Alternative splicing in the lung influences COVID-19 severity and respiratory diseases.

Hospital admission for COVID-19 remains common despite the successful development of vaccines and treatments. Thus, there is an ongoing need to identify targets for new COVID-19 therapies. Alternative splicing is an essential mechanism for generating functional diversity in protein isoforms and influences immune response to infection. However, the causal role of alternative splicing in COVID-19 severity and its potential therapeutic relevance is not fully understood. In this study, we evaluated the causal role of alternative splicing in COVID-19 severity and susceptibility using Mendelian randomization (MR). To do so, we performed two-sample MR to assess whether cis-sQTLs spanning 8,172 gene splicing in 5,295 genes were associated with COVID-19 outcomes in the COVID-19 Host Genetics Initiative, including up to 158,840 COVID-19 cases and 2,782,977 population controls. We identified that alternative splicing in lungs, rather than total RNA expression of OAS1, ATP11A, DPP9 and NPNT, was associated with COVID-19 severity. MUC1 splicing was associated with COVID-19 susceptibility. Further colocalization analyses supported a shared genetic mechanism between COVID-19 severity with idiopathic pulmonary fibrosis at ATP11A and DPP9 loci, and with chronic obstructive lung diseases at NPNT. We lastly showed that ATP11A, DPP9, NPNT, and MUC1 were highly expressed in lung alveolar epithelial cells, both in COVID-19 uninfected and infected samples. Taken together, these findings clarify the importance of alternative splicing of proteins in the lung for COVID-19 and other respiratory diseases, providing isoform-based targets for drug discovery.

Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity

Obesity is a major risk factor for COVID-19 severity; however, the underlying mechanism is not fully understood. Considering that obesity influences the human plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity. We first screened 4,907 plasma proteins to identify proteins influenced by body mass index (BMI) using Mendelian randomization (MR). This yielded 1,216 proteins, whose effects on COVID-19 severity were assessed, again using MR. This two-step approach identified nephronectin (NPNT), for which a one standard deviation increase was associated with severe COVID-19 (odds ratio = 1.71, 95% CI: 1.45-2.02, P = 1.63 x 10-10). Colocalization analyses indicated that an NPNT splice isoform drove this effect. Overall, NPNT mediates 3.7% of the total effect of BMI on severe COVID-19. Finally, we found that decreasing body fat mass and increasing fat-free mass can lower NPNT levels and thus may improve COVID-19 outcomes. These findings provide actionable insights into how obesity influences COVID-19 severity.

Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection

Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Using measurements of [~]4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury. Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.

Circulating proteins to predict adverse COVID-19 outcomes

Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4,701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict adverse COVID-19 outcomes in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4,701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different adverse COVID-19 outcomes were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of adverse COVID-19 outcomes. Further research is needed to understand how to incorporate protein measurement into clinical care.

Integrated immunovirological profiling validates plasma SARS-CoV-2 RNA as an early predictor of COVID-19 mortality

Despite advances in COVID-19 management, it is unclear how to recognize patients who evolve towards death. This would allow for better risk stratification and targeting for early interventions. However, the explosive increase in correlates of COVID-19 severity complicates biomarker prioritisation. To identify early biological predictors of mortality, we performed an immunovirological assessment (SARS-CoV-2 viral RNA, cytokines and tissue injury markers, antibody responses) on plasma samples collected from 144 hospitalised COVID-19 patients 11 days after symptom onset and used to test models predicting mortality within 60 days of symptom onset. In the discovery cohort (n=61, 13 fatalities), high SARS-CoV-2 vRNA, low RBD-specific IgG levels, low SARS-CoV-2-specific antibody-dependent cellular cytotoxicity, and elevated levels of several cytokines and lung injury markers were strongly associated with increased mortality in the entire cohort and the subgroup on mechanical ventilation. Model selection revealed that a three-variable model of vRNA, age and sex was very robust at identifying patients who will succumb to COVID-19 (AUC=0.86, adjusted HR for log-transformed vRNA=3.5; 95% CI: 2.0-6.0). This model remained robust in an independent validation cohort (n=83, AUC=0.85). Quantification of plasma SARS-CoV-2 RNA can help understand the heterogeneity of disease trajectories and identify patients who may benefit from new therapies.

Understanding the development status of ophthalmic artificial intelligence, holding the challenges and opportunities / 中华眼底病杂志

With the rapid development of artificial intelligence (AI), especially deep learning, AI research in the field of ophthalmology has presented a trend of diversification in disease types, generalization in scenarios and deepening in researches. The AI algorithm has showed a good performance in the studies of diabetic retinopathy, age-related macular degeneration, glaucoma and other ocular diseases, yielding up the great potential of ophthalmic AI. However, most studies are still in their infancy, and the application of ophthalmic AI still faces many challenges such as lack of interpretability for results, deficiency of data standardization, and insufficiency of clinical applicability. At the same time, it should also be noted that the development of multi-modal imaging, the innovation of digital technologies (such as 5G and the Internet of Things) and telemedicine, and the new discovery that retina status can reflect systemic diseases have brought new opportunities for the development of ophthalmic AI. Learn the current status of AI research in the field of ophthalmology, grasp the new challenges and opportunities in its development process, successfully realizing the transformation of ophthalmic AI from research to practical application.

Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes 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 1,934 COVID-19 cases (713 with severe and 1,221 with mild disease) and 15,251 ancestry-matched population controls across four independent COVID-19 biobanks. We then tested if rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only one rare pLOF mutation across these genes amongst 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 find no evidence of association of rare loss-of-function variants in the proposed 13 candidate genes with severe COVID-19 outcomes.

Circulating Proteins Influencing COVID-19 Susceptibility and Severity: a Mendelian Randomization Study

Proteins detectable in peripheral blood may influence COVID-19 susceptibility or severity. However, understanding which circulating proteins are etiologically involved is difficult because their levels may be influenced by COVID-19 itself and are also subject to confounding factors. To identify circulating proteins influencing COVID-19 susceptibility and severity we undertook a large-scale two-sample Mendelian randomization (MR) study, since this study design can rapidly scan hundreds of circulating proteins and reduces bias due to reverse causation and confounding. We identified genetic determinants of 931 circulating proteins in 28,461 SARS-CoV-2 uninfected individuals, retaining only single nucleotide polymorphism near the gene encoding the circulating protein. We found that a standard deviation increase in OAS1 levels was associated with reduced COVID-19 death or ventilation (N = 4,336 cases / 623,902 controls; OR = 0.54, P = 7x10-8), COVID-19 hospitalization (N = 6,406 / 902,088; OR = 0.61, P = 8x10-8) and COVID-19 susceptibility (N = 14,134 / 1,284,876; OR = 0.78, P = 8x10-6). Results were consistent in multiple sensitivity analyses. We then measured OAS1 levels in 504 patients with repeated plasma samples (N=1039) with different COVID-19 outcomes and found that increased OAS1 levels in a non-infectious state were associated with protection against very severe COVID-19, hospitalization and susceptibility. Further analyses suggested that a Neanderthal isoform of OAS1 affords this protection. Thus, evidence from MR and a case-control study supported a protective role for OAS1 in COVID-19 outcomes. Available medicines, such as phosphodiesterase-12 inhibitors, increase OAS1 and could be explored for their effect on COVID-19 susceptibility and severity.

Vitamin D and Covid-19 Susceptibility and Severity: a Mendelian Randomization Study

BackgroundIncreased vitamin D levels, as reflected by 25OHD measurements, have been proposed to protect against COVID-19 disease based on in-vitro, observational, and ecological studies. However, vitamin D levels are associated with many confounding variables and thus associations described to date may not be causal. Vitamin D Mendelian randomization (MR) studies have provided results that are concordant with large-scale vitamin D randomized trials. Here, we used two-sample MR to assess evidence supporting a causal effect of circulating 25OHD levels on COVID-19 susceptibility and severity. Methods and findingsGenetic variants strongly associated with 25OHD levels in a genome-wide association study (GWAS) of 443,734 participants of European ancestry (including 401,460 from the UK Biobank) were used as instrumental variables. GWASs of COVID-19 susceptibility, hospitalization, and severe disease from the COVID-19 Host Genetics Initiative were used as outcome GWASs. These included up to 14,134 individuals with COVID-19, and 1,284,876 without COVID-19, from 11 countries. SARS-CoV-2 positivity was determined by laboratory testing or medical chart review. Population controls without COVID-19 were also included in the control groups for all outcomes, including hospitalization and severe disease. Analyses were restricted to individuals of European descent when possible. Using inverse-weighted MR, genetically increased 25OHD levels by one standard deviation on the logarithmic scale had no clear association with COVID-19 susceptibility (OR = 0.97; 95% CI: 0.95, 1.10; P=0.61), hospitalization (OR = 1.11; 95% CI: 0.91, 1.35; P=0.30), and severe disease (OR = 0.93; 95% CI: 0.73, 1.17; P=0.53). We used an additional 6 meta-analytic methods, as well as sensitivity analyses after removal of variants at risk of horizontal pleiotropy and obtained similar results. These results may be limited by weak instrument bias in some analyses. Further, our results do not apply to individuals with vitamin D deficiency. ConclusionIn this two-sample MR study, we did not observe evidence to support an association between 25OHD levels and COVID-19 susceptibility, severity, or hospitalization. Hence, vitamin D supplementation as a mean of protecting against worsened COVID-19 outcomes is not supported by genetic evidence. Other therapeutic or preventative avenues should be given higher priority for COVID-19 randomized controlled trials. Author SummaryO_LIWhy was this study done? - Vitamin D levels have been associated with COVID-19 outcomes in multiple observational studies, though confounders are likely to bias these associations. - By using genetic instruments which limit such confounding, Mendelian randomization studies have consistently obtained results concordant with vitamin D supplementation randomized trials. This provides rationale to undertake vitamin D Mendelian randomization studies for COVID-19 outcomes. C_LIO_LIWhat did the researchers do and find? - We used the genetic variants obtained from the largest consortium of COVID-19 cases and controls, and the largest study on genetic determinants of vitamin D levels. We used Mendelian randomization to estimate the effect of increased vitamin D on COVID-19 outcomes, while limiting confounding. - In multiple analyses, our results consistently showed no evidence for an association between genetically predicted vitamin D levels and COVID-19 susceptibility, hospitalization, or severe disease. C_LIO_LIWhat do these findings mean? - Vitamin D is a highly confounded variable, and traditional observational studies are at high risk of biased estimates. - We did not find evidence that vitamin D supplementation would improve COVID-19 outcomes. - Given Mendelian randomizations past track-record of anticipating the results of vitamin D randomized controlled trials, other therapeutic and preventative avenues should be prioritized for COVID-19 trials. C_LI

Clinical analysis of 66 patients of retinoblastoma / 中华眼底病杂志

Objective To observe the clinical characteristics ofretinoblastoma (RB) in Southwest China.Methods A retrospective clinical study.From January 2010 to December 2017,66 RB patients diagnosed in Ophthalmology Department of West China Hospital of Sichuan University were included in the study.All the patients underwent ocular B-ultrasound,orbital CT or MRI examination.Ten patients underwent RetCam examination at the same time.Twenty-nine patients were diagnosed by histopathological examination,and 37 patients were diagnosed by clinical symptoms and imaging examination.According to whether the tumor invaded the orbit and optic nerve,it could be divided into extraocular stage and intraocular stage.Intraocular tumors were divided into A-E stages according to the international intraocular RB classification.Treatments were performed according to different stages.The general information,age at diagnosis,course of diseases (the time between onset symptoms and diagnosis),causes of visiting a doctor,classification,treatment methods and eyeball preservation rate were retrospectively analyzed.Results Patients all came from Southwest China (56 patients from Sichuan Province,2 patients from Yunnan Province,2 patients from Guizhou Province,and 6 patients from Tibet).The permanent residence were identified in 43 patients,including 27 patients (62.8％) from rural areas.There were 38 males (57.6％);50 unilateral tumors (75.8％) and 16 bilateral tumors (24.2％);51 firstvisiting patients (77.3％) and 15 re-visiting patients (22.7％).The average diagnostic age of first-visiting patients was 20.9 ± 14.4 months,with 23.2 ± 14.7 and 11.2 ± 7.6 months for unilateral and bilateral tumors,respectively.There were 41 patients had definite course and causes,of whom the average course was 90.6± 115.2 days.The most common cause was leucocoria in 32 patients (62.7％),followed by redness and swelling in 4 patients (9.8％),and other causes in 5 patients (12.2％).Among the 15 re-visiting patients,the average diagnostic age was 63.6± 46.8 months,the average course was 32.8 ± 45.5 months.Recurrence was occurred in 5 patients (33.3％),leucocoria in 4 patients (26.7％),postoperative complication in 3 patients (20.0％),protrusion in 2 patients (13.3％) and redness in 1 (6.7％) patient,respectively.Fifty out of 82 eyes were admitted to hospital,including 37 eyes of first-visiting patients and 13 eyes of re-visiting patients.Among 37 first-visiting eyes,there were 5 eyes (13.5％) in stage A-C,26 eyes (70.3％) in stage D-E,6 eyes (16.2％) in extraocular stage.Five eyes in stage A-C were treated with laser photocoagulation and (or) cryotherapy combined with systemic chemotherapy.Four eyes in stage D were treated with intraocular arterial chemotherapy.Nineteen eyes (51.3％) were performed with enucleation,2 eyes (5.4％) with evisceration and 7 eyes (18.9％) abandoned treatment.Among 13 re-visiting eyes,6 eyes (46.2％,with 5 eyes of recurrence) had been enucleated before,4 eyes (30.8％) were in extraocular stage and 3 eyes (23.1％) in stage D-E.Five eyes (38.5％) were treated with evisceration,4 eyes (30.8％) with enucleation,1 eye with oculoplastic surgery and 3 eyes (23.1％) abandoned treatment.The rate of eye preservation was 18.0％,29.0％ for intraocular stage and 0％ for extraocular stage,respectively.Conclusion RB patients in Southwest China have a longer course between onset symptoms and diagnosis,more advanced classification and lower rate of eye preservation.

Contrast observation of optical coherence tomography angiography between neovascular age-related macular degeneration and myopic choroidal neovascularization before and after intravitreal anti-vascular endothelial growth factor treatment / 中华眼底病杂志

Objective To compare the features of OCT angiography (OCTA) between neovascular agerelated macular degeneration (nAMD) and myopic ehoroidal neovascularization (mCNV) patients before and after intravitreal anti-VEGF treatment.Methods A prospective cohort study.Twenty-nine patients (37 eyes) with nAMD (19 males and 10 females,aged 68.20±8.76) and 31 patients (34 eyes) with mCNV (9 males and 22 females,aged 43.10± 11.80,with the mean diopter of-9.71 ± 1.20 D) from Department of Ophthalmology,West China Hospital of Sichuan University during May and December 2017 were included in this study.Ranibizumab or Conbercept (0.5 mg/0.05 ml) was intravitreally injected in all eyes.The patients were follow-up for 3-6 months.The OCTA was conducted before treatment and 1 day,1 week,1 month and 3-6 months after treatment.In order to ensure that the scanning position was the same,the tracking mode was adopted for each scanning.According to the OCTA images,the lesion area,parafoveal superficial vessel density and perfusion area were measured and analyzed contrastively between nAMD and mCNV patients.Results The mean lesion area before and 1 month after treatment in nAMD patients were 0.38± 1.87 mum2 and 0.06±0.12 mm2,while in mCNV patients,those were 0.26± 1.06 mm2 and 0.03 ± 0.05 mm2,respectively.There were statistically significant differences (Z=4.181,4.475;P＜0.001) in CNV lesion area before and 1 month after treatment between nAMD and mCNV patients.Compared with those before treatment,the absolute change (Z=1.853,P=0.064) and the percentage changes (t=2.685,P=0.010) of CNV lesion area l month after treatment in nAMD and mCNV patients show a statistical meaning.There were significantly decreases in both parafoveal superficial vessel density (F=8.997,P=0.003) and perfusion area (F=7.887,P=0.015) 3 months after treatment in nAMD patients,while decreases in parafoveal superficial vessel density (F=11.142,P=0.004) and perfusion area (F=7.662,P=0.013) could be detected 1 day after treatment in mCNV patients,before rising 1 month after treatment.Conclusions There are significantly differences in lesion area before and after the treatment of intravitreal anti-VEGF between nAMD and mCNV patients by OCTA examination.Moreover,the changes of both parafoveal superficial vessel density and perfusion area after anti-VEGF treatment are statistically different in two groups.

Clinical diagnosis and treatment for age-related macular degeneration: a brief analysis of the guidelines / 中国医师杂志

Age-related macular degeneration (AMD) is a common cause of blindness among people over 65 in developed countries.With the rapidity of population aging process,the prevalence of AMD will be further increased.The application of anti-vascular endothelial factor growth medicine in ophthalmology has made great progress in the therapeutic effect and prognosis of wet AMD.In this context,many countries and regions have successively formulated guidelines for the AMD clinical diagnosis and treatment,especially the United States,Europe and Australia.Through the analysis of AMD clinical guidelines of American Academy of Ophthalmology (AAO) in 2015,and by comparing it with AMD analysis and treatment guidelines of European Society of Retina Specialists (EURETINA) in 2014,this paper provides an accurate,effective and comprehensive diagnosis strategy and lays a foundation for providing AMD patients with quality diagnosis and treatment plans.