How to Cite this Article: Griesi-Oliveira K, Moreira DdP, Davis-Wright N, Sanders S, Mason C, Orabona GM, Vadasz E, Bertola DR, State MW, Passos-Bueno MR. 2012. A Complex Chromosomal Rearrangement Involving Chromosomes 2, 5, and X in Autism Spectrum Disorder. Am J Med Genet Part B 159B:529–536.
A complex chromosomal rearrangement involving chromosomes 2, 5, and X in autism spectrum disorder†
Article first published online: 16 MAY 2012
Copyright © 2012 Wiley Periodicals, Inc.
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
Volume 159B, Issue 5, pages 529–536, July 2012
How to Cite
Griesi-Oliveira, K., Moreira, D. d. P., Davis-Wright, N., Sanders, S., Mason, C., Orabona, G. M., Vadasz, E., Bertola, D. R., State, M. W. and Passos-Bueno, M. R. (2012), A complex chromosomal rearrangement involving chromosomes 2, 5, and X in autism spectrum disorder. Am. J. Med. Genet., 159B: 529–536. doi: 10.1002/ajmg.b.32059
- Issue published online: 5 JUN 2012
- Article first published online: 16 MAY 2012
- Manuscript Accepted: 18 APR 2012
- Manuscript Received: 29 MAY 2011
- balanced translocation;
- uniparental disomy chromosome 5;
- duplication 5q11;
Here, we describe a female patient with autism spectrum disorder and dysmorphic features that harbors a complex genetic alteration, involving a de novo balanced translocation t(2;X)(q11;q24), a 5q11 segmental trisomy and a maternally inherited isodisomy on chromosome 5. All the possibly damaging genetic effects of such alterations are discussed. In light of recent findings on ASD genetic causes, the hypothesis that all these alterations might be acting in orchestration and contributing to the phenotype is also considered. © 2012 Wiley Periodicals, Inc.
Autism spectrum disorders (ASD) are a group of neurodevelopmental diseases with onset in early childhood, characterized by impairments in social and communicative skills and a repertoire of repetitive behaviors. The latest studies have consistently provided an estimated prevalence of 0.6% for these disorders [Fombonne, 2009]. It is widely accepted that ASD have a strong genetic component, with a high heritability index [El-Fishawy and State, 2010]. However, their genetic architecture is very heterogeneous, and both multifactorial and Mendelian models seem to play a role in ASD etiology. Despite the enormous effort to identify the genetic factors and mechanisms involved in ASD, still very few genes have been definitely associated with this complex disorder.
It is estimated that chromosomal abnormalities, such as translocations, inversions, deletions, and duplications, are present in around 3% of ASD cases [Vorstman et al., 2006]. More recently, an increasing number of rare potentially pathogenic submicroscopic duplications or deletions, the copy number variations (CNVs), have been identified in approximately 5–10% of ASD patients [Szatmari et al., 2007; Marshall et al., 2008; Pinto et al., 2010; van Daalen et al., 2011]. Mapping of the boundaries of chromosomal translocations, examination of overlapping regions among duplications or deletions of different sizes and analysis of CNVs have allowed the identification of genes that have become strong candidates for ASD, such as SHANK3, NLGN3/4, and NRXN1 [Laumonnier et al., 2004; Durand et al., 2007; Kim et al., 2008]. Thus, chromosomal alterations represent an important etiological mechanism associated with ASD and their molecular and genomic analysis is a useful approach to investigate the genetics of these disorders.
In this report, we describe the clinical features and molecular characterization of chromosomal abnormalities of a female patient with ASD, developmental delay, and craniofacial dysmorphism.
MATERIALS AND METHODS
A detailed anamnesis and a three-generation pedigree, as well as a physical examination were performed. Blood from the proband and her parents was collected for DNA and karyotype analysis. The study was approved by the Ethical Committee of Bioscience Institute—University of São Paulo.
Karyotype and FISH Studies
Metaphase slides were obtained from peripheral blood lymphocytes treated with colchicine and conventional G-banded karyotype was performed for the patient and her parents.
For breakpoint mapping, FISH analysis (fluorescent in situ hybridization) was carried out using bacterial artificial chromosomes (BACs) from the RPCI-11 library. BACs were selected from UCSC genome Browser (http://genome.ucsc.edu/, hg18) and labeled using nick translation reaction [Lichter et al., 1990]. Hybridization of the probes to the patient's metaphase slides was performed following standard procedures. Images were analyzed with the Openlab v.5.5 software and in silico analysis were performed using the UCSC genome browser and National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) databases. All the genes localized 1 Mb distal or proximal from the breakpoint were investigated in regard to their function, site of expression, interaction with other genes, associated diseases, animal models and relation to neurological function and psychiatric diseases.
SNP-Based Microarray Analysis
Patient's DNA sample was hybridized on Illumina Human CNV 370k BeadChips, following the manufacturer's protocol. Data were analyzed using PennCNV [Wang et al., 2007] and QuantiSNP [Colella et al., 2007] software packages. The CNVs found were compared to the Database of Genomic Variants (http://projects.tcag.ca/variation/), Autism CNV Database (http://projects.tcag.ca/autism_500k/) and Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER; http://decipher.sanger.ac.uk/) to identify common and rare variants, as well as recurrence of variants in other autistic patients.
Patient, mother, and father were genotyped for the markers D5S1981, D5S416, D5S644, D5S2027, D5S408 (ABI PRISM Linkage Mapping Set version 2.0; Perking Elmer, Applied Biosystems, Foster City, CA), D5S2092, D5S2076, D5S2102, and D5S2107 (M-13 tailed primers). The results were analyzed with GeneMapper Software v4.0 (Applied Biosystems).
Isolation of Human Dental Pulp Stem Cells
Dental pulp stem cells (DPSCs) lineages were obtained after digestion of dental pulp tissues with a solution of 0.25% trypsin for 30 min at 37°C. The cells were cultivated in DMEM/F12 media (Gibco, Carlsbad, CA) supplemented with 15% fetal bovine serum (Hyclone, Logan, UT), 1% penicillin/streptomycin and 1% non-essential amino acids and maintained under standard conditions (37°C, 5% CO2).
RNA Isolation and Quantitative Real-Time PCR
RNA samples were extracted from DPSCs using the NucleoSpin RNA II (Macherey-Nagel, Düren, Germany) extraction kit. Samples concentration and quality were evaluated by Nanodrop 1000 and gel electrophoresis. RNA samples were reversely transcribed into cDNA using the Super Script II First Strand Synthesis System (Invitrogen, Carlsbad, CA) according to manufacturer's instructions. Primers were designed using PrimerExpress v. 2.0 software and their specificity was verified by melting curve analysis on 7500 System SDS v. 1.2 Software (Applied Biosystems; Table I). Reactions were run on an Applied Biosystems 7500 sequence detection system using SYBR-Green Master Mix (Applied Biosystems). Quantitative analysis was performed using the comparative threshold cycle method [Livak and Schmittgen, 2001]. The geNorm applet (www.medgen.ugent.be/genorm/) was used to determine the stability of the reference genes GAPDH, HPRT1, SDHA, and HMBS and generate a normalization factor for the expression values of the target genes. The principles of analysis of geNorm are described in Vandesompele et al. .
|Gene||Primer F||Primer R|
The patient, a girl who is currently 10 year-old, was born to a 27-year-old mother and 33-year-old father, both healthy and non-consanguineous. She was born at term after an uncomplicated pregnancy except for placental infarction at the 30th week. There was no history of medication use or alcohol consumption during pregnancy. Birth weight and length was 2.355 kg (<10th percentile) and 45 cm (<10th percentile), respectively, and her Apgar scores were 9 at 1 min and 10 at 5 min. Her older sister is healthy and the parents did not report any case of developmental delay or psychiatric diseases in their first relatives.
The first signs of developmental problems noted by the parents were hypotonia, motor delay, and excessive crying at night. She sat without support at 8 months of age, walked at 24 months and still suffers from lack of sphincter control. No alterations were found in neuroimaging exams (cranial CT scan and brain MRI). She has lack of spoken language, weakly compensated by other forms of communication, a low level of cognitive functioning, poor eye contact and impaired social interaction skills. The patient met the DSM-IV criteria for pervasive developmental disorder not otherwise specified (PDDNOS), one of the categories within ASD. This diagnosis was supported by the administration of the Childhood Autism Rating Scale (CARS) [Schopler et al., 1980] and a questionnaire based on Autism Diagnosis Interview–Revised (ADI-R) [Lord et al., 1994].
On physical examination, the patient shows dysmorphic facial features, comprising blepharophimosis, short philtrum, everted lips, prominent central incisors and ears. Ophthalmologic evaluation disclosed high myopia. The craniofacial alterations do not fulfill clinical criteria for any known genetic syndrome.
G-banded karyotype revealed a balanced translocation between chromosome 2 and X [46,XX, t(2;X)(q11;q24)] in the proband (Fig. 1A). Parent karyotypes were normal.
The BAC clone RP11-34G16 spans the breakpoint on chromosome 2 (Fig. 1B). In the region covered by this BAC, there are three transcripts of non-characterized proteins: BC016831, AK 057596, and AL832439.
The BAC clone RP11-42G22 hybridized to both derivative 2 and derivative X as well as to normal X, and BAC RP11-631P19 was found to be distal to the breakpoint (Fig. 1C). This result indicates the disruption of the transcript AK123976 and places the breakpoint in a region that also spans two other genes: RHOXF1 (Rhox homeobox family, member 1, originally called OTEX) and RHOXF2 (Rhox homeobox family, member 2, originally called PEPP2). We were unable to confirm if these genes were disrupted since no probes were available to narrow down the breakpoint area.
Microarray data revealed that the patient is homozygous for all the SNP markers on chromosome 5, suggesting uniparental isodisomy (UPD) (Fig. 2A). Patient and parents were genotyped for five microsatellite markers, distributed along the entire chromosome, which showed that the isodisomy was maternally inherited (Fig. 2B). Furthermore, we also identified a duplication on chromosome 5q11, ranging from ∼49.5 to ∼52.1 Mb (Fig. 2A,C). The duplication was confirmed by the presence of a microsatellite marker (D5S2107) in heterozygosity in this region (Fig. 2B), which was the only informative marker out of the four tested.
Near the breakpoints there are two functionally important genes, UBE2A and GLUD2. GLUD2 is not abundantly transcribed in DPSC, and therefore we only investigated the expression levels of UBE2A. qPCR analysis showed that transcriptional levels of UBE2A in DPSCs from the studied patient are not significantly different from the controls (Normalized expression values—patient: 1.02; controls: 1.22 ± 0.22; Mann–Whitney test P = 0.78).
We identified a girl with ASD who has a de novo balanced translocation involving the chromosomes 2q11 and Xq24. By FISH analysis, we could only confirm the disruption of AK123976, located on chromosome X, which is yet a very poorly characterized transcript. The breakpoint region on chromosome X also spans RHOXF1 and RHOXF2 genes. Although it has not been tested in neuronal tissue yet, there are evidences that RHOXF2 can regulate the expression of genes that play important roles in nervous system, such as axonal guidance, neuronal migration and signal transduction in neurons [Liu et al., 1999; Vuletic et al., 2005; Round and Stein, 2007; Hu et al., 2008; Hu et al., 2010].
It is possible that chromosomal balanced translocations disrupt regulatory elements important to control the surrounding genes of the breakpoint regions [Fenton et al., 2006; Cinquetti et al., 2008]. We notice that there are potential candidates near the chromosome X breakpoint: UBE2A at 468 kb and GLUD2, at 845 kb distal. Nonsense mutation in UBE2A seems to be a cause of mental retardation [Nascimento et al., 2006]. This gene encodes an ubiquitin-conjugating enzyme (E2), which interacts with UBE3A, the gene responsible for Angelman Syndrome, a phenotype that frequently presents ASD as comorbidity [Veltman et al., 2005]. On the other hand, GLUD2 encodes the enzyme glutamate dehydrogenase 2, important for the metabolism of the neurotransmitter glutamate. Several lines of evidence implicate glutamatergic neurotransmission system in ASD etiology [Jamain et al., 2002; Serajee et al., 2003; Shuang et al., 2004]. Although our data on the expression levels of GLUD2 were inconclusive, we observed that UBE2A did not differ between patient and control cells suggesting that the translocation does not affect UBE2A regulation.
The patient also presents a duplication of approximately 2.5 Mb on chromosome 5q11. The duplication is of paternal origin, suggesting that this alteration and the UPD was very possibly generated by an incomplete rescue of trisomy on chromosome 5. On karyotyping, we did not detect supernumerary chromosomes, suggesting that this segment is probably inserted somewhere in the genome, for instance on chromosomes involved in the translocation or on chromosome 5. Therefore, disruption of genes or regulatory regions caused by the insertion of this segment might be also contributing to phenotype. Although the genes located within this segment seem not be involved in neuronal development, we cannot exclude gene dosage effect as an additional mechanism contributing to the psychiatry alterations of this patient. In this regard, it is worthy to mention that at least two other cases of patients presenting mental retardation have been reported to have copy number variations involving this region [DECIPHER database http://decipher.sanger.ac.uk/patient/253998 and Barbosa-Melo et al., 2011].
To our knowledge, the studied case represents the second case in the literature of UPD on the entire chromosome 5, but the first of maternal origin. A first report on UPD on the entire chromosome 5, however of paternal origin, was described in a boy with spinal muscular atrophy (SMA) [Brzustowicz et al., 1994], a disorder mostly caused by homozygous deletions at the SMN1 gene, located at 5q11.2-q13.3 [Matthijs et al., 1996]. It was suggested that SMA in this boy was probably caused by the transmission of two copies of a paternal defective gene, instead of parental imprinting effects, since the patient does not present any other developmental abnormalities.
A case of paternal segmental isodisomy on chromosome 5q32-qter was identified in a patient diagnosed with childhood onset schizophrenia (COS) [Seal et al., 2006], a disorder that presents clinical symptoms and etiological mechanisms that overlaps with ASD [Ching et al., 2010; Gauthier et al., 2010]. In the region involved in the segmental isodisomy seen in the COS patient, more exactly on chromosome 5q34-q35.1, there is a cluster of gamma-aminobutyric acid (GABA) receptor subunit genes: GABRB2, GABRA6, GABRA1, GABRG2, and GABRP. GABAergic neurotransmission system has been implicated in the etiology of autism and schizophrenia [Ma et al., 2005; Schmitz et al., 2005; Fatemi et al., 2009; Gonzalez-Burgos et al., 2010].
Considering that UPD on chromosome 5 does not necessarily lead to behavioral abnormalities, it seems more likely that recessive mutations on maternal chromosome 5 inherited by this girl could be leading to ASD symptoms instead of imprinting effects caused by the UPD. In this regard, several candidate genes and regions on chromosome 5 have already been related to ASD and are summarized in Table II.
|NIPBL (5p13.2)||Cornelia de Lange syndrome (47–67% of individuals with de Lange syndrome have ASD)|
Basile et al. [2007
]; Berney et al. [1999
]; Bhuiyan et al. [2006
]; Moss et al. [2008
]; Oliver et al. [2008
|MEF2C (5q14)||5q14 microdeletion syndrome|
Berland and Houge [2010
]; Novara et al. [2010
]; Nowakowska et al. [2010
]; Zweier et al. [2010
|ALDH7A1 (5q23.2)||Pyridoxine-dependent epilepsy (3 out of 64 cases described are reported to have ASD)|
Bennett et al. [2009
]; Burd et al. [2000
]; Mills et al. [2010
|NSD1 (5q35.2-q35.3)||Sotos syndrome|
Battaglia and Carey [2006
]; Bolton et al. [2004
]; Kielinen et al. [2004
|SEMA5A (5p15)||Association study||Weiss et al. |
|PITX1 (5q31)||Association study|
Philippi et al. [2007
|5p15.2-p15.33||Cri du Chat syndrome (39% of individuals with Cri du Chat syndrome have ASD)|
Cantu et al. [1990
]; Dykens and Clarke [1997
]; Marshall et al. [2008
]; Moss et al. [2008
St Pourcain et al. [2010
]; Ma et al. ; Wang et al. [2009
In face of the genetic complexity of this case and the almost uniqueness of such alterations, even among ASD cohorts, we cannot rule out the possibility that all of the alterations found in this patient might contribute to the behavioral phenotype. In this regard, some examples of apparently oligogenic model of inheritance in ASD have been listed in the literature [Bakkaloglu et al., 2008; Poot et al., 2010; Leblond et al., 2012], and a deeper discussion on this theme can be found elsewhere [Jones and Szatmari, 2002; Cook and Scherer, 2008; Girirajan and Eichler, 2010; Poot et al., 2011]. Functional studies of the genes involved in the translocation and duplication as well as next generation sequencing of chromosome 5 might help in the near future to elucidate some of these questions.
We would like to thank the patient and her family, as well as Cassio Eduardo Raposo do Amaral for their contribution to this study. This work was supported by CNPq and FAPESP/CEPID grants.
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