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An 800тАЙkb deletion at 17q23.2 including the MED13 (THRAP1) gene revealed by aCGH in a patient with a SMC 17p

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CLINICAL REPORT
An 800 kb Deletion at 17q23.2 Including the MED13
(THRAP1) Gene, Revealed by aCGH in a Patient
With a SMC 17p
Nadia Boutry-Kryza,1,2 Audrey Labalme,3 Marianne Till,3 Caroline Schluth-Bolard,3 Jacques Langue,4
Catherine Turleau,5 Patrick Edery,2,3 and Damien Sanlaville2,3*
1
Hospices Civils de Lyon, Service de Genetique Moleculaire et Clinique, Lyon, France
2
INSERM, U1028; CNRS, UMR5292; UCBL1, Lyon Neuroscience Research Center, TIGER Team, Lyon, France
3
Hospices Civils de Lyon, Service de Cytogenetique Constitutionnelle, Bron Cedex, France
Hospices Civils de Lyon, Service de Neuropediatrie, Lyon, France
4
5
AP-HP, Service de Cytogenetique, H^opital Necker Enfants Malades, Paris, France
Received 10 March 2010; Accepted 22 May 2011
We report on clinical and cytogenetic studies in a 7-year-old child
with moderate intellectual disability, short stature, mild dysmorphism, and hearing loss. R-chromosome banding showed a
de novo autosomal marker originating from the 17p chromosome segment in all cells analyzed. Array comparative genome
hybridization (aCGH) was used to determine the gene content
and proximal and distal breakpoints of the small supernumerary
marker chromosome (SMC). These breakpoints mapped to the
centromere of chromosome 17 and the 17p11.2 region, respectively. Unexpectedly, aCGH analysis also revealed a de novo
deletion of 800 kb encompassing six genes in the 17q23.2 region,
including MED13 (also known as THRAP1). We compared our
patient with other reported cases of SMC(17), to determine the
respective contributions of the duplication and the deletion to
the phenotype. We cannot entirely exclude a minor role for the
SMC(17), but we suggest that MED13 haploinsufficiency was
responsible for the phenotype of the patient particularly the
cataract, hearing loss and semicircular canal dysplasia. Moreover, this report highlights the usefulness of aCGH for the
specification of gene content in cases of abnormality, facilitating
the establishment of accurate phenotype–genotype correlations
and the detection of other, complex rearrangements.
How to Cite this Article:
Boutry-Kryza N, Labalme A, Till M, SchluthBolard C, Langue J, Turleau C, Edery P,
Sanlaville D. 2012. An 800 kb deletion at
17q23.2 including the MED13 (THRAP1)
gene, revealed by aCGH in a patient with a
SMC 17p.
Am J Med Genet Part A 158A:400–405.
INTRODUCTION
correlation results from the extreme diversity of SMCs (degree of
mosaicism, size, structure, origin, gene content) and the limitations
of classical cytogenetic investigations [Crolla et al., 2005]. However,
the development in recent years of cytogenetic tools, including
array comparative genome hybridization (aCGH) in particular, has
made it possible to characterize imbalanced chromosome abnormalities with a higher resolution (size, breakpoints), even in cases of
mosaicism [Ballif et al., 2006; Menten et al., 2006]. Moreover,
aCGH sometimes reveals other unexpected abnormalities associated with the markers [Baldwin et al., 2008; Tsuchiya et al., 2008]
and the considerable phenotypic variability of patients with SMCs
may be accounted for by these other ‘‘hidden’’ imbalanced rearrangements, which remained undetected before karyotyping. The
case reported below illustrates this point.
We report here on clinical, cytogenetic and molecular studies in a
girl with both a de novo SMC derived from the proximal short arm
The characterization of small supernumerary marker chromosomes (SMCs) discovered on karyotyping is a real challenge and
is necessary for the establishment of genotype-phenotype correlations and for accurate genetic counseling. Indeed, only one third of
SMCs are associated with a precise phenotype (e.g.: tetrasomy 12p
and Pallister-Killian syndrome, chromosome 22 inversion-duplication, and cat-eye syndrome). This lack of phenotype–genotype
*Correspondence to:
Damien Sanlaville, Service de Cytogenetique Constitutionnelle, Centre de
Biologie et de Pathologie Est, 59, Boulevard Pinel, 69677 Bron Cedex,
France. E-mail: damien.sanlaville@chu-lyon.fr
Published online 7 December 2011 in Wiley Online Library
(wileyonlinelibrary.com).
DOI 10.1002/ajmg.a.34222
Ó 2011 Wiley Periodicals, Inc.
Key words: SMC; chromosome 17; aCGH; MED13 gene
Ó 2011 Wiley Periodicals, Inc.
400
BOUTRY-KRYZA ET AL.
of chromosome 17 and a de novo 800 kb 17q23.2 deletion detected
by aCGH. We also present additional evidence that the genes
present on this SMC(17) probably have little, if any, phenotypic
effect.
CLINICAL REPORT
This 7-year-old child was the second child of nonconsanguineous
parents of French background with no informative family history.
Her father was 34 and her mother was 31 years old at the time of
conception. Intrauterine growth retardation was observed during
pregnancy. The child was delivered normally at term. Her birth
weight was 2,560 g ( 2 SD), her birth length was 44.5 cm ( 2 SD),
and her head circumference was 32.2 cm ( 2 SD). Blood lymphocyte karyotyping was performed at birth, due to possible sexual
ambiguity (abnormality of the clitoris, subsequently considered to
be an anatomic variant). A supernumerary marker chromosome
was found in all the metaphase cells observed (40/40). Parental
karyotypes were normal. Clinical follow-up showed significant
feeding difficulties and recurrent bronchiolitis. Growth retardation
( 2.5 SD), developmental delay (the patient sat unsupported at the
age of 10 months walked at the age of 21 months), and delayed
speech acquisition were noted at the age of three years. The patient
also had a hearing loss, with prolonged latencies in auditory evoked
potential tests. MRI scan showed bilateral semicircular canal dysplasia, with ossicular malformations. On clinical examination, we
noted minor craniofacial abnormalities: temporal retraction, small
ears with posterior rotation, unilateral preauricular fistula, small
mouth, short nose, small hands and feet (no picture of the patient is
provided because the required informed written consent could not
be obtained).
On examination at the age of four years, the patient presented
with pes equinus of the right foot, with loss of the Achilles and
patellar tendon reflexes. Pes equinus was resolved by physiotherapy.
A recent clinical examination of this child at the age of six years
showed bilateral peripheral cataract and right conduction hearing
loss (60–70 dB) requiring the use of a hearing aid. Speech and motor
development improved with time. This patient had attention deficit
and hyperactivity disorder (ADHD), which was improved by
risperidone treatment. No sleep disorder was noted.
MATERIALS AND METHODS
Classical Cytogenetic Investigations
Peripheral blood lymphocytes were karyotyped by RHG banding,
with standard techniques. Chromosome analyses were also performed on cultured blood lymphocytes from both parents.
Fluorescence In Situ Hybridization (FISH)
We initially carried out FISH with commercial probes, according to
the manufacturer’s instructions, to characterize the origin and gene
content of the SMC. We used three probes: a chromosome 17
centromeric probe (D17Z1, KREATECHÒ), a Smith–Magenis
locus-specific probe (FLI, SMR CYTOCELLÒ), and a Miller–
Dieker locus-specific probe (LIS1, MDR CYTOCELLÒ)).
401
For confirmation of the aCGH data, we carried out FISH with the
BAC clones RP11-458P8 (17p11.2), RP11-93H8 (17p11.2), and
RP11-769P22 (17q21.31, control probe), as previously described
[Romana et al., 1994]. We then used the RP11-342K2 BAC clone
(17q23) encompassing the MED13 (THRAP1) locus, to check for
MED13 deletion in the patient and for rearrangements of 17q23 in
the samples from the parents.
Array Comparative Genomic Hybridization (aCGH)
Oligonucleotide aCGH was performed with the Agilent Human
Genome CGH Microarray Kit 244K, according to the manufacturer’s instructions (protocol version 4.0), as previously
described [Schluth-Bolard et al., 2008]. Data were analyzed with
the CGH Analytics software platform (AgilentÒ, Santa Clara, USA).
Data were extracted with Feature ExtractionÒ 9.1 software and
analyzed with CGH analyticsÒ 4.5 software, with the following
parameters: window 0.2 MB, ADM2 threshold 6.0.
Quantitative PCR Analysis (qPCR)
qPCR was performed to confirm the DNA loss detected by aCGH
analysis. We used probes binding to exon 8 of the MED13 gene, in
accordance with the instructions provided with the kit (Quantitect
SYBR GREEN PCR, QiagenÒ, Courtabeouf, France). All qPCR were
run on a LightCycler 2000 (Roche Applied ScienceÒ, Indianapolis,
USA).
Microsatellite DNA Marker Analysis
We analyzed four microsatellites, to determine the parental origin
of the abnormalities. We extracted genomic DNA from peripheral
blood leukocytes from the patient and her parents. One of the
microsatellites used (D17S1811; GenBank Accession No.: Z52802)
mapped to the deletion and the other three microsatellites mapped
to the duplicated region (D17S689: GenBank Accession No.:
L29364; D17S1871: GenBank Accession No.: Z51496 and
GATA70H05: GenBank Accession No.: G15778). Allele sizes
were determined with GeneMapperÒ software.
RESULTS
The postnatal karyotype revealed the presence of two X chromosomes and a supernumerary small chromosome in all cells (40/40).
This additional marker was too small for identification on the
basis of its banding pattern (Fig. 1a). The karyotypes of the parents
were normal. We therefore determined the origin of this de novo
SMC by FISH with centromeric probes. The supernumerary chromosome hybridized with the chromosome 17 centromeric probe
but not with the Smith–Magenis and Miller–Dieker microdeletion
syndrome probes (Fig. 1c). We then carried out aCGH analysis,
which revealed a gain of about 1.6 Mb of chromosomal material
on 17p11.2, between the binding sites of oligonucleotides
A_16_P40777061 and A_14_P113402 (respective positions
20,404,913 and 22,004,995 Mb; hg18, NCBI36; Fig. 1c), confirming
partial trisomy 17p with the inclusion of euchromatic sequences.
This result was confirmed by FISH (Fig. 1b). Interestingly, aCGH
analysis also revealed the unexpected loss of 800 kb from the
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
402
FIG. 1. a: Partial karyotype (RHG banding) of the proband. The size of the SMC(17), indicated by an arrow, is compared with that of chromosome 20. b:
FISH results for the RP11-93H8 (17p11.2, red) and RP11-769P22 (17q21.31, green) probes. The arrow indicates the SMC(17); c: aCGH analysis. The
red arrow indicates the gain on 17p11.2. The green arrow indicates the loss on 17q23.2. * indicates a known CNP in a control DNA.
genomic sequence of 17q23.2, between the binding sites for oligonucleotides A_16_P03272064 and A_16_P20698245 (respective
positions 57,372,913 and 58,206,595 Mb; hg18, NCBI36). This
result was confirmed by qPCR with a primer binding to exon 8
of the MED13 gene and was shown to be a de novo modification
(data not shown).
An analysis of parental samples with the BAC clone RP11-342K2
(17q23) revealed no major chromosome rearrangement, such as
large inversions (data not shown). This clone was found to be absent
from the patient’s cells (data not shown).
The microsatellite analysis revealed that the deletion was of
maternal origin. Unfortunately, the three microsatellites located
in the same region of the genome as the SMC were not informative
(Table I).
DISCUSSION
Eleven cases of chromosome 17-derived SMCs have been reported
[Yatsenko et al., 2005; Kogan et al., 2009]. The 17p11.2 region is
particularly rich in low-copy number repeats (LCRs). LCRs are
DNA sequences involved in nonallelic homologous recombination
(NAHR), a mechanism responsible for DNA rearrangements, such
as deletions, duplications, inversions and SMCs. In the 17p11.2
region, the proximal and distal Smith–Magenis LCRs (SMS-REP)
mediate the common deletion and reciprocal duplication resulting
in the Smith–Magenis [Park et al., 2002] and Potocki–Lupski
syndromes [Potocki et al., 2007], respectively. We describe here
a case of SMC(17) with a distal breakpoint mapping to the
centromere region and a proximal breakpoint mapping close to
TABLE I. Results of the Microsatellite Marker Studies Performed in the Patient and Her Parents
Microsatellite marker
D17S1811
D17S689
D17S1871
GATA70H05
NI, not informative.
Location
17q23.2
17p11.2
17p11.2
17p11.2
Proband
82
169/169/169
353/353/353
142/146/146
Father
82/82
169/171
353/371
142/146
Mother
88/88
169/169
353/353
132/146
Parental origin
Maternal
NI
NI
NI
BOUTRY-KRYZA ET AL.
the proximal SMS-REP in the LCR17pD (Fig. 2). This SMC(17)
therefore did not include the region generally implicated in
Potocki–Lupski syndrome (PLS). To our knowledge, only two
cases of SMC(17) that did not include the this region have been
described to date [Shaw et al., 2004; Kogan et al., 2009].The case of
Shaw et al. [2004] 2,170 had a distal breakpoint between the binding
sites of clones CTD-2010G8 (19.9 Mb) and RP5-836L9 (20.1 Mb)
and a centromeric proximal breakpoint. In our case, the distal
breakpoint was located at 20.4 Mb, so the SMC had a lower
euchromatin content (Fig. 2). In the other case, described by Kogan
et al., there was a distal breakpoint in the proximal SMS-REP, as in
our patient, but a proximal breakpoint in the 17q11.2 band.
In addition to the mosaic SMC(17), the patient also displayed
mosaicism for an SMC(13). The clinical features of these patients
were not consistent with the phenotype of our patient. In particular,
our patient presented with cataracts, severe hearing loss and semicircular canal dysplasia, which have never previously been reported
in patients with SMC(17).
The duplicated region in our patient contained nine genes:
MGC87631, USP22, DHRS7B, TMEM11, MGC33894, MAP2K3,
KCNJ12, C17orf51, and FAM27L (RefSeqGenes, UCSC hg18). Six of
these genes are encompassed by two copy number polymorphisms
(CNPs) described by Redon et al. (CNPs 1218 and 1219). The other
three genes (TMEM11, DHRS7B, and MGC33894) encode proteins
with poorly characterized functions: TMEM11 encodes a protein
thought to regulate the morphogenesis of mitochondria, particularly during cell stress (hypoxia, infection) [Rival et al., 2011].
DHRS7B (dehydrogenase/reductase member 7B) and MGC33894
encode proteins of unknown function (UCSC genome browser). In
addition, a girl with a de novo min(17) encompassing the chromosomal region found in our patient was reported on Thomas
Liehr’s marker site (http://www.med.uni-jena.de/fish/sSMC/
17.htm#Start17, case 17-O-p11.2/3-1). At the age of two years,
403
the patient displayed no malformations, dysmorphism, or retardation of psychomotor development. We cannot entirely exclude
the possibility that the SMC(17) plays a role in the intellectual
disability of this patient, but we suggest that the phenotype observed
in our patient, including the hearing loss and ocular abnormalities,
was due to the de novo 800 kb 17q23.2 deletion rather than the
SMC.
To our knowledge, no other small deletion has ever been
described in this chromosomal region. This 17q23.2 deletion
encompasses six genes (EFCAB3, MED13, METTL2A, TLK2,
MRC2, and MARCH10, RefSeqGenes, UCSC hg18). A copy number
polymorphism (CNP 1238) has been described in this region, but it
is smaller than the observed deletion and includes only the EFCAB3
gene. The other five genes are absent from this CNP and are
potential candidate genes underlying the clinical symptoms of
this child. One of these genes, MED13 (OMIM 603808), is of
particular interest with respect to the phenotype of the patient.
Indeed, the product of this gene probably forms a subcomplex with
the products of the MED12, CDK8, and Cyclin C genes—the human
CDK8 subcomplex—which is thought to downregulate transcription [Knuesel et al., 2009]. These four genes appear to be essential
for embryo development, but not for cell viability. In Drosophila,
alteration to this complex cause malformations of the eyes and
external sensory organs [Loncle et al., 2007]. Indeed, mutant
Med13-Drosophilia display a lack of photoreceptor differentiation
in the eye discs, leading to malformation of the ommatidia
[Treisman, 2001]. These Med13-mutants also display downregulation of the bab gene in the leg discs. This gene is required for
development of the proximo-distal leg axis and its downregulation
results in distal leg shortening. A loss of bristle differentiation has
also been observed in the adult notum: in Med13-mutants, expression of the sens gene, which is required for sensory organ precursor
differentiation, is undetectable. Malformations of wings and
FIG. 2. Schematic diagram of the 17p chromosomal region, derived from Yatsenko et al. [2005]. The black arrow shows the region most frequently
involved in the Smith–Magenis and Potocki–Lupski syndromes. The purple arrows indicate the limits of the SMC(17) in the patient studied here (JH).
The blue and green arrows indicate the limits of the SMC(17) reported by Shaw et al. [2004], the orange arrow indicates the limits of the SMC(17)
corresponding to Kogan’s patient [Kogan et al., 2009] (KP); the gray arrow indicates the boundaries of the SMC(17) reported in Thomas Liehr’s
chromosome marker website.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
404
antennas have also been noted. Interestingly, our patient presented
with neurosensorial loss (hearing loss and cataracts). Moreover,
one of the partners of MED13, MED12, interacts with Mediator, a
protein involved in regulating neuronal gene expression [Ding
et al., 2008]. MED12 mutations have been shown to be responsible
for two X-linked intellectual disability disorders: the Opitz–
Kaveggia and Lujan syndromes [Risheg et al., 2007; Schwartz
et al., 2007].
Three other deletions of the MED13 gene were found in the
DECIPHER database (Patients 249 237, 250 379, and 253 402).
These three deletions were more proximal, but the only deleted
region common to our patient contained only the MED13 locus.
Two of the patients with these deletions presented mental retardation and deafness (Patients 249,237 and 250,379). No clinical data
were available for case 253,402.
Our results provide no conclusive proof concerning the parental
origin of the SMC. The chromosomal deletion was found to be of
maternal origin, but our analyses of the parental samples found no
chromosomal rearrangement involving the deleted region. We
cannot exclude the possibility of a small parental inversion, but
the presence of such an inversion could not account for the presence
of both the SMC(17) and the 17q23 deletion. An in silico analysis of
the deleted region with the TCAG website identified no highly
similar duplicated sequences that might account for this deletion
through an NAHR-based mechanism.
In summary, this patient’s report highlights the complexity of
phenotype-genotype correlations in microdeletion and microduplication syndromes. Our attention was initially drawn to the
SMC(17), which was thought likely to be responsible for the
patient’s phenotype. However, our findings suggest that the basis
of the abnormal phenotype in this patient, particularly as concerns
the ocular and hearing abnormalities, is actually haploinsufficiency
of the MED13 gene.
INTERNET ADDRESSES
UCSC: www.genome.ucsc.edu.
Thomas Liehr’s marker site: www.med.uni-jena.de/fish/sSMC/
17.htm#Start17.
TCAG site: http://projects.tcag.ca/cgi-bin/variation/gbrowse/
hg18/.
DECIPHER site: http://decipher.sanger.ac.uk/.
ACKNOWLEDGMENTS
We thank the members of this family for their continuing interest
and cooperation. We thank the DGOS (Direction Ge ne rale de
l’Organisation des Soins) for their support for the development
of the aCGH platform at Lyon. We thank Prof. Zeynep T€
umer
(Center for Applied Human Molecular Genetics, Glostrup,
Denmark) and Dr Anne Ronan (Hunter Genetic Unit from
Waratah, NSW 2298, Australia), for accepting the citation of their
DECIPHER Consortium cases (Numbers 250379 and 249237,
respectively) in our discussion. Descriptions of these two cases
will be provided elsewhere. We also thank the DECIPHER
Consortium.
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