Leveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance.

The genetic heterogeneity of Mendelian disorders results in a significant proportion of patients that are unable to be assigned a confident molecular diagnosis after conventional exon sequencing and variant interpretation. Here, we evaluated how many patients with an inherited retinal disease (IRD) have variants of uncertain significance (VUS) that are disrupting splicing in a known IRD gene by means other than affecting the canonical dinucleotide splice site. Three in silico splice-affecting variant predictors were leveraged to annotate and prioritize variants for splicing functional validation. An in vitro minigene system was used to assay each variant's effect on splicing. Starting with 745 IRD patients lacking a confident molecular diagnosis, we validated 23 VUS as splicing variants that likely explain disease in 26 patients. Using our results, we optimized in silico score cutoffs to guide future variant interpretation. Variants that alter base pairs other than the canonical GT-AG dinucleotide are often not considered for their potential effect on RNA splicing but in silico tools and a minigene system can be utilized for the prioritization and validation of such splice-disrupting variants. These variants can be overlooked causes of human disease but can be identified using conventional exon sequencing with proper interpretation guidelines.

Leber congenital amaurosis, from darkness to light: An ode to Irene Maumenee.

This article is dedicated to Irene Hussels Maumenee, Professor of Human Genetics and Ophthalmology, Johns Hopkins' Wilmer Eye Institute, Ocular Genetics Fellowship director in 1994-1995. Leber congenital amaurosis (LCA) has almost come full circle, from a profound and molecularly uncharacterized form of congenital retinal blindness to one in which a large number of causative genes and disease pathways are known, and the world's first human retinal disease to be treated by gene therapy. Dr. Maumenee's insights, efforts, and leadership have contributed significantly to this remarkable scientific journey. In this manuscript, we present a short summary of the known LCA genes, LCA disease subtypes, and emerging treatment options. Our manuscript consolidates previous knowledge with current findings in an attempt to provide a more comprehensive understanding of LCA.

Choroideremia Is a Systemic Disease With Lymphocyte Crystals and Plasma Lipid and RBC Membrane Abnormalities.

PURPOSE: Photoreceptor neuronal degenerations are common, incurable causes of human blindness affecting 1 in 2000 patients worldwide. Only half of all patients are associated with known mutations in over 250 disease genes, prompting our research program to identify the remaining new genes. Most retinal degenerations are restricted to the retina, but photoreceptor degenerations can also be found in a wide variety of systemic diseases. We identified an X-linked family from Sri Lanka with a severe choroidal degeneration and postulated a new disease entity. Because of phenotypic overlaps with Bietti's crystalline dystrophy, which was recently found to have systemic features, we hypothesized that a systemic disease may be present in this new disease as well. METHODS: For phenotyping, we performed detailed eye exams with in vivo retinal imaging by optical coherence tomography. For genotyping, we performed whole exome sequencing, followed by Sanger sequencing confirmations and cosegregation. Systemic investigations included electron microscopy studies of peripheral blood cells in patients and in normal controls and detailed fatty acid profiles (both plasma and red blood cell [RBC] membranes). Fatty acid levels were compared to normal controls, and only values two standard deviations above or below normal controls were further evaluated. RESULTS: The family segregated a REP1 mutation, suggesting choroideremia (CHM). We then found crystals in peripheral blood lymphocytes and discovered significant plasma fatty acid abnormalities and RBC membrane abnormalities (i.e., elevated plasmalogens). To replicate our discoveries, we expanded the cohort to nine CHM patients, genotyped them for REP1 mutations, and found the same abnormalities (crystals and fatty acid abnormalities) in all patients. CONCLUSIONS: Previously, CHM was thought to be restricted to the retina. We show, to our knowledge for the first time, that CHM is a systemic condition with prominent crystals in lymphocytes and significant fatty acid abnormalities.

A Review of Secondary Photoreceptor Degenerations in Systemic Disease.

Photoreceptor neuronal degenerations are common and incurable causes of human blindness with one in 2000 affected. Approximately, half of all patients are associated with known mutations in more than 200 disease genes. Most retinal degenerations are restricted to the retina (primary retinal degeneration) but photoreceptor degeneration can also be found in a wide variety of systemic and syndromic diseases. These are called secondary retinal degenerations. We review several well-known systemic diseases with retinal degenerations (RD). We discuss RD with hearing loss, RD with brain disease, and RD with musculoskeletal disease. We then postulate which retinal degenerations may also have previously undetected systemic features. Emerging new and exciting evidence is showing that ubiquitously expressed genes associated with multitissue syndromic disorders may also harbor mutations that cause isolated primary retinal degeneration. Examples are RPGR, CEP290, CLN3, MFSD5, and HK1 mutations that cause a wide variety of primary retinal degenerations with intact systems.

Regulation of uncoupling protein-2 mRNA in L6 myotubules: I: Thiazolidinediones stimulate uncoupling protein-2 gene expression by a mechanism requiring ongoing protein synthesis and an active mitogen-activated protein kinase.

The mitochondrial uncoupling protein-2 (UCP2) can uncouple phosphorylation to subserve several functions. It has been reported that the insulin sensitizers, thiazolidinediones (TZDs), increase UCP2 mRNA levels and, more recently, that TZDs stimulate UCP2 reporter genes but that the sequences involved do not bind peroxisome proliferator-activated receptor gamma (PPARgamma). We report here that TZDs stimulated UCP2 gene (ucp2) transcription in L6 myotubules involving an indirect mechanism. L6 cells contained comparatively small amounts of PPARgamma mRNA but clearly detectable amounts of PPARgamma2 protein. UCP2 mRNA levels were increased in a time- and concentration-dependent manner by TZDs. UCP2 mRNA had slow turnover (t 1/2 approximately 38 h), and this was not affected by TZDs. Bisphenol A diglycidyl ether, a PPARy antagonist, concentration dependently inhibited the TZD-induced increase in UCP2 mRNA. Blockade of protein synthesis with cycloheximide as well as abrogation of mitogen-activated protein kinase (MAPK) activity with PD98059 or U0126 also prevented the TZD-induced increase in UCP2 mRNA. As with autologous UCP2 mRNA, TZDs stimulated reporter gene expression directed by ucp2 sequences in transiently transfected L6 cells. The effect was enhanced by cotransfection of PPARgamma + retinoid X receptor gamma and prevented by MEK blockade. TZDs, however, did not increase the activation of MAPK, nor did its activation by other means (change of medium, insulin-like growth factor-1, insulin) increase UCP2 mRNA, indicating that phosphorylation is not limiting. These results suggest that TZDs indirectly stimulate ucp2 transcription by inducing-via PPARgamma-limiting amounts of a protein, which must be phosphorylated by MAPK to stimulate the gene.

Regulation of uncoupling protein-2 mRNA in L6 myotubules: II: Thyroid hormone amplifies stimulation of uncoupling protein-2 gene by thiazolidinediones and other peroxisome proliferator-activated receptor ligands in L6 myotubules: evidence for a priming effect.

The stimulation of the uncoupling protein-2 gene (ucp2) by thyroid hormone (triiodothyronine [T3]) in vivo is variable, suggesting complex interactions and even the possibility of indirect effects. We investigated the effect of T3 on ucp2 expression in L6 myotubules. Alone, T3 did not significantly stimulate ucp2 expression in L6 cells, but it amplified the stimulation by thiazolidinediones (TZDs). L6 cells expressed both alpha1 and beta1 thyroid hormone receptors and the data were consistent with the effect being mediated by these receptors. T3 also enhanced the stimulation of ucp2 by the nonselective peroxisome proliferator-activated receptor (PPAR) ligands bezafibrate and carbacyclin, but not that by oleic acid or norepinephrine. L6 cells expressed PPARbeta and PPARgamma, but not PPARalpha. As short as a 1-h preexposure of L6 cells to T3 was sufficient to amplify the effect of PPAR ligands. Neither transcription nor translation was needed for this effect of T3. T3 did not affect the t1/2 of UCP2 mRNA. The histone deacetylases inhibitor trichostatin A (TSA) stimulated the expression of ucp2 but did not add to the effect of T3 nor did this hormone enhance the effect of TSA. These results suggest that T3 selectively enhances the transcriptional stimulation of ucp2 by TZDs and nonselective PPAR ligands by priming the gene to a transactivating signal(s) generated by such ligands.