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Ophthalmic Molecular Genetics |

Novel Compound Heterozygous TULP1 Mutations in a Family With Severe Early-Onset Retinitis Pigmentosa FREE

Anneke I. den Hollander, PhD; Janneke J. C. van Lith-Verhoeven, MD, PhD; Maarten L. Arends, BSc; Tim M. Strom, MD, PhD; Frans P. M. Cremers, PhD; Carel B. Hoyng, MD, PhD
[+] Author Affiliations

Author Affiliations: Departments of Human Genetics (Drs den Hollander and Cremers, and Mr Arends) and Ophthalmology (Drs van Lith-Verhoeven and Hoyng), and Nijmegen Centre for Molecular Life Sciences (Drs den Hollander and Cremers), Nijmegen Medical Centre, Radboud University, Nijmegen, the Netherlands; and Institute of Human Genetics, German Science Foundation National Research Center for Environment and Health, Munich-Neuherberg, and Institute of Human Genetics, Technical University, Munich, Germany (Dr Strom).


Section Editor: Janey L Wiggs, MD, PhD

More Author Information
Arch Ophthalmol. 2007;125(7):932-935. doi:10.1001/archopht.125.7.932.
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Published online

Objective  To describe the clinical characteristics and determine the genetic defect in a Surinamese family with autosomal recessive retinitis pigmentosa.

Methods  Family members underwent blood sampling and ophthalmologic examinations. After exclusion of all known mutations in all genes involved in autosomal recessive retinitis pigmentosa, a genome-wide linkage scan was performed using 11 555 single-nucleotide polymorphisms spread throughout the genome. Mutation analysis of the TULP1 gene was performed by direct sequencing.

Results  All affected family members had a severe retinal dystrophy with a history of nystagmus, low visual acuity, and nyctalopia since infancy. The scotopic and photopic responses were nonrecordable on electroretinography. A genome-wide scan suggested linkage to the chromosomal region containing the TULP1 gene. Mutation analysis of TULP1 identified novel compound heterozygous mutations (p.Arg482Trp and p.Leu504fsX140) in all affected family members.

Conclusions  The affected members of the Surinamese family have a severe early-onset form of autosomal recessive retinitis pigmentosa, which is caused by compound heterozygous mutations in the TULP1 gene.

Clinical Relevance  Clinical and molecular genetic characterization of autosomal recessive retinitis pigmentosa may help to provide a more accurate prognosis in individual patients. This study confirms that TULP1 mutations cause a severe early-onset form of autosomal recessive retinitis pigmentosa.

Figures in this Article

Retinitis pigmentosa (RP) is a heterogeneous group of progressive retinal dystrophies, which has a prevalence of approximately 1 in 4000 individuals. Retinitis pigmentosa is characterized by nyctalopia, a progressive constriction of the visual fields, pigment depositions in the midperipheral retina, and a gradual reduction of visual acuity. The disease can be inherited in an autosomal recessive, autosomal dominant, or X-linked fashion. Mutations in 19 genes have been reported to cause autosomal recessive RP, and 5 loci have been reported for which the causative gene has not yet been identified.1

Mutations in the TULP1 gene are found in approximately 1% to 2% of patients with autosomal recessive RP.26 To date, 14 different mutations have been found in the TULP1 gene.28 In comparison with other forms of RP, patients with TULP1 mutations have a very severe visual handicap, which may be better described as Leber congenital amaurosis.3,4,8,9

TULP1 is a member of the tubby-like protein (TULP) family. The TULP proteins are characterized by a highly conserved C-terminal tubby domain; their expression is mainly restricted to neuronal tissues. Expression of TULP1 is confined to the retina, where it localizes primarily to the inner segments and connecting cilium of the photoreceptor cells. TULP1 is involved in protein trafficking and is essential for the transport of rhodopsin from its site of synthesis in the inner segments through the connecting cilium to the outer segments.10,11

In this study, we describe a Surinamese family with multiple members who were affected by a severe early-onset form of autosomal recessive RP. The involvement of all known mutations in all known autosomal recessive RP genes was excluded. A genome-wide linkage suggested linkage to a region on chromosome 6, which contains the TULP1 gene. Mutation analysis of the TULP1 gene identified 2 novel compound heterozygous mutations in all affected individuals.

PATIENTS AND OPTHALMOLOGICAL EXAMINATIONS

Five affected and 5 unaffected members of a Surinamese family with autosomal recessive RP participated in this study. All affected family members underwent complete ophthalmologic examinations, including best-corrected projected Snellen visual acuities, slitlamp biomicroscopy, dilated fundus examinations, Goldmann visual fields, and International Society for Clinical Electrophysiology of Vision–standardized electroretinography and electrooculography. Informed consent was obtained from all participating individuals, consistent with the tenets of the Declaration of Helsinki. This study was approved by the institutional review board of the Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands.

MOLECULAR ANALYSIS

Standard protocols were used to extract DNA from peripheral blood leukocytes.12 The proband (II-8) of the Surinamese family was screened for 505 known mutations and sequence variants in 16 genes known to be involved in autosomal recessive RP (CERKL, CNGA1, CNGB1, MERTK, PDE6A, PDE6B, PNR, RDH12, RGR, RLBP1, SAG, TULP1, CRB1, RPE65, USH2A, and USH3A) with a genotyping microarray based on arrayed primer extension technology (AR-RP Chip; Asper Ophthalmics, Tartu, Estonia).13 Ten members of the Surinamese family underwent genotyping, with 11 555 single nucleotide polymorphisms spread throughout the genome (Affymetrix GeneChip Human Mapping 10K Array Xba142 2.0; Affymetrix, Santa Clara, California). Multipoint parametric linkage analysis was performed with Allegro v1.2c (Decode Genetics, Reykjavik, Iceland)14 in the EasyLinkage Plus v4.00b software package (University of Würzburg, Würzburg, Germany)15 using the Decode Genetics genetic single nucleotide polymorphism map and the white allele frequencies. An autosomal recessive mode of inheritance with complete penetrance was assumed, as none of the children (third generation) of the 5 affected siblings (second generation) are affected. The disease-allele frequency was estimated at 0.001. Haplotypes were constructed with HaploPainter V.024 (University of Cologne, Cologne, Germany).16

Primers for amplification of the TULP1 coding exons and splice junctions were designed with ExonPrimer (Technical University, Munich, Germany; http://ihg.gsf.de/ihg/ExonPrimer.html) and Primer3 (Whitehead Institute, Cambridge, Massachusetts).17 Primer sequences and polymerase chain reaction conditions can be requested from the authors. Polymerase chain reaction products were purified with the QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany). Sequencing was performed with BigDye Terminator Chemistry, version 3 (Applied Biosystems, Foster City, California), on a 3730 or 3100 DNA Analyzer (Applied Biosystems). The p.Arg482Trp missense mutation was analyzed in control individuals by digestion of the exon 14 polymerase chain reaction product with restriction enzyme HpaII.

CLINICAL EXAMINATION

All affected individuals of the Surinamese family had severe retinal dystrophy. They had a history of nystagmus, low visual acuity, and nyctalopia since infancy. On the last examinations (ages, 39-63 years), their visual acuities ranged from light perception to 1/300 OU. The 3 youngest affected family members (II-4, II-8, and II-10) had myopic refractions, varying from a spherical equivalent of − 2.5 to − 2.0 diopters. They all had nonrecordable scotopic and photopic electroretinography responses and a flat line on electrooculogram. The visual fields showed a general and central decline in sensitivity with progression to a constricted visual field of 10°. On examination of the anterior segments, posterior subcapsular cataracts were found (Figure 1A). The oldest affected individual (II-1) already underwent cataract surgery. Retinal examination revealed narrowed arterioles, optic disc pallor, atrophy of the pigment epithelium, and diffuse bone spicule pigmentation extending to the macular region (Figure 1B).

Place holder to copy figure label and caption
Figure 1.

A, Posterior subcapsular cataract in patient II-4. B, Fundus photograph of the left eye of patient II-1 showing diffuse bone spicule pigmentation extending to the macular region, narrowed arterioles, disc pallor, and atrophy of the pigment epithelium.

Graphic Jump Location
MOLECULAR ANALYSES

The proband (II-8) of the family was analyzed with the autosomal recessive RP mutation chip13 and did not carry any mutations in the genes known to be involved in autosomal recessive RP. Genome-wide linkage analysis revealed 2 regions with a maximum multipoint logarithm of the odds score of 2.9. Haplotype analysis confirmed that the single nucleotide polymorphism alleles at both of these regions completely segregated with the disease. One region is located on chromosome 5p15 between single nucleotide polymorphisms rs4487467 and rs2008011, spans 6.6 megabase pairs (Mb) of genomic DNA, and contains 11 genes. The second region is located on chromosome 6p21 between single nucleotide polymorphisms rs3871466 and rs726108, spans 7.8 Mb of genomic DNA, and contains more than 150 genes, including the TULP1 gene (Figure 2A).

Place holder to copy figure label and caption
Figure 2.

Molecular analysis of the genetic defect in a Surinamese family with autosomal recessive retinitis pigmentosa. A, Pedigree structure and haplotype analysis at chromosome 6p21. Mutations in the TULP1 gene segregate with the disease in the family. Mutation 1 (M1), p.Leu504fsX140; mutation 2 (M2), p.Arg482Trp. Black bars indicate uninformative single nucleotide polymorphism alleles. B, Genomic sequence of the TULP1 gene in proband II-8 and a control individual. The proband carries a heterozygous missense mutation p.Arg482Trp in exon 14 and a heterozygous 11–base pair (bp) deletion in exon 15. C, Alignment of a part of the C-terminal tubby domain of TULP1 orthologs and TULP family members and position of all missense mutations identified in the TULP1 gene to date, including the novel p.Arg482Trp mutation. Identical amino acids are indicated in black boxes, conserved residues in gray boxes. Amino acid positions are shown after mutation names.

Graphic Jump Location

Mutation analysis of the TULP1 gene in the proband (II-8) of the family revealed a novel heterozygous missense mutation in exon 14 (c.1444C>T, p.Arp482Trp) and a novel heterozygous 11–base pair (bp) deletion leading to a frameshift in exon 15 (c.1511_1521delTGCAGTTCGGC, p.Leu504fsX140) (Figure 2B). All affected individuals were compound heterozygous for these mutations, while the unaffected individuals were either heterozygous for p.Arg482Trp or did not carry these mutations (Figure 2A). The p.Arg492Trp mutation was not detected in 92 control individuals.

To date, 14 different mutations have been found in the TULP1 gene, including 4 splice-site mutations, 2 frameshift mutations, 1 nonsense mutation, and 7 missense mutations.28 All missense mutations are located in the C-terminal tubby domain, which is highly conserved between all TULP family members.18

In this study, we describe a Surinamese family with a severe early-onset form of autosomal recessive RP, which is caused by novel compound heterozygous mutations in the TULP1 gene. The 11-bp deletion in exon 15 (c.1511_1521delTGCAGTTCGGC) causes a frameshift and replaces the 39 C-terminal amino acids by 140 aberrant amino acid residues (p.Leu504fsX140). The missense mutation p.Arg482Trp affects a conserved amino acid residue in the C-terminal tubby domain of TULP1 orthologs and tubby-related proteins (Figure 2C). Similar to other TULP1 missense mutations, the p.Arg482Trp mutation converts a positively charged side chain to a neutral one. It has been postulated that an important biological function, such as DNA or protein binding, is dependent on the maintenance of a positive surface, which may be disrupted by this mutation.18

The severe phenotype observed in the Surinamese family is in agreement with previous reports, which also describe a severe early-onset retinal dystrophy in patients with TULP1 mutations. The addition of novel TULP1 mutations to the autosomal recessive RP mutation chip13 will enhance its efficiency in the future.

Correspondence: Anneke I. den Hollander, PhD, Department of Human Genetics, Radboud University, Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands (a.denhollander@antrg.umcn.nl).

Submitted for Publication: November 2, 2006; final revision received December 21, 2006; accepted December 28, 2006.

Financial Disclosure: None reported.

Funding/Support: This work was supported by grant 916.56.160 from the Netherlands Organisation for Scientific Research (Dr den Hollander) and grant 543 from the British Retinitis Pigmentosa Society (Drs den Hollander and Cremers).

Additional Contributions: Arjan P. de Brouwer, PhD, provided helpful discussions, and Mrs Christel Beumer and Mrs Saskia van der Velde-Visser provided technical assistance.

 RetNet: Retinal Information Network Web site. http://www.sph.uth.tmc.edu/Retnet/ Accessed November 1, 2006
Gu  SLennon  ALi  Y  et al.  Tubby-like protein-1 mutations in autosomal recessive retinitis pigmentosa. Lancet 1998;351 (9109) 1103- 1104
PubMed
Hagstrom  SANorth  MANishina  PMBerson  ELDryja  TP Recessive mutations in the gene encoding the tubby-like protein TULP1 in patients with retinitis pigmentosa. Nat Genet 1998;18 (2) 174- 176
PubMed
Paloma  EHjelmqvist  LBayés  M  et al.  Novel mutations in the TULP1 gene causing autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci 2000;41 (3) 656- 659
PubMed
Kondo  HQin  MMizota  A  et al.  A homozygosity-based search for mutations in patients with autosomal recessive retinitis pigmentosa, using microsatellite markers. Invest Ophthalmol Vis Sci 2004;45 (12) 4433- 4439
PubMed
Mandal  MNHeckenlively  JRBurch  T  et al.  Sequencing arrays for screening multiple genes associated with early-onset human retinal degenerations on a high-throughput platform. Invest Ophthalmol Vis Sci 2005;46 (9) 3355- 3362
PubMed
Banerjee  PKleyn  PWKnowles  JA  et al.  TULP1 mutation in two extended Dominican kindreds with autosomal recessive retinitis pigmentosa. Nat Genet 1998;18 (2) 177- 179
PubMed
Hanein  SPerrault  IGerber  S  et al.  Leber congenital amaurosis: comprehensive survey of the genetic heterogeneity, refinement of the clinical definition, and genotype-phenotype correlations as a strategy for molecular diagnosis. Hum Mutat 2004;23 (4) 306- 317
PubMed
Lewis  CABatlle  IRBatlle  KG  et al.  Tubby-like protein 1 homozygous splice-site mutation causes early-onset severe retinal degeneration. Invest Ophthalmol Vis Sci 1999;40 (9) 2106- 2114
PubMed
Hagstrom  SAAdamian  MScimeca  M  et al.  A role for the Tubby-like protein 1 in rhodopsin transport. Invest Ophthalmol Vis Sci 2001;42 (9) 1955- 1962
PubMed
Xi  QPauer  GJMarmorstein  ADCrabb  JWHagstrom  SA Tubby-like protein 1 (TULP1) interacts with F-actin in photoreceptor cells. Invest Ophthalmol Vis Sci 2005;46 (12) 4754- 4761
PubMed
Miller  SADykes  DDPolesky  HF A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988;16 (3) 1215
PubMed
Allikmets  RZernant  JJaakson  K  et al.  Analysis of autosomal recessive retinitis pigmentosa patients on the ARRP genotyping (disease chip) [ARVO abstract 1700]. Invest Ophthalmol Vis Sci 2006;47
Gudbjartsson  DFJonasson  KFrigge  MLKong  A Allegro: a new computer program for multipoint linkage analysis. Nat Genet 2000;25 (1) 12- 13
PubMed
Hoffmann  KLindner  TH easyLINKAGE-Plus: automated linkage analyses using large-scale SNP data. Bioinformatics 2005;21 (17) 3565- 3567
PubMed
Thiele  HNürnberg  P HaploPainter: a tool for drawing pedigrees with complex haplotypes. Bioinformatics 2005;21 (8) 1730- 1732
PubMed
Rozen  SSkaletsky  H Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000;132365- 386
PubMed
Boggon  TJShan  WSSantagata  SMyers  SCShapiro  L Implication of Tubby proteins as transcription factors by structure-based functional analysis. Science 1999;286 (5447) 2119- 2125
PubMed

Figures

Place holder to copy figure label and caption
Figure 1.

A, Posterior subcapsular cataract in patient II-4. B, Fundus photograph of the left eye of patient II-1 showing diffuse bone spicule pigmentation extending to the macular region, narrowed arterioles, disc pallor, and atrophy of the pigment epithelium.

Graphic Jump Location
Place holder to copy figure label and caption
Figure 2.

Molecular analysis of the genetic defect in a Surinamese family with autosomal recessive retinitis pigmentosa. A, Pedigree structure and haplotype analysis at chromosome 6p21. Mutations in the TULP1 gene segregate with the disease in the family. Mutation 1 (M1), p.Leu504fsX140; mutation 2 (M2), p.Arg482Trp. Black bars indicate uninformative single nucleotide polymorphism alleles. B, Genomic sequence of the TULP1 gene in proband II-8 and a control individual. The proband carries a heterozygous missense mutation p.Arg482Trp in exon 14 and a heterozygous 11–base pair (bp) deletion in exon 15. C, Alignment of a part of the C-terminal tubby domain of TULP1 orthologs and TULP family members and position of all missense mutations identified in the TULP1 gene to date, including the novel p.Arg482Trp mutation. Identical amino acids are indicated in black boxes, conserved residues in gray boxes. Amino acid positions are shown after mutation names.

Graphic Jump Location

Tables

References

 RetNet: Retinal Information Network Web site. http://www.sph.uth.tmc.edu/Retnet/ Accessed November 1, 2006
Gu  SLennon  ALi  Y  et al.  Tubby-like protein-1 mutations in autosomal recessive retinitis pigmentosa. Lancet 1998;351 (9109) 1103- 1104
PubMed
Hagstrom  SANorth  MANishina  PMBerson  ELDryja  TP Recessive mutations in the gene encoding the tubby-like protein TULP1 in patients with retinitis pigmentosa. Nat Genet 1998;18 (2) 174- 176
PubMed
Paloma  EHjelmqvist  LBayés  M  et al.  Novel mutations in the TULP1 gene causing autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci 2000;41 (3) 656- 659
PubMed
Kondo  HQin  MMizota  A  et al.  A homozygosity-based search for mutations in patients with autosomal recessive retinitis pigmentosa, using microsatellite markers. Invest Ophthalmol Vis Sci 2004;45 (12) 4433- 4439
PubMed
Mandal  MNHeckenlively  JRBurch  T  et al.  Sequencing arrays for screening multiple genes associated with early-onset human retinal degenerations on a high-throughput platform. Invest Ophthalmol Vis Sci 2005;46 (9) 3355- 3362
PubMed
Banerjee  PKleyn  PWKnowles  JA  et al.  TULP1 mutation in two extended Dominican kindreds with autosomal recessive retinitis pigmentosa. Nat Genet 1998;18 (2) 177- 179
PubMed
Hanein  SPerrault  IGerber  S  et al.  Leber congenital amaurosis: comprehensive survey of the genetic heterogeneity, refinement of the clinical definition, and genotype-phenotype correlations as a strategy for molecular diagnosis. Hum Mutat 2004;23 (4) 306- 317
PubMed
Lewis  CABatlle  IRBatlle  KG  et al.  Tubby-like protein 1 homozygous splice-site mutation causes early-onset severe retinal degeneration. Invest Ophthalmol Vis Sci 1999;40 (9) 2106- 2114
PubMed
Hagstrom  SAAdamian  MScimeca  M  et al.  A role for the Tubby-like protein 1 in rhodopsin transport. Invest Ophthalmol Vis Sci 2001;42 (9) 1955- 1962
PubMed
Xi  QPauer  GJMarmorstein  ADCrabb  JWHagstrom  SA Tubby-like protein 1 (TULP1) interacts with F-actin in photoreceptor cells. Invest Ophthalmol Vis Sci 2005;46 (12) 4754- 4761
PubMed
Miller  SADykes  DDPolesky  HF A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988;16 (3) 1215
PubMed
Allikmets  RZernant  JJaakson  K  et al.  Analysis of autosomal recessive retinitis pigmentosa patients on the ARRP genotyping (disease chip) [ARVO abstract 1700]. Invest Ophthalmol Vis Sci 2006;47
Gudbjartsson  DFJonasson  KFrigge  MLKong  A Allegro: a new computer program for multipoint linkage analysis. Nat Genet 2000;25 (1) 12- 13
PubMed
Hoffmann  KLindner  TH easyLINKAGE-Plus: automated linkage analyses using large-scale SNP data. Bioinformatics 2005;21 (17) 3565- 3567
PubMed
Thiele  HNürnberg  P HaploPainter: a tool for drawing pedigrees with complex haplotypes. Bioinformatics 2005;21 (8) 1730- 1732
PubMed
Rozen  SSkaletsky  H Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000;132365- 386
PubMed
Boggon  TJShan  WSSantagata  SMyers  SCShapiro  L Implication of Tubby proteins as transcription factors by structure-based functional analysis. Science 1999;286 (5447) 2119- 2125
PubMed

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