Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Kinetic modelling of the role of the aldehyde dehydrogenase enzyme and the breast cancer resistance protein in drug resistance and transport

A compartmental model for the in vitro uptake kinetics of the anti-cancer agent topotecan (TPT) has been extended from a previously published model. The extended model describes the drug activity and delivery of the pharmacologically active form to the DNA target as well as the catalysis of the aldehyde dehydrogenase (ALDH) enzyme and the elimination of drug from the cytoplasm via the efflux pump. Verification of the proposed model is achieved using scanning-laser microscopy data from live human breast cancer cells. Before estimating the unknown model parameters from the experimental in vitro data it is essential to determine parameter uniqueness (or otherwise) from this imposed output structure. This is formally performed as a structural identifiability analysis, which demonstrates that all of the unknown model parameters are uniquely determined by the output structure corresponding to the experiment

Abdominal aortic diameter and vascular atherosclerosis: the Multi-Ethnic Study of Atherosclerosis.

International audienceOBJECTIVES: To gain insight into early mechanisms of aortic widening, we examined associations between the diameter of the abdominal aorta (AD) and cardiovascular disease (CVD) risk factors and biomarkers, as well as measures of subclinical atherosclerosis, in a multi-ethnic population. DESIGN: Cross-sectional cohort. METHODS: A total of 1926 participants (mean age 62, 50% women) underwent chest and abdomen scanning by computed tomography, ultrasound of the carotid arteries, and CVD risk factor assessment. AD was measured 5 cm above and at the bifurcation. RESULTS: In a model containing traditional CVD risk factors, biomarkers and ethnicity, only age (standardized β = 0.97), male sex (β = 1.88), body surface area (standardized β = 0.92), current smoking (β = 0.42), D-dimer levels (β = 0.19) and hypertension (β = 0.53) were independently and significantly associated with increasing AD (in mm) at the bifurcation; use of cholesterol-lowering medications predicted smaller AD (β = -0.70) (P < 0.01 for all). These findings were similar for AD 5 cm above the bifurcation with one exception: compared to Caucasian-Americans, Americans of Chinese, African and Hispanic descent had significantly smaller AD 5 cm above the bifurcation (β's = -0.59, -0.49, and -0.52, respectively, all P < 0.01), whereas AD at the bifurcation did not differ by ethnicity. Physical activity, alcohol consumption, diabetes and levels of IL-6, CRP and homocysteine were not independently associated with AD. Higher aortic and coronary artery calcium burden, but not common carotid artery intima-media thickness, were independently, but modestly (β = 0.11 to 0.19), associated with larger AD. CONCLUSIONS: Incremental widening of the aortic diameter shared some, but not all, risk factors for occlusive vascular disease

Styrene, an Unpalatable Substrate with Complex Regulatory Networks

Styrene, a volatile organic compound (VOC), is an important industrial material involved in the production of plastic, synthetic rubber and resin, insulation and other industrial materials containing molecules such as polystyrene, butadiene-styrene latex, styrene copolymers and unsaturated polyester resins. Styrene exposure may cause contact-based skin inflammation, irritation of eyes, nose and respiratory tract. Neurological effects such as alterations in vision, hearing loss and longer reaction times, have been associated with styrene exposure in the workplace. In addition, styrene oxide may act as an established mutagen and carcinogen (www.epa.gov/chemfact/styre-sd.pdf). It has been reported that, in 2002, 22,323 tons of styrene were released to the environment (82), in spite of the US Clean Air Act mandate on reduction in the volume of allowable styrene emission (www.epa.gov/chemfact/styre-sd.pdf). Among a variety of emerging air pollution technologies, biofiltration is an attractive option for the treatment of VOCs, because it is cost-effective and does not generate secondary contaminants (45). Moreover, microbial biodegradation is the major route for the removal of non-aqueous compounds from soils. Styrene is also naturally present in non polluted environments, since it derives from fungal decarboxylation of cinnamic acid (90). Therefore it is not surprising that microorganisms of different families have been found to be able to degrade this compound (31). The promising results obtained in the removal of styrene from contaminated waste-gases by biofiltration (5, 39, 103) have led to an increasing attention to the regulatory mechanisms underlying styrene degradation, with the aim to improve bioremediation processes. Despite the diffusion in nature of this degradative capability, only few strains, mainly belonging to the Pseudomonas genus, have been characterized (66). This chapter is focused on the up-to-now discovered regulatory mechanisms underlying the expression of the styrene-catabolism genes. Moreover, open questions on environmental and metabolic constrains that govern styrene degradation are discussed. Biotechnological relevance of styrene-degrading strains in fine chemicals production and bioremediation processes is not examined here. Main topics on these application fields have recently been reviewed by Dobson and co-workers (66)

Vascular and neuronal development: Intersecting parallelisms and rossroads

Two key events during evolution allowed vertebrates to develop specialized tissues able to perform complex tasks: the formation of a highly branched vascular system ensuring that all tissues receive adequate blood supply, and the development of a nervous system in which nerves branches to transmit electrical signal to peripheral organs. Both networks are laid down in a complex and stereotyped manner, which is tightly controlled by a series of shared developmental cues. Vessels and nerves use similar signals and principles to grow, differentiate and navigate toward their final targets. Moreover, the vascular and the nervous system cross-talk and, when deregulated, they contribute to medically relevant diseases. The emerging evidence that both systems share several molecular pathways not only provides an important link between vascular biology and neuroscience, but also promises to accelerate the discovery of new pathogenetic insights and therapeutic strategies