Molecular and clinical characterization of a founder mutation causing G6PC3 deficiency.

Background: G6PC3 deficiency is a rare genetic disorder that causes syndromic congenital neutropenia. It is driven by the intracellular accumulation of a metabolite named 1,5-anhydroglucitol-6-phosphate (1,5-AG6P) that inhibits glycolysis. Patients display heterogeneous extra-hematological manifestations, contributing to delayed diagnosis. Objective: The G6PC3 c.210delC variant has been identified in patients of Mexican origin. We set out to study the origin and functional consequence of this mutation. Furthermore, we sought to characterize the clinical phenotypes caused by it. Methods: Using whole-genome sequencing data, we conducted haplotype analysis to estimate the age of this allele and traced its ancestral origin. We examined how this mutation affected G6PC3 protein expression and performed extracellular flux assays on patient-derived cells to characterize how this mutation impacts glycolysis. Finally, we compared the clinical presentations of patients with the c.210delC mutation relative to other G6PC3 deficient patients published to date. Results: Based on the length of haplotypes shared amongst ten carriers of the G6PC3 c.210delC mutation, we estimated that this variant originated in a common ancestor of indigenous American origin. The mutation causes a frameshift that introduces a premature stop codon, leading to a complete loss of G6PC3 protein expression. When treated with 1,5-anhydroglucitol (1,5-AG), the precursor to 1,5-AG6P, patient-derived cells exhibited markedly reduced engagement of glycolysis. Clinically, c.210delC carriers display all the clinical features of syndromic severe congenital neutropenia type 4 observed in prior reports of G6PC3 deficiency. Conclusion: The G6PC3 c.210delC is a loss-of-function mutation that arose from a founder effect in the indigenous Mexican population. These findings may facilitate the diagnosis of additional patients in this geographical area. Moreover, the in vitro 1,5-AG-dependent functional assay used in our study could be employed to assess the pathogenicity of additional G6PC3 variants.

The landscape of rare genetic variation associated with inflammatory bowel disease and Parkinson's disease comorbidity.

BACKGROUND: Inflammatory bowel disease (IBD) and Parkinson's disease (PD) are chronic disorders that have been suggested to share common pathophysiological processes. LRRK2 has been implicated as playing a role in both diseases. Exploring the genetic basis of the IBD-PD comorbidity through studying high-impact rare genetic variants can facilitate the identification of the novel shared genetic factors underlying this comorbidity. METHODS: We analyzed whole exomes from the BioMe BioBank and UK Biobank, and whole genomes from a cohort of 67 European patients diagnosed with both IBD and PD to examine the effects of LRRK2 missense variants on IBD, PD and their co-occurrence (IBD-PD). We performed optimized sequence kernel association test (SKAT-O) and network-based heterogeneity clustering (NHC) analyses using high-impact rare variants in the IBD-PD cohort to identify novel candidate genes, which we further prioritized by biological relatedness approaches. We conducted phenome-wide association studies (PheWAS) employing BioMe BioBank and UK Biobank whole exomes to estimate the genetic relevance of the 14 prioritized genes to IBD-PD. RESULTS: The analysis of LRRK2 missense variants revealed significant associations of the G2019S and N2081D variants with IBD-PD in addition to several other variants as potential contributors to increased or decreased IBD-PD risk. SKAT-O identified two significant genes, LRRK2 and IL10RA, and NHC identified 6 significant gene clusters that are biologically relevant to IBD-PD. We observed prominent overlaps between the enriched pathways in the known IBD, PD, and candidate IBD-PD gene sets. Additionally, we detected significantly enriched pathways unique to the IBD-PD, including MAPK signaling, LPS/IL-1 mediated inhibition of RXR function, and NAD signaling. Fourteen final candidate IBD-PD genes were prioritized by biological relatedness methods. The biological importance scores estimated by protein-protein interaction networks and pathway and ontology enrichment analyses indicated the involvement of genes related to immunity, inflammation, and autophagy in IBD-PD. Additionally, PheWAS provided support for the associations of candidate genes with IBD and PD. CONCLUSIONS: Our study confirms and uncovers new LRRK2 associations in IBD-PD. The identification of novel inflammation and autophagy-related genes supports and expands previous findings related to IBD-PD pathogenesis, and underscores the significance of therapeutic interventions for reducing systemic inflammation.

Evaluation of unilateral corneal collagen cross-linking on fellow untreated eyes of patients with keratoconus / A avaliação da reticulação unilateral do colágeno corneano em olhos não tratados de pacientes com ceratocone

ABSTRACT Purpose: This study aimed to examine the effects of unilateral corneal collagen cross-linking treatment on visual acuity and the topographic findings of the fellow untreated eye of patients who had bilateral progressive keratoconus. Methods: Patients with progressive keratoconus who underwent cross-linking treatment were screened retrospectively. A total of 188 untreated eyes of 188 patients whose eyes were treated unilaterally with either standard or accelerated cross-linking and refused cross-linking procedure for the fellow eye were included. Visual acuity and topographic findings of the fellow untreated eyes were obtained preoperatively and postoperatively at the 1st, 3rd, 6th, 12th, 24th, 30th, and 36th months. Results: The change over time of variables examined was similar in the untreated eyes of patients who received standard and accelerated cross-linking methods (p>0.05). At the 12th month, 136 (95.8%) untreated eyes were stable according to progression criteria. Only 4 (8%) eyes were progressive at the 24th month. No progression was observed in any of the 16 patients with a 36-month follow up. Conclusions: The results showed that the fellow untreated eyes of patients with bilateral progressive keratoconus did not have significant progression rates after unilateral cross-linking treatment.

RESUMO Objetivo: Examinar os efeitos do tratamento de reticulação unilateral do colágeno corneano na acuidade visual e os achados topográficos em olhos não tratados de pacientes com ceratocone progressivo bilateral. Métodos: Foram rastreados retrospectivamente pacientes com ceratocone progressivo submetidos a tratamento de reticulação. Foram incluídos no estudo 188 olhos não tratados de 188 pacientes tratado unilateralmente com reticulação padrão ou acelerada e que recusaram o procedimento de reticulação no outro olho. A acuidade visual e os achados topográficos dos olhos não tratados foram obtidos no pré- e pós-operatório no 1º, 3º, 6º, 12º, 24º, 30º e 36º mês. Resultados: As alterações ao longo do tempo foram semelhantes para as variáveis examinadas nos olhos não tratados de pacientes tratados com métodos de reticulação padrão e acelerado (p>0,05). No 12º mês, 136 olhos não tratados (95,8%) estavam estáveis, de acordo com os critérios de progressão. Apenas quatro olhos (8%) mostraram progressão no 24º mês. Nenhuma progressão foi observada nos 16 pacientes que tiveram um acompanhamento de 36 meses. Conclusões: O estudo mostrou que os olhos não tratados de pacientes com ceratocone progressivo bilateral não apresentaram taxas de progressão significativas após o tratamento unilateral com reticulação.

Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set.

Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. Experimental approaches for identifying GOF and LOF are generally slow and costly, whilst available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, a machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants, trained on a broad range of gene-, protein-, and variant-level features describing diverse biological characteristics. LoGoFunc outperforms other tools trained solely to predict pathogenicity for identifying pathogenic GOF and LOF variants and is available at https://itanlab.shinyapps.io/goflof/ .

Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients.

Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.

Evaluation of unilateral corneal collagen cross-linking on fellow untreated eyes of patients with keratoconus.

PURPOSE: This study aimed to examine the effects of unilateral corneal collagen cross-linking treatment on visual acuity and the topographic findings of the fellow untreated eye of patients who had bilateral progressive keratoconus. METHODS: Patients with progressive keratoconus who underwent cross-linking treatment were screened retrospectively. A total of 188 untreated eyes of 188 patients whose eyes were treated unilaterally with either standard or accelerated cross-linking and refused cross-linking procedure for the fellow eye were included. Visual acuity and topographic findings of the fellow untreated eyes were obtained preoperatively and postoperatively at the 1st, 3rd, 6th, 12th, 24th, 30th, and 36th months. RESULTS: The change over time of variables examined was similar in the untreated eyes of patients who received standard and accelerated cross-linking methods (p>0.05). At the 12th month, 136 (95.8%) untreated eyes were stable according to progression criteria. Only 4 (8%) eyes were progressive at the 24th month. No progression was observed in any of the 16 patients with a 36-month follow up. CONCLUSIONS: The results showed that the fellow untreated eyes of patients with bilateral progressive keratoconus did not have significant progression rates after unilateral cross-linking treatment.

Electrolyte, Nitric Oxide and Oxidative Stress Levels of Aqueous Humor in Patients with Retinal Detachment and Silicone Oil Tamponade.

Purpose: To enlighten the pathogenesis of silicone oil (SiO)-related complications via measuring aqueous humor levels of electrolytes, nitric oxide (NO), and oxidative stress in SiO, retinal detachment (RD), and control groups. Materials and Methods: In this prospective study, 56 patients were grouped as SiO (n = 29), RD (n = 12), and control (n = 15). The results of pre- and post-operative ophthalmological examinations, aqueous humor electrolyte and NO levels, total antioxidant and oxidant status (TAS, TOS) and oxidative stress index (OSI) were analyzed. Results: SiO group had a higher mean Na+ level compared to controls (144.77 ± 11.48 vs 137.56 ± 6.57 mmol/kg, p = .02). Also, the mean Na+ and Cl- levels of RD group were higher than controls (149.04 ± 12.05 vs. 137.56 ± 6.57 mmol/kg, p = .02, 115.2 ± 7.79 vs 106.23 ± 8.99 mmol/kg, p = .031 for Na+ and Cl-, respectively). The mean NO level of RD group was higher than that of SiO group (51.07 ± 19.56 vs. 34.07 ± 13.84 µM, p = .009). The mean TAS and TOS were lower in SiO group compared to controls (1.92 ± 0.64 vs. 2.49 ± 0.56 µmolTroloxEqv./L, p = .021, 34.98 ± 26.55 vs. 61.46 ± 22.69 µmolH2O2Eqv./L, p = .004 for TAS and TOS, respectively). Intraocular retention time of SiO demonstrated positive correlation with post-operative visual acuity (logMAR) and negative correlation with TOS. Conclusions: Elevated aqueous humor Na+ and Cl- in RD patients might reflect abolished function of ion channels on detached retina. Increased Na+ and lack of NO response to elevated intraocular pressure in SiO-filled eyes might contribute to secondary cataract and glaucoma formation. SiO is associated with low levels of oxidative stress in aqueous humor; however, increased intraocular retention time of SiO is related to a poor visual outcome.

Clinical evaluation of different types of contact lenses in keratoconus management.

PURPOSE: To compare the clinical and topographical findings of the keratoconus patients according to the prescribed contact lens type and to investigate the effects of corneal collagen cross-linking (CXL) and cone location on lens selection. METHODS: The records of 301 eyes of 195 keratoconus patients who were prescribed contact lenses were analyzed retrospectively. The eyes were grouped according to the lens type: Soft toric contact lens (STCL), rigid gas-permeable contact lens (RGPCL), hybrid contact lens (HCL) and mini-scleral contact lens (MSCL). The history of having CXL, ophthalmological examination findings, and the topographical findings were compared between the groups. Brown-Forsythe, Chi-square, and post-hoc tests were used to compare the groups. Mann-Whitney U test was used for subgroup analysis. Comparison of the lens-corrected visual acuity (LCVA) and spectacle-corrected visual acuity (SCVA) levels was made with Wilcoxon signed-ranks test. RESULTS: There was no significant difference between the groups regarding topographical cone location, CXL history, spherical refraction, and LCVA. The difference between spectacle-corrected visual acuity and LCVA was higher in RGPCL and MSCL groups than STCL group (p=0.01). Keratometry of RGPCL and MSCL groups were higher than STCL and HCL groups (p=0.01, p<0.001). In RGPCL group, eyes with central cones had a higher increase in visual acuity with contact lenses compared to eyes with paracentral cones (p=0.043). STCL and MSCL were mostly prescribed in mild and severe keratoconic eyes, respectively. In RGPCL group, the increase in visual acuity with contact lens was higher in eyes treated with CXL (p= <0.01). CONCLUSIONS: While STCL and HCL were mostly prescribed in mild keratoconus, RGPCL and MSCL were selected for moderate or advanced disease. If appropriately chosen, all types of contact lenses could result in a good visual acuity level. CXL history did not affect the prescribed lens type. Having central cone location and CXL history in RGPCL group improved visual acuity more efficiently.

An assessment of ocular elasticity using real time ultrasound and ocular response analyzer in active or remission rheumatoid arthritis.

PURPOSE: To investigate the elasticity of ocular structures in patients with rheumatoid arthritis (RA) without ocular involvement. METHODS: The study included 56 RA patients (study group) and 24 healthy volunteers as the control group. The rheumatoid arthritis patients were divided into two subgroups as those in active phase (Group 1, n = 25) or in remission phase (Group 2, n = 31) according to the disease activity index (DAS 28) score. The elastography values of the ratio of orbital fat-sclera (ROF/S) were measured with real-time US elastography, and corneal mechanical values were measured with the Reichert Ocular Response Analyzer in each eye. RESULTS: The mean ROF/S value was 5.2 ± 1.8 in Group 1, 0.7 ± 0.4 Group 2, and 0.6 ± 0.1 in the control group. There was a significant difference between the Group 1 and control group with regard to ROF/S (p < 0.001), but no significant difference was determined between Group 2 and control group (p > 0.05). The mean ROF/S value was a significant difference between the Group 1 and 2 (p < 0.001). ROF/S was significantly correlated with DAS-28 and C-reactive protein (CRP) (r = 0.816, p < 0.001 and r = 0.259, p = 0.006). CONCLUSIONS: ROF/S was significantly increased in patients in the active phase of RA. Findings revealed that ocular tissue structural changes may occur in the active phase and these could be related to ocular complications as a prognostic factor.

Blood coagulation parameters after intravitreal injection of aflibercept in patients with neovascular age-related macular degeneration.

PURPOSE: The aim of this study was to evaluate the effect of intravitreal injection of aflibercept (IVA) on blood coagulation tests in neovascular age-related macular degeneration (AMD) patients. METHODS: Thirty-four patients with neovascular AMD (study group) and 32 healthy individuals (control group) were enrolled. Prothrombin time (PT) and activated partial thromboplastin time (aPTT) were measured at different times in patients with neovascular AMD. RESULTS: The levels of PT and aPTT after IVA were decreased at 1 month after the first injection and 1 month after the second injection compared to the baseline measurement in the study group. CONCLUSIONS: IVA may cause a decrease in the levels of PT and aPTT at 1 month after the first injection and 1 month after the second injection although these results are not statistically significant in our study.