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1.  The G18V CRYGS mutation associated with human cataracts increases γS-crystallin sensitivity to thermal and chemical stress 
Biochemistry  2009;48(30):7334-7341.
γS-Crystallin, important in maintaining lens transparency, is a monomeric βγ-crystallin comprising two paired homologous domains, each with two Greek key motifs. An autosomal dominant cortical progressive cataract has been associated with a G18V mutation in human γS-crystallin. To investigate the molecular mechanism of this cataract and confirm the causative nature of the G18V mutation we examined resultant changes in conformation and stability. Human γS-crystallin cDNA was cloned into pET-20b(+) and the G18V mutant was generated by site-directed mutagenesis. Recombinant HγS-crystallins were expressed in E. coli and purified by ion-exchange and size-exclusion chromatography. By analytical ultracentrifugation wild type and mutant HγS-crystallin are monomers of about 21.95±0.21kDa and 20.89 ± 0.18kDa respectively and have similar secondary structures by far-UV CD. In increasing levels of guanidinium hydrochloride (GuHCl), a sharp red shift in fluorescence λmax and increase in emission correlating with exposure of tryptophans to the protein surface is detected earlier in the mutant protein. Under thermal stress, the G18V mutant begins to show changes in tryptophan fluorescence above 42°C and shows a Tm of 65°C as monitored by CD at 218 nm, while wild type HγS-crystallin is very stable with Tm values of 75.5°C and 75.0°C as measured by fluorescence and CD respectively. Equilibrium unfolding/refolding experiments as a function of GuHCl confirm the relative instability of the G18V mutant. Wild type HγS-crystallin exhibits a two-state transition and reversible refolding above 1.0M GuHCl, but the unfolding transition of mutant HγS-crystallin shows an intermediate state. The first transition (N→I) shows a [GuHCl]1/2 of 0.5 M while the second transition (I→U) has the same [GuHCl]1/2 as wild type HγS-crystallin, about 2.0 M. Our present study confirms the high stability of wild type HγS-crystallin and demonstrates that the G18V mutation destabilizes the protein towards heat and GuHCl induced unfolding. These biophysical characteristics are consistent with the progressive cataract formation seen in the family members carrying this mutation.
doi:10.1021/bi900467a
PMCID: PMC2735583  PMID: 19558189
lens; crystallin; cataract; human; protein stability
2.  Association of Pathogenic Mutations in TULP1 With Retinitis Pigmentosa in Consanguineous Pakistani Families 
Archives of ophthalmology  2011;129(10):1351-1357.
Objective
To identify pathogenic mutations responsible for autosomal recessive retinitis pigmentosa in 5 consanguineous Pakistani families.
Methods
Affected individuals in the families underwent a detailed ophthalmological examination that consisted of fundus photography and electroretinography. Blood samples were collected from all participating family members, and genomic DNA was extracted. A genome-wide linkage scan was performed, followed by exclusion analyses among our cohort of nuclear consanguineous families with microsatellite markers spanning the TULP1 locus on chromosome 6p. Two-point logarithm of odds scores were calculated, and all coding exons of TULP1 were sequenced bidirectionally.
Results
The results of ophthalmological examinations among affected individuals in these 5 families were suggestive of retinitis pigmentosa. The genome-wide linkage scan localized the disease interval to chromosome 6p, harboring TULP1 in 1 of 5 families, and sequential analyses identified a single base pair substitution in TULP1 that results in threonine to alanine substitution (p.T380A). Subsequently, we investigated our entire cohort of families with autosomal recessive retinitis pigmentosa and identified 4 additional families with linkage to chromosome 6p, all of them harboring a single base pair substitution in TULP1 that results in lysine to arginine substitution (p.K489R). Results of single-nucleotide polymorphism haplotype analyses were suggestive of a common founder in these 4 families.
Conclusion
Pathogenic mutations in TULP1 are responsible for the autosomal recessive retinitis pigmentosa phenotype in these consanguineous Pakistani families, with a single ancestral mutation in TULP1 causing the disease phenotype in 4 of 5 families.
Clinical Relevance
Clinical and molecular characterization of pathogenic mutations in TULP1 will increase our understanding of retinitis pigmentosa at a molecular level.
doi:10.1001/archophthalmol.2011.267
PMCID: PMC3463811  PMID: 21987678
3.  Mutations in RLBP1 associated with fundus albipunctatus in consanguineous Pakistani families 
The British journal of ophthalmology  2011;95(7):1019-1024.
Objective
To identify disease-causing mutations in two consanguineous Pakistani families with fundus albipunctatus.
Methods
Affected individuals in both families underwent a thorough clinical examination including funduscopy and electroretinography. Blood samples were collected from all participating members and genomic DNA was extracted. Exclusion analysis was completed with microsatellite short tandem repeat markers that span all reported loci for fundus albipunctatus. Two-point logarithm of odds (LOD) scores were calculated, and coding exons and exon–intron boundaries of RLBP1 were sequenced bi-directionally.
Results
The ophthalmic examination of affected patients in both families was consistent with fundus albipunctatus. The alleles of markers on chromosome 15q flanking RLBP1 segregated with the disease phenotype in both families and linkage was further confirmed by two-point LOD scores. Bi-directional sequencing of RLBP1 identified a nonsense mutation (R156X) and a missense mutation (G116R) that segregated with the disease phenotype in their respective families.
Conclusions
These results strongly suggest that mutations in RLBP1 are responsible for fundus albipunctatus in the affected individuals of these consanguineous Pakistani families.
doi:10.1136/bjo.2010.189076
PMCID: PMC3459316  PMID: 21447491
4.  A new locus for autosomal recessive congenital cataract identified in a Pakistani family 
Molecular Vision  2010;16:240-245.
Purpose
To identify the disease locus for autosomal recessive congenital cataract in a consanguineous Pakistani family.
Methods
All affected individuals underwent detailed ophthalmologic and medical examination. Blood samples were collected and DNA was extracted. A genome-wide scan was performed with polymorphic microsatellite markers on genomic DNA from affected and unaffected family members, and logarithm of odds (LOD) scores were calculated.
Results
The clinical records and ophthalmological examinations suggested that all affected individuals have nuclear cataracts. Maximum LOD scores of 5.01, 4.38, and 4.17 at θ=0 were obtained with markers D7630, D7S657, and D7S515, respectively. Fine mapping refined the critical interval and suggested that markers in a 27.78 cM (27.96 Mb) interval are flanked by markers D7S660 and D7S799, which co-segregate with the disease phenotype in family PKCC108.
Conclusions
We have identified a new locus for autosomal recessive congenital cataract, localized to chromosome 7q21.11-q31.1 in a consanguineous Pakistani family.
PMCID: PMC2822550  PMID: 20161816
5.  GNAT1 Associated with Autosomal Recessive Congenital Stationary Night Blindness 
Congenital stationary night blindness is characterized by impaired night vision, decreased visual acuity, nystagmus, myopia, and strabismus. A genome-wide linkage scan was completed that localized the critical interval to the short arm of chromosome 3 and sequencing identified a novel missense mutation in GNAT1.
Purpose.
Congenital stationary night blindness is a nonprogressive retinal disorder manifesting as impaired night vision and is generally associated with other ocular symptoms, such as nystagmus, myopia, and strabismus. This study was conducted to further investigate the genetic basis of CSNB in a consanguineous Pakistani family.
Methods.
A consanguineous family with multiple individuals manifesting cardinal symptoms of congenital stationary night blindness was ascertained. All family members underwent detailed ophthalmic examination, including fundus photographic examination and electroretinography. Blood samples were collected and genomic DNA was extracted. Exclusion and genome-wide linkage analyses were completed and two-point LOD scores were calculated. Bidirectional sequencing of GNAT1 was completed, and quantitative expression of Gnat1 transcript levels were investigated in ocular tissues at different postnatal intervals.
Results.
The results of ophthalmic examinations were suggestive of early-onset stationary night blindness with no extraocular anomalies. The genome-wide scan localized the critical interval to chromosome 3, region p22.1-p14.3, with maximum two-point LOD scores of 3.09 at θ = 0, flanked by markers D3S3522 and D3S1289. Subsequently, a missense mutation in GNAT1, p.D129G, was identified, which segregated within the family, consistent with an autosomal recessive mode of inheritance, and was not present in 192 ethnically matched control chromosomes. Expression analysis suggested that Gnat1 is expressed at approximately postnatal day (P)7 and is predominantly expressed in the retina.
Conclusions.
These data suggest that a homozygous missense mutation in GNAT1 is associated with autosomal recessive stationary night blindness.
doi:10.1167/iovs.11-8026
PMCID: PMC3339909  PMID: 22190596
6.  Association Properties of βB1- and βA3-Crystallins: Ability to Form Heterotetramers 
Biochemistry  2008;47(42):11062-11069.
As major constituents of the mammalian lens, β-crystallins associate into dimers, tetramers, and higher-order complexes in order to maintain lens transparency and refractivity. A previous study has shown that dimerization of βB2- and βA3-crystallins is energetically highly favored and entropically driven. While heterodimers further associate into higher order complexes in vivo, a significant level of reversibly associated tetrameric crystallin has not been previously observed in vitro. In order to enhance our understanding of the interactions between β-crystallins, this study characterizes the association of βB1-crystallin, a major component of large β-crystallin complexes (β-high) with itself and with βA3-crystallin. Mouse βB1- and human βA3-crystallins were expressed in E. coli and purified chromatographically. Their association was then characterized using size-exclusion chromatography, native gel electrophoresis, isoelectric focusing, and analytical sedimentation equilibrium centrifugation. When present alone, each β-crystallin associates into homodimers but no tetramer formation is seen. Upon mixing, heterocomplex formation between βB1- and βA3-crystallins is observed using size-exclusion chromatography, native gel electrophoresis, isoelectric focusing, and sedimentation equilibrium. In contrast to results previously obtained upon mixing βB2- and βA3-crystallins, mixed βB1- and βA3-crystallins show a dimer-tetramer equilibrium with a Kd of 1.1 μM, indicating that these two β-crystallins associate predominantly into heterotetramers in vitro. Thus, while each purified β-crystallin associates only into homodimers and mixed βB2- and βA3-crystallins form a mixture of homo- and heterodimers, mixed βB1- and βA3-crystallins associate predominantly into heterotetramers in equilibrium with heterodimers. These findings suggest a unique role for βB1-crystallin in promoting higher-order crystallin association in the lens.
doi:10.1021/bi8012438
PMCID: PMC2752815  PMID: 18823128
7.  A Novel Locus for Autosomal Recessive Retinitis Pigmentosa in a Consanguineous Pakistani Family Maps to Chromosome 2p 
American Journal of Ophthalmology  2010;149(5):861-866.
OBJECTIVE
To identify a disease locus for autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family.
DESIGN
Prospective linkage study.
METHODS
Blood samples were collected and genomic DNA was extracted. A genome-wide scan was performed using 382 polymorphic microsatellite markers on genomic DNA from 4 affected and 5 unaffected family members, and logarithm of odds scores were calculated.
RESULTS
A maximum 2-point logarithm of odds score of 3.14 at θ = 0 was obtained for marker D2S165 during the genome-wide scan. Fine mapping markers identified a 20.92-cM (19.98-Mb) interval flanked by D2S149 and D2S367 that cosegregates with the disease phenotype. Haplotype analyses further refined the critical interval, distal to D2S220 in a 12.31-cM (13.35-Mb) region that does not harbor any genes that previously have been associated with retinitis pigmentosa.
CONCLUSIONS
Linkage analysis identified a new locus for autosomal recessive retinitis pigmentosa that maps to chromosome 2p22.3-p24.1 in a consanguineous Pakistani family.
doi:10.1016/j.ajo.2009.12.034
PMCID: PMC3399686  PMID: 20227676
8.  Ectopia Lentis in a Consanguineous Pakistani Family and a Novel Locus on Chromosome 8q 
Archives of Ophthalmology  2010;128(8):1046-1049.
Objective
To investigate the genetic basis and molecular characteristics of the isolated form of ectopia lentis.
Methods
We ascertained a consanguineous Pakistani family with multiple individuals with ectopia lentis. All affected as well as unaffected members with isolated ectopia lentis underwent detailed ophthalmologic and medical examination. Blood samples were collected and DNA was extracted. A genome-wide scan was completed with 382 polymorphic microsatellite markers, and logarithm of odds (LOD) scores were calculated.
Results
Maximum 2-point LOD scores of 5.68 and 2.88 at θ=0 were obtained for markers D8S285 and D8S260, respectively, during the genome-wide scan. Additional microsatellite markers refined the disease locus to a 16.96-cM (14.07-Mb) interval flanked by D8S1737 proximally and D8S1117 distally.
Conclusions
We report on a new locus for nonsyndromic autosomal recessive ectopia lentis on chromosome 8q11.23-q13.2 in a consanguineous Pakistani family.
Clinical Relevance
Identification of genetic loci and genes involved in ectopia lentis will enhance our understanding of the disease at a molecular level, leading to better genetic counseling and family screening and possible future development of better treatment.
doi:10.1001/archophthalmol.2010.165
PMCID: PMC3398798  PMID: 20697006
9.  Nonsense mutation in MERTK causes autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family 
The British Journal of Ophthalmology  2010;94(8):1094-1099.
Background
Retinitis pigmentosa (RP) is one of the most common ophthalmic disorders affecting one in approximately 5000 people worldwide. A nuclear family was recruited from the Punjab province of Pakistan to study the genetic basis of autosomal recessive RP.
Methods
All affected individuals underwent a thorough ophthalmic examination and the disease was characterised based upon results for fundus photographs and electroretinogram recordings. Genomic DNA was extracted from peripheral leucocytes. Exclusion studies were performed with short tandem repeat (STR) markers flanking reported autosomal recessive RP loci. Haplotypes were constructed and results were statistically evaluated.
Results
The results of exclusion analyses suggested that family PKRP173 was linked to chromosome 2q harbouring mer tyrosine kinase protooncogene (MERTK), a gene previously associated with autosomal recessive RP. Additional STR markers refined the critical interval and placed it in a 13.4 cM (17 Mb) region flanked by D2S293 proximally and D2S347 distally. Significant logarithm of odds (LOD) scores of 3.2, 3.25 and 3.18 at θ=0 were obtained with markers D2S1896, D2S2269 and D2S160. Sequencing of the coding exons of MERTK identified a mutation, c.718G→T in exon 4, which results in a premature termination of p.E240X that segregates with the disease phenotype in the family.
Conclusion
Our results strongly suggest that the nonsense mutation in MERTK, leading to premature termination of the protein, is responsible for RP phenotype in the affected individuals of the Pakistani family.
doi:10.1136/bjo.2009.171892
PMCID: PMC3393880  PMID: 20538656
10.  Crystallin gene mutations in Indian families with inherited pediatric cataract 
Molecular Vision  2008;14:1157-1170.
Purpose
Pediatric cataract is the most common form of treatable childhood blindness and is both clinically and genetically heterogeneous. Autosomal dominant and recessive forms of cataract have been reported to be caused by mutations in 22 different genes so far. Of the cataract mutations reported to date, about half the mutations occur in crystallins, a quarter of the mutations in connexins, and the remainder is evenly divided between intrinsic membrane proteins, intermediate filament proteins, and transcription factors. This study is aimed at identification of the spectrum and frequency of crystallin gene mutations in cataractous patients in an Indian population.
Methods
Genetic analysis was extended to screen the entire coding region of the CRYAA, CRYAB, CRYBA1, CRYBA4, CRYBB1, CRYBB2, CRYBB3, CRYGC, CRYGD, and CRYGS genes using single stranded conformational polymorphism (SSCP) analysis as a screening technique followed by direct sequencing of all subjects that displayed an electrophoretic shift.
Results
This report describes the first simultaneous mutation analysis of 10 crystallin genes in the same population, represented by 60 south Indian families. The analysis allowed the identification of causative mutations in 10 of the families (three novel and six reported). This includes six missense mutations (CRYAA-R12C, R21W, R54C, CRYAB- A171T, CRYGC-R168W, CRYGS- S39C), two nonsense mutations (CRYBB2- Q155X, CRYGD- R140X), and one splice mutation, which was identified in two families (CRYBA1-IVS3+1G>A).
Conclusions
Crystallin mutations are responsible for 16.6% of the inherited pediatric cataract in this population. As causative mutations have not been found in many of the families analyzed, this study suggests the presence of further novel genes or sequence elements involved in the pathogenesis of cataract in these families.
PMCID: PMC2435160  PMID: 18587492
11.  Functional Validation of Hydrophobic Adaptation to Physiological Temperature in the Small Heat Shock Protein αA-crystallin 
PLoS ONE  2012;7(3):e34438.
Small heat shock proteins (sHsps) maintain cellular homeostasis by preventing stress and disease-induced protein aggregation. While it is known that hydrophobicity impacts the ability of sHsps to bind aggregation-prone denaturing proteins, the complex quaternary structure of globular sHsps has made understanding the significance of specific changes in hydrophobicity difficult. Here we used recombinant protein of the lenticular sHsp α A-crystallin from six teleost fishes environmentally adapted to temperatures ranging from -2°C to 40°C to identify correlations between physiological temperature, protein stability and chaperone-like activity. Using sequence and structural modeling analysis we identified specific amino acid differences between the warm adapted zebrafish and cold adapted Antarctic toothfish that could contribute to these correlations and validated the functional consequences of three specific hydrophobicity-altering amino acid substitutions in αA-crystallin. Site directed mutagenesis of three residues in the zebrafish (V62T, C143S, T147V) confirmed that each impacts either protein stability or chaperone-like activity or both, with the V62T substitution having the greatest impact. Our results indicate a role for changing hydrophobicity in the thermal adaptation of α A-crystallin and suggest ways to produce sHsp variants with altered chaperone-like activity. These data also demonstrate that a comparative approach can provide new information about sHsp function and evolution.
doi:10.1371/journal.pone.0034438
PMCID: PMC3315530  PMID: 22479631
12.  Molecular Analysis of Bardet-Biedl Syndrome Families: Report of 21 Novel Mutations in 10 Genes 
The authors describe the screening of 55 families of European, Tunisian, and Arab descent for mutations in 15 BBS and 5 additional ciliopathy genes. The spectrum of mutations is described with a discussion of possible third-allele effects.
Purpose.
Bardet-Biedl syndrome (BBS) is genetically heterogeneous with 15 BBS genes currently identified, accounting for approximately 70% of cases. The aim of our study was to define further the spectrum of BBS mutations in a cohort of 44 European-derived American, 8 Tunisian, 1 Arabic, and 2 Pakistani families (55 families in total) with BBS.
Methods.
A total of 142 exons of the first 12 BBS-causing genes were screened by dideoxy sequencing. Cases in which no mutations were found were then screened for BBS13, BBS14, BBS15, RPGRIP1L, CC2D2A, NPHP3, TMEM67, and INPP5E.
Results.
Forty-three mutations, including 8 frameshift mutations, 10 nonsense mutations, 4 splice site mutations, 1 deletion, and 20 potentially or probably pathogenic missense variations, were identified in 46 of the 55 families studied (84%). Of these, 21 (2 frameshift mutations, 4 nonsense mutations, 4 splice site mutations, 1 deletion, and 10 missense variations) were novel. The molecular genetic findings raised the possibility of triallelic inheritance in 7 Caucasian families, 1 Arabian family, and 1 Tunisian patient. No mutations were detected for BBS4, BBS11, BBS13, BBS14, BBS15, RPGRIP1L, CC2D2A, NPHP3, TMEM67, or INPP5E.
Conclusions.
This mutational analysis extends the spectrum of known BBS mutations. Identification of 21 novel mutations highlights the genetic heterogeneity of this disorder. Differences in European and Tunisian patients, including the high frequency of the M390R mutation in Europeans, emphasize the population specificity of BBS mutations with potential diagnostic implications. The existence of some BBS cases without mutations in any currently identified BBS genes suggests further genetic heterogeneity.
doi:10.1167/iovs.11-7554
PMCID: PMC3176075  PMID: 21642631
13.  Overexpression of Human γC-crystallin 5 bp Duplication Disrupts Lens Morphology in Transgenic Mice 
Expression of c.119_123dup CRYGC, associated with autosomal dominant human cataracts, causes degeneration and vacuolization of lens fiber cells and cataracts in transgenic mice. This confirms the causative nature of this mutation and suggests that it acts through a direct toxic effect on lens fiber cells.
Purpose.
To delineate the molecular mechanisms underlying autosomal dominant congenital cataracts caused by a 5 bp duplication in human CRYGC.
Methods.
c.119_123dup (CRYGC5bpd) and wild-type human γC-crystallin (CRYGC) were expressed in transgenic mouse lenses by the chicken βB1-crystallin promoter. Lenses were characterized histologically, by real-time PCR, SDS-PAGE, and Western blot. pET and Tet-on expression systems were used to express human CRYGC and CRYGC5bpd proteins in Escherichia coliand HeLa cells, respectively.
Results.
Transgenic expression of CRYGC5bpd mutant γC-crystallin results in nuclear cataracts in which lens fiber cells begin to show variable degrees of degeneration and vacuolization by postnatal day 21. By 6 weeks of age all CRYGC5bpd lenses exhibit abnormalities of varying severity, comprising large vacuoles in cortical fiber cells, swelling and disorganization of fiber cells, and defective fiber cell migration and elongation. Levels of CRYGC5bpd mRNA are 3.7- and 14.1-fold higher than endogenous Crygc mRNA in postnatal day 1 and 6-week CRYGC5bpd mice lens, respectively. Crygc, Crygb, Crybb2, and Crybb3 mRNA levels are decreased in CRYGC5bpd mice compared with wild-type and CRYGC mice. Both wild-type and mutant human γC crystallin are uniformly distributed in the cytosol of HeLa cells, but CRYGC5bpd is degraded when expressed in E. coli BL21(DE3).
Conclusions.
Transgenic expression of mutant CRYGC5bpd γ-crystallin at near-physiological levels causes lens opacities and fiber cell defects, confirming the pathogenicity of this mutation. These results further suggest that HCG5pbd γ-crystallin causes cataracts through a direct toxic or developmental effect on lens cells causing damaged microstructure rather than through formation of HMW aggregates with resultant light scattering.
doi:10.1167/iovs.11-7168
PMCID: PMC3176079  PMID: 21436266
14.  Spatial expression patterns of autophagy genes in the eye lens and induction of autophagy in lens cells 
Molecular Vision  2012;18:1773-1786.
Purpose
Mutation of the autophagy gene FYVE (named after the four cysteine-rich proteins: Fab 1 [yeast orthologue of PIKfyve], YOTB, Vac 1 [vesicle transport protein], and EEA1) and coiled coil containing 1 (fyco1) causes human cataract suggesting a role for autophagy in lens function. Here, we analyzed the range and spatial expression patterns of lens autophagy genes and we evaluated whether autophagy could be induced in lens cells exposed to stress.
Methods
Autophagy gene expression levels and their spatial distribution patterns were evaluated between microdissected human lens epithelium and fibers at the mRNA and protein levels by microarray data analysis, real-time PCR and western blot analysis. Selected autophagy protein spatial expression patterns were also examined in newborn mouse lenses by immunohistochemistry. The autophagosomal content of cultured human lens epithelial cells was determined by counting the number of microtubule-associated protein 1 light chain 3B (LC3B)-positive puncta in cells cultured in the presence or absence of serum.
Results
A total of 42 autophagy genes were detected as being expressed by human lens epithelium and fibers. The autophagosomal markers LC3B and FYCO1 were detected throughout the newborn mouse lens. Consistently, the autophagy active form of LC3B (LC3B II) was detected in microdissected human lens fibers. An increased number of LC3B-positive puncta was detected in cultured lens cells upon serum starvation suggesting induction of autophagy in lens cells under stress conditions.
Conclusions
The data provide evidence that autophagy is an important component for the function of lens epithelial and fiber cells. The data are consistent with the notion that disruption of lens autophagy through mutation or inactivation of specific autophagy proteins could lead to loss of lens resistance to stress and/or loss of lens differentiation resulting in cataract formation.
PMCID: PMC3398491  PMID: 22815631
15.  An Atypical Form of Bietti Crystalline Dystrophy 
Ophthalmic genetics  2011;32(2):118-121.
Purpose
To describe clinical and functional features of a patient with Bietti crystalline dystrophy and atypical electroretinogram responses.
Methods
The patient underwent a thorough medical anamnesis, genetic counseling, peripheral blood draw for CYP4V2 gene analysis and electron microscopy, and a complete ophthalmological assessment including optical coherence tomography, indocyanine green angiography, microperimetry, full-field electroretinogram and multifocal electroretinogram.
Results
The most striking features of the retina were deposits of yellowish-white glistening crystals and focal lobular areas of choriocapillary atrophy at the posterior pole and midperiphery. The full-field electroretinogram was normal and the multifocal electroretinogram showed extinguished central recordings. Mutation analysis revealed a homozygous c. 332T>C p.I111T mutation in exon 3 of the CYP4V2 gene. Typical cytoplasmic inclusions containing crystalline-like structure and large degenerative lysosomes were seen on electron microscopy of peripheral leukocytes.
Conclusion
Here we describe a patient with Bietti crystalline dystrophy with a CYP4V2 gene mutation and typical leukocyte inclusions who showed the classical retinal lesions but had a normal electroretinogram. This suggests the existence of less severe forms of BCD related to relatively mild CYP4V2 mutations.
doi:10.3109/13816810.2011.559653
PMCID: PMC3155699  PMID: 21385027
bietti; electroretinogram; CYP4V2 gene
16.  Mutations in the β-subunit of rod phosphodiesterase identified in consanguineous Pakistani families with autosomal recessive retinitis pigmentosa 
Molecular Vision  2011;17:1373-1380.
Purpose
This study was designed to identify pathogenic mutations causing autosomal recessive retinitis pigmentosa (RP) in consanguineous Pakistani families.
Methods
Two consanguineous families affected with autosomal recessive RP were identified from the Punjab Province of Pakistan. All affected individuals underwent a thorough ophthalmologic examination. Blood samples were collected, and genomic DNAs were extracted. Exclusion analysis was completed, and two-point LOD scores were calculated. Bidirectional sequencing of the β subunit of phosphodiesterase 6 (PDE6β) was completed.
Results
During exclusion analyses both families localized to chromosome 4p, harboring PDE6β, a gene previously associated with autosomal recessive RP. Sequencing of PDE6β identified missense mutations: c.1655G>A (p.R552Q) and c.1160C>T (p.P387L) in families PKRP161 and PKRP183, respectively. Bioinformatic analyses suggested that both mutations are deleterious for the native three-dimensional structure of the PDE6β protein.
Conclusions
These results strongly suggest that mutations in PDE6β are responsible for the disease phenotype in the consanguineous Pakistani families.
PMCID: PMC3108895  PMID: 21655355
17.  Lack of phenotypic effect of triallelic variation in SPATA7 in a family with Leber congenital amaurosis resulting from CRB1 mutations 
Molecular Vision  2011;17:3326-3332.
Purpose
To identify the causative gene for autosomal recessive Leber congenital amaurosis (LCA) in a Chinese family.
Methods
One Chinese LCA family was identified and an ophthalmologic examination was performed. The genetic defects were analyzed simultaneously by a genome-wide linkage scan with 382 polymorphic microsatellite markers, as well as by comprehensive mutational screening of 15 genes known to associate with LCA on the genomic DNA of this family.
Results
Suggestive linkages were found in 13 chromosomal regions, of which only one harbored a known causative gene, crumbs homolog 1 (CRB1), on chromosome 1. Sanger sequencing of CRB1 identified two novel heterozygous mutations, c.3221T>C (p.L1074S) and c.2677–2A>C. In addition, a novel missense heterozygous mutation, c.938C>A (p.A313D), in spermatogenesis associated 7 (SPATA7), was detected in the proband after screening of the other 14 LCA causative genes. All three affected individuals of the family had compound heterozygous CRB1 mutations, and one of the three (the proband) had an additional mutation in SPATA7. The unaffected mother had the heterozygous c.3221T>C mutation in CRB1 and the heterozygous c.938C>A mutation in SPATA7. The unaffected father could not be tested, but presumably had the heterozygous c.2677–2A>C mutation in CRB1. The proband, with triallelic mutations in CRB1 and SPATA7, had a phenotype similar to other two affected brothers, suggesting the additional mutant allele in SPATA7 might not contribute to the disease. Similarly, the mother, with digenic mutations in CRB1 and SPATA7, had normal vision and fundi, suggesting the digenic mutations in these two genes might not cause disease.
Conclusions
Digenic and triallelic mutations of CRB1 and SPATA7 were detected in a family with LCA. Our results imply that CRB1 and SPATA7 may not interact with each other directly. This emphasizes that care should be taken in invoking a mutation–disease association for digenic and triallelic mutations.
PMCID: PMC3247167  PMID: 22219627
18.  Association analysis of nine candidate gene polymorphisms in Indian patients with type 2 diabetic retinopathy 
BMC Medical Genetics  2010;11:158.
Background
Diabetic retinopathy (DR) is classically defined as a microvasculopathy that primarily affects the small blood vessels of the inner retina as a complication of diabetes mellitus (DM).It is a multifactorial disease with a strong genetic component. The aim of this study is to investigate the association of a set of nine candidate genes with the development of diabetic retinopathy in a South Indian cohort who have type 2 diabetes mellitus (T2DM).
Methods
Seven candidate genes (RAGE, PEDF, AKR1B1, EPO, HTRA1, ICAM and HFE) were chosen based on reported association with DR in the literature. Two more, CFH and ARMS2, were chosen based on their roles in biological pathways previously implicated in DR. Fourteen single nucleotide polymorphisms (SNPs) and one dinucleotide repeat polymorphism, previously reported to show association with DR or other related diseases, were genotyped in 345 DR and 356 diabetic patients without retinopathy (DNR). The genes which showed positive association in this screening set were tested further in additional sets of 100 DR and 90 DNR additional patients from the Aravind Eye Hospital. Those which showed association in the secondary screen were subjected to a combined analysis with the 100 DR and 100 DNR subjects previously recruited and genotyped through the Sankara Nethralaya Hospital, India. Genotypes were evaluated using a combination of direct sequencing, TaqMan SNP genotyping, RFLP analysis, and SNaPshot PCR assays. Chi-square and Fisher exact tests were used to analyze the genotype and allele frequencies.
Results
Among the nine loci (15 polymorphisms) screened, SNP rs2070600 (G82S) in the RAGE gene, showed significant association with DR (allelic P = 0.016, dominant model P = 0.012), compared to DNR. SNP rs2070600 further showed significant association with DR in the confirmation cohort (P = 0.035, dominant model P = 0.032). Combining the two cohorts gave an allelic P < 0.003 and dominant P = 0.0013). Combined analysis with the Sankara Nethralaya cohort gave an allelic P = 0.0003 and dominant P = 0.00011 with an OR = 0.49 (0.34 - 0.70) for the minor allele. In HTRA1, rs11200638 (G>A), showed marginal significance with DR (P = 0.055) while rs10490924 in LOC387715 gave a P = 0.07. No statistical significance was observed for SNPs in the other 7 genes studied.
Conclusions
This study confirms significant association of one polymorphism only (rs2070600 in RAGE) with DR in an Indian population which had T2DM.
doi:10.1186/1471-2350-11-158
PMCID: PMC2994838  PMID: 21067572
19.  Cataract- and Lens-Specific Upregulation of ARK Receptor Tyrosine Kinase in Emory Mouse Cataract 
Purpose
The Emory mouse is a well-characterized model for age-onset cataract. The purpose of the present study was to identify differentially expressed genes between pre- and post-cataract Emory mouse lenses.
Methods
Eyes were extracted from Emory mice at 3 weeks (precataract) and 7.5 months (postcataract) of age, and lenses were dissected. Lens RNA was compared for gene expression differences by RT-PCR differential display, and transcripts exhibiting altered levels of gene expression were cloned and identified by sequencing. The levels of two transcripts were further evaluated by RT-PCR in 3-week- and 7.5-month-old lenses and the remainder of the eye. The same transcripts were also measured in lenses from three non–Emory mouse strains (FVB/N, 129Sv, and CD1) ages 4 weeks to 11.5 months.
Results
Three transcripts were identified as exhibiting altered levels of gene expression between 3-week- and 7.5-month-old Emory mouse lenses. These encoded αA-crystallin (decreased), βA3/A1-crystallin (decreased), and adhesion-related kinase (ARK) receptor tyrosine kinase (increased). Decreased αA-crystallin and increased ARK expression were not detected in lenses isolated from three non–Emory mouse strains of similar age. Increased expression of ARK was not detected between 3-week- and 7.5-month-old Emory mouse eye nonlens tissues.
Conclusions
The present data confirm that expression of the αA-crystallin gene is decreased in cataract in the Emory mouse lens relative to age-matched control lenses and they provide evidence for cataract- and lens-specific upregulation of the ARK receptor tyrosine kinase in the Emory mouse.
PMCID: PMC2957826  PMID: 12036992
20.  Mutations in ASCC3L1 on 2q11.2 Are Associated with Autosomal Dominant Retinitis Pigmentosa in a Chinese Family 
Linkage of adRP to the ASCC3L1 region of chromosome 2 and identification of a mutation in hBrr2p associated with RP in this Chinese family add mutations in another splicing factor to the known causes of RP.
Purpose.
To localize and identify the gene and mutations causing autosomal dominant retinitis pigmentosa in a Chinese Family.
Methods.
Families were ascertained and patients underwent complete ophthalmic examinations. Blood samples were collected and DNA was extracted. A linkage scan of genomic regions containing known candidate genes was performed by using 34 polymorphic microsatellite markers on genomic DNA from affected and unaffected family members, and lod scores were calculated. Candidate genes were sequenced and mutations analyzed.
Results.
A genome-wide scan yielded a lod score of 3.5 at θ = 0 for D2S2333 and 3.46 at θ = 0 for D2S2216. This region harbors the ASCC3L1 gene. Sequencing of ASCC3L1 in an affected family member showed a heterozygous single-base-pair change; c.3269G→T, predicted to result in an Arg1090Leu amino acid change.
Conclusions.
The results provide strong evidence that mutations in ASCC3L1 have resulted in autosomal dominant retinitis pigmentosa in this Chinese family.
doi:10.1167/iovs.09-3725
PMCID: PMC2868455  PMID: 19710410
21.  Autosomal recessive corneal endothelial dystrophy (CHED2) is associated with mutations in SLC4A11 
Journal of Medical Genetics  2006;44(1):64-68.
Objective
To map and identify the gene for autosomal recessive congenital hereditary endothelial dystrophy (CHED2, OMIM 217700), a disorder characterised by diffuse bilateral corneal clouding that may lead to visual impairment and requiring corneal transplantation.
Methods
Members of 16 families with autosomal recessive CHED were genotyped for 13 microsatellite markers at the CHED2 locus on chromosome 20p13‐12. Two‐point linkage analysis was carried out using the FASTLINK version of the MLINK program. Mutation screening was carried out by amplification of exons and flanking regions by polymerase chain reaction, followed by direct automated sequencing.
Results
Linkage and haplotype analysis placed the disease locus within a 2.2 cM (1.3 Mb) interval flanked by D20S198 and D20S889, including SLC4A11. The maximum limit of detection score of 11.1 was obtained with D20S117 at θ = 0. Sequencing of SLC4A11 showed homozygotic mutations in affected members from 12 of 16 families.
Conclusion
These results confirm that mutations in the SLC4A11 gene cause autosomal recessive CHED.
doi:10.1136/jmg.2006.044644
PMCID: PMC2597914  PMID: 16825429
22.  Autosomal recessive congenital cataract linked to EPHA2 in a consanguineous Pakistani family 
Molecular Vision  2010;16:511-517.
Purpose
To investigate the genetic basis of autosomal recessive congenital cataracts in a consanguineous Pakistani family.
Methods
All affected individuals underwent a detailed ophthalmological and clinical examination. Blood samples were collected and genomic DNAs were extracted. A genome-wide scan was performed with polymorphic microsatellite markers. Logarithm of odds (LOD) scores were calculated, and Eph-receptor type-A2 (EPHA2), residing in the critical interval, was sequenced bidirectionally.
Results
The clinical and ophthalmological examinations suggested that all affected individuals have nuclear cataracts. Genome-wide linkage analyses localized the critical interval to a 20.78 cM (15.08 Mb) interval on chromosome 1p, with a maximum two-point LOD score of 5.21 at θ=0. Sequencing of EPHA2 residing in the critical interval identified a missense mutation: c.2353G>A, which results in an alanine to threonine substitution (p.A785T).
Conclusions
Here, we report for the first time a missense mutation in EPHA2 associated with autosomal recessive congenital cataracts.
PMCID: PMC2846848  PMID: 20361013
23.  Autosomal recessive congenital cataract in consanguineous Pakistani families is associated with mutations in GALK1 
Molecular Vision  2010;16:682-688.
Purpose
To identify the pathogenic mutations responsible for autosomal recessive congenital cataracts in consanguineous Pakistani families.
Methods
All affected individuals underwent detailed ophthalmologic and medical examination. Blood samples were collected and genomic DNA was extracted. A genome-wide scan was performed with polymorphic microsatellite markers on genomic DNA from affected and unaffected family members and logarithm of odds (LOD) scores were calculated. All coding exons of galactokinase (GALK1) were sequenced to identify pathogenic lesions.
Results
Clinical records and ophthalmological examinations suggested that affected individuals have nuclear cataracts. Linkage analysis localized the critical interval to chromosome 17q with a maximum LOD score of 5.54 at θ=0, with D17S785 in family PKCC030. Sequencing of GALK1, a gene present in the critical interval, identified a single base pair deletion: c.410delG, which results in a frame shift leading to a premature termination of GALK1: p.G137fsX27. Additionally, we identified a missense mutation: c.416T>C, in family PKCC055 that results in substitution of a leucine residue at position 139 with a proline residue: p.L139P, and is predicted to be deleterious to the native GALK1 structure.
Conclusions
Here, we report pathogenic mutations in GALK1 that are responsible for autosomal recessive congenital cataracts in consanguineous Pakistani families.
PMCID: PMC2855732  PMID: 20405025
24.  Cat-Map: putting cataract on the map 
Molecular Vision  2010;16:2007-2015.
Lens opacities, or cataract(s), may be inherited as a classic Mendelian disorder usually with early-onset or, more commonly, acquired with age as a multi-factorial or complex trait. Many genetic forms of cataract have been described in mice and other animal models. Considerable progress has been made in mapping and identifying the genes and mutations responsible for inherited forms of cataract, and genetic determinants of age-related cataract are beginning to be discovered. To provide a convenient and accurate summary of current information focused on the increasing genetic complexity of Mendelian and age-related cataract we have created an online chromosome map and reference database for cataract in humans and mice (Cat-Map).
PMCID: PMC2965572  PMID: 21042563
25.  Mapping of a new locus associated with autosomal recessive congenital cataract to chromosome 3q 
Molecular Vision  2010;16:2634-2638.
Purpose
To localize the disease interval for autosomal recessive congenital cataracts in a consanguineous Pakistani family.
Methods
All affected individuals underwent detailed ophthalmologic examination. Blood samples were collected and genomic DNA was extracted. A genome-wide scan was performed with fluorescently-labeled microsatellite markers on genomic DNA from affected and unaffected family members and logarithm of odds (LOD) scores were calculated.
Results
Clinical records and ophthalmological examinations suggested that affected individuals have bilateral congenital cataracts. Genome-wide linkage analysis localized the critical interval to chromosome 3q with a maximum LOD score of 3.87 at θ=0; with marker D3S3609. Haplotype analyses refined the critical interval to a 23.39 cM (18.01 Mb) interval on chromosome 3q, flanked by D3S1614 proximally and D3S1262, distally.
Conclusions
Here, we report a new locus for autosomal recessive congenital cataract localized to chromosome 3q in a consanguineous Pakistani family.
PMCID: PMC3002966  PMID: 21179239

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