Re-analysis and meta-analysis of summary statistics from gene-environment interaction studies.

MOTIVATION: statistics from genome-wide association studies enable many valuable downstream analyses that are more efficient than individual-level data analysis while also reducing privacy concerns. As growing sample sizes enable better-powered analysis of gene-environment interactions, there is a need for gene-environment interaction-specific methods that manipulate and use summary statistics. RESULTS: We introduce two tools to facilitate such analysis, with a focus on statistical models containing multiple gene-exposure and/or gene-covariate interaction terms. REGEM (RE-analysis of GEM summary statistics) uses summary statistics from a single, multi-exposure genome-wide interaction study to derive analogous sets of summary statistics with arbitrary sets of exposures and interaction covariate adjustments. METAGEM (META-analysis of GEM summary statistics) extends current fixed-effects meta-analysis models to incorporate multiple exposures from multiple studies. We demonstrate the value and efficiency of these tools by exploring alternative methods of accounting for ancestry-related population stratification in genome-wide interaction study in the UK Biobank as well as by conducting a multi-exposure genome-wide interaction study meta-analysis in cohorts from the diabetes-focused ProDiGY consortium. These programs help to maximize the value of summary statistics from diverse and complex gene-environment interaction studies. AVAILABILITY AND IMPLEMENTATION: REGEM and METAGEM are open-source projects freely available at https://github.com/large-scale-gxe-methods/REGEM and https://github.com/large-scale-gxe-methods/METAGEM.

Genetic dissection of the pluripotent proteome through multi-omics data integration.

Genetic background drives phenotypic variability in pluripotent stem cells (PSCs). Most studies to date have used transcript abundance as the primary molecular readout of cell state in PSCs. We performed a comprehensive proteogenomics analysis of 190 genetically diverse mouse embryonic stem cell (mESC) lines. The quantitative proteome is highly variable across lines, and we identified pluripotency-associated pathways that were differentially activated in the proteomics data that were not evident in transcriptome data from the same lines. Integration of protein abundance to transcript levels and chromatin accessibility revealed broad co-variation across molecular layers as well as shared and unique drivers of quantitative variation in pluripotency-associated pathways. Quantitative trait locus (QTL) mapping localized the drivers of these multi-omic signatures to genomic hotspots. This study reveals post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome and provides a regulatory map for mESCs that can provide a basis for future mechanistic studies.

Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut.

The molecular bases of how host genetic variation impacts the gut microbiome remain largely unknown. Here we used a genetically diverse mouse population and applied systems genetics strategies to identify interactions between host and microbe phenotypes including microbial functions, using faecal metagenomics, small intestinal transcripts and caecal lipids that influence microbe-host dynamics. Quantitative trait locus (QTL) mapping identified murine genomic regions associated with variations in bacterial taxa; bacterial functions including motility, sporulation and lipopolysaccharide production and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and caecal levels of ornithine lipids. Follow-up in vitro and in vivo studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that ornithine lipids have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits including Atf3, which encodes for a transcription factor that plays vital roles in modulating metabolism and immunity. Collectively, these results suggest that ornithine lipids are potentially important for A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.

Spatially Resolved Transcriptomes of Mammalian Kidneys Illustrate the Molecular Complexity and Interactions of Functional Nephron Segments.

Available transcriptomes of the mammalian kidney provide limited information on the spatial interplay between different functional nephron structures due to the required dissociation of tissue with traditional transcriptome-based methodologies. A deeper understanding of the complexity of functional nephron structures requires a non-dissociative transcriptomics approach, such as spatial transcriptomics sequencing (ST-seq). We hypothesize that the application of ST-seq in normal mammalian kidneys will give transcriptomic insights within and across species of physiology at the functional structure level and cellular communication at the cell level. Here, we applied ST-seq in six mice and four human kidneys that were histologically absent of any overt pathology. We defined the location of specific nephron structures in the captured ST-seq datasets using three lines of evidence: pathologist's annotation, marker gene expression, and integration with public single-cell and/or single-nucleus RNA-sequencing datasets. We compared the mouse and human cortical kidney regions. In the human ST-seq datasets, we further investigated the cellular communication within glomeruli and regions of proximal tubules-peritubular capillaries by screening for co-expression of ligand-receptor gene pairs. Gene expression signatures of distinct nephron structures and microvascular regions were spatially resolved within the mouse and human ST-seq datasets. We identified 7,370 differentially expressed genes (p adj < 0.05) distinguishing species, suggesting changes in energy production and metabolism in mouse cortical regions relative to human kidneys. Hundreds of potential ligand-receptor interactions were identified within glomeruli and regions of proximal tubules-peritubular capillaries, including known and novel interactions relevant to kidney physiology. Our application of ST-seq to normal human and murine kidneys confirms current knowledge and localization of transcripts within the kidney. Furthermore, the generated ST-seq datasets provide a valuable resource for the kidney community that can be used to inform future research into this complex organ.

GEM: scalable and flexible gene-environment interaction analysis in millions of samples.

MOTIVATION: Gene-environment interaction (GEI) studies are a general framework that can be used to identify genetic variants that modify the effects of environmental, physiological, lifestyle or treatment effects on complex traits. Moreover, accounting for GEIs can enhance our understanding of the genetic architecture of complex diseases and traits. However, commonly used statistical software programs for GEI studies are either not applicable to testing certain types of GEI hypotheses or have not been optimized for use in large samples. RESULTS: Here, we develop a new software program, GEM (Gene-Environment interaction analysis in Millions of samples), which supports the inclusion of multiple GEI terms, adjustment for GEI covariates and robust inference, while allowing multi-threading to reduce computation time. GEM can conduct GEI tests as well as joint tests of genetic main and interaction effects for both continuous and binary phenotypes. Through simulations, we demonstrate that GEM scales to millions of samples while addressing limitations of existing software programs. We additionally conduct a gene-sex interaction analysis on waist-hip ratio in 352 768 unrelated individuals from the UK Biobank, identifying 24 novel loci in the joint test that have not previously been reported in combined or sex-specific analyses. Our results demonstrate that GEM can facilitate the next generation of large-scale GEI studies and help advance our understanding of the genetic architecture of complex diseases and traits. AVAILABILITY AND IMPLEMENTATION: GEM is freely available as an open source project at https://github.com/large-scale-gxe-methods/GEM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Determinants of COVID-19 vaccine acceptance in a high infection-rate country: a cross-sectional study in Russia.

BACKGROUND: COVID-19 vaccine development is proceeding at an unprecedented pace. Once COVID-19 vaccines become widely available, it will be necessary to maximize public vaccine acceptance and coverage. OBJECTIVE: This research aimed to analyze the predictors of COVID-19 vaccine acceptance in Russia. METHODS: A cross-sectional online survey was conducted among Russian adults from September 26th to November 9th, 2020. Predictors of the intent to take up COVID-19 vaccination were explored using logistic regression. RESULTS: Out of 876 participants, 365 (41.7%) would be willing to receive the vaccine if it became available. Acceptance increased for a vaccine with verified safety and effectiveness (63.2%). Intention to receive the COVID-19 vaccine was relatively higher among males (aOR=2.37, 95% CI 1.41-4.00), people with lower monthly income (aOR=2.94, 95%CI 1.32-6.57), and with positive trust in the healthcare system (aOR=2.73, 95% CI 1.76-4.24). The Russian people were more likely to accept the COVID-19 vaccine if they believed that the vaccine reduces the risk of virus infection (aOR=8.80, 95%CI 5.21-14.87) or relieves the complications of the disease (aOR=10.46, 95%CI 6.09-17.96). Other barriers such as being unconcerned about side-effects (aOR=1.65, 95%CI 1.03-2.65) and the effectiveness and safety of the vaccination (aOR=2.55, 95%CI 1.60-4.08), also affected acceptance. CONCLUSIONS: The study showed the usefulness of the health belief model constructs in understanding the COVID-19 vaccination acceptance rate in the Russian population. This rate was influenced by sociodemographic and health-related characteristics, and health beliefs. These findings might help guide future efforts for policymakers and stakeholders to improve vaccination rates by enhancing trust in the healthcare system.

Determinants of COVID-19 vaccine acceptance in a high infection-rate country: a cross-sectional study in Russia

BACKGROUND: COVID-19 vaccine development is proceeding at an unprecedented pace. Once COVID-19 vaccines become widely available, it will be necessary to maximize public vaccine acceptance and coverage. OBJECTIVE: This research aimed to analyze the predictors of COVID-19 vaccine acceptance in Russia. METHODS: A cross-sectional online survey was conducted among Russian adults from September 26th to November 9th, 2020. Predictors of the intent to take up COVID-19 vaccination were explored using logistic regression. RESULTS: Out of 876 participants, 365 (41.7%) would be willing to receive the vaccine if it became available. Acceptance increased for a vaccine with verified safety and effectiveness (63.2%). Intention to receive the COVID-19 vaccine was relatively higher among males (aOR=2.37, 95% CI 1.41-4.00), people with lower monthly income (aOR=2.94, 95%CI 1.32-6.57), and with positive trust in the healthcare system (aOR=2.73, 95% CI 1.76-4.24). The Russian people were more likely to accept the COVID-19 vaccine if they believed that the vaccine reduces the risk of virus infection (aOR=8.80, 95%CI 5.21-14.87) or relieves the complications of the disease (aOR=10.46, 95%CI 6.09-17.96). Other barriers such as being unconcerned about side-effects (aOR=1.65, 95%CI 1.03-2.65) and the effectiveness and safety of the vaccination (aOR=2.55, 95%CI 1.60-4.08), also affected acceptance. CONCLUSIONS: The study showed the usefulness of the health belief model constructs in understanding the COVID-19 vaccination acceptance rate in the Russian population. This rate was influenced by sociodemographic and health-related characteristics, and health beliefs. These findings might help guide future efforts for policymakers and stakeholders to improve vaccination rates by enhancing trust in the healthcare system

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Regulation of protein abundance in genetically diverse mouse populations.

Genetically diverse mouse populations are powerful tools for characterizing the regulation of the proteome and its relationship to whole-organism phenotypes. We used mass spectrometry to profile and quantify the abundance of 6,798 proteins in liver tissue from mice of both sexes across 58 Collaborative Cross (CC) inbred strains. We previously collected liver proteomics data from the related Diversity Outbred (DO) mice and their founder strains. We show concordance across the proteomics datasets despite being generated from separate experiments, allowing comparative analysis. We map protein abundance quantitative trait loci (pQTLs), identifying 1,087 local and 285 distal in the CC mice and 1,706 local and 414 distal in the DO mice. We find that regulatory effects on individual proteins are conserved across the mouse populations, in particular for local genetic variation and sex differences. In comparison, proteins that form complexes are often co-regulated, displaying varying genetic architectures, and overall show lower heritability and map fewer pQTLs. We have made this resource publicly available to enable quantitative analyses of the regulation of the proteome.

Exploring the influence of meteorological conditions on the performance of a waste stabilization pond at high altitude with structural equation modeling.

Algal photosynthesis plays a key role in the removal mechanisms of waste stabilization ponds (WSPs), which is indicated in the variations of three parameters, dissolved oxygen, pH, and chlorophyll a. These variations can be considerably affected by extreme climatic conditions at high altitude. To investigate these effects, three sampling campaigns were conducted in a high-altitude WSP in Cuenca (Ecuador). From the collected data, the first application of structure equation modeling (SEM) on a pond system was fitted to analyze the influence of high-altitude characteristics on pond performance, especially on the three indicators. Noticeably, air temperature appeared as the highest influencing factors as low temperature at high altitude can greatly decrease the growth rate of microorganisms. Strong wind and large diurnal variations of temperature, 7-20 °C, enhanced flow efficiency by improving mixing inside the ponds. Intense solar radiation brought both advantages and disadvantages as it boosted oxygen level during the day but promoted algal overgrowth causing oxygen depletion during the night. From these findings, the authors proposed insightful recommendations for future design, monitoring, and operation of high-altitude WSPs. Moreover, we also recommended SEM to pond engineers as an effective tool for better simulation of such complex systems like WSPs.

Sequence-Based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen-Specific Antibodies.

We created a novel transgenic rat that expresses human antibodies comprising a diverse repertoire of heavy chains with a single common rearranged kappa light chain (IgKV3-15-JK1). This fixed light chain animal, called OmniFlic, presents a unique system for human therapeutic antibody discovery and a model to study heavy chain repertoire diversity in the context of a constant light chain. The purpose of this study was to analyze heavy chain variable gene usage, clonotype diversity, and to describe the sequence characteristics of antigen-specific monoclonal antibodies (mAbs) isolated from immunized OmniFlic animals. Using next-generation sequencing antibody repertoire analysis, we measured heavy chain variable gene usage and the diversity of clonotypes present in the lymph node germinal centers of 75 OmniFlic rats immunized with 9 different protein antigens. Furthermore, we expressed 2,560 unique heavy chain sequences sampled from a diverse set of clonotypes as fixed light chain antibody proteins and measured their binding to antigen by ELISA. Finally, we measured patterns and overall levels of somatic hypermutation in the full B-cell repertoire and in the 2,560 mAbs tested for binding. The results demonstrate that OmniFlic animals produce an abundance of antigen-specific antibodies with heavy chain clonotype diversity that is similar to what has been described with unrestricted light chain use in mammals. In addition, we show that sequence-based discovery is a highly effective and efficient way to identify a large number of diverse monoclonal antibodies to a protein target of interest.

Multispecific Antibody Development Platform Based on Human Heavy Chain Antibodies.

Heavy chain-only antibodies (HCAbs) do not associate with light chains and their VH regions are functional as single domains, forming the smallest active antibody fragment. These VH regions are ideal building blocks for a variety of antibody-based biologics because they tolerate fusion to other molecules and may also be attached in series to construct multispecific antibodies without the need for protein engineering to ensure proper heavy and light chain pairing. Production of human HCAbs has been impeded by the fact that natural human VH regions require light chain association and display poor biophysical characteristics when expressed in the absence of light chains. Here, we present an innovative platform for the rapid development of diverse sets of human HCAbs that have been selected in vivo. Our unique approach combines antibody repertoire analysis with immunization of transgenic rats, called UniRats, that produce chimeric HCAbs with fully human VH domains in response to an antigen challenge. UniRats express HCAbs from large transgenic loci representing the entire productive human heavy chain V(D)J repertoire, mount robust immune responses to a wide array of antigens, exhibit diverse V gene usage and generate large panels of stable, high affinity, antigen-specific molecules.

Influence of corneal curvature on central and paracentral pachymetry with optical coherence tomography.

PURPOSE: Optical coherence tomography (OCT) has been found to be valuable to measure the corneal thickness (CT). The purpose of this clinical study was to determine the influence of corneal curvature on central and paracentral pachymetry with slit lamp-adapted OCT using a linear scanning geometry. METHODS: In a prospective, comparative observational study, a total of 77 consecutive patients (77 eyes) participated. Central and paracentral (4 mm) CT with slit lamp-adapted OCT (Heidelberg Engineering, Heidelberg, Germany) and with ultrasound (US) pachymetry were performed. The corneal curvature was determined with manual keratometry, and the influence of the corneal curvature on CT with OCT was compared with curvature-independent US values. RESULTS: The overall mean central CT values were 533 +/- 53 microm (OCT) and 546 +/- 56 microm (US) and paracentrally 562 +/- 55 microm (OCT) and 569 +/- 55 microm (US). The mean central and paracentral differences (P < 0.001) between both methods were 12.7 and 6.4 microm, respectively. The mean corneal curvature was 7.79 +/- 0.30 mm corresponding to a mean corneal power of 43.39 +/- 1.69 diopters. In the central area, there was no influence on the OCT measurements (r = -0.01, P = 0.935), whereas there was a minimal influence (r = 0.131, P = 0.021) on paracentral pachymetry with OCT using a linear scanning module. In paracentral areas, the systematic difference between OCT and US decreased from 8.4 microm in flat corneas (P < 0.001) to 5.0 microm in steeper corneas (P = 0.06). CONCLUSIONS: Slit lamp-adapted OCT allowed noncontact central and paracentral CT measurements. Although there were significant differences between OCT and US measurements, the corneal curvature had only a minimal influence on paracentral pachymetry with OCT using a linear scanning geometry. For more peripheral measurements or in marked alterations of the corneal curvature, correction factors may be needed.

[Scanning electron microscopy findings in explanted posterior chamber lenses]. / Rasterelektronenmikroskopische Befunde explantierter Hinterkammerlinsen.

Five explanted posterior chamber lenses were examined under the scanning electron microscope to determine the changes. The intraocular time of the lenses was 1 week to 3 years. The polypropylene loops showed superficial cracks in all cases, but only in the curve and the insertion areas. The findings therefore indicated that the morphological changes are more likely caused by mechanical stress than by biological degradation alone.

[Tonography and fluorophotometry in the clinical study of aqueous humor dynamics]. / Tonographie und Fluorophotometrie zur klinischen Untersuchung der Kammerwasserdynamik.

We used Grant's tonography and fluorophotometry (the Jones and Maurice method) to study the aqueous humor dynamics in normal and glaucomatous eyes. The results of the two methods were compared. The mean facility and rate of aqueous flow in normal eyes were similar. In glaucomatous eyes the tonographic outflow facility (C-value) varied greatly, and the calculated rate of aqueous flow (F-value) also had a large standard deviation. To study the inflow rate, fluorophotometry is a more accurate method. Further calculation of uveoscleral flow and the "pseudofacility" from the tonographic F-value and fluorophotometric C-value was therefore of only limited accuracy.

[Long-term follow-up following posterior chamber lens implantation with defective or absent posterior chamber]. / Langzeitbeobachtungen nach HKL-Implantation mit defekter oder fehlender Hinterkapsel.

41 patients were follow up in whom a posterior chamber lens was implanted despite of ruptured posterior capsule. Follow-up period was 9 months to 5 years: 30 lenses were well centered, 7 were slightly decentrated, 2 were strongly decentrated. In 2 cases the lens was luxated into the vitreous. CME was observed in two cases and retinal detachment in 5 cases. In 6 selected patients without posterior capsule, a 2-loop PCL (Simcoe-type) was implanted by controlled suture-fixation into the ciliary sulcus. The inferior haptic was sutured directly in the 6 o'clock position while the superior haptic (12 o'clock) was fixed indirectly by an "iris flap" (made from the "iridectomy") which was turned posteriorly. Follow-up period of 1-2 years: no decentration, vitreous in the anterior chamber in 2 cases.

[Cyclocryotherapy in chronic glaucoma]. / Zyklokryotherapie beim chronischen Glaukom.

For the last 10 years, cyclocryotherapy has been performed on nearly 700 glaucomatous eyes using practically the same technique. The cyclocryotherapy was standardized: six applications in the lower half of the globe, 4 mm posterior to the limbus as measured from the center of the 2.5 mm diameter cryoprobe. Freezing lasted 60 s; the temperature of the cryoprobe in the air was -65 degrees C and about -55 degrees C during the application. The cryo-induced lesion was found macroscopically, as well as with the microscope, in the pars plana and both epithelial layers were destroyed. The ciliary processes were only slightly affected. Alterations were also seen in the posterior part of Schlemm's canal and in the trabecular meshwork. The trabecular meshwork showed wide intertrabecular spaces. The trabecular lamella were partially interrupted with destroyed cellular elements. Tonographic and fluorophotometric findings showed a transient reduction in the formation of the intraocular fluid in the early postoperative stage. During the same plan there was a considerable breakdown of the blood aqueous barrier. Clinically, one can see a reaction in the anterior chamber with or without fibrinoid exudation. In the late stage, the inflow of the intraocular fluid mostly reached the preoperative level, whereas the outflow improved significantly. Following cyclocryotherapy, a IOP reduction of about 40% was achieved. In 85% of the treated glaucomatous eyes, if was possible to bring the IOP under control. However, in half of these eyes medical therapy was also needed. Cyclocryotherapy represents an alternative to the filtering operation, and it is not necessary to enter the bulb with this procedure.

[Endophthalmitis and toxic lens syndrome. Differential diagnosis and therapy]. / Endophthalmitis und Toxic lens-Syndrom. Differentialdiagnose und Therapie.

Inflammatory reactions following cataract extraction and implantation of an intraocular lens are rare complications. In a group of 10,000 patients the incidence of toxic lens syndrome was 0.15%; infections were seen in 0.07% of the cases. Except for two patients with toxic lens syndrome associated with cystoid macular edema, all ultimately had good visual acuity. While toxic lens syndrome is seen in the first postoperative week or recurs at a later date and responds very well to corticosteroids, bacterial endophthalmitis usually develops on the first postoperative day, with fulminant progress. Mycotic infections occur after a longer interval and temporarily respond better to corticosteroids. The endophthalmitis should be treated early with a vitrectomy to eliminate micro-organisms and toxic agents, and to achieve a high intraocular level of antibiotics and antimycotics. From June 1982 to June 1987, thirteen patients with endophthalmitis after cataract extraction were vitrectomized. Navigating visual acuity was ultimately achieved in eight cases. Two patients developed a phthisis bulbi and one a recurrent mycosis. Thus, altogether, an inflammation-free eye with navigating visual acuity can be achieved in over 50% of cases.

[Capsular lesions in extracapsular cataract operation and implantation of posterior chamber lenses]. / Kapselläsion bei e.c. Kataraktoperation und Implantation von Hinterkammerlinsen.

The present paper reports follow-up findings up to five years postoperatively in 41 cases following capsular-zonular rupture with implantation of a posterior chamber lens after extracapsular cataract extraction. Capsular disruption occurred most frequently (in 32 cases) during cortical aspiration. The capsular defects were localized in the periphery in 18 cases and in the central area in ten. Dialysis of the zonular fibers was seen in 13 cases. The intraocular lens (IOL) was well centered in 30 eyes and slightly off-center in seven. Only two cases with decentered IOLS required surgical centering of the lenses. In two eyes dislocation of the IOL into the vitreous was observed. Cystoid macular edema developed in two cases. In five cases retinal detachment occurred.