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

Rethinking soil water repellency and its management

Soil water repellency (SWR) is a widespread challenge to plant establishment and growth. Despite considerable research, it remains a recalcitrant problem for which few alleviation technologies or solutions have been developed. Previous research has focused on SWR as a problem to be overcome, however, it is an inherent feature of many native ecosystems where it contributes to ecosystem functions. Therefore, we propose a shift in the way SWR is perceived in agriculture and in ecological restoration, from a problem to be solved, to an opportunity to be harnessed. A new focus on potential ecological benefits of SWR is particularly timely given increasing incidence, frequency and severity of hotter droughts in many regions of the world. Our new way of conceptualising SWR seeks to understand how SWR can be temporarily alleviated at a micro-scale to successfully establish plants, and then harnessed in the longer term and at larger spatial scales to enhance soil water storage to act as a “drought-proofing” tool for plant survival in water-limited soils. For this to occur, we suggest research focusing on the alignment of physico-chemical and microbial properties and dynamics of SWR and, based on this mechanistic understanding, create products and interventions to improve success of plant establishment in agriculture, restoration and conservation contexts. In this paper, we outline the rationale for a new way of conceptualising SWR, and the research priorities needed to fill critical knowledge gaps in order to harness the ecological benefits from managing SWR

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

Localized non-Hodgkin's lymphoma with B-cell histology:Cure without cyclophosphamide? A report of the United Kingdom Children's Cancer Study Group on studies NHL 8501 and NHL 9001 (1985-1996)

We have examined the outcome for children treated on two consecutive United Kingdom Children's Cancer Study Group studies of localized B-cell non-Hodgkin's lymphoma (NHL). The first study (NHL 8501; 1985-1989) included cyclophosphamide in the treatment regimen ata total cumulative dose of 4 g/m2 whereas the regimen in the succeeding study (NHL 9001; 1990-1996) did not include cyclophosphamide. Ninety children with confirmed B-cell NHL were treated in the two studies (NHL 8501, n = 33 and NHL9001, n = 57). With a median follow-up of 7.5 years, overall survival for localized B-cell NHL did not differ between the two regimens with observed 3-year survivals of 94% [95% confidence interval (CI) 80-98%] and 89% (95% CI 79-95%) respectively (P = 0.47). There was also no difference in the event-free survival between children treated on regimen NHL 8501 and NHL 9001 [91% (95% CI 76-97%) vs 84% (95% CI 73-92%) after 3 years; P = 0.34]. Although the difference in the number of failed remissions between NHL 8501 and 9001 (0/33 vs 6/57) approached statistical significance (P = 0.08. Fisher's exact test), there was no overall statistical difference between the treatment failures on either regimen (P = 0.34). Substantial long-term survival can be achieved for many children with localized B-cell NHL without the use of cyclophosphamide. Further studies are needed to identify whether all clinical or histopathological subgroups will benefit equally from the omission of cyclophosphamide.</p

Isolated parenchymal lung involvement in children with stage IV Hodgkin's disease: results of the UKCCSG HD8201 and HD9201 studies

We retrospectively reviewed the case notes of 27 patients who were diagnosed with stage IV Hodgkin's disease (HD) because of isolated parenchymal pulmonary involvement on chest radiograph and computerized tomography scan (excluding subcategory E). Ten were boys and 15 had B symptoms. Median age at diagnosis was 13.6 years (range 6.1-16.2). All received 6-8 cycles of ChlVPP (chlorambucil, vinblastine, procarbazine and prednisolone) and two had additional whole lung irradiation (12 Gy). Ten patients (37%) relapsed or progressed. Seven survive following second-line therapy while three died, two of HD and one of secondary acute myeloid leukaemia 4 years from diagnosis. At the time of analysis, the median follow-up of patients was 56 months (range 9-127). The event-free survival (EFS) was 58.4% (95% CI 38.5-75.8%) at both 5 and 10 years from diagnosis, and the overall survival (OS) was 84.2% (95% CI 61.8-94.6%) at both 5 and 10 years from diagnosis. We conclude that the outcome for HD patients defined as stage IV, because of isolated parenchymal lung involvement, is encouraging and compares favourably with other extra lymphatic organ involvement. Combination chemotherapy is effective in achieving long-term remission and whole lung irradiation is unnecessary

High dose melphalan in the treatment of advanced neuroblastoma: results of a randomised trial (ENSG-1) by the European Neuroblastoma Study Group

High dose myeloablative chemotherapy ("megatherapy"), with haematopoietic stem cell support, is now widely used to consolidate response to induction chemotherapy in patients with advanced neuroblastoma. In this study (European Neuroblastoma Study Group, ENSG1), the value of melphalan myeloablative "megatherapy" was evaluated in a randomised, multi-centre trial. Between 1982 and 1985, 167 children with stages IV and III neuroblastoma (123 stage IV > 1 year old at diagnosis and 44 stage III and stage IV from 6 to 12 months old at diagnosis) were treated with oncovin, cisplatin, epipodophyllotoxin, and cyclophosphamide (OPEC) induction chemotherapy every 3 weeks. After surgical excision of primary tumour, the 90 patients (69% of the total) who achieved complete response (CR) or good partial response (GPR) were eligible for randomisation either to high dose melphalan (180 mg per square meter) with autologous bone marrow support or to no further treatment. Sixty-five (72%) of eligible children were actually randomised and 21 of these patients were surviving at time of this analysis, with median follow-up from randomisation of 14.3 years. Five year event-free survival (EFS) was 38% (95% confidence interval (CI) 21-54%) in the melphalan-treated group and 27% (95% CI 12-42%) in the "no-melphalan" group. This difference was not statistically significant (P = 0.08, log rank test) but for the 48 randomised stage IV patients aged >1 year at diagnosis outcome was significantly better in the melphalan-treated group-5 year EFS 33% versus 17% (P = 0.01, log rank test). In this trial, high dose melphalan improved the length of EFS and overall survival of children with stage IV neuroblastoma >1 year of age who achieved CR or GPR after OPEC induction therapy and surgery. Multi-agent myeloablative regimens are now widely used as consolidation therapy for children with stage IV disease and in those with other disease stages when the MYCN gene copy number in tumour cells is amplified. Because they are more toxic, complex, and costly these combination megatherapy regimens should be compared with single agent melphalan in randomised clinical trial