Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.This work was supported by Ministry of Health of the Czech Republic, grant no. 16-34272A; computational resources were provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the programme “Projects of Large Research, Development, and Innovations Infrastructures”. Analyses in Prague (JT, EF and MS) were supported by Ministry of Health, Czech Republic, grant no. 00064203, and by PRIMUS/17/MED/11. Analyses in the Monza (Centro Ricerca Tettamanti, SS, AG and GC) laboratory were supported by the Italian Association for Cancer Research (AIRC) and Comitato Maria Letizia Verga

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

Background: State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings: The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance: The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution fo

Untargeted metabolomics based on ultra-high-performance liquid chromatography–high-resolution mass spectrometry merged with chemometrics: A new predictable tool for an early detection of mycotoxins

In order to explore the early detection of mycotoxins in wheat three standardized approaches (Fusarium disease severity, PCR assays for Fusarium spp. identification and mycotoxin quantification) and a novel untargeted metabolomics strategy were jointly assessed. In the first phase of this research, standardized approaches were able to quantify mycotoxins and identify Fusarium spp. Then, an UHPLC-QTOF metabolic fingerprinting method was developed to investigate plant-pathogen cross-talk. At the same time, chemometrics analysis demonstrated to be a powerful tool in order to distinguish low and strong infection levels. Combining these results, the cross-talk plant pathogen related to the early detection of mycotoxins was discovered. As a rapid response to fungal infection an overexpression of phosphatidic acids was discovered. By contrast, when the infection became stronger an increase of oxylipins and diacylglycerols was revealed

The potential applications of fibrin-coated electrospun polylactide nanofibers in skin tissue engineering

Marketa Bacakova,1,2 Jana Musilkova,1 Tomas Riedel,3 Denisa Stranska,4 Eduard Brynda,3 Margit Zaloudkova,5 Lucie Bacakova1 1Department of Biomaterials and Tissue Engineering, Institute of Physiology, Czech Academy of Sciences, 2Second Faculty of Medicine, Charles University in Prague, 3Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, 4InStar Technologies, Liberec, 5Institute of Rock Structure and Mechanics, Czech Academy of Sciences, Prague, Czech Republic Abstract: Fibrin plays an important role during wound healing and skin regeneration. It is often applied in clinical practice for treatment of skin injuries or as a component of skin substitutes. We prepared electrospun nanofibrous membranes made from poly(L-lactide) modified with a thin fibrin nanocoating. Fibrin surrounded the individual fibers in the membrane and also formed a thin fibrous mesh on several places on the membrane surface. The cell-free fibrin nanocoating remained stable in the cell culture medium for 14 days and did not change its morphology. On membranes populated with human dermal fibroblasts, the rate of fibrin degradation correlated with the degree of cell proliferation. The cell spreading, mitochondrial activity, and cell population density were significantly higher on membranes coated with fibrin than on nonmodified membranes, and this cell performance was further improved by the addition of ascorbic acid in the cell culture medium. Similarly, fibrin stimulated the expression and synthesis of collagen I in human dermal fibroblasts, and this effect was further enhanced by ascorbic acid. The expression of beta1-integrins was also improved by fibrin, and on pure polylactide membranes, it was slightly enhanced by ascorbic acid. In addition, ascorbic acid promoted deposition of collagen I in the form of a fibrous extracellular matrix. Thus, the combination of nanofibrous membranes with a fibrin nanocoating and ascorbic acid seems to be particularly advantageous for skin tissue engineering. Keywords: electrospun nanofibers, nanocoating, skin tissue engineering, fibroblasts, fibrin, ascorbic acid, nanotechnology, nanomedicine, collagen I synthesis, beta1-integrin

A novel approach based on untargeted lipidomics reveals differences in the lipid pattern among durum and common wheat

In the present work the possibility of using an untargeted metabolomic strategy to discriminate between common and durum wheat lipidome for an authenticity purpose was explored. A first study was conducted by analyzing 52 samples from two durum and common wheat varieties. Afterwards, an extended and independent sample set (173 samples and five varieties) was used as a confirmatory study to verify the stability and consistency of the models obtained. Putatively identified markers were evaluated applying ROC curves resulting in individual marker AUC >90% both in preliminary and confirmatory study. In addition, digalactosyl diglyceride (DGDG) 36:4 was shown to be an effective marker differentiating between authentic durum wheat and its adulterated admixture down to 3% adulteration level, which is the maximum contamination level allowed by Italian legislation. The results demonstrated that untargeted lipidomics, in conjunction with chemometric tools has a significant potential for screening and detection of wheat fraud

Protein nanocoatings on synthetic polymeric nanofibrous membranes designed as carriers for skin cells

Marketa Bacakova,1,2 Julia Pajorova,1,2 Denisa Stranska,3 Daniel Hadraba,1,4 Frantisek Lopot,4 Tomas Riedel,5 Eduard Brynda,5 Margit Zaloudkova,6 Lucie Bacakova1 1Department of Biomaterials and Tissue Engineering, Institute of Physiology, Czech Academy of Sciences, 2Second Faculty of Medicine, Charles University, Prague, 3InStar Technologies, Liberec, 4Department of Anatomy and Biomechanics, Faculty of Physical Education and Sport, Charles University, 5Department of Chemistry and Physics of Surfaces and Biointerfaces, Institute of Macromolecular Chemistry, 6Department of Composites and Carbon Materials, Institute of Rock Structure and Mechanics, Czech Academy of Sciences, Prague, Czech Republic Abstract: Protein-coated resorbable synthetic polymeric nanofibrous membranes are promising for the fabrication of advanced skin substitutes. We fabricated electrospun polylactic acid and poly(lactide-co-glycolic acid) nanofibrous membranes and coated them with fibrin or collagen I. Fibronectin was attached to a fibrin or collagen nanocoating, in order further to enhance the cell adhesion and spreading. Fibrin regularly formed a coating around individual nanofibers in the membranes, and also formed a thin noncontinuous nanofibrous mesh on top of the membranes. Collagen also coated most of the fibers of the membrane and randomly created a soft gel on the membrane surface. Fibronectin predominantly adsorbed onto a thin fibrin mesh or a collagen gel, and formed a thin nanofibrous structure. Fibrin nanocoating greatly improved the attachment, spreading, and proliferation of human dermal fibroblasts, whereas collagen nanocoating had a positive influence on the behavior of human HaCaT keratinocytes. In addition, fibrin stimulated the fibroblasts to synthesize fibronectin and to deposit it as an extracellular matrix. Fibrin coating also showed a tendency to improve the ultimate tensile strength of the nanofibrous membranes. Fibronectin attached to fibrin or to a collagen coating further enhanced the adhesion, spreading, and proliferation of both cell types. Keywords: skin-tissue engineering, nanocoating, nanofibers, skin cells, fibrin, collage

Immune response to E7 protein of human papillomavirus type 16 anchored on the cell surface

To target the E7 protein of human papilloma virus 16 to the cell surface, a fusion gene was constructed. It encodes the signal peptide, part of the immunoglobulin (IgG)-like domain, the transmembrane anchor of vaccinia virus (VV) hemagglutinin (HA), and the complete E7-coding sequence. The fusion gene was expressed under the HA late promoter by a recombinant VV, designated VV-E7-HA. The E7-HA protein was displayed on the surface of cells infected with the recombinant virus and was more stable than unmodified E7. The biological properties of the VV-E7-HA virus were compared with those of a VV-E7 virus that expressed the unmodified E7 and with a VV expressing the Sig-E7-LAMP fusion protein. While the first two of these recombinants were based on VV strain Praha, the third was derived from the WR strain of VV. Infection of mice with the VV-E7-HA virus induced the formation of E7-specific antibodies with the predominance of the IgG2a isotype, whereas the other two viruses did not induce the formation of E7-specific antibodies. Unlike the other two viruses, VV-E7-HA did not induce a response of cytotoxic T lymphocytes or Th1 cells and did not protect mice against the growth of E7-expressing tumors. Thus, VV-E7-HA induced a differently polarized immune response to the E7 protein than the other two viruses.status: publishe