Molecular Vision 2006; 12:499-505 ©2006 Molecular Vision Received 30 September 2005 | Accepted 26 April 2006 | Published 12 May 2006

Fine mapping of the keratoconus with cataract locus on chromosome 15q and candidate gene analysis

Durga Prasad Dash,1 Giuliana Silvestri,2 Anne E. Hughes1

Departments of 1Medical Genetics and 2Ophthalmology, Queen’s University of Belfast, Belfast, United Kingdom

Purpose: To report the fine mapping of the keratoconus with cataract locus on chromosome 15q and the mutational analysis of positional candidate genes. Methods: Genotyping of two novel microsatellite markers and a single nucleotide polymorphism (SNP) in the critical region of linkage for keratoconus with cataract on 15q was performed. Positional candidate genes (MORF4L1, KIAA1055, ETFA, AWP1, REC14, KIAA1199, RCN2, FA H , IDH3A, MTHFS, ADAMTS7, MAN2C1, PTPN9, KIAA1024, ARNT2, BCL2A1, ISL2, C15ORF22 (P24B), DNAJA4, FLJ14594, CIB2 (KIP2), C15ORF5, and PSMA4) prioritized on the basis of ocular expression and probable function were screened by PCR-based DNA sequencing methods. Results: We report the refinement of the linkage region for keratoconus with cataract to an interval of approximately 5.5 Mb flanked by the MAN2C1 gene and the D15S211 marker on chromosome 15q. Mutational analysis of positional candi- date genes detected many sequence variations and single nucleotide polymorphisms. None of the sequence variants were considered pathogenic as they were also found in unaffected family members and normal control DNA samples. Conclusions: Fine mapping of the keratoconus with cataract locus on 15q has reduced the linked region to 5.5 Mb, thereby excluding 28 candidate genes. A further 23 candidate genes were excluded by direct sequencing methods, al- though a pathogenic genomic rearrangement or exonic deletion would not have been detected.

Keratoconus (KC; OMIM 148300), the most common Mutations in the VSX-1 transcription factor (OMIM corneal dystrophy, is a bilateral, noninflammatory progressive 605020) were identified in 4.7% of patients with keratoconus corneal ectasia. Clinically, the cornea becomes progressively (KTCN1; OMIM 148300) and also in posterior polymorphous thin and conical which leads to myopia, irregular astigma- corneal dystrophy (PPCD1; OMIM 122000) [11]. However, tism, and corneal scarring. The transparency and refractive traditional mapping methods to identify the genetic basis of state of the cornea is a prerequisite for normal vision. The KC have been limited by the lack of large multigeneration disease usually arises in the teenage years, eventually stabi- families for study. Genome-wide scans to localize the KC gene lizing in the third and fourth decades [1]. It occurs with no or genes had not been reported until our group identified a ethnic or gender preponderance and causes significant visual large three-generation family with KC and anterior polar cata- impairment in young adults. No specific treatment exists ex- ract and reported linkage to chromosome 15q22.32-24.2 [12]. cept to replace the corneal tissue by surgery (corneal trans- Recently loci for autosomal dominantly inherited keratoco- plantation) when the visual acuity can no longer be corrected nus have been mapped to chromosomes 21 [13], 16q22.3-q23.1 by contact lenses. In the Western world, KC is the most com- (KTCN2; OMIM 608932) [10], 3p14-q13 (KTCN3; OMIM mon indication for corneal transplantation [2]. The underly- 608586) [14], 2p24 (KTCN4; OMIM 609271) [15] and 5q14.1- ing biochemical processes and pathobiology of keratoconus q21.3 (NCBI). remain poorly understood. The keratoconus with cataract locus on chromosome 15q The incidence of KC is 1 in 2,000 in the general popula- was identified in a large Northern Irish family of three gen- tion [1,3]. A family history is present only in a minority of erations affected by combined autosomal dominant early on- cases, however, one of the major etiological factors is genetic set anterior polar cataract and clinically severe keratoconus [1,4-6]. KC is believed to be inherited autosomally, because [12]. The disease gene in this family was successfully mapped of familial occurrence [7], a higher concordance rate of the to chromosome 15q22.32-24.2 within a 6.5 Mb region flanked trait in monozygotic twins then dizygotic twins [8] and its by markers CYP11A and D15S211 [12]. CTSH, CRABP1, prevalence in first degree relatives is 15-67 times higher than IREB2, and RASGRF1 were excluded previously as the caus- the general population [6]. Most studies describe autosomal ative gene for keratoconus with cataract [12]. The purpose of dominant inheritance, with incomplete penetrance or variable the present study was to narrow the critical region of linkage expressivity [1,9,10]. of keratoconus with cataract by genotyping novel microsatellite markers and single nucleotide polymorphisms identified dur- Correspondence to: Durga Prasad Dash, Department of Ophthalmol- ing sequencing of candidate genes. Fine mapping of a kerato- ogy, Institute of Clinical Science, Block A, Queen’s University of conus with cataract locus on 15q has reduced the linked re- Belfast, Royal Victoria Hospital, Grosvenor Road, Belfast, BT12 gion to 5.5 Mb, thereby excluding 28 potential candidate genes. 6BA, United Kingdom; Phone: 0044-7754404969; FAX: 0044- A further 23 positional candidate genes were prioritized for 2890632699; email: [email protected] 499 Molecular Vision 2006; 12:499-505 ©2006 Molecular Vision analysis based on expression studies, molecular and biochemi- purification kit (Gentra Systems, Inc., Minneapolis, MN). cal evidence (Table 1) and excluded by PCR-based DNA se- Single nucleotide polymorphism typing: The single nucle- quencing. otide polymorphism (SNP) rs1128933 in exon 20 of MAN2C1 (GenBank NM_006715) was typed in key recombinants us- METHODS ing the forward primer 5'-CTG GAG ACA CGG TAT AGG Genomic DNA was extracted from the peripheral blood leu- CTG G-3' and the reverse primer 5'-AGT GTA CCT GGG kocytes of all available family members using Puregene DNA AGT GGG AAG G-3'. Cycle sequencing was performed with

TABLE 1. LIST OF POSITIONAL CANDIDATE GENES IN KERATOCONUS WITH CATARACT LOCUS SCREENED FOR MUTATION Gene Full name of the gene OMIM ------

MORF4L1(MRG15) Mortality factor 4 like 1 607303

KIAA1055 Transmembrane protein 2-like gene

ETFA Electron-transfer-flavoprotein, alpha polypeptide (glutaric 608053 aciduria II)

AWP1 Protein associated with PRK1

REC14 Recombination protein REC14

KIAA1199 KIAA1199 608366

RCN2 Reticulocalbin 2, EF-hand calcium binding domain 602584

FAH Fumarylacetoacetate hydrolase (fumarylacetoacetase) 276700

IDH3A Isocitrate dehydrogenase 3 (NAD+) alpha 601149

MTHFS 5,10-methenyltetrahydrofolate synthetase 604197 (5-formyltetrahydrofolate cycloligase)

ADAMTS7 A disintegrin-like and metalloprotease (reprolysin type) 605009 with thrombospondin type 1 motif, 7

MAN2C1 Mannosidase, alpha, class 2C, member 1 154580

PTPN9 Protein tyrosine phosphatase, nonreceptor type 9 600768

KIAA1024 KIAA1024 protein

ARNT2 Aryl-hydrocarbon receptor nuclear translocator 2 606036

BCL2A1 BCL2-related protein A1 601056

ISL2 ISL2 transcription factor, LIM/homeodomain, (islet-2)

C15ORF22(P24B) Chromosome 15 open reading frame 22

DNAJA4 DnaJ (Hsp40) homolog, subfamily A, member 4

FLJ14594 Leucine rich repeat neuronal 6A

CIB2 (KIP2) Calcium and integrin binding family member 2 605564

C15ORF5 Chromosome 15 open reading frame 5

PSMA4 proteasome (prosome, macropain) subunit, alpha type, 4 Gene name and corresponding OMIM (wherever possible) is given in the disease linked region of keratoconus with cataract on chromosome 15q. 500 Molecular Vision 2006; 12:499-505 ©2006 Molecular Vision the BigDye Terminator Cycle Sequencing kit (Applied PCR-based DNA sequencing: Analysis of positional can- Biosystems, Foster City, CA) on PCR products using the for- didate genes was carried out by PCR-based DNA sequencing ward PCR primer and analyzed on the ABI Prism 3100 DNA using dye terminator chemistry (ABI). Primers were designed Sequencing System (Applied Biosystems). using Primer Detective, version 1.01 (Clontech Labs Inc., CA) Identification and typing of microsatellite markers: Two for all individual exons plus at least 50 bp of flanking intronic novel microsatellite markers on chromosome 15 located at 73.8 sequence, and 5' and 3' untranslated regions. For ADAMTS7, Mb between MAN2C1 and ETFA and at 78.4 Mb (within long-range PCR using Elongase (Invitrogen, Paisley, UK) was ARNT2) were identified from the human genome database carried out as a preliminary step, using gene-specific primers (HGD). PCR was performed on genomic DNA from family that did not amplify related pseudogenes. After dilution of members using the following primers: 5'-Fam-CTG TAT GCA product (1 in 1000) nested PCR was performed before sequenc- GCG ATC AGT GAG C-3' and 5'-GTA GGA GAC AGA GAC ing as already described. All primer pairs and PCR conditions ACT CAG TCC-3' for the marker at 73.8 Mb and 5'-Fam- are available on request. TTA CAT CAC TTG CAT TGC TTC C-3' and 5'-AAT CAC AGC CAA ACA TAG ATG C-3' for the ARNT2 intragenic RESULTS marker. Diluted PCR products were electrophoresed on an ABI One SNP and two novel microsatellite markers were identi- 3100 genetic analyzer. Alleles were sized by Genotyper soft- fied toward the extremities of the previously linked interval ware (ABI) and scored using in-house software, C-allele (C- on chromosome 15q [12] in a family with autosomal domi- ALLELE program, Dr. Shane Mckee, Department of Medical nant keratoconus and cataract. Utilizing these markers, fam- Genetics, Queen’s University of Belfast, UK). Linkage analy- ily members were genotyped to clarify the position of the re- sis was performed using the Fastlink linkage program version combination in key individuals. Typing of rs1128933 (Figure

5.1. 1) within exon 20 of MAN2C1 showed III23 is recombinant at

Figure 1. Haplotyping of polymorphic markers on chromosome 15q. The af-

fected mother (II9) genotyped “CT” for rs1128933 within MAN2C1 and the in-

ferred haplotype of the normal father (II8) is “CC” based on the paternal haplotype

inherited by (III25) and (III27). The “C” allele of rs1128933 is associated with the

disease haplotype. II9 has passed the “C” allele to all of her affected offspring ex-

cept (III23). III23 is therefore recombinant

at the MAN2C1 locus, whereas III21 is not recombinant at this locus. Thus affected

parent (II9) and offspring infer that the disease gene is distal of rs1128933 in the MAN2C1 gene. The disease haplotype inherited from the affected parent is shown by vertical bars.

501 Molecular Vision 2006; 12:499-505 ©2006 Molecular Vision

the MAN2C1 locus and more proximal markers, whereas III21, without identifying a causative mutation. There is limited scope previously shown to be recombinant at CYP11A, is not re- for further refinement of the linkage region, which cannot be combinant at MAN2C1. The novel microsatellite markers lo- reduced below a core interval of 4.6 Mb with the present fam- cated at 73.8 and 78.4 Mb (ARNT2) were fully informative ily members. One family has been reported in the literature for tracking haplotypes inherited by the crucial individuals in with corneal pathology and congenital cataract which maps to this family; however, none showed recombination at these loci. chr15q [16]. The authors of this study have proposed the term The further haplotype analysis described here has reduced the EDICT syndrome for the clinical findings of endothelial dys- candidate interval of the keratoconus with cataract locus by trophy, iris hypoplasia, congenital cataract, and stromal thin- 1.0 Mb, to the region flanked by rs1128933 (within MAN2C1) ning (EDICT) which were inherited as an autosomal domi- and D15S211. nant trait in their family. The locus for EDICT syndrome maps Candidate genes positioned within this 5.5 Mb region to a 26 Mb region of chromosome 15q which overlaps our (Figure 2) were identified and prioritized for analysis based region, and may therefore be allelic, however the small size on expression studies, molecular, and biochemical evidence of this family restricts its potential for improved mapping. (Table 1). Numerous sequence variations were found (Table Although the clinical phenotype in this family shows consid- 2) in positional candidate genes (MORF4L1, KIAA1055, ETFA, erable differences from the EDICT syndrome [16], it is pos- AWP1, REC14, KIAA1199, RCN2, FAH, IDH3A, MTHFS, sible that both families share a common genetic basis. The ADAMTS7, MAN2C1, PTPN9, KIAA1024, ARNT2, BCL2A1, EDICT syndrome includes features of significant anterior dys- ISL2, C15ORF22 (P24B), DNAJA4, FLJ14594, CIB2 (KIP2), genesis such as microcornea, iris hypoplasia, endothelial ab- C15ORF5, and PSMA4). None of the sequence variants were normalities and importantly the snydrome been reported to considered pathogenic as they were also found in unaffected have congenital anterior polar cataract. Our family differs in family members and unrelated, ethnically matched normal that those affected have been documented as having no ab- control DNA samples. normalities or signs of anterior segment dysgenesis at birth, with the corneal and lens changes developing after the age of DISCUSSION 5 years. Sequential examination of our family has indicated The refinement of the linkage region for the keratoconus with that the anterior polar cataract and keratoconus are develop- cataract locus on chromosome 15q [15] to 5.5 Mb between mental and not congenital. The ocular phenotype in our fam- MAN2C1 and D15S211 has excluded 28 positional candidate ily is also unusual as the occurrence of keratoconus and de- genes. CTSH, CRABP1, IREB2, and RASGRF1 which re- velopmental anterior polar cataract has not to our knowledge mained within the refined disease interval were excluded pre- been previously described. Isolated congenital cataracts are viously by direct sequencing [15]. The reduced disease gene usually inherited in an autosomal dominant fashion with mu- interval is exceedingly gene rich containing a total of 75 posi- tations predominantly reported in the lens crystallins and tional candidate genes, of which 27 have now been screened connexins [17]. Anterior polar cataracts are developmental lens opacities and have been mapped to 14q24-qter (CTAA1; OMIM 115650) [18] and 17p13 (CTAA2; OMIM 601202) [19]. Corneal guttata (focal thickenings of the Descemet’s membrane of the corneal endothelium) have been reported in association with anterior polar cataract (OMIM 121390) [20,21]. Developmentally the human lens is derived from sur- face ectoderm and the cornea from surface ectoderm and neu- roectoderm. The ocular phenotype in this family may reflect a single developmental anomaly. Pathogenic mutations have been reported in a number of transcription factors which re- sult in ocular phenotypes combining cataract, anterior seg- ment dysgenesis and specific iris defects (aniridia, coloboma) [22-24]. Human VSX-1 (OMIM 605020) is a member of the Vsx1 group of vertebrate paired-like homeodomain transcription factors [25,26]. Mutations in the VSX-1 transcription factor were identified in 7% [11] of keratoconus patients [27]. To date, five pathogenic heterozygous missense mutations have been reported in VSX-1 associated with keratoconus: L17P, R166W, L159M, D144E, and P247R [11,27]. The aryl hydro- carbon receptor nuclear translocator (ARNT2) in our candi- Figure 2. Map of the linked region of keratoconus with cataract on chromosome 15q. The linkage markers used in this study are shown date interval is also member of a novel transcription factor on the left with their relative positions (NCBI Build 35.1 map) on the family consisting of a conserved basic helix-loop-helix (bHLH) right. The heavy bar (5.5 Mb) represents the critical region of the structural motif contiguous with a PAS domain. A W278X locus for keratoconus with cataract. mutation in the aryl hydrocarbon receptor-interacting protein- 502 Molecular Vision 2006; 12:499-505 ©2006 Molecular Vision like 1 (AIPL1) gene on 17p was found in a Pakistani family The pathogenic mutation for keratoconus with cataract in with Leber’s congenital amaurosis and anterior keratoconus this family may be in one of the lower priority genes that have [28]. We have not found any pathogenic mutation in ARNT2 not yet been screened, however, the possibility of a mutation or in ISL2 or MORF4L1 (also called MRG15) which also code in a high priority gene that is not amenable to detection by for transcription factors. PCR-based sequencing must also be considered. Exonic dele- ADAMTS7 was a strong candidate gene as the ADAMTS tions, duplications and other rearrangements would fall into (a disintegrin-like and metalloprotease domain with this category. We have applied multiplex ligation-dependent thrombospondin type 1 motif) families are secreted enzymes probe amplification (MLPA) [31-34] to three genes (data not metalloproteases with a prominent role in extracellular ma- shown) and have found no evidence of copy number change. trix proteolysis [29] The proteolytic activity of this gene may The mutation may also be located in a conserved intergenic be related to development of keratoconus in which there is region of regulatory importance. Chromosome 15q shows a evidence implicating matrix metalloproteinases in the patho- high frequency of neocentromeres, which harbour a high den- genesis [30]. Other ADAMTS7 family members such as sity of clinically important duplicons, indicating a significant ADAMTS18 (16q22.3-q23.1) and ADAMTS9 (3p14-q13) have evolutionary history of this region [35]. Rearrangements in been mapped within other reported keratoconus loci [10,13]. this region have previously been associated with diseases [36- ADAMTS7 presented sequencing difficulties because of its 41]. extremely close homology to several genes located on chro- Quantitative analysis of SNP genotypes at numerous loci mosome 15q and elsewhere, necessitating the use of long-range spanning the critical region of the keratoconus with cataract PCR to ensure specificity. Although no causative mutation was locus is included in future research plans. This will enable found in ADAMTS7, several novel SNPs were identified. more precise mapping of the linkage interval and also provide The most interesting of the remaining positional candi- evidence of any anomalous dosage effects that may be of rel- date genes are RNUT1, IMP3 (C15orf12), CSPG4, FBXO22, evance to the disease process. Identification of genes impli- PSTPIP1, HMG20A, LRRN6A, ACSBG1 (BG1), CHRNA5, cated in the pathogenesis of keratoconus is vital for the devel- CHRNA3, CHRNB4, transcription factor genes ZNF291 and opment of novel treatments and early preventative strategies SIN3A1 and will be studied in the future. for this common corneal disorder.

TABLE 2. SEQUENCE VARIATIONS SEGREGATED WITH DISEASE HAPLOTYPE OF KERATOCONUS WITH CATARACT Location Amino acid Gene DNA change in the gene change Comment ------MTHFS -475A>C Promoter Novel SNP ARNT2 c.1503+27G>C Intron 8 Novel SNP ARNT2 c.2028 G>A Exon 19 Known SNP (rs4072568) (Untranslated) P24B -249G>T Promoter Novel SNP P24B -82G>A Promoter Novel SNP ADAMTS7 c.1468-4G>A Intron 9 Novel SNP ADAMTS7 c.1530C>T Exon 10 p.Ala510Ala Novel synonymous SNP ADAMTS7 c.2223T>C Exon 15 p.Ser741Ser Novel synonymous SNP ADAMTS7 c.2645+179C>T Intron 17 Novel SNP ADAMTS7 c.4267-42A>G Intron 19 Novel SNP ADAMTS7 c.4267-44C>T Intron 19 Novel SNP ADAMTS7 c.4419+5 A>G Intron 20 Novel SNP ADAMTS7 3'+42C>T (c.5061+42C>T) 3' UTR Novel SNP ADAMTS7 3'+4T>C (c.5061+4T>C) 3' UTR Known SNP (rs12286) CTSH c.77C>G Exon 1 p.Ser29Ser Known synonymous SNP (rs3190230) CTSH c.1-1T>G 5' UTR Known SNP (rs1036939) RASGRF1 c.1826+37T>A Intron 13 Known SNP (rs3816283) IREB2 c.20-127A>G Intron 1 Novel SNP IREB2 c.583+58G>A Intron 7 Known SNP (rs8036042) IREB2 c.583+19 A>G Intron 7 Known SNP (rs3817092) PSMA4 c.1-97 G>T 5' UTR Known SNP (rs3813571) PSMA4 c.720 C>T Exon 9 p.His240His Known synonymous SNP (rs8053) These sequence variants did not reveal a clear pathogenic mutation causing the disease. The naming systems of DNA change is from the nomenclature of the (Human Genome Variation Society). 503 Molecular Vision 2006; 12:499-505 ©2006 Molecular Vision

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The print version of this article was created on 12 May 2006. This reflects all typographical corrections and errata to the article through that date. Details of any changes may be found in the online version of the article. α 505