Modifiers of notch transcriptional activity identified by genome-wide RNAi

<p>Abstract</p> <p>Background</p> <p>The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in <it>Drosophila </it>cell culture to identify genes that modify Notch-dependent transcription.</p> <p>Results</p> <p>Employing complementary data analyses, we found 399 putative modifiers: 189 promoting and 210 antagonizing Notch activated transcription. These modifiers included several known Notch interactors, validating the robustness of the assay. Many novel modifiers were also identified, covering a range of cellular localizations from the extracellular matrix to the nucleus, as well as a large number of proteins with unknown function. Chromatin-modifying proteins represent a major class of genes identified, including histone deacetylase and demethylase complex components and other chromatin modifying, remodeling and replacement factors. A protein-protein interaction map of the Notch-dependent transcription modifiers revealed that a large number of the identified proteins interact physically with these core chromatin components.</p> <p>Conclusions</p> <p>The genome-wide RNAi screen identified many genes that can modulate Notch transcriptional output. A protein interaction map of the identified genes highlighted a network of chromatin-modifying enzymes and remodelers that regulate Notch transcription. Our results open new avenues to explore the mechanisms of Notch signal regulation and the integration of this pathway into diverse cellular processes.</p

Comparisons of anemia, thrombocytopenia, and neutropenia at initiation of HIV antiretroviral therapy in Africa, Asia, and the Americas

SummaryBackgroundHematological abnormalities are common manifestations of advanced HIV-1 infection that could affect the outcomes of highly-active antiretroviral therapy (HAART). Although most HIV-1-infected individuals live in resource-constrained countries, there is little information about the frequency of hematological abnormalities such as anemia, neutropenia, and thrombocytopenia among individuals with advanced HIV-1 disease.MethodsThis study compared the prevalence of pre-antiretroviral therapy hematological abnormalities among 1571 participants in a randomized trial of antiretroviral efficacy in Africa, Asia, South America, the Caribbean, and the USA. Potential covariates for anemia, neutropenia, and thrombocytopenia were identified in univariate analyses and evaluated in separate multivariable models for each hematological condition.ResultsThe frequencies of neutropenia (absolute neutrophil count ≤1.3×109/l), anemia (hemoglobin ≤10g/dl), and thrombocytopenia (platelets ≤125×109/l) at initiation of antiretroviral therapy were 14%, 12%, and 7%, respectively, and varied by country (p<0.0001 for each). In multivariable models, anemia was associated with gender, platelet count, and country; neutropenia was associated with CD4+ lymphocyte and platelet counts; and thrombocytopenia was associated with country, gender, and chronic hepatitis B infection.ConclusionsDifferences in the frequency of pretreatment hematological abnormalities could have important implications for the choice of antiretroviral regimen in resource-constrained settings

A twostep qualityimprovement intervention to address Pap smear quality at public health facilities in South Africa

Background. The endocervical component of a Pap smear is an important indicator of sample quality – or ‘adequacy’. However, only 6 of 52 districts in South Africa (SA) meet the Department of Health (DoH) performance benchmark: a 70% adequacy rate. We implemented a quality-improvement (QI) intervention to address suboptimal Pap smear quality in Tshwane District, Gauteng Province, SA.Objectives. To determine whether training with the wooden Ayre spatula (step 1) or introduction of the cytobroom (step 2) resulted in greater improvements in Pap smear adequacy rates.Methods. Two Tshwane District health facilities participated in our QI project between May 2016 and February 2017. In step 1, staff received training on the Ayre spatula. In step 2, the spatula was replaced with the cytobroom. Pap smear volumes, adequacy rates and results are reported for the pre-intervention period and after each QI step. We compared adequacy rates using Fisher’s exact test, with a significance level of p=0.05.Results. In the pre-intervention period, 304 of 965 Pap smears were deemed adequate (32%; 95% confidence interval (CI) 29 - 35%). After step 1, the proportion increased to 109 of 191 (57%; 95% CI 50 - 64%; p&lt;0.01). Similarly, after step 2, the proportion increased to 155 of 192 (81%; 95% CI 74 - 86%; p&lt;0.01). The proportion of abnormal smears increased from 13% before the QI intervention to 17% after step 1 and 22% after step 2.Conclusion. Although training in Pap smear collection using the Ayre spatula resulted in modest improvements in quality, facilities only achieved the DoH benchmark of a 70% adequacy rate after the introduction of the cytobroom

Prevalence of Anal HPV and Anal Dysplasia in HIV-Infected Women from Johannesburg, South Africa

Background: Anal cancer is a relatively common cancer among HIV-infected populations. There are limited data on the prevalence of anal high-risk human papillomavirus (HR-HPV) infection and anal dysplasia in HIV-infected women from resource-constrained settings. Methods: A cross-sectional study of HIV-infected women aged 25-65 years recruited from an HIV clinic in Johannesburg, South Africa. Cervical and anal swabs were taken for conventional cytology and HR-HPV testing. Women with abnormal anal cytology and 20% of women with negative cytology were seen for high-resolution anoscopy with biopsy of visible lesions. Results: Two hundred women were enrolled. Anal HR-HPV was found in 43%. The anal cytology results were negative in 51 (26%); 97 (49%) had low-grade squamous intraepithelial lesions (SIL), 32 (16%) had atypical squamous cells of unknown significance, and 19 (9.5%) had high-grade SIL or atypical squamous cells suggestive of high-grade SIL. On high-resolution anoscopy, 71 (36%) had atypia or low-grade SIL on anal histology and 17 (8.5%) had high-grade SIL. Overall, 31 (17.5%) had high-grade SIL present on anal cytology or histology. Abnormal cervical cytology was found in 70% and cervical HR-HPV in 41%. Conclusions: We found a significant burden of anal HR-HPV infection, abnormal anal cytology, and high-grade SIL in our cohort. This is the first study of the prevalence of anal dysplasia in HIV-infected women from sub-Saharan Africa. Additional studies are needed to define the epidemiology of these conditions, as well as the incidence of anal cancer, in this population

Xpert human papillomavirus test is a promising cervical cancer screening test for HIV-seropositive women

This study investigated the performance of Cepheid Xpert human papillomavirus (HPV) assay in South African human immunodeficiency virus (HIV)-infected women and compared its performance with that of hybrid capture-2 (hc2). Methods: Stored cervical specimens from HIV-infected women that had previously been tested using hc2 were tested using Xpert. Results: The overall HR-HPV prevalence was found to be 62.0% (720/1161) by Xpert and 61.2% (711/1161) by hc2. 13.6% (158/1161) were HPV16 positive, 18.8% (218/1161) were HPV18/45, 37.3% (434/1161) were HPV31/33/35/52/58, 12.7% (147/1161) were HPV51/59 and 23.3% (270/1161) were HPV39/68/56/66. Overall agreement with hc2 was 90%; Cohen's kappa was 0.78 (95% CI 0.74-0.82) indicating substantial agreement. Detection of HPV16, HPV18/45, and HPV31/33/35/52/58 were independently associated with cervical intraepithelial neoplasia (CIN)-2+ (P<0.0001 for each); while HPV51/59 and HPV39/68/56/66 were not. Women infected with HPV16, HPV18/45 or HPV31/33/35/52/58 were found to have significantly higher amounts of HPV DNA detected for those with CIN2+ compared to those without CIN2+, P<0.0001 for each. Xpert and hc2 were similarly sensitive (88.3% and 91.5%, respectively) and specific (48.4% and 51.0%) for CIN2+ and CIN3 (sensitivity: 95.8% and 97.9%; specificity: 41.4% and 42.8%). Conclusions: Xpert is a promising screening test in HIV-infected women that performs similarly to hc2

Estimating the burden of cervical disease among HIV-infected women accessing screening services in South Africa: A model-based analysis

Background. Cervical cancer remains the second most common cancer among women worldwide, with much of the global burden occurring in low- and middle-income countries. HIV-infected women are at increased risk of human papillomavirus infection, preinvasive cervical disease and invasive cervical cancer (ICC). Funded through the United States President’s Emergency Plan for AIDS Relief (PEPFAR) and working in collaboration with the South African (SA) Department of Health, our team supports cervical screening integrated within public sector HIV clinics in SA.Objectives. To estimate the burden of cervical disease among HIV-infected women accessing screening services supported through our programme.Methods. We constructed conditional probability models to estimate the burden of grade 1 and grades 2/3 cervical intraepithelial lesions (CIN1 and CIN2/3) and ICC among two cohorts: one consisting of 3 190 HIV-infected women for whom only cytology results were available for analysis, and another consisting of 75 358 HIV-infected women for whom neither cytology nor histology results were available. Parameter estimates for the models were derived from routinely collected programmatic data and published clinical trials.Results. Between January 2009 and November 2015, 75 358 HIV-infected women underwent Pap smear screening in public sector clinics supported by our cervical cancer prevention programme. Based on modelling analysis, we estimate that 46 123 cases of CIN1 (range 45 500 - 49 608), 13 598 cases of CIN2/3 (range 12 749 - 14 828), and 104 cases of ICC (range 61 - 186) occurred in this population.Conclusions. Our findings highlight the magnitude of cervical disease among HIV-infected women in SA.

Efficacy and Safety of Three Antiretroviral Regimens for Initial Treatment of HIV-1: A Randomized Clinical Trial in Diverse Multinational Settings

Background: Antiretroviral regimens with simplified dosing and better safety are needed to maximize the efficiency of antiretroviral delivery in resource-limited settings. We investigated the efficacy and safety of antiretroviral regimens with once-daily compared to twice-daily dosing in diverse areas of the world. Methods and Findings: 1,571 HIV-1-infected persons (47% women) from nine countries in four continents were assigned with equal probability to open-label antiretroviral therapy with efavirenz plus lamivudine-zidovudine (EFV+3TC-ZDV), atazanavir plus didanosine-EC plus emtricitabine (ATV+DDI+FTC), or efavirenz plus emtricitabine-tenofovir-disoproxil fumarate (DF) (EFV+FTC-TDF). ATV+DDI+FTC and EFV+FTC-TDF were hypothesized to be non-inferior to EFV+3TC-ZDV if the upper one-sided 95% confidence bound for the hazard ratio (HR) was ≤1.35 when 30% of participants had treatment failure. An independent monitoring board recommended stopping study follow-up prior to accumulation of 472 treatment failures. Comparing EFV+FTC-TDF to EFV+3TC-ZDV, during a median 184 wk of follow-up there were 95 treatment failures (18%) among 526 participants versus 98 failures among 519 participants (19%; HR 0.95, 95% CI 0.72–1.27; p = 0.74). Safety endpoints occurred in 243 (46%) participants assigned to EFV+FTC-TDF versus 313 (60%) assigned to EFV+3TC-ZDV (HR 0.64, CI 0.54–0.76; p<0.001) and there was a significant interaction between sex and regimen safety (HR 0.50, CI 0.39–0.64 for women; HR 0.79, CI 0.62–1.00 for men; p = 0.01). Comparing ATV+DDI+FTC to EFV+3TC-ZDV, during a median follow-up of 81 wk there were 108 failures (21%) among 526 participants assigned to ATV+DDI+FTC and 76 (15%) among 519 participants assigned to EFV+3TC-ZDV (HR 1.51, CI 1.12–2.04; p = 0.007). Conclusion: EFV+FTC-TDF had similar high efficacy compared to EFV+3TC-ZDV in this trial population, recruited in diverse multinational settings. Superior safety, especially in HIV-1-infected women, and once-daily dosing of EFV+FTC-TDF are advantageous for use of this regimen for initial treatment of HIV-1 infection in resource-limited countries. ATV+DDI+FTC had inferior efficacy and is not recommended as an initial antiretroviral regimen

A multinational study of neurological performance in antiretroviral therapy-naïve HIV-1-infected persons in diverse resource-constrained settings

Little is known about how the prevalence and incidence of neurological disease in HIV-infected patients in resource-limited settings. We present an analysis of neurological and neurocognitive function in antiretroviral naïve individuals in multinational resource-limited settings