Evaluation of polyplexes as gene transfer agents

Non-viral transfection systems based on the complexes of DNA and polycations (‘polyplexes’) were evaluated with respect to their effectiveness, toxicity and cell type dependence in a variety of in vitro models. The panel of polycations examined included branched and linear polyethyleneimines, poly[N-ethyl-4-vinyl pyridinium bromide], polyamidoamine dendrimer (Superfect™), poly(propyleneimine) dendrimer (Astramol™) and a conjugate of Pluronic® P123 and polyethyleneimine (P123-g-PEI(2K)), having a graft-block copolymer architecture. Using a panel of cell lines the linear polyethyleneimine ExGen™ 500, Superfect™, branched polyethyleneimine 25 kDa, and P123-g-PEI(2K) were determined as systems displaying highest transfection activity while exhibiting relatively low cytotoxicity. These systems had activity higher than or comparable to lipid transfection reagents (Lipofectin®, LipofectAMINE™, CeLLFECTIN® and DMRIE-C) but did not reveal serum dependence and were less toxic than the lipids. Overall, this study demonstrates good potential of structurally diverse polyplex systems as transfection reagents with relatively low cytotoxicity

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

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Implementation of a T4 Extraction Control for Molecular Assays of Cerebrospinal Fluid and Stool Specimens

The use of appropriate extraction and amplification controls for acellular specimens is not standardized in the clinical laboratory community. Extraction controls and checks for inhibitors of amplification in cellular specimens are most often accomplished by amplification of an internal human genomic target. This approach is not feasible for acellular specimens, which may contain little or no amplifiable genomic material. Other specimen types, such as stool, frequently contain amplification inhibitors. Failure to test for these inhibitors can result in the reporting of false-negative results. The goal of this study was to evaluate the use of a T4 bacteriophage as an extraction and amplification control for acellular specimens. The T4 bacteriophage assay was evaluated for use as a control in 290 specimens, including cerebrospinal fluid, serum, and filtered stool. Extraction procedures on two automated instruments were assessed, including the Roche MagNAPure Compact (Roche Diagnostics, Indianapolis, IN) and the QIAGEN BioRobot M48 (QIAGEN, Valencia, CA), along with the manual QIAGEN extraction method. The T4 bacteriophage can be extracted reliably and reproducibly from cerebral spinal fluid, serum, and filtered stool and, therefore, is useful as both an extraction control and inhibitor check for these specimen sources

Human hepatocyte depletion in the presence of HIV-1 infection in dual reconstituted humanized mice

Human immunodeficiency virus type 1 (HIV-1) infection impairs liver function, and liver diseases have become a leading cause of morbidity in infected patients. The immunopathology of liver damage caused by HIV-1 remains unclear. We used chimeric mice dually reconstituted with a human immune system and hepatocytes to address the relevance of the model to pathobiology questions related to human hepatocyte survival in the presence of systemic infection. TK-NOG males were transplanted with mismatched human hematopoietic stem/progenitor cells and hepatocytes, human albumin concentration and the presence of human immune cells in blood were monitored for hepatocytes and immune reconstitution, and mice were infected with HIV-1. HIV-1-infected animals showed a decline in human albumin concentration with a significant reduction in percentage of human hepatocytes compared to uninfected mice. The decrease in human albumin levels correlated with a decline in CD4+ cells in the liver and with an increase in HIV-1 viral load. HIV-1 infection elicited proinflammatory response in the immunological milieu of the liver in HIV-infected mice compared to uninfected animals, as determined by upregulation of IL23, CXCL10 and multiple toll-like receptor expression. The inflammatory reaction associated with HIV-1 infection in vivo could contribute to the depletion and dysfunction of hepatocytes. The dual reconstituted TK-NOG mouse model is a feasible platform to investigate hepatocyte-related HIV-1 immunopathogenesis. This article has an associated First Person interview with the first author of the paper

TOP2A protein by quantitative immunofluorescence as a predictor of response to epirubicin in the neoadjuvant treatment of breast cancer

Anthracyclines are commonly used in breast cancer, although they lack validated predictive biomarkers. We explored the interaction between TOP2A protein by quantitative immunofluorescence (QIF) and anthracycline sensitivity.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Overall survival benefit for sequential doxorubicin-docetaxel compared with concurrent doxorubicin and docetaxel in node-positive breast cancer-8-year results of the breast international group 02-98 phase III trial

Background: In women with node-positive breast cancer, the Breast International Group (BIG) 02-98 tested the incorporation of docetaxel (Taxotere) into doxorubicin (Adriamycin)-based chemotherapy, and compared sequential and concurrent docetaxel. At 5 years, there was a trend for improved disease-free survival (DFS) with docetaxel. We present results at 8-year median follow-up and exploratory analyses within biologically defined subtypes. Methods: Patients were randomly assigned to one of four treatments: (i) sequential control: doxorubicin (A) (75 mg/m. 2) × 4 → classical cyclophosphamide, methotrexate, 5-fluorouracil (CMF); (ii) concurrent control: doxorubicin, cyclophosphamide (AC)(60/600 mg/m. 2) × 4 →CMF; (iii) sequential docetaxel: A (75 mg/m. 2) × 3 → docetaxel (T) (100 mg/m. 2) × 3 → CMF and (iv) concurrent docetaxel: AT(50/75 mg/m. 2) × 4 →CMF. The primary comparison evaluated docetaxel efficacy regardless of the schedule. Exploratory analyses were undertaken within biologically defined subtypes. Results: Two thousand eight hundred and eighty-seven patients were enrolled. After 93.4 months of median follow-up, there were 916 DFS events. For the primary comparison, there was no significant improvement in DFS from docetaxel [hazard ratio (HR) = 0.91, 95% confidence interval (CI) = 0.80-1.05, P = 0.187]. In secondary comparisons, sequential docetaxel significantly improved DFS compared with sequential control (HR = 0.81, 95% CI = 0.67-0.99, P = 0.036), and significantly improved DFS (HR = 0.84, 95% CI = 0.72-0.99, P = 0.035) and overall survival (OS) (HR = 0.79, 95% CI = 0.65-0.98, P = 0.028) compared with concurrent doxorubicin-docetaxel. Luminal-A disease had the best prognosis. HRs favored addition of sequential docetaxel in all subtypes, except luminal-A; but this observation was not statistically supported because of limited numbers. Conclusion: With further follow-up, the sequential docetaxel schedule resulted in significantly better OS than concurrent doxorubicin-docetaxel, and continued to show better DFS than sequential doxorubicin-based control. © The Author 2013. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved.SCOPUS: ar.jinfo:eu-repo/semantics/publishe