Age at antiretroviral therapy initiation and cell-associated HIV-1 DNA levels in HIV-1-infected children

Background The latent viral reservoir is the major obstacle to achieving HIV remission and necessitates life-long antiretroviral therapy (ART) for HIV-infected individuals. Studies in adults and children have found that initiating ART soon after infection is associated with a reduction in the size of the HIV-1 reservoir. Here we quantified cell-associated HIV-1 DNA in early-treated but currently older HIV-infected children suppressed on ART. Methods The study participants comprised of a cohort of 146 early-treated children with HIV-1 RNA <50 copies/ml enrolled as part of a clinical trial in Johannesburg, South Africa. A stored buffy coat sample collected after a median 4.3 years on ART and where HIV-1 RNA was <50 copies/ml was tested for cell-associated HIV-1 DNA levels. An in-house, semi-nested real-time quantitative hydrolysis probe PCR assay to detect total HIV-1 subtype C proviral DNA was used. Children were followed prospectively for up to 3 years after this measurement to investigate subsequent HIV-1 RNA rebound/failure while remaining on ART. Age at ART initiation, HIV-1 RNA decline prior to HIV-1 DNA measurement and other factors were investigated. Results A gradient between age at ART initiation and later HIV-1 DNA levels was observed. When ART was started 50 copies/ml whilst on ART within 3 years after the DNA measurement was 2.07 (95% CI: 1.352–3.167) times greater if the HIV-1 DNA level was above the median of 55 copies/106 cells. Conclusions Cell-associated HIV-1 DNA levels measured after more than 4 years on ART were lower the younger the age of the child when ART was initiated. This marker of the size of the viral reservoir also predicted subsequent viral rebound/treatment failure while ART was sustained. The results provide additional evidence of the benefits of prompt diagnosis and early ART initiation in newborns and infants

Repression of human papillomavirus oncogene expression under hypoxia is mediated by PI3K/mTORC2/AKT signaling

Oncogenic HPV types are major human carcinogens. Under hypoxia, HPV-positive cancer cells can repress the viral E6/E7 oncogenes and induce a reversible growth arrest. This response could contribute to therapy resistance, immune evasion, and tumor recurrence upon reoxygenation. Here, we uncover evidence that HPV oncogene repression is mediated by hypoxia-induced activation of canonical PI3K/mTORC2/AKT signaling. AKT-dependent downregulation of E6/E7 is only observed under hypoxia and occurs, at least in part, at the transcriptional level. Quantitative proteome analyses identify additional factors as candidates to be involved in AKT-dependent E6/E7 repression and/or hypoxic PI3K/mTORC2/AKT activation. These results connect PI3K/mTORC2/AKT signaling with HPV oncogene regulation, providing new mechanistic insights into the cross talk between oncogenic HPVs and their host cells.Hypoxia is linked to therapeutic resistance and poor clinical prognosis for many tumor entities, including human papillomavirus (HPV)-positive cancers. Notably, HPV-positive cancer cells can induce a dormant state under hypoxia, characterized by a reversible growth arrest and strong repression of viral E6/E7 oncogene expression, which could contribute to therapy resistance, immune evasion and tumor recurrence. The present work aimed to gain mechanistic insights into the pathway(s) underlying HPV oncogene repression under hypoxia. We show that E6/E7 downregulation is mediated by hypoxia-induced stimulation of AKT signaling. Ablating AKT function in hypoxic HPV-positive cancer cells by using chemical inhibitors efficiently counteracts E6/E7 repression. Isoform-specific activation or downregulation of AKT1 and AKT2 reveals that both AKT isoforms contribute to hypoxic E6/E7 repression and act in a functionally redundant manner. Hypoxic AKT activation and consecutive E6/E7 repression is dependent on the activities of the canonical upstream AKT regulators phosphoinositide 3-kinase (PI3K) and mechanistic target of rapamycin (mTOR) complex 2 (mTORC2). Hypoxic downregulation of E6/E7 occurs, at least in part, at the transcriptional level. Modulation of E6/E7 expression by the PI3K/mTORC2/AKT cascade is hypoxia specific and not observed in normoxic HPV-positive cancer cells. Quantitative proteome analyses identify additional factors as candidates to be involved in hypoxia-induced activation of the PI3K/mTORC2/AKT signaling cascade and in the AKT-dependent repression of the E6/E7 oncogenes under hypoxia. Collectively, these data uncover a functional key role of the PI3K/mTORC2/AKT signaling cascade for viral oncogene repression in hypoxic HPV-positive cancer cells and provide new insights into the poorly understood cross talk between oncogenic HPVs and their host cells under hypoxia

Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways

BACKGROUND: Interpreting large-scale studies from microarrays or next-generation sequencing for further experimental testing remains one of the major challenges in quantitative biology. Combining expression with physical or genetic interaction data has already been successfully applied to enhance knowledge from all types of high-throughput studies. Yet, toolboxes for navigating and understanding even small gene or protein networks are poorly developed. RESULTS: We introduce two Cytoscape plug-ins, which support the generation and interpretation of experiment-based interaction networks. The virtual pathway explorer viPEr creates so-called focus networks by joining a list of experimentally determined genes with the interactome of a specific organism. viPEr calculates all paths between two or more user-selected nodes, or explores the neighborhood of a single selected node. Numerical values from expression studies assigned to the nodes serve to score identified paths. The pathway enrichment analysis tool PEANuT annotates networks with pathway information from various sources and calculates enriched pathways between a focus and a background network. Using time series expression data of atorvastatin treated primary hepatocytes from six patients, we demonstrate the handling and applicability of viPEr and PEANuT. Based on our investigations using viPEr and PEANuT, we suggest a role of the FoxA1/A2/A3 transcriptional network in the cellular response to atorvastatin treatment. Moreover, we find an enrichment of metabolic and cancer pathways in the Fox transcriptional network and demonstrate a patient-specific reaction to the drug. CONCLUSIONS: The Cytoscape plug-in viPEr integrates –omics data with interactome data. It supports the interpretation and navigation of large-scale datasets by creating focus networks, facilitating mechanistic predictions from –omics studies. PEANuT provides an up-front method to identify underlying biological principles by calculating enriched pathways in focus networks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2017-z) contains supplementary material, which is available to authorized users

Virus/Host Cell Crosstalk in Hypoxic HPV-Positive Cancer Cells

Oncogenic types of human papillomaviruses (HPVs) are major human carcinogens. The expression of the viral E6/E7 oncogenes plays a key role for HPV-linked oncogenesis. It recently has been found that low oxygen concentrations (“hypoxia”), as present in sub-regions of HPV-positive cancers, strongly affect the interplay between the HPV oncogenes and their transformed host cell. As a result, a state of dormancy is induced in hypoxic HPV-positive cancer cells, which is characterized by a shutdown of viral oncogene expression and a proliferative arrest that can be reversed by reoxygenation. In this review, these findings are put into the context of the current concepts of both HPV-linked carcinogenesis and of the effects of hypoxia on tumor biology. Moreover, we discuss the consequences for the phenotype of HPV-positive cancer cells as well as for their clinical behavior and response towards established and prospective therapeutic strategies

Performance Comparison of Distributed Injection Methods for Hypersonic Film-Cooling

Film-cooling is one of the promising technologies proposed to help mitigate the heat-transfer load experienced by hypersonic vehicles. To investigate this phenomena, fundamental testing of three different distributed Boundary-Layer (BL) injection methods was carried out in the T4 Stalker Tube using hydrogen injectant. A flat plate model was tested, using a cross-flow of air, at Mach 7.6; a dynamic pressure of 48 kPa; and a flight enthalpy of Mach 10. This fundamental testing was done to help characterize the performance and injection characteristics of different distributed injection methods. The three different injectors selected for this study were a porous Carbon/Carbon (C/C) Ceramic-Matrix-Composite (CMC); a porous oxygen compatible CMC; and a Multi-Port Injector Array (MPIA) optimised for scramjet conditions. Of these, the C/C CMC performed the best, overall, when examining the heat-transfer reduction for both a laminar and transitional-turbulent BL in a hypersonic cross-flow

The impact of Holocene deglaciation and glacial dynamics on the landscapes and geomorphology of Potter Peninsula, King George Island (Isla 25 Mayo), NW Antarctic Peninsula

The timing and impact of deglaciation and Holocene readvances on the terrestrial continental margins of the Antarctic Peninsula (AP) have been well-studied but are still debated. Potter Peninsula on King George Island (KGI) (Isla 25 de Mayo), South Shetland Islands (SSI), NW Antarctic Peninsula, has a detailed assemblage of glacial landforms and stratigraphic exposures for constraining deglacial landscape development and glacier readvances. We undertook new morphostratigraphic mapping of the deglaciated foreland of the Warszawa Icefield, an outlet of the Bellingshausen (Collins) Ice Cap on Potter Peninsula, using satellite imagery and new lithofacies recognition and interpretations, combined with new chronostratigraphic analysis of stratigraphic sections, lake sediments, and moraine deposits. Results show that the deglaciation on Potter Peninsula began before c. 8.2 ka. Around c. 7.0 ka, the Warszawa Icefield and the marine-facing Fourcade Glacier readvanced across Potter Peninsula and to the outer part of Potter Cove. Evidence of further readvances on Potter Peninsula was absent until the Warszawa Icefield margin was landward of its present position on three occasions: c. 1.7–1.4 ka, after c. 0.7 ka (most likely c. 0.5–0.1 ka), and by 1956 CE. The timing of Holocene deglaciation and glacier fluctuations on Potter Peninsula are broadly coeval with other glacier- and ice-free areas on the SSI and the northern AP and likely driven by interactions between millennial–centennial-scale changes in solar insolation and irradiance, the southern westerlies, and the Southern Annular Mode

Scatterplots showing associations between HIV-1 DNA log₁₀ copies/10⁶ cells and a: Time on ART in years; b: Pre-ART HIV-1 RNA copies/ml and c: Pre-ART CD4 count in cells/mm3.

<p>LOcally WEighted Scatter-plot Smoother (LOWESS) and linear regression prediction lines shown in blue and red, respectively.; grey area shows the 95% prediction elipse.</p

Characteristics of 146 treated HIV-infected children in Johannesburg, South Africa, at the time of measurement of cell-associated HIV-1 DNA (current time) and at the time of antiretroviral therapy (ART) initiation.

<p>Characteristics of 146 treated HIV-infected children in Johannesburg, South Africa, at the time of measurement of cell-associated HIV-1 DNA (current time) and at the time of antiretroviral therapy (ART) initiation.</p