magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing.

Recently, novel biotechnologies to quantify RNA modifications became an increasingly popular choice for researchers who study epitranscriptome. When studying RNA methylations such as N6-methyladenosine (m6A), researchers need to make several decisions in its experimental design, especially the sample size and a proper statistical power. Due to the complexity and high-throughput nature of m6A sequencing measurements, methods for power calculation and study design are still currently unavailable. In this work, we propose a statistical power assessment tool, magpie, for power calculation and experimental design for epitranscriptome studies using m6A sequencing data. Our simulation-based power assessment tool will borrow information from real pilot data, and inspect various influential factors including sample size, sequencing depth, effect size, and basal expression ranges. We integrate two modules in magpie: (i) a flexible and realistic simulator module to synthesize m6A sequencing data based on real data; and (ii) a power assessment module to examine a set of comprehensive evaluation metrics.

The Role of the Ophthalmic Genetics Multidisciplinary Team in the Management of Inherited Retinal Degenerations-A Case-Based Review.

(1) Background: Inherited retinal degenertions are rare conditions which may have a dramatic impact on the daily life of those affected and how they interact with their environment. Coordination of clinical services via an ophthalmic genetics multidisciplinary team (OG-MDT) allows better efficiency of time and resources to reach diagnoses and facilitate patient needs. (2) Methods: This clinical case series was conducted by a retrospective review of patient records for patients enrolled in the Target 5000 programme and managed by the OG-MDT, at the Mater Hospital Dublin, Ireland (n = 865) (3) Results: Herein we describe clinical cases and how the use of the OG-MDT optimizes care for isolated and syndromic IRD pedigrees. (4) Conclusions: this paper demonstrates the benefits of an OG-MDT to patients with IRDs resulting in the holistic resolution of complex and syndromic cases. Furthermore, we demonstrate that this format can be adopted/developed by similar centres around the world, bringing with it the myriad benefits.

Ethno-racial variations in mental health symptoms among sexually-active gay, bisexual, and other men who have sex with men in Vancouver, Canada: a longitudinal analysis.

BACKGROUND: Minority stress from racism and heterosexism may uniquely interact to impact the mental health of racialized sexual minorities. We examined variations in anxiety and depressive symptoms by reported by ethno-racial identity among gay, bisexual, and other men who have sex with men (gbMSM) in Vancouver, Canada. METHODS: We recruited gbMSM aged ≥ 16 years from February 2012 to February 2015 using respondent-driven sampling (RDS). Participants completed computer assisted self-interviews (CASI) at enrollment and every 6 months until February 2017. We examined factors associated with moderate/severe anxiety and depression scores (> 10) on the Hospital Anxiety and Depression Scale (HADS) and differences in key explanatory variables including sociodemographic, psychosocial, and substance use factors. We used multivariable mixed effects models to assess whether moderate/severe scores were associated with ethno-racial identity across all visits. RESULTS: After RDS-adjustment, of 774 participants, 79.9% of participants identified as gay. 68.6% identified as white, 9.2% as Asian, 9.8% as Indigenous, 7.3% as Latin American, and 5.1% as other ethno-racial identities. Participants contributed a median of 6 follow-up visits (Q1-Q3: 4-7). In the multivariable analysis, Asian participants had decreased odds of moderate/severe anxiety scores compared to white participants (aOR = 0.39; 95% CI: 0.18-0.86), and Latin American participants had decreased odds of moderate/severe depression scores compared to both white (aOR = 0.17; 95% CI: 0.08-0.36) and Asian (aOR = 0.07; 95% CI: 0.02-0.20) participants. CONCLUSION: Asian and Latino gbMSM reported decreased mental health symptoms compared to white participants. Asian and Latino gbMSM in Vancouver appear to manage multiple minority stressors without adversely affecting their mental health.

It's all about connection: Determinants of social support and the influence on HIV treatment interruptions among people living with HIV in British Columbia, Canada.

BACKGROUND: Social support has previously been found to be associated with improved health outcomes of individuals managing chronic illnesses, including amongst people living with HIV (PLWH). For women and people who use injection drugs who continue to experience treatment disparities in comparison to other PLWH, social support may have potential in facilitating better treatment engagement and retention. In this analysis, we examined determinants of social support as measured by the Medical Outcomes Study - Social Support Survey (MOS-SSS) scale, and quantified the relationship between MOS-SSS and HIV treatment interruptions (TIs) among PLWH in British Columbia, Canada. METHODS: Between January 2016 and September 2018, we used purposive sampling to enroll PLWH, 19 years of age or older living in British Columbia into the STOP HIV/AIDS Program Evaluation study. Participants completed a baseline survey at enrolment which included the MOS-SSS scale, where higher MOS-SSS scores indicated greater social support. Multivariable linear regression modeled the association between key explanatory variables and MOS-SSS scores, whereas multivariable logistic regression modeled the association between MOS-SSS scores and experiencing TIs while controlling for confounders. RESULTS: Among 644 PLWH, we found that having a history of injection drug use more than 12 months ago but not within the last 12 months, self-identifying as Indigenous, and sexual activity in the last 12 months were positively associated with MOS-SSS, while being single, divorced, or dating (vs. married), experiences of lifetime violence, and diagnosis of a mental health disorder were inversely associated. In a separate multivariable model adjusted for gender, ethnicity, recent homelessness, sexual activity in the last 12 months, and recent injection drug use, we found that higher MOS-SSS scores, indicating more social support, were associated with a lower likelihood of HIV treatment interruptions (adjusted odds ratio: 0.90 per 10-unit increase, 95% confidence interval: 0.83, 0.99). CONCLUSIONS: Social support may be an important protective factor in ensuring HIV treatment continuity among PLWH. Future research should examine effective means to build social support among communities that have potential to promote increased treatment engagement.

A feasibility study on the efficacy of a patient-owned wound surveillance system for diabetic foot ulcer care (ePOWS study).

Objective: Wound image analysis tools hold promise in helping patients to monitor their wounds. We aim to perform a novel feasibility study on the efficacy of a patient-owned wound surveillance system for diabetic foot ulcer (DFU) care. Methods: This two-institutional, prospective, single-arm pilot study examined patients with DFU. An artificial intelligence-enabled image analysis app calculating the wound surface area was installed and patients or caregivers were instructed to take pictures of wounds during dressing changes. Patients were followed until wound deterioration, wound healing, or wound stability at 6 months occurred and the outcomes of interest included study adherence, algorithm performance, and user experience. Results: Between January 2021 and December 2021, 39 patients were enrolled in the study, with a mean age of 61.6 ± 8.6 years, and 69% (n = 27) of subjects were male. All patients had documented diabetes and 85% (n = 33) of them had peripheral arterial disease. A mean follow-up for those completing the study was 12.0 ± 8.5 weeks. At the conclusion of the study, 80% of patients (n = 20) had primary wound healing whilst 20% (n = 5) had wound deterioration. The study completion rate was 64% (n = 25). Usage of the app for surveillance of DFU healing, as compared to physician evaluation, yielded a sensitivity of 100%, specificity of 20%, positive predictive value of 83%, and negative predictive value of 100%. Of those who provided user experience feedback, 59% (n = 10) felt the app was easy to use, 47% (n = 8) would recommend the wound analysis app to others but only 6% would pay for the app out of pocket (n = 1). Conclusion: Implementation of a patient-owned wound surveillance system is feasible. Most patients were able to effectively monitor wounds using a smartphone app-based solution. The image analysis algorithm demonstrates strong performance in identifying wound healing and is capable of detecting deterioration prior to interval evaluation by a physician. Patients generally found the app easy to use but were reluctant to pay for the use of the solution out of pocket.

Fatal injuries associated with rear step riding among municipal solid waste collection workers (United States, 1984-2020).

BACKGROUND: United States solid waste workers suffer a high fatal injury rate due to their frequent exposures to refuse-vehicle-related hazards. The Occupational Safety and Health Administration (OSHA) allows workers to ride on the rear steps of a garbage truck (exterior riding) if employers abide by American National Standard Z245.1 (ANSI Z245.1). The State of California (CA) has banned exterior riding since 1984, and the City of New York (NYC) has implemented its own initiatives to prevent exterior riding deaths. METHODS: Fatal exterior riding incidents were identified from two online databases. Variables relating to deceased workers, employers, and injury circumstances were analyzed. RESULTS: The study identified 181 exterior riding deaths from 604 refuse-vehicle-related fatal incidents (deaths either directly caused by a refuse vehicle or one in which the victim was performing a refuse-vehicle-related task) in the United States (1984-2020). A total of 50 (27.6%) of the exterior riding deaths had no ANSI Z245.1 violations. Risk factors other than those addressed by ANSI Z245.1 contributed to these worker deaths. CONCLUSIONS: Exterior riding deaths identified by this study were all preventable. Temporary workers and workers in the public sector may be at higher risk for exterior riding deaths. Both CA and NYC had taken measures to prohibit the practice of exterior riding, and both had lower numbers of exterior riding deaths. ANSI Z245.1 and current OSHA enforcement policy do not address the inherent dangers of falling off a moving heavy vehicle while standing on a small and elevated platform, and are not effective in preventing fatal exterior riding incidents.

Usher Syndrome on the Island of Ireland: A Genotype-Phenotype Review.

Purpose: Usher syndrome (USH) is a genetically heterogeneous group of autosomal recessive (AR) syndromic inherited retinal degenerations (IRDs) representing 50% of deaf-blindness. All subtypes include retinitis pigmentosa, sensorineural hearing loss, and vestibular abnormalities. Thorough phenotyping may facilitate genetic diagnosis and intervention. Here we report the clinical/genetic features of an Irish USH cohort. Methods: USH patients were selected from the Irish IRD registry (Target 5000). Patients were examined clinically (deep-phenotyping) and genetically using a 254 IRD-associated gene target capture sequencing panel, USH2A exon, and whole genome sequencing. Results: The study identified 145 patients (24.1% USH1 [n = 35], 73.8% USH2 [n = 107], 1.4% USH3 [n = 2], and 0.7% USH4 [n = 1]). A genetic diagnosis was reached in 82.1%, the majority (80.7%) being MYO7A or USH2A genotypes. Mean visual acuity and visual field (VF) were 0.47 ± 0.58 LogMAR and 31.3° ± 32.8°, respectively, at a mean age of 43 years. Legal blindness criteria were met in 40.7%. Cataract was present in 77.4%. ADGRV1 genotypes had the most VF loss, whereas USH2A patients had greater myopia and CDH23 had the most astigmatism. Variants absent from gnomAD non-Finnish Europeans and ClinVar represented more than 20% of the variants identified and were detected in ADGRV1, ARSG, CDH23, MYO7A, and USH2A. Conclusions: USH is a genetically diverse group of AR IRDs that have a profound impact on affected individuals and their families. The prevalence and phenotype/genotype characteristics of USH in Ireland have, as yet, gone unreported. Understanding the genotype of Irish USH patients may guide clinical and genetic characterization facilitating access to existing/novel therapeutics.

Detailed analysis of an enriched deep intronic ABCA4 variant in Irish Stargardt disease patients.

Over 15% of probands in a large cohort of more than 1500 inherited retinal degeneration patients present with a clinical diagnosis of Stargardt disease (STGD1), a recessive form of macular dystrophy caused by biallelic variants in the ABCA4 gene. Participants were clinically examined and underwent either target capture sequencing of the exons and some pathogenic intronic regions of ABCA4, sequencing of the entire ABCA4 gene or whole genome sequencing. ABCA4 c.4539 + 2028C > T, p.[= ,Arg1514Leufs*36] is a pathogenic deep intronic variant that results in a retina-specific 345-nucleotide pseudoexon inclusion. Through analysis of the Irish STGD1 cohort, 25 individuals across 18 pedigrees harbour ABCA4 c.4539 + 2028C > T and another pathogenic variant. This includes, to the best of our knowledge, the only two homozygous patients identified to date. This provides important evidence of variant pathogenicity for this deep intronic variant, highlighting the value of homozygotes for variant interpretation. 15 other heterozygous incidents of this variant in patients have been reported globally, indicating significant enrichment in the Irish population. We provide detailed genetic and clinical characterization of these patients, illustrating that ABCA4 c.4539 + 2028C > T is a variant of mild to intermediate severity. These results have important implications for unresolved STGD1 patients globally with approximately 10% of the population in some western countries claiming Irish heritage. This study exemplifies that detection and characterization of founder variants is a diagnostic imperative.

Treatment patterns and healthcare costs among patients with psoriasis initiating apremilast or biologics: a retrospective claims database cohort analysis.

OBJECTIVE: This study aimed to compare treatment patterns and healthcare costs for patients with psoriasis who initiate apremilast, tumor necrosis factor inhibitor, or interleukin inhibitor. METHODS: This retrospective cohort study used Optum Clinformatics® Data Mart to identify propensity score-matched patients initiating apremilast, tumor necrosis factor inhibitors, or interleukin inhibitors, with 12-month baseline and 24-month follow-up data. Switch, discontinuation, persistence, healthcare resource utilization, and total healthcare costs were assessed. RESULTS: Twenty-four-month switch rates were highest for tumor necrosis factor inhibitors (32%), followed by apremilast (21%) then interleukin inhibitors (14%). Mean (SD) per-patient-per-month costs for switchers were lowest for apremilast ($4213 [$2304]), higher for tumor necrosis factor inhibitors ($5274 [$2280]), and highest for interleukin inhibitors ($5539 [$2296]; p < .001), primarily attributable to pharmacy costs: $3466 (apremilast), $4432 (tumor necrosis factor inhibitor), and $4721 (interleukin inhibitor). LIMITATIONS: Psoriasis severity is absent from claims data; cost outcomes may be influenced by more severe psoriasis being more costly. CONCLUSION: Switching psoriasis treatment is common and increases over time. Apremilast initiators had lower switch rates and costs compared with tumor necrosis factor inhibitors, despite lower effectiveness reported in previous studies, perhaps indicating patient preference for oral treatment. Additional oral options may be desirable for this population.

Factors associated with improvements in symptoms of anxiety and depression among gay, bisexual and other men who have sex with men (gbMSM) in Vancouver, Canada: A prospective cohort study.

BACKGROUND: Depression and anxiety are commonly experienced among gay, bisexual and other men-who-have-sex-with-men (gbMSM). We explored factors associated with improvements in mental health symptoms among gbMSM with abnormal depression and anxiety scores over a period of four years, in Vancouver, Canada. METHODS: Sexually active gbMSM ≥16 years of age were recruited using respondent-driven sampling from February 2012 to February 2015. Participants completed a computer-assisted questionnaire which included the Hospital Anxiety and Depression Scale (HADS), and psychometric scales to measure loneliness, self-esteem and social connectedness, every 6 months until July 2019. Generalized linear mixed models were used to assess factors associated with normal/borderline HADS scores (<11) following a previous abnormal score (≥11) for each of anxiety and depression subscales. RESULTS: We recruited 694 participants, of whom 580 had at least one follow-up visit. Across all visits, 43.6 % of participants ever had abnormal anxiety scores and 16.2 % ever had abnormal depression scores. Among those with abnormal anxiety scores, 34.9 % of follow-up visits demonstrated reductions in anxiety scores. Among those with abnormal depression scores 51.0 % of follow-up visits demonstrated reductions in depression scores. Reductions in anxiety scores were associated with increased self-esteem, decreased loneliness and the number of gbMSM seen/spoken to in the previous month. Reductions in depression scores were associated with increased self-esteem, decreased loneliness and having a regular partner. CONCLUSION: Improvements in mental health symptoms were frequently observed. Social connectedness was related with improved anxiety and depression symptoms. Interventions to improve social connectedness may help to improve mental health for gbMSM.

Limited Impact of First-Line Drug Resistance Mutations on Virologic Response Among Patients Receiving Second-Line Antiretroviral Therapy in Rural Uganda.

BACKGROUND: Delayed detection of ART failure in settings without access to viral load (VL) monitoring has been hypothesized to lead to suboptimal response to second-line therapy due to accumulated drug resistance mutations (DRMs). We tested this hypothesis in a program setting in rural Uganda. METHODS: From June 2012 to January 2014, we enrolled participants receiving nonnucleoside reverse transcriptase inhibitor-based first-line ART for ≥4 years, without access to VL monitoring. Participants who had a measured VL ≥ 1000 copies/mL on two occasions were switched to protease inhibitor-based regimens and followed every 6 months until September 2016. We measured VL at study exit. We conducted DRM testing at enrollment and study exit and examined factors associated with virologic failure. RESULTS: We enrolled 137 participants (64.3% female) with a median age of 44 years and a median duration on ART of 6.0 years. In a median of 2.8 years of follow-up, 7 (5%) died, 5 (3.6%) voluntarily withdrew, and 9 (6.6%) became lost to follow-up. Of 116 participants with a VL result at study exit, 20 (17%) had VL > 1000 copies/mL. Virologic failure was associated with reporting suboptimal adherence ( P = 0.028). Of patients with DRM data at enrollment, 103 of 105 (98%) had at least 1 DRM. Participants with thymidine analog mutations at enrollment were less likely to have virologic failure at study exit (11% vs. 36%; P = 0.007). No other DRMs were associated with failure. CONCLUSION: Even in the presence of multiple DRMs on first-line therapy, virologic failure after 3 years of protease inhibitor-based ART was infrequent. Suboptimal adherence to ART was associated with virologic failure.

Impact of apixaban treatment discontinuation on the risk of hospitalization among patients with nonvalvular atrial fibrillation and COVID-19.

INTRODUCTION: This study evaluated the risk of hospitalization among nonvalvular atrial fibrillation (NVAF) patients with an outpatient COVID-19 diagnosis who discontinued vs continued apixaban treatment. METHODS: Adult patients with NVAF with an apixaban prescription prior to an outpatient COVID-19 diagnosis were identified from Optum Clinformatics claims database (1 April 2020-31 March 2021). Continuers were those who continued apixaban as of the index date (date of initial outpatient COVID-19 diagnosis) and discontinuers were those who had the last day of apixaban supply on or before index. Patients were followed from COVID-19 diagnosis to change of continuation/discontinuation status, switch, death, end of continuous coverage or study end, whichever occurred first. Inverse probability treatment weighting (IPTW) was performed to balance cohorts. Cox proportional hazard models were used to compare the risk of all-cause hospitalization and hospitalization for ischemic stroke (IS), venous thromboembolism (VTE), myocardial infarction (MI), bleeding and mortality. RESULTS: A total of 7869 apixaban patients with COVID-19 were included: 6676 continuers (84.8%) and 1193 discontinuers (15.2%). Compared with continuers, discontinuers had a higher risk of all-cause hospitalization (hazard ratio [HR]: 1.23; 95% confidence interval [CI]: 1.08-1.40), IS (HR: 2.00; 95% CI: 1.03-3.87), VTE (HR: 2.37; 95% CI: 1.06-5.27) and mortality (HR: 2.28; 95% CI: 1.85-2.80). There were no significant differences in the risk of MI (HR: 1.01; 95% CI: 0.54-1.90) or bleeding-related hospitalization (HR: 1.13; 95% CI: 0.73-1.76). CONCLUSION: NVAF patients with COVID-19 who discontinued apixaban had a higher risk of hospitalization and thrombotic events vs those who continued apixaban, with no significant difference in bleeding-related hospitalization.

A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions.

Active mutations in the RAS genes are found in ∼30% of human cancers. Although thought to have overlapping functions, RAS isoforms show preferential activation in human tumors, which prompted us to employ a comparative and quantitative proteomics approach to generate isoform-specific and nucleotide-dependent interactomes of the four RAS isoforms, KRAS4A, KRAS4B, HRAS, and NRAS. Many isoform-specific interacting proteins were identified, including HRAS-specific CARM1 and CHK1 and KRAS-specific PIP4K2C and IPO7. Comparing the interactomes of WT and constitutively active G12D mutant of RAS isoforms, we identified several potential previously unknown effector proteins of RAS, one of which was recently reported while this article was in preparation, RADIL. These interacting proteins play important roles as knockdown or pharmacological inhibition leads to potent inhibition of cancer cells. The HRAS-specific interacting protein CARM1 plays a role in HRAS-induced senescence, with CARM1 knockdown or inhibition selectively increasing senescence in HRAS-transformed cells but not in KRAS4B-transformed cells. By revealing new isoform-specific and nucleotide-dependent RAS interactors, the study here provides insights to help understand the overlapping functions of the RAS isoforms.

Oxygen level regulates N-terminal translation elongation of selected proteins through deoxyhypusine hydroxylation.

Hypusine is a post-translational modification on eukaryotic translation initiation factor 5A (eIF5A). The last step of hypusine biosynthesis, deoxyhypusine hydroxylation, is an oxygen-dependent reaction. Here we show that deletion of the deoxyhypusine hydroxylase Lia1 compromises yeast respiration through translation downregulation of selected proteins in the respiration pathway. The translation suppression, because of the lack of deoxyhypusine hydroxylation, mainly affects translation of the N termini of the proteins, independent of the presence of proline residues but likely dependent on the interaction between the N-terminal nascent peptide and the ribosomal peptide exit tunnel. Proteomics and biochemical studies reveal that Lia1 deletion decreases N-terminal translation of proteins involved in mitochondrial respiration, oxidative stress response, and protein folding. Our work uncovers functions of the hypusine modification by considering the substrate requirement of the post-translational modification, highlights the unique challenges of translating the N termini of proteins, and reveals an oxygen-sensing mechanism in eukaryotic cells.

The cost impact of disease progression to metastatic castration-sensitive prostate cancer.

BACKGROUND: Metastatic prostate cancer (PC) is associated with declining survival rates and increased health care expenditure. However, there are few studies quantifying these increased costs. OBJECTIVE: To estimate overall health care resource utilization and costs associated with progression to metastatic disease in Medicare or commercially insured patients with nonmetastatic castration-sensitive PC (nmCSPC) or previously undiagnosed PC. METHODS: In this retrospective, observational cohort study, we used data from the IBM MarketScan Commercial and MarketScan Medicare Supplemental Databases. Included patients were aged 18 years or older, had 2 or more health care claims associated with a diagnosis of PC, and had a diagnosis of metastatic disease (index date) between January 1, 2014, and December 31, 2016. Patients with PC were identified at index as either progressing from a localized disease state (nmCSPC) without evidence of castration resistance (progressors) or de novo metastatic without a prior PC diagnosis. Unadjusted all-cause direct health care costs for the 2-year pre-index period and up to 2 years post-index were summarized. Metastasis-related incremental all-cause direct health care costs were estimated using regression modeling to adjust for patient baseline characteristics, follow-up duration, and possible selection bias. RESULTS: We identified 3,854 patients who met the criteria for CSPC at metastasis: 2,766 Medicare patients (mean age 78.8 ± 7.6 years) and 1,088 commercial patients (mean age 57.6 ± 4.3 years), with de novo patients accounting for 28.9% and 34.5% of the 2 analysis populations, respectively. Mean unadjusted total all-cause health care costs over the 24-month pre-index period among progressors were $52,661 (Medicare) and $43,111 (commercial); those among de novo patients were $39,756 (Medicare) and $22,090 (commercial). Mean unadjusted post-index costs for progressors were $100,331 (Medicare) and $127,374 (commercial) over a mean follow-up duration of 14.63 and 18.41 months, respectively, and $124,538 (Medicare) and $173,408 (commercial) over a mean follow-up duration of 14.14 and 17.29 months for patients with de novo disease. After multivariate adjustment, incremental cost increases due to metastasis in patients with CSPC pre-index were estimated at $104,051 (Medicare) and $93,334 (commercial), assuming data are available for 24 months post-index. Allowing for variation in the postindex observation period, estimates were $71,308 (Medicare) and $82,336 (commercial). Among de novo patients, cost increases due to metastasis were estimated at $180,932 (Medicare) and $215,397 (commercial), assuming all patients have data for 24 months postindex. Allowing for variable follow-up, estimates were $113,253 (Medicare) and $161,714 (commercial). CONCLUSIONS: Development of metastatic CSPC is associated with considerable costs over a 24-month follow-up period. Cost increases are greater for de novo patients than for those who progressed from localized disease. DISCLOSURES: Q.-D. Trinh received personal fees from Astellas, Bayer, and Janssen and grants from Intuitive Surgical. L. Passos Chaves, Q. Feng, J. Zhu, and T. Abbott are employees of Astellas Pharma Global Development, Inc. R. Sandin is an employee of, and holds stock in, Pfizer AB. This study was funded by Astellas Pharma Inc. (Northbrook, IL) and Pfizer Inc., the codevelopers of enzalutamide. Astellas Pharma Inc. was involved in the study design, data collection, analysis, interpretation of data, and decision to present these results.

Electrophysiology-Guided Genetic Characterisation Maximises Molecular Diagnosis in an Irish Paediatric Inherited Retinal Degeneration Population.

Inherited retinal degenerations (IRDs) account for over one third of the underlying causes of blindness in the paediatric population. Patients with IRDs often experience long delays prior to reaching a definitive diagnosis. Children attending a tertiary care paediatric ophthalmology department with phenotypic (i.e., clinical and/or electrophysiologic) evidence suggestive of IRD were contacted for genetic testing during the SARS-CoV-2-19 pandemic using a "telegenetics" approach. Genetic testing approach was panel-based next generation sequencing (351 genes) via a commercial laboratory (Blueprint Genetics, Helsinki, Finland). Of 70 patient samples from 57 pedigrees undergoing genetic testing, a causative genetic variant(s) was detected for 60 patients (85.7%) from 47 (82.5%) pedigrees. Of the 60 genetically resolved IRD patients, 5% (n = 3) are eligible for approved therapies (RPE65) and 38.3% (n = 23) are eligible for clinical trial-based gene therapies including CEP290 (n = 2), CNGA3 (n = 3), CNGB3 (n = 6), RPGR (n = 5) and RS1 (n = 7). The early introduction of genetic testing in the diagnostic/care pathway for children with IRDs is critical for genetic counselling of these families prior to upcoming gene therapy trials. Herein, we describe the pathway used, the clinical and genetic findings, and the therapeutic implications of the first systematic coordinated round of genetic testing of a paediatric IRD cohort in Ireland.

Trends in characteristics and outcomes among US adults hospitalised with COVID-19 throughout 2020: an observational cohort study.

OBJECTIVES: To examine the temporal patterns of patient characteristics, treatments used and outcomes associated with COVID-19 in patients who were hospitalised for the disease between January and 15 November 2020. DESIGN: Observational cohort study. SETTING: COVID-19 subset of the Optum deidentified electronic health records, including more than 1.8 million patients from across the USA. PARTICIPANTS: There were 51 510 hospitalised patients who met the COVID-19 definition, with 37 617 in the laboratory positive cohort and 13 893 in the clinical cohort. PRIMARY AND SECONDARY OUTCOME MEASURES: Incident acute clinical outcomes, including in-hospital all-cause mortality. RESULTS: Respectively, 48% and 49% of the laboratory positive and clinical cohorts were women. The 50- 65 age group was the median age group for both cohorts. The use of antivirals and dexamethasone increased over time, fivefold and twofold, respectively, while the use of hydroxychloroquine declined by 98%. Among adult patients in the laboratory positive cohort, absolute age/sex standardised incidence proportion for in-hospital death changed by -0.036 per month (95% CI -0.042 to -0.031) from March to June 2020, but remained fairly flat from June to November, 2020 (0.001 (95% CI -0.001 to 0.003), 17.5% (660 deaths /3986 persons) in March and 10.2% (580/5137) in October); in the clinical cohort, the corresponding changes were -0.024 (95% CI -0.032 to -0.015) and 0.011 (95% CI 0.007 0.014), respectively (14.8% (175/1252) in March, 15.3% (189/1203) in October). Declines in the cumulative incidence of most acute clinical outcomes were observed in the laboratory positive cohort, but not for the clinical cohort. CONCLUSION: The incidence of adverse clinical outcomes remains high among COVID-19 patients with clinical diagnosis only. Patients with COVID-19 entering the hospital are at elevated risk of adverse outcomes.

C19orf12 ablation causes ferroptosis in mitochondrial membrane protein-associated with neurodegeneration.

Mitochondrial membrane protein-associated with neurodegeneration (MPAN) is a rare genetic disease characterized by aggressive neurodegeneration and massive iron accumulation in patients' brains. Genetics studies identified defects in C19orf12 locus being associated with MPAN which likely caused loss of function although underlying pathogenic mechanism(s) remain elusive. In the present study, we investigated C19orf12 knockout (KO) M17 neuronal cells and primary skin fibroblasts from MPAN patients with C19orf12 homozygous G58S or heterozygous C19orf12 p99fs*102 mutations as cellular models of MPAN. C19orf12 KO cells and MPAN fibroblast cells demonstrated mitochondrial fragmentation and dysfunction, iron overload and increased oxidative damage. Antioxidant NAC and iron chelator DFO rescued both oxidative stress and mitochondrial deficits. Moreover, C19orf12 KO cells and MPAN fibroblast cells were susceptible to erastin- or RSL3-induced ferroptosis which could be almost completely prevented by pretreatment of iron chelator DFO. Importantly, we also found mitochondrial fragmentation and increased ferroptosis related oxidative damage in neurons in the biopsied cortical tissues from an MPAN patient. Collectively, these results supported the notion that iron overload and ferroptosis likely play an important role in the pathogenesis of MPAN.

Usher syndrome type IV: clinically and molecularly confirmed by novel ARSG variants.

Usher syndrome (USH) is an autosomal recessively inherited disease characterized by sensorineural hearing loss (SNHL) and retinitis pigmentosa (RP) with or without vestibular dysfunction. It is highly heterogeneous both clinically and genetically. Recently, variants in the arylsulfatase G (ARSG) gene have been reported to underlie USH type IV. This distinct type of USH is characterized by late-onset RP with predominantly pericentral and macular changes, and late onset SNHL without vestibular dysfunction. In this study, we describe the USH type IV phenotype in three unrelated subjects. We identified three novel pathogenic variants, two novel likely pathogenic variants, and one previously described pathogenic variant in ARSG. Functional experiments indicated a loss of sulfatase activity of the mutant proteins. Our findings confirm that ARSG variants cause the newly defined USH type IV and support the proposed extension of the phenotypic USH classification.