PurposeNext-generation sequencing (NGS) based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques have not been fully defined with regard to test accuracy and reproducibility.MethodsWe developed a targeted enrichment and NGS approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy and glaucoma. In preparation for providing this Genetic Eye Disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, reproducibility as well as the clinical sensitivity of the test.ResultsThe GEDi test is highly reproducible and accurate, with sensitivity and specificity for single nucleotide variant detection of 97.9% and 100%, respectively. The sensitivity for variant detection was notably better than the 88.3% achieved by whole exome sequencing (WES) using the same metrics, due to better coverage of targeted genes in the GEDi test compared to commercially available exome capture sets. Prospective testing of 192 patients with IRDs indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%.ConclusionThe data suggest that based on quantified performance metrics, selective targeted enrichment is preferable to WES for genetic diagnostic testing.

Background: The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease.

Mutations in the ubiquitously expressed pre-mRNA processing factors 3, 8, and 31 (PRPF3, PRPF8, and PRPF31) cause nonsyndromic dominant retinitis pigmentosa in humans, an inherited retinal degeneration. It is unclear what mechanisms, or which cell types of the retina, are affected. Transgenic mice with the human mutations in these genes display late-onset morphological changes in the retinal pigment epithelium (RPE). To determine whether the observed morphological changes are preceded by abnormal RPE function, we investigated its phagocytic function in Prpf3(T494M/T494M), Prpf8(H2309P/H2309P), and Prpf31(+/-) mice. We observe decreased phagocytosis in primary RPE cultures from mutant mice, and this is replicated by shRNA-mediated knockdown of PRPF31 in human ARPE-19 cells. The diurnal rhythmicity of phagocytosis is almost lost, indicated by the marked attenuation of the phagocytic burst 2 hours after light onset. The strength of adhesion between RPE apical microvilli and photoreceptor outer segments also declined during peak adhesion in all mutants. In all models, at least one of the receptors involved in binding and internalization of shed photoreceptor outer segments was subjected to changes in localization. Although the mechanism underlying these changes in RPE function is yet to be elucidated, these data are consistent with the mouse RPE being the primary cell affected by mutations in the RNA splicing factors, and these changes occur at an early age.

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It is known that alternating magnetic field applications on eukaryotic cells loaded with single domain iron oxide nanoparticles result in high hyperthermic citotoxicity leading to cell dead. Although magnetic hyperthermia therapy for cancer tumours is being developed under this idea, some in vitro assays have shown controversial results indicating that alternating magnetic field triggers large apoptotic effect without significant culture-temperature increase. In agreement with these observations a huge lowering in nanoparticle specific heating rates, when going from the colloidal suspension to cell endosomes, together with cell death, has been reported. Here, we propose a new methodology to determine the occurrence of local heating in cells when alternating magnetic fields in the radiofrequency field range are applied to cell cultures holding very low iron oxide concentrations, being these concentrations insufficient to produce a global cell-culture temperature increase up to therapeutic values. To this end, human lung adenocarcinoma cells (A549 cell line) were transduced with a lentiviral vector encoding the expression of the enhanced green fluorescence protein, EGFP, under the action of the inducible human heat shock protein 70B promoter. This modified A549 cell line was incubated with aqueous suspensions of magnetite core nanoparticles (uncoated or covered with coating agents like citric acid or silicon oxide), and exposed to radiofrequency fields. The application of an alternating magnetic field to cell cultures loaded with nanoparticles resulted in no global temperature increase but EGFP expression. Stress-inducible gene expression scales with uptake

Long intervening non-coding RNAs (lincRNAs) are increasingly being implicated as important factors in many aspects of cellular development, function, and disease, but remain poorly understood. In this study, we examine the human retinal pigment epithelium (RPE) lincRNA transcriptome using RNA-Seq data generated from human fetal RPE (fRPE), RPE derived from human induced pluripotent stem cells (iPS-RPE), and undifferentiated iPS (iPS). In addition, we determine the suitability of iPS-RPE, from a transcriptome standpoint, as a model for use in future studies of lincRNA structure and function. A comparison of gene and isoform expression across the whole transcriptome shows only minimal differences between all sample types, though fRPE and iPS-RPE show higher concordance than either shows with iPS. Notably, RPE signature genes show the highest degree of fRPE to iPS-RPE concordance, indicating that iPS-RPE cells provide a suitable model for use in future studies. An analysis of lincRNAs demonstrates high concordance between fRPE and iPS-RPE, but low concordance between either RPE and iPS. While most lincRNAs are expressed at low levels (RPKM < 10), there is a high degree of concordance among replicates within each sample type, suggesting the expression is consistent, even at levels subject to high variability. Finally, we identified and annotated 180 putative novel genes in the fRPE samples, a majority of which are also expressed in the iPS-RPE. Overall, this study represents the first characterization of lincRNA expression in the human RPE, and provides a model for studying the role lincRNAs play in RPE development, function, and disease.

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Purpose Primary human corneal endothelial cells (HCEnCs) cultured in room air are exposed to significantly higher O 2 concentrations [O 2 ] than what is normally present in the eye. We evaluated the growth and metabolism of HCEnCs cultured under physiological [O 2 ] (2.5%; [O 2 ] 2.5 ) and room air ([O 2 ] A ). Methods Primary cultures of HCEnCs from normal donors and donors with Fuchs dystrophy were grown at [O 2 ] 2.5 and [O 2 ] A . Growth and morphology were compared using phase-contrast microscopy, zonula occludens (ZO-1) localization, cell density measurements, and senescence marker staining. CD44 (cell quality) and HIF-1α (hypoxia-inducible factor-1α) levels were evaluated by Western blotting. Cell adaptability to a reversal of [O 2 ] growth conditions was measured with cell viability assays, and cell metabolism was assessed via oxygen consumption and extracellular acidification rates. Results HCEnCs grown at [O 2 ] A and [O 2 ] 2.5 displayed similar morphologies, ZO-1 localization, CD44 expression, and senescence. Cells from donors with Fuchs dystrophy grew better at [O 2 ] 2.5 than at [O 2 ] A . HIF-1α was undetectable. Cells displayed greater viability at [O 2 ] 2.5 than at [O 2 ] A . HCEnCs showed significantly greater proton leak ( P < 0.01), nonmitochondrial oxygen consumption ( P < 0.01), and spare capacity ( P < 0.05) for oxygen consumption rates, and greater basal glycolysis ( P < 0.05) with a decreased glycolytic reserve capacity ( P < 0.05) for extracellular acidification rates. Conclusions Primary HCEnCs show unique metabolic characteristics at physiologic [O 2 ]. The effect of [O 2 ] for optimization of HCEnC culture conditions should be considered. Translational Relevance With the advance of cell-based therapeutics for corneal endothelial diseases, [O 2 ] should be considered an important variable in the optimization of HCEnC culture conditions.