Biomedical subjects

Anand Swaroop

Publications and source records attributed to Anand Swaroop.

60 records · Page 4Linked to original sources

PubMed2002

A comprehensive mutation analysis of RP2 and RPGR in a North American cohort of families with X-linked retinitis pigmentosa.

X-linked retinitis pigmentosa (XLRP) is a clinically and genetically heterogeneous degenerative disease of the retina. At least five loci have been mapped for XLRP; of these, RP2 and RP3 account for 10%-20% and 70%-90% of genetically identifiable disease, respectively. However, mutations in the respective genes, RP2 and RPGR, were detected in only 10% and 20% of families with XLRP. Mutations in an alternatively spliced RPGR exon, ORF15, have recently been shown to account for 60% of XLRP in a European cohort of 47 families. We have performed, in a North American cohort of 234 families with RP, a comprehensive screen of the RP2 and RPGR (including ORF15) genes and their 5' upstream regions. Of these families, 91 (39%) show definitive X-linked inheritance, an additional 88 (38%) reveal a pattern consistent with X-linked disease, and the remaining 55 (23%) are simplex male patients with RP who had an early onset and/or severe disease. In agreement with the previous studies, we show that mutations in the RP2 gene and in the original 19 RPGR exons are detected in <10% and approximately 20% of XLRP probands, respectively. Our studies have revealed RPGR-ORF15 mutations in an additional 30% of 91 well-documented families with X-linked recessive inheritance and in 22% of the total 234 probands analyzed. We suggest that mutations in an as-yet-uncharacterized RPGR exon(s), intronic changes, or another gene in the region might be responsible for the disease in the remainder of this North American cohort. We also discuss the implications of our studies for genetic diagnosis, genotype-phenotype correlations, and gene-based therapy.

Carrier Proteins↗

PubMed2002

Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays.

PURPOSE: To evaluate and optimize methods of target labeling and microarray hybridization using eye gene microarrays. Standardized protocols that consistently produce low background and high intensity hybridization with small amounts of starting RNA are needed to extract differentially expressed genes from a pool of thousands of unaltered genes. METHODS: Two identical aliquots of RNA from P19 cell line were labeled with Cy3 or Cy5 dyes using four different methods and self-against-self hybridization was performed on mouse eye gene arrays. The validity and reproducibility of these protocols were further examined using target RNAs isolated from wild-type or neural retinal leucine zipper (Nrl) knockout mouse retinas. Hybridizations were also carried out on human gene array slides with different amounts of starting RNA from human retina. RESULTS: Using self-against-self hybridization, we optimized the protocols for direct labeling (R-square = 0.93), aminoallyl indirect labeling (R-square = 0.97), Genisphere 3DNA labeling (R-square = 0.96), and for microarray hybridization and washing. Although small amounts of initial RNA can be used in TSA method, inconsistent labeling was encountered under our experimental conditions. When retinal RNA targets from Nrl+/+ and Nrl-/- mice were tested by direct and aminoallyl indirect labeling protocols, both produced varying hybridization results with low intensity spots and non-uniform backgrounds. However, the Genisphere 3DNA labeling procedure consistently yielded strong hybridization and R-square values of 0.92 or higher. Furthermore, expression profiles were compatible with prior knowledge of this mouse model. Serial analysis of hybridizations with various starting amounts of RNA showed that the Genisphere 3DNA protocol could produce reliable signal intensity with 3 microgram of total RNA. CONCLUSIONS: We have systematically evaluated and optimized methods for target labeling, microarray hybridization and washing. These procedures have been used for expression profiling with 3 microgram of starting RNA. Our studies should encourage further use of microarray technology for gene profiling during eye development and in retinal diseases.

Adult↗

PubMed2002

Mouse eye gene microarrays for investigating ocular development and disease.

Microarray technology can facilitate simultaneous expression analysis of thousands of genes and assist in delineating cellular pathways involved in development or disease pathogenesis. Since public databases and commercial cDNA microarrays have an under-representation of eye-expressed genes, we generated over 3000 expressed sequence tags from three unamplified mouse eye/retina cDNA libraries. These eye-expressed genes were used to produce cDNA microarrays. Methodology for printing of slides, hybridization, scanning and data analysis has been optimized. The I-gene microarrays will be useful for establishing expression profiles of the mouse eye/retina and provide a resource for defining molecular pathways involved in development, aging and disease.

Animals↗

PubMed2002

Gene expression profile of native human retinal pigment epithelium.

PURPOSE: To generate a profile of genes expressed in the native human retinal pigment epithelium and identify candidate genes for retinal and macular diseases. METHODS: Two cDNA libraries (one amplified, the other unamplified) were constructed using RNA isolated from native human RPE sheets. The sequence from the 5' end was obtained for randomly selected clones from the two libraries. Of these, more than 2000 expressed sequence tags (ESTs) were analyzed for similarity to sequences and gene clusters in public databases. RESULTS: EST analysis revealed several known RPE-expressed genes and more than 500 genes that have been characterized previously but were not known to be expressed in the RPE. Transthyretin and 90-kDa heat shock protein represent the most abundant transcripts identified in these RPE libraries. More than 200 novel ESTs and putative proteins were identified. An additional 344 sequences matched only the human genomic sequence. CONCLUSIONS: High-complexity cDNA libraries were generated from native human RPE. Analysis of ESTs generated from these libraries has yielded a profile of genes expressed in the native RPE. Several of the identified genes are known to play a significant role in the RPE. Novel ESTs, putative proteins, and genomic hits may represent as yet unidentified RPE-expressed genes and many of these, mapping in the region of retinal disease loci, may serve as candidate genes. In addition, the nonredundant set of more than 1100 genes and ESTs described herein will be a valuable resource for generating gene microarrays, which can assist in delineating RPE expression profiles during human disease pathogenesis.

Child↗

PubMed2002

Microarray analysis of gene expression in the aging human retina.

PURPOSE: To develop gene expression profiles of young and elderly human retinas and identify candidate genes for aging-associated retinal diseases. METHODS: Gene microarray slides containing 2400 human genes (primarily neuronal) were hybridized to biotin or dinitrophenyl (DNP)-labeled target cDNAs that were synthesized using total RNAs from young (13-14 years) and elderly (62-74 years) human retinas. Hybridization signals were visualized with cyanine (Cy)-5 or Cy-3 fluorescent reporter molecules, and the fluorescence intensities of the images were analyzed by computer. Northern blot analysis and real-time quantitative reverse transcription PCR (qRT-PCR) were performed to validate the microarray results. RESULTS: Of the 2400 genes represented on the microarray slides, more than 50% hybridized to the retinal cDNA targets. Expression of a majority of these genes was not altered during aging; nonetheless, changes in the expression of 24 genes were detected between young and elderly retinas. These genes could be clustered into four categories: energy metabolism, stress response, cell growth, and neuronal transmission/signaling. Northern blot analysis and qRT-PCR results confirmed the changes in expression of 8 of 10 genes examined. CONCLUSIONS: Using commercially available slide microarrays, the authors show that aging of the human retina is associated with changes in patterns of gene expression. This analysis suggests that pathways involved in stress response and energy metabolism play key roles in retinal aging. These studies demonstrate the utility of gene microarrays in identifying global patterns of retinal gene expression and lay the foundation for future studies defining the genetic basis of aging-associated retinal diseases, such as age-related macular degeneration.

Adolescent↗

PubMed2002

Retinal histopathology of an XLRP carrier with a mutation in the RPGR exon ORF15.

X-linked retinitis pigmentosa comprises the severe forms of RP, with early onset of night blindness, rapid constriction of visual fields and eventual loss of central acuity. Of the five distinct XLRP loci identified on the X chromosome, mutations have been found only in the RP2 and RPGR genes. Of these, mutations in RPGR are more common, particularly in a mutational hot spot that was identified in the newly discovered exon ORF15. We report on an extended family with a microdeletion in RPGR exon ORF15 and the retinal histopathology of a female carrier of this mutation. We found a 1bp deletion at position 632 in exon ORF15 in affected members of family XLRP-319. This mutation alters the reading frame of the predicted RPGR protein, resulting in a premature stop codon. The mutation segregated with disease in three generations of the family and was associated with severe early onset retinal disease in affected men. The retina from a 75 year old carrier female donor had slight photoreceptor loss in the less diseased areas. More severe atrophy with retinal pigment epithelium (RPE) migration was present in areas of the mid- and far periphery. By immunocytochemistry, loss of rhodopsin labelling in rods was found in the areas of focal atrophy and loss of uniform cone spacing was apparent even in well preserved regions. Small multifocal areas of outer retinal degeneration were present in the better preserved regions of the eye. In these foci, rod and cone loss did not coincide. The dissociation of rod and cone degeneration in areas of focal disease is consistent with random X-inactivation early in embryonic development and the occurrence of distinct patterns of radial (rod) and tangential (cone) dispersion during clonal expansion early in photoreceptor differentiation.

Adult↗