Human Molecular Genetics, 2003, Vol. 12, No. 13 1463-1474
DOI: 10.1093/hmg/ddg165
© 2003 Oxford University Press
CALL interrupted in a patient with non-specific mental retardation: gene dosage-dependent alteration of murine brain development and behavior
1Flanders Interuniversity Institute for Biotechnology (VIB) and 2University Hospital Leuven, Center for Human Genetics, Leuven, Belgium, 3Zentrum für Molekulare Neurobiologie, Eppendorf Clinic, University of Hamburg, Hamburg, Germany and 4Laboratory of Neurochemistry and Behavior, Born-Bunge Foundation, Department of Biomedical Sciences and Department of Neurology/Memory Clinic, Middelheim Hospital, University of Antwerp, Antwerp, Belgium
Received November 12, 2002; Revised April 22, 2003; Accepted April 30, 2003
| ABSTRACT |
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Investigation of MR patients with 3p aberrations led to the identification of the translocation breakpoint in intron five of the neural Cell Adhesion L1-Like (CALL or CHL1) gene in a man with non-specific mental retardation and 46,Y, t(X;3)(p22.1;p26.3). The Xp breakpoint does not seem to affect a known or predicted gene. Moreover, a fusion transcript with the CALL gene could not be detected and no mutations were identified on the second allele. CALL is highly expressed in the central and peripheral nervous system, like the mouse ortholog close homolog to L1 (Chl1). Chl1 expression levels in the hippocampus of Chl1+/- mice were half of those obtained in wild-type littermates, reflecting a gene dosage effect. Timm staining and synaptophysin immunohistochemistry of the hippocampus showed focal groups of ectopic mossy fiber synapses in the lateral CA3 region, outside the trajectory of the infra-pyramidal mossy fiber bundle in Chl1-/- and Chl1+/- mice. Behavioral assessment demonstrated mild alterations in the Chl1-/- animals. In the probe trial of the Morris Water Maze test, Chl1-/- mice displayed an altered exploratory pattern. In addition, these mice were significantly more sociable and less aggressive as demonstrated in social exploration tests. The Chl1+/- mice showed a phenotypic spectrum ranging from wild-type to knockout behavior. We hypothesize that a 50% reduction of CALL expression in the developing brain results in cognitive deficits. This suggests that the CALL gene at 3p26.3 is a prime candidate for an autosomal form of mental retardation. So far, mutation analysis of the CALL gene in patients with non-specific MR did not reveal any disease-associated mutations.
| INTRODUCTION |
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Subtelomeric deletions usually result in contiguous gene syndromes with mental retardation (MR) as a clinical feature (1). More than 70 patients with 3p- syndrome (2,3) or partial 3p trisomies (4) have been reported. Molecular analysis shows that the deleted or duplicated regions vary in size (3). It is thus assumed that in the 3p chromosomal region a number of genes contribute to the MR phenotype (5,6). MR can be classified as either syndromic or non-specific. In patients with syndromic forms of MR, the clinical manifestations include MR associated with other physical features (such as neurological symptoms, skeletal defects or facial dysmorphism), whereas in patients with non-specific MR no distinctive clinical or biochemical manifestations occur, apart from the cognitive impairment. In the last 6 years, several genes have been identified in non-specific X-linked MR (reviewed in 7). Recently, the neurotrypsin (PRSS12, MIM no. 606709) gene at 4q24 has been found to be responsible for an autosomal recessive form of non-specific MR (8). We present data on a patient with non-specific MR and an interruption of one allele of the neural cell adhesion L1-like (CALL or CHL1; hereafter referred to as CALL) gene. The CALL gene has already been reported as a candidate for autosomal-recessive non-specific MR (9). Moreover, it is proposed as a gene which may be associated with schizophrenia (10). Furthermore, CALL is most frequently deleted in patients with the 3p- syndrome (5,11,12). We provide evidence that the CALL gene might be involved in cognitive and behavioral functions, through CALL and Chl1 mRNA expression studies in brain combined with histology and behavioral studies in Chl1-/- and Chl1+/- mice. Finally, a mutation analysis was performed in patients with non-specific MR and with no family history for the disease.
| RESULTS |
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FISH analysis of a t(X;3)(p22.1;p26.3)
We investigated patients with 3p chromosomal aberrations in order to identify autosomal candidate genes for non-specific MR in the 3p subtelomeric region. A 3p25.3
pter map was constructed in silico (Fig. 1). This region contains several brain-expressed genes such as CALL (GenBank accession no. NM_006614), contactin 6 (CNTN6), contactin 4 [an axonal-associated (AXCAM-related) cell adhesion molecule], a novel neuronal leucine-rich repeat (NLRR-1)-like, inositol 1,4,5-triphosphate receptor type 1 (ITPR1, MIM no. 147265), a Class B basic helixloophelix 2 (BHLHB2/DEC1, MIM no. 604256) and a KIAA0212 transcript. FISH analysis was performed with four BAC clones and one cosmid clone (Fig. 1, P1P5). In one patient with non-specific MR and translocation 46,Y,t(X;3)(p22.1;p26.3), signals of probe P2 were present on either side of the breakpoint, indicating that the CALL gene is affected in this patient.
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Cloning of the breakpoints
We used standard positional cloning strategies to clone the breakpoints in the patient with translocation 46,Y, t(X;3)(p22.1;p26.3). The Xp22.1 breakpoint was mapped to PAC clone RP6-102C13 (Fig. 2A). On 3p, the CALL gene was interrupted between exon 4 and exon 16 since a split signal was observed by FISH with BAC RP11166F3 (Fig. 2B and C). The aberrant HindIII band detected by Southern blot analysis with a probe derived from RP6-102C13 (Fig. 2D), was cloned and sequenced. A 26 bp insertion, ACATATATAT ATATATCCTT ATATAT was identified at the breakpoint in CALL intron 5 (BAC RP11-114K9 nucleotide position 16068). PCR with primer pairs (XpF1+3pR1 and 3pF1+XpR1), annealing at either side of the breakpoints, revealed the expected PCR products with gDNA of the patient but not with normal controls (Fig. 2E). RACE experiments starting from CALL exon 3 or 5 (3'-RACE) and exon 6 or 7 (5'-RACE) resulted in the exclusive amplification of the CALL gene derived from the intact second allele, indicating that no fusion transcript was present. Sequence analysis of the open reading frame (cDNA position 2723946) of the CALL cDNA of the patient did not reveal any mutation of the CALL gene on the second, wild-type allele. Finally, position effects by the 3p breakpoint were not expected since the nearest gene, contactin 6 (CNTN6) (13), was at 1 Mb from the CALL gene. So far, CALL seems to be the most telomeric gene on chromosome 3p.
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A contig map was constructed at the Xp breakpoint combining our data with information available via public (NCBI, Sanger) and private (Celera) databases. The Xp breakpoint was situated in a THE1-internal LTR/MaLR-class repeat (RP11-617O8 nucleotide position 85696). Using various gene prediction programs such as BLAST/unigene, GRAIL-1.3, GENSCAN, Fgene, Genefinder, Hexon and GeneMark, the first predicted genes are located 87 kb upstream (MAGE-B6) and 148 kb downstream (NA88-A pseudogene) with respect to the breakpoint. None of the two predicted genes are expressed in human brain (1416). However, expression of both genes could not be investigated in the presented patient since they are not expressed in peripheral blood leukocytes (PBLs) or fibroblasts. Our data strongly suggest that no gene on the X-chromosome is involved and that CALL is the only affected gene in this patient.
CALL and Chl1 expression
The CALL gene has been proposed as a candidate gene for non-specific MR because it is highly expressed in brain (11). Real-time quantitative PCR demonstrated high CALL expression in total fetal and adult brain, and in a Schwann cell culture, compared to other human tissues or cell lines (Fig. 3). mRNA expression levels of the CALL gene in PBLs, EpsteinBarr virus (EBV)-transformed cell lines or fibroblasts were very low to undetectable so we were unable to evaluate relative CALL expression levels in the only available material obtained from the patient.
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CALL has been identified as the mouse Chl1 ortholog in humans (11,17). Chl1 shows high expression levels in brain regions such as cerebral cortex, thalamus, hippocampus and amygdala (18,19). The Chl1-/- mouse (20), allowed us to investigate a Chl1 gene dosage effect in the hippocampus. Using real-time quantitative PCR, we could demonstrate that, in one-day-old (P1) Chl1+/- mice, the expression levels were half of those present in Chl1+/+ littermates. As expected, Chl1-/- mice did not show any Chl1 mRNA expression (Fig. 4A). Furthermore, we could detect a 2-fold decrease of Chl1 expression in the hippocampus of 6-day-old (P6) Chl1+/+ littermates compared to P1 Chl1+/+ mice (Fig. 4B). The observed Chl1 mRNA expression differences between the P1 and P6 littermates were very constant; a finding not observed for another L1 family member, Ncam180 (data not shown).
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Ectopic bundles of mossy fibers in Chl1-/- and Chl1+/- mice
Mouse hippocampi were dissected, fixed and embedded for histological and immunochemical examination. No morphological abnormalities were noticed using markers GFAP and F4/80 in P6 and adult brains of Chl1-/- and Chl1+/- mice (data not shown). However, in Chl1-/- and Chl1+/- adult brains, between one and three focal groups of bundles of mossy fiber synapses per section were situated outside of the trajectory of the infra-pyramidal mossy fiber bundles of the lateral CA3 region of the hippocampus, as detected by Timm staining. These ectopic mossy fiber synapses were detected in seven out of 10 Chl1-/- (Fig. 5E and J) and in three out of nine Chl1+/- mice (Fig. 5B, D, G and I), compared to one in seven Chl1+/+ mice. Synaptophysin staining in the same brains confirmed these ectopic mossy fiber synapses.
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Altered exploratory and social adaptive behavior in Chl1-/- and Chl1+/- mice
Male Chl1-/-, Chl1+/- and Chl1+/+ mice were subjected to a whole set of behavioral assessment studies (Table 1) and alterations were observed in the Chl1-/- mice. In the probe trial of the Morris Water Maze test, Chl1-/- mice displayed an altered exploratory pattern. In addition, the Chl1-/- mice were significantly more sociable and less aggressive, as demonstrated in the social exploration tests. The Chl1+/- mice showed a phenotypic spectrum ranging from wild-type to knockout behavior. A detailed description of the methods and results obtained with these studies can be found online, in the Supplementary Material.
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Screening for disease-associated mutations
We screened for mutations in all 26 coding exons (exons 328) and intronic boundaries in 20 patients with non-specific MR and with no family history for the disease. In comparison to the reference sequences, eight variants (Table 2) were identified of which five occurred at high frequency (>30%). These include one missense alteration in exon 3 (c.320C>T; p.L17F) with an allele frequency of 0.75/0.25, and four intronic variants namely IVS4+10G>C (0.83/0.17), IVS8-25C>T (0.70/0.30), IVS9+127 C>T (0.30/0.70) and IVS9-41G>A (0.73/0.27). The intronic variation (IVS27+18T>C) was detected in two patients only (0.95/0.05) while IVS12-33G>A was restricted to one single patient (0.98/0.02). Finally, an interesting missense variant in exon 14 (c.1711A>T, p.K480N) was noticed in one patient leading to heterozygosity at this position (0.98/0.02). This nucleotide change affects a non-conserved residue in the Ig5 domain of CALL. This variation was not found in 100 control samples (200 chromosomes) as revealed by sequence analysis of this exon, but was detected in the normally intelligent mother of this patient, indicating it to be a rare polymorphism.
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| DISCUSSION |
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Most patients with partial 3p monosomy show a contiguous gene deletion syndrome with constant clinical findings of severe MR, pre- and postnatal growth retardation and facial dysmorphism. Additional clinical features include deafness, digital abnormalities, renal and gastrointestinal anomalies and congenital heart defects, depending on the extent of the deletion (21). Patients with partial 3p trisomy are usually moderately to severely mentally retarded, show facial dysmorphism and often include clinical features of the associated partial monosomy (2224). However, in some patients the phenotype is not associated with major dysmorphic features (25). Patients with MR and apparently balanced translocations involving the 3p chromosomal region have not been reported so far. Taken together with various observations (3,6,26,27), this study shows that the 3p chromosomal region is a hot-spot in the etiology of autosomal forms of MR.
Several patients with MR and 3p aberrations were investigated by fluorescent in situ hybridization (FISH) analysis. Through positional cloning of a translocation t(X;3)(p22.1;p26.3), we provide strong evidence that the CALL gene is involved in non-specific MR. With real-time quantitative PCR we demonstrated that the CALL gene is highly expressed in the central and peripheral nervous systems, confirming that it is a candidate gene for a functional role in the nervous system. The CALL gene was cloned and mapped (11) based on knowledge of the mouse ortholog Chl1 (17). CALL belongs to the L1 family of immunoglobulin (Ig)-like neural cell adhesion molecules. It has several isoforms and contains six Ig-like domains, four fibronectin type III-like domains, a single-pass transmembrane domain and a short cytoplasmic tail (11). CALL is most closely related to L1CAM and shows an overall 32% identity (49% similarity). Like L1CAM, CALL has recognition sites for integrins, fibroblast growth factor receptors and phosphotyrosine kinases (28). Neural cell adhesion molecules, such as L1, are involved in neurite outgrowth (29,30), axonal guidance (31), cell migration and adhesion (32). These actions are processed via specific signal transduction pathways (reviewed in 33,34). Mutations in neural cell adhesion molecules have been implicated for several neurological disorders. L1CAM mutations, responsible for the L1-syndrome, mainly affect the central nervous system. This allelic X-linked MR (XLMR) disorder includes X-linked SPG1, MASA syndrome and X-linked hydrocephalus (3539). Mutations in L1CAM have been found to interfere with ligand interactions and cell-surface expression (40). Heterozygous L1CAM mutations in women can be associated with a variable phenotype including MR, abnormal brain development, spastic paraplegia and adducted thumbs (41). Occasionally, MR is the only clinical feature in woman carriers (28,42). Functional analysis in mice and humans have been reported, including promoter (43), ligand interaction (44) and genotypephenotype correlation studies (41,45,46).
Since one allele of the CALL gene is interrupted in the patient, and no mutation was found on the second allele, we propose that the pathogenic mechanism in this patient is haplo-insufficiency. Angeloni et al. (5) already suggested that CALL haplo-insufficiency could be the pathogenic mechanism in 3p- syndrome based on its location in the deleted regions. Presumably, the MR phenotype of patients with partial 3p trisomy could also be the result of disturbed CALL gene dosage. Because of the very low expression levels in PBLs, EBV-transformed or fibroblast cell lines we could not investigate a possible gene dosage effect of CALL mRNA expression. For the same reason, potential position effects of the nearest flanking genes at the Xp breakpoint could not be investigated. The nearest gene, CNTN6, is located at
1 Mb of the 3p breakpoint and it is thus unlikely that it is affected by the rearrangement (47,48). This can not be excluded, however, as a long-range effect of a chromosomal anomaly at a distance of 1 Mb has recently been reported (49).
The phenotype of the Chl1-/- mice shows subtle brain abnormalities in the form of aberrant projection of mossy fibers in the CA3 subfield of the hippocampus (20) and an altered exploratory behavior, suggesting that cognitive processes involving spatial memory are disturbed. Since Chl1+/- mice were not included in their study (20), we initiated tests in Chl1-/- and Chl1+/- mice in order to support the hypothesis of haplo-insufficiency by analyzing the Chl1 expression levels and studying their behavior. Chl1 has an overall identity of 83% with CALL (97% identity in the C-terminal 105 amino acids). Their mRNA expression patterns are similar with highest expression in brain and in neural cell cultures (11,17). Chl1 promotes neurite outgrowth in vitro (19,50) and prevents neuronal death (51). In contrast to L1, Chl1 does not bind to itself, nor does it bind heterophilically to L1 (19). However, both Chl1 and L1 show overlapping expression patterns (19) and their expression is up-regulated in axonal regeneration (52,53).
By real-time quantification we could clearly demonstrate a gene dosage effect in mouse hippocampi. The Chl1 mRNA levels of Chl1+/- mice were
50% of those found in Chl1+/+ controls. Liu et al. (18) demonstrated a strictly regulated gradient of Chl1 expression with a high-caudal to low-rostral pattern in rat brain during embryonic development and noticed highest Chl1 levels at P1P7. Thereafter, the expression drops significantly but mRNA levels sustain during adulthood. Both findings support the importance of the spatial and temporal availability of the correct amount of Chl1 during brain development. Indeed, we also find highly constant expression levels at the time points investigated (Fig. 4). The question then arises whether a 50% reduction of Chl1 mRNA expression could result in a disturbed development of neurons leading to abnormal cognitive function and behavior.
Histological examination of the brains of Chl1-/- and Chl1+/- mice demonstrated an aberrant mossy fiber organization in the CA3 region of the hippocampus. However, the aberrant pattern seen in the Chl1-/- mice was different from the one reported by Montag-Sallaz (20). They described a disorganized CA3 region of the hippocampus with individual thin mossy fibers or some axons forming small bundles, which traveled in a disorganized way through the CA3 region between supra and infra-pyramidal mossy fiber bundles. We detected significantly more bundles of ectopic mossy fiber synapses in the lateral CA3 region of the hippocampus of Chl1-/- and Chl1+/- mice. Ectopic mossy fibers have already been reported in Ncam180-/- mice (54). However, in other Ncam180 null mutant mice, a reduction of mossy fibers in the CA3 subregion was noticed (55). Similarly, the Gdi1-/- mice, the only knockout mouse model for X-linked non-specific MR so far, did not show gross brain abnormalities (56), but a trilamination of the infra-pyramidal mossy fibers and disorganized CA3 pyramidal cell layer in the hippocampus of these mice was reported. Moreover, they showed decreased synaptic potential of hippocampal neurons in these knockout mice. Further experiments are necessary to define the situation in Chl1-/- and Chl1+/- mice.
We subsequently investigated whether the histological aberrant brain organization resulted in altered behavior of Chl1-/- and Chl1+/- mice. In the probe trial of the Morris Water Maze test, the Chl1-/- mice were less efficient in exploratory searching behavior, a result in agreement with the observations by Montag-Sallaz (20). However, the swimming patterns in their study were different from the retention pattern we observed. Impaired probe trial performance could be indicative of alterations in exploratory behavior or behavioral flexibility that are not due to hippocampal defects (57). In the resident-intruder test, Chl1-/- mice were less aggressive, more sociable and showed mating behavior, a finding that was not observed in Chl1+/+ mice. Interestingly, in all social exploration and interaction tests, the Chl1+/- mice showed a behavioral spectrum ranging from wild-type to knockout, resulting in a mean that reflects the intermediate score. Behavioral studies with Ncam-/- and Ncam+/- mice also demonstrated altered aggressive responses in these animals compared to wild-type mice (58), indicating that the phenotypic outcome of other genes of the immunoglobulin superfamilies could be gene dosage-dependent and that these genes affect social interactions, which often involve the amygdala and the hippocampus. Moreover, increased social and mating behavior has also been described for the Gdi1-/- mouse (heterozygous mice not tested) in the residentintruder test (56).
The discrepancies in mossy fiber projections and in the behavior in the Morris Water Maze as well as in open field experiments between our mice of a mixed Sv129/C57BL/6J background and mice having an almost pure C57BL/6J background (20) illustrate the importance of the genetic background (59,60). However, in both mouse strains an aberrant mossy fiber projection and an altered exploratory behavior of Chl1-/- mice was observed. Amongst many other examples, genetic background differences were also observed for mossy fiber terminal configuration in Fmr1-/- mice (61,62) as well as for the extent of ventricular enlargement in L1-/- mice (45,63,64). As mentioned earlier, more than one gene has been proposed as a candidate gene for the MR phenotype in the 3p- syndrome. Centromeric to the CALL gene, several other candidate genes for MR can be predicted based on their relatively high expression in the (developing) brain and their functional involvement in signaling pathways and/or presumed role in growth regulation of neurons. Two genes, the CNTN4 and NLRR-l-like genes, are predicted in the 3p25.3 chromosomal region. These genes are promising candidates for autosomal dominant and/or recessive forms of MR. Both genes (but not CALL) are deleted in a child with developmental delay and a 3p25.3p26.2 interstitial deletion (6), and both are linked to the mapped interval in a six-generation family with autosomal-recessive MR described by Higgins and co-workers (9). In this family, the CALL gene was excluded by single-strand conformation polymorphism analysis (J. Higgins, personal communication). Further investigations on patients with MR and apparently balanced 3p translocations might lead to the discovery of novel MR genes in the proximal 3p21p25 chromosomal region. Indeed, the novel gene MEGAP/srGAP3 has recently been proposed as one candidate gene for MR associated with the 3p- syndrome (65), but others might still be discovered.
Mutation analysis of the CALL gene in 20 MR patients with non-specific MR did not reveal any disease-associated mutations. Eight polymorphisms were identified (six intronic and two missense changes) including one rare missense change (p. K480N). Recently, sequence analysis of the CALL gene in 24 schizophrenia patients reported only four nucleotide variants (66), of which two were also identified by our screen. In their study, the polymorphic missense alteration in exon 3 (n.320C>T, p.L17F) was correlated with schizophrenia (note that they use a different exon numbering). The Leu allele was present at higher frequencies in schizophrenic patients (0.71/0.29) compared with controls (0.63/0.37). The frequency of the Leu17 allele in our (small) MR subpopulation was even higher (0.75/0.25).
In conclusion, we provide evidence that the CALL gene is involved in non-specific MR. In Chl1+/- mice a gene dosage effect was clearly demonstrated. Since the strictly regulated spatial and temporal Chl1 expression is important for axonal development, abnormalities in Chl1 expression may lead to the subtle histological and behavioral phenotypes in Chl1-/- and Chl1+/- mice. This suggests that CALL haplo-insufficiency is a likely mechanism contributing to the MR phenotype in the reported patient with translocation 46,Y,t(X;3)(p22.1;p26.3). Although it is likely that there are other MR genes in the 3pter chromosomal region, we propose the CALL gene as a first candidate gene for an autosomal dominant form of non-specific MR. The detection of mutations in other patients will have to prove this hypothesis.
| MATERIALS AND METHODS |
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Patients with 3p aberrations
The local Research and Medical Ethical Committee of the University Hospital of Leuven approved the study and informed consent was obtained from the participants or their guardians. Fourteen patients with MR and 3p aberrations were investigated by FISH after conventional G-, T- and high resolution banding was performed on blood lymphocytes.
FISH analysis
FISH analysis was performed on metaphase spreads of blood leukocytes or of EBV-transformed blood lymphocytes, following standard procedures (67). A lysamine-labeled alpha-satellite probe of chromosome 3 (Appligene Oncor, Darra, Australia) was used with the 3p25.3
pter probes RP11-731E12 (GenBank accession no. AC055763), including the 5' region of the CALL gene at 3p26.3 (probe P1), RP11-114K9 (GenBank accession no. AC011609), including the 3' region of CALL (probe P2), RP11-497I24 (GenBank accession no. AC018833), close and centromeric to CNTN6 at 3p26.3 (probe P3), CTC-243A6, partially including the OXTR gene at 3p25.3 (probe P4) and a cosmid clone containing the Von Hippel Lindau (VHL) locus at 3p25.3 (probe P5) (GenBank accession no. NT_005927). Both breakpoint regions of the patient with 46,Y,t(X;3)(p22.1;p26.3) were further analyzed with the 3p26.3 BAC clones RP11-306H5 (GenBank accession no. AC026187) and RP11-166F3 (GenBank accession no. AC026171) and with the Xp22.1 BAC/PAC clones GS1-466O1 (GenBank accession no. AC005297), RP6-102C13, RP11-617O8 (GenBank accession no. AC073614) and RP11-702C7 (GenBank accession no. AC079178).
Clinical report of the patient with 46,Y,t(X;3)(p22.1;p26.3)
One of the eight investigated patients with non-specific MR is a 76-year-old man, who is a resident in the Psychiatric Institute in Geel (Belgium). He was the second child of non-consanguinous Caucasian parents. Two younger brothers and one sister died during early childhood of unknown causes, and the mother had had three miscarriages. Two other brothers have normal intelligence and a normal 46,XY karyotype. Physical measurements of the patient are all normal. Neurological examination showed overall bradykinesia. Tendon reflexes were brisk and there were no pathological reflexes. His spontaneous hand position was with his thumbs adducted, but no contraction of the thumbs, or spasticity of the hands or legs was present. Coordination was intact. Because of his low mental level, psychiatric assessment was obtained from the nursing personnel and through clinical observation. We saw an emotionally dull and passive old man with adequate social contact, orientation appropriate for his mental level, bradyphrenia and poor attention span. He spoke in short sentences and displayed mild echolalia. The subject's history mentions several episodes of anxiety with agitation that responded well to haloperidol. However, a psychiatric diagnosis for these past episodes was not available. A brain CT-scan showed non-specific and age-related findings. Intelligence tests indicated that he was moderately mentally retarded (50<TIQ<70), with a developmental age equivalent of 45 years and a balanced developmental profile on McCarthy's Developmental Scale (68). The level of adaptive functioning (AAA test) (69) was situated 2 SD below the mean scores of the standard population with MR. His weakest characteristics (>2 SD below the mean) were community use and home-living.
Cloning of the 46,Y,t(X;3)(p22.1;p26.3) breakpoints
A map of the Xp22 breakpoint region was constructed with obtained sequences and sequences available from human genome databases. For Southern blotting, genomic DNA was digested with BamHI, HindII or HindIII. 32P-labeled probes were used for hybridization. The hybridized membranes were exposed to Biomax hypersensitive films (Kodak) at -70°C. High molecular weight genomic DNA of the patient was digested with HindII or HindIII and used for long distance inverse PCR (70). First round PCR was performed with primers LDI2-F1 and -R1, and second round with nested primers LDI2-F2 and -R2, using buffer 3 of the Expand Long Template PCR System (Roche Applied Science, Basel, Switzerland). PCR conditions were as follows: denaturation at 94°C for 4 min, annealing at 63°C for 30 s and elongation at 68°C for 14 min for 30 cycles. The PCR products were cloned and sequenced. A map of the 3p26 breakpoint region was constructed in silico using the available databases. (All primer sequences are available online, see Supplementary Material Table 3.)
RACE experiments and mutation analysis in the patient
Total RNA for rapid amplification of cDNA ends (RACE) was extracted from an EBV-transformed cell line of the patient using Trizol (Life Technologies, Gaithersburg, MD). RACE experiments were performed as described earlier (71). Briefly, first-strand cDNA was generated with the oligo (dT)-adaptor primer 465 (for 3' RACE) or the CALL-specific primers CALL-ex9R1 and -ex7R1 (for 5' RACE). The latter first-strand product was extended with an A-tail using the Terminal Deoxynucleotide Transferase kit (Roche), followed by the second-strand synthesis with the primer mixture 1748+1749+1750 (dT8)V. A first round of PCR was performed with the RACE adaptor primer 467 in combination with the CALL-specific primer CALL-ex3F1 or -ex5F1 for 3' RACE, or CALL-ex7R1 or -ex9R1 for 5' RACE. Nested PCR was performed with the RACE adaptor primer 468 and other internal CALL-specific primers. RACE PCR products were ligated in pGEM-T Easy (Promega, Madison, WI) and sequenced.
For mutation screening of the second CALL allele, cDNA synthesis was performed with random hexamer primers (Life Technologies) starting from total RNA of an EBV-transformed cell line of the patient. Overlapping PCR products for the CALL open reading frame were generated, using primer sets (CALL-ex1F1+-ex5R1, -ex5F1+-ex10R1, -ex10F1+-ex14R1, -ex14F1+-Tmr, -Tmf+-ex23R1, -ex20F1+-ex27R1 and -ex26F1+-ex28R1) for 40 cycles with annealing at 63°C. PCR products were directly sequenced on an automated ABI-PRISM 310 sequencer (Applied BioSystems, Foster City, CA).
Real-time quantitative PCR
Total RNA from human adult tissues was commercially obtained (BD BioSciences Clontech, Palo Alto, CA); total RNA from human fetal brain, lung, liver and muscle was a kind gift of Dr V. Kalscheuer (Max-Planck-Institute for Molecular Genetics, Berlin, Germany). Total RNA from a human Schwann cell line (kindly provided by Dr E. Legius, Leuven, Belgium), the glioma HTB-138 and neuroblastoma CCL-127 cell lines, and from mouse hippocampi was extracted with the RNeasy® mini kit (Qiagen) according to the manufacturer's recommendations. First-strand cDNA synthesis was performed on 1 µg total RNA with 80 U Superscript II using random hexamer primers (Life Technologies) in a final volume of 20 µl. Real-time quantitative PCR was performed with CALL and Chl1 (GenBank accession no. NM_007697) gene-specific primers on an ABI PRISM 7700 SDS apparatus (Applied BioSystems) as described elsewhere (72). The mRNA levels were normalized to the housekeeping genes GAPDH and/or ß-ACTIN and relative differences were calculated according to the comparative CT method (SDS User Bulletin 2; Applied Biosystems).
Immunohistochemistry
The mice were deeply anesthetized and perfused transcardially with 60 ml 1 : 4 Bouin solution in phosphate buffered saline pH 7.4 (PBS) or alternately with 20 ml 1% Na2S, NaH2PO4 and 20 ml 4% paraformaldehyde in PBS solution, twice each, for Timm staining. Brains were fixed overnight at room temperature in the respective perfusion solution. One hemisphere was cryo-preserved in deep-frozen 2-methyl butane and the other was paraffin-embedded after dehydration in ethanol using methyl benzoate as an intermediate. For immunohistochemistry, paraffin-embedded brain sections were used as described previously (73), with primary antibodies directed against glial fibrillary acid protein (GFAP as a marker for astroglia; Sternberger Inc., Lutherville, MD, USA), F4/80 (a marker for microglia and macrophages, obtained from ATCC number HB-198) or synaptophysin (a marker for presynaptic boutons; Synaptic Systems, Göttingen, Germany). Timm staining was performed as described (74) for either cryo-preserved or paraffin-embedded brain sections.
Behavioral studies in mice
Chl1-/- mice were generated and genotyped as described previously (20). In contrast to the mice described in their study (almost pure C57BL/6J background), we obtained mice that were crossed in a mixed Sv129/C57BL/6J background. The behavioral studies focused on hippocampal functions in ten Chl1-/-, 15 Chl1+/- and 10 Chl1+/+ male mice using spatial, exploratory and contextual memory tasks, and tests of anxiety and social exploration. Statistical analysis of the behavioral data was performed using one- and two-way analysis of variance (ANOVA) with Tukey HSD test for pair wise comparison, and the Fisher's exact test. To examine the effect of genotype and trial on escape latency, path length and proportional search times in the Morris Water Maze task, a two-way ANOVA for repeated measures (RM) was used. Data are reported as mean values±SEM, and P-values below 0.05 were considered significant. More details on the methods used are available as Supplementary Material.
Mutation screening of the CALL gene
Mutation screening of CALL was performed by sequence analysis of all 26 coding exons with their flanking intronic sequences. The PCR primers (in Supplementary Material, Table 4) were designed by Vector NTi (Informax, Bethesda, MD) and PCR was performed on 50 ng genomic DNA for 35 cycles on a 9700 thermal cycler (Applied Biosystems). PCR products were directly sequenced with either of both PCR primers using the BigDye v3.1 sequencing kit and ran on an ABI-PRISM 3100 capillary sequencer (Applied Biosystems). Sequences were assembled and analyzed with the ContigExpress sequence assembly software (Informax) towards the genomic (GenBank accession no. AC011609) and cDNA (GenBank accession no. NM_006614) reference sequences. Identified nucleotide changes were verified by sequencing the opposite strand from a new PCR product.
| SUPPLEMENTARY MATERIAL |
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Supplementary Material is available at HMG Online.
| ACKNOWLEDGEMENTS |
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We would like to thank all the patients and family members, which were involved in this study, as well as the medical staff including Rudy Theulinx, from the Psychiatric Institute of Geel (Belgium) for their cooperation. Furthermore, we want to acknowledge Phillipe Demaerel for his expert opinion on the CT-scan, Martine Borghgraef and Bernice de Vos for the IQ testing, Lut van den Berghe for clinical assistance, Myriam Welkenhuysen for psychological support, Reinhilde Thoelen, Giselle Degeest and Bernadette Vanderschueren for technical assistance and Frieda Franck for excellent assistance with the behavioral studies in mice. This project was supported by Research grants (G-0299-01 and G-0027-97) of the Fund for Scientific Research, Flanders (FWO, Vlaanderen), Belgium and the German Research Society.
| FOOTNOTES |
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* To whom correspondence should be addressed at: Human Genome Laboratory, VIB4, Center for Human Genetics, Herestraat 49, B-3000 Leuven, Belgium. Tel: +32 16345948; Fax: +32 16347166; Email: guy.froyen{at}med.kuleuven.ac.be
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