The 9-cis retinoic acid receptor (retinoid X receptor, RXR) forms heterodimers with the all-trans retinoic acid receptor (RAR) and other nuclear receptors on DNA regulatory sites composed of tandem binding elements. We describe the 1.70 A resolution structure of the ternary complex of RXR and RAR DNA-binding regions in complex with the retinoic acid response element DR1. The receptors recognize identical half-sites through extensive base-specific contacts; however, RXR binds exclusively to the 3' site to form an asymmetric complex with the reverse polarity of other RXR heterodimers. The subunits associate in a strictly DNA-dependent manner using the T-box of RXR and the Zn-II region of RAR, both of which are reshaped in forming the complex. The protein-DNA contacts, the dimerization interface and the DNA curvature in the RXR-RAR complex are distinct from those of the RXR homodimer, which also binds DR1. Together, these structures illustrate how the nuclear receptor superfamily exploits conformational flexibility and locally induced structures to generate combinatorial transcription factors.
\n \n\n \n \nThe stepwise approach to pharmacological treatment in adult asthma mandates that asthma treatment is progressively stepped up to achieve symptom control and reduce the risk of exacerbations, and stepped down after a period of prolonged control. This review proposes that in adults without good asthma control, 'well-controlled' asthma can only be achieved in around 70% of patients across the strata of severity, and only if there is a progressive increase in ICS/LABA therapy to a maintenance ICS dose which causes the same magnitude of systemic side effects as oral prednisone at a 5mg daily dose. Another consideration is that in a person with asthma, there are numerous overlapping disorders that can present with symptoms indistinguishable from asthma, comorbidities that contribute to poor control and lifestyle/environmental factors that require treatment in their own right, and that if specifically managed might lead to better outcomes. The disparity between patients' perceptions and guideline assessment of control may be due to 'partially controlled' asthma being associated with near maximal levels of quality of life, with minimal impairment. Finally it is widely assumed that asthma symptom control equates to elimination of risk of asthma attacks, an assumption that may not apply to many patients, particularly those with more severe asthma. We propose that further research is undertaken to determine the optimal levels of asthma control, and the potential value of different treatment targets such as control of type-2 airway inflammation, that can be achieved with currently available treatment, based on efficacy, side effects and cost.
\n \n\n \n \nOBJECTIVE:To characterise the clinical features of patients admitted to hospital with coronavirus disease 2019 (covid-19) in the United Kingdom during the growth phase of the first wave of this outbreak who were enrolled in the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) World Health Organization (WHO) Clinical Characterisation Protocol UK (CCP-UK) study, and to explore risk factors associated with mortality in hospital. DESIGN:Prospective observational cohort study with rapid data gathering and near real time analysis. SETTING:208 acute care hospitals in England, Wales, and Scotland between 6 February and 19 April 2020. A case report form developed by ISARIC and WHO was used to collect clinical data. A minimal follow-up time of two weeks (to 3 May 2020) allowed most patients to complete their hospital admission. PARTICIPANTS:20\u2009133 hospital inpatients with covid-19. MAIN OUTCOME MEASURES:Admission to critical care (high dependency unit or intensive care unit) and mortality in hospital. RESULTS:The median age of patients admitted to hospital with covid-19, or with a diagnosis of covid-19 made in hospital, was 73 years (interquartile range 58-82, range 0-104). More men were admitted than women (men 60%, n=12\u2009068; women 40%, n=8065). The median duration of symptoms before admission was 4 days (interquartile range 1-8). The commonest comorbidities were chronic cardiac disease (31%, 5469/17\u2009702), uncomplicated diabetes (21%, 3650/17\u2009599), non-asthmatic chronic pulmonary disease (18%, 3128/17\u2009634), and chronic kidney disease (16%, 2830/17\u2009506); 23% (4161/18\u2009525) had no reported major comorbidity. Overall, 41% (8199/20\u2009133) of patients were discharged alive, 26% (5165/20\u2009133) died, and 34% (6769/20\u2009133) continued to receive care at the reporting date. 17% (3001/18\u2009183) required admission to high dependency or intensive care units; of these, 28% (826/3001) were discharged alive, 32% (958/3001) died, and 41% (1217/3001) continued to receive care at the reporting date. Of those receiving mechanical ventilation, 17% (276/1658) were discharged alive, 37% (618/1658) died, and 46% (764/1658) remained in hospital. Increasing age, male sex, and comorbidities including chronic cardiac disease, non-asthmatic chronic pulmonary disease, chronic kidney disease, liver disease and obesity were associated with higher mortality in hospital. CONCLUSIONS:ISARIC WHO CCP-UK is a large prospective cohort study of patients in hospital with covid-19. The study continues to enrol at the time of this report. In study participants, mortality was high, independent risk factors were increasing age, male sex, and chronic comorbidity, including obesity. This study has shown the importance of pandemic preparedness and the need to maintain readiness to launch research studies in response to outbreaks. STUDY REGISTRATION:ISRCTN66726260.
\n \n\n \n \n<jats:p>Hepatitis B virus (HBV) infection is a major global health problem with over 240 million infected individuals at risk of developing progressive liver disease and hepatocellular carcinoma. HBV is an enveloped DNA virus that establishes its genome as an episomal, covalently closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Currently available standard-of-care treatments for chronic hepatitis B (CHB) include nucleos(t)ide analogues (NA) that suppress HBV replication but do not target the cccDNA and hence rarely cure infection. There is considerable interest in determining the lifespan of cccDNA molecules to design and evaluate new curative treatments. We took a novel approach to this problem by developing a new mathematical framework to model changes in evolutionary rates during infection which, combined with previously determined within-host evolutionary rates of HBV, we used to determine the lifespan of cccDNA. We estimate that during HBe-antigen positive (HBeAgPOS) infection the cccDNA lifespan is 61 (36-236) days, whereas during the HBeAgNEG phase of infection it is only 26 (16-81) days. We found that cccDNA replicative capacity declined by an order of magnitude between HBeAgPOS and HBeAgNEG phases of infection. Our estimated lifespan of cccDNA is too short to explain the long durations of chronic infection observed in patients on NA treatment, suggesting that either a sub-population of long-lived hepatocytes harbouring cccDNA molecules persists during therapy, or that NA therapy does not suppress all viral replication. These results provide a greater understanding of the biology of the cccDNA reservoir and can aid the development of new curative therapeutic strategies for treating CHB.</jats:p>
\n \n\n \n \nThe DNA damage response (DDR) is central to the cell survival and it requires post-translational modifications, in part, to sense the damage, amplify the signaling response and recruit and regulate DNA repair enzymes. Lysine methylation of histones such as H4K20 and non-histone proteins including p53 has been shown to be essential for the mounting of the DDR. It is well-known that the lysine methyltransferase SET7 regulates the DDR, as cells lacking this enzyme are hypersensitive to chemotherapeutic drugs. To define addition substrates of SET7 involved in the DDR, we screened a peptide array encompassing potential lysine methylation sites from >100 key DDR proteins and identified peptides from 58 proteins to be lysine methylated defining a methylation consensus sequence of [S>K-2; S>R-1; K0] consistent with previous findings. We focused on K377 methylation of the Flap endonuclease 1 (FEN1), a structure specific endonuclease with important functions in Okazaki fragment processing during DNA replication as a substrate of SET7. FEN1 was monomethylated by SET7 in vivo in a cell cycle dependent manner with levels increasing as cells progressed through S phase and decreasing as they exited S phase, as detected using K377me1 specific antibodies. Although K377me1 did not affect the enzymatic activity of FEN1, it was required for the cellular response to replicative stress by FEN1. These finding define FEN1 as a new substrate of SET7 required for the DDR.
\n \n\n \n \n<jats:p>PALB2 [partner and localizer of BRCA2 (breast cancer early-onset 1)] has emerged as a key player in the maintenance of genome integrity. Biallelic mutations in PALB2 cause FA (Fanconi's anaemia) subtype FA-N, a devastating inherited disorder marked by developmental abnormalities, bone marrow failure and childhood cancer susceptibility, whereas monoallelic mutations predispose to breast, ovarian and pancreatic cancer. The tumour suppressor role of PALB2 has been intimately linked to its ability to promote HR (homologous recombination)-mediated repair of DNA double-strand breaks. Because PALB2 lies at the crossroads between FA, HR and cancer susceptibility, understanding its function has become the primary focus of several studies. The present review discusses a current synthesis of the contribution of PALB2 to these pathways. We also provide a molecular description of FA- or cancer-associated PALB2 mutations.</jats:p>
\n \n\n \n \nConcerted multidisciplinary efforts have led to the development of Cyclin-Dependent Kinase inhibitors (CDKi's) as small molecule drugs and chemical probes of intracellular CDK function. However, conflicting data has been reported on the inhibitory potency of CDKi's and a systematic characterization of affinity and selectivity against intracellular CDKs is lacking. We have developed a panel of cell-permeable energy transfer probes to quantify target occupancy for all 21 human CDKs in live cells, and present a comprehensive evaluation of intracellular isozyme potency and selectivity for a collection of 46 clinically-advanced CDKi's and tool molecules. We observed unexpected intracellular activity profiles for a number of CDKi's, offering avenues for repurposing of highly potent molecules as probes for previously unreported targets. Overall, we provide a broadly applicable method for evaluating the selectivity of CDK inhibitors in living cells, and present a refined set of tool molecules to study CDK function.
\n \n\n \n \nPast studies on the relationship between Killer cell Immunoglobulin-like Receptor (KIR) and Human Leukocyte Antigen (HLA) genetic variation and chronic immune activation (CIA) in HIV infection are not uniformly consistent. Moreover, interferon-\u03b3-induced protein 10 (IP-10) is a soluble biomarker of immune activation, with high plasma concentrations predicting accelerated disease progression in HIV infection. Thus, we investigated the association of KIR and HLA-C genetic polymorphisms with plasma IP-10 concentration in 183 treatment-naive chronically HIV-infected adults of Bantu origin from Zimbabwe. KIR genetic variation was determined using allele-specific primer PCR while HLA-C typing was characterized by sequencing. Plasma IP-10 was quantified using enzyme-linked immunosorbent assay. The KIR2DL3 gene was significantly associated with CIA as observed from IP-10 concentrations among KIR2DL3 carriers (265.20\u2009pg/mL, IQR: 179.99-385.19) compared with KIR2DL3 noncarriers (183.56\u2009pg/mL; IQR: 110.98-230.81; p\u2009=\u20090.001) and among KIR2DL3+HLA-C2 carriers (226.23\u2009pg/mL, IQR: 187.96-394.73) compared with KIR2DL3+HLA-C2 noncarriers (212.86\u2009pg/mL, IQR: 160.15-344.99; p\u2009=\u20090.017), respectively. Similarly, IP-10 concentrations were significantly higher (p\u2009=\u20090.030) in the KIR3DS1 carriers (313.86\u2009pg/mL, IQR: 230.05-469.20) compared with KIR3DS1 noncarriers (246.01\u2009pg/mL, IQR: 169.58-373.32). Thus, KIR and HLA-C could be playing important roles in HIV-associated immune activation. The elevation of IP-10 in KIR2DL3 and KIR2DL3+C2 could potentially be explained by increased IFN-\u03b3 secretion from activated NK cell activation due to the absence of KIR2DL3's cognate C1 ligand. To the best of our knowledge, this is the first study on a potential link between KIR and HLA-C genetic determinants and plasma IP-10 concentration in this population sample. Future studies are called for in other world populations for biomarkers of disease progression and mechanisms of IP-10 variability in HIV infection.
\n \n\n \n \n\u00a9 2017, Ibadan Biomedical Communications Group. All rights reserved. Human Leukocyte Antigen (HLA), particularly HLA-B and class II alleles have been differentially associated with disease outcomes in different populations following infection with the malaria Plasmodium falciparum. However, the effect of HLA-A on malaria infection and/or disease is not fully understood. Recently, HLA-A alleles have been suggested to play a role in the outcome of P. falciparum malaria infection in a Malian study. Herein, we investigated the association between HLA-A alleles and the outcome of malaria infection in children in Ibadan southwest Nigeria. HLA-A genotyping was performed on 393 children samples (DNA) using the sequence-based method. We compared genotype and allele frequencies data obtained from these Nigerian children; 176 with asymptomatic malaria infection (controls), 124 with uncomplicated malaria and 93 children with severe malaria (51 severe malarial anaemia and 42 cerebral malaria). We found a high frequency of HLA-A*36:01 (13.5%) in the entire studied population and also confirmed the high frequency of a previously reported allele of African origin (HLA-A*30:01). After adjusting for age and parasite density, we found a significant association between HLA-A*20:01:01 (OR = 3.19, p < 0.001) and susceptibility to severe malarial anaemia. We also found significant associations between HLA-A* 29:02:01 (OR = 7.26, p = 0.008) and A* 66:02 (Or = 4.19, p = 0.03) and susceptibility to cerebral malaria. Our findings suggest that HLA-A alleles play a role in the outcome of malaria in children in Ibadan. These findings may help elucidate the molecular background of malaria resistance in the study population.
\n \n\n \n \nOBJECTIVE:To describe the features of HIV-associated chronic lung disease (CLD) in older children and adolescents living with HIV and to examine the clinical factors associated with CLD. This is a post hoc analysis of baseline data from the BREATHE clinical trial (ClinicalTrials.gov, NCT02426112). METHODS:Children and adolescents aged 6-19\u00a0years were screened for CLD (defined as a FEV1 z-score <-1 with no reversibility post-bronchodilation with salbutamol) at two HIV clinics in Harare, Zimbabwe, and Blantyre, Malawi. Eligible participants with CLD (cases) were enrolled, together with a control group without CLD [frequency-matched by age group and duration on antiretroviral therapy (ART)] in a 4:1 allocation ratio. A clinical history and examination were undertaken. The association between CLD and a priori-defined demographic and clinical covariates was investigated using multivariable logistic regression. RESULTS:Of the 1585 participants screened, 419 (32%) had a FEV1 z-score <-1, of whom 347 were enrolled as cases [median age 15.3\u00a0years (IQR 12.7-17.7); 48.9% female] and 74 with FEV1 z-score >0 as controls [median age 15.6\u00a0years (IQR 12.1-18.2); 62.2% female]. Among cases, current respiratory symptoms including cough and shortness of breath were reported infrequently (9.3% and 1.8%, respectively). However, 152 (43.8%) of cases had a respiratory rate above the 90th centile for their age. Wasting and taking second-line ART were independently associated with CLD. CONCLUSIONS:The presence of CLD indicates the need to address additional treatment support for youth living with HIV, alongside ART provision, to ensure a healthier adulthood.
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