The PARP inhibitor AZD2461 provides insights into the role of PARP3 inhibition for both synthetic lethality and tolerability with chemotherapy in preclinical models

The PARP inhibitor AZD2461 was developed as a next-generation agent following olaparib, the first PARP inhibitor approved for cancer therapy. In BRCA1-deficient mouse models, olaparib resistance predominantly involves overexpression of P-glycoprotein,so AZD2461 was developed as a poor substrate for drug transporters. Here we demonstrate the efficacy of this compound against olaparib-resistant tumors that overexpress P-glycoprotein. In addition, AZD2461 was better tolerated in combination with chemotherapy than olaparib in mice, which suggests that AZD2461 could have significant advantages over olaparib in the clinic. However, this superior toxicity profile did not extend to rats. Investigations of this difference revealed a differential PARP3 inhibitory activity for each compound and a higher level of PARP3 expression in bone marrow cells from mice as compared with rats and humans. Our findings have implications for the use of mouse models to assess bone marrow toxicity for DNA-damaging agents and inhibitors of the DNA damage response. Finally, structural modeling of the PARP3-active site with different PARP inhibitors also highlights the potential to develop compounds with different PARP family member specificity profiles for optimal antitumor activity and tolerability

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

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Appropriate management of acute gastroenteritis in Australian children: a population-based study

Objectives: To determine the proportion of care provided to children with acute gastroenteritis (AGE) in Australia consistent with clinical practice guidelines. Methods: Indicators were developed from national and international clinical practice guideline (CPG) recommendations and validated by an expert panel. Medical records from children ≤15 years presenting with AGE in three healthcare settings-Emergency Department (ED), hospital admissions and General Practitioner (GP) consultations-from randomly selected health districts across three Australian States were reviewed. Records were audited against 35 indicators by trained paediatric nurses, to determine adherence to CPGs during diagnosis, treatment, and ongoing management. Results: A total of 14,434 indicator assessments were performed from 854 healthcare visits for AGE by 669 children, across 75 GPs, 34 EDs and 26 hospital inpatient services. Documented adherence to guidelines across all healthcare settings was 45.5% for indicators relating to diagnosis (95% CI: 40.7-50.4), 96.1% for treatment (95% CI: 94.8-97.1) and 57.6% for ongoing management (95% CI: 51.3-63.7). Adherence varied by healthcare setting, with adherence in GPs (54.6%; 95% CI: 51.1-58.1) lower than for either ED settings (84.7%; 95% CI: 82.4-86.9) or for inpatients (84.3%; 95% CI: 80.0-87.9); p<0.0001 for both differences. The difference between settings was driven by differences in the diagnosis and ongoing management phases of care. Conclusions: Adherence to clinical guidelines for children presenting to healthcare providers with AGE varies according to phase of care and healthcare setting. Although appropriate diagnostic assessment and ongoing management phase procedures are not well documented in medical records (particularly in the GP setting), in the treatment phase children are treated in accordance with guidelines over 90% of the time.Neroli Sunderland, Johanna Westbrook, Rachel Urwin, Zoe Knights, Jonny Taitz, Helena Williams, Louise K. Wiles, Charlotte Molloy, Peter Hibbert, Hsuen P. Ting, Kate Churruca, Gaston Arnolda, Jeffrey Braithwaite (on behalf of the CareTrack Kids investigative team

Quantitative Chemical Proteomic Profiling of Ubiquitin Specific Proteases in Intact Cancer Cells

Deubiquitinating enzymes play an important role in a plethora of therapeutically relevant processes and are emerging as pioneering drug targets. Herein, we present a novel probe, Ubiquitin Specific Protease (USP) inhibitor, alongside an alkyne-tagged activity-based probe analogue. Activity-based proteome profiling identified 12 USPs, including USP4, USP16, and USP33, as inhibitor targets using submicromolar probe concentrations. This represents the first intact cell activity-based profiling of deubiquitinating enzymes. Further analysis demonstrated functional inhibition of USP33 and identified a synergistic relationship in combination with ATR inhibition, consistent with USP4 inhibition

Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy.

Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy BRCA1 and BRCA2 are important for DNA double-strand break repair by homologous recombination(1), and mutations in these genes predispose to breast and other cancers(2). Poly(ADP- ribose) polymerase ( PARP) is an enzyme involved in base excision repair, a key pathway in the repair of DNA single- strand breaks(3). We show here that BRCA1 or BRCA2 dysfunction unexpectedly and profoundly sensitizes cells to the inhibition of PARP enzymatic activity, resulting in chromosomal instability, cell cycle arrest and subsequent apoptosis. This seems to be because the inhibition of PARP leads to the persistence of DNA lesions normally repaired by homologous recombination. These results illustrate how different pathways cooperate to repair damage, and suggest that the targeted inhibition of particular DNA repair pathways may allow the design of specific and less toxic therapies for cancer

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals

BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. - RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus’ microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. - CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.Background Results - Sample information and dating - General metagenomic assessment - Mycobacterium leprae (individual Abusir1630) - Hepatitis B virus (individual Abusir1543) - Oral microbiome assessment Discussion Conclusions Methods - Sample extraction and radiocarbon dating - Sample extraction and library preparation - Metagenomic screening - Authentication of ancient DNA - Content of endogenous DNA (SourceTracker2) - Data processing of sample Abusir1630b (M. leprae) -- Read processing, mapping, and variant calling -- SNP typing -- Anthropological analysis -- Phylogeny -- Beast analysis -- Temporal signal - Data processing individual Abusir1543 (hepatitis B virus) -- Read processing, mapping, and variant calling -- Phylogeny -- Recombination analysis -- Beast analysis -- Temporal signa