Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy

Gene-corrected patient-specific induced pluripotent stem (iPS) cells offer a unique approach to gene therapy. Here, we begin to assess whether the mutational load acquired during gene correction of iPS cells is compatible with use in the treatment of genetic causes of retinal degenerative disease. We isolated iPS cells free of transgene sequences from a patient with gyrate atrophy caused by a point mutation in the gene encoding ornithine-δ-aminotransferase (OAT) and used homologous recombination to correct the genetic defect. Cytogenetic analysis, array comparative genomic hybridization (aCGH), and exome sequencing were performed to assess the genomic integrity of an iPS cell line after three sequential clonal events: initial reprogramming, gene targeting, and subsequent removal of a selection cassette. No abnormalities were detected after standard G-band metaphase analysis. However, aCGH and exome sequencing identified two deletions, one amplification, and nine mutations in protein coding regions in the initial iPS cell clone. Except for the targeted correction of the single nucleotide in the OAT locus and a single synonymous base-pair change, no additional mutations or copy number variation were identified in iPS cells after the two subsequent clonal events. These findings confirm that iPS cells themselves may carry a significant mutational load at initial isolation, but that the clonal events and prolonged cultured required for correction of a genetic defect can be accomplished without a substantial increase in mutational burden.

Ophthalmologic heterogeneity in subjects with gyrate atrophy of choroid and retina harboring the L402P mutation of ornithine aminotransferase

OBJECTIVE/PURPOSE

To investigate clinical variation in a genetically homogenous group of subjects with gyrate atrophy of choroid and retina with hyperornithinemia (GA). The group was made up of homozygotes and compound heterozygotes for mutation L402P in the ornithine aminotransferase (OAT) gene.

DESIGN

Cross-sectional study.

PARTICIPANTS

Thirty-five Finnish subjects (18 men) with GA with a mean age of 33 years (range, 5-74 years) carrying the Finnish founder mutation L402P.

METHODS

All subjects were examined between 1993 and 1995. The analysis was composed of, in addition to careful clinical evaluation, studies of visual fields with Goldmann perimeter, photographing of the eye fundi, and corneal electroretinography (ERG) recordings.

MAIN OUTCOME MEASURES

The changes in eye fundi, visual acuity, cataract changes in the lens, visual field constriction, and ERG responses were determined.

RESULTS

Myopia, early cataracts, and highly abnormal ERG were typical for the GA subjects. The changes progressed rather uniformly with age. However, visual acuity, funduscopic findings, and visual fields showed great phenotypic variation. Despite the great interindividual variation, both eyes of each subject were always similarly affected.

CONCLUSIONS

This study of 35 subjects with GA carrying a single mutation shows that the ophthalmologic symptoms and findings vary widely. The data also reveal that GA subjects are already affected by severe visual impairment in young adulthood. However, the diagnosis is often made very late.

Characteristics of L-ornithine: 2-oxoacid aminotransferase and potential prenatal diagnosis of gyrate atrophy of the choroid and retina by first trimester chorionic villus sampling

A deficiency of the mitochondrial matrix enzyme L-ornithine: 2-oxoacid aminotransferase causes gyrate atrophy of the choroid and retina with hyperornithinemia (MIM 258870), a blinding degenerative disease, which is inherited as an autosomal recessive trait. We have developed a sensitive microradioisotopic method for enzyme assay by using 2-oxo-[5-14C] glutarate as the substrate and performing the separation of the product, [5-14C] glutamate from the substrate on a cation-exchange column. The enzyme activity was determined in human and rat tissues and in cultured cells. The enzyme activity in fibroblasts from a patient was deficient and that of the parents ranged between 25 and 60% of the control values. In addition we have found the enzyme expressed in native and cultured chorionic villi indicating a potential detection of the disease during the first trimester of pregnancy.

Gyrate atrophy of the choroid and retina: lymphocyte ornithine-delta-aminotransferase activity in different mutations and carriers

Deficiency of omithine-delta-aminotransferase (OAT) causes gyrate atrophy of the choroid and retina with hyperornithinemia (GA; McKusick 258870), a progressive autosomal recessive chorioretinal degeneration leading to early blindness. As residual enzyme activity may vary in different mutations of the OAT gene and explain individual variations in disease progression, a sensitive HPLC modification of the OAT assay in lymphocytes was developed, based on measurement of the dihydroquinozolinium reaction product. The OAT activities (ranges) of 43 Finnish GA patients with mutations L402P/L402P, R180T/L402P, N89K/ L402P, and L402P/x (x = previously unknown allele), were <1-10, <1-13, <1-17, and <1 pmol x min(-1) mg protein(-1), respectively. The OAT activities (mean+/-SD) of nine L402P/ wild heterozygotes were 70+/-50 (range 33-193), and those of 15 healthy control subjects 184+/-60 (range 85-291) pmol x min(-1) mg protein(-1). This lymphocyte assay is an easy, rapid, and sensitive method for reliable recognition of GA homozygotes. OAT mutations of the Finnish patients show similar residual enzyme activity in the lymphocytes. OAT activities in the L402P heterozygotes and healthy control subjects overlap, suggesting that, for reliable carrier detection, the OAT alleles have to be studied. However, as all OAT mutations are not known, direct measurement of enzyme activity has a role in heterozygote identification and possibly also in prenatal diagnosis of GA.

Retrovirus-mediated gene transfer of ornithine-delta-aminotransferase into keratinocytes from gyrate atrophy patients

Gyrate atrophy is a progressive blindness associated with deficiency of ornithine aminotransferase (OAT). The strategy of using an autologous keratinocyte graft, modified to express high levels of OAT as an ornithine-catabolizing skin-based enzyme sink, is investigated. Two OAT-containing retroviral vectors were constructed with or without a resistance gene. When packaged in a retroviral vector particle generated with the gibbon ape leukemia (GALV) virus envelope (PG13), these vectors could readily transduce >50% of target keratinocytes. The transduced keratinocytes in culture expressed up to 75-fold more OAT than normal control keratinocytes and these gene-modified cells extracted [14C]ornithine more efficiently than controls. The vector prepared without neo transduced cells more efficiently and led to higher levels of OAT expression than the neo-containing vector. Ornithine catabolism was maintained at high levels when the transduced patient keratinocytes were differentiated in vitro as a multilayered cutaneous organoid.

Human ornithine aminotransferase complexed with L-canaline and gabaculine: structural basis for substrate recognition

BACKGROUND

Ornithine aminotransferase (OAT) is a 45 kDa pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of L-ornithine and 2-oxoglutarate to glutamate-delta-semialdehyde and glutamic acid, respectively. In humans, loss of OAT function causes an accumulation of ornithine that results in gyrate atrophy of the choroid and retina, a disease that progressively leads to blindness. In an effort to learn more about the structural basis of this enzyme's function, we have determined the X-ray structures of OAT in complex with two enzyme-activated suicide substrates: L-canaline, an ornithine analog, and gabaculine, an irreversible inhibitor of several related aminotransferases.

RESULTS

The structures of human OAT bound to the inhibitors gabaculine and L-canaline were solved to 2.3 A at 110K by difference Fourier techniques. Both inhibitors coordinate similarly in the active site, binding covalently to the PLP cofactor and causing a 20 degrees rotation in the cofactor tilt relative to the ligand-free form. Aromatic-aromatic interactions occur between the bound gabaculine molecule and active-site residues Tyr85 and Phe177, whereas Tyr55 and Arg180 provide specific contacts to the alpha-amino and carboxyl groups of L-canaline.

CONCLUSIONS

The OAT-L-canaline complex structure implicates Tyr55 and Arg180 as the residues involved in coordinating with the natural substrate ornithine during normal enzyme turnover. This correlates well with two enzyme-inactivating point mutations associated with gyrate atrophy, Tyr55-->His and Arg180-->Thr. The OAT-gabaculine complex provides the first structural evidence that the potency of the inhibitor is due to energetically favourable aromatic interactions with residues in the active site. This aromatic-binding mode may be relevant to structure-based drug design efforts against other omega-aminotransferase targets, such as GABA aminotransferase.

Heterogeneity and uniqueness of ornithine aminotransferase mutations found in Japanese gyrate atrophy patients

PURPOSE

To identify mutations in ornithine aminotransferase (OAT) in seven Japanese families with gyrate atrophy (GA), an autosomal recessive chorioretinal degeneration of the eye caused by a generalized biochemical deficiency in OAT; mutations in the OAT gene have shown a high degree of molecular heterogeneity.

METHODS

DNA was prepared from patients' fibroblasts and analyzed by polymerase-chain-reaction amplification of the OAT gene sequence, denaturing gradient gel electrophoresis, and direct sequencing for identification of the mutations.

RESULTS

Eight different mutations were identified in seven unrelated Japanese GA patients with hyperornithinemia, confirming the high genetic heterogeneity of this disease. Five of these mutations were new, including one causing a pyridoxine-responsive disease, and all eight mutations have been found only in Japanese GA patients. Consistent with some similarity between the Japanese and Finnish populations in genetic isolation and homogeneity, there was a preponderance of homozygous mutations (five out of seven patients) as was previously reported for 16 Finnish GA pedigrees.

CONCLUSION

The eight Japanese OAT mutations represent a group of heterogenous mutations unique to a specific population pool.

Pyridoxine-responsive gyrate atrophy of the choroid and retina: clinical and biochemical correlates of the mutation A226V

We discovered the missense mutation, A226V, in the ornithine-delta-aminotransferase (OAT) genes of two unrelated patients with gyrate atrophy of the choroid and retina (GA). One patient, who was a compound for A226V and for the premature termination allele R398ter, showed a significant (P < .01) decrease in mean plasma ornithine levels, following pyridoxine supplementation with a constant protein intake: 826 +/- 128 microM (n = 5; no pyridoxine supplementation) versus 504 +/- 112 microM (n = 6; 500 mg pyridoxine/d) and 546 +/- 19 microM (n = 6; 1,000 mg pyridoxine/d). In extracts of fibroblasts from a second GA patient homozygous for A226V and from Chinese hamster ovary cells expressing an OAT-cDNA-containing A226V, we found that OAT activity increased from undetectable levels to approximately 10% of normal when the concentration of pyridoxal phosphate was increased from 50 to 600 microM. A226V is the fourth disease-causing pyridoxine-responsive human mutation to be reported.

Rapid and efficient molecular analysis of gyrate atrophy using denaturing gradient gel electrophoresis

PURPOSE

A generalized biochemical deficiency of the mitochondrial matrix enzyme ornithine aminotransferase (OAT) is the inborn error in gyrate atrophy (GA), an autosomal recessive blinding disease of the retina and choroid of the eye. Because mutations in the OAT gene show a high degree of molecular heterogeneity in GA, the authors set out to determine the mutations by rapid and efficient methods.

METHODS

The mutations in the OAT gene were determined by a combination of polymerase chain reaction (PCR) amplification of gene sequences, analysis by denaturing gradient gel electrophoresis (DGGE), and direct DNA sequencing.

RESULTS

Eleven different mutations in 21 (95.5%) out of 22 mutant OAT alleles from 11 patients were identified: six missense mutations, three nonsense mutations, one 2 bp-deletion, and one splice acceptor mutation. A silent polymorphism of Asn (AAC)378 to Asn (AAT) was also observed. CONCLUSIONS. The combination of PCR amplification of the gene sequences, DGGE analysis, and direct sequencing is a rapid and efficient method for detection of mutations in GA cases. The diversity of the mutations attests to the enormous genetic heterogeneity in this disease.

A deletion in the ornithine aminotransferase gene in gyrate atrophy

Gyrate atrophy (GA) is an autosomal recessive chorioretinal degenerative disease of the eye caused by an inborn defect of the nuclear encoded mitochondrial enzyme ornithine aminotransferase (OAT). We have described previously a GA patient with a 5.0-kilobase pair truncated EcoRI OAT gene fragment and the absence of OAT mRNA on Northern blot analysis. Cloning and sequencing analysis of the truncated gene fragment revealed a 1,072-base pair (bp) deletion including the entire exon 6, starting in intron 5, 172 bp upstream of exon 6 and ending in intron 6, 772 bp downstream of exon 6. A short direct repeat sequence (AGGAGC), resembling the sequence shown to cause DNA polymerase alpha to pause, and sequences capable of forming hairpin loops were both present at the 5' and 3' break-points of the deletion. Reverse transcription-polymerase chain reaction amplification of the patient's RNA with OAT primers yielded DNA fragments of two different sizes, consistent with a low level expression of OAT mRNA. Direct sequencing of the smaller fragment demonstrated the complete absence of exon 6 sequence in the mRNA predicted from the deletion, causing a reading frame shift which results in a premature termination codon at position 192. The mutation in the other allele has been demonstrated by polymerase chain reaction, denaturing gradient gel electrophoresis, and direct sequencing also to be a premature termination codon in exon 6. The absence of detectable OAT mRNA in this patient is consistent with these premature termination mutations because they have been shown to decrease the level of mRNA, especially if present early in the coding sequence.

Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences

Ornithine delta-aminotransferase is a nuclear-encoded mitochondrial matrix enzyme which catalyzes the reversible interconversion of ornithine and alpha-ketoglutarate to glutamate semialdehyde and glutamate. Inherited deficiency of ornithine delta-aminotransferase results in ornithine accumulation and a characteristic chorioretinal degeneration, gyrate atrophy of the choroid and retina. We have surveyed the ornithine delta-aminotransferase genes of gyrate atrophy patients for mutations. Using a variety of techniques, we discovered and molecularly characterized 21 newly recognized ornithine delta-aminotransferase alleles. We determined the consequences of these and three previously described mutations on ornithine delta-aminotransferase mRNA, antigen, and enzyme activity in cultured fibroblasts. The majority (20/24) of these alleles produce normal amounts of normally sized ornithine delta-aminotransferase mRNA. By contrast, only 2/24 had normal amounts of ornithine delta-aminotransferase antigen. Reproducing these mutations by site-directed mutagenesis and expressing the mutant ornithine delta-aminotransferase in Chinese hamster ovary cells confirms that several of these mutations inactivate ornithine delta-aminotransferase and cause gyrate atrophy in these patients.

A 15-bp deletion in exon 5 of the ornithine aminotransferase (OAT) locus associated with gyrate atrophy

Gyrate atrophy of the choroid and retina (GA) is an autosomal recessive disorder in which a deficiency of the mitochondrial matrix enzyme ornithine aminotransferase (OAT) leads to progressive blindness. Previously, we and others have reported a number of missense mutations and splice defects in the OAT gene associated with GA. In the present case, through sequencing of the PCR amplified cDNA products, we have detected a novel 15-bp deletion within exon 5 of the OAT gene which retains the original reading frame. The deleted PCR product is the only one produced from the patient's mRNA, while mRNA from the patient's mother yields both deleted and normal length PCR products. The alternate, apparently nonexpressing OAT allele in this patient was inherited from the father, who displays only the normal length PCR product. The codon at the deletion joint remains unaltered, predicting the loss of the pentapeptide Tyr-Thr-Val-Lys-Gly without any other amino acid change. The breakpoints are adjacent to or within two copies of a 4-bp direct repeat, which may have implications for the mechanism of deletion.

Molecular pathology of gyrate atrophy of the choroid and retina due to ornithine aminotransferase deficiency

Gyrate atrophy (GA) is an autosomal recessive eye disease characterized by progressive loss of vision due to chorioretinal degeneration. It is associated with a deficiency of the mitochondrial enzyme ornithine aminotransferase (OATase) with consequent hyperornithinemia. Although the clinical phenotype is largely confined to the eye, OATase deficiency is a systemic disorder. A step toward delineation of the enzyme defect in GA at the molecular level has been made by cloning and characterizing the cDNA and structural gene for OATase. The structural gene for OATase maps to chromosome 10 (10q26) and OATase-related sequences map to the X chromosome (Xp11.2). A diverse number of mutations at the OATase locus in GA patients of varied ethnic origins have been defined employing polymerase chain reaction and other molecular biological techniques. The majority of these mutations are of the missense type although a splicing mutation in one patient has recently been identified. The functional consequences of some of these mutations have been tested and confirmed in a eukaryotic expression system. These mutations demonstrate the allelic heterogeneity, which extends to both pyridoxine responsive and non-responsive forms of GA, reflecting the clinical and biochemical heterogeneity observed in this disease. The molecular studies in addition to providing information on the structure/function of the enzyme will facilitate understanding of the retinal pathophysiology in this disorder.

Point mutation affecting processing of the ornithine aminotransferase precursor protein in gyrate atrophy

A generalized deficiency of the mitochondrial enzyme, ornithine aminotransferase (OAT) is the inborn error in gyrate atrophy, an autosomal recessive degenerative disease of the choroid and retina of the eye that leads to blindness. Southern analysis, using the OAT cDNA probe, of the OAT gene in a gyrate atrophy patient whose level of OAT protein is markedly decreased indicated the functional gene to be grossly intact. Northern analysis of his OAT mRNA demonstrated only half the normal level of OAT message, suggesting expression of only one of the two alleles of the OAT gene. A functional assay of the expressed OAT mRNA by in vitro translation and immunoprecipitation with anti-human OAT antibody indicated synthesis of an OAT protein from the message. The expressed message was cloned and sequenced and was shown to contain a single base change from C to T, resulting in an amino acid codon change from CAT (histidine) to TAT (tyrosine) at position 319 in the translated OAT protein. The mutant and normal OAT precursors were synthesized using transcriptional expression clones of OAT and in vitro translation of the expressed mRNA and tested in an in vitro mitochondrial transport/processing system. The results indicate that the mutant OAT precursor from the gyrate atrophy patient can be transported to the mitochondria but is minimally processed there, which would lead to degradation of the labile precursor and loss of OAT activity as phenotypically observed.