Corneal Vascularization Associated With a Novel PDGFRB Variant.

Purpose: The purpose of this study was to identify the genetic cause of aggressive corneal vascularization in otherwise healthy children in one family. Further, to study molecular consequences associated with the identified variant and implications for possible treatment. Methods: Exome sequencing was performed in affected individuals. HeLa cells were transduced with the identified c.1643C>A, p.(Ser548Tyr) variant in the platelet-derived growth factor receptor beta gene (PDGFRB) or wild-type PDGFRB. ELISA and immunoblot analysis were used to detect the phosphorylation levels of PDGFRß and downstream signaling proteins in untreated and ligand-stimulated cells. Sensitivity to various receptor tyrosine kinase inhibitors (TKIs) was determined. Results: A novel c.1643C>A, p.(Ser548Tyr) PDGFRB variant was found in affected family members. HeLa cells transduced with this variant did not have increased baseline levels of phosphorylated PDGFRß. However, upon stimulation with ligand, excessive activation of PDGFRß was observed compared to cells transduced with the wild-type variant. PDGFRß with the p.(Ser548Tyr) amino acid substitution was successfully inhibited with tyrosine kinase inhibitors (axitinib, dasatinib, imatinib, and sunitinib) in vitro. Conclusions: A novel c.1643C>A, p.(Ser548Tyr) PDGFRB variant was found in family members with isolated corneal vascularization. Cells transduced with the newly identified variant showed increased phosphorylation of PDGFRß upon ligand stimulation. This suggests that PDGF-PDGFRß signaling in these patients leads to overactivation of PDGFRß, which could lead to abnormal wound healing of the cornea. The examined TKIs prevented such overactivation, introducing the possibility for targeted treatment in these patients.

Factors that influence a patient's decision to engage in genetic research.

Introduction: The most challenging step in clinical research studies is patient recruitment. Many research studies do not reach their targets because of participant rejection. The purpose of this study was to assess patient as well as the community knowledge, motivation, and barriers to participate in genetic research. Methods: A cross-section study was conducted between September 2018 and February 2020 using face-to-face interviews with candidate patients from outpatient clinics at King Fahad Medical City (KFMC), Riyadh, Saudi Arabia. Additionally, an online survey was conducted to assess the community's knowledge, motivation and barriers to participate in genetic research studies. Results: In total, 470 patients were interviewed for this study, with 341 being successfully recruited for the face to face interview, and the other patients being refused owing to time constraints. The majority percentage of the respondents were females. The respondents' mean age was 30, and 52.6% reported having a college degree. The survey results from 388 participants illustrated that around 90% of the participants, participated voluntarily due to a good understanding of genetics studies. The majority held positive attitudes toward being part of genetic research, which exceeded the reported motivation score of >75%. The survey indicated that >90% of individuals were willing to participate to acquire therapeutic benefits or to receive continued aftercare. However, 54.6% of survey participants were worried about the side effects and the risks involved in genetic testing. A higher proportion (71.4%) of respondents reported that lack of knowledge about genetic research was one of the barriers to rejecting participation. Conclusion: Respondents reported relatively high motivation and knowledge for participation in genetic research. However, study participants reported "do not know enough about genetic research" and "lack of time during clinic visit" as a barrier for participation in genetic research.

Isolated Congenital Anosmia: Case Report and Literature Review.

Isolated congenital anosmia (ICA) is a rare entity worldwide with poorly understood genetic variation. The diagnosis of ICA is made by exclusion of acquired causes of anosmia. Additionally, magnetic resonance imaging in ICA is essential for diagnosis, as it shows reduced or absent development of olfactory bulbs and shallow olfactory sulci. Here, we present the case of a 21-year-old man who presented to our clinic with complete anosmia since birth. The patient's history was negative for acquired causes of anosmia, and the physical examinations of the ears, nose, throat, head, and neck were all not remarkable. Smell testing revealed complete anosmia. The CT imaging was unremarkable; however, magnetic resonance imaging of the anterior brain and olfactory region showed bilaterally absent olfactory bulbs and olfactory tracts, with a shallow olfactory groove. The patient was then subjected to whole exome sequencing. Bioinformatics analysis was performed on the 37 genes associated with olfactory dysfunction, in which a missense variant was identified in the HS6ST1(NM_004807.3) gene was identified, which insilico tools predicted to be likely pathogenic. The results of this patient's genetic analysis add to the possible genetic culprits reported in ICA cases. Additional genetic analyses are required to validate mutations and understand the heterogeneity of disease representation.

Expression of Programmed Cell Death-L1 (PD-L1) Protein and Mismatch Repair Mutations in Orbital Tumours-a Pilot Study.

PURPOSE: Programmed cell death protein 1 (PD-1) and DNA mismatch repair (MMR) deficiency play an important role in tumour progression and response to treatment.Both markers have been studied in some ocular tumours but little is known about these markers in orbital tumours. This pilot study reports on PD-L1 expression and MMR mutations using next generation sequencing (NGS) in specific orbital tumours. METHODS: We reviewed surgical specimens from patients with rhabdomyosarcoma, adenoid cystic carcinoma (ACC), pleomorphic adenoma (PA) and biopsy negative tissue from orbital tumours used as a control. immunohistochemistry (IHC) was performed on Formalin fixed paraffin embedded tissue using a PD-L1 antibody. DNA was extracted for targeted gene panel NGS of the MMR genes PMS2, MLH1, MSH6 and MSH2. RESULTS: The study included 17 orbital specimens. Scattered membrane PD-L1 staining was noted in 3/6 rhabdomyosarcoma specimens without an accompanying lymphocytic infiltrate. PD-L1 immunostaining was absent in 3/3 ACC, and 5/6 PA specimens. PD-L1 immunostaining was not detected in 2/2 control specimens. 4/17 samples shared the same pathogenic mutation in the MLH1 gene, including 3/6 rhabdomyosarcoma and 1/3 ACC samples. 1/6 PA samples had a mutation in MSH6. CONCLUSIONS: Our study demonstrated scattered, non-quantifiable or absent PD-L1 staining in a limited sample of orbital tumours suggesting that PD-1/PD-L1 inhibitor therapy may not be useful in treatment of malignant orbital tumours (rhabdomyosarcoma and ACC) when refractory to conventional therapy. Our pilot study suggest that PD-L1/MMR axis might not play a major role in the pathogenesis of primary orbital tumour.

Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19.

A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry-matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes.

Methylation Profiling of Medulloblastoma in a Clinical Setting Permits Sub-classification and Reveals New Outcome Predictions.

Medulloblastoma (MB) is the most common childhood malignant brain tumor and is a leading cause of cancer-related death in children. DNA methylation profiling has rapidly advanced our understanding of MB pathogenesis at the molecular level, but assessments in Saudi Arabian (SA)-MB cases are sparse. MBs can be sub-grouped according to methylation patterns from FPPE samples into Wingless (WNT-MB), Sonic Hedgehog (SHH-MB), Group 3 (G3), and Group 4 (G4) tumors. The WNT-MB and SHH-MB subgroups are characterized by gain-of function mutations that activate oncogenic cell signaling, whilst G3/G4 tumors show recurrent chromosomal alterations. Given that each subgroup has distinct clinical outcomes, the ability to subgroup SA-FPPE samples holds significant prognostic and therapeutic value. Here, we performed the first assessment of MB-DNA methylation patterns in an SA cohort using archival biopsy material (FPPE n = 49). Of the 41 materials available for methylation assessments, 39 could be classified into the major DNA methylation subgroups (SHH, WNT, G3, and G4). Furthermore, methylation analysis was able to reclassify tumors that could not be sub-grouped through next-generation sequencing, highlighting its superior accuracy for MB molecular classifications. Independent assessments demonstrated known clinical relationships of the subgroups, exemplified by the high survival rates observed for WNT tumors. Surprisingly, the G4 subgroup did not conform to previously identified phenotypes, with a high prevalence in females, high metastatic rates, and a large number of tumor-associated deaths. Taking our results together, we demonstrate that DNA methylation profiling enables the robust sub-classification of four disease sub-groups in archival FFPE biopsy material from SA-MB patients. Moreover, we show that the incorporation of DNA methylation biomarkers can significantly improve current disease-risk stratification schemes, particularly concerning the identification of aggressive G4 tumors. These findings have important implications for future clinical disease management in MB cases across the Arab world.

DIFFUSE RETINAL VASCULAR LEAKAGE AND CONE-ROD DYSTROPHY IN A FAMILY WITH THE HOMOZYGOUS MISSENSE C.1429G>A (P.GLY477ARG) MUTATION IN CRB1.

PURPOSE: To describe a specific cone-rod dystrophy phenotype in a family with the homozygous c.1429G>A; p.Gly477Arg mutation in CRB1. The detailed phenotype of subjects with this specific mutation has not been described previously. METHODS: Clinical examination included full-field electroretinography and high-resolution and widefield retinal imaging and uveitis workup. Molecular genetic analysis included next-generation sequencing of known retinal dystrophy genes and Sanger sequencing for segregation analysis. RESULTS: Three affected male siblings (26, 16, and 8 years old) were diagnosed with cone-rod dystrophy, featuring bilateral macular hypoautofluorescent lesions. In addition, the eldest brother was found to have retinal vascular leakage throughout the retina without telangiectasia. Uveitis laboratory workup was unremarkable. The homozygous c.1429G>A; p.Gly477Arg mutation in CRB1 was found to segregate with disease in this family. CONCLUSION: To the best of our knowledge, diffuse vascular leakage without telangiectasia or exudation, with bull's eye maculopathy, has not been reported previously in CRB1-cone rod dystrophy. This expands the phenotype complexity associated with CRB1 mutations and confirms that dystrophies associated with mutations in this gene may appear with features of uveitis.

Advanced coats-like retinopathy as the initial presentation of Familial Retinal Arterial Macroaneurysms.

PURPOSE: To describe two young Saudi brothers with bilateral progressive retinal arterial aneurysms and a subtotal exudative retinal detachment with Coats-like presentation in the older sibling as the initial presentation of Familial Retinal Arterial Macroaneurysms (FRAM). OBSERVATIONS: Two young Saudi brothers with a family history of consanguinity presented with the classic clinical presentation and genetic identification of FRAM. In this report, we describe the presence of prominent peripheral retinal capillary changes mimicking Coats' disease. CONCLUSIONS AND IMPORTANCE: FRAM can present similar to bilateral Coats' disease and should be considered in the differential diagnosis of Coats-like retinopathy. The diagnosis of FRAM may have a significant implication because of the associated cardiac abnormality, such as supravalvular pulmonary stenosis, which should be evaluated by echocardiography and managed accordingly.

Rod-Cone Dystrophy with Initially Preserved Visual Acuity Despite Early Macular Involvement Suggests Recessive CERKL Mutations.

PURPOSE: To highlight that recessive CERKL mutations cause an early-onset rod-cone dystrophy with initially preserved visual acuity despite early macular involvement, an unusual and distinct initial phenotypic presentation. METHODS: A retrospective case series. RESULTS: Two young Saudi Arabian adults complained of worsening night blindness over the preceding few years, one of whom had been symptomatic since early childhood. Both had retinal pigment epithelium (RPE) mottling/granularity, vascular attenuation, few bone spicules, and frank macular RPE atrophic changes despite relatively preserved visual acuity. Electroretinography was non-recordable, and ocular coherence tomography confirmed retinal thinning, particularly of the outer nuclear layer in the fovea. Each patient harbored a different homozygous CERKL mutation (p.L245P, p.C333*). The few prior reports that detail the presenting phenotype of CERKL mutations describe children or young adults with the similar unusual presenting constellation of findings: rod-cone dystrophy and frank macular atrophy but relatively preserved visual acuity. With time, central vision is affected. CONCLUSIONS: The initial presenting features of CERKL-related retinopathy are distinct and unusual. Recognition of this initial presenting phenotype can facilitate earlier molecular diagnosis and genetic counseling.

Childhood cone-rod dystrophy with macular cystic degeneration from recessive CRB1 mutation.

PURPOSE: To describe three siblings with childhood cone-rod dystrophy and macular cystic degeneration in a family with apparently variable phenotypes of CRB1-related recessive retinal dystrophy. METHODS: Ophthalmologic examination (including electroretinography (ERG), ocular coherence tomography (OCT), and intravenous fluorescein angiography when possible) and homozygosity analysis guided candidate gene testing. RESULTS: When the proband was evaluated at 7 years old for progressive visual loss, fundus exam was unremarkable (including no macular thickening clinically or by OCT) but ERG revealed cone-rod dysfunction with an electronegative waveform. Four years later repeat examination was significant for bilateral macular cystic degeneration and immediate family members were evaluated. Both the older sister (15 years old) and the younger brother (7 years old) had cone-rod dystrophy with macular cystic degeneration. Both the father (45 years old) and mother (35 years old) had had early adult-onset nyctalopia with later eventual loss of central vision; examination revealed dystrophic retinas with mostly peripheral clumped and/or nummular pigment and macular atrophy. ERG for both the older sister and younger brother confirmed cone-rod dysfunction (without an electronegative waveform) and was non-recordable for both the parents. Homozygosity analysis guided candidate gene analysis and confirmatory Sanger sequencing for the family uncovered a homozygous CRB1 mutation (c.80G > T [p.Cys27Phe]) in affected family members. CONCLUSIONS: The phenotypic spectrum of recessive CRB1 mutation includes childhood cone-rod dystrophy with macular cystic degeneration and the associated ERG can be electronegative.

The RPGRIP1-related retinal phenotype in children.

AIM: To characterise the childhood retinal phenotype associated with recessive mutations in retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1), a gene that has been infrequently associated with Leber congenital amaurosis, the most severe form of childhood non-syndromic retinal dystrophy. METHODS: This was a retrospective case series analysis. RESULTS: Nine children (seven families) with homozygous RPGRIP1 mutations were identified. All were noted by their families to have had shaking eyes, variable eye turn and/or poor vision at or soon after birth and to be more comfortable in darkness than daylight. At the age of examination (2-7 years of age) fixation was poor or non-existent with hemeralopia, nystagmus, variable strabismus and often an oculodigital sign (6/9). Electroretinography was non-recordable. The posterior pole was grossly normal with mild vascular attenuation, but one girl did have a subtle abnormal macular reflex associated with decreased autofluorescence. Retinal pigment epithelium changes were seen in the periphery, ranging from mottling to bone spicules, and cycloplaegic refraction was hyperopic (+3 to +10 diopters). Two children were photophobic and two were developmentally delayed. One boy had oesotropia and nystagmus that decreased when hyperopic spectacles were worn. One girl decreased her nystagmus amplitude by adopting a particular gaze preference. CONCLUSIONS: Recessive RPGRIP1 mutations cause a severe cone-rod Leber congenital amaurosis phenotype, often with poor or no fixation and an oculodigital sign. In the first decade of life retinal changes are clinically most evident in the periphery. Despite the typical severity of the phenotype, fixation can improve for some affected children with wear of the associated hyperopic refraction or by a null point that dampens nystagmus. Spectacle correction of high refractive errors should be encouraged.

Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes.

Retinal dystrophy (RD) is a heterogeneous group of hereditary diseases caused by loss of photoreceptor function and contributes significantly to the etiology of blindness globally but especially in the industrialized world. The extreme locus and allelic heterogeneity of these disorders poses a major diagnostic challenge and often impedes the ability to provide a molecular diagnosis that can inform counseling and gene-specific treatment strategies. In a large cohort of nearly 150 RD families, we used genomic approaches in the form of autozygome-guided mutation analysis and exome sequencing to identify the likely causative genetic lesion in the majority of cases. Additionally, our study revealed six novel candidate disease genes (C21orf2, EMC1, KIAA1549, GPR125, ACBD5, and DTHD1), two of which (ACBD5 and DTHD1) were observed in the context of syndromic forms of RD that are described for the first time.

Molecular characterization of Joubert syndrome in Saudi Arabia.

Joubert syndrome (JS) is a ciliopathy that is defined primarily by typical cerebellar structural and ocular motility defects. The genetic heterogeneity of this condition is significant with 16 genes identified to date. We have used a combination of autozygome-guided candidate gene mutation analysis and exome sequencing to identify the causative mutation in a series of 12 families. The autozygome approach identified mutations in RPGRIP1L, AHI1, TMEM237, and CEP290, while exome sequencing revealed families with truncating mutations in TCTN1 and C5ORF42. Our study, the largest comprehensive molecular series on JS, provides independent confirmation of the recently reported TCTN1, TMEM237, and C5ORF42 as bona fide JS disease genes, and expands the allelic heterogeneity of this disease.

RP1 and retinitis pigmentosa: report of novel mutations and insight into mutational mechanism.

BACKGROUND/AIM: Retinitis pigmentosa (RP) is the commonest form of retinal dystrophy and is usually inherited as a monogenic trait but with remarkable genetic heterogeneity. RP1 is one of the earliest identified disease genes in RP with mutations in this gene known to act both recessively and dominantly although the mutational mechanism remains unclear. This study is part of our ongoing effort to characterise RP in Saudi Arabia at the molecular level. METHODS: Homozygosity mapping and candidate gene analysis. RESULTS: The authors have identified four novel mutations, all recessive, in a number of families with a typical RP phenotype. CONCLUSION: The distribution of these novel and previously reported RP1 mutations makes it challenging to describe a unifying mutational mechanism for dominant versus recessive RP1-related RP.

In search of triallelism in Bardet-Biedl syndrome.

Bardet-Biedl syndrome (BBS) is a model disease for ciliopathy in humans. The remarkable genetic heterogeneity that characterizes this disease is consistent with accumulating data on the interaction between the proteins encoded by the 14 BBS genes identified to date. Previous reports suggested that such interaction may also extend to instances of oligogenic inheritance in the form of triallelism which defies the long held view of BBS as an autosomal recessive disease. In order to investigate the magnitude of triallelism in BBS, we conducted a comprehensive analysis of all 14 BBS genes as well as the CCDC28B-modifier gene in a cohort of 29 BBS families, most of which are multiplex. Two in trans mutations in a BBS gene were identified in each of these families for a total of 20 mutations including 12 that are novel. In no instance did we observe two mutations in unaffected members of a given family, or observe the presence of a third allele that convincingly acted as a modifier of penetrance and supported the triallelic model of BBS. In addition to presenting a comprehensive genotype/phenotype overview of a large set of BBS mutations, including the occurrence of nonsyndromic retinitis pigmentosa in a family with a novel BBS9 mutation, our study argues in favor of straightforward autosomal recessive BBS in most cases.

Autozygome maps dispensable DNA and reveals potential selective bias against nullizygosity.

PURPOSE: Copy number variants are an important source of human genome diversity. The widespread distribution of hemizygous copy number variants in the DNA of healthy humans suggests that haploinsufficiency is largely tolerated. However, little is known about the extent to which corresponding nullizygosity (two-copy deletion) is similarly tolerated. METHODS: We analyzed a cohort of first cousin unions to enrich for shared parental hemizygous events and tested their Mendelian inheritance in offspring. RESULTS: Analysis of autozygous DNA blocks (autozygome) in the offspring not only proved an efficient method of mapping "dispensable" DNA but also revealed potential selective bias against the occurrence of nullizygous changes. This bias was not restricted to genic copy number variants and was not accounted for by a high rate of miscarriages. CONCLUSIONS: The autozygome is an efficient way to map dispensable segments of DNA and may reveal selective bias against nullizygosity in healthy individuals.

Mutation of IGFBP7 causes upregulation of BRAF/MEK/ERK pathway and familial retinal arterial macroaneurysms.

Insulin-like growth factor binding proteins (IGFBPs) play important physiological functions through the modulation of IGF signaling as well as IGF-independent mechanisms. Despite the established role of IGFs in development, a similar role for the seven known IGFBPs has not been established in humans. Here, we show that an autosomal-recessive syndrome that consists of progressive retinal arterial macroaneurysms and supravalvular pulmonic stenosis is caused by mutation of IGFBP7. Consistent with the recently established inhibitory role of IGFBP7 on BRAF signaling, the BRAF/MEK/ERK pathway is upregulated in these patients, which may explain why the cardiac phenotype overlaps with other disorders characterized by germline mutations in this pathway. The retinal phenotype appears to be mediated by a role in vascular endothelium, where IGFBP7 is highly expressed.

Later retinal degeneration following childhood surgical aphakia in a family with recessive CRYAB mutation (p.R56W).

PURPOSE: To describe later retinal degeneration following childhood cataract surgery without intraocular lens implantation in a consanguineous family with developmental cataract from homozygous p.R56W mutation in CRYAB, a gene that encodes a heat-shock protein (alphaB-crystallin) in both retina and the lens. METHODS: Prospective ophthalmologic examination and venous blood sampling for diagnostic CRYAB sequencing in the 12 available family members (7 siblings and their 2 parents, the siblings' maternal aunt and her son, and the siblings' maternal grandmother). RESULTS: Those who underwent childhood cataract surgery (2 siblings, their mother, their maternal aunt) or who had visually-insignificant lens opacities (2 siblings, their maternal grandmother) were homozygous for p.R56W CRYAB mutation. Among these 7 affected family members, clinically-obvious rod-cone degeneration was present only in the only 2 adults who were aphakic since childhood from cataract surgery. CONCLUSIONS: Recessive p.R56W CRYAB mutation shows variable expressivity for lens opacity. Decades of aphakia increases retinal light exposure and may be an environmental risk factor for significant retinal degeneration in patients homozygous for the mutation.

Methylation-specific multiplex-ligation-dependent probe amplification as a rapid molecular diagnostic tool for pseudohypoparathyroidism type 1b.

Pseudohypoparathyroidism type 1b (PHP1b) is a rare metabolic bone disorder characterized by isolated renal parathyroid hormone resistance. The disorder is almost always associated with an imprinting defect or deletions in the differentially methylated region of the GNAS locus located on chromosome 20q13. In addition to the epigenetic and genetic aberrations of the differentially methylated region, PHP1b can also result from a deletion of STX16, a long-range control element of methylation at the GNAS locus located centromeric of GNAS. This report describes the utilization of a recently described methylation-specific multiplex-ligation-dependent probe amplification assay for high-throughput molecular analysis of a patient with the clinical diagnosis of PHP1b. Although more patients will need to be tested to confirm this, methylation-specific multiplex-ligation-dependent probe amplification in our hands proved to be a rapid, sensitive, and fairly easy-to-interpret assay that can be used in lieu of Southern blot analysis to diagnose PHP1b.