TAPESTRY: A De-centralized Service for Trusted Interaction Online

Engineering and Physical Sciences Research Council EPSRC Grant Ref: EP/N02799X/1 under the UKRI Digital Economy Programme

Monoallelic Expression of Multiple Genes in the CNS

The inheritance pattern of a number of major genetic disorders suggests the possible involvement of genes that are expressed from one allele and silent on the other, but such genes are difficult to detect. Since DNA methylation in regulatory regions is often a mark of gene silencing, we modified existing microarray-based assays to detect both methylated and unmethylated DNA sequences in the same sample, a variation we term the MAUD assay. We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS. Selected genes were then tested for allele-specific expression in clonal neural stem cell lines derived from reciprocal F1 (C57BL/6×JF1) hybrid mice. In addition, using a separate approach, we directly analyzed allele-specific expression of a group of genes interspersed within clusters of OlfR genes, since the latter are subject to allelic exclusion. Altogether, of the 500 known genes in the chromosomal region surveyed, five show monoallelic expression, four identified by the MAUD assay (Agc1, p (pink-eyed dilution), P4ha3 and Thrsp), and one by its proximity to OlfR genes (Trim12). Thrsp (thyroid hormone responsive SPOT14 homolog) is expressed in hippocampus, but the human protein homolog, S14, has also been implicated in aggressive breast cancer. Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci. Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification

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 hospitalization2–4 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

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

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

Reproductive biology of Melaleuca alternifolia (Myrtaceae) 1. Floral biology

Melaleuca alternifolia (Maiden Betche) Cheel is commercially important as the source of essential oil for the Australian tea tree-oil industry. Information on reproductive biology of M. alternifolia is important to the Australian breeding program directed at improving the quality and quantity of tea tree oil. Flowering in three geographically separated sites-two planted seed orchards and one managed natural population, all in NSW was observed in the present study, with supporting data obtained from glasshouse-grown plants in Canberra. The majority of the work was conducted from 2004 to 2007, although the study also drew on some prior observations. M. alternifolia has spikes of flowers that open acropetally over a 6-day period. No strong separation of male and female phases was found in any individual flower; pollen was shed by 1.4 days after anthesis and the stigma reached peak receptivity 3-5 days after anthesis. Dichogamy and acropetal floral development may lead to geitonogamy. Flowering occurred during the months of OctoberNovember, with the peak in November, and was synchronous across all three sites. Flowering intensity and success in producing capsules appeared to be associated with total spring rainfall. Initiation of flowering in M. alternifolia appears to be correlated with daylength, or an environmental parameter closely correlated with daylength. Flowering intensity varied considerably among the years surveyed, sites and families, and appears to be promoted by a period of winter minimum temperatures below 5°C. In M. alternifolia, the morphological development of buds, flowers and fruit leading to the development of mature seed takes place over a period 16-18 months from flowering. M. alternifolia differed significantly in the number of viable seeds per capsule from individual trees, from 26±3.8 to 57±3.8 germinants

Reproductive biology of Melaleuca alternifolia (Myrtaceae) 2. Incompatibility and pollen transfer in relation to the breeding system

The onset of stigma receptivity in Melaleuca alternifolia (Maiden Betche) Cheel was evaluated by observing pollen-tube growth and seed set following controlled pollination. Pollen-tube numbers in the style, following controlled pollinations, increased from Day 1 to Day 6, then declining rapidly. The stigma was most receptive during Days 3-6, and still receptive at low levels as early as shortly after anthesis and as late as 10 days after pollination. The present study found that individuals of M. alternifolia differed in their degree of expression of self-incompatibility. Artificial self-pollination, with emasculation, in several families resulted in complete self-incompatibility, with no capsule retention. The microscopic observation of pollen-tube development revealed a mechanism of self-incompatibility in M. alternifolia. A self-incompatibility system operates in the style, although a few self-pollen grains are capable of germinating and producing pollen tubes. It also appears that late-acting self-incompatibility mechanisms discriminate against self-pollen tubes when they descend to the ovary. Artificial cross-pollination of selected parents produced seed with greater germination capacity and seedlings that grew faster than the corresponding open-pollinated seed and seedlings from the same parent. Freeze-dried pollen stored at -18C maintained viability (22%) over 1 year of storage. This finding will allow greater flexibility in undertaking controlled pollinations, because stored pollen can be substituted for fresh pollen when insufficient quantities are available from new-season flowers. A wide variety of insects was observed visiting the flowers of M. alternifolia, and capsule set was high even in bags that excluded flower visitors greater than 2mm. Thrips species seem likely to be important pollinators of this species because they are small and were abundant inside and outside of exclusion bags, although several other insect species such as bees, flies and wasps were also identified as frequent floral visitors