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Transition from lens epithelial cells to lens fiber cell is accompanied by numerous changes in gene expression critical for lens transparency. We identify expression patterns of highly prevalent genes including ubiquitous and enzyme crystallins in the embryonic day 13 chicken lens.Embryonic day 13 chicken lenses were dissected into central epithelial cell (EC), equatorial epithelial cell (EQ), cortical fiber cell (FP), and nuclear fiber cell (FC) compartments. Total RNA was prepared, subjected to high-throughput unidirectional mRNA sequencing, analyzed, mapped to the chicken genome, and functionally grouped.A total of 77,097 gene-specific transcripts covering 17,450 genes were expressed, of which 10,345 differed between two or more lens subregions. Ubiquitous crystallin gene expression increased from EC to EQ and was similar in FP and FC. Highly expressed crystallin genes fell into three coordinately expressed groups with R2 ≥ 0.93: CRYAA, CRYBB2, CRYAB, and CRYBA2; CRYBB1, CRYBA4, CRYGN, ASL1, and ASL; and CRYBB3 and CRYBA1. The highly expressed transcription factors YBX1, YBX3, PNRC1, and BASP1 were coordinately expressed with the second group of crystallins (r20.88).Although it is well known that lens crystallin gene expression changes during the epithelial to fiber cell transition, these data identify for the first time three distinct patterns of expression for specific subsets of crystallin genes, each highly correlated with expression of specific transcription factors. The results provide a quantitative basis for designing functional experiments pinpointing the mechanisms governing the landscape of crystallin expression during fiber cell differentiation to attain lens transparency.

Purpose To identify the genetic origins of autosomal recessive congenital cataracts (arCC) in the Pakistani population. Methods Based on the hypothesis that most arCC patients in consanguineous families in the Punjab areas of Pakistan should be homozygous for causative mutations, affected individuals were screened for homozygosity of nearby highly informative microsatellite markers and then screened for pathogenic mutations by DNA sequencing. A total of 83 unmapped consanguineous families were screened for mutations in 33 known candidate genes. Results Patients in 32 arCC families were homozygous for markers near at least 1 of the 33 known CC genes. Sequencing the included genes revealed homozygous cosegregating sequence changes in 10 families, 2 of which had the same variation. These included five missense, one nonsense, two frame shift, and one splice site mutations, eight of which were novel, in EPHA2, FOXE3, FYCO1, TDRD7, MIP, GALK1, and CRYBA4. Conclusions The above results confirm the usefulness of homozygosity mapping for identifying genetic defects underlying autosomal recessive disorders in consanguineous families. In our ongoing study of arCC in Pakistan, including 83 arCC families that underwent homozygosity mapping, 3 mapped using genome-wide linkage analysis in unpublished data, and 30 previously reported families, mutations were detected in approximately 37.1% (43/116) of all families studied, suggesting that additional genes might be responsible in the remaining families. The most commonly mutated gene was FYCO1 (14%), followed by CRYBB3 (5.2%), GALK1 (3.5%), and EPHA2 (2.6%). This provides the first comprehensive description of the genetic architecture of arCC in the Pakistani population.

Retinitis pigmentosa (RP) represents a group of inherited retinal dystrophies characterized by night blindness followed by progressive narrowing of the visual fields, often culminating in vision loss. Retinitis pigmentosa is genetically heterogeneous; currently mutations in at least 63 genes have been implicated.1 Identification of these genes and mutations causing RP has provided unique insights not only into the pathophysiology of retinal degenerations, but also into the basic biology of the retina and the visual pathways within it. Sullivan et al.2 identified a Glu847Lys hexokinase 1 (HK1) mutation in five families with autosomal recessive retinitis pigmentosa (adRP), all of which shared a common extended haplotype, suggesting common ancestry. The severity of RP in affected family members was highly variable, with one individual homozygous for the mutation having severe retinal disease, although no extraocular abnormalities were identified in any individual affected with RP. The Glu847Lys mutation is on the surface of the HK1 molecule, far from any identified functional site, and is not predicted to impair either enzymatic activity or protein stability. Absence of the nonspherocytic hemolytic anemia seen in autosomal recessive HK1 deficiency in affected individuals is consistent with preservation of kinase activity and normal glucose metabolism in the Glu847Lys mutant HK1, and the absence of extraretinal abnormalities suggests gain of a deleterious property specific to the retina. There is precedent for this, as mutations in HK1 have also been associated with Russe hereditary motor and sensory neuropathy,3 and HK1 is known to interact with a number of proteins active in regulating apoptosis, including VDAC1, DREAM, RANBP2, and COX11. While requiring functional confirmation, in addition to expanding our understanding of the genetic architecture of RP, this report suggests that although heavily studied for decades, HK1 has a previously unknown molecular function perhaps active in a novel metabolic or regulatory pathway critical to retinal homeostasis and function.

Purpose Glaucoma comprises a heterogeneous group of optic neuropathies with a complex genetic basis. It is the second leading cause of irreversible blindness in the world. This study investigates the association of SNPs on chromosome 2p with primary open angle glaucoma (POAG) in a Southern Indian population. Methods Case-control analysis was performed using 220 unrelated POAG cases and 220 age-matched unaffected controls recruited through the Aravind Eye Hospital and its outlying clinics. Five SNPs (rs1533428, rs12994401, rs10202118, rs11125375, and rs11889995) on chromosome 2p were evaluated in these two groups and genotyped using Taq Man SNP genotyping assay. Statistical analysis was performed using the SVS program package by Golden Helix to identify the distributions of allele and genotype frequencies, Fisher exact test P values, and odds ratios and to check Hardy-Weinberg equilibrium. Results Among the five SNPs screened, SNP rs10202118, showed a P = 0.026 for the basic allelic test, P = 0.004 for the genotypic test, and P = 0.0014 for the recessive model. The second suggestive marker was rs11125375, which also showed P = 0.033 for the recessive model. The associated SNPs formed a common disease haplotype. The remaining three SNPs showed insignificant association in this study population. Conclusions This was the first study to demonstrate the association of SNPs on chromosome 2p in patients with POAG in the Indian population. The two tagging SNPs (rs10202118 and rs11125375) on chromosome 2p are the most likely sites underlying the significant association with POAG in this study population.

The γ-crystallins, together with α- and β-crystallins, comprise the major water-soluble proteins of the ocular lens.1,2 The crystallins play a critical role in development and the maintenance of lens transparency.3 α-crystallins are synthesized at high levels by epithelial and fiber cells and are expressed first at the lens vesicle stage. Morphologically, the vertebrate lens is composed of the anterior epithelial cells, which cover the anterior surface of the lens, and fiber cells, which are terminally differentiated cells derived from the epithelial cells. The numerous specializations of fiber cells, including elongation, loss of organelles, and synthesis of large amounts of lens crystallins, are critical for the normal clarity and refractive properties of the lens. β-crystallins and γ-crystallins are most highly expressed in lens fiber cells; the γ-crystallins show their highest concentration in the central nucleus, while the β-crystallins generally have their highest concentration in the cortical fiber cells.4 Several mutations in γC-crystallin associated with autosomal dominant cataract have been identified in humans.5 Previously we have demonstrated that a 5-bp insertion in exon 2 of the γC-crystallin gene (c.119_123dup CRYGC) is associated with autosomal dominant variable zonular pulverulent cataracts.6 This mutation is predicted to shift the reading frame of the γC-crystallin coding sequence, resulting in synthesis of a truncated polypeptide consisting of 41 amino acids of the first Greek key motif followed by 63 novel amino acids. Truncation of the polypeptide in the connecting region between the first two motifs would be predicted to destabilize the structure of the first motif, so that no Greek key motifs are expected to be formed correctly. One interesting clinical aspect of these cataracts is the extreme variation in phenotype of individuals carrying the five-base insertion, including both bilateral and unilateral cataracts and ranging from completely asymptomatic adult individuals with no or minimal cataract detected by slit lamp examination to severe congenital total cataracts.7 To elucidate the in vivo effects of human mutant γC-crystallin (CRYGC5bpd) in the eye lens, transgenic mice expressing mutant and wild-type human γC-crystallin under control of a highly efficient lens-specific chicken βB1-crystallin promoter that consistently has been able to drive high-level expression of transgenes in lens fiber cells8 were generated. Expression of CRYGC5bpd results in high levels of mutant mRNA and synthesis of the mutant γC-crystallin, which disrupts normal lens morphology and causes cataract. Furthermore, the high degree of variation in the severity of the cataracts in humans is recapitulated in the transgenic mice, even those originating from the same founder.

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 theta = 0 for D2S2333 and 3.46 at theta = 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.

PURPOSE: To characterize the ocular phenotype resulting from mutation of Rab38, a candidate gene for Hermansky-Pudlak syndrome.METHODS: Chocolate mice (cht, Rab38(cht/cht)) and control heterozygous (Rab38(cht/)(+)) and wild-type mice were examined clinically, histologically, ultrastructurally, and electrophysiologically. Mice homozygous for both the Rab38(cht) and the Tyrp1(b) alleles were similarly examined.RESULTS: Rab38(cht/cht) mice showed variable peripheral iris transillumination defects at 2 months of age. Patches of RPE hypopigmentation were noted clinically in 57% of Rab38(cht/cht) eyes and 6% of Rab38(cht/)(+) eyes. Rab38(cht/cht) mice exhibited thinning of the iris and RPE and larger b-wave amplitudes in the scotopic range when compared with the control animals. Compared with wild-type mice, Rab38(cht/cht) melanosomes were smaller and there were fewer in neuroectodermally derived retinal pigment epithelium; in neural crest-derived choroid melanocytes, they were smaller in size only. Mutation of both Rab38 and Tyrp1 produced mice with ocular and coat color pigment dilution greater than that seen with either mutation alone. Comprehensive clinical and pathologic analyses showed no other organ system or blood defects in Rab38(cht/cht) mice.CONCLUSIONS: Rab38(cht/cht) mice show ocular characteristics reminiscent of human oculocutaneous albinism, as well as iris and RPE thinning. The synergistic effects of the Rab38(cht) and Tyrp1(b) alleles suggest that TYRP1 is not the only target of RAB38 trafficking. This mouse line provides a useful model for studying melanosome biology and its role in human ocular diseases. (Less)

PURPOSE. To unravel the molecular genetic background in families with congenital cataract in association with microcornea (CCMC, OMIM 116150). METHODS. CCMC families were recruited from a national database on hereditary eye diseases; DNA was procured from a national gene bank on hereditary eye diseases and by blood sampling from one large family. Genomewide linkage analysis, fine mapping, and direct genomic DNA sequencing of nine cataract candidate genes were applied. Restriction enzyme digests confirmed identified mutations. RESULTS. Analyses of 10 Danish families with hereditary congenital cataract and microcornea revealed five novel mutations. Three of these affected the crystallin, -A gene (CRYAA), including two mutations (R12C and R21W) in the crystallin domain and one mutation (R116H) in the small heat shock domain. One mutation (P189L) affected the gap junction protein 8( GJA8), and one mutation (Y134X) was detected in crystallin -D (CRYGD). CONCLUSIONS. The identification of a CRYGD mutation adds another gene to those that may be mutated in CCMC and underscores the genetic heterogeneity of this condition. Three CRYAA mutations at the R116 position, in association with CCMC, suggest that R116 represents a CCMC-mutational hotspot. The CCMC phenotype demonstrates variable expression with regard to cataract morphology and age of appearance. Clinical heterogeneity, including additional malformation of the anterior segment of the eye, confirm that dedicated cataract genes may be involved in the largely unknown developmental molecular mechanisms involved in lens-anterior segment interactions. (Invest Ophthalmol Vis Sci. 2007;48: 3937‐3944) DOI:10.1167/iovs.07-0013

PURPOSE. To study Bardet-Biedl syndrome (BBS) in the Tunisian population and determine the presence of triallelism in the eight identified BBS genes. METHODS. DNA samples were collected from 19 consanguineous Tunisian families with BBS. Genome-wide scans were performed with microsatellite markers in 12 families, and two-point linkage analyses were performed. Direct sequencing was used to screen patients with BBS for mutations in all eight identified BBS genes. RESULTS. Mutations in the BBS genes were identified in nine families. In addition, a large consanguineous family (57004) showed linkage to the BBS7 locus, although no mutation was identified. Five novel mutations were present in the nine families: one in BBS2 (c.565C>T, p.ArgR189Stop), one in BBSS (c.123delA, p.Gly42GlufsX11), one in BBS7 (g.47247455_47267458del20004insATA, p.Met284LysfsX7), and two in BBSS (c.459+1G>A, p.Pro101LeufsX12 and c.355_356inSGGTGGAAGGCCAGGCA, p.Thr124ArgfsX43). CONCLUSIONS. All families in which mutations were identified show changes in both copies of the mutant gene, and inheritance patterns in all families are consistent with autosomal recessive inheritance excluding any evidence of triallelism in the BBS genes in Tunisia.

PURPOSE. To localize and identify the gene and mutations causing autosomal recessive retinitis pigmentosa in three consanguineous Pakistani families. METHODS. Blood samples were collected and DNA was extracted. A genome-wide scan was performed by using 382 polymorphic microsatellite markers on genomic DNA from affected and unaffected family members, and lod scores were calculated. RESULTS. A genome-wide scan of 25 families gave an hlod = 4.53 with D8S260. Retinitis pigmentosa in all three families mapped to a 14.21-cM (21.19-Mb) region on chromosome 8 at q 11, flanked by D8S532 and D8S260. This region harbors RP1, which is known to cause autosomal dominant retinitis pigmentosa. Sequencing of the coding exons of RP1 showed mutations in all three families: two single-base deletions, c.4703delA and c.5400delA, resulting in a frame shift, and a 4-bp insertion, c.1606insTGAA, all causing premature termination of the protein. All affected individuals in these families are homozygous for the mutations. Parents and siblings heterozygous for the mutant allele did not show any signs or symptoms of RP. CONCLUSIONS. These results provide strong evidence that mutations in RP1 can result in recessive as well as dominant retinitis pigmentosa. The findings suggest that truncation of RP1 before the BIF motif or within the terminal portion results in a simple loss of RP1 function, producing a recessive inheritance pattern. In contrast, disruption of RP1 within or immediately after the BIF domain may result in a protein with a deleterious effect and hence a dominant inheritance pattern.

Purpose To identify the disease locus for autosomal recessive congenital cataracts in consanguineous Pakistani families. Methods Two Pakistani families were ascertained, patients were examined, blood samples were collected, and DNA was isolated. A genome-wide scan was performed using >382 polymorphic microsatellite markers on genomic DNA from affected and unaffected family members. Two-point lod scores were calculated, haplotypes were formed by inspection, and candidate genes were sequenced. Real-time quantitative PCR techniques were used to determine the mRNA levels, and molecular modeling was performed to gain a better understanding of the significance of the disease-causing mutation. Results In the genome-wide scan, maximum lod scores of 2.67 and 2.77 for family 60004 and 2.02 and 2.04 for family 60006 were obtained for markers D22S539 and D22S315, respectively. The linked region, 22.7 cM (10 Mb) flanked by markers D22S420 and D22S1163, contains the beta-crystallin gene cluster including the genes CRYBA4, CRYBB1, CRYBB2, and CRYBB3. Sequencing of these genes showed a G-->C transition in exon 6 of CRYBB3 resulting in a p.G165R change in the betaB3-crystallin protein that cosegregates with the disease in both families. Real-time PCR analysis suggested that betaB3-crystallin mRNA levels approximate those of other betagamma-crystallins. Molecular modeling predicted changes in electrostatic potential that would be expected to reduce the stability of the fourth Greek-key motif, and hence the entire protein, dramatically. Conclusions For the first time, a mutation in CRYBB3 is reported in two consanguineous Pakistani families with autosomal recessive congenital cataracts.

To identify the disease locus of autosomal recessive congenital nuclear cataracts in a consanguineous Pakistani family.A large Pakistani family with multiple individuals affected by autosomal recessive congenital cataracts was ascertained. Patients were examined, blood samples were collected, and DNA was isolated. A genome-wide scan was performed using 382 polymorphic microsatellite markers on genomic DNA from affected and unaffected family members. Two-point lod scores were calculated, and haplotypes were formed by inspection.In the genome-wide scan, a maximum lod score of 2.89 was obtained for marker D19S414 on 19q13. Fine mapping using D19S931, D19S433, D19S928, D19S225, D19S416, D19S213, D19S425, and D19S220 markers from the Généthon database showed that markers in a 14.3-cM (12.66-Mb) interval flanked by D19S928 and D19S420 cosegregated with the cataract locus. Lack of homozygosity further suggests that the cataract locus may lie in a 7-cM (4.3-Mb) interval flanked by D19S928 proximally and D19S425 distally. On fine mapping, a maximum lod score of 3.09 was obtained with D19S416 at theta = 0.Linkage analysis identified a new locus for autosomal recessive congenital nuclear cataracts on chromosome 19q13 in a consanguineous Pakistani family.

PURPOSE To map the locus and identify the gene causing autosomal recessive congenital cataracts in a large consanguineous Tunisian family. METHODS DNA was extracted from blood samples from a large Tunisian family with an autosomal recessive, congenital, total white cataract. A genome-wide scan was performed with microsatellite markers. All exons and the splice sites of the HSF4 gene were sequenced in all members of the Tunisian family and in control individuals. RT-PCR was used to detect different transcripts of the HSF4 gene in the human lens. The transcripts were cloned in a TA cloning vector and sequenced. RESULTS Two-point linkage analyses showed linkage to markers on 16q22 with a maximum lod score of 17.78 at theta = 0.01 with D16S3043. Haplotype analysis refined the critical region to a 1.8-cM (4.8-Mb) interval, flanked by D16S3031 and D16S3095. This region contains HSF4, some mutations of which cause the autosomal dominant Marner cataract. Sequencing of HSF4 showed a homozygous mutation in the 5' splice site of intron 12 (c.1327+4A-->G), which causes the skipping of exon 12. A more detailed study of the transcripts resulting from alternative splicing of the HSF4 gene in the lens is also reported, showing the major transcript HSF4b. CONCLUSIONS This is the first report describing association of an autosomal recessive cataract with the HSF4 locus on 16q21-q22.1 and the first description of HSF4 splice variants in the lens showing that HSF4b is the major transcript.

PURPOSE To identify the genetic defect associated with autosomal recessive congenital cataract in four Arab families from Israel. METHODS Genotyping was performed using microsatellite markers spaced at approximately 10 cM intervals. Two-point lod scores were calculated using MLINK of the LINKAGE program package. Mutation analysis of the glucosaminyl (N-acetyl) transferase 2 gene (GCNT2) gene was performed by direct sequencing of PCR-amplified exons. RESULTS The cataract locus was mapped to a 13.0-cM interval between D6S470 and D6S289 on Chr. 6p24. A maximum two-point lod score of 8.75 at theta = 0.019 was obtained with marker D6S470. Sequencing exons of the GCNT2 gene, mutations of which have been associated with cataracts and the i blood group phenotype, revealed in these families a homozygous G-->A substitution in base 58 of exon-2, resulting in the formation of premature stop codons W328X, W326X, and W328X, of the GCNT2A, -B, and -C isoforms, respectively. Subsequent blood typing of affected family members confirmed the possession of the rare adult i blood group phenotype. CONCLUSIONS A nonsense mutation in the GCNT2 gene isoforms is associated with autosomal recessive congenital cataract in four distantly related Arab families from Israel. These findings provide further insight into the dual role of the I-branching GCNT2 gene in the lens and in reticulocytes.