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

Involvement of DNA polymerase beta in repair of ionizing radiation damage as measured by in vitro plasmid assays.

Contains fulltext : 51692.pdf (publisher's version ) (Open Access)Characteristic of damage introduced in DNA by ionizing radiation is the induction of a wide range of lesions. Single-strand breaks (SSBs) and base damages outnumber double-strand breaks (DSBs). If unrepaired, these lesions can lead to DSBs and increased mutagenesis. XRCC1 and DNA polymerase beta (polbeta) are thought to be critical elements in the repair of these SSBs and base damages. XRCC1-deficient cells display a radiosensitive phenotype, while proliferating polbeta-deficient cells are not more radiosensitive. We have recently shown that cells deficient in polbeta display increased radiosensitivity when confluent. In addition, cells expressing a dominant negative to polbeta have been found to be radiosensitized. Here we show that repair of radiation-induced lesions is inhibited in extracts with altered polbeta or XRCC1 status, as measured by an in vitro repair assay employing irradiated plasmid DNA. Extracts from XRCC1-deficient cells showed a dramatically reduced capacity to repair ionizing radiation-induced DNA damage. Extracts deficient in polbeta or containing a dominant negative to polbeta also showed reduced repair of radiation-induced SSBs. Irradiated repaired plasmid DNA showed increased incorporation of radioactive nucleotides, indicating use of an alternative long-patch repair pathway. These data show a deficiency in repair of ionizing radiation damage in extracts from cells deficient or altered in polbeta activity, implying that increased radiosensitivity resulted from radiation damage repair deficiencies

Radiobiology: state of the present art. A conference report.

Contains fulltext : 89538.pdf (publisher's version ) (Closed access)PURPOSE: To review the present state of the art of the major current research areas in radiobiology in the form of a conference report. BACKGROUND: To celebrate their 50th anniversary, the Dutch Radiobiology Society recently held a meeting entitled "50 Years of Radiation Science in The Netherlands: From Molecular Research to Medical Application". Speakers were attracted from the USA and various European countries, covering topics including hypoxia, genomics and proteomics, DNA repair, DNA damage and signalling, chromosomal instability, stem cells, and normal tissue responses. Given the occasion, a history of Dutch radiobiology was also presented. CONCLUSION: Understanding the molecular pathways influencing the radiation response of cells, tumours and normal tissues has progressed dramatically over the last decades. Papers presented at this meeting showed that this understanding is leading to new and more effective ways to treat cancer with radiation.1 januari 201

Predicting response to radiotherapy: Evolutions and revolutions.

Contains fulltext : 81932.pdf (publisher's version ) (Closed access)Purpose: To review the many changes which have occurred in the past decades in the field of predicting outcome after radiotherapy from biological characteristics of the tumour or normal tissue. This review will also describe the present state of the art and emerging trends for the future. Conclusions: From using explanted cells, glass electrodes, exogenous proliferation and hypoxia tracers, and others, there has been a move towards monitoring expression and mutation of genes. Initially this was possible for just one or a few genes, but methods are now available which allow genome-wide monitoring at either the DNA or RNA level. The potential advantage of this evolution is not only to predict but also to understand potential causes of failure, allowing more rational and effective interventions. Comparative genomic hybridisation, mRNA expression profiling, microRNA profiling and promoter methylation profiling have all shown promise in finding signatures correlating with outcome, including after treatment involving radiotherapy. Expected trends for the future are: more signatures relevant to radiotherapy will be discovered; signatures will be refined and reduced to their essentials, such that genome-wide screening will give way to tailored signatures, quantifiable by routine non-array technology; more focus will be on assays predicting which pathway-specific radiosensitising drugs will be effective (exploiting tumour weaknesses); more signatures will be subjected to validation in randomised trials; and proteomics, DNA sequencing and imaging methods will play progressively increasing roles

Predicting recurrence after radiotherapy in head and neck cancer

Item does not contain fulltextHead and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Radiotherapy is a mainstay of treatment, either alone for early stage tumors or combined with chemotherapy for late stage tumors. An overall 5-year survival rate of around 50% for HNSCC demonstrates that treatment is often unsuccessful. Prediction of outcome is, therefore, aimed at sparing patients from ineffective and toxic treatments on the one hand, and indicating more successful treatment modalities on the other. Both functional and genetic assays have been developed to predict intrinsic radiosensitivity, hypoxia, and repopulation rate. Few, however, have shown consistent correlations with outcome across multiple studies. Messenger RNA and microRNA profiling show promise for predicting hypoxia, whereas epidermal growth factor receptor expression combined with other measures of tumor differentiation grade shows promise for predicting repopulation rate. Intrinsic radiosensitivity assays have not proven useful to date, although development of repair protein foci assays indicates promise from preclinical studies. Assays for cancer stem cell content have shown promise in several clinical studies. In addition, 2 assays showing robustness as predictors for outcome in HNSCC are human papilloma virus status and epidermal growth factor receptor expression. Neither these nor stem cell assays, however, can as yet reliably indicate alternative and better treatments for poor prognosis patients. It would be of great value to have assays that predict the benefit for an individual from combining new molecularly targeted agents with radiotherapy to increase response, in particular those that exploit tumor mutations to provide tumor specificity. Predictive assays are being developed for detecting defects in repair pathways for single- and double-strand DNA breaks, which should allow selection of drugs targeting the appropriate backup pathway, thus exploiting the concept of synthetic lethality. This is one of the most promising areas for prediction, both currently and in the future

Ionizing radiation sensitivity of DNA polymerase lambda-deficient cells.

Contains fulltext : 51693.pdf (publisher's version ) (Open Access)Ionizing radiation induces a diverse spectrum of DNA lesions, including strand breaks and oxidized bases. In mammalian cells, ionizing radiation-induced lesions are targets of non-homologous end joining, homologous recombination, and base excision repair. In vitro assays show a potential involvement of DNA polymerase lambda in non-homologous end joining and base excision repair. In this study, we investigated whether DNA polymerase lambda played a significant role in determining ionizing radiation sensitivity. Despite increased sensitivity to hydrogen peroxide, lambda-deficient mouse embryonic fibroblasts displayed equal survival after exposure to ionizing radiation compared to their wild-type counterparts. In addition, we found increased sensitivity to the topoisomerase inhibitors camptothecin and etoposide in the absence of polymerase lambda. These results do not reveal a major role for DNA polymerase lambda in determining radiosensitivity in vivo

Editorial radiotherapy and oncology 2002: predictive assays for normal tissue damage.

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Prognostic and predictive markers in oncology. Introduction.

Contains fulltext : 71368.pdf (publisher's version ) (Closed access