Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity.

Plasma RNAemia, delayed antibody responses and inflammation predict COVID-19 outcomes, but the mechanisms underlying these immunovirological patterns are poorly understood. We profile 782 longitudinal plasma samples from 318 hospitalized patients with COVID-19. Integrated analysis using k-means reveals four patient clusters in a discovery cohort: mechanically ventilated critically-ill cases are subdivided into good prognosis and high-fatality clusters (reproduced in a validation cohort), while non-critical survivors segregate into high and low early antibody responders. Only the high-fatality cluster is enriched for transcriptomic signatures associated with COVID-19 severity, and each cluster has distinct RBD-specific antibody elicitation kinetics. Both critical and non-critical clusters with delayed antibody responses exhibit sustained IFN signatures, which negatively correlate with contemporaneous RBD-specific IgG levels and absolute SARS-CoV-2-specific B and CD4+ T cell frequencies. These data suggest that the "Interferon paradox" previously described in murine LCMV models is operative in COVID-19, with excessive IFN signaling delaying development of adaptive virus-specific immunity.

The level of protein in the maternal murine diet modulates the facial appearance of the offspring via mTORC1 signaling.

The development of craniofacial skeletal structures is fascinatingly complex and elucidation of the underlying mechanisms will not only provide novel scientific insights, but also help develop more effective clinical approaches to the treatment and/or prevention of the numerous congenital craniofacial malformations. To this end, we performed a genome-wide analysis of RNA transcription from non-coding regulatory elements by CAGE-sequencing of the facial mesenchyme of human embryos and cross-checked the active enhancers thus identified against genes, identified by GWAS for the normal range human facial appearance. Among the identified active cis-enhancers, several belonged to the components of the PI3/AKT/mTORC1/autophagy pathway. To assess the functional role of this pathway, we manipulated it both genetically and pharmacologically in mice and zebrafish. These experiments revealed that mTORC1 signaling modulates craniofacial shaping at the stage of skeletal mesenchymal condensations, with subsequent fine-tuning during clonal intercalation. This ability of mTORC1 pathway to modulate facial shaping, along with its evolutionary conservation and ability to sense external stimuli, in particular dietary amino acids, indicate that the mTORC1 pathway may play a role in facial phenotypic plasticity. Indeed, the level of protein in the diet of pregnant female mice influenced the activity of mTORC1 in fetal craniofacial structures and altered the size of skeletogenic clones, thus exerting an impact on the local geometry and craniofacial shaping. Overall, our findings indicate that the mTORC1 signaling pathway is involved in the effect of environmental conditions on the shaping of craniofacial structures.

The genetic changes that shaped Neandertals, Denisovans, and modern humans.

Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.

A genome-wide association study for survival from a multi-centre European study identified variants associated with COVID-19 risk of death.

The clinical manifestations of SARS-CoV-2 infection vary widely among patients, from asymptomatic to life-threatening. Host genetics is one of the factors that contributes to this variability as previously reported by the COVID-19 Host Genetics Initiative (HGI), which identified sixteen loci associated with COVID-19 severity. Herein, we investigated the genetic determinants of COVID-19 mortality, by performing a case-only genome-wide survival analysis, 60 days after infection, of 3904 COVID-19 patients from the GEN-COVID and other European series (EGAS00001005304 study of the COVID-19 HGI). Using imputed genotype data, we carried out a survival analysis using the Cox model adjusted for age, age2, sex, series, time of infection, and the first ten principal components. We observed a genome-wide significant (P-value < 5.0 × 10-8) association of the rs117011822 variant, on chromosome 11, of rs7208524 on chromosome 17, approaching the genome-wide threshold (P-value = 5.19 × 10-8). A total of 113 variants were associated with survival at P-value < 1.0 × 10-5 and most of them regulated the expression of genes involved in immune response (e.g., CD300 and KLR genes), or in lung repair and function (e.g., FGF19 and CDH13). Overall, our results suggest that germline variants may modulate COVID-19 risk of death, possibly through the regulation of gene expression in immune response and lung function pathways.

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago.

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.

In Vitro Comparison of Ulotaront (SEP-363856) and Ralmitaront (RO6889450): Two TAAR1 Agonist Candidate Antipsychotics.

BACKGROUND: Trace amine-associated receptor-1 (TAAR1) agonists have been proposed as potential antipsychotics, with ulotaront and ralmitaront having reached clinical trials. While ulotaront demonstrated efficacy in a recent Phase II trial, a corresponding study studies of ralmitaront failed to show efficacy as a monotherapy or as an adjunct to atypical antipsychotics. In addition to TAAR1 agonism, ulotaront is a partial agonist at the serotonin 1A receptor (5-HT1AR). However, little is known about ralmitaront. METHODS: We compared ulotaront and ralmitaront at TAAR1, 5-HT1AR, and dopamine D2 using luciferase complementation-based G protein recruitment, cAMP accumulation, and G protein-coupled inward rectifier potassium channel activation assays. RESULTS: Ralmitaront showed lower efficacy at TAAR1 in G protein recruitment, cAMP accumulation, and GIRK activation assays. Moreover, ralmitaront lacked detectable activity at 5-HT1AR and dopamine D2. CONCLUSIONS: Compared with ulotaront, ralmitaront shows lower efficacy and slower kinetics at TAAR1 and lacks efficacy at 5-HT1AR. These data may be relevant to understanding differences in clinical profiles of these 2 compounds.

Major Genetic Risk Factors for Dupuytren's Disease Are Inherited From Neandertals.

Dupuytren's disease is characterized by fingers becoming permanently bent in a flexed position. Whereas people of African ancestry are rarely afflicted by Dupuytren's disease, up to ∼30% of men over 60 years suffer from this condition in northern Europe. Here, we meta-analyze 3 biobanks comprising 7,871 cases and 645,880 controls and find 61 genome-wide significant variants associated with Dupuytren's disease. We show that 3 of the 61 loci harbor alleles of Neandertal origin, including the second and third most strongly associated ones (P = 6.4 × 10-132 and P = 9.2 × 10-69, respectively). For the most strongly associated Neandertal variant, we identify EPDR1 as the causal gene. Dupuytren's disease is an example of how admixture with Neandertals has shaped regional differences in disease prevalence.

A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology.

In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.

Functional dissection of two amino acid substitutions unique to the human FOXP2 protein.

The transcription factor forkhead box P2 (FOXP2) is involved in the development of language and speech in humans. Two amino acid substitutions (T303N, N325S) occurred in the human FOXP2 after the divergence from the chimpanzee lineage. It has previously been shown that when they are introduced into the FOXP2 protein of mice they alter striatal synaptic plasticity by increasing long-term depression in medium spiny neurons. Here we introduce each of these amino acid substitutions individually into mice and analyze their effects in the striatum. We find that long-term depression in medium spiny neurons is increased in mice carrying only the T303N substitution to the same extent as in mice carrying both amino acid substitutions. In contrast, the N325S substitution has no discernable effects.

Response to Comment on "Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals".

Herai et al. discuss the known fact that a low percentage of modern humans who lack any overt phenotypes carry the ancestral TKTL1 allele. Our paper demonstrates that the amino acid substitution in TKTL1 increases neural progenitor cells and neurogenesis in the developing brain. It is another question if, and to what extent, this has consequences for the adult brain.

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 Coronavirus disease (COVID-19) severity; however, the mechanisms underlying this relationship are not fully understood. As obesity influences the plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity in humans. Here, we screened 4,907 plasma proteins to identify proteins influenced by body mass index using Mendelian randomization. This yielded 1,216 proteins, whose effect on COVID-19 severity was assessed, again using Mendelian randomization. We found that an s.d. increase in nephronectin (NPNT) was associated with increased odds of critically ill COVID-19 (OR = 1.71, P = 1.63 × 10-10). The effect was driven by an NPNT splice isoform. Mediation analyses supported NPNT as a mediator. In single-cell RNA-sequencing, NPNT was expressed in alveolar cells and fibroblasts of the lung in individuals who died of COVID-19. Finally, decreasing body fat mass and increasing fat-free mass were found to lower NPNT levels. These findings provide actionable insights into how obesity influences COVID-19 severity.

How students discern anatomical structures using digital three-dimensional visualizations in anatomy education.

Learning anatomy holds specific challenges, like the appreciation of three-dimensional relationships between anatomical structures. So far, there is limited knowledge about how students construct their understanding of topographic anatomy. By understanding the processes by which students learn anatomical structures in 3D, educators will be better equipped to offer support and create successful learning situations. Using video analysis, this study investigates how students discern anatomical structures. Sixteen students at different levels of education and from different study programs were recorded audiovisually while exploring 3D digital images using a computerized visualization table. Eleven hours of recorded material were analyzed using interaction analysis and phenomenography. Seven categories were identified during data analysis, describing the qualitatively different patterns of actions that students use to make sense of anatomy: decoding the image; positioning the body in space; purposeful seeking, using knowledge and experience; making use of and creating variation; aimless exploration, and arriving at moments of understanding. The results suggest that anatomy instruction should be organized to let the students decide how and at what pace they examine visualized images. Particularly, the discovery process of decoding and positioning the body in space supports a deep learning approach for learning anatomy using visualizations. The students' activities should be facilitated and not directed.

Prevalence and characteristics of unipolar mania in a low-income country setting: population-based data from the Butajira cohort, rural Ethiopia.

PURPOSE: Previous research suggests unipolar mania, i.e., bipolar disorder without depression, to be more common in low-income countries. However, longitudinal population-based studies on unipolar mania from low-income countries are lacking. This study therefore examined unipolar mania, in Butajira, Ethiopia, and associations with possible determinants. METHODS: Key informants and 68,378 screenings with the Composite International Diagnostic Interviews (CIDI 2.1) identified suspected cases of bipolar disorder. Diagnosis was confirmed using the Schedules for Clinical Assessment in Neuropsychiatry (SCAN 2.1) (n = 2,285). 315 participants with bipolar disorder were recruited and followed up for an average of 2.5 years. Unipolar mania was defined when illness episodes consisted of at least two manic relapses. 240 cases had sufficient data to ascertain course of disorder. RESULTS: 41.7% (100 of 240 cases) of participants had unipolar mania. Unipolar mania was associated with less suicidal ideation (0% vs. 26.4%, p < 0.001), less suicidal thoughts (occasionally/often: 1%/3% vs. 19.6%/21%, p < 0.001), and less history of suicide attempt (2% vs. 11.6%, p = 0.01). The participants with unipolar mania tended to have better social functioning (OR = 2.05, p = 0.07) and less alcohol use (20.8% vs. 31.4%, p = 0.07). The study was partly based on retrospective data liable to recall bias. Some cases defined as unipolar mania in our study may later develop depression. CONCLUSION: Previous cross-sectional studies finding high proportions of unipolar mania in low-income countries appear supported. Unipolar mania trended towards better social functioning and was associated with lower suicidality. Future unipolar mania specifications could inform treatment and prognostic estimates of bipolar disorder.

Transfer of anatomy during surgical clerkships: an exploratory study of a student-staff partnership.

Objectives: This qualitative study aims to explore how fourth-year medical students on the surgery course perceived a clinical anatomy workshop organised by near-peer student teachers in partnership with faculty. Methods: Forty-seven medical students participated in a workshop on clinical anatomy in the dissection laboratory. A voluntary response sampling method was used. The students' perceptions of the workshop were explored through a thematic content analysis of transcribed, semi-structured group interviews and written comments. Results: A majority of the students had not revisited the dissection laboratory since their second year, and all students described the workshop as a unique opportunity to vertically integrate anatomical knowledge. Four main themes were identified as most valuable for the students' learning experience, namely that the workshop 1) was taught by knowledgeable and friendly near-peer tutors (NPTs), 2) consisted of highly relevant anatomical content, 3) offered a hands-on experience of cadavers in the dissection laboratory, and 4) was taught in a focused session in the middle of the surgery course. Conclusions:  This study shows how hands-on workshops in clinical anatomy, developed in student-staff partnerships and taught by NPTs, can enable senior medical students to recall and vertically integrate anatomical knowledge during surgical clerkships. The results have implications for curriculum design, giving voice to senior students' wishes for spaced repetition and vertical integration of pre-clinical anatomy knowledge during their clinical training. Moreover, this study may inspire other students and faculty to develop similar near-peer teaching activities through student-staff partnerships.

ELF5 is a potential respiratory epithelial cell-specific risk gene for severe COVID-19.

Despite two years of intense global research activity, host genetic factors that predispose to a poorer prognosis of COVID-19 infection remain poorly understood. Here, we prioritise eight robust (e.g., ELF5) or suggestive but unreported (e.g., RAB2A) candidate protein mediators of COVID-19 outcomes by integrating results from the COVID-19 Host Genetics Initiative with population-based plasma proteomics using statistical colocalisation. The transcription factor ELF5 (ELF5) shows robust and directionally consistent associations across different outcome definitions, including a >4-fold higher risk (odds ratio: 4.88; 95%-CI: 2.47-9.63; p-value < 5.0 × 10-6) for severe COVID-19 per 1 s.d. higher genetically predicted plasma ELF5. We show that ELF5 is specifically expressed in epithelial cells of the respiratory system, such as secretory and alveolar type 2 cells, using single-cell RNA sequencing and immunohistochemistry. These cells are also likely targets of SARS-CoV-2 by colocalisation with key host factors, including ACE2 and TMPRSS2. In summary, large-scale human genetic studies together with gene expression at single-cell resolution highlight ELF5 as a risk gene for severe COVID-19, supporting a role of epithelial cells of the respiratory system in the adverse host response to SARS-CoV-2.

Fluorescence-Based Measurements of Membrane-Bound Angiotensin Converting Enzyme 2 Activity Using Xenopus Laevis Oocytes.

Functional investigations of enzymes involving cellular expression systems are important for pharmacological studies. The precise control of expression is challenging in transiently transfected mammalian cell lines. Here, we explored the ability of Xenopus laevis oocytes to express a membrane-bound enzyme for functional characterization using standard 96-well plates and a fluorescence-based plate reader assay. We microinjected oocytes with cRNA encoding the angiotensin converting enzyme 2 (ACE2) and measured the enzymatic activity in single oocytes using a commercial fluorescence-based assay. The injected oocytes showed up to a 50-fold increase in fluorescence compared to uninjected oocytes. This fluorescence intensity was dose-dependent on the amount of ACE2 cRNA. These results suggest that Xenopus oocytes can be used for the functional evaluation of membrane-bound enzymes, decreasing the experimental workload.

The clinically relevant CYP2C8*3 and CYP2C9*2 haplotype is inherited from Neandertals.

Genetic variation in genes encoding cytochrome P450 enzymes influences the metabolism of drugs and endogenous compounds. The locus containing the cytochrome genes CYP2C8 and CYP2C9 on chromosome 10 exhibits linkage disequilibrium between the CYP2C8*3 and CYP2C9*2 alleles, forming a haplotype of ~300 kilobases. This haplotype is associated with altered metabolism of several drugs, most notably reduced metabolism of warfarin and phenytoin, leading to toxicity at otherwise therapeutic doses. Here we show that this haplotype is inherited from Neandertals.

Three-dimensional visualisation of authentic cases in anatomy learning - An educational design study.

BACKGROUND: Many studies have investigated the value of three-dimensional (3D) images in learning anatomy. However, there is a lack of knowledge about students learning processes using technology and 3D images. To understand how to facilitate and support the learning of anatomy, there is a need to know more about the student perspectives on how they can use and benefit from 3D images. METHODS: This study used designed educational sessions informed by Educational Design Research to investigate the role of technology-enhanced 3D images in students' anatomy learning. Twenty-four students representing different health professions and multiple study levels, and one tutor, participated in the study. A visualisation table was used to display the images of real patient cases related to disorders associated with the abdomen and the brain. Students were asked to explore the images on their own and audio/video capture was used to record their words and actions. Directly following the session, students were interviewed about their perceptions and different ways of learning and studying anatomy. The tutor was interviewed about his reflections on the session and his role as a facilitator on two occasions. Content analysis was used in its manifest and latent form in the data analysis. RESULT: Two main categories describing the students' and tutor's accounts of learning using the visualisation table were identified: 1. Interpreting 3D images and 2. Educational sessions using visualisation tables. Each category had signifying themes representing interpretations of the latent meaning of the students' and tutor's accounts. These were: Realism and complexity; Processes of discernment; References to previous knowledge; Exploring on one's own is valuable; Context enhances learning experiences; Combinations of learning resources are needed and Working together affects the dynamics. CONCLUSIONS: This study identifies several important factors to be considered when designing effective and rewarding educational sessions using a visualization table and 3D images in anatomy education. Visualisation of authentic images has the potential to create interest and meaningfulness in studying anatomy. Students need time to actively explore images but also get tutor guidance to understand. Also, a combination of different resources comprises a more helpful whole than a single learning resource.