|
|
||||||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1From the Laboratory for Retinal Regeneration, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan; and the 2Department of Ophthalmology and Visual Science, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
| Abstract |
|---|
|
|
|---|
METHODS. Experiments were performed to investigate the gene and allele copy numbers of FSCN2 in patients with RP who have the c.72delG mutation as well as healthy subjects with or without the mutation. A real-time PCR-based genotyping approach was established that used a real-time PCR assay to qualify the copy numbers of both the wild-type and mutant alleles of the FSCN2 gene.
RESULTS. Three patients with RP and three normal subjects had an equal ratio of the alleles. Of interest, another patient had an asymmetric allele ratio (4:1) of the copy number of the wild-type allele, compared with that of the mutant allele. These findings were further verified using quantitative assays. An allele-specific methylation assay demonstrated a random methylation pattern in the FSCN2 gene.
CONCLUSIONS. The copy numbers of the FSNC2 gene and of each allele in the mutant samples were quantified. The findings excluded the possibility that allelic CNV was associated with RP, suggesting that the c.72delG variant is not the primary cause of RP. It is not likely that the FSCN2 gene is imprinted differentially. The real-time PCR-based genotyping method developed in this study is useful for investigations of allelic asymmetries within genomic regions with CNVs.
Genetic screening of FSCN2 generally uses PCR or SSCP analysis, together with direct DNA sequencing. These qualitative methods, which are capable of determining the presence or absence of the gene and the nucleotide change in the target amplicons, do not quantitatively evaluate the gene copy number. Copy number variation (CNV) has been increasingly recognized as an important genetic cause of some inherited diseases and complex disorders. CNVs in the FSCN2 gene were recently discovered in normal populations using whole-genome array-based comparative genomic hybridization (array CGH) analysis.10 11 Therefore, it is possible that gene or allele CNVs affect the disease phenotypes observed in patients or healthy subjects carrying the c.72delG mutation. For instance, allelic asymmetry with more mutant than wild-type alleles could lead to retinal degeneration.
Imprinting is a non-Mendelian form of inheritance characterized by monoallelic expression depending on the maternal or paternal origin. The imprinted genes always show a differentially methylated pattern. So far, at least 52 genes with parental imprinting have been identified in humans (http://www.geneimprint.org; maintained in the public domain by the Jirtle Laboratory, Duke University, Durham, NC) and no imprinted gene has been identified in patients with RP. It is also possible that imprinting status affects phenotype expression in the patients or normal subjects with the c.72delG mutation. To our knowledge, these possibilities have yet to be addressed.
In this study, we used a real-time PCR-based genotyping approach to analyze the allelic ratio of FSCN2, and performed a reproducible real-time PCR assay (Taqman; Applied Biosystems, Inc. [ABI], Foster City, CA) in both patients with RP and normal subjects. We found no difference in the allelic ratios of the patients with RP and the healthy individuals. Of interest, allelic asymmetry present in a RP patient and our results indicate the presence of multiple copy numbers of the FSCN2 gene in subjects from the normal population. In addition, methylation analysis was performed to address the imprinting possibility.
| Methods |
|---|
|
|
|---|
Screening for the FSCN2 Mutation
Genomic DNA was extracted from peripheral blood samples (QIAamp DNA Blood Mini Kits; Qiagen, Hilden, Germany). Amplification of the genomic region-spanning exon 1 of FSCN2 and flanking upstream or intronic regions was performed using PCRs with appropriate primers as described in a previous study.2 The amplified products were sequenced according to standard protocols (model 3130; ABI). Sequencing data were assembled automatically (SeqMan module of the Lasergene program; DNAStar, Madison, WI).
DNA Subcloning
The PCR product, including c.72delG from the DNA sample of 0075, was cloned into a plasmid vector (pCR4-TOPO; Invitrogen, Carlsbad, CA) according to the provided protocols. Plasmids were purified (Wizard Plus Minipreps DNA Purification System; Promega, Madison, WI), then digested with EcoRI and electrophoresed on agarose gels for verification or sequenced as described earlier. Vector DNA representing the mutant or the wild-type sequence was used as authentic control samples to generate a mixture of serial allelic ratios from 4:1 to 1:4. Each mixture was then diluted to 1:10, 1:102, 1:103, and 1:104 with TE buffer.
Allele-Specific Genotyping
The allele-specific probe (Table 1) for either the wild-type or mutant allele was designed and synthesized by ABI Japan (Tokyo, Japan). Primers corresponding to the probes (Table 1) were designed on computer (Primer Express 3.0; ABI). Genotyping was performed with real-time PCR (TaqMan StepOne; ABI), according to the recommended protocol. In brief, 5 µL of genotyping master mix (TaqMan; ABI) was mixed with forward and reverse primers (900 nM), two probes (200 nM TaqMan) for each allele, and the DNA sample. The mixture of the vector DNA, including either the mutant allele or the wild-type allele, was prepared as the standard (4:1, 3:1, 2:1, 1:1, 1:2, 1:3, and 1:4). A thermal profile was set up as one prereading cycle of 60°C for 30 seconds and a hot-start cycle of 95°C for 10 minutes, to activate the enzyme, followed by 40 cycles of 95°C for 15 seconds, 60°C for 1 minute, and 70°C for 30 seconds, and a postreading cycle of 60°C for 30 seconds. Data were automatically analyzed (StepOne program; ABI). All tests were repeated independently at least twice.
|
Data Analysis
A comparative CT method of quantitation (
Ct) was used according to the manufacturers instructions (StepOne Real-Time PCR system; ABI). The 
Ct was calculated separately for FSCN2 and RNaseP for each sample. The 
Ct for FSCN2 and the 
Ct for RNaseP can then be reported as a simple ratio (the 
Ct FSCN2 value divided by the 
Ct RNaseP value), from which the copy number of FSCN2 was calculated. The PCR amplification efficiencies for RNaseP, wild-type FSCN2, and mutant FSCN2 were evaluated separately using standard curves.
Pseudogene Analysis
To exclude the possibility that the normal human genome contains an FSCN2 pseudogene, we designed a series of primers to amplify the coding region of exon 1 (Table 1 , Fig. 1 ), and the PCR products were sequenced as described earlier. In addition, the genomic sequence of the FSCN2 gene was analyzed using BLASTN homology searches (www.ncbi.nlm.nih.gov/BLAST/, provided in the public domain by the National Center for Biotechnology Information, Bethesda, MD). Transcripts or genomic sequences that showed both significant homology and similar lengths were chosen as possible pseudogenes.
|
|
| Results |
|---|
|
|
|---|
Allele-Specific Genotyping
Prepared mixtures containing a series of ratios of mutant and wild-type sequence plasmids were tested as scaling standards for allele-specific genotyping (Fig. 3A) . DNA samples from patients with RP and normal control subjects, together with no-sample negative control samples, were subjected to genotyping tests. Allelic discrimination plot analysis using the PCR system software (StepOne; ABI) showed the separation of each allele ratio; normal controls without the c.72delG mutation were clustered near the horizontal axis, whereas the samples from the three patients and two normal controls heterozygous for the mutation were centered in the 1:1 allele ratio area (Fig. 3B) . Of interest, P0302 demonstrated a 4:1 ratio of wild-type to mutant alleles (Fig. 3B) .
|
|
To investigate the gene copy number of FSCN2 in the healthy population, we screened 54 phenotypically and genotypically normal samples and seven samples from phenotypically normal subjects or patients with RP known to carry the mutation using the P2 and P3 primer/probe sets (Table 1) . The results showed that all the individuals carried four copies of the FSCN2 gene. One patient (P0302) who carried the mutation was found to have four copies of the wild-type allele and one copy of the mutant allele when the P2 set was used, whereas they had only four copies of the wild-type allele with the P3 set, indicating the presence of a shorter copy of the gene with a forward breakpoint between the P2 and P3 regions (Fig. 1) . To locate the terminal breakpoint, the P4 and P5 primers (Table 1) were used to examine the corresponding regions in P0302 and a normal control subject. As shown in Figures 1 and 4B , P0302 had more copies of the P4 region compared with the normal control sample, whereas no difference in the copy numbers of the P5 regions were observed. This result indicates that the terminal breakpoint was located between the P4 and P5 regions.
Pseudogene Tests
BLASTN analysis did not identify any transcripts or genomic sequences with both a significant homology score and a similar length. Although pseudogenes have DNA sequences similar to those of their functional counterparts, most of them have multiple sequence variations located throughout the gene. We performed PCRs with a forward primer specific for the 5' end of exon 1 and eight different reverse primers specific for sequences in exon 1 or intron 1. If the c.72delG allele was located in an unknown pseudogene, some of the amplified products would harbor the mutation together with other neighboring sequence variations. All the amplified products, however, contained a unique heterozygous single-base deletion, suggesting that c.72delG is not located in a pseudogene.
Bisulfite Sequencing of Cloned DNA Fragments
Bisulfite-treated DNAs from patients P0302, P0100 and a normal subject, N-ST, and another normal control subject (without the mutation) were amplified by using the three primer sets. The MSP and USP primers specifically anneal to the methylated and unmethylated alleles respectively while the M3 primer amplify both alleles. Among the 20 clones derived from the MSP or USP products, we did not find a deviated ratio of the methylation pattern in all tested samples (Table 2) . In P0302, approximately 20% of the methylated clones and 25% of the unmethylated clones were found to have the mutation, which is consistent with the 4:1 allelic CNV and indicates a random methylation pattern of either mutant or wild-type allele. Furthermore, no preferential methylation pattern was observed in both the patients and healthy individuals in the M3 clones (Fig. 2) .
|
| Discussion |
|---|
|
|
|---|
CNV has recently been identified as a cause of global genetic variation in the human genome. CNVs have been estimated to occur in approximately 12% of the genome,17 and have been reported to be associated with various diseases and variations in drug efficacies.18 19 Over 2000 CNVs have been identified to date, and both increased and decreased CNVs covering the FSCN2 gene in chromosome 17 have been reported recently.10 11 This finding led us to hypothesize that CNVs of FSCN2 may be associated with retinal degeneration. Furthermore, copy number alterations of the wild-type or mutant allele may underlie the differences between affected patients and healthy subjects who carry the c.72delG variant. In this study, we examined both the gene and the allele copy numbers of FSCN2 in patients with RP and healthy subjects. We did not find a CNV between the RP patients and the normal subjects. It should be noted that we did not investigate the cosegregation of the mutation and the disease in the families, because the cases were either isolated, or the DNA samples from the other family members were not available. Therefore, whether the mutation is associated with the disease in these family cases is unknown.
In agreement with our hypothesis, allelic asymmetry was observed in a severely affected patient with RP who showed an unusual allelic variation, with four copies of the wild-type allele and one copy of the mutant allele. To our knowledge, this type of variation has not been described previously. The other 54 normal individuals showed the same copy numbers, suggesting that normal Japanese individuals carry at least four copies of the FSCN2 gene. Wong et al.10 have described 22 subjects with decreased CNVs spanning the FSCN2 gene among 95 normal subjects using array CGH. In the group of normal individuals, however, no decreased CNVs were identified with the real-time PCR assay. This bias indicates the type and frequency of CNVs depend on the ethnicity of the examined population.
It is important to quantify the allelic copy numbers in CNVs to understand how they contribute to genetic disorders, because CNVs may alter the functional effects of heterozygous mutations. In the present study, we established an efficient genotyping method based on real-time PCRs, to investigate the allelic ratio of a heterozygous sequence change. As mentioned, three RP patients and three normal subjects carrying the c.72delG mutation were found to have a 1:1 ratio of the alleles. One patient, however, was found to have a 4:1 wild-type to mutant allelic ratio. These results were further confirmed following the quantification of each allele by real-time PCR assays. Our results suggest that the allele CNV identified in this study is unlikely to be associated with the pathogenicity of the disease. The current method based on conventional, reliable assays, however, may facilitate investigations into the allelic ratios of specific regions containing CNVs and their roles in other genomic disorders. Although the chromosomal array CGH is extensively used for the genome-wide detection of CNVs,10 11 it uses a relatively large amount of genomic DNA and may fail to detect relatively small CNVs as well as slight changes in allelic ratios. In contrast, the quantitative real-time PCR-based method we used in the present study is more sensitive and specific. Padiath et al.19 and Hosono et al.20 recently developed a SNP-based invader assay to detect allele asymmetries within CNV regions. It is believed that both of these new methods will be useful for studying the detailed allelic functions associated with individual disease susceptibilities.
We had to exclude the possibility of an FSCN2 pseudogene in the human genome. The mammalian genome contains pseudogenes that correspond to several functional genes, including such commonly used internal controls as β-actin, GAPDH, and cyclophilin. There are three main types of pseudogenes: processed (or retransposed) pseudogenes, nonprocessed (or duplicated) pseudogenes, and unitary pseudogenes. Because most of the known pseudogenes have several sequence disparities compared with the functional gene, we amplified the coding exon 1 by using multiple flanking primers to test whether the c.72delG mutation is located in a pseudogene. Sequencing of all the PCR products consistently detected only the current sequence variant, strongly suggesting that there were no relevant pseudogenes. Furthermore, direct PCR sequencing of exons 2 to 5 with flanking primers did not identify any other sequence alterations. BLASTN analysis of the current human genome sequence database did not detect any sequences that were highly similar to FSCN2. Together, these findings make it unlikely that an FSCN2 pseudogene in the human genome influenced our results. It must be noted, however, that we could not exclude the presence of a duplicate pseudogene that had all the same characteristics as the FSCN2 gene. Furthermore, bisulfite sequencing analysis of the DNAs from patients or normal subjects failed to find a preferential methylation in either allele. Based on this result, we conclude that it is not likely that the FSCN2 gene is imprinted with monoallelic expression in the patients or healthy subjects examined in the present study.
In brief, our analysis of CNVs as well as variations in the number of alleles with or without the c.72delG mutation in the FSCN2 gene among Japanese subjects suggests that FSCN2 is unlikely to be the pathogenic genetic cause of retinal degeneration. We believe the method established in this study, which is based on a real-time PCR assay, is useful for identifying allelic and genomic CNVs that may underlie various genomic disorders.
| Acknowledgements |
|---|
| Footnotes |
|---|
Submitted for publication December 26, 2007; revised February 15 and March 24, 2008; accepted June 23, 2008.
Disclosure: Z.-B. Jin, None; M. Mandai, None; K. Homma, None; C. Ishigami, None; Y. Hirami, None; N. Nao-i, None; M. Takahashi, None
The publication costs of this article were defrayed in part by page charge payment. This article must therefore be marked "advertisement" in accordance with 18 U.S.C.
1734 solely to indicate this fact.
Corresponding author: Zi-Bing Jin, Laboratory for Retinal Regeneration, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047 Japan; jinzb{at}cdb.riken.jp.
| References |
|---|
|
|
|---|
This article has been cited by other articles:
![]() |
C. Li, E. Mizutani, T. Ono, and T. Wakayama An Efficient Method for Generating Transgenic Mice Using NaOH-Treated Spermatozoa Biol Reprod, February 1, 2010; 82(2): 331 - 340. [Abstract] [Full Text] [PDF] |
||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |