deleted allele is critical for the gain of the abnormal methylation and penetrance of the clinical phenotype. Furthermore, we observe that the hypermethylation resulting from the deletions is always mosaic, suggesting that the epigenetic defect at the IGF2-H19 locus is established post-zygotically and may cause body asymmetry and heterogeneity of the clinical phenotype. Finally, the IC1 microdeletions are associated with a high incidence of Wilms' tumour, making their molecular diagnosis particularly important for genetic counselling and tumour surveillance at follow-up.

The centromeric 11p15 imprinting centre is also involved in Silver-Russell syndrome

Silver-Russell syndrome (SRS) is a heterogeneous disorder characterised by severe intrauterine and postnatal growth retardation, limb and body asymmetry, a typical facial appearance and less common dysmorphisms. Recently, epimutations and maternal duplications affecting the short arm of chromosome 11 have been shown to have a crucial role in the aetiology of the disease. Disturbances in the same genomic region cause the overgrowth disorder Beckwith-Wiedemann syndrome (BWS). In BWS, mutations in the telomeric as well as in the centromeric imprinting centres (ICR1 and ICR2) in 11p15 can be observed. In SRS, methylation defects in the imprinted region in 11p15 were considered to be restricted to the telomeric ICR1. They can be detected in about 30% of patients. This article reports on the first patient with SRS with a cryptic duplication restricted to the centromeric ICR2 domain in 11p15. The maternally inherited duplication in this patient included a region of 0.76-1 Mbp and affected the genes regulated by the ICR2, among them CDKN1C and LIT1. This study provides evidence for a role for this imprinting centre in the aetiology of SRS and shows that SRS presents a picture genetically opposite to that of BWS.

Tumour surveillance in Beckwith-Wiedemann syndrome and hemihyperplasia: a critical review of the evidence and suggested guidelines for local practice

There is strong evidence for an association between overgrowth disorders such as Beckwith-Wiedemann syndrome and the development of neoplasia. An increased cancer risk has also been observed in individuals with isolated hemihyperplasia. We critically review the evidence for tumour surveillance in Beckwith-Wiedemann syndrome and isolated hemihyperplasia and suggest local practice guidelines.

A maternal hypomethylation syndrome presenting as transient neonatal diabetes mellitus

The expression of imprinted genes is mediated by allele-specific epigenetic modification of genomic DNA and chromatin, including parent of origin-specific DNA methylation. Dysregulation of these genes causes a range of disorders affecting pre- and post-natal growth and neurological function. We investigated a cohort of 12 patients with transient neonatal diabetes whose disease was caused by loss of maternal methylation at the TNDM locus. We found that six of these patients showed a spectrum of methylation loss, mosaic with respect to the extent of the methylation loss, the tissues affected and the genetic loci involved. Five maternally methylated loci were affected, while one maternally methylated and two paternally methylated loci were spared. These patients had higher birth weight and were more phenotypically diverse than other TNDM patients with different aetiologies, presumably reflecting the influence of dysregulation of multiple imprinted genes. We propose the existence of a maternal hypomethylation syndrome, and therefore suggest that any patient with methylation loss at one maternally-methylated locus may also manifest methylation loss at other loci, potentially complicating or even confounding the clinical presentation.

Epigenetic deregulation of imprinting in congenital diseases of aberrant growth

Human chromosome 11p15 comprises two imprinted domains important in the control of fetal and postnatal growth. Novel studies establish that imprinting at one of these, the IGF2-H19 domain, is epigenetically deregulated (with loss of DNA methylation) in Silver-Russell Syndrome (SRS), a congenital disease of growth retardation and asymmetry. Previously, the exact opposite epigenetic alteration (gain of DNA methylation) had been detected at the domain's 'imprinting control region' (ICR) in patients with Beckwith-Wiedemann Syndrome (BWS), a complex disorder of fetal overgrowth. However, more frequently, BWS is caused by loss of DNA methylation at the ICR that regulates the second imprinted domain at 11p15. Interestingly, a similar epigenetic alteration (with loss of methylation) at a putative ICR on human chromosome 6q24, is involved in transient neonatal diabetes mellitus (TNDM), a congenital disease with intrauterine growth retardation and a transient lack of insulin. Thus, fetal and postnatal growth is epigenetically controlled by different ICRs, at 11p15 and other chromosomal regions.