Checklist for studies of HIV drug resistance prevalence or incidence: rationale and recommended use

HIV drug resistance (HIVDR) is a major challenge to the effectiveness of antiretroviral therapy. Global efforts in addressing HIVDR require clear, transparent, and replicable reporting in HIVDR studies. We describe the rationale and recommended use of a checklist that should be included in reports of HIVDR incidence and prevalence. After preliminary consultations with experts on HIVDR and establishing the need for guidance on HIVDR reporting, we used a sequential, explanatory, mixed methods approach to create the checklist; together with the accompanying articles, the checklist was reviewed by the authors and validated externally. The checklist for studies on HIVDR prevalence or incidence (CEDRIC-HIV) includes 15 recommended items that would enhance transparency and facilitate interpretation, comparability, and replicability of HIVDR studies. CEDRIC-HIV will help authors of HIVDR studies prepare research reports and assist reviewers and editors in assessments of completeness of reporting. The checklist will also facilitate statistical pooling and interpretation of HIVDR data.

How well do polygenic risk scores identify men at high risk for prostate cancer? Systematic review and meta-analysis

OBJECTIVES

Genome-wide association studies have revealed over 200 genetic susceptibility loci for prostate cancer (PCa). By combining them, polygenic risk scores (PRS) can be generated to predict risk of PCa. We summarize the published evidence and conduct meta-analyses of PRS as a predictor of PCa risk in Caucasian men.

PATIENTS AND METHODS

Data were extracted from 59 studies, with 16 studies including 17 separate analyses used in the main meta-analysis with a total of 20,786 cases and 69,106 controls identified through a systematic search of ten databases. Random effects meta-analysis was used to obtain pooled estimates of area under the receiver-operating characteristic curve (AUC). Meta-regression was used to assess the impact of number of single-nucleotide polymorphisms (SNPs) incorporated in PRS on AUC. Heterogeneity is expressed as I² scores. Publication bias was evaluated using funnel plots and Egger tests.

RESULTS

The ability of PRS to identify men with PCa was modest (pooled AUC 0.63, 95% CI 0.62-0.64) with moderate consistency (I² 64%). Combining PRS with clinical variables increased the pooled AUC to 0.74 (0.68-0.81). Meta-regression showed only negligible increase in AUC for adding incremental SNPs. Despite moderate heterogeneity, publication bias was not evident.

CONCLUSION

Typically, PRS accuracy is comparable to PSA or family history with a pooled AUC value 0.63 indicating mediocre performance for PRS alone.

Recommendations for the diagnosis and management of vaccine-induced immune thrombotic thrombocytopenia

There have recently been safety concerns regarding an increased risk of vaccine-induced immune thrombotic thrombocytopenia (VITT) following administration of SARS-CoV-2 adenoviral vector vaccines. The Southern African Society of Thrombosis and Haemostasis reviewed the emerging literature on this idiosyncratic complication. A draft document was produced and revised by consensus agreement by a panel of professionals from various specialties. The recommendations were adjudicated by independent international experts to avoid local bias. We present concise, practical guidelines for the clinical management of VITT.

Phylogenetic Clustering among Asylum Seekers with New HIV-1 Diagnoses in Montreal, QC, Canada

Migrants are at an increased risk of HIV acquisition. We aimed to use phylogenetics to characterize transmission clusters among newly-diagnosed asylum seekers and to understand the role of networks in local HIV transmission. Retrospective chart reviews of asylum seekers linked to HIV care between 1 June 2017 and 31 December 2018 at the McGill University Health Centre and the Jewish General Hospital in Montreal were performed. HIV-1 partial pol sequences were analyzed among study participants and individuals in the provincial genotyping database. Trees were reconstructed using MEGA10 neighbor-joining analysis. Clustering of linked viral sequences was based on a strong bootstrap support (>97%) and a short genetic distance (<0.01). Overall, 10,645 provincial sequences and 105 asylum seekers were included. A total of 13/105 participant sequences (12%; n = 7 males) formed part of eight clusters. Four clusters (two to three people) included only study participants (n = 9) and four clusters (two to three people) included four study participants clustered with six individuals from the provincial genotyping database. Six (75%) clusters were HIV subtype B. We identified the presence of HIV-1 phylogenetic clusters among asylum seekers and at a population-level. Our findings highlight the complementary role of cohort data and population-level genotypic surveillance to better characterize transmission clusters in Quebec.

Comparative clinical prognosis of massive and non-massive pulmonary embolism: A registry-based cohort study

AIMS

Little is known about the prognosis of patients with massive pulmonary embolism (PE) and its risk of recurrent venous thromboembolism (VTE) compared with non-massive PE, which may inform clinical decisions. Our aim was to compare the risk of recurrent VTE, bleeding, and mortality after massive and non-massive PE during anticoagulation and after its discontinuation.

METHODS AND RESULTS

We included all participants in the RIETE registry who suffered a symptomatic, objectively confirmed segmental or more central PE. Massive PE was defined by a systolic hypotension at clinical presentation (<90 mm Hg). We compared the risks of recurrent VTE, major bleeding, and mortality using time-to-event multivariable competing risk modeling. There were 3.5% of massive PE among 38 996 patients with PE. During the anticoagulation period, massive PE was associated with a greater risk of major bleeding (subhazard ratio [sHR] 1.72, 95% confidence interval [CI] 1.28-2.32), but not of recurrent VTE (sHR 1.15, 95% CI 0.75-1.74) than non-massive PE. An increased risk of mortality was only observed in the first month after PE. After discontinuation of anticoagulation, among 11 579 patients, massive PE and non-massive PE had similar risks of mortality, bleeding, and recurrent VTE (sHR 0.85, 95% CI 0.51-1.40), but with different case fatality of recurrent PE (11.1% versus 2.4%, P = .03) and possibly different risk of recurrent fatal PE (sHR 3.65, 95% CI 0.82-16.24).

CONCLUSION

In this large prospective registry, the baseline hemodynamic status of the incident PE did not influence the risk of recurrent VTE, during and after the anticoagulation periods, but was possibly associated with recurrent PE of greater severity.

D-dimer levels and risk of recurrence following provoked venous thromboembolism: findings from the RIETE registry

BACKGROUND

Patients with venous thromboembolism (VTE) secondary to transient risk factors may develop VTE recurrences after discontinuing anticoagulation. Identifying at-risk patients could help to guide the duration of therapy.

METHODS

We used the RIETE database to assess the prognostic value of d-dimer testing after discontinuing anticoagulation to identify patients at increased risk for recurrences. Transient risk factors were classified as major (postoperative) or minor (pregnancy, oestrogen use, immobilization or recent travel).

RESULTS

In December 2018, 1655 VTE patients with transient risk factors (major 460, minor 1195) underwent d-dimer measurements after discontinuing anticoagulation. Amongst patients with major risk factors, the recurrence rate was 5.74 (95% CI: 3.19-9.57) events per 100 patient-years in those with raised d-dimer levels and 2.68 (95% CI: 1.45-4.56) in those with normal levels. Amongst patients with minor risk factors, the rates were 7.79 (95% CI: 5.71-10.4) and 3.34 (95% CI: 2.39-4.53), respectively. Patients with major risk factors and raised d-dimer levels (n = 171) had a nonsignificantly higher rate of recurrences (hazard ratio [HR]: 2.14; 95% CI: 0.96-4.79) than those with normal levels. Patients with minor risk factors and raised d-dimer levels (n = 382) had a higher rate of recurrences (HR: 2.34; 95% CI: 1.51-3.63) than those with normal levels. On multivariate analysis, raised d-dimers (HR: 1.74; 95% CI: 1.09-2.77) were associated with an increased risk for recurrences in patients with minor risk factors, not in those with major risk factors.

CONCLUSIONS

Patients with raised d-dimer levels after discontinuing anticoagulant therapy for VTE provoked by a minor transient risk factor were at an increased risk for recurrences.

Hypertrophic cardiomyopathy MYH7 mutation R723G alters mRNA secondary structure

Point mutation R723G in the MYH7 gene causes hypertrophic cardiomyopathy (HCM). Heterozygous patients with this mutation exhibit a comparable allelic imbalance of the MYH7 gene. On average 67% of the total MYH7 mRNA are derived from the MYH7^R723G-allele and 33% from the MYH7^WT allele. Mechanisms underlying mRNA allelic imbalance are largely unknown. We suggest that a different mRNA lifetime of the alleles may cause the allelic drift in R723G patients. A potent regulator of mRNA lifetime is its secondary structure. To test for alterations in the MYH7^R723G mRNA structure we used selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. We show significantly different SHAPE reactivity of wild-type and MYH7^R723G RNA, which is in accordance with bioinformatically predicted structures. Thus, we provide the first experimental evidence for mRNA secondary structure alterations by the HCM point mutation. We assume that this may result in a prolonged lifetime of MYH7^R723G mRNA in vivo and subsequently in the determined allelic imbalance.

Cisplatin and 5-fluorouracil with or without epidermal growth factor receptor inhibition panitumumab for patients with non-resectable, advanced or metastatic oesophageal squamous cell cancer: a prospective, open-label, randomised phase III AIO/EORTC trial (POWER)

BACKGROUND

Palliative chemotherapy of advanced oesophageal squamous cell cancer (ESCC) consists of cisplatin/5-fluorouracil (CF) to target epidermal growth factor receptor (EGFR) with panitumumab (P); chemotherapy enhanced overall survival (OS) in advanced colorectal or squamous cell head and neck cancers. With prospective serum and tumour biomarkers, we tested if P added to CF (CFP) improved OS in advanced ESCC.

PATIENTS AND METHODS

Eligible patients with confirmed ESCC that was not curatively resectable or did not qualify for definitive radiochemotherapy, were randomised 1 : 1 to receive CF [cisplatin (C) 100 mg/m² i.v., day 1; 5-fluorouracil (F) 1000 mg/m² i.v., days 1-4] or CF plus P (9 mg/kg, i.v., day 1, each q3-week cycle) until progressive disease or unacceptable toxicity. Safety was reviewed by the Data Safety Monitoring Board after 40, 70 and 100 patients who completed at least one cycle. After 53 enrolled patients, cisplatin was reduced from 100 mg/m² to 80 mg/m².

RESULTS

The trial was stopped early based on interim efficacy results triggered by the third safety analysis: median OS (mOS) favoured CF over CFP, regardless of cisplatin dose [hazard ratio (HR) 1.77, 95% confidence interval (CI) 1.06-2.98; P = 0.028]. In the final analysis, mOS was 10.2 versus 9.4 months for CF versus CFP, respectively (HR 1.17, 95% CI 0.79-1.75; P = 0.43). One hundred (70.4%) of 142 patients in the safety population died, 51 (51.0%) with CFP. Most deaths were related to disease progression [44/49 (90%) deaths in CF versus 34/51 (67%) deaths in CFP]; objective responses [27/73 (37.0%)] were identical. The most common serious adverse events were kidney injury [3 (4.3%) versus 7 (9.7%)], general health deterioration [5 (7.1%) versus 5 (6.9%)] and dysphagia [4 (5.7%) versus 4 (5.6%)] in CF versus CFP, respectively. There were three (4.3%) and 17 (23.6%) common terminology criteria for adverse events (CTCAE) grade 5 events in CF versus CFP, respectively. Low soluble (s)EGFR levels were associated with better progression-free survival; sEGFR was induced under CFP.

CONCLUSION

EGFR inhibition added to CF did not improve survival in unselected advanced ESCC patients. The results support further liquid biopsy studies.

TRIAL REGISTRATION

ClinicalTrials.gov (NCT01627379) and EudraCT (2010-020606-15).

Assessing the role of transmission chains in the spread of HIV-1 among men who have sex with men in Quebec, Canada

BACKGROUND

Phylogenetics has been used to investigate HIV transmission among men who have sex with men. This study compares several methodologies to elucidate the role of transmission chains in the dynamics of HIV spread in Quebec, Canada.

METHODS

The Quebec Human Immunodeficiency Virus (HIV) genotyping program database now includes viral sequences from close to 4,000 HIV-positive individuals classified as Men who have Sex with Men (MSMs), collected between 1996 and early 2016. Assessment of chain expansion may depend on the partitioning scheme used, and so, we produce estimates from several methods: the conventional Bayesian and maximum likelihood-bootstrap methods, in combination with a variety of schemes for applying a maximum distance criterion, and two other algorithms, DM-PhyClus, a Bayesian algorithm that produces a measure of uncertainty for proposed partitions, and the Gap Procedure, a fast non-phylogenetic approach. Sequences obtained from individuals in the Primary HIV Infection (PHI) stage serve to identify incident cases. We focus on the period ranging from January 1st 2012 to February 1st 2016.

RESULTS AND CONCLUSION

The analyses reveal considerable overlap between chain estimates obtained from conventional methods, thus leading to similar estimates of recent temporal expansion. The Gap Procedure and DM-PhyClus suggest however moderately different chains. Nevertheless, all estimates stress that longer older chains are responsible for a sizeable proportion of the sampled incident cases among MSMs. Curbing the HIV epidemic will require strategies aimed specifically at preventing such growth.

In-depth Sampling of High-risk Populations to Characterize HIV Transmission Epidemics Among Young MSM Using PrEP in France and Quebec

Background

A better understanding of HIV transmission dynamics among populations at high risk is important for development of prevention strategies. We determined HIV transmission networks from infected individuals enrolled in the pre-exposure prophylaxis (PrEP) IPERGAY trial in combination with the ANRS PRIMO and Montreal PHI cohorts to identify and characterize active clusters of transmission in this high-risk population.

Methods

Genotypic resistance tests were performed on plasma samples from 31 IPERGAY participants. Reverse transcriptase sequences were analyzed in combination with unique HIV pol sequences from 1351 individuals enrolled in the PRIMO ANRS cohort (1999–2014) and 511 individuals enrolled in the Montreal PHI cohort (1996–2016). Network analyses were performed to infer putative relationships between all participants.

Results

Overall, 1893 participants were included. Transmission network analyses revealed that 14 individuals (45.2%) from the IPERGAY trial were involved in 13 clusters sampled over a median period (interquartile range) of 2 (0.3–7.8) years, including 7 dyads and 6 larger clusters ranging from 4 to 28 individuals. When comparing characteristics between clustering individuals enrolled in the PRIMO cohort (n = 377) and in IPERGAY (n = 14), we found that IPERGAY participants had a higher viral load (5.93 vs 5.20 log₁₀ copies/mL, P = .032) and reported a higher number of partners in the last 2 months (P < .01).

Conclusions

These results demonstrate high rates of HIV transmission clustering among young high-risk MSM enrolled in the IPERGAY trial. In-depth sampling of high-risk populations may help to uncover unobserved transmission intermediaries and improve prevention efforts that could be targeted to the most active clusters.

New Challenges in HIV Research: Combining Phylogenetic Cluster Size and Epidemiological Data

An exciting new direction in HIV research is centered on using molecular phylogenetics to understand the social and behavioral drivers of HIV transmission. SPOT was an intervention designed to offer HIV point of care testing to men who have sex with men at a community-based site in Montreal, Canada; at the time of testing, a research questionnaire was also deployed to collect data on socio-demographic and behavioral characteristics of participating men. The men taking part in SPOT could be viewed, from the research perspective, as having been recruited via a convenience sample. Among men who were found to be HIV positive, phylogenetic cluster size was measured using a large cohort of HIV-positive individuals in the province of Quebec. The cluster size is likely subject to under-estimation. In this paper, we use SPOT data to evaluate the association between HIV transmission cluster size and the number of sex partners for MSM, after adjusting for the SPOT sampling scheme and correcting for measurement error in cluster size by leveraging external data sources. The sampling weights for SPOT participants were calculated from another study of men who have sex with men in Montreal by fitting a weight-adjusted model, whereas measurement error was corrected using the simulation-extrapolation conditional on covariates approach.

DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

Background

Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they often produce conflicting measures of confidence in clusters. The current study proposes a new Bayesian phylogenetic clustering algorithm, which we refer to as DM-PhyClus (Dirichlet-Multinomial Phylogenetic Clustering), that identifies sets of sequences resulting from quick transmission chains, thus yielding easily-interpretable clusters, without using any ad hoc distance or confidence requirement.

Results

Simulations reveal that DM-PhyClus can outperform conventional clustering methods, as well as the Gap procedure, a pure distance-based algorithm, in terms of mean cluster recovery. We apply DM-PhyClus to a sample of real HIV-1 sequences, producing a set of clusters whose inference is in line with the conclusions of a previous thorough analysis.

Conclusions

DM-PhyClus, by eliminating the need for cutpoints and producing sensible inference for cluster configurations, can facilitate transmission cluster detection. Future efforts to reduce incidence of infectious diseases, like HIV-1, will need reliable estimates of transmission clusters. It follows that algorithms like DM-PhyClus could serve to better inform public health strategies.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2347-3) contains supplementary material, which is available to authorized users.

Thromboxane A2 and Prostacyclin Generation in the Microvasculature of Patients with Atherosclerosis – Effect of Low-Dose Aspirin

Generation of thromboxane A2 (TxA2) and prostacyclin (PGI2) at the site of platelet-vessel wall interaction, i.e. in blood emerging from a standardized injury of the microvasculature made to determine skin bleeding time was investigated in 7 patients with atherosclerosis (angiographically verified obstructions of the femoral arteries) and in 7 normal control subjects apparently free of atherosclerotic lesions. Similar amounts of TxA2 (measured as thromboxane B2, TxB2) were generated at the site of plug formation in the patients with peripheral vascular disease (PVD) and in the control subjects. Significantly lower levels of PGI2 (measured as 6-keto-prostaglandin F1α, 6-keto- PGF1α) were found in blood from an injury of the microvasculature in the patients compared with the controls. These data do not suggest a major role of the platelet prostaglandin metabolism in the development of atherosclerosis. However, decreased synthesis of PGI2 by endothelial cells might contribute to the development and/or progression of atherosclerotic lesions. In the patients with PVD, low-dose aspirin (50 mg/day for 7 days) resulted in a >90% inhibition of the TxB2 production at the site of plug formation. Following low-dose aspirin 6-keto-PcF1α levels were below 20 pg/ml (limit of sensitivity of our radioimmunoassay procedure) in the majority of the samples.

We therefore conclude that in patients with PVD a decreased synthesis of PGI2 by endothelial cells might contribute to the progression of atherosclerosis. Furthermore, low-dose aspirin treatment results in a similar inhibition of the platelet prostaglandin generation as recently observed in healthy subjects.

Von Willebrand Factor Multimer Patterns in Pregnancy-Induced Hypertension

Microangiopathy and disseminated platelet aggregation have been reported in thrombotic thrombocytopenic purpura (TIP) and pregnancy-induced hypertension (PIH). Since unusually large von Willebrand factor (vWF) multimers have been implicated in the evolvement of TTP, we analyzed factor VIII/vWF parameters in patients with PIH. Mean vWF: Ag level was significantly higher in 27 patients with PIH as compared to 20 matched healthy pregnant women (358 ± 160 u/dl vs. 274 ± 125 u/dl, p < 0.05). Moreover, plasma vWF: Ag levels and the ratio of vWF: Ag to factor VIII were found to be linearly correlated to the severity of PIH. In contrast, no significant differences in mean levels of factor VIII and ristocetin cofactor were observed between these groups. Crossed immunoelectrophoresis of vWF revealed a higher incidence of a pre-peak and an increased migration index in the PIH group as compared to the control group (60% vs. 44% and 1.27 ± 0.26 vs. 1.19 ± 0.18, p < 0.01 respectively). Analysis of plasma vWF multimer patterns by 1.4% agarose electrophoresis in 0.1% SDS revealed excessive amounts of large, medium and small size multimers in the PIH patients. Conceivably, the quantitative changes in vWF multimers reflect endothelial injury and may play a role in the microangiopathy observed in PIH.

Successful knock-in of Hypertrophic Cardiomyopathy-mutation R723G into the MYH7 gene mimics HCM pathology in pigs

Familial Hypertrophic Cardiomyopathy (HCM) is the most common inherited cardiac disease. About 30% of the patients are heterozygous for mutations in the MYH7 gene encoding the ß-myosin heavy chain (MyHC). Hallmarks of HCM are cardiomyocyte disarray and hypertrophy of the left ventricle, the symptoms range from slight arrhythmias to sudden cardiac death or heart failure. To gain insight into the underlying mechanisms of the diseases' etiology we aimed to generate genome edited pigs with an HCM-mutation. We used TALEN-mediated genome editing and successfully introduced the HCM-point mutation R723G into the MYH7 gene of porcine fibroblasts and subsequently cloned pigs that were heterozygous for the HCM-mutation R723G. No off-target effects were determined in the R723G-pigs. Surprisingly, the animals died within 24 h post partem, probably due to heart failure as indicated by a shift in the a/ß-MyHC ratio in the left ventricle. Most interestingly, the neonatal pigs displayed features of HCM, including mild myocyte disarray, malformed nuclei, and MYH7-overexpression. The finding of HCM-specific pathology in neonatal R723G-piglets suggests a very early onset of the disease and highlights the importance of novel large animal models for studying causative mechanisms and long-term progression of human cardiac diseases.

Thrombophilic Polymorphisms Are Common in Women with Fetal Loss without Apparent Cause

An association between fetal loss and thrombophilia has recently been described but has not been yet fully elucidated. We have evaluated prospectively the prevalence of the three common thrombophilic polymorphisms (TP) factor V G1691A (Leiden), thermolabile-methyl-enetetrahydrofolate reductase (TL-MTHFR) C677T and factor II G20210A mutations, in 76 women with fetal loss (≥3 in first, ≥2 in second, ≥1 in third trimester) without apparent cause and 106 controls without fetal loss. Thirty seven out of 76 (49%) of the women in the fetal loss group had at least one TP compared to only 23/106 (22%) in the control group (p = 0.0001). Factor V-Leiden was more common in the fetal loss group 24/76 (32%) compared to the control group 11/106 (10%) (OR = 4.0, 95% CI: 1.8-8.8, p <0.001). Five of the 76 patients (7%) were homozygous for factor V-Leiden compared to none of the controls (p = 0.012). A trend, albeit no statistically significant difference was found between women with fetal loss and control groups regarding factor II G20210A (8% vs. 4% respectively, OR = 2.2, 95% CI: 0.6-8.0, p = 0.23) and MTHFR C677T (18% vs. 10% respectively, OR = 1.95, 95% CI: 0.83-4.6, p = 0.12). Combined TP were documented in 6/76 (8%) patients compared to 1/106 (1%) in controls (OR = 9.0, 95% CI: 1.1-76, p = 0.02). Second or third trimester fetal loss were more common cause of pregnancy termination in 37 patients with TP compared to 39 patients without TP (57/158 (36%) vs. 23/135 (17%) respectively, (p = 0.0004). Thrombophilic polymorphisms are common in women with fetal loss without apparent cause and are associated with late pregnancy wastage. Combinations of TP increase the risk for fetal loss.

Gestational Outcome in Thrombophilic Women with Recurrent Pregnancy Loss Treated by Enoxaparin

Inherited and acquired thrombophilia are associated with recurrent pregnancy loss (RPL). We have evaluated the efficacy and safety of the low molecular weight heparin enoxaparin in 50 women, (mean age 26 ± 3 years) with RPL (>3 losses in 1st, >2 losses in 2nd and >1 loss in 3rd trimester) who were found to harbor thrombophilia. Twentyseven had a solitary thrombophilic defect, and twenty-three women had combined thrombophilic defects: 17 – two defects and 6 – three defects. Following diagnosis of thrombophilia, sixty-one subsequent pregnancies were treated with the low molecular weight heparin enoxaparin throughout gestation until 4 weeks after delivery. Dosage was 40 mg/day in women with solitary defect and 80 mg/day in combined defects. Aspirin, 75 mg daily was given in addition to enoxaparin to women with antiphospholipid syndrome. Forty-six out of 61 (75%) gestations treated by enoxaparin resulted in live birth compared to only 38/193 (20%) of the untreated pregnancies in these 50 women prior to diagnosis of thrombophilia (p <0.00001). In 23 women without a single living child following 82 untreated gestations, antithrombotic therapy resulted in 26/31 (84%) successful deliveries (p <0.0001). In 20 women with a prior living child, antithrombotic therapy improved successful delivery from 33/86 (38%) to 20/21 (95%) (p <0.0001). Enoxaparin dose of 40 mg/day resulted in live birth in 24/35 (69%) of gestations, compared to 19/23 (83%) gestations in women treated with 80 mg/day (p = 0.37). Only one thrombotic episode and one mildbleeding episode were noticed during enoxaparin therapy. Enoxaparin is safe and effective in prevention of pregnancy loss in women with inherited and acquired thrombophilia.

Purification of Zika virus RNA-dependent RNA polymerase and its use to identify small-molecule Zika inhibitors

Background

The viral RNA-dependent RNA polymerase (RdRp) enzymes of the Flaviviridae family are essential for viral replication and are logically important targets for development of antiviral therapeutic agents. Zika virus (ZIKV) is a rapidly re-emerging human pathogen for which no vaccine or antiviral agent is currently available.

Methods

To facilitate development of ZIKV RdRp inhibitors, we have established an RdRp assay using purified recombinant ZIKV NS5 polymerase.

Results

We have shown that both the hepatitis C virus (HCV) nucleoside inhibitor sofosbuvir triphosphate and a pyridoxine-derived non-nucleoside small-molecule inhibitor, DMB213, can act against ZIKV RdRp activity at IC 50 s of 7.3 and 5.2 μM, respectively, in RNA synthesis reactions catalysed by recombinant ZIKV NS5 polymerase. Cell-based assays confirmed the anti-ZIKV activity of sofosbuvir and DMB213 with 50% effective concentrations (EC 50 s) of 8.3 and 4.6 μM, respectively. Control studies showed that DMB213 did not inhibit recombinant HIV-1 reverse transcriptase and showed only very weak inhibition of HIV-1 integrase strand-transfer activity. The S604T substitution in motif B of the ZIKV RdRp, which corresponds to the S282T substitution in motif B of HCV RdRp, which confers resistance to nucleotide inhibitors, also conferred resistance to sofosbuvir triphosphate, but not to DMB213. Enzyme assays showed that DMB213 appears to be competitive with natural nucleoside triphosphate (NTP) substrates.

Conclusions

Recombinant ZIKV RdRp assays can be useful tools for the screening of both nucleos(t)ide compounds and non-nucleotide metal ion-chelating agents that interfere with ZIKV replication.

Involvement of the heparanase procoagulant domain in bleeding and wound healing

Essentials Heparanase forms a complex with tissue factor and enhances the generation of factor Xa. The present study was aimed to identify the procoagulant domain of heparanase. Procoagulant peptides significantly shortened bleeding time and enhanced wound healing. Tissue factor pathway inhibitor (TFPI)-2 derived peptides inhibited the procoagulant peptides.

SUMMARY

Background Heparanase, which is known to be involved in angiogenesis and metastasis, was shown to form a complex with tissue factor (TF) and to enhance the generation of activated factor X (FXa). Our study demonstrated that peptides derived from TF pathway inhibitor (TFPI)-2 impeded the procoagulant effect of heparanase, and attenuated inflammation, tumor growth, and vascularization. Aims To identify the procoagulant domain in the heparanase molecule, and to evaluate its effects in a model of wound healing that involves inflammation and angiogenesis. Methods Twenty-four potential peptides derived from heparanase were generated, and their effect was studied in an assay of FXa generation. Peptides 14 and 16, which showed the best procoagulant effect, were studied in a bleeding mouse model and in a wound-healing mouse model. Results Peptides 14 and 16 increased FXa levels by two-fold to three-fold, and, at high levels, caused consumption coagulopathy. The TFPI-2-derived peptides explored in our previous study were found to inhibit the procoagulant effect induced by peptides 14 and 16. In the bleeding model, time to clot formation was shortened by 50% when peptide 14 or peptide 16 was topically applied or injected subcutaneously. In the wound-healing model, the wound became more vascular, and its size was reduced to one-fifth as compared with controls, upon 1 week of exposure to peptide 14 or peptide 16 applied topically or injected subcutaneously. Conclusions The putative heparanase procoagulant domain was identified. Peptides derived from this domain significantly shortened bleeding time and enhanced wound healing.

Correcting covariate-dependent measurement error with non-zero mean

There are many settings in which the distribution of error in a mismeasured covariate varies with the value of another covariate. Take, for example, the case of HIV phylogenetic cluster size, large values of which are an indication of rapid HIV transmission. Researchers wish to find behavioral correlates of HIV phylogenetic cluster size; however, the distribution of its measurement error depends on the correctly measured variable, HIV status, and does not have a mean of zero. Further, it is not feasible to obtain validation data or repeated measurements. We propose an extension of simulation-extrapolation, an estimation technique for bias reduction in the presence of measurement error that does not require validation data and can accommodate errors whose distribution depends on other, error-free covariates. The proposed extension performs well in simulation, typically exhibiting less bias and variability than either regression calibration or multiple imputation for measurement error. We apply the proposed method to data from the province of Quebec in Canada to examine the association between HIV phylogenetic cluster size and the number of reported sex partners. Copyright © 2017 John Wiley & Sons, Ltd.

Outcome of Patients with Venous Thromboembolism and Factor V Leiden or Prothrombin 20210 Carrier Mutations During the Course of Anticoagulation

BACKGROUND

Individuals with factor V Leiden or prothrombin G20210A mutations are at a higher risk to develop venous thromboembolism. However, the influence of these polymorphisms on patient outcome during anticoagulant therapy has not been consistently explored.

METHODS

We used the Registro Informatizado de Enfermedad TromboEmbólica database to compare rates of venous thromboembolism recurrence and bleeding events occurring during the anticoagulation course in factor V Leiden carriers, prothrombin mutation carriers, and noncarriers.

RESULTS

Between March 2001 and December 2015, 10,139 patients underwent thrombophilia testing. Of these, 1384 were factor V Leiden carriers, 1115 were prothrombin mutation carriers, and 7640 were noncarriers. During the anticoagulation course, 160 patients developed recurrent deep vein thrombosis and 94 patients developed pulmonary embolism (16 died); 154 patients had major bleeding (10 died), and 291 patients had nonmajor bleeding. On multivariable analysis, factor V Leiden carriers had a similar rate of venous thromboembolism recurrence (adjusted hazard ratio [HR], 1.16; 95% confidence interval [CI], 0.82-1.64), half the rate of major bleeding (adjusted HR, 0.50; 95% CI, 0.25-0.99) and a nonsignificantly lower rate of nonmajor bleeding (adjusted HR, 0.66; 95% CI, 0.43-1.01) than noncarriers. Prothrombin mutation carriers and noncarriers had a comparable rate of venous thromboembolism recurrence (adjusted HR, 1.00; 95% CI, 0.68-1.48), major bleeding (adjusted HR, 0.75; 95% CI, 0.42-1.34), and nonmajor bleeding events (adjusted HR, 1.10; 95% CI, 0.77-1.57).

CONCLUSIONS

During the anticoagulation course, factor V Leiden carriers had a similar risk for venous thromboembolism recurrence and half the risk for major bleeding compared with noncarriers. This finding may contribute to decision-making regarding anticoagulation duration in selected factor V Leiden carriers with venous thromboembolism.

The Clinical Course of Venous Thromboembolism May Differ According to Cancer Site

BACKGROUND

We hypothesized that the clinical course of venous thromboembolism in patients with active cancer may differ according to the specificities of primary tumor site.

AIM AND METHODS

We used data from RIETE (international registry of patients with venous thromboembolism) to compare the clinical venous thromboembolism-related outcomes during the course of anticoagulation in patients with one of the 4 more frequent cancers (breast, prostate, colorectal, or lung cancer).

RESULTS

As of September 2014, 3947 cancer patients were recruited, of whom 938 had breast, 629 prostate, 1189 colorectal, and 1191 lung cancer. Overall, 55% had metastatic disease (42%, 36%, 53%, and 72%, respectively). During the course of anticoagulant therapy (mean duration, 139 days), the rate of thromboembolic recurrences was similar to the rate of major bleeding in patients with breast (5.6 [95% confidence interval (CI), 3.8-8.1] vs 4.1 [95% CI, 2.7-5.9] events per 100 patient-years) or colorectal cancer (10 [95% CI, 7.6-13] vs 12 [95% CI, 9.4-15] per 100 patient-years). In contrast, in patients with prostate cancer, the rate of venous thromboembolic recurrences was half the rate of major bleeding (6.9 [95% CI, 4.4-10] vs 13 [95% CI, 9.2-17] events per 100 patient-years), whereas in those with lung cancer, the rate of thromboembolic recurrences was twofold higher than the rate of major bleeding (27 [95% CI, 22-23] vs 11 [95% CI, 8.6-15] per 100 patient-years).

CONCLUSIONS

Significant differences in the clinical profile of venous thromboembolic-related outcomes were observed according to the site of cancer. These findings suggest the development of cancer-specific anticoagulant strategies as an area for further research.

Abstract P2-07-11: The association between angiotensin receptor blockers usage and breast cancer characteristics

Background: Data regarding the impact of angiotensin receptor blockers (ARB) on breast cancer are inconsistent. We evaluate the association between ARB usage and breast cancer characteristics and outcomes.

Methods: All patients who were treated in our institute for estrogen receptor positive, human epidermal growth factor receptor 2 negative early breast cancer between 4/2005 and 3/2012 and whose tumors were sent for Oncotype-DX analysis were included. Medical records were retrospectively reviewed for clinical-pathological parameters, related comorbidities, treatment and outcomes. Data regarding ARB usage was retrieved. Usage of several pre-specified medications for hypertension including angiotensin converting enzyme inhibitors (ACEI), mineralocorticoid receptor antagonists (MRA), and β-blockers (BB) was also evaluated. Each medication group was compared to the rest of the study population.

Results:671 patients were included in the study cohort. Forty six (7%) were treated with ARB, 93 (14.2%) with ACEI, 14 (2.1%) with MRA, and 115 (17.5%) with BB. ARB usage was associated with different histological subtype distribution (P=0.009), higher incidence of macroscopic nodal involvement (P&lt;0.001) and more advanced stage at diagnosis (p&lt;0.001). These findings remained significant on multivariate analysis. Patients treated with ARB had worse 5-year breast cancer specific survival (94.7% vs. 98.8%, P=0.024) and worse 5-year overall survival (94.6% vs. 98.8%, p=0.015), but these differences were not demonstrated on multivariate analysis (p=0.251 and p=0.441. respectively).

Conclusions: Patients treated with ARB presented with more advanced breast cancer disease and some distinct histological features. Further research is required to elucidate the effect of ARB treatment on breast cancer.

Tumor burdenPopulation (no.)Tumor size, cm (SD)Macroscopic node posotive1Stage Mean, cm (SD)P, univariate analysis%P, univariate analysisI, %II, %P, univariate analysisAll (671)1.68 (0.8)-9-71.228.3-ARB (46)1.89 (0.81)0.05423.9&lt;0.0013763&lt;0.001ACEI (93)1.93 (0.93)0.0048.50.86363.835.10.355MRA (14)1.88 (0.67)0.32914.30.36357.142.90.907BB (115)1.77 (0.95)0.21613.20.08766.731.60.0911Macroscopic nodes: lymph node metastases&gt; 2 millimeter

Histological characteristicsPopulation (no.)Ki67 (%)Estrogen recepator stain intensityHistology subtype Mean, (SD)P, univariate analysisMean, (SD)P, univariate analysisIDC (%)ILC (%)P, univariate analysisAll (671)15.91 (13.58)-2.47 (0.57)-80.912.2-ARB (46)12.27 (7.19)0.0052.57 (0.59)0.24665.226.10.009ACEI (93)17.1 (14.24)0.4032.44 (0.55)0.51575.5160.358MRA (14)21.4 (11.2)0.1972.63 (0.42)0.30385.87.10.841BB (115)15.93 (12.93)0.992.51 (0.58)0.49675.713.90.186IDC- invasive ductal carcinoma, ILC- invasive lobular carcinoma

Citation Format: Goldvaser H, Rizel S, Hendler D, Neiman V, Shepshelovich D, Shochat T, Sulkes A, Brenner B, Yerushalmi R. The association between angiotensin receptor blockers usage and breast cancer characteristics [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-07-11.

Abstract P5-08-25: The association between smoking and breast cancer characteristics and outcome

Background: Smoking is associated with an increased incidence of hormone receptor positive breast cancer. Data regarding worse breast cancer outcome in smokers are accumulating. Current literature regarding the impact of smoking on breast cancer characteristics is limited. The aim of this study was to evaluate the impact of smoking on the characteristics and outcome of estrogen receptor positive, human epidermal growth factor receptor 2 (HER2) negative early breast cancer.

Methods: This was a retrospective single center study. All patients diagnosed from 4/2005 through 3/2012 and treated in our institute for early, estrogen receptor positive, HER2 negative breast cancer, whose tumors were sent for Oncotype DX analysis were included. Medical records were reviewed for demographics, clinico-pathological parameters, treatment and outcome. Patients were grouped and compared according to smoking history (present or past smokers vs. never smokers) and status (current vs. former and never smokers). Heavy smokers (pack years ≥30) were analyzed separately.

Results: A total of 671 patients were included. 28.7% had a history of smoking, 17% were current smokers and 11.5% were heavy smokers. Smoking had no impact on tumor size, nodal involvement and Oncotype DX recurrence score. Angiolymphatic and perineural invasion rates were higher in current smokers than in the rest of the cohort (11% vs. 5.1%, p=0.023, 9% vs. 3.45%, p=0.013, respectively). Smoking had no other impact regarding histological characteristics. Five-year disease free survival and overall survival rates were 95.7% and 98.5%, respectively. Smoking had no impact on outcome.

Conclusions: In patients with estrogen receptor positive, HER2 negative, early breast cancer, smoking had no clinically significant influence on tumor characteristics and outcome. As the study was limited to a specific subgroup of the breast cancer population in this heterogeneous disease and since smoking is a modifiable risk factor for the disease, further research is required to clarify the possible impact of smoking on breast cancer.

Breast cancer characteristics according to history of smoking, smoking status and pack yearsPopulation (no.)Mean tumor size, cm (SD)Macroscopic N + (%)Oncotype Dx RS, mean (SD)Histology, IDC (%)Angiolymphatic invasion (%)Perniural invasion (%)Ki67 (%), mean (SD)Hx smoking (178)1.66 (0.9)10.718.9 (9.4)817.75.915.8 (13.5)No Hx of smoking (443)1.7 (0.8)8.419.33 (10.8)805.43.816 (14.1)Active smokers (104)1.76 (1)9.619.7 (9)8211916.5 (14.6)Never/former smokers (513)1.68 (0.8)919.1 (10.5)805.13.515.8 (13.7)PY 0-29 (523)1.69 (0.8)9.419.2 (10.7)806416.2 (14.2)PY≥30 (67)1.67 (1)918.3 (8.8)859913.8 (12.1)

Citation Format: Goldvaser H, Gal O, Rizel S, Hendler D, Neiman V, Shochat T, Sulkes A, Brenner B, Yerushalmi R. The association between smoking and breast cancer characteristics and outcome [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-08-25.

Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study

BACKGROUND

Codon usage bias has been described for various organisms and is thought to contribute to the regulation of numerous biological processes including viral infections. HIV-1 codon usage has been previously shown to be different from that of other viruses and man. It is evident that the antiretroviral drugs used to restrict HIV-1 replication also select for resistance variants. We wanted to test whether codon frequencies in HIV-1 sequences from treatment-experienced patients differ from those of treatment-naive individuals due to drug pressure affecting codon usage bias.

RESULTS

We developed a JavaScript to determine the codon frequencies of aligned nucleotide sequences. Irrespective of subtypes, using HIV-1 pol sequences from 532 treatment-naive and 52 treatment-experienced individuals, we found that pol sequences from treatment-experienced patients had significantly increased AGA (arginine; p = 0.0002***) and GGU (glycine; p = 0.0001***), and decreased AGG (arginine; p = 0.0001***) codon frequencies. The same pattern was not observed when subtypes B and C sequences were analyzed separately. Additionally, irrespective of subtypes, using HIV-1 gag sequences from 524 treatment-naive and 54 treatment-experienced individuals, gag sequences from treatment-experienced patients had significantly increased CUA (leucine; p < 0.0001***), CAG (glutamine; p = 0.0006***), AUC (isoleucine; p < 0.0001***) and UCU (serine; p = 0.0005***), and decreased AUA (isoleucine; p = 0.0003***) and CAA (glutamine; p = 0.0006***) codon frequencies.

CONCLUSION

Using pol and gag genes derived from the same HIV-1 genome, we show that antiretroviral therapy changed certain HIV-1 codon frequencies in a subtype specific way.

Beyond Condoms: Risk Reduction Strategies Among Gay, Bisexual, and Other Men Who Have Sex With Men Receiving Rapid HIV Testing in Montreal, Canada

Gay, bisexual, and other men who have sex with men (MSM) have adapted their sexual practices over the course of the HIV/AIDS epidemic based on available data and knowledge about HIV. This study sought to identify and compare patterns in condom use among gay, bisexual, and other MSM who were tested for HIV at a community-based testing site in Montreal, Canada. Results showed that while study participants use condoms to a certain extent with HIV-positive partners and partners of unknown HIV status, they also make use of various other strategies such as adjusting to a partner's presumed or known HIV status and viral load, avoiding certain types of partners, taking PEP, and getting tested for HIV. These findings suggest that MSM who use condoms less systematically are not necessarily taking fewer precautions but may instead be combining or replacing condom use with other approaches to risk reduction.