Mutational analysis of patients with the diagnosis of choroideremia

Contiguous Gene Syndromes and Hearing Loss: A Clinical Report of Xq21 Deletion and Comprehensive Literature Review

Given the crucial role of the personalized management and treatment of hearing loss (HL), etiological investigations are performed early on, and genetic analysis significantly contributes to the determination of most syndromic and nonsyndromic HL cases. Knowing hundreds of syndromic associations with HL, little comprehensive data about HL in genomic disorders due to microdeletion or microduplications of contiguous genes is available. Together with the description of a new patient with a novel 3.7 Mb deletion of the Xq21 critical locus, we propose an unreported literature review about clinical findings in patients and their family members with Xq21 deletion syndrome. We finally propose a comprehensive review of HL in contiguous gene syndromes in order to confirm the role of cytogenomic microarray analysis to investigate the etiology of unexplained HL.

Cell-based Therapies for Corneal and Retinal Disorders

Maintenance of the visual function is the desired outcome of ophthalmologic therapies. The shortcomings of the current treatment options, like partial recovery, post-operation failure, rigorous post-operative care, complications, etc., which are usually encountered with the conventional treatment options has warranted newer treatment options that may eliminate the root cause of diseases and minimize the side effects. Cell therapies, a class of regenerative medicines, have emerged as cutting-edge treatment option. The corneal and retinal dystrophies during the ocular disorders are the major cause of blindness, worldwide. Corneal disorders are mainly categorized mainly into corneal epithelial, stromal, and endothelial disorders. On the other hand, glaucoma, retinitis pigmentosa, age-related macular degeneration, diabetic retinopathy, Stargardt Disease, choroideremia, Leber congenital amaurosis are then major retinal degenerative disorders. In this manuscript, we have presented a detailed overview of the development of cell-based therapies, using embryonic stem cells, bone marrow stem cells, mesenchymal stem cells, dental pulp stem cells, induced pluripotent stem cells, limbal stem cells, corneal epithelial, stromal and endothelial, embryonic stem cell-derived differentiated cells (like retinal pigment epithelium or RPE), neural progenitor cells, photoreceptor precursors, and bone marrow-derived hematopoietic stem/progenitor cells etc. The manuscript highlights their efficiency, drawbacks and the strategies that have been explored to regain visual function in the preclinical and clinical state associated with them which can be considered for their potential application in the development of treatment.

Choroideremia Carriers: Dark-Adapted Perimetry and Retinal Structures

Purpose

In choroideremia (CHM) carriers, scotopic sensitivity was assessed by dark adapted chromatic perimetry (DACP) and outer retinal structure was evaluated by multimodal imaging.

Methods

Nine carriers (18 eyes) and 13 healthy controls (13 eyes) underwent DACP testing with cyan and red stimuli. Analysis addressed peripapillary (4 test locations closest to the optic disc), macular (52 locations), and peripheral (60 locations outside the macula) regions. Responses were considered to be rod-mediated when cyan relative to red sensitivity was >5 dB. Fundus imaging included spectral domain optical coherence tomography (SD-OCT), short-wavelength (SW-AF), near-infrared (NIR-AF), ultrawide-field (200 degrees) pseudocolor fundus imaging, and quantitative (qAF) fundus autofluorescence.

Results

Detection of the cyan stimulus was rod mediated in essentially all test locations (99.7%). In the macular and peripheral areas, DACP sensitivity values were not significantly different from healthy eyes. In the peripapillary area, sensitivities were significantly decreased (P < 0.05). SD-OCT imaging ranged from hyper-reflective lesions and discontinuities of the outer retinal bands to hypertransmission of signal. SW-AF and NIR-AF images presented with peripapillary atrophy in seven patients (14 eyes). Mosaicism was detectable in SW-AF images in seven patients and in NIR-AF images in five patients. Frank hypo-autofluorescence was visible in eight patients with distinct chorioretinopathy in seven patients. The qAF values were below the 95% confidence interval (CI) of healthy age-matched individuals in 12 eyes.

Conclusions

Rod mediated scotopic sensitivity was comparable to that in control eyes in macular and peripheral areas but was decreased in the peripapillary area where changes in retinal structure were also most severe.

Clinical Manifestations and Genetic Analysis of 5 Korean Choroideremia Patients Initially Diagnosed With Retinitis Pigmentosa

BACKGROUND

To investigate the clinical findings of choroideremia patients and perform genetic analysis by whole-exome sequencing (WES).

METHODS

A total of 94 patients initially diagnosed with retinitis pigmentosa (RP) at another hospital, and who visited our hospital for genetic analysis by WES, were included in the study, along with 64 family members. All subjects underwent comprehensive ophthalmic evaluation, including best-corrected visual acuity, slit lamp examination, fundus photography, fundus autofluorescence (FAF), fluorescein angiography (FAG), visual field (VF), electroretinogram (ERG), and optical coherence tomography (OCT).

RESULTS

In six male patients with suspected choroideremia, extensive retinal pigment epithelium (RPE) and severe loss of choroid were observed in the fundus, but not in the macula. CHM gene mutation was confirmed in five patients. A novel single nucleotide variant at a splice site was observed in one patient. OCT showed marked thinning of the outernuclear layer and choroid, except in the macula. FAF showed a small area of hyperfluorescence in the posterior pole. In addition, characteristic interlaminar bridges were observed in four patients. On FAG, hypofluorescence was seen up to the far-peripheral retina in five patients.

CONCLUSION

Of the 94 patients initially diagnosed with RP, CHM mutation was identified in five (5.3%) by WES. Choroideremia should be considered as a differential diagnosis of RP. WES would be useful for identifying the causes of hereditary retinal disease.

CHM mutation spectrum and disease: An update at the time of human therapeutic trials

Choroideremia is an X-linked inherited retinal disorder (IRD) characterized by the degeneration of retinal pigment epithelium, photoreceptors, choriocapillaris and choroid affecting males with variable phenotypes in female carriers. Unlike other IRD, characterized by a large clinical and genetic heterogeneity, choroideremia shows a specific phenotype with causative mutations in only one gene, CHM. Ongoing gene replacement trials raise further interests in this disorder. We describe here the clinical and genetic data from a French cohort of 45 families, 25 of which carry novel variants, in the context of 822 previously reported choroideremia families. Most of the variants represent loss-of-function mutations with eleven families having large (i.e. ≥6 kb) genomic deletions, 18 small insertions, deletions or insertion deletions, six showing nonsense variants, eight splice site variants and two missense variants likely to affect splicing. Similarly, 822 previously published families carry mostly loss-of-function variants. Recurrent variants are observed worldwide, some of which linked to a common ancestor, others arisen independently in specific CHM regions prone to mutations. Since all exons of CHM may harbor variants, Sanger sequencing combined with quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification experiments are efficient to achieve the molecular diagnosis in patients with typical choroideremia features.

Expanding the genetic spectrum of choroideremia in an Australian cohort: report of five novel CHM variants

Choroideremia is an X-linked chorioretinal dystrophy caused by mutations in the CHM gene. Several CHM gene replacement clinical trials are in advanced stages. In this study, we report the molecular confirmation of choroideremia in 14 Australian families sourced from the Australian Inherited Retinal Disease Registry and DNA Bank. Sixteen males (14 symptomatic) and 18 females (4 symptomatic; 14 obligate carriers) were identified for analysis. Participants' DNA was analyzed for disease-causing CHM variants by Sanger sequencing, TaqMan qPCR and targeted NGS. We report phenotypic and genotypic data for the 14 symptomatic males and four females manifesting disease symptoms. A pathogenic or likely pathogenic CHM variant was detected in all families. Eight variants were previously reported, and five were novel. Two de novo variants were identified. We previously reported the molecular confirmation of choroideremia in 11 Australian families. This study expands the CHM genetically confirmed Australian cohort to 32 males and four affected carrier females.

Whole exome sequencing of a family revealed a novel variant in the CHM gene, c.22delG p.(Glu8Serfs*4), which co-segregated with choroideremia

Choroideremia is a complex form of blindness-causing retinal degeneration. The aim of the present study was to investigate the pathogenic variant and molecular etiology associated with choroideremia in a Chinese family. All available family members underwent detailed ophthalmological examinations. Whole exome sequencing, bioinformatics analysis, Sanger sequencing, and co-segregation analysis of family members were used to validate sequencing data and confirm the presence of the disease-causing gene variant. The proband was diagnosed with choroideremia on the basis of clinical manifestations. Whole exome sequencing showed that the proband had a hemizygous variant in the CHM gene, c.22delG p. (Glu8Serfs*4), which was confirmed by Sanger sequencing and found to co-segregate with choroideremia. The variant was classified as likely pathogenic and has not previously been described. These results expand the spectrum of variants in the CHM gene, thus potentially enriching the understanding of the molecular basis of choroideremia. Moreover, they may provide insight for future choroideremia diagnosis and gene therapy.

Patterns and Intensities of Near-Infrared and Short-Wavelength Fundus Autofluorescence in Choroideremia Probands and Carriers

Purpose

To ascertain cellular constituents within islands of preserved retina in choroideremia (CHM) by multimodal imaging.

Methods

CHM probands (16) and female carriers (9) of CHM were studied. Near-infrared autofluorescence (NIR-AF; 787-nm excitation; emission, >830 nm), short-wavelength autofluorescence (SW-AF; 488-nm excitation, 500- to 680-nm emission), and spectral-domain optical coherence tomography (SD-OCT) images were acquired with a confocal scanning laser ophthalmoscope. SW-AF intensities were measured by quantitative fundus autofluorescence (qAF), and NIR-AF intensity profiles were analyzed. Retinal thicknesses and visual acuity were measured.

Results

In 19 of 31 eyes of affected males, islands of preserved NIR-AF signal were also visible as fluorescence signal in SW-AF images. Notable in 12 eyes were areas of speckled SW-AF that was hypoautofluorescent in the NIR-AF image. Islands of preserved NIR-AF and SW-AF signal were often associated with the presence of visible but thinned outer nuclear layer and discontinuous interdigitation zone, ellipsoid zone, and external limiting membrane. NIR-AF profiles revealed that even in areas of preserved retina, the NIR-AF signal from retinal pigment epithelium (RPE) melanin is greatly reduced. qAF was reduced overall. The fundus of carriers was characterized by a mosaicism in which patches of reduced NIR-AF colocalized with reduced SW-AF.

Conclusions

In CHM-affected males, the presence of RPE was indicated by an NIR-AF signal and the absence of hypertransmission of OCT signal into the choroid. RPE preservation was associated with better visual acuity. In carriers, patches of reduced SW-AF colocalized with decreased NIR-AF and qAF was severely reduced.

Optical coherence tomography (OCT) features of cystoid spaces in choroideremia (CHM)

PURPOSE

To investigate the prevalence and features of cystoid spaces (CS) in patients with confirmed genetic diagnosis of choroideremia (CHM) using swept source optical coherence tomography (OCT).

METHODS

We retrospectively reviewed CHM patients examined at the Regional Reference Center for Hereditary Retinal Degenerations at the Eye Clinic in Florence. We took into consideration genetically confirmed CHM patients with ophthalmological and swept source optical coherence tomography (OCT) examinations. The presence/absence and location of cystoid spaces in the retina of each eye were reported.

RESULTS

A total of 42 eyes of 21 CHM patients were included in our series. The average age of the patients was 36.5 ± 20.1 (range, 13-73 years). The average best-corrected visual acuity (BCVA) for all patients was 0.63 ± 1.00 logMar (range, 0-2,80). CS were present in 15 eyes of eight patients (8/21, 38%). In all cases, CS were located in inner nuclear layer (INL); in five eyes of three patients, CS were detected also in ganglion cell layer (GCL). CS appeared as microcistoyd abnormalities and were detected in retinal areas characterized by retinal pigment epithelium (RPE) and outer retinal layers atrophy at the transition zone.

CONCLUSIONS

Cystoid spaces in choroideremia showed peculiar features; they are clusters of small-size extrafoveal degenerative cysts mainly located in inner nuclear layer at the transition zone where outer retinal layers and RPE are severely damaged.

Near-infrared autofluorescence in young choroideremia patients

Purpose: To study near-infrared autofluorescence (NIR-AF) and short- wave autofluorescence (SW-AF) imaging modalities in young patients affected with choroideremia (CHM).Methods: NIR-AF and SW-AF images, Optical coherence tomography (OCT) and color fundus images were acquired from 3 young CHM patients (6 eyes) enrolled at the Regional Reference Center for Hereditary Retinal Degenerations of the Eye Clinic in Florence.Results: We studied 3 young CHM patients (6 eyes). The mean age of the patients was 17,3 years. Using NIR-AF, patient P1 was characterized by speckled hypo-autofluorescent areas at the posterior pole with a preserved central hyper-autofluorescence while patient P2 and P3 were characterized by a preserved NIR-AF signal only at the fovea. Using SW-AF, patient P1 was characterized by a normal macular autofluorescence and by a speckled FAF pattern involved the vascular arcades while patient P2 and P3 showed well-demarcated hypo-autofluorescence areas involving the posterior pole with a preserved macular autofluorescence. The differences between NIR-AF and SW-AF were more pronounced in advanced stages. In correspondence of preserved NIR-AF, the OCT examination showed regular and continuous outer retinal hyperreflective bands. We observed abnormal RPE/Bruch's membrane complex and EZ band externally to the NIR-AF signal area.Conclusions: NIR-AF imaging confirms an early RPE involvement allowing us to identify and to quantify the RPE pigment loss in choroideremia. For this reason, NIR-AF imaging can be useful for monitoring the progression of the disease and to study the effect of future treatments.

Visual Function at the Atrophic Border in Choroideremia Assessed with Adaptive Optics Microperimetry

PURPOSE

Recent advances in retinal imaging allow visualization of structural abnormalities in retinal disease at the cellular level. This study used adaptive optics (AO) microperimetry to assess visual sensitivity with high spatial precision and to examine how function varies across 2 phenotypic features observed in choroideremia: atrophic lesion borders and outer retinal tubulations (ORTs).

DESIGN

Cross-sectional study.

PARTICIPANTS

Twelve choroideremia patients.

METHODS

A custom AO scanning light ophthalmoscope (AOSLO) equipped with both confocal and nonconfocal split-detection imaging methods was used to image the photoreceptor inner and outer segment mosaics. For AO microperimetry, circular 550-nm stimuli were presented through the AOSLO system; stimuli were either 9.6 or 38.3 arcmin² (approximately 60 or 15 times smaller than a Goldman III stimulus). Test locations were identified in structural images and stimuli were targeted to these locations using real-time retinal tracking combined with measurements of transverse chromatic aberration. Psychophysical detection thresholds were measured at the atrophic border in 12 patients. Additionally, visual sensitivity was probed along ORTs in 4 patients.

MAIN OUTCOME MEASURE

Visual sensitivity thresholds measured with AO microperimetry at retinal locations corresponding to structural phenotypes observed on AOSLO retinal images.

RESULTS

In choroideremia, sharp borders between intact central islands of the photoreceptor mosaic and complete atrophy of the outer retina and retinal pigment epithelium were observed in both split-detection and confocal structural images. Adaptive optics microperimetry at locations spanning these borders showed a commensurately sharp decrease in function, with readily measurable visual sensitivity on one side and dense scotoma on the other. These functional transitions often occurred over a distance smaller than the diameter of the Goldman III stimulus. Thresholds measured along ORTs showed dense scotoma over the tubule in all 4 participants, despite the visibility of remnant cone inner segments on the AO images.

CONCLUSIONS

Choroideremia patients exhibited sharp functional transitions that collocated with structural transitions from intact to severely degenerated retina. We found no evidence of visual sensitivity over ORTs. Measuring cone function with high resolution offered insight into disease mechanisms and may enable precise assessment of whether experimental therapies, such as gene therapy, provide a functional benefit.

CHOROIDEREMIA ASSOCIATED WITH A NOVEL SYNONYMOUS MUTATION IN GENE ENCODING REP-1

PURPOSE

To report a novel synonymous mutation in CHM and the associated phenotype in an affected man and carrier mother.

METHODS

Case report.

RESULTS

A 34-year-old man with a long history of progressive night blindness and visual field constriction was diagnosed with choroideremia based on ocular examination and multimodal retinal imaging. Extensive chorioretinal degeneration was noted on spectral domain optical coherence tomography and fundus autofluorescence imaging. Candidate CHM gene sequencing revealed a hemizygous c.1359C>T, p.(S453S) variant. This variant was heterozygous in the mother of the proband who exhibited the classic carrier phenotype of choroideremia on fundus autofluorescence imaging.

CONCLUSION

A novel c.1359C>T, p.(S453S) variant in CHM is the first-identified synonymous mutation associated with disease manifestation in an affected man and carrier phenotype in a heterozygous mother.

THE NATURAL HISTORY OF FULL-FIELD STIMULUS THRESHOLD DECLINE IN CHOROIDEREMIA

PURPOSE

To evaluate full-field sensitivity thresholds (FSTs) across a wide range of choroideremia (CHM) disease stages and to determine their applicability as functional endpoints for CHM clinical trials.

METHODS

Thirty CHM subjects (60 eyes) and 50 healthy controls (50 eyes) underwent FST testing under dark-adapted conditions to determine rod- and cone-mediated FSTs. Central retinal structure and function were assessed using fundus autofluorescence and microperimetry. Correlation and regression analyses were performed to compare FST responses with the residual area of retinal pigment epithelium in the peri- and parafoveal regions, as well as the mean and highest macular microperimetry sensitivity.

RESULTS

All patients with CHM had a baseline of 18 dB elevation in dark-adapted rod FSTs, including the least affected individuals. Further FST sensitivity loss was exponentially associated with decrease in the area of residual peri- and parafoveal retinal pigment epithelium, with precipitous loss of sensitivity noted for fundus autofluorescence areas less than 5 mm. Cone FSTs were comparable with controls, except for advanced stages of CHM. Full-field sensitivity threshold responses showed high correlation with both mean and highest macular microperimetry thresholds (P < 0.001). In some cases of absent macular fundus autofluorescence, the peripheral retina could contribute to detectable rod FST responses but with severely diminished cone-driven responses.

CONCLUSION

Full-field sensitivity threshold testing demonstrated a baseline level of rod dysfunction in CHM present in all rod photoreceptors. Further decline in FST responses correlated strongly with the extent of central retina structural and functional loss. Full-field sensitivity threshold allowed quantification of residual rod function in peripheral islands of vision, which cannot be reliably achieved with other conventional tests. As such, the FST can serve as a complimentary tool to guide patient selection and expand the eligibility criteria for current and future CHM clinical trials.

Genetic testing for choroideremia

We studied the scientific literature and disease guidelines in order to summarize the clinical utility of the genetic test for choroideremia (CHM). CHM is an inherited X-linked recessive disorder associated with variations in the CHM gene. The overall prevalence of CHM varies from 1 in 50 000 to 1 in 100 000. Clinical diagnosis is based on clinical findings, ophthalmological examination, visual field, fundus autofluorescence, optical coherence tomography and electroretinography. The genetic test is useful for confirming diagnosis and for differential diagnosis, couple risk assessment and access to clinical trials.

Genetic analysis and clinical phenotype of two Indian families with X-linked choroideremia

Purpose:

This study aims to describe the phenotype and genotype of two Indian families affected with X-linked choroideremia (CHM).

Materials and Methods:

In these two families, the affected individuals and unaffected family members underwent a comprehensive ophthalmic examination including an optical coherence tomography (OCT) and electroretinogram. Blood samples were collected from the families for genetic analysis. Next generation sequencing (NGS) was done using a panel of 184 genes, which covered previously associated genes with retinal dystrophies. Sequencing data were analyzed for the CHM, RPGR, and RP2 genes that have been implicated in CHM and X-linked retinitis pigmentosa (XLRP), respectively. The identified variants were confirmed by Sanger sequencing in available individuals and unrelated controls.

Results:

In two unrelated male patients, NGS analysis revealed a previously reported 3’-splice site change c.820-1G>C in the CHM gene in the first family and hemizygous mutation c.653G>C (p.Ser218X) in the second family. The asymptomatic family members were carriers for these mutations. Spectral domain-OCT showed loss of outer retina, preservation of the inner retina, and choroidal thinning in the affected males and retinal pigment epithelial changes in the asymptomatic carriers. The identified mutations were not present in 100 controls of Indian origin. There were no potential mutations found in XLRP-associated (RPGR and RP2) genes.

Conclusion:

This report describes the genotype and phenotype findings in patients with CHM from India. The identified genetic mutation leads to lack of Rab escort protein-1 (REP-1) or affects the production of a REP-1 protein that is likely to cause retinal abnormalities in patients.

A maternally inherited 8.05 Mb Xq21 deletion associated with Choroideremia, deafness, and mental retardation syndrome in a male patient

Background

Deletions in Xq21 cause various congenital defects in males including choroideremia, deafness and mental retardation, depending on their size and gene content. Until now only a limited number of patients with Xq21 deletions has been reported.

Case presentation

Here we describe a 17-year-old male with choroideremia, deafness, and mental retardation syndrome. Using SNP arrays, an 8.05 Mb deletion in Xq21 was identified inherited from the apparently healthy mother. The deleted region harbors 12 OMIM genes, of which POU3F4, CHM, and ZNF711 might have contributed to the patient’s phenotype including hearing loss, poor vision, and intellectual disability. Moreover, the patient’s mother exhibits a normal phenotype while carrying the same deletion, which is often observed in previous studies on female carriers in families with this syndrome.

Conclusions

Our study confirms the causative effect between the Xq21 deletion in males and choroideremia, deafness and mental retardation.

Novel non-contiguous exon duplication in choroideremia

The importance of establishing a genetic diagnosis in patients with a choroideremia phenotype has been underscored by the advent of gene replacement therapy for this condition. Here, we describe a complex imbalance at the CHM locus in a male patient with classical disease. At the DNA level, this imbalance consists of 2 non-contiguous duplications (exons 1-2 and 9-12). Further characterization suggests the generation of 2 independent CHM transcriptional units, one of which may produce a deleted form of the Rab escort protein 1 protein. Expression of such a type of aberrant protein in photoreceptors may have important implications when considering gene therapy for this disorder.

Single-base substitutions in the CHM promoter as a cause of choroideremia

Although over 150 unique mutations affecting the coding sequence of CHM have been identified in patients with the X-linked chorioretinal disease choroideremia (CHM), no regulatory mutations have been reported, and indeed the promoter has not been defined. Here, we describe two independent families affected by CHM bearing a mutation outside the gene's coding region at position c.-98: C>A and C>T, which segregated with the disease. The male proband of family 1 was found to lack CHM mRNA and its gene product Rab escort protein 1, whereas whole-genome sequencing of an affected male in family 2 excluded the involvement of any other known retinal genes. Both mutations abrogated luciferase activity when inserted into a reporter construct, and by further employing the luciferase reporter system to assay sequences 5' to the gene, we identified the CHM promoter as the region encompassing nucleotides c.-119 to c.-76. These findings suggest that the CHM promoter region should be examined in patients with CHM who lack coding sequence mutations, and reveals, for the first time, features of the gene's regulation.

Multimodal Imaging of Photoreceptor Structure in Choroideremia

PURPOSE

Choroideremia is a progressive X-linked recessive dystrophy, characterized by degeneration of the retinal pigment epithelium (RPE), choroid, choriocapillaris, and photoreceptors. We examined photoreceptor structure in a series of subjects with choroideremia with particular attention to areas bordering atrophic lesions.

METHODS

Twelve males with clinically-diagnosed choroideremia and confirmed hemizygous mutations in the CHM gene were examined. High-resolution images of the retina were obtained using spectral domain optical coherence tomography (SD-OCT) and both confocal and non-confocal split-detector adaptive optics scanning light ophthalmoscope (AOSLO) techniques.

RESULTS

Eleven CHM gene mutations (3 novel) were identified; three subjects had the same mutation and one subject had two mutations. SD-OCT findings included interdigitation zone (IZ) attenuation or loss in 10/12 subjects, often in areas with intact ellipsoid zones; RPE thinning in all subjects; interlaminar bridges in the imaged areas of 10/12 subjects; and outer retinal tubulations (ORTs) in 10/12 subjects. Only split-detector AOSLO could reliably resolve cones near lesion borders, and such cones were abnormally heterogeneous in morphology, diameter and density. On split-detector imaging, the cone mosaic terminated sharply at lesion borders in 5/5 cases examined. Split-detector imaging detected remnant cone inner segments within ORTs, which were generally contiguous with a central patch of preserved retina.

CONCLUSIONS

Early IZ dropout and RPE thinning on SD-OCT are consistent with previously published results. Evidence of remnant cone inner segments within ORTs and the continuity of the ORTs with preserved retina suggests that these may represent an intermediate state of retinal degeneration prior to complete atrophy. Taken together, these results supports a model of choroideremia in which the RPE degenerates before photoreceptors.

The Spectrum of CHM Gene Mutations in Choroideremia and Their Relationship to Clinical Phenotype

PURPOSE

We report the underlying genotype and explore possible genotypic-phenotypic correlations in a large cohort of choroideremia patients.

METHODS

We studied prospectively a cohort of 79 patients diagnosed within a tertiary referral service for patients with retinal dystrophies. Phenotypic evaluation consisted of clinical examination, including visual acuity and residual retinal area by fundus autofluorescence (FAF). Genotype was established by sequencing. We also investigated whether particular genotypes were associated with more severe phenotypes by performing analysis of covariance (ANCOVA), with visual acuity and FAF as the dependent variables and age as the covariant.

RESULTS

A total of 74 (94%) of patients in our cohort had causative mutations by sequencing, the majority of which were anticipated to be null. Of these, 35 (47%) had insertions and deletions, 13 (18%) had mutations predicted to affect splicing, and 26 (35%) had single point mutations. In the latter case, 13 of 21 (62%) pedigrees with single point mutations were C to T transitions at C-phosphate-G (CpG) dinucleotides. These mutations were spread across 5 of only 24 CpG dinucleotides in the entire CHM cDNA. Furthermore, these 5 locations are the only sites at which C to T transitions result in a stop codon. No clear evidence was found for genotype-phenotype correlation except in the instance of a patient with a large deletion involving neighbouring sequences.

CONCLUSIONS

In patients with a diagnosis of choroideremia made by a specialty service, there is a high likelihood of establishing a genetic diagnosis. The majority of causative mutations appear to be null and, therefore, may benefit from gene replacement therapy. A disproportionate number of single point mutations observed were C to T transitions, consistent with the evolutionary decay of CpG dinucleotides through methylation and subsequent deamination. Hence, the development of choroideremia in such patients may represent the unwanted consequence of human evolution; de novo mutations are predicted to arise at these sites in future generations. (ClinicalTrials.gov number, NCT01461213.).

A Comprehensive Analysis of Choroideremia: From Genetic Characterization to Clinical Practice

Choroideremia (CHM) is a rare X-linked disease leading to progressive retinal degeneration resulting in blindness. The disorder is caused by mutations in the CHM gene encoding REP-1 protein, an essential component of the Rab geranylgeranyltransferase (GGTase) complex. In the present study, we evaluated a multi-technique analysis algorithm to describe the mutational spectrum identified in a large cohort of cases and further correlate CHM variants with phenotypic characteristics and biochemical defects of choroideremia patients. Molecular genetic testing led to the characterization of 36 out of 45 unrelated CHM families (80%), allowing the clinical reclassification of four CHM families. Haplotype reconstruction showed independent origins for the recurrent p.Arg293* and p.Lys178Argfs*5 mutations, suggesting the presence of hotspots in CHM, as well as the identification of two different unrelated events involving exon 9 deletion. No certain genotype-phenotype correlation could be established. Furthermore, all the patients´ fibroblasts analyzed presented significantly increased levels of unprenylated Rabs proteins compared to control cells; however, this was not related to the genotype. This research demonstrates the major potential of the algorithm proposed for diagnosis. Our data enhance the importance of establish a differential diagnosis with other retinal dystrophies, supporting the idea of an underestimated prevalence of choroideremia. Moreover, they suggested that the severity of the disorder cannot be exclusively explained by the genotype.

Analysis of a large choroideremia dataset does not suggest a preference for inclusion of certain genotypes in future trials of gene therapy

Background

Choroideremia (CHM) is an X‐linked degeneration of the retinal pigment epithelium, photoreceptors, and choroid, which causes nyctalopia and progressive constriction of visual fields leading to blindness. The CHM gene encodes Rab escort protein 1 (REP‐1). In this work, we reviewed the phenotypes and genotypes of affected males with the purpose of understanding the functional effects of CHM mutations and their relationship with the phenotypes.

Methods

A retrospective review of 128 affected males was performed analyzing the onset of symptoms, visual acuity, and visual fields with respect to their mutations in the CHM gene.

Results

In rank order, reflecting data from this report, the most common mutations found in the CHM gene were nonsense mutations (41%), exon deletions (37%), and splice sites (14%) associated with a loss of functional protein. In the pool of 106 CHM mutations, we discovered four novel missense mutations (c.238C>T; p.L80F, c.819G>T; p.Q273H, c.1327A>G; p.M443V, and c.1370C>T; p.L457P) predicted to be severe changes affecting protein stability and folding with the effect similar to that of other types of mutations. No significant genotype–phenotype correlation was found with respect to the onset of nyctalopia, the onset of other visual symptoms, visual acuity, or width of visual fields.

Conclusion

There is no evidence to support exclusion of CHM patients from clinical trials based on their genotypes or any potential genotype–phenotype correlations.

Pathogenic mechanisms and the prospect of gene therapy for choroideremia

INTRODUCTION

Choroideremia is a rare, X-linked disorder recognized by its specific ocular phenotype as a progressive degenerative retinopathy resulting in blindness. New therapeutic approaches, primarily based on genetic mechanisms, have emerged that aim to prevent the progressive vision loss.

AREAS COVERED

This article will review the research that has progressed incrementally over the past two decades from mapping to gene discovery, uncovering the presumed mechanisms triggering the retinopathy to preclinical testing of potential therapies.

EXPERT OPINION

While still in an evaluative phase, the introduction of gene replacement as a potential therapy has been greeted with great enthusiasm by patients, advocacy groups and the medical community.

Retinal dystrophies, genomic applications in diagnosis and prospects for therapy

Retinal dystrophies (RDs) are degenerative diseases of the retina which have marked clinical and genetic heterogeneity. Common presentations among these disorders include night or colour blindness, tunnel vision and subsequent progression to complete blindness. The known causative disease genes have a variety of developmental and functional roles with mutations in more than 120 genes shown to be responsible for the phenotypes. In addition, mutations within the same gene have been shown to cause different disease phenotypes, even amongst affected individuals within the same family highlighting further levels of complexity. The known disease genes encode proteins involved in retinal cellular structures, phototransduction, the visual cycle, and photoreceptor structure or gene regulation. This review aims to demonstrate the high degree of genetic complexity in both the causative disease genes and their associated phenotypes, highlighting the more common clinical manifestation of retinitis pigmentosa (RP). The review also provides insight to recent advances in genomic molecular diagnosis and gene and cell-based therapies for the RDs.

Gene therapy for choroideremia using an adeno-associated viral (AAV) vector

Choroideremia is an outer retinal degeneration with a characteristic clinical appearance that was first described in the nineteenth century. The disorder begins with reduction of night vision and gradually progresses to blindness by middle age. The appearance of the fundus in sufferers is recognizable by the characteristic pale color caused by the loss of the outer retina, retinal-pigmented epithelium, and choroidal vessels, leading to exposure of the underlying sclera. Choroideremia shows X-linked recessive inheritance and the choroideremia gene (CHM) was one of the first to be identified by positional cloning in 1990. Subsequent identification and characterization of the CHM gene, which encodes Rab escort protein 1 (REP1), has led to better comprehension of the disease and enabled advances in genetic diagnosis. Despite several decades of work to understand the exact pathogenesis, no established treatments currently exist to stop or even slow the progression of retinal degeneration in choroideremia. Encouragingly, several specific molecular and clinical features make choroideremia an ideal candidate for treatment with gene therapy. This work describes the considerations and challenges in the development of a new clinical trial using adeno-associated virus (AAV) encoding the CHM gene.

Retinal nerve fiber thickness measurements in choroideremia patients with spectral-domain optical coherence tomography

PURPOSE

To evaluate the presence of peripapillary retinal nerve fiber layer (RNFL) defects in patients with choroideremia by using spectral-domain optical coherence tomography (SD-OCT).

METHODS

Twenty-nine eyes of 16 patients with choroideremia underwent peripapillary RNFL thickness measurements by using SD-OCT.

RESULTS

The mean (±SD) age of the study population was 44.0 ± 16.0 years (range, 13-63 years). Thirteen eyes (45%) showed a thinning of the peripapillary RNFL in at least 1 quadrant in either 1 or both eyes. Thinning was most commonly found in the superior (13 eyes) and inferior (10 eyes) quadrants. Twenty-one eyes (72%) showed a thickening of the peripapillary RNFL in at least 1 quadrant in either 1 or both eyes. Of these 21 eyes, all had thickening in the temporal quadrant. Additionally, 2 eyes in each of the other 3 quadrants were found to be abnormally thick.

CONCLUSION

Our study demonstrated the presence of defects in the peripapillary RNFL thickness in patients with choroideremia by using SD-OCT. It would be clinically prudent that choroideremia patients considered for various treatment options be considered for RNFL thickness measurements.

Choroideremia in a woman with ectodermal dysplasia and complex translocations involving chromosomes X, 1, and 3

BACKGROUND

Choroideremia is an X-linked recessive disorder characterized by vision loss with progressive atrophy of the retinal photoreceptors, retinal pigment epithelium (RPE), and choriocapillaris. Ectodermal dysplasia is a heterogeneous group of disorders characterized by a deficiency of two or more ectodermal derivatives. We report on the phenotypic and genetic characteristics of a 29-year-old woman with both choroideremia and ectodermal dysplasia.

MATERIALS AND METHODS

Observational case report with physical and ophthalmic examination, fluorescein angiography (FA), visual field testing, electroretinography, and cytogenetic analysis. This study adhered to the tenets of the Declaration of Helsinki and The New York Eye and Ear Infirmary Institutional Review Board guidelines.

RESULTS

Physical and ocular examination revealed hypotrichosis, hypohidrosis, full dentures, meibomian gland hypoplasia, and a decrease in corneal tear film. Visual acuity was hand motions in the right eye and 20/50 in the left eye. Fundus examination and fluorescein angiography were consistent with advanced choroideremia and revealed diffuse bilateral RPE and chorioretinal atrophy with sparing of the fovea. Visual field testing had less than 10-degree central islands in both eyes. Scotopic electroretinogram (ERG) was flat with a small flicker response. Cytogenetic analysis showed a complex translocation involving chromosomes X, 1, and 3: 46,X,t(X;1;3)(q13;q24;q21),inv(9)(p11q13). Selective inactivation of the normal X chromosome was present in blood and skin. Chromosomal analyses of the proband's family (mother and two brothers) were normal.

CONCLUSION

An X-autosome chromosomal translocation combined with non-random inactivation of the normal X-chromosome in a woman resulted in the phenotypic findings of choroideremia and ectodermal dysplasia.

The molecular basis of human retinal and vitreoretinal diseases

During the last two to three decades, a large body of work has revealed the molecular basis of many human disorders, including retinal and vitreoretinal degenerations and dysfunctions. Although belonging to the group of orphan diseases, they affect probably more than two million people worldwide. Most excitingly, treatment of a particular form of congenital retinal degeneration is now possible. A major advantage for treatment is the unique structure and accessibility of the eye and its different components, including the vitreous and retina. Knowledge of the many different eye diseases affecting retinal structure and function (night and colour blindness, retinitis pigmentosa, cone and cone rod dystrophies, photoreceptor dysfunctions, as well as vitreoretinal traits) is critical for future therapeutic development. We have attempted to present a comprehensive picture of these disorders, including biological, clinical, genetic and molecular information. The structural organization of the review leads the reader through non-syndromic and syndromic forms of (i) rod dominated diseases, (ii) cone dominated diseases, (iii) generalized retinal degenerations and (iv) vitreoretinal disorders, caused by mutations in more than 165 genes. Clinical variability and genetic heterogeneity have an important impact on genetic testing and counselling of affected families. As phenotypes do not always correlate with the respective genotypes, it is of utmost importance that clinicians, geneticists, counsellors, diagnostic laboratories and basic researchers understand the relationships between phenotypic manifestations and specific genes, as well as mutations and pathophysiologic mechanisms. We discuss future perspectives.

Loss-of-function mutations in Rab escort protein 1 (REP-1) affect intracellular transport in fibroblasts and monocytes of choroideremia patients

Background

Choroideremia (CHM) is a progressive X-linked retinopathy caused by mutations in the CHM gene, which encodes Rab escort protein-1 (REP-1), an escort protein involved in the prenylation of Rabs. Under-prenylation of certain Rabs, as a result of loss of function mutations in REP-1, could affect vesicular trafficking, exocytosis and secretion in peripheral cells of CHM patients.

Methodology/Principal Findings

To evaluate this hypothesis, intracellular vesicle transport, lysosomal acidification and rates of proteolytic degradation were studied in monocytes (CD14+ fraction) and primary skin fibroblasts from the nine age-matched controls and thirteen CHM patients carrying 10 different loss-of-function mutations. With the use of pHrodo™ BioParticles® conjugated with E. coli, collagen I coated FluoSpheres beads and fluorescent DQ™ ovalbumin with BODYPY FL dye, we demonstrated for the first time that lysosomal pH was increased in monocytes of CHM patients and, as a consequence, the rates of proteolytic degradation were slowed. Microarray analysis of gene expression revealed that some genes involved in the immune response, small GTPase regulation, transcription, cell adhesion and the regulation of exocytosis were significantly up and down regulated in cells from CHM patients compared to controls. Finally, CHM fibroblasts secreted significantly lower levels of cytokine/growth factors such as macrophage chemoattractant protein-1 (MCP-1), pigment epithelial derived factor (PEDF), tumor necrosis factor (TNF) alpha, fibroblast growth factor (FGF) beta and interleukin (lL)-8.

Conclusions/Significance

We demonstrated for the first time that peripheral cells of CHM patients had increased pH levels in lysosomes, reduced rates of proteolytic degradation and altered secretion of cytokines. Peripheral cells from CHM patients expose characteristics that were not previously recognized and could used as an alternative models to study the effects of different mutations in the REP-1 gene on mechanism of CHM development in human population.

CHM gene molecular analysis and X-chromosome inactivation pattern determination in two families with choroideremia

Choroideremia is an X-linked recessive retinal dystrophy characterized by progressive loss of the photoreceptor, the retinal pigment epithelium, and the choriocapillaris layers which ultimately can result in blindness by the fifth decade of life. The disease is caused by mutations in the gene CHM, which encodes a protein involved in the regulation of intracellular vesicular traffic. Typically, hemizygous males are affected by the disease and female carriers are asymptomatic with only a diffuse mottled pattern of hyperpigmentation on funduscopy. Uncommon instances of fully affected females have been described previously and these cases are proposed to arise from an skewed Lyonization mechanism preferentially inactivating the X chromosome carrying the normal CHM allele. In this work, the clinical and molecular features of two Mexican families with choroideremia are described. A novel and a previously described CHM mutation were identified. X-chromosome inactivation assays were performed in a total of 12 heterozygous carriers from the two families. In an affected female from family A, a random X-inactivation pattern was demonstrated; on the other hand, in a female carrier from family B displaying a conspicuous pattern of pigment epithelium mottling at the peripheral retina, a skewed X-inactivation pattern was found. However, the X-chromosome preferentially inactivated in this female was the one carrying the mutated allele. Our results add to the genotypic spectrum in choroideremia and does not support a correlation between X-inactivation status and abnormal retinal phenotype in heterozygous female carriers from these two families.

Choroideremia: new findings from ocular pathology and review of recent literature

Histopathology of young individuals affected by choroideremia is rarely available to allow correlation with the clinical presentation. A 30-year-old man with choroideremia died in a motor vehicle accident and one eye was subjected to histopathological examination. Immunoblot analysis of protein derived from white blood cells of a living brother, also affected with choroideremia, confirmed the absence of Rab escort protein-1, the normal CHM gene product. Direct sequencing of the coding region and adjacent splice sites of the CHM gene was undertaken on genomic DNA from the living brother and revealed a transition mutation, C to T, in exon 6 (R253X) which resulted in a stop codon and was predicted to truncate the protein product. Histopathological examination of the eye of the deceased brother showed relative independent degeneration of choriocapillaris, retinal pigment epithelium, and retina, similar to observations in the mouse model of choroideremia. In addition, mild T-lymphocytic infiltration was found within the choroid. The ophthalmic features and the pathology of choroideremia are discussed in light of new findings in the current case.

Rab escort protein 1 (REP1) in intracellular traffic: a functional and pathophysiological overview

The intracellular distribution of proteins, compartments, substrates, and products is an active process called intracellular traffic. Control of intracellular traffic is established by small GTP-binding proteins (Rab proteins). Rab proteins are modified by geranyl-geranyl moieties necessary for membrane association and target-protein recognition. Geranyl-geranyl groups are transferred to Rab proteins by geranyl-geranyl transferase 2 (GGTase2). GGTase2 requires Rab escort protein 1 (REP1) to bind Rab proteins. REP1 null mutations underlie an X-linked retinal degeneration called choroideremia (CHM). This review summarizes the current biochemical and clinical knowledge on REP1 and CHM.

The functional effect of pathogenic mutations in Rab escort protein 1

Choroideremia (CHM) is a chorioretinal degeneration with an X-linked pattern of inheritance. Affected males experience progressive atrophy of the choroid, retinal pigment epithelium and retina leading to eventual blindness. The CHM gene encodes Rab escort protein 1 (REP-1). REP-1 is involved in trafficking of Rab proteins in the cell. To date, the majority of reported mutations in the CHM gene cause a complete loss of REP-1 function. Here we report pathogenic mutations: a novel missense mutation, L550P; a truncation c.1542T>A, STOP; and two deletions (c.525_526delAG and c.1646delC) in the CHM gene and their phenotypic effect. To analyze the effect of mutations, the 3D structure of human REP-1 and the proteins associated with REP-1 function were modeled using sequence homology with rat proteins. In silico analysis of the missense mutation L550P suggests that the proline residue at position 550 destabilizes the beta-structural elements, and the REP-1 tertiary structure. Truncation and deletion mutants are associated with a partial or total loss of the REP-1 essential activity and protein-protein interactions as predicted by the analysis of the structure and stability of these protein products. The presumptive loss of protein was confirmed by Western Blot analysis of protein from mononuclear cells and fibroblasts (FB) from CHM patients.

A novel mutation (967-970+2)delAAAGGT in the choroideremia gene found in a Japanese family and related clinical findings

PURPOSE

To investigate the choroideremia (CHM) gene of one affected male and one obligate carrier in a Japanese family with choroideremia, and to characterize the related clinical features.

METHODS

We examined one affected man and one carrier woman from a Japanese family. Genomic DNA was extracted from leukocytes of peripheral blood collected from the affected man and his daughter, who is an obligate carrier of choroideremia. Exons 1-15 of the CHM gene were amplified by polymerase chain reaction (PCR) and directly sequenced. We performed ophthalmic examinations including best-corrected visual acuity, slit-lamp examination, fundus examination, electroretinography, and Goldmann perimetry.

RESULTS

A novel (967-970+2)delAAAGGT mutation was detected in the CHM gene. The affected man was hemizygous and had night-blindness, chorioretinal atrophy spreading from the posterior pole to the mid-periphery, and bareness of the sclera. His daughter was a heterozygous carrier who had chorioretinal atrophy and mottled appearance of the retinal pigment epithelium.

CONCLUSION

A novel (967-970+2)delAAAGGT mutation existed in the CHM gene of a Japanese family with choroideremia.

Choroideremia carriers maintain a normal electro-oculogram (EOG)

PURPOSE

To assess the functional integrity of the retinal pigment epithelium and outer retina in choroideremia (CHM) carriers with confirmed mutations in the REP-1 gene, by recording the EOG.

METHODS

The visual function of 17 choroideremia carriers ages 25-61 was assessed by determining their Snellen visual acuity and by recording the Arden ratio of the EOG. The 15 exons of the CHM gene were PCR-amplified from DNA from each of the carriers and their sequences were compared to the normal sequence to identify mutations.

RESULTS

The 17 CHM carriers had normal logMAR visual acuity (average of 0.07: Snellen equivalent of 20/25; with no acuities lower than 20/40). The average of the Arden ratio recorded from the 17 carriers was 2.71, which is not significantly different from the average value of 2.46 recorded in our lab. Fundus examination revealed mottled areas of chorioretinal degeneration consistent with the carrier status of CHM. Mutations in the CHM gene were identified in all CHM carriers by sequencing.

CONCLUSIONS

Whereas clinical observation suggests that progressive fundus changes are present in female carriers, these carriers do not show a change in the Arden ratio of the EOG over the ages studied (25-61 years).

De novo mutation in a choroideremia carrier

PURPOSE

To describe a de novo gene mutation in a female patient with clinically characteristic findings of choroideremia (CHM).

METHODS

Determination of best-corrected visual acuity, fundus examination, visual field analysis, and electroretinography were performed on a female patient with an advanced CHM phenotype. Blood samples were obtained from the patient and both her parents, and direct genomic sequencing for DNA analysis was performed on the blood samples.

RESULTS

A single base-pair sequence change was identified in codon 293 in exon 7 (R293X) of the CHM gene in the proband. This mutation was not found to occur in her clinically unaffected parents.

CONCLUSION

These findings document that a de novo point mutation should be considered when an isolated female family member is found to have CHM.

Choroideremia: variability of clinical and electrophysiological characteristics and first report of a negative electroretinogram

PURPOSE

To analyze the variability of clinical and electrophysiological characteristics in X-linked choroideremia and provide the first report of a negative electroretinogram in choroideremia.

DESIGN

Retrospective study.

PARTICIPANTS

The records of 18 male patients with choroideremia and 8 female carriers were evaluated.

METHODS

The data were reviewed regarding visual acuity (VA), color vision, perimetry, fundus autofluorescence, and full-field electroretinography (according to standards of the International Society for Clinical Electrophysiology of Vision).

MAIN OUTCOME MEASURES

Morphological and functional phenotype characteristics, fundus autofluorescence, electroretinography, and Rab escort protein 1 (REP-1) mutations.

RESULTS

Four unrelated families with choroideremia (9 affected males, 7 carriers) and 10 unrelated individuals (9 affected males, 1 carrier) were included. Mutational analysis, performed in 2 families and 3 individual males, revealed REP-1 mutations in all except 1 male. The age of the males ranged from 5.9 to 63.0 years (mean, 33.9), and VA ranged from hand movements to 1.0 (median, 0.7). Fundus autofluorescence (n = 7) showed defects in the retinal pigment epithelium in all males. Electroretinography (n = 13) was almost undetectable in 6 males and reduced in 6, indicating a rod-cone dystrophy. A further male showed a negative electroretinogram, with a b:a wave ratio of 0.5. Visual acuity of the 8 carriers (age, 4.8-56.8 years [mean, 24.0]) ranged from light perception to 1.2 (median, 1.0). Light perception was present in 1 carrier manifesting choroideremia with distinct chorioretinal atrophy. Pigmentary stippling, seen in the other carriers, was seen in fundus autofluorescence (n = 1) with a distinct speckled pattern. Electroretinograms were normal in 6 of 7 and reduced in the manifesting carrier. Defects in color vision and visual field were found in affected males and in the female carriers.

CONCLUSIONS

The phenotype of choroideremia presents with high variability. In addition to the previously reported findings, we observed a negative electroretinogram, indicating a postreceptoral retinal dysfunction, in 1 affected male; severe course of choroideremia with early blindness in 1 manifesting carrier; color vision deficits in the majority of affected males and carriers; and characteristic alterations in fundus autofluorescence.

Automated splicing mutation analysis by information theory

Information theory-based software tools have been useful in interpreting noncoding sequence variation within functional sequence elements such as splice sites. Individual information analysis detects activated cryptic splice sites and associated splicing regulatory sites and is capable of distinguishing null from partially functional alleles. We present a server (https://splice.cmh.edu) designed to analyze splicing mutations in binding sites in either human genes, genome-mapped mRNAs, user-defined sequences, or dbSNP entries. Standard HUGO-approved gene symbols and HGVS-approved systematic mutation nomenclature (or dbSNP format) are entered via a web portal. After verifying the accuracy of input variant(s), the surrounding interval is retrieved from the human genome or user-supplied reference sequence. The server then computes the information contents (Ri) of all potential constitutive and/or regulatory splice sites in both the reference and variant sequences. Changes in information content are color-coded, tabulated, and visualized as sequence walkers, which display the binding sites with the reference sequence. The software was validated by analyzing approximately 1,300 mutations from Human Mutation as well as eight mapped SNPs from dbSNP designated as splice site variants. All of the splicing mutations and variants affected splice site strength or activated cryptic splice sites. The server also detected several missense mutations that were unexpectedly predicted to have concomitant effects on splicing or appeared to activate cryptic splicing.