Epigenetic contribution to birth
defects
David Amor
20th June 2011
Genomic imprinting
•
•
Genomic imprinting is the
biological process whereby a
gene or genomic domain is
biochemically marked with
information about its parental
origin.
Genomic imprints may be
covalent (DNA methylation) or
non-covalent (DNA-protein and
DNA-RNA interactions, genomic
localization in nuclear space),
and are maintained throughout
the cell cycle.
Genomic Imprinting
•
•
•
•
Parental imprints are established during
gametogenesis as homologous DNA passes
uniquely through sperm or egg, and are maintained
into adulthood
Genomic imprints have the significant functional
consequence of stifling gene expression from one of
the parental alleles, resulting in unbalanced gene
expression between homologous alleles.
As a result of imprinting, there is biased allelic
expression that favours expression from one parental
locus over the other.
Imprinting may not be 100% efficient, and there may
be ‘leaky’ expression from the ‘silenced allele’.
Imprinted genes
•
Role of imprinting in ‘normal’ development
– Cell-cycle regulation- altered growth and development
– Organogenesis : neurogenesis genes over-represented
– Cell growth and/or maintenance
– Regulation of biological and cellular processes
– Chromatin architecture
•
Errors in imprinting have been implicated in
– human genetic disease
• rare birth defects, imprinting syndromes
– progression of certain cancers
– some neurological disorders – where condition more
common in one parental line e.g. AZ, bipolar disorder,
male sexual orientation, obesity, schizophrenia
How many
imprinted genes?
Approx 60
identified + 150
predicted =
approx 1% of the
human genome
Genome-wide distribution of genes
proved (filled triangles) or predicted with
high confidence (unfilled triangles) to be
imprinted. Red downward triangles, blue
upward triangles, and black dots indicate
genes predicted to be maternally,
paternally, or biallelically expressed,
respectively.
Philippe P. Luedi et al. Genome Res. 2007; 17: 17231730
9 Imprinting disorders now recognised
Locus
1.
2.
3.
4.
5.
6.
7.
8.
9.
Prader-Willi syndrome
Angelman syndrome
Transient neonatal diabetes
Beckwith-Wiedemann syndrome
Russell-Silver syndrome
matUPD14
patUPD14
Pseudohypoparathyroidism 1B
Maternal hypomethylation syndrome
15q11-13
15q11-13
6q24
11p15.5
11p15.5, matUPD7
14q32
14q32
20q13
6p22
Diverse genetic and epigenetic changes
underlie recognised imprinting disorders
•
•
•
•
•
Large deletions or duplications of chromosome
regions that contain imprinted genes
DNA mutations in genes that are usually imprinted
DNA mutations in imprinting control centres
Uniparental disomy (UPD)
Alteration in epigenetic marks at imprinted loci
without alteration in DNA sequence = epimutation
For each imprinting disorder, the relative contributions of
the above mechanisms is different
Uniparental disomy
Uniparental disomy: When both copies of a chromosome pair are derived from the
same parent. One cause of abnormal imprinting patterns.
Typically a result of ‘trisomy rescue’ in early embryonic life
Example: Chromosome 15
x
x
9
9
x
x
9
Methylation status of the
SNRPN gene
x methylated
9 unmethylated
Maternally derived
chromosome 15
Paternally derived
chromosome 15
x
x
This child would have Prader-Willi
syndrome
Angelman syndrome
•
•
Clinical features
– 1 in 16,000
– Intellectual disability
– Impaired speech
– Ataxia, seizures, microcephaly
– Happy demeanour
Mechanism
– 70% deletion 15q
– 11% UBE3A mutation
– 7% patUPD15
– 3% epimutations (loss of
maternal methylation)
– 0.3% imprinting centre deletion
– (Remainder unknown)
Prader-Willi syndrome
•
Clinical features
– 1 in 17,500
– Neonatal hypotonia
– Obesity
– Cognitive impairment
– Distinctive
behavioural
characteristics
– Hypogonadism
– Facial appearance
Prader-Willi syndrome
•
Mechanism
– 70% deletion 15q
– 25% matUPD15
– <1% epimutations
Beckwith-Wiedemann syndrome
•
Clinical features
– Macroglossia
– Pre/post natal
overgrowth
– Anterior abdominal wall
defects
– Neonatal
hypoglycaemia
– Ear pits/creases
– Hemihypertrophy
– Facial naeveus
flammeus
– Increased risk of
abdominal tumours
Beckwith-Wiedemann syndrome
•
Mechanisms
– > 50% have epimutation on maternal allele
• 50% loss of methylation at DMR2
• 2-7% have gain of methylation at DMR1
– 20% patUPD11 (mosaic, segmental)
– 10% mutation in maternal allele of CDKN1C
– 1-2% cytogenetically visible deletion/duplication
DMR1
DMR2
H19
Mat
IGF2
Expressed
Silenced
H19DMR
Pat
Silenced
Meth
Expressed
LIT1
CDKN1C
Meth
Silenced
Expressed
KvDMR1
Expressed
Silenced
Russell-Silver syndrome
•
Clinical features
– Growth retardation
(IUGR and postnatal)
– clinodactyly
– limb length
asymmetry
– triangular facies
– CALS
– variable learning
difficulties
Russell-Silver syndrome
•
Mechanisms
– 11p locus
• 45% have epimutation (LOM) of paternal allele of DMR1
• Maternally inherited duplications involving DMR1
DMR1
DMR2
H19
Mat
IGF2
Expressed
Silenced
LIT1
Silenced
H19DMR
Pat
Silenced
Meth
Expressed
CDKN1C
Meth
Expressed
KvDMR1
Expressed
– Chomosome 7 loci (2 imprinted loci on 7p/7q)
• 5% have matUPD7
• maternal duplication of 7p has similar phenoptype
• epimutations not reported
Silenced
Maternal UPD14 syndrome
•
Clinical features
– Approx 50 patients
reported
– Pre and postnatal
growth retardation
– hypotonia
– Facial dysmorphism
– Early onset puberty
– Variable learning
difficulties
Mitter et al. AJMG 2006
Maternal UPD14 syndrome
•
Mechanisms
– Altered gene
expression at 14q
DMR
– Most cases have UPD
– 3 recent reports of
paternal chromosome
deletions (Kagami et al Nat
Genet 2008)
– 1 report of
epimutation (LOM on
paternal allele)
10 yo patient with matUPD14 syndrome due to epimutation
Temple, I K et al. J Med Genet 2007;44:637-640
Paternal UPD14 syndrome
•
Clinical features
– Approx 30 patients
reported
– Polyhydramnios
– Premature labour
– Skeletal abnormalies
– Usually early death
Chu et al AJMG 2003
Figure 1. The patient as a neonate. A: Note narrow chest, protuberant abdomen
with diastasis recti, and mild rhizomelic shortening of upper limbs. B: Note broad
nasal bridge, hirsute forehead. C: Note short AP diameter of chest, short broad
thumb. D: Note small thorax with bowing of ribs.
Paternal UPD14 syndrome
•
Mechanisms
– Most pat UPD14
– 5 chromosome
deletions on maternal
allele (see Kagami et al Nat
Genet 2008)
– 3 epimutations (GOM
on maternal allele) (see
Kagami et al Nat Genet 2008)
Mattes AJMG (2007)
Figure 1. a,b: Chest X-ray at birth demonstrating bell-shaped rib cage with a
characteristic arched appearance of the ribs due to caudal bowing anteriorly
and cranial bowing posteriorly, elongated clavicles, stippled epiphyses of the
humeri, and kyphoscoliosis. c,d: X-ray of the forearms demonstrating
contractures of the wrists with ulnar deviation, digit extensor contractures, and
swan neck deformity. e,f: Prominent philtrum, prominent midline beak of upper
lip, vertical creases under the lower lips, anteverted flared nares, and a broad
nasal bridge.
Pseudohypoparathyroidism 1B
•
•
Clinical features
– hypocalcaemia and
hyperphosphataemia
due to resistance to
parathyroid hormone
Mechanism
– Caused by mutations or
epimutations in the
regulatory regions of the
gene GNAS1
– GNAS1 encodes the
alpha subunit of the
stimulatory G-protein,
and in the proximal renal
tubule, transcripts of the
alpha subunit are
derived only from the
maternal allele.
Pseudohypoparathyroidism 1B
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•
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•
PHP-1b occurs in familial and
sporadic forms
Most familial cases result from
a 3-kb microdeletion upstream
of GNAS, leading to LOM on
the maternal allele
Sporadic cases are likely to be
caused by epimutation (LOM of
the maternal allele)
To date there has been only
one PHP-1b patient with
patUPD of 20q
Other disorder at GNAS locus
Albright Hereditary
osteodystrophy
Inactivating
mutations
Progressive osseous
heterotopia
Inactivating
mutations
McCune-Albright
syndrome
Activating
mutations
Transient neonatal diabetes mellitus (TND)
•
•
Clinical features
– presents in the neonatal period with growth
retardation and hypoglycaemia
Mechanism
– At 6q24 there is a DMR that is methylated on the
maternal allele and unmethylated on the paternal
allele
– TND results from a ‘double dose’ of the paternal
epigenotype
– 40% paternal chromosome duplication
– 40% patUPD6
– 20% epimutation: maternal LOM
Maternal hypomethylation syndrome
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•
•
From Boonen et al.,
EJHG 2008
Relatively new syndrome resulting
from maternal LOM at multiple loci
Ascertained either through
– BWS (with features of other
imprinting disorders) (Rossignol
et al., 2006)
– TND (with features of other
imprinting disorders) (MacKay
et al., 2006)
Homozygous mutations in the gene
ZFP57
– 10 families reported to date,
most consanguineous
– Phenotypes highly variable
Maternal hypomethylation syndrome
“Hypomethylation phenotypes” from Mackay,
Temple
Mean birth weight
Macroglossia*
Abdominal wall defects0/4
Developmental delay
‘Severe’ intellectual disability*
Speech delay*
Abnormal corpus callosum
Growth delay
Mat age >35 years
Infertility/IVF
LOM6q24 only
2060
1/4
1/4
0/4
0/4
1/4
*Also deafness, hypospadius, CHD
LOM multiple Loci
2342
6/9
2/6
2/6
2/9
5/9
2/9
1/6
3/6
1/6
Other genetic loci that influence imprinting
NLRP7
Homozygous (maternal) mutations in the gene
NLRP7 cause familial recurrent hydatidiform mole
hydatidiform mole is diploid and biparental, but
phenotype is that of androgenetic hydatidiform
mole
NLRP2
Single case report of mother with homozygous
mutations in NLRP2 who had two children with
BWS due to epimutation at 11p15.5
Imprinting disorders and ART
•Factors linked to subfertility?
Primordial germ cell
Imprint
establishment
•Use of immature germ cells
•Ovarian hyperstimulation
•Germ cells in vitro manipulation
•Germ cells cryopreservation
Zygote
Mechanical
stress
•Culture conditions
•Embryo cryopreservation
Mature gametes
Fertilisation
IVF/ICSI
Imprint maintenance
AS
PWS
BWS
RSS
Mat
UPD14
Pat
UPD14
PHP-1b
TND
Mat
Hypometh
synd
Cytogenetic
70%
70%
1-2%
<1%
3
patients
5
patients
0
40%
0
UPD
7%
25%
20%
5%
>90%
>50%
1 patient
40%
0
DNA mutation
5-10%
<1%
10%
?
0
0
Most
familial
0
0
Mat LOM
3%
0
50-60%
0
0
0
? Most
sporadic
20%
100%
Mat GOM
0
0
2-7%
0
0
3
patients
0
0
Pat LOM
0
<1%
0
64%
1 patient
0
0
0
Pat GOM
0
0%
0
1 patient
0
0
0
0
Epimutation