Molecular breakpoint cloning and gene expression studies of a novel translocation t(4;15)(q27;q11.2) associated with Prader-Willi syndrome

Cytogenetic and FISH analysis

Metaphase spreads obtained from short-term blood lymphocyte cultures and Epstein-Barr virus (EBV)-transformed lymphoblastoid cells (LCL) were processed for high-resolution GTG- banding by standard methods. For FISH studies, Bacterial Artificial Chromosomes (BACs) were sourced from the RPCI-11 library and selected using the UCSC Genome Browser, Assemblies: July 2003 and May 2004). Fluorescence labelling, hybridization procedures and imaging were performed as previously described [29].

DNA methylation study

Genomic DNA was purified by phenol-chloroform extraction from LCLs from the study subject, a normal control, and a PWS individual (Patient E in [6], Coriell Human Mutant Cell Repository # GM12134). To investigate methylation at exon 1 of SNRPN, 50 μg DNA were used for the bisulfite reaction and PCR with primers according to standard protocols [30, 31]. PCR products were separated on a 3% agarose gel, stained with ethidium bromide, and visualized under UV illumination.

Expression studies by RT-PCR and quantitative RT-PCR

For a subset of exons in the SNPRN gene and the snoRNAs HBII-13, HBII-437, and PWCR1/HBII-85, quantitative RT-PCR assays were performed with SYBR Green I™ dye in an ABI 7700 cycler (Applied Biosystems) by using standard protocols [32, 33]. Primers were designed to amplify products of 50 bp in length. GAPDH expression was used as a reference. Each sample was run at least in triplicate. The results were interpreted as described previously [28].

LCL RNA samples from a PWS individual with a microdeletion of the imprinting center (GM12134), a normal individual, an individual with an intrachromosomal triplication of the PWS region on the paternally-derived chromosome 15 (Patient 1 in [34], Coriell Human Mutant Cell Repository # GM12135), and fibroblast RNA from another t(4;15) PWS individual with the breakpoint in intron 2 of SNRPN [27, 28] served as controls.

Southern blot analysis

Southern blot analysis was performed according to standard methods with ExpressHyb™ solution (BD Biosciences). Genomic DNA from a normal individual and the t(4;15) carrier was cleaved in a double digestion with restriction enzymes NheI and BsaWI to release a 6.4 kb fragment, and with NheI and ApaI to release a 10 kb fragment in the normal chromosome. The DNA probes were synthesized by PCR from genomic DNA and cloned into a pCRII T/A-vector (Invitrogen). The probes were designed to hybridize within intron 16 (SB-1) and upstream of the ApaI restriction site (SB-3) (Table 1).

Breakpoint cloning with a PCR-based method

Genomic DNA from a normal individual and the t(4;15) carrier was cleaved in a double digestion with restriction enzymes EcoRV and ApaI, followed by adapter ligation according to the manufacturer's instructions (BD Genome Walker Universal Kit) [35]. A nested PCR reaction with adapter primers and sequence-specific primers was performed and the amplification products were cloned into the pC2.1 T/A-vector (Invitrogen) after gel purification. The clones were sequenced from both directions with universal primers from the vector (M13) and sequence specific primers.

Clinical case report

The patient (Fig. 2) was born at 41 weeks of gestation with a birth weight of 8 lb. Pregnancy was uneventful, but fetal movements were somewhat reduced. In the newborn, poor muscle tone, weak cry, excessive sleepiness, and undescended testes were observed. During infancy, he had poor suck and prolonged feeding times, but his weight gain was satisfactory and he did not require tube feeding. He was suspected to have absence seizures of about 20 seconds duration, along with proneness to giggling, sometimes with eye-rolling. These episodes resolved by four years of age, and an EEG was normal.

He had a left esotropia that was surgically corrected. During childhood, sticky saliva, dry mouth, skin picking and a marked tolerance to pain were noted and have persisted.

Excessive daytime somnolence continued beyond infancy and treatment with amphetamine was started at 9 years of age. A sleep study, at 13 years of age, was normal. In 2002, a further sleep study and a multiple sleep latency tests confirmed the diagnosis of narcolepsy. His daytime sleepiness has continued to respond to dexamphetamine.

Regarding his body weight, there was no rapid weight gain between 1 and 6 years. Around 8 years of age, his interest in food increased, and now he would keep eating if he had unrestricted access to favorite sweet foods. He lives with his parents who help to control his food intake. At 14.5 years, he had small hands and feet, at the 20^th percentile and 5^th percentile, respectively, and showed mild truncal obesity. His head circumference of 56.7 cm was at the 98^th percentile. Brain MRI scan was normal. At age 16 years, his height was 155.7 cm and weight 65 kg. At the age of 22 years, his height is approximately 164 cm and his weight has increased to 90 kg (BMI = 33.5).

At 13 years of age, he was found to have delayed puberty and reduced linear growth velocity with his height falling below the 3^rd centile. Treatment with testosterone resulted in improved height gain and genital development. At 15 years of age, he had a left orchidopexy and removal of a dysplastic intra-abdominal right testis. He remains on 6 monthly testosterone implants because of reduced hypothalamic function. He has never been on growth hormone treatment.

Developmentally he had a mild delay in comparison to his older siblings. He attended normal school but had some difficulties due to rigid behaviours and poor peer interactions. Psychological testing (WISC 111, Wide Range Achievement test and BASC self report) revealed an overall normal intellect. However, he had some involuntary fluctuation in attention and significant visual perceptual difficulties, e.g. deficits in visual organization, in making sense of his visual world and transcribing visual material. These perceptual problems have had a significant effect on his learning and social life. At the age of 22, he is attending a mainstream high school requiring extra time and assistance in completing a diploma in information technology. He is good at dismantling computers and installing hardware, and prefers working on his computer to socializing. Hyperphagia and skin picking are still a challenge for him.

Cytogenetic analysis

High-resolution chromosome analysis showed an apparently balanced reciprocal translocation between the long arm of chromosome 4 and the proximal long arm of chromosome 15. The breakpoints were assigned to chromosome bands 4q27 and 15q11: 46, XY, t(4;15)(q27;q11) (Fig. 3a). Parental chromosomes were normal, indicating that the patient's translocation was de novo.

DNA methylation analysis

To exclude alternative explanations for the phenotype, such as an imprinting defect, DNA methylation analysis was performed. Methylation-specific PCR of the SNURF-SNRPN exon 1 region revealed a normal bi-parental methylation pattern (Fig. 3b).

Mapping of the translocation breakpoint by FISH

We performed cytogenetic and molecular studies to characterize the breakpoint at 15q11 in detail. Preliminary FISH analysis showed that the breakpoint in 15q11 was located between D15S11 and GABRB3, which flank the SNRPN locus (data not shown). On this basis, a chromosome walking strategy was used across this region to narrow down the breakpoint region. We identified two BACs, RP11-160D9 (current position 22577151-22735621 on UCSC Genome Browser, May 2004 release) and RP11-876N20 (current position 22857334-23036552), that flanked the breakpoint and, thus, mapped it to a ~122 kb interval (Fig. 1b).

Fine mapping of the breakpoint by SNRPN expression and Southern blot analysis

To further refine the breakpoint, we carried out quantitative RT-PCR and RT-PCR experiments using RNA from an LCL and skin fibroblasts (FB) for expression of SNRPN transcripts. As shown in Figure 4 and Table 2, we found expression of SNPRN exons 2, 3, and 14 to 17, but no expression of exons 18 to 20, and concluded that the breakpoint falls within intron 17. For mapping intron 17, we designed a Southern blot using unique restriction sites. DNA cleaved with NheI and BsaWI showed a 6.4 kb band for the t(4;15) carrier and the normal control (Fig. 5b, lanes 1 and 2), indicating that the breakpoint is located downstream of the BsaWI site. Samples doubly digested with NheI and ApaI (Fig. 5b, lanes 3–6), revealed additional bands for the translocation carrier. Besides the expected 10 kb band derived from the normal chromosome 15, there was a ~11.5 kb band in lane 4, detected with the SB-1 probe, and a ~7 kb band in lane 6, detected with probe SB-3 (Fig. 5b). The novel ~11.5 kb band arose from the der(15) chromosome, with an NheI site on the chromosome 15 portion and an ApaI site on the chromosome 4 portion (Fig. 5c, upper panel). The novel band of ~7 kb arose from the der(4) chromosome, with an ApaI site on the chromosome 15-part and an NheI site on the chromosome 4-part. Taken together, these results delimit the breakpoint region to ~3.6 kb between the BsaWI and ApaI sites (Fig. 5a).

Amplification product	PWS	Normal control	t-PWS (4;15)	PWS triplication	t-PWS intron 2	t-PWS (4;15)
	LCL	LCL	LCL	LCL	FB	FB
SNURF Ex 2	0.0001	0.53	0.54	2	0.002	0.56
SNURF Ex 3	0.0002	1.1	1.43	6.4	0.0004	0.56
HBII-437	0.00003	0.86	1.13	4.9	0.00008	0.1
SNRPN 14/15	0.0013	4.7	4.91	17.23	-	-
SNRPN 19/20a	0.005	1.34	0.003	4.7	0.007	0.007
HBII-438	0.03	1.5	0.02	6.2	0.07	0.07
PWCR1/HBII-85	0.03	3.7	0.02	16.8	0.04	0.06

Sample identification: PWS: PWS with an IC microdeletion (patient E in [5]); t(4;15) PWS: the PWS case reported here; PWS-triplication: intrachromosomal triplication of the PWS region [33]; t-PWS intron 2: previously reported PWS case with t(4;15)(q27;q11.2) and breakpoint in SNRPN intron 2 [26, 27]; LCL, lymphoblastoid cell line, FB, fibroblast strain. The numbers represent the ratio of target product to GAPDH control product.

Breakpoint mapping at the nucleotide level

By DNA sequencing, we mapped the breakpoint to SNRPN intron 17 (position chr 15: 22803227) and to chromosome 4 at position chr. 4:123965881 (UCSC Genome Browser, May 2004) (Fig. 6). On chromosome 4, a long terminal repeat (LTR) retrotransposon, LTR1B, spans the breakpoint. On chromosome 15, we found a short interspersed element (SINE), AluY, and a long interspersed element (LINE), L1M4, surrounding the breakpoint (Fig. 6a). Thirty-nine bp upstream of the breakpoint on chromosome 15 starts a common 26 bp core sequence of Alu elements (Alu-DEIN) in an inverted orientation. This sequence is known to be involved in gene rearrangements [36]. While the sequence across the breakpoint is contiguous on the der(15), an extra A is inserted on the der(4) chromosome (Fig. 6b). Furthermore, the breakpoint on chromosome 4 falls in a large intron between exons 10 and 11 of a spliced transcript (BC045668). By RT-PCR, we found that this transcript is expressed in fibroblasts, but not in LCLs (data not shown).

Expression of upstream genes MKRN3, MAGEL2, and NDN

Expression of the three imprinted genes MKRN3, MAGEL2, and NDN upstream of SNRPN was tested by RT-PCR in t(4;15) fibroblasts and found to be indistinguishable from expression in normal control fibroblasts (data not shown).

Expression of C/D box snoRNAs and intron-encoded ESTs

When testing for the intron-encoded C/D box snoRNAs, we were able to document expression of HBII-13 and HBII-437 and lack of expression for HBII-438A/B and HBII-85/PWCR1 (Fig. 7). By use of a more sensitive method, quantitative real-time RT-PCR, we obtained similar results for the SNRPN exons and snoRNAs tested (Table 2). Two ESTs, AK094315 and AB061718 (= HBT8) located in the 30 kb SNRPN intron 20 were not expressed in the PWS control [6] and t(4;15) LCLs, but were expressed in the normal control LCL (Fig. 7).

Breakpoint mapping and mechanism of the translocation event

Dissecting the PWS deletion region and identifying individual genes as responsible for parts of the phenotype represent a challenge because all reported smaller deletions inactivate all imprinted genes on the paternally- derived chromosome 15. Rare reciprocal translocations, therefore, provide unique insights. We here report our studies of a 22 year old male with features of PWS who has a de novo balanced reciprocal translocation t(4;15)(q27;q11.2). This is the first such case where the translocation breakpoints have been identified at the DNA sequence level. The cytogenetic breakpoint designations in this individual are identical to those in another male PWS-like case with t(4;15)(q27;q11.2), previously reported by Kuslich and colleagues [27] and restudied by Gallagher and colleagues [28], which raised the intriguing possibility of a recurrent translocation that may be facilitated by genomic repeats or other distinct molecular features.

The translocation is de novo, as is true for all the previously described cases with translocation breakpoints involving the SNPRN gene. Given the PWS-like phenotype, the translocation was assumed to be of paternal origin. This assumption was confirmed by the expression studies. Paternal origin of the translocation was formally proven in 2 of the 5 previously reported cases [26, 27].

Karyotype – phenotype correlations

Two individuals with SNRPN intron 2 breakpoints were described as having classical PWS, meeting the major clinical criteria by age 3.5 years and additional minor clinical criteria [25, 27]. The individuals with a breakpoint in SNRPN Exon 20/Intron 20 were described as having a milder or atypical form of PWS (Table 3 and Table 4). The weight gain started later than in classical PWS, at 7 and 5 years, respectively, for the patients described by Schulze et al. 1996 and Wirth et al. 2001, and at 8 years in our case. The characteristic facial features were absent in the case of Wirth et al. 2001, and also in the present case. But this is not a consistent feature in classical PWS, as in a retrospective evaluation of 90 molecularly-proven PWS cases, only 49% had the characteristic facial gestalt [39].

It is apparent from the review of the previously reported cases and the individual reported here (Table 3 and Table 4) that some of these translocation cases tend to have a milder, 'atypical' clinical picture, in comparison with classical PWS. There is not a complete absence of any of the major phenotypic features (neonatal hypotonia and feeding difficulty, hyperphagia from early childhood, obesity, cognitive compromise, hypogenitalism), but the degree of affection may be lower. None of the reported translocation cases had any additional features that might possibly be attributed to disruption of a gene on the reciprocal chromosome, and in no prior case had an attempt been made to identify a gene at this location.

Our sequence data mapped the breakpoint on chromosome 4 within intron 10 of a spliced polyadenylated transcript (BC045668). This unique cDNA clone represents a 3764 bp mRNA from a human testis library that does not appear to encode a protein. Its 5' end overlaps the interleukin 21 (IL21) transcript by 511 bp in the opposite direction (UCSC Genome Browser, May 2004). It appears unlikely that heterozygous disruption of this gene contributes to the phenotype in our patient.

Translocation has no effect on imprinting center methylation and upstream genes

To assess whether the translocation event had affected the allele-specific methylation pattern at the imprinting center (IC), and/or to exclude a coincident imprinting defect, we carried out methylation studies of the SNRPN exon 1 region that revealed a normal bi-parental methylation pattern. Similar results were reported for each of the other five PWS individuals who had translocation breakpoints within the SNRPN gene. These results predict that expression of the genes located centromeric to the SNRPN exon 1/ IC region, NDN, MAGEL2 and MKRN3, should not be affected in these individuals. By studying t(4;15) fibroblasts by RT-PCR, we indeed found expression of all three genes. Previously, only MKRN3 was reported to be expressed in the three PWS translocation cases in which it was studied [20, 25, 27].

In t(4;15) lymphoblasts, the SNRPN transcript was detectable by RT-PCR and quantitative RT-PCR and found to extend all the way to exon 17. The major transcript that encodes the SNURF/SNRPN proteins terminates in exon 10 [20] and, therefore, should be unaffected by this t(4;15) translocation. With the caveat that studies on peripheral tissues, fibroblasts and lymphoblasts, may not accurately reflect gene expression in the brain, our results indicate that SNURF/SNRPN and the centromeric genes MKRN3, NDN and MAGEL2 are unlikely to play a prime role in the causation of PWS-associated features, although it remains an open question whether their loss or non-functioning might contribute to the more marked phenotypic expression that is seen in typical PWS.

Genes downstream of the breakpoint are not expressed

With respect to expression of downstream transcripts, the reported results on LCLs with breakpoints in exon 20/intron 20 were consistent, whereas for the two patients with breakpoints in intron 2, the reported results were conflicting for expression of downstream transcripts IPW and PAR-1. In a re-evaluation of the t(4;15) case reported by Kuslich and colleagues [26], no expression of these transcripts and of the PWCR1/HBII-85 snoRNA cluster was detected by real-time quantitative RT-PCR [28].

Therefore, we focused our analysis on the snoRNAs and two ESTs in intron 20. As for the intron-encoded C/D box snoRNAs, HBII-13 and HBII-437 were expressed, and HBII-438A/B and HBII-85/PWCR1 were not. HBII-52 snoRNAs were not studied, as they are not expressed in the available tissues and have previously been excluded from contributing to the PWS phenotype [40, 41]. The two ESTs in the large intron 20 that are highly expressed in brain tissues [42] were found to be expressed in a normal control LCL, but not in the t(4;15) LCL. This result suggests that these ESTs do not have their own promoter but are dependent on transcription from the SNRPN promoter that is located on the other translocation derivative in these cells. Therefore, these ESTs most likely represent stable derivatives of large alternatively spliced non-coding SNRPN transcripts.