PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2

In search for broad-spectrum antivirals, we discovered a small molecule inhibitor, RMC-113, that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrated selective dual inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Advanced lipidomics revealed alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and linked its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We discovered PIP4K2C's roles in SARS-CoV-2 entry, RNA replication, and assembly/egress, validating it as a druggable antiviral target. Integrating proteomics, single-cell transcriptomics, and functional assays revealed that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced impairment of autophagic flux. Reversing this autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C, an understudied kinase, and propose dual inhibition of PIP4K2C and PIKfyve as a candidate strategy to combat emerging viruses.

Chemical inactivation strategies for SARS-CoV-2-infected cells and organoids

Infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) research, conducted in high-containment laboratories, requires transferring samples to lower containment labs for downstream applications, mandating sample inactivation. Here, we present a stepwise protocol for chemical inactivation of SARS-CoV-2 virus in culture supernatants or within infected cells and organoids, using eight chemical reagents validated via plaque assays. Additionally, we describe steps for troubleshooting virus inactivation, titer calculation, and log reduction. This protocol offers valuable resources for the COVID-19 research community, providing essential tools to advance research on this virus.

An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations

Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.

Back-pocket optimization of 2-aminopyrimidine-based macrocycles leads to potent dual EPHA2/GAK kinase inhibitors with antiviral activity

Macrocyclization of acyclic compounds is a powerful strategy for improving inhibitor potency and selectivity. Here, we developed a 2-aminopyrimidine-based macrocyclic dual EPHA2/GAK kinase inhibitor as a chemical tool to study the role of these two kinases in viral entry and assembly. Starting with a promiscuous macrocyclic inhibitor, 6, we performed a structure-guided activity relationship and selectivity study using a panel of over 100 kinases. The crystal structure of EPHA2 in complex with the developed macrocycle 23 provided a basis for further optimization by specifically targeting the back pocket, resulting in compound 55 as a potent dual EPHA2/GAK inhibitor. Subsequent front-pocket derivatization resulted in an interesting in cellulo selectivity profile, favoring EPHA4 over the other ephrin receptor kinase family members. The dual EPHA2/GAK inhibitor 55 prevented dengue virus infection of Huh7 liver cells, mainly via its EPHA2 activity, and is therefore a promising candidate for further optimization of its activity against dengue virus.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Anticancer pan-ErbB inhibitors reduce inflammation and tissue injury and exert broad-spectrum antiviral effects

Targeting host factors exploited by multiple viruses could offer broad-spectrum solutions for pandemic preparedness. Seventeen candidates targeting diverse functions emerged in a screen of 4,413 compounds for SARS-CoV-2 inhibitors. We demonstrated that lapatinib and other approved inhibitors of the ErbB family of receptor tyrosine kinases suppress replication of SARS-CoV-2, Venezuelan equine encephalitis virus (VEEV), and other emerging viruses with a high barrier to resistance. Lapatinib suppressed SARS-CoV-2 entry and later stages of the viral life cycle and showed synergistic effect with the direct-acting antiviral nirmatrelvir. We discovered that ErbB1, ErbB2, and ErbB4 bind SARS-CoV-2 S1 protein and regulate viral and ACE2 internalization, and they are required for VEEV infection. In human lung organoids, lapatinib protected from SARS-CoV-2-induced activation of ErbB-regulated pathways implicated in non-infectious lung injury, proinflammatory cytokine production, and epithelial barrier injury. Lapatinib suppressed VEEV replication, cytokine production, and disruption of blood-brain barrier integrity in microfluidics-based human neurovascular units, and reduced mortality in a lethal infection murine model. We validated lapatinib-mediated inhibition of ErbB activity as an important mechanism of antiviral action. These findings reveal regulation of viral replication, inflammation, and tissue injury via ErbBs and establish a proof of principle for a repurposed, ErbB-targeted approach to combat emerging viruses.

Conventional vs. Hypo-Fractionated, Radiotherapy for High-Risk Prostate Cancer (PCS5), Randomized, Non-Inferiority, Phase 3 Trial: Posthoc Analysis of IMRT vs. 3D-CRT Radiation Therapy Associated Toxicities

PURPOSE/OBJECTIVE(S)

The Prostate Cancer Study number 5 (PCS5), is a multi-centric non-inferiority, phase 3, randomized controlled trial of high-risk prostate cancer patients of treated with either conventionally fractionated radiotherapy (CFRT) or hypofractionated radiotherapy (HFRT). The 7 years' pre-planned analysis showed that HFRT (68 Gy in 25 fractions) was as effective and well tolerated as CFRT (76 Gy in 38 fractions). In this posthoc analysis we aim to report the genitourinary (GU) and gastrointestinal (GI) toxicities associated with radiation therapy techniques: intensity-modulated radiotherapy (IMRT) and 3D-conformal radiotherapy (3D-CRT).

MATERIALS/METHODS

PCS5 randomized patients in a 1:1 ratio to receive either CFRT or HFRT. All patients received long term neoadjuvant, concurrent and adjuvant androgen suppression, with a median duration of 24 months. The toxicities were reported as per the Common Terminology Criteria for Adverse Events version 4. Acute toxicities were defined as presenting ≤ 180 days post-RT start and delayed > 180 days. The cumulative acute and delayed GI and GU toxicities were classified in grade groups: grade 1 or higher (G1+), G2+, and G3+. For each grade group, acute and delayed, we performed multivariable logistic regression analyses, adjusting for age, CTV volume, diabetes, fractionation (CRFT or HFRT), hypertension, and stage < T3b or ≥ T3b. For efficacy analyses cox-regression was utilized. A p-value < 0.05 was considered significant.

RESULTS

Three hundred twenty of the 329 patients enrolled in the trial were included in this posthoc analyses. The mean age was 71.4 ± 6.1 years, and the mean CTV volume (n = 219) was 47.25 ± 19.9 cc. IMRT was used in 195 (60.6%) patients and 3D-CRT in 125 (39.1%) patients. Multivariable logistic regression showed a significant difference in favor of IMRT for GI G2+ acute toxicity (OR = 0.285 [0.14-0.59]; CI: 95%; p<0.001) and GI G2+ delayed toxicity (OR = 0.202 [0.60-0.69]; CI: 95%; p = 0.01). There were no differences in G3+ GI or GU toxicities and there were no grade 4 toxicities. There were no differences in efficacy at 7 years between the two treatment technics. Outcomes for IMRT vs. 3D-CRT respectively, overall survival (81.5% vs 79.2%; HR: 0.92 [0.55-1.53]; CI: 95%; p-value: 0.74), distant metastasis free survival (90,7% vs 92.8%; HR: 1.4 [0.63-3.1]; CI: 95%; p-value: 0.42), prostate cancer mortality (95.8% vs. 92.2%; HR: 0.93 [0.32-2.67]; CI: 95%; p-value: 0.89), and biochemical failure (85.1% vs 88%; HR: 1.35 [0.72-2.52]; CI: 95%; p-value: 0.35).

CONCLUSION

This is the first phase 3 randomized controlled trial assessing the use of HFRT vs. CFRT, exclusively in high-risk prostate cancer patients. Given that our efficacy data at 7 years follow-up establishes moderate HFRT as a new standard of care and no difference between IMRT and 3D-CRT, we strongly recommend that patients who are treated with EBRT should receive IMRT, given the reduced acute and delayed grade 2 or higher GI toxicities.

Preparing for the next viral threat with broad-spectrum antivirals

There is a large global unmet need for the development of countermeasures to combat hundreds of viruses known to cause human disease and for the establishment of a therapeutic portfolio for future pandemic preparedness. Most approved antiviral therapeutics target proteins encoded by a single virus, providing a narrow spectrum of coverage. This, combined with the slow pace and high cost of drug development, limits the scalability of this direct-acting antiviral (DAA) approach. Here, we summarize progress and challenges in the development of broad-spectrum antivirals that target either viral elements (proteins, genome structures, and lipid envelopes) or cellular proviral factors co-opted by multiple viruses via newly discovered compounds or repurposing of approved drugs. These strategies offer new means for developing therapeutics against both existing and emerging viral threats that complement DAAs.

Anticancer pan-ErbB inhibitors reduce inflammation and tissue injury and exert broad-spectrum antiviral effects

Targeting host factors exploited by multiple viruses could offer broad-spectrum solutions for pandemic preparedness. Seventeen candidates targeting diverse functions emerged in a screen of 4,413 compounds for SARS-CoV-2 inhibitors. We demonstrated that lapatinib and other approved inhibitors of the ErbB family receptor tyrosine kinases suppress replication of SARS-CoV-2, Venezuelan equine encephalitis virus (VEEV), and other emerging viruses with a high barrier to resistance. Lapatinib suppressed SARS-CoV-2 entry and later stages of the viral life cycle and showed synergistic effect with the direct-acting antiviral nirmatrelvir. We discovered that ErbB1, 2 and 4 bind SARS-CoV-2 S1 protein and regulate viral and ACE2 internalization, and they are required for VEEV infection. In human lung organoids, lapatinib protected from SARS-CoV-2-induced activation of ErbB-regulated pathways implicated in non-infectious lung injury, pro-inflammatory cytokine production, and epithelial barrier injury. Lapatinib suppressed VEEV replication, cytokine production and disruption of the blood-brain barrier integrity in microfluidic-based human neurovascular units, and reduced mortality in a lethal infection murine model. We validated lapatinib-mediated inhibition of ErbB activity as an important mechanism of antiviral action. These findings reveal regulation of viral replication, inflammation, and tissue injury via ErbBs and establish a proof-of-principle for a repurposed, ErbB-targeted approach to combat emerging viruses.

Numb-associated kinases are required for SARS-CoV-2 infection and are cellular targets for antiviral strategies

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose serious threats to global health. We previously reported that AAK1, BIKE and GAK, members of the Numb-associated kinase family, control intracellular trafficking of multiple RNA viruses during viral entry and assembly/egress. Here, using both genetic and pharmacological approaches, we probe the functional relevance of NAKs for SARS-CoV-2 infection. siRNA-mediated depletion of AAK1, BIKE, GAK, and STK16, the fourth member of the NAK family, suppressed SARS-CoV-2 infection in human lung epithelial cells. Both known and novel small molecules with potent AAK1/BIKE, GAK or STK16 activity suppressed SARS-CoV-2 infection. Moreover, combination treatment with the approved anti-cancer drugs, sunitinib and erlotinib, with potent anti-AAK1/BIKE and GAK activity, respectively, demonstrated synergistic effect against SARS-CoV-2 infection in vitro. Time-of-addition experiments revealed that pharmacological inhibition of AAK1 and BIKE suppressed viral entry as well as late stages of the SARS-CoV-2 life cycle. Lastly, suppression of NAKs expression by siRNAs inhibited entry of both wild type and SARS-CoV-2 pseudovirus. These findings provide insight into the roles of NAKs in SARS-CoV-2 infection and establish a proof-of-principle that pharmacological inhibition of NAKs can be potentially used as a host-targeted approach to treat SARS-CoV-2 with potential implications to other coronaviruses.

The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection

The signaling pathways and cellular functions regulated by the four Numb-associated kinases are largely unknown. We reported that AAK1 and GAK control intracellular trafficking of RNA viruses and revealed a requirement for BIKE in early and late stages of dengue virus (DENV) infection. However, the downstream targets phosphorylated by BIKE have not yet been identified. Here, to identify BIKE substrates, we conducted a barcode fusion genetics-yeast two-hybrid screen and retrieved publicly available data generated via affinity-purification mass spectrometry. We subsequently validated 19 of 47 putative BIKE interactors using mammalian cell-based protein-protein interaction assays. We found that CLINT1, a cargo-specific adapter implicated in bidirectional Golgi-to-endosome trafficking, emerged as a predominant hit in both screens. Our experiments indicated that BIKE catalyzes phosphorylation of a threonine 294 CLINT1 residue both in vitro and in cell culture. Our findings revealed that CLINT1 phosphorylation mediates its binding to the DENV nonstructural 3 protein and subsequently promotes DENV assembly and egress. Additionally, using live-cell imaging we revealed that CLINT1 cotraffics with DENV particles and is involved in mediating BIKE's role in DENV infection. Finally, our data suggest that additional cellular BIKE interactors implicated in the host immune and stress responses and the ubiquitin proteasome system might also be candidate phosphorylation substrates of BIKE. In conclusion, these findings reveal cellular substrates and pathways regulated by the understudied Numb-associated kinase enzyme BIKE, a mechanism for CLINT1 regulation, and control of DENV infection via BIKE signaling, with potential implications for cell biology, virology, and host-targeted antiviral design.

Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription

Cellular exonucleases involved in the processes that regulate RNA stability and quality control have been shown to restrict or to promote the multiplication cycle of numerous RNA viruses. Influenza A viruses are major human pathogens that are responsible for seasonal epidemics, but the interplay between viral proteins and cellular exonucleases has never been specifically studied. Here, using a stringent interactomics screening strategy and an siRNA-silencing approach, we identified eight cellular factors among a set of 75 cellular proteins carrying exo(ribo)nuclease activities or involved in RNA decay processes that support influenza A virus multiplication. We show that the exoribonuclease ERI1 interacts with the PB2, PB1 and NP components of the viral ribonucleoproteins and is required for viral mRNA transcription. More specifically, we demonstrate that the protein-protein interaction is RNA dependent and that both the RNA binding and exonuclease activities of ERI1 are required to promote influenza A virus transcription. Finally, we provide evidence that during infection, the SLBP protein and histone mRNAs co-purify with vRNPs alongside ERI1, indicating that ERI1 is most probably recruited when it is present in the histone pre-mRNA processing complex in the nucleus.

BIKE regulates dengue virus infection and is a cellular target for broad-spectrum antivirals

Global health is threatened by emerging viruses, many of which lack approved therapies and effective vaccines, including dengue, Ebola, and Venezuelan equine encephalitis. We previously reported that AAK1 and GAK, two of the four members of the understudied Numb-associated kinases (NAK) family, control intracellular trafficking of RNA viruses. Nevertheless, the role of BIKE and STK16 in viral infection remained unknown. Here, we reveal a requirement for BIKE, but not STK-16, in dengue virus (DENV) infection. BIKE mediates both early (postinternalization) and late (assembly/egress) stages in the DENV life cycle, and this effect is mediated in part by phosphorylation of a threonine 156 (T156) residue in the μ subunit of the adaptor protein (AP) 2 complex. Pharmacological compounds with potent anti-BIKE activity, including the investigational anticancer drug 5Z-7-oxozeaenol and more selective inhibitors, suppress DENV infection both in vitro and ex vivo. BIKE overexpression reverses the antiviral activity, validating that the mechanism of antiviral action is, at least in part, mediated by BIKE. Lastly, 5Z-7-oxozeaenol exhibits antiviral activity against viruses from three unrelated RNA viral families with a high genetic barrier to resistance. These findings reveal regulation of poorly understood stages of the DENV life cycle via BIKE signaling and establish a proof-of-principle that pharmacological inhibition of BIKE can be potentially used as a broad-spectrum strategy against acute emerging viral infections.

Overview of acute renal manifestations in cancer patients

Acute kidney injury is frequently encountered in patients with malignancy and is associated with prolonged hospitalization, significant morbidity, and increased mortality. Thorough evaluation is required to identify possible contributing factors, which may range from relatively easily reversible pre-renal causes to complex cancer-specific aetiologies. This review will serve as a practical guide for acute care physicians on the acute medical unit to the assessment and initial management of cancer patients presenting with acute kidney injury.

P5505Inflammation implicated in the aetiology of major vascular and non-vascular diseases in East Asians

Background

Mendelian randomisation (MR) studies using genetic variants in the IL6R gene encoding the interleukin-6 (IL-6) receptor have demonstrated that IL-6 plays a causal role in the aetiology of coronary heart disease (CHD) in European populations, with implications for the development of drugs targeting inflammation-related pathways. It is less clear whether IL-6 signalling plays a causal role in vascular disease or major non-vascular diseases in East Asians.

Purpose

Using an MR approach, we investigated associations of altered IL-6 signalling with subtypes of CHD, stroke, cancer and respiratory disease in a large East Asian cohort.

Methods

In approximately 150,000 Chinese adults from the China Kadoorie Biobank, we investigated associations of rs7529229 (in strong linkage disequilibrium, r2=0.99, with the IL6R Asp358Ala variant rs2228145) with blood biomarkers and selected disease events in which inflammation has previously been implicated. First, we used linear regression to quantify the per-allele association of rs7529229 with levels in plasma of log-transformed C-reactive protein (CRP) (n=17,866), fibrinogen (n=9,255), and IL-6 protein (n=633). Second, we used logistic regression to evaluate the association of rs7529229 with incidence of CHD, stroke, cancer, and respiratory disease events. All models were adjusted for age, age-squared, sex (except breast cancer), and case ascertainment (for CRP and fibrinogen), and stratified by recruitment region. We assessed significance at a 5% false discovery rate.

Results

IL6R rs7529229 C-allele was associated with lower log CRP (–0.11 SDs per C-allele; p=4.9x10–25) and log fibrinogen (–0.07 SDs; p=2.2x10–7), and higher log IL-6 (0.15 SDs; p=0.011) (Figure 1), mimicking therapeutic blockade of IL6R. IL6R rs7529229 was associated with a lower risk of acute myocardial infarction (n=4,047 cases; OR: 0.92 [95% CI 0.88–0.96] per C-allele; p=2.8x10–4), with the association similar for fatal and non-fatal cases (Figure 2). There was no evidence of association with ischaemic stroke (n=18,315; OR: 1.00 [0.98–1.03]; p=0.90) or intracerebral haemorrhage (n=7,372; OR: 1.03 [0.99–1.07]; p=0.10). For non-cardiovascular diseases, the IL6R rs7529229 was associated with a lower risk of oesophageal (n=824; OR: 0.88 [0.79–0.97] per C-allele; p=0.013) and colorectal (n=1,151; OR: 0.89 [0.82–0.97]; p=8.3x10–3) cancers, but a higher risk of tuberculosis (n=1,017; OR: 1.15 [1.05–1.26]; p=2.4x10–3).

Conclusion

The results of the present study are consistent with a causal role for the IL-6 signalling pathway in the aetiology of myocardial infarction and some cancers, but not of stroke. These findings provide further genetic support for drug development targeting inflammation in the prevention and treatment of coronary and selected cancer outcomes.

Acknowledgement/Funding

Kadoorie Charitable Foundation, UK Wellcome Trust, Chinese Ministry of Science and Technology, BHF, CRUK, NIHR

In silico analysis revealed Zika virus miRNAs associated with viral pathogenesis through alteration of host genes involved in immune response and neurological functions

BACKGROUND

The concurrent Zika Virus (ZIKV) outbreaks in the United States and Northeast Brazil have evoked global surveillance. Zika infection has been correlated with severe clinical symptoms, such as microcephaly, Guillain-Barré syndrome, and other congenital brain abnormalities. Recent data suggest that ZIKV predominantly targets neural progenitor cells leading to neurological impairment. Despite the clinical evidence, detailed experimental mechanism of ZIKV neurotropic pathogenesis has not been fully understood yet. Here we hypothesized that ZIKV produces miRNAs, which target essential host genes involved in various cellular pathways facilitating their survival through immune evasion and progression of disease during brain development.

METHODS

From genome sequence information using several bioinformatic tools, we predicted pri-miRNAs, pre-miRNAs, and finally the mature miRNAs produced by ZIKV. We also identified their target genes and performed functional enrichment analysis to identify the biological processes associated with these genes. Finally, we analyzed a publicly available RNA-seq data set to determine the altered expression level of the targeted genes.

RESULTS

From ZIKV genome sequence, we identified and validated 47 putative novel miRNAs. Functional enrichment of the targeted genes demonstrates the involvement of various biological pathways regulating cellular signaling, neurological functions, cancer, and fetal development. The expression analysis of these genes showed that ZIKV-produced miRNAs downregulate the key genes involved in these pathways, which in turn may lead to impaired brain development.

CONCLUSIONS

Our finding proposes novel ZIKV miRNAs and their targets, which upon experimental validation could help developing new therapeutics to combat ZIKV infection and minimize ZIKV-mediated pathologies.

Screening and identification of quorum sensing degraders from live feed Artemia

Quorum sensing (QS) is bacterial cell-to-cell communication with small signal molecules such as acyl-homoserine lactones (AHL) that control a number of phenotypes including the regulation of virulence determinants in pathogenic bacteria. Therefore, quorum sensing degrader has been suggested as one of the biocontrol strategies to fight bacterial infections. In the present study, different bacterial QS degrader strains were isolated from Artemia and screened using Chromobacterium violaceum CV026 bioassay. The results showed that six bacterial strains (four Gram-positive and two Gram-negative) isolated from Artemia were able to degrade AHL in two different in vitro assays. All the strains were later identified through 16S rRNA gene sequencing as Rhodococcus opacus, Strepsporangium roseum, Streptomyces alboniger, Enterobacter clocae and Bacillus litoralis. Highest bacterial AHL degrader, Bacillus litoralis BP-ART/6 fully degraded 10 ppm AHL in 9 hrs. The present study showed that bacterial strains isolated from Artemia can act as a QS degrader. ?

Characteristics of Feeding Practices and Nutritional Status of Infants in Selected Villages at Dhamrai

Infants are the most vulnerable group among all the age groups in our society. Breastfeeding decisions and practices are influenced by multiple factors including knowledge, attitude and beliefs. This rural based cross sectional descriptive study carried out among 320 mothers having infant up to 1 year of selected villages at Dhamrai from 7th August to 31 th January 2014, to determine the characteristics of feeding practices and nutritional status of infants. Near fifty. percent infants belonged to age group 9-12 months and of them one third were more than 8 kg. Regarding feeding status 284(88.8%) of respondents got colostrum's bit about fifty-five percent mother did not know the benefit of exclusive breastfeeding. The observation regarding complementary feeding 142(50.9%) infants were started after six months of age and the common types of complementary food were khichuri (49.7%), shagu, suji (21.5%), fruit juice (6.8%) given as family food. It was found that 208(65%) mothers were encouraged by doctors to practice weaning food. The prevalence of severe underweight and moderate underweight in the studied children were 10.9% and 14.1% respectively, the prevalence of moderate and severe wasting children was 6.2% and 3.2% respectively and the prevalence of severely and moderately stunted children were 8.3% and 10.9% respectively. Proper breastfeeding practices are effective ways for reducing infant morbidity and mortality. So it may be concluded that correct breast feeding practices should be supported and promoted to improve the well-being of infants.

Gender Differentials In Nutritional Status of Elderly People In Selected Rural Areas of Bangladesh

Background: The present cross sectional study was undertaken to assess the food habits and nutritional status among elderly people in rural Bangladesh and to compare the same between male and female. A simple random sampling and geographical re-conciliation method was used to select the study population. All the patients in a pre-publicized medical camp were approached and a total of 186 male and 237 female participated in the study. Data were collected through face to face interview with a semi-structured questionnaire and anthropometric measures were collected using instruments. Associations between dietary intake and World Health Organization (WHO) referred Body Mass Index (BMI) range was done using cross tabulation. Results: The mean age of male was 67.69 years and that of female was 65.46 years. The female subjects were higher than males in number in this study. The rate of male literacy was found to be 39.8% where literacy among the female was 13.9%. Among all, 79.6% males were found to be living with their spouse where the rate of living with spouse among the female amounted 53.2%. About half of elderly people were found to be living under poor and 32% in low middle class socio-economic condition. Study revealed that 80.6% male and 78.9% female got no opportunity to take protein-rich food more than three days per week. Again 95.7% male and 97.5% female had no opportunity take more than two servings of protein rich food per week. The similar case occurred in case of taking fatty food, vegetable and fruits per week. Similarly 100 % male and 99.6% female reported that they were taking more than two servings of fatty food per week. No significant association was found between BMI and food intake. The significance was tested by Pearson chi-square. In this test the p –value for protein rich food was 0.234 (p?0.05), while fatty food (0.712), vegetable (0.502) and fruits (0.274) which was more than referred significance p-value ?0.05. Hence, the study confirmed that malnutrition remains a common problem among older people living in rural Bangladesh though there is no significant association was found between food intake and nutrition. Conclusion: Management of malnutrition in case of elderly population requires a multidisciplinary approach that treats pathology and uses both social and dietary forms of intervention. Bangladesh Journal of Medical Science Vol. 12 No. 02 April’13 Page 150-157 DOI: http://dx.doi.org/10.3329/bjms.v12i2.14943

Search for new physics with same-sign isolated dilepton events with jets and missing transverse energy

A search for new physics is performed in events with two same-sign isolated leptons, hadronic jets, and missing transverse energy in the final state. The analysis is based on a data sample corresponding to an integrated luminosity of 4.98 fb(-1) produced in pp collisions at a center-of-mass energy of 7 TeV collected by the CMS experiment at the LHC. This constitutes a factor of 140 increase in integrated luminosity over previously published results. The observed yields agree with the standard model predictions and thus no evidence for new physics is found. The observations are used to set upper limits on possible new physics contributions and to constrain supersymmetric models. To facilitate the interpretation of the data in a broader range of new physics scenarios, information on the event selection, detector response, and efficiencies is provided.

Azimuthal anisotropy of charged particles at high transverse momenta in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

The azimuthal anisotropy of charged particles in Pb-Pb collisions at sqrt[s(NN)]=2.76  TeV is measured with the CMS detector at the LHC over an extended transverse momentum (p(T)) range up to approximately 60  GeV/c. The data cover both the low-p(T) region associated with hydrodynamic flow phenomena and the high-p(T) region where the anisotropies may reflect the path-length dependence of parton energy loss in the created medium. The anisotropy parameter (v2) of the particles is extracted by correlating charged tracks with respect to the event-plane reconstructed by using the energy deposited in forward-angle calorimeters. For the six bins of collision centrality studied, spanning the range of 0-60% most-central events, the observed v2 values are found to first increase with p(T), reaching a maximum around p(T)=3  GeV/c, and then to gradually decrease to almost zero, with the decline persisting up to at least pp(T)=40  GeV/c over the full centrality range measured.

Search for dark matter and large extra dimensions in pp collisions yielding a photon and missing transverse energy

Results are presented from a search for new physics in the final state containing a photon (γ) and missing transverse energy (E[combininb /](T)). The data correspond to an integrated luminosity of 5.0 fb(-1) collected in pp collisions at √[s]=7 TeV by the CMS experiment. The observed event yield agrees with standard-model expectations for the γ+E[combininb /](T) events. Using models for the production of dark-matter particles (χ), we set 90% confidence level (C.L.) upper limits of 13.6-15.4 fb on χ production in the γ+E[combininb /](T) state. These provide the most sensitive upper limits for spin-dependent χ-nucleon scattering for χ masses (M(χ)) between 1 and 100 GeV. For spin-independent contributions, the present limits are extended to M(χ)<3.5 GeV. For models with 3-6 large extra dimensions, our data exclude extra-dimensional Planck scales between 1.64 and 1.73 TeV at 95% C.L.

SU-E-J-28: Comparison of IGRT Shift Data Between Prostate Gland and Prostate Bed Obtained from Ct-On-Rails

PURPOSE

The daily shifts of prostate gland have been intensively reported in literatures. However, few papers reported daily shifts of prostate bed due to several practical difficulties (e.g. limited soft tissue contrast in MVCT and CBCT and significant deformation of prostate cavity). We have routinely performed IGRT for both prostate gland and bed with ct-on-rails, and the superior image quality allows us not only to differentiate both bony anatomy and soft tissue contrast of prostate gland and bed. In this study, we investigated if the shift of prostate bed is signifiant difference from that of prostate gland.

METHODS

we reviewed shift data of 50 prostate gland patients who underwent 43 fractions and 22 patients of prostatectomy underwent 37 fractions. In total 2150 CT scans were reviewed for prostate gland and 814 scans for prostate bed.

RESULTS

Of the reviewed 814 CT images from 22 prostate bed patients, the standard deviation of shift was found to be 5.9 mm in AP direction (ranges from -22.4mm to 22mm), 3.2mm in SI direction (ranges from -14mm to 14mm), and 4.1mm in lateral direction (ranges from -15mm to 22mm). Of the 2150 CT images of prostate gland from 50 patients, the standard deviation of the shift was found to be 5.4 mm in AP direction (-20mm to 18 mm), 5.0mm in SI direction (-26mm to 20mm), and 4.3mm in lateral direction (range from-15 to 30mm). F tests of systematic /random shift distribution in three orthogonal directions between prostate gland and prostate bed were subsequently performed, it was found that the systematic shift in SI direction for prostate bed is smaller than for prostate gland (p=0.003).

CONCLUSIONS

Our result suggests no significant difference existing in shift between prostate bed and gland. Therefore strategies for daily prostate gland motion can be directly applied to prostate bed.

Search for the standard model Higgs boson in the decay channel H→ZZ→4ℓ in pp collisions at √s=7 TeV

A search for a Higgs boson in the four-lepton decay channel H→ZZ, with each Z boson decaying to an electron or muon pair, is reported. The search covers Higgs boson mass hypotheses in the range of 110<m(H)<600 GeV. The analysis uses data corresponding to an integrated luminosity of 4.7 fb(-1) recorded by the CMS detector in pp collisions at √s=7 TeV from the LHC. Seventy-two events are observed with four-lepton invariant mass m(4ℓ)>100 GeV (with 13 below 160 GeV), while 67.1±6.0 (9.5±1.3) events are expected from background. The four-lepton mass distribution is consistent with the expectation of standard model background production of ZZ pairs. Upper limits at 95% confidence level exclude the standard model Higgs boson in the ranges of 134-158 GeV, 180-305 GeV, and 340-465 GeV. Small excesses of events are observed around masses of 119, 126, and 320 GeV, making the observed limits weaker than expected in the absence of a signal.

Search for signatures of extra dimensions in the diphoton mass spectrum at the large hadron collider

A search for signatures of extra spatial dimensions in the diphoton invariant-mass spectrum has been performed with the CMS detector at the LHC. No excess of events above the standard model expectation is observed using a data sample collected in proton-proton collisions at √s=7 TeV corresponding to an integrated luminosity of 2.2 fb(-1). In the context of the large-extra-dimensions model, lower limits are set on the effective Planck scale in the range of 2.3-3.8 TeV at the 95% confidence level. These limits are the most restrictive bounds on virtual-graviton exchange to date. The most restrictive lower limits to date are also set on the mass of the first graviton excitation in the Randall-Sundrum model in the range of 0.86-1.84 TeV, for values of the associated coupling parameter between 0.01 and 0.10.

Search for a vectorlike quark with charge 2/3 in t+Z events from pp collisions at √s=7 TeV

A search for pair-produced heavy vectorlike charge-2/3 quarks, T, in pp collisions at a center-of-mass energy of 7 TeV, is performed with the CMS detector at the LHC. Events consistent with the flavor-changing-neutral-current decay of a T quark to a top quark and a Z boson are selected by requiring two leptons from the Z-boson decay, as well as an additional isolated charged lepton. In a data sample corresponding to an integrated luminosity of 1.14  fb(-1), the number of observed events is found to be consistent with the standard model background prediction. Assuming a branching fraction of 100% for the decay T→tZ, a T quark with a mass less than 475  GeV/c(2) is excluded at the 95% confidence level.

Search for supersymmetry at the LHC in events with jets and missing transverse energy

A search for events with jets and missing transverse energy is performed in a data sample of pp collisions collected at √s=7 TeV by the CMS experiment at the LHC. The analyzed data sample corresponds to an integrated luminosity of 1.14 fb(-1). In this search, a kinematic variable α(T) is used as the main discriminator between events with genuine and misreconstructed missing transverse energy. No excess of events over the standard model expectation is found. Exclusion limits in the parameter space of the constrained minimal supersymmetric extension of the standard model are set. In this model, squark masses below 1.1 TeV are excluded at 95% C.L. Gluino masses below 1.1 TeV are also ruled out at 95% C.L. for values of the universal scalar mass parameter below 500 GeV.

Search for new physics with a monojet and missing transverse energy in pp collisions at √s = 7 TeV

A study of events with missing transverse energy and an energetic jet is performed using pp collision data at a center-of-mass energy of 7 TeV. The data were collected by the CMS detector at the LHC, and correspond to an integrated luminosity of 36 pb(-1). An excess of these events over standard model contributions is a signature of new physics such as large extra dimensions and unparticles. The number of observed events is in good agreement with the prediction of the standard model, and significant extension of the current limits on parameters of new physics benchmark models is achieved.

Search for B(s)(0) → μ+ μ- and B(0) → μ+ μ- decays in pp collisions at sqrt[s] = 7 TeV

A search for the rare decays B(s)(0) → μ+ μ- and B(0) → μ+ μ- is performed in pp collisions at sqrt[s] = 7 TeV, with a data sample corresponding to an integrated luminosity of 1.14 fb(-1), collected by the CMS experiment at the LHC. In both cases, the number of events observed after all selection requirements is consistent with expectations from background and standard-model signal predictions. The resulting upper limits on the branching fractions are B(B(s)(0) → μ+ μ-) < 1.9 × 10(-8) and B(B(0) → μ+ μ-)<4.6 × 10(-9), at 95% confidence level.