Complex intrachromosomal rearrangement in 1q leading to 1q32.2 microdeletion: a potential role of SRGAP2 in the gyrification of cerebral cortex
© Rincic et al. 2016
Received: 28 December 2015
Accepted: 30 January 2016
Published: 20 February 2016
Van der Woude syndrome (MIM: 119300, VWS) is a dominantly inherited and the most common orofacial clefting syndrome; it accounts for ~2 % of all cleft lip and palate cases. Intellectual disability (ID) is characterized by significant limitations, both in intellectual functioning (cognitive deficit) and in adaptive behavior as expressed in conceptual, social and practical adaptive skills. Karyotyping has been the first standard test for the detection of genetic imbalance in patients with ID for more than 35 years. Advances in genetic diagnosis have laid chromosomal microarrays (CMA) as a new standard and first first-line test for diagnosis of patients with ID, as well as other conditions, such as autism spectrum disorders or multiple congenital anomalies.
The present case was initially studied due to unexplained cognitive deficit. Physical examination at the age of 18 years revealed cleft palate, lower lip pits and hypodontia, accompanied with other dysmorphic features and absence of speech. Brain MRI uncovered significantly reduced overall volume of gray matter and cortical gyrification. Banding cytogenetics revealed an indistinct intrachromosomal rearrangement in the long arm of one chromosome 1, and subsequent microarray analyses identified a 5.56 Mb deletion in 1q32.1-1q32.3, encompassing 52 genes; included were the entire IRF6 gene (whose mutations/deletions underlay VWS) and SRGAP2, a gene with an important role in neuronal migration during development of cerebral cortex. Besides, a duplication in 3q26.32 (1.9 Mb in size) comprising TBL1XR1 gene was identified. Multicolor banding for chromosome 1 and molecular cytogenetics applying a battery of locus-specific probes covering 1q32.1 to 1q44 characterized a four breakpoint-insertional-rearrangement-event, resulting in 1q32.1-1q32.3 deletion.
Considering that the human-specific three-fold segmental duplication of SRGAP2 gene evolutionary corresponds to the beginning of neocortical expansion, we hypothesize that aberrations in SRGAP2 are strong candidates underlying specific brain abnormalities, namely reduced volume of grey matter and reduced gyrification.
Van der Woude syndrome (MIM: 119300, VWS) is a dominantly inherited and the most common orofacial clefting syndrome; it accounts for ~2 % of all cleft lip and palate cases . A clinical synopsis for VWS predominantly includes mouth and teeth abnormalities (lower lip pits, cleft lip and/or palate and hypodontia). In addition, abnormalities of limb, skin, nails and genital and/or hearing loss could be present . 1q32-41 chromosomal location was mapped as being critical for VWS in 1987, when a patient with an interstitial deletion of chromosome 1q32-41 was reported . Only in 2002, by direct sequencing, mutations in the IRF6 gene were detected and linked to VWS and popliteal pterygium syndrome . About 70 % of VWS causal mutations occur in IRF6 gene , however, in less than 2 % of individuals with VWS entire IRF6 gene is deleted .
Nowadays it is worldwide recognized that IQ test score of 70–75 and lower, indicates a limitation in intellectual functioning or cognitive deficit. Intellectual disability (ID) is characterized by significant limitations, both in intellectual functioning (cognitive deficit) and in adaptive behavior as expressed in conceptual, social and practical adaptive skills . ID is divided into five categories based on IQ (mild, moderate, severe, profound and unable to classify) . In addition to that, ID can be grouped into syndromic (patients with one or multiple additional clinical features) and non-syndromic (i.e. ID as sole clinical feature). Karyotyping has been the first standard test for the detection of genetic imbalance in patients with ID for more than 35 years. Advances in genetic diagnosis have laid chromosomal microarrays (CMA) as a new standard and first first-line test for diagnosis of patients with ID. Cytogenetic and CMA as a “state-of-the-art” molecular-cytogenetic method are used in other conditions as well, such as autism spectrum disorders, multiple congenital anomalies and diverse brain diseases. Genetic findings in children with autistic disorders support conclusion that cytogenetic and molecular-cytogenetic studies should be considered as compulsory in terms of detecting possible genetic causes of cognitive deficit and brain diseases [9, 10].
At the age of 18 years the female patient was studied due to unexplained cognitive deficit. She was born after an uneventful pregnancy after 32 weeks of gestation (birth weight: 2400 g, birth length: 40 cm) as a child of closely related parents (3rd degree). According to scant data on her early development, she started to walk at the age of 2 years and her language development was severely delayed. The girl was born with palathoshisis which was surgically corrected at the age of 3 years, when also the encephalopathy, vesicoureteral reflux, expressive (motor) dysphasia and developmental delay were diagnosed. At the age of 9 years she still could not control the sphincters and was diagnosed with moderate to severe cognitive deficit and undeveloped speech (due to articulation disorder), and was moved from socially deprived environment in foster care homes. In addition to cleft palate as the primary clinical feature, she had thin lips with bilateral pits, indistinct and short philtrum, flat midface, narrow palpebral fissures, hypodontia (missing upper incisor) with irregular dental growth, acne-prone skin, hirsutism, broad thumbs, and short and tapering fingers. By the age of 18 years she developed some limited communication skills, but due to articulation irregularities the speech was rather incomprehensible and reduced to short sentences. Graphomotor development was delayed; no writing and reading skills were developed. She was deprived in spatial orientation and was not able to understand the concept of time.
Materials and methods
Cytogenetics and molecular cytogenetics
This patient was studied within the project approved by the ethics committee of the School of Medical, University of Zagreb and the institution from which the patient comes. Peripheral blood was taken with a written informed consent by the institution from which the patient comes. Banding cytogenetics from peripheral blood lymphocytes was done according to the standard procedure. Fluorescence in situ hybridization (FISH) was done according to standard protocols using multicolor-banding probe-sets (MCB) and bacterial artificial chromosome (BACs) probes [9, 10]. All BACs used in this study are listed in Additional file 1. Genomic DNA was extracted from whole blood by Puregene DNA Purification Kit (Gentra Systems, Minneapolis, MN, USA) following manufactureinstructions. Multiplex ligation dependent probe amplification (MLPA) analysis was performed according to the manufacturer’s instructions (MRC-Holland, the Netherlands) using ABI-PRISM 3130XL Genetic Analyzer (Applied Biosystems, Foster City, USA). MLPA data analysis was done by use of GeneMarker software package (SoftGenetics, USA). Subtelomeric MLPA (P036-E2, P070-B2) and microdeletion/microduplication (P245-B1, P297-B2) probe sets were used. Arraycomparative genomic hybridization (aCGH) was performed on Agilent oligonucleotide SurePrint G3 Human Genome microarray 4X180 K (Agilent Technologies, Santa Clara, CA, USA). The array was processed following the manufacturer’s recommended protocol, and a sex-matched non-disease control sample (Promega, Mannheim, Germany) was used as a reference. Array results were analyzed using Cytogenomics software setting ADM2 aberration algorithm. Publicly available data for spatio-temporal expression profiles in brain  was screened by specially designed algorithm for all detected genes with aberrant copy number as previously described .
Magnetic resonance imaging was performed on a 3T MR device (Magnetom TrioTim, Siemens; Germany), with 32-channel head coil, using standard set of sequences that included sagittal 3D magnetizationprepared rapid acquisition gradient echo (MPRAGE) sequence with voxel size 1 mm x 1 mm x 1 mm (TR = 2300 ms; TE = 3 ms; flip angle = 9 degrees; matrix : 256 x 256). Volumetric processing of MR images was conducted by using the CIVET (version 1.1.11) pipeline developed at Montreal Neurological Institute, Brain Imaging Centre . This automated pipeline provided tools for observer independent corticometric analysis [14–28]. The calculated measurements included volumes of the grey and white matter tissue, of cerebrospinal fluid, and gyrification index for both hemispheres. Quantification of regional cortical thicknessaverages where lobe borders were determined by sulcal landmarks and detected by the CIVET pipeline, and regional/lobar cortical volume and surface area estimates were made for parietal, occipital, frontal, and temporal lobes, and for isthmus of cingulate gyrus, parahippocampal and cingulate gyrus, and insula. The gyrification index is a metric that quantifies the amount of cortex buried within the sulci compared to the amount of surface visible cortex. The gyrification index was computed by dividing the total cortical surface area with the area of the convex hull.
Genes important for clinical phenotype of the patient from OMIM database
laminin subunit beta 3
Junctional Epidermolysis Bullosa, Herlitz Type and Non-Herlitz Type;
Amelogenesis imperfecta, type IA
Junctional Epidermolysis – autosomal recessive skin disorder in which blisters occur at the level of the lamina lucida in the skin basement membrane, Herlitz type is more severe than Non-Herlitz type and often results in early death;
Amelogenesis imperfecta IA is characterized by enamel that may not develop to normal thickness
G0/G1 switch 2
?Van der Woude syndrome (VWS)
VWS is dominantly inherited developmental disorder characterized by pits and/or sinuses of the lower lip, and cleft lip and/or cleft palate (CL/P, CP)
interferon regulatory factor 6
Van der Woude syndrome;
Popliteal pterygium syndrome 1 (PPS);
Orofacial cleft 6
VWS is dominantly inherited developmental disorder characterized by pits and/or sinuses of the lower lip, and cleft lip and/or cleft palate (CL/P, CP);
PPS has a highly variable clinical presentation including orofacial, cutaneous, musculoskeletal, and genital anomalies;
Orofacial cleft 6 is nonsyndromic cleft lip with or without cleft palate
retinal degeneration 3
Leber congenital amaurosis 12
early-onset childhood retinal dystrophies characterized by vision loss, nystagmus, and severe retinal dysfunction
NIMA-related kinase 2
?retinitis pigmentosa 67;
?Van der Woude syndrome
hereditary retinal conditions in which degeneration of rod photoreceptors is more pronounced than that of cone photoreceptors
potassium channel, voltage gated eag related subfamily H, member 1
Zimmermann-Laband syndrome 1
Zimmermann-Laband - rare disorder characterized by gingival fibromatosis, dysplastic or absent nails, hypoplasia of the distal phalanges, scoliosis, hepatosplenomegaly, hirsutism, abnormalities of the cartilage of the nose and/or ears and developmental delay
Temple-Baraitser syndrome - rare developmental disorder, severe mental retardation and anomalies of the first ray of the upper and lower limbs with absence/hypoplasia of the nails.
Volumetric brain MRI analysis
gyrification index gray
gyrification index white
gyrification index mid
Clinical physical presentation - van der Woude syndrome
Here we report a 1q32.1-1q32.3 deletion of 5.56 Mb in a girl patient presenting a main features of VWS accompanied with severe cognitive deficit. Most prominent VWS phenotypic characteristics in the present case are well described in the literature and could be assigned to at least several genes (LAMB3, G0S2, IRF6, RD3, NEK2 and KCNH1) described in Table 2. Haploinsufficiency score1 for IRF6 gene is extremely low (HI score 2.02 %), it is therefore most likely that in present case phenotype characteristics (cleft palate, lower bilateral pits and hypodontia) are consisted with the literature descriptions of VWS, and are repercussions of IRF6 haploinsufficiency. Besides, some cases with small deletions in IRF6 gene were described as well. Three cases with a microdeletion (0.1–1 Mb in size) were detected by CMA in a large cohort of patients with clinical diagnosis of VWS [29, 30]. Mutation in G0S2 and NEK2 genes were associated with phenotype of VWS , but contribution of haploinsufficiency of these genes in our case is questionable due to two facts: I) high HI score for booth genes (G0S2 88,45 and NEK2 25,91), and II) NEK2 is only partly deleted. Mutations in LAMB3 gene causes autosomal recessive skin disorder with blisters on the skin – Junctional Epidermolysis (JEB) . In presented case LAMB3 deletion might have unmasked the recessive allele, as the HI score is high (58.66). Therefore, the phenotype manifestations restricted to acne-prone skin could represent a very mild form of Non-Herlitz type of JEB (MIM 226650). Conformation of Non-Herlitz type of JEB could be done only by direct sequencing of affected LAMB3 gene. Mutations in KCNH1 gene are responsible for two severe phenotypes, Temple-Baraitser syndrome (MIM: 611816) and Zimmermann-Laband syndrome 1 (MIM: 135500), respectively; both characterized by similar clinical synopses and severe cognitive deficit (Table 2.). The HI score for KCNH1 is relatively high (22.53) but in the present case distinct physical phenotype ((wide mouth, broad nasal bridge, hirsutism, broad thumbs and short and tapering fingers) could be due to KCNH1 haploinsufficiency.
Research of cognitive function has shown that group of patients with clinical VWS diagnosis have just a slightly wider distribution of full-scale IQ (84 to 118) compared to controls (96 to 123) . The evaluation of brain morphology in patients with clinical diagnosis of nonsyndromic clefts of the lip and/or palate have pointed to some brain abnormalities. The most severely affected region was the left temporal lobe with decreased gray matter volume . In presented case, brain MRI showed reduced temporal lobe in all volumetric measurements (Additional file 3), but this finding alone cannot sufficiently explain a cognitive deficit.
Only two reported cases were studied by high resolution array technique. Tan et al.  reported a patient with de novo 2.3 Mb 1q32.2 microdeletion, presenting orofacial VWS phenotype. He was otherwise healthy individual, followed up closely for the last 20 years and there was no evidence of cognitive deficit . Gene content shared with our case included PLXNA2 and SYT14 (Fig. 6). Since there was no evidence of cognitive deficit in case of Tan et al. , we may only discuss the contribution of PLXNA2 and SYT14 genes to the cognitive phenotype in our case. PLXNA2 mediates signals from two semaphorins (SEMA3 and SEMA6) and plays a role in axon guidance (guiding axonal growth cones), invasive growth and cell migration. Although PLXNA2 HI score is 5.01, the lack of cognitive phenotype in case reported by Tan et al. could be due to incomplete penetrance, as knockout mice for SEMA3 and SEMA6 show the neural abnormalities to some extent. It is possible that plexin-semaphorn diversity and brain “plasticity” could prenatally compensate for PLXNA2 haploinsufficiency, meaning that a signal transduction of SEMA3 and SEMA6 could go via other receptors during neurodevelopment. SYT14 is expressed prenatally, has HI score of 18.19, and has a role in prenatal neurotransmission. In case of Tan et al.  distal breakpoint is disrupting SYT14, so the haploid state might possibly be sufficient for the normal development. The second case studied with CMA, was a 22-month-old baby presenting with a 2.98 Mb deletion in 1q32.2–q32.3 region, who in addition to VWS, displayed developmental delay and dysmorphism . KCNH1 and RCOR3 genes were the only two deleted genes enriched in human brain and overlapped with present case (Fig. 6). Mutations in aforementioned KCNH1 gene are responsible for two syndromes, the Temple-Baraitser (MIM 611816) and Zimmermann-Laband (MIM 135500) syndrome 1, both being developmental disorders characterized by severe cognitive and physical abnormalities (Table 1.). RCOR3 gene important for restricting the neural features to neuron has HI score of 13.05 and is prenatally expressed. Taking into account the above mentioned facts, KCNH1 and ROCR3 are good candidate genes whose haploinsufficiency may be liable for severe cognitive deficit combined with dysmorphism.
The main players for cognitive deficit (1q32.1 :SRGAP2 and CD55; 3q26.33 :TBL1XR1)
In comparison to two cases studied by array, our case has a proximal breakpoint further extended in 1q32.1, and the deletion covers additional genes including SRGAP2 and CD55.
Short description on ancestral SRGAP2 function
↑ Proliferative zone (VZ and SVZ)
↑ Postmitotic regions (CP)
↑ throughout cortical development culminating at P1 corresponding to the peak of neuronal migration in the cortex
negatively regulate the rate of radial migration by promoting LP branching and dynamics
stage 1 neurons:
through its F-BAR domain, induces filopodia
stage 2 neurons:
↑ significantly increased the total number of primary neurites emerging from the cell body
↑ increase the number of primary neurite branches
mice are viable (although born significantly below the expected Mendelian ratio)
No abnormality in cortical lamination
dendritic spine morphology:
↑ neck length
↑ spine density
Juvenile: ↓ head width
Adult: ↑ head width
↓ in cortical neurons led to a significant decrease in both axonal and dendritic branching
↑significant increase in the percentage of neurons that have reached the dense CP and a corresponding decreased percentage of neurons in the IZ
↑ accelerated radial migration
↓ LP in layer 5/6 was significantly less branched and less complex
dendritic spine morphology:
↑ neck length
↑ spine density
Juvenile: ↓ head width
Adult: ↑ head width
significantly reduced the number of cells reaching the CP
↓severely inhibited radial migration
↑increase in the percentage of neurons with multiple processes emerging from the cell body – induce excessive branching of radially migrating neurons
no transition from multipolar cells to a full LP (no cell body translocation)
↑ spine heads
↓ spine neck
↑ enlargement of dendritic spines
Short overview of SRGAP2 paralogs
Estimated time of duplication
Expression in human braina
protein sequence is highly constrained (no changes among non-human primates, and only a single amino-acid change between human and mouse orthologs)
N-terminal F-BAR domain – involved in membrane deformation;
central Rho-GAP domain – specifically stimulates GTPase activity of Rac1;
C-terminal tail with SH3 domain – interacts with
F-BAR domain = autoinhibition?
↑in the germinal layers and cortical plate
controls cortical neural migration
~3.4 million years
promoter and 1–9 exons of ancestral SRGAP2
3'-breakpoint located in intron 9 → truncated
interacts with SRGAP2A
~2.4 million years
duplication of SRGAP2B to 1p11.2
3'-breakpoint located in intron 9 → truncated F-BAR domainb
↑in the germinal layers (in culture longer maintains a high level of expression than SRGAP2A)
inhibits SRGAP2A - SRGAP2 knockdown
~1 million years
duplication of SRGAP2B and additional deletion of exons 2 and 3 → premature termination codonb
most likely no function – probably subjected to nonsense-mediated decay
CD55 (CD55 molecule, decay accelerating factor for complement, HGNC: 2665, 1q32) gene encodes glycoprotein that has a physiological role to inhibit the complement cascade, protecting autologous cells and tissues from complement-mediated damage. It was recently demonstrated that certain number of genes belonging to macrophages/immune system (including CD55) show differential expression between ages of 3 to 6 months after birth (time of intense overshoot-type synaptic formation – number of synapses reach the peak, and pruning taking place after this peak) . The process of synaptic phagocytosis by microglia which is occurring at the time of the overshoot-type synaptic formations could cause damage to normal tissue and mitochondria. The fact that CD55 shows the higher expression at 6 months than at 3 months, may suggests that normal brain tissue is more protected at 6 M . The deletion of CD55 gene in our case could have potential role in the “fine tuning” of synaptic pruning in a negative way. Reduced level of the glycoprotein, due to a deletion, could hypothetically make normal brain tissue more prone to negative side effects of phagocytosis during pruning period. Further functional analysis could shed more light on this process and reveal the neuro-protective genes.
TBL1XR1 (transducin (beta)-like 1 X-linked receptor 1, HGNC:29529, 3q26.33) is essential in mediating transcription silencing by unliganded nuclear receptors (NRs) and other regulated transcription factors (TFs) [44–46]. Through the recruitment of the specific proteasome complex, TBL1XR1 can act as a transcription activator which mediates the exchange of corepressors for coactivators [47, 48]. TBL1XR1 haploinsufficiency was so far described in only three patients, all characterized by facial dysmorphism, speech delay, mild to moderate cognitive deficit, and lack of autistic behaviors [49, 50]. Interestingly, mutations in TBL1XR1 gene were recently identified in three patients displaying ASD and severe ID, but without any obvious dysmorphism or recurrent comorbidities [51, 52]. HI score for TBL1XR1 is 6.81.
The deletion in our patient appeared to be a very rare event and provides a valuable insight for genotype-phenotype correlations in genetic disorders. The phenotype in presented case points on the importance of looking for the recessive disorders when deletion is detected. The deletion might in turn unmask recessive disorder; even when the HI score is low. Only by combining the GTG-banding, FISH and CMA analyses we were able to fully characterize the structural rearrangement within 1q. Brain MRI is crucial for the patients with cognitive deficit, as it allows better genotype-phenotype correlations and understanding of gene aberration consequences. Finally, the aberrations in SRGAP2 are strong candidates underlying specific brain abnormalities, namely reduced volume of grey matter and reduced gyrification. Further analyses of the cases with SRGAP2 aberrations should be highly informative in this respect.
Haploinsufficiency score (HI score) of less than ten, indicating that genes are dosage sensitive and expected to have phenotypic effect. From https://decipher.sanger.ac.uk/
We are grateful to the patient and her foster parents for participating in this study. We want to thank Professor Ivica Kostovic for all the help and constructive conversation during the writing. This work was supported in parts by the Croatian Ministry of Science Education and Sport (LB); Business Innovation Croatian Agency – Croatian Institute for Technology BICRO-HIT (FB) and Croatian Academy of Sciences and Arts Foundation and University of Zagreb research support (ZK).
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