|
|
||||||||
1 From the Jules Stein Eye Institute and the 6 Molecular Biology Institute, University of California Los Angeles School of Medicine; the 2 Biology Department, Loyola Marymount University, Los Angeles, California; the 3 Molecular Medicine Unit, University of Leeds, United Kingdom; 4 Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago; and the 5 Scheie Eye Institute, University of Pennsylvania, Philadelphia.
| Abstract |
|---|
|
|
|---|
METHODS. DNAs from family members were genotyped for markers covering the entire genome at an average spacing of approximately 9 centimorgans (cM). The data were input into a pedigree computer program to produce output files used to calculate lod scores. Significant linkage was revealed at 8cen, prompting the genotyping of a number of additional markers. Exons of a candidate gene were sequenced directly by standard fluorescent dideoxy methods. Haplotype analysis was performed with markers in this locus in 13 multiplex and 2 simplex CRD families in which neither parent had disease.
RESULTS. Four-point linkage analysis gave a maximum lod score of approximately 7.6 at both D8S1769 and GATA101H09 in the large consanguineous family. Recombination events defined an interval of 8.7 cM between D8S1820 and D8S532 within which the gene must lie. This 8p11 locus (CORD9) is immediately distal to but distinct from the RP1 autosomal dominant RP (adRP) locus. Two islands of homozygosity were found in this locus: The alleles of 6 of 10 markers in one of the islands and 2 of 4 in the other were homozygous. The UniGene cluster Hs.8719 (UniGene System, provided by the National Center for Biotechnology Information and available at http://www.ncbi.nlm.nih.gov/UniGene), which tags a gene with significant homology to Dual Specificity Phosphatase 3, maps within the CORD9 interval and is highly expressed in the retina. To evaluate this gene as a potential disease candidate, intronexon structure was determined, and exons were screened in the consanguineous family. No variants were found that could be related to disease. Haplotype analysis of 15 other families with CRD, using markers at CORD9, excluded this locus in 9 of 15.
CONCLUSIONS. A new arCRD locus (CORD9) has been identified corresponding to a yet unidentified gene in the 8.7-cM interval D8S1820-D8S532. No mutations were found in one candidate gene in affected members of the primary study family. Haplotype analysis of a cohort of 13 multiplex and 2 simplex families with CRD ruled out the CORD9 gene in 9 of 15 of the families. To date, a total of 126 loci carrying gene mutations causing various forms of retinal degeneration have been mapped, and the mutant gene has been identified in 64 of them. However, only 2 loci for arCRD have been documented. This is the report of a third.
| Introduction |
|---|
|
|
|---|
To date, RP has been associated with mutations in 24 different genes and 16 chromosomal loci for which the defective gene has not yet been found.6 The causes of CRD appear to be less numerous, but still quite diverse: four genes and six loci.6 Two of these are of autosomal recessive inheritance: CORD8 on chromosome 1q12-q247 and the locus corresponding to the ABCA4 gene on chromosome 1p.8 Therefore, when we found an informative, consanguineous family with an autosomal recessive conerod dystrophy phenotype, we first demonstrated that the disease was not linked to either of the known recessive CRD loci. We then performed a whole genome linkage search, leading to the identification of a new locus, CORD9, on chromosome 8p11.
| Materials and Methods |
|---|
|
|
|---|
|
The study protocol adhered to the tenets of the Declaration of Helsinki for all individuals. Informed consent for all procedures was obtained from all subjects after the nature of the studies had been fully explained.
Genotyping
DNAs were extracted from blood leukocytes by standard
methods. The DNAs of the primary family were analyzed for the alleles
of 400 polymorphic, high-quality, short tandem repeat markers spanning
the genome, with an average spacing of approximately 9 centimorgans
(cM) by the Marshfield Mammalian Genotyping Service (provided in the
public domain by Marshfield Clinic, Marshfield, WI, and available
at
http://www.marshfieldclinic.org/research/genetics/genotyping_service/mgsver2.htm).
The data were input directly to the Cyrillic pedigree information
package (Exeter Software; Setauket, NY) to produce output files for the
Linkage program suite (provided by the Human Genome Mapping Project
Resources Center, Cambridge, UK and available at
http://www.hgmp.mrc.ac.uk/genomeweb/linkage.html). PCR primers for
additional markers tested in the 8p12-q12 locus (determined as the
critical interval by analysis of the Marshfield data) and selected from
the Marshfield genetic map of chromosome 8 (provided in the public
domain by Marshfield Clinic, and available at
http://www.marshfieldclinic.org/research/genetics/map_markers/maps/indexmapframes.html)
were purchased from Research Genetics (Huntsville, AL). The
markers were amplified by PCR from genomic DNAs in the presence
of [
-32P]dCTP, electrophoresed in 7%
acrylamide denaturing gels, and exposed to x-ray film, as described
previously.10
For each marker, all members of the family
were run side by side in the same gel.
Haplotype analysis was performed on the 15 other CRD-affected families using the markers D8S499, D8S2319, and D8S1125. Genomic DNAs were extracted, amplified with the appropriate markers and electrophoresed as described for the markers of the primary family. All members of these families were also run side by side in the same gel.
RT-PCR Analysis
Total RNA was extracted from retinal tissue using extraction
reagent (TRIzol; Gibco BRL, Grand Island, NY), according to the
manufacturers instructions. The tissue had been dissected from human
eyes and snap frozen in liquid nitrogen. One microgram of this RNA was
incubated with 100 ng of random primer at 70°C for 10 minutes. The
samples were placed on ice and Moloney murine leukemia virus (MMLV)
reverse transcriptase buffer, 10 mM dithiothreitol (DTT), 1 mM each of
the dNTPs (all from Gibco BRL), and 0.5 U RNAsin (Promega,
Madison, WI) were added. After equilibration at 37°C for 2 minutes,
200 U MMLV reverse transcriptase was added, and the reactions were
incubated at 37°C for 1 hour. The samples were heated to 95°C and 2
µl of the cDNA was used in PCR reactions.
Mutation Screening
The coding exons of DUS3-like and the flanking splice
junctions were screened for mutations by direct sequencing. The
following primers were used: exon 1, 5'-CGCTTTGTAATTGGTGCAGCTC-3' and
5'-CCAGCGTGGAGAGCC-AGCTG-3' (PCR product, 416 bp); exon 2,
5'- GCTGCTCTGGACTCACTCAAG-3' and
5'-CCTGTCTGCCACCCTTCT-CC-3' (PCR product, 425 bp); exon 3,
5'-GTCTTCCCCAACAACCTGGC-3' and 5'-CAAATTCCAGGCACCCTGTTC-3'
(PCR product, 319 bp); and exon 4, 5'-GCCCCATGTCACCCTTTCCC-3'
and 5'-CCT-ATCTCCAGCTGGGAGCC-3' (PCR product, 343 bp). Reactions
were performed in a 50-µl volume with 50 ng of genomic DNA; 20 pmol
of each primer; 200 µM each dATP, dCTP, dGTP, dTTP; 10 mM Tris-HCl
(pH 8.3); 50 mM KCl, 1.5 mM MgCl2, 0.01% gelatin
and 1 U Taq DNA polymerase (Gibco BRL). After the initial
denaturation step at 96°C for 3 minutes, the samples were processed
through 35 cycles of 92°C for 30 seconds, 55°C for 30 seconds, and
72°C for 30 seconds. A final extension step was performed at 72°C
for 10 minutes. After amplification, PCR products were processed using
a PCR purification kit (Qiaquick; Qiagen, Valencia, CA) according to
the manufacturers instructions. The PCR product was eluted into 30
µl of 10 mM Tris (pH 8.5), and 5 µl of this purified product was
used in a sequencing reaction. Both the forward and reverse strands of
the PCR products were directly sequenced (ABI 377 sequencer, using the
ABI Prism BigDye Terminator cycle sequencing ready-reaction kit; PE
Applied Biosystems, Foster City, CA). Sequencing reactions were set up
according to the manufacturers instructions, using either the forward
or reverse primers detailed earlier.
| Results |
|---|
|
|
|---|
|
|
Visual function test results are shown in Figure 3 . Compared with ERGs of a representative normal subject, all waveforms of the two patients were severely abnormal (Fig. 3A) . Patient A showed reduced amplitudes but normal timing of both rod and cone ERGs. Patient B had greater reductions in amplitude. Figure 3B shows kinetic perimetry (top panels) and static threshold perimetry in the dark-adapted (middle panels) and light-adapted (bottom panels) states. Sensitivity losses for rods (500-nm stimulus, dark-adapted) and long- (L) and middle (M)-wavelength cones (600-nm stimulus, light-adapted) were calculated from locus-specific normal values and are shown as gray-scale maps (03 log units). The psychophysical tests were conducted to position the anatomic fovea at the central fixation target (central scotoma thus truly "central"). Patients otherwise used eccentric fixation loci of approximately 20° from the fovea. By kinetic perimetry, both patients retained midperipheral islands of vision and could see both a large bright target (V-4e) and a smaller bright target (I-4e). Static perimetry also indicated detectable rod and cone sensitivity mainly in the nasal midperiphery. Some loci had no loss of rod or cone sensitivity, whereas other loci showed losses of 1 to 3 log units.
Additional CRD-Affected Families
All 15 probands reported symptoms of decreasing central vision. In
addition to reduced visual acuity, these individuals and their affected
family members showed color vision disturbances, relative or absolute
central scotomas with minimal-to-moderate peripheral field restriction
by kinetic perimetry, and ERG abnormalities. ERG b-wave results in
patients with detectable signals conformed to the two patterns we have
described in CRD3
5
: cone responses substantially worse
than those of rods or cone and rod responses equally reduced. A
spectrum of macular changes were observed that varied from a blunted
foveal reflex or nonspecific mottling of the foveal retinal pigment
epithelium, to bulls eyeappearing macular lesions, to geographic
atrophy. Most but not all patients had peripheral retinopathy, which
ranged from regions of hypopigmentation to pigment clumping (anterior
to the vascular arcades) to large patches of atrophy. Despite a
spectrum of visual function and clinical findings in the different
families, there was intrafamilial consistency of phenotype with those
members at advanced stages showing a more severe version of the disease
pattern found in their younger less-affected relatives.
Genotyping of the Primary Family
Analysis of the initial genome-wide scan suggested a locus in a
large region around the centromere of chromosome 8 from 8p12 to 8q12.
This locus has been named CORD9 (Hugo Gene Nomenclature
Committee, http://www.gene.ucl.ac.uk/nomenclature/).
Two-point lod scores were calculated for markers in this region from
the original genotyping and from additional markers tested by us. There
were two peaks: one at D8S1769 (60.3 cM from the p telomere in the
Marshfield genetic map) and the other at GATA101H09 (64.6 cM).
Multipoint analysis showed a flat approximately 4-cM peak from D8S1769
to GATA101H09 with a lod score of approximately 7.6 for both markers
(Fig. 4) . The pedigree (Fig. 1)
reveals a consanguineous family with three
informative sibships. The three fathers of the sibships are brothers,
whereas two of the mothers are sisters and the third is their first
cousin. Each of the fathers is third cousin to each of the mothers.
Crossovers at D8S1820 and D8S532 place the mutant gene proximal to
(below) the former and distal to (above) the latter (legend to Fig. 1
).
According to the Marshfield genetic map, the distance between D8S1820
and D8S532 is 8.7 cM (Fig. 5)
.
|
|
Gene Candidate
At the time the CORD9 locus was first discovered,
examination of Genemap 99 (provided by NCBI and available at
http://www.ncbi.nlm.nih.gov/genemap/) identified the expressed sequence
tag (EST) stSG4713 within the candidate region. This EST was part of
the UniGene cluster Hs.8719 (ESTs, weakly similar to dual-specificity
protein phosphatase 3; UniGene System provided by NCBI at
http://www.ncbi.nlm.nih.gov/UniGene). Of the ESTs within this cluster,
48% (43/89) originated from eye or brain cDNA, making this EST,
hereafter referred to as dual-specificity protein phosphatase 3-like
(DUS3-like), a good candidate for the CORD9 gene.
The complete coding sequence of DUS3-like was obtained on
the basis of overlapping EST sequences available within
GenBank (provided by NCBI and available at
http://www.ncbi.nlm.nih.gov/GenBank) and RT-PCR analysis. The mRNA
obtained was 1689 bp, contained an open reading frame (ORF) between
nucleotide 135 and nucleotide 1008, and encoded a predicted protein of
211 amino acids. The genomic organization of DUS3-like was
determined by comparing the sequence of the cDNA with the genomic
sequence of clone RP11-2I13 available in GenBank (accession number
AC015779). DUS3-like contains four exons and spans 7.5 kb.
RT-PCR analysis confirmed a high level of expression of this gene in
retina and brain but also showed it was widely expressed in many other
tissues (Fig. 6)
. Therefore, because the complete genome structure for this relatively
short retinally expressed gene was available, we directly sequenced it
in family members, but no DNA changes were observed.
|
Genotyping of the 15 Additional CRD-Affected Families
To estimate the frequency of the CORD9 mutation in
arCRD, we performed genotype analysis on 13 multiplex and 2 simplex
families in which neither parent had disease, using markers from the
locus. We first tested D8S499 because it is a tetranucleotide repeat
and was among the markers in the region of homozygosity at 60.3 cM
(Fig. 5)
. If D8S499 was uninformative, we also tested D8S2319 and
D8S1125, tetranucleotide and trinucleotide repeats, respectively, in
the same region of homozygosity. In eight of the families, D8S499 did
not segregate with disease and in one additional family that was
uninformative for D8S499 and D8S2319, D8S1125 did not segregate with
disease. This locus could not be ruled out from segregating with
disease in the other six families. We use the phrase "could not be
ruled out from segregating with disease" because even though the
affected individuals in these six families inherited the same unique
pair of alleles for the markers tested, the probability of this
occurring by chance is high. For example, in a sibship of one
unaffected and two affected siblings, the chance that the two affected
siblings will uniquely inherit the same pair of alleles of a marker is
almost 5 in 100. Therefore, based on our very small sample of 15
families, the frequency of CORD9 mutations can be no more
than 6 (40%) of 15 and is almost certainly much lower.
| Discussion |
|---|
|
|
|---|
Haplotype analysis of 13 multiplex and 2 simplex North American CRD-affected families using markers from the CORD9 locus, ruled out 9 of them, leaving a maximum of 6 (40%) that could have disease-causing mutations in the gene at this locus. It is likely that the actual percentage of mutations is substantially lower. In studies of the PDE6B gene in 30 families with autosomal recessive retinal degeneration, the gene could be ruled out from segregating with disease in 21 families. Exon screening by single-strand conformation polymorphism (SSCP) of the probands from the nine remaining families revealed a homozygous mutation in one and no mutations in either allele of the other eight probands.16
There are at least 40 genes that can cause nonsyndromic RP when mutated (24 genes and 16 additional loci for which the mutant gene has not yet been discovered). Of the 17 arRP genes that have been identified, not one has been shown to have mutations causing more than a small percentage of all arRP.17 18 19 20 21 22 23 24 There are four genes and six additional loci for nonsyndromic CRD.6 Only one gene and one locus (with the gene not yet identified) have been associated with arCRD. Mutations in this one gene (ABCA4) have been estimated to account for as much as 70% of cases of arCRD in one study25 but a lesser percentage in another.26 Further molecular studies of patients diagnosed with CRD using published classification schemes3 5 should clarify the frequency of the different genotypes and their relation to phenotype.
In summary, we have identified a new locus for arCRD (CORD9) at 8p11. We have shown that disease can be caused by mutations in the gene at this locus in no more than 6 (40%) of a cohort of 13 multiplex and 2 simplex CRD-affected families, and suggest that this maximum frequency will turn out to be considerably lower for the gene. We have also identified the DUS3-like candidate gene in the CORD9 locus, determined its exonintron structure, screened it, and found no mutations associated with disease in the primary arCRD family. Although CRD is relatively rare, the pathogenesis of this disease resembles many aspects of the more common age-related macular degeneration. Identification of the gene mutated in CORD9 will, therefore, highlight a new candidate for possible involvement in susceptibility to this increasingly significant disease of older adults.
| Acknowledgements |
|---|
| Footnotes |
|---|
Submitted for publication April 13, 2001; revised June 22, 2001; accepted July 6, 2001.
Commercial relationships policy: N.
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: Michael Danciger, Department of Biology, Loyola Marymount University, 7900 Loyola Boulevard, Los Angeles, CA 90045-8220. mdancige{at}lmu.edu
| References |
|---|
|
|
|---|
This article has been cited by other articles:
![]() |
A. C. Wiik, C. Wade, T. Biagi, E.-O. Ropstad, E. Bjerkas, K. Lindblad-Toh, and F. Lingaas A deletion in nephronophthisis 4 (NPHP4) is associated with recessive cone-rod dystrophy in standard wire-haired dachshund Genome Res., September 1, 2008; 18(9): 1415 - 1421. [Abstract] [Full Text] [PDF] |
||||
![]() |
M Michaelides, G E Holder, D M Hunt, F W Fitzke, A C Bird, and A T Moore A detailed study of the phenotype of an autosomal dominant cone-rod dystrophy (CORD7) associated with mutation in the gene for RIM1 Br. J. Ophthalmol., February 1, 2005; 89(2): 198 - 206. [Abstract] [Full Text] [PDF] |
||||
![]() |
A Hameed, A Abid, A Aziz, M Ismail, S Q Mehdi, and S Khaliq Evidence of RPGRIP1 gene mutations associated with recessive cone-rod dystrophy J. Med. Genet., August 1, 2003; 40(8): 616 - 619. [Full Text] |
||||
![]() |
G. A. Fishman, E. M. Stone, D. A. Eliason, C. M. Taylor, M. Lindeman, and D. J. Derlacki ABCA4 Gene Sequence Variations in Patients With Autosomal Recessive Cone-Rod Dystrophy Arch Ophthalmol, June 1, 2003; 121(6): 851 - 855. [Abstract] [Full Text] [PDF] |
||||
![]() |
B. J. Klevering, A. Blankenagel, A. Maugeri, F. P. M. Cremers, C. B. Hoyng, and K. Rohrschneider Phenotypic Spectrum of Autosomal Recessive Cone-Rod Dystrophies Caused by Mutations in the ABCA4 (ABCR) Gene Invest. Ophthalmol. Vis. Sci., June 1, 2002; 43(6): 1980 - 1985. [Abstract] [Full Text] [PDF] |
||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |