Boceprevir in combination with HIV protease inhibitors in patients with advanced fibrosis-altered drug-drug interactions?

In HIV/HCV co-infected patients improved treatment outcomes have been reported for the HCV protease inhibitors (PIs) boceprevir (BOC) and telaprevir (TVR), reaching SVR rates of up to 70% in pilot trials. Due to complex drug-drug-interactions triple therapy is substantially limited in HIV/HCV-coinfected individuals. Co-administration of BOC with the commonly available HIV PIs has been reported not only to decrease the level of BOC but also to lead to relevant decreases in the respective HIV PI. Here, we report on two patients who received BOC-containing HCV triple therapy in combination with a HIV PI. Patient 1 was on darunavir 800 mg/ritonavir 100 mg once-daily mono-therapy. Using FibroScan a liver stiffness of 34 kPa suggested liver cirrhosis prior to start of HCV triple therapy. At week 5 of HCV triple therapy darunavir trough concentration was measured in the reference range with 3777 ng/ml (reference trough concentration 2400–4600 ng/ml). HCV-RNA became negative at week 10 and HIV-RNA was below detection limit (<40 copies/ml) at all times. Patient 2 was on a simplified FTC qd and fos-amprenavir 700 mg/ritonavir 100 mg bid regimen. Liver disease had also progressed to liver cirrhosis, confirmed in FibroScan, with a liver stiffness of 32 kPa. At week 8 of HCV triple therapy fos-amprenavir trough level was measured in the normal reference range with 1699 ng/ml (reference trough concentration 750–2500 ng/ml). At week 11 HCV-RNA was <12 IU/ml and HIV viral load was below detection limit of <40 copies/ml at all times. Our clinical data suggest that in patients with advanced liver disease possibly drug levels of HIV PIs which are coadministered with BOC may be within the normal range. In order to better understand the true amount of drug interactions between BOC and commonly used HIV PIs in HIV/HCV-coinfected patients with more advanced liver fibrosis, urgently more PK studies are required to make HCV triple therapy accessible for a wider number of HIV/HCV-coinfected patients in desperate need of these drugs

The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery

<p>Background: The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans.</p> <p>Results: Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates.</p> <p>Conclusions: The H. contortus genome and transcriptome provides an essential platform for postgenomic research in this and other important strongylid parasites. </p&gt

A transcriptomic analysis of Echinococcus granulosus larval stages:implications for parasite biology and host adaptation

The cestode Echinococcus granulosus--the agent of cystic echinococcosis, a zoonosis affecting humans and domestic animals worldwide--is an excellent model for the study of host-parasite cross-talk that interfaces with two mammalian hosts. To develop the molecular analysis of these interactions, we carried out an EST survey of E. granulosus larval stages. We report the salient features of this study with a focus on genes reflecting physiological adaptations of different parasite stages.We generated ~10,000 ESTs from two sets of full-length enriched libraries (derived from oligo-capped and trans-spliced cDNAs) prepared with three parasite materials: hydatid cyst wall, larval worms (protoscoleces), and pepsin/H(+)-activated protoscoleces. The ESTs were clustered into 2700 distinct gene products. In the context of the biology of E. granulosus, our analyses reveal: (i) a diverse group of abundant long non-protein coding transcripts showing homology to a middle repetitive element (EgBRep) that could either be active molecular species or represent precursors of small RNAs (like piRNAs); (ii) an up-regulation of fermentative pathways in the tissue of the cyst wall; (iii) highly expressed thiol- and selenol-dependent antioxidant enzyme targets of thioredoxin glutathione reductase, the functional hub of redox metabolism in parasitic flatworms; (iv) candidate apomucins for the external layer of the tissue-dwelling hydatid cyst, a mucin-rich structure that is critical for survival in the intermediate host; (v) a set of tetraspanins, a protein family that appears to have expanded in the cestode lineage; and (vi) a set of platyhelminth-specific gene products that may offer targets for novel pan-platyhelminth drug development.This survey has greatly increased the quality and the quantity of the molecular information on E. granulosus and constitutes a valuable resource for gene prediction on the parasite genome and for further genomic and proteomic analyses focused on cestodes and platyhelminths

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

[Image: see text] Proteogenomics has the potential to advance genome annotation through high quality peptide identifications derived from mass spectrometry experiments, which demonstrate a given gene or isoform is expressed and translated at the protein level. This can advance our understanding of genome function, discovering novel genes and gene structure that have not yet been identified or validated. Because of the high-throughput shotgun nature of most proteomics experiments, it is essential to carefully control for false positives and prevent any potential misannotation. A number of statistical procedures to deal with this are in wide use in proteomics, calculating false discovery rate (FDR) and posterior error probability (PEP) values for groups and individual peptide spectrum matches (PSMs). These methods control for multiple testing and exploit decoy databases to estimate statistical significance. Here, we show that database choice has a major effect on these confidence estimates leading to significant differences in the number of PSMs reported. We note that standard target:decoy approaches using six-frame translations of nucleotide sequences, such as assembled transcriptome data, apparently underestimate the confidence assigned to the PSMs. The source of this error stems from the inflated and unusual nature of the six-frame database, where for every target sequence there exists five “incorrect” targets that are unlikely to code for protein. The attendant FDR and PEP estimates lead to fewer accepted PSMs at fixed thresholds, and we show that this effect is a product of the database and statistical modeling and not the search engine. A variety of approaches to limit database size and remove noncoding target sequences are examined and discussed in terms of the altered statistical estimates generated and PSMs reported. These results are of importance to groups carrying out proteogenomics, aiming to maximize the validation and discovery of gene structure in sequenced genomes, while still controlling for false positives

FrameDP: sensitive peptide detection on noisy matured sequences

Summary: Transcriptome sequencing represents a fundamental source of information for genome-wide studies and transcriptome analysis and will become increasingly important for expression analysis as new sequencing technologies takes over array technology. The identification of the protein-coding region in transcript sequences is a prerequisite for systematic amino acid-level analysis and more specifically for domain identification. In this article, we present FrameDP, a self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities

Complement stimulates Retinal Pigment Epithelial Cells to undergo Pro-inflammatory Changes as in Early Age-Related Macular Degeneration

Purpose. A polymorphism in the complement factor H gene, leading to increased complement activation, is associated with the development of age-related macular degeneration (AMD). We therefore examined the effect of human complement sera (HCS) on retinal pigment epithelial (RPE) cells with respect to pro-inflammatory mediators relevant in early AMD. Methods. RPE cells were treated with HCS or heat-inactivated (HI)-HCS as a complement-deficient control. Cells were stained for C5b-9 using immunocytochemistry and immunofluorescence, and cell viability was determined. Interleukin (IL) -6, -8 and monocyte chemoattractant protein-1 (MCP-1) were quantified by ELISA and their expression was determined by RT-PCR. Intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1) and tumour necrosis factor-α (TNF-α) were analysed by western blotting. The intracellular distribution of nuclear factor (NF)-ƙB was investigated by immunofluorescence. Results. Concentration-dependent increased staining for C5b-9 was observed after HCS treatment, whereas cell viability decreased. ELISA and RT-PCR analysis revealed increased secretion and expression of IL-6, -8 and MCP-1. Western blot analysis showed a concentration-dependent enhancement in ICAM-1, VCAM-1 and TNF-α in response to HCS, and immunofluorescence staining revealed cytosolic to nuclear translocation of NF-ƙB. Conclusions. This study suggests that complement may stimulate RPE cells to create a pro-inflammatory environment via NF-ƙB activation which may support early AMD development

Human Complement Sera stimulates Basolateral Secretion of VEGF by Retinal Pigment Epithelial Cells

Purpose. A mutation in the complement factor H (CFH) gene, leading to increased complement activation, is correlated with the development of age-related macular degeneration (AMD). Therefore, the influence of complement on human retinal pigment epithelial (RPE) cells was examined in respect to their polarized secretion of vascular endothelial growth factor (VEGF). Methods. RPE cells were cultured on transwell filters with DMEM and 1 % foetal calf serum. At six weeks post confluence, when the RPE have pigmented, the density of the cell monolayer was measured by a permeability assay using sodium fluorescein. The cells were treated with human complement sera for 24 hours. The amount of VEGF secreted into the media was quantified by enzyme-linked immunosorbent assay. Furthermore, the cellular distribution of VEGF in complement treated cells grown in chamber slides was detected by immunocytochemistry, and PCR analysis was used to determine the expression of the growth factor in RPE cells. Results. Untreated RPE cells produced VEGF constitutively. Basal stimulation of polarized cells with human complement sera led to a concentration dependent increased release of the growth factor towards the basal compartment. Immunocytochemical staining and PCR analysis for VEGF also demonstrated a concentration dependent enhancement in response to complement. Conclusions. VEGF production towards the basal side was strongly increased when RPE cells were exposed to human complement sera applied to the basal side. Therefore, complement might play a significant role in AMD, as VEGF is known to stimulate vessel growth in the choroid and support pro-angiogenic processes

Liver fibrosis in HIV patients receiving a modern cART:Which factors play a role?

Liver-related death in human immunodeficiency virus (HIV)-infected individuals is about 10 times higher compared with the general population, and the prevalence of significant liver fibrosis in those with HIV approaches 15%. The present study aimed to assess risk factors for development of hepatic fibrosis in HIV patients receiving a modern combination anti-retroviral therapy (cART). This cross-sectional prospective study included 432 HIV patients, of which 68 (16%) patients were anti-hepatitis C virus (HCV) positive and 23 (5%) were HBsAg positive. Health trajectory including clinical characteristics and liver fibrosis stage assessed by transient elastography were collected at inclusion. Liver stiffness values &gt;7.1 kPa were considered as significant fibrosis, while values &gt;12.5 kPa were defined as severe fibrosis. Logistic regression and Cox regression uni- and multivariate analyses were performed to identify independent factors associated with liver fibrosis. Significant liver fibrosis was detected in 10% of HIV mono-infected, in 37% of HCV co-infected patients, and in 18% of hepatitis B virus coinfected patients. The presence of diabetes mellitus (odds ratio [OR]=4.6) and FIB4 score (OR=2.4) were independently associated with presence of significant fibrosis in the whole cohort. Similarly, diabetes mellitus (OR=5.4), adiposity (OR=4.6), and the FIB4 score (OR=3.3) were independently associated with significant fibrosis in HIV mono-infected patients. Importantly, cumulative cART duration protected, whereas persistent HIV viral replication promoted the development of significant liver fibrosis along the duration of HIV infection. Our findings strongly indicate that besides known risk factors like metabolic disorders, HIV may also have a direct effect on fibrogenesis. Successful cART leading to complete suppression of HIV replication might protect from development of liver fibrosis.</p

Chemical effects during the formation of various types of femtosecond laser-generated surface structures on titanium alloy

Abstract In this contribution, chemical, structural, and mechanical alterations in various types of femtosecond laser-generated surface structures, i.e., laser-induced periodic surface structures (LIPSS, ripples), Grooves, and Spikes on titanium alloy, are characterized by various surface analytical techniques, including X-ray diffraction and glow-discharge optical emission spectroscopy. The formation of oxide layers of the different laser-based structures inherently influences the friction and wear performance as demonstrated in oil-lubricated reciprocating sliding tribological tests (RSTTs) along with subsequent elemental mapping by energy-dispersive X-ray analysis. It is revealed that the fs-laser scan processing (790 nm, 30 fs, 1 kHz) of near-wavelength-sized LIPSS leads to the formation of a graded oxide layer extending a few hundreds of nanometers into depth, consisting mainly of amorphous oxides. Other superficial fs-laser-generated structures such as periodic Grooves and irregular Spikes produced at higher fluences and effective number of pulses per unit area present even thicker graded oxide layers that are also suitable for friction reduction and wear resistance. Ultimately, these femtosecond laser-induced nanostructured surface layers efficiently prevent a direct metal-to-metal contact in the RSTT and may act as an anchor layer for specific wear-reducing additives contained in the used engine oil

Transmission of Human Immunodeficiency Virus I Drug Resistance - a Case Report. What are the Clinical Implications?

The success of first-line antiretroviral therapy can be challenged by the acquisition of primary drug resistance. Here we report a case where baseline genotypic resistance testing detected resistance conferring nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-associated mutations, but no primary mutations for protease inhibitor (PI). Subsequent PI-based HAART with boosted saquinavir led to virological treatment success with persistently undetectable viral load. After treatment simplification from saquinavir to an atazanavir based PI-therapy and no change in backbone therapy rapid virological breakthrough occurred. Retrospective analysis displayed preexisting gag cleavage site mutations which may have reduced the genetic barrier in a clinical relevant manner in combination with the already existing NRTI resistance mutations. Alternatively, this effect could be explained with a different antiviral potency for the respective PIs used