Cell-free DNA in plasma as an essential immune system regulator.

The cell-free DNA (cfDNA) is always present in plasma, and it is biomarker of growing interest in prenatal diagnostics as well as in oncology and transplantology for therapy efficiency monitoring. But does this cfDNA have a physiological role? Here we show that cfDNA presence and clearance in plasma of healthy individuals plays an indispensable role in immune system regulation. We exposed THP1 cells to healthy individuals' plasma with (NP) and without (TP) cfDNA. In cells treated with NP, we found elevated expression of genes whose products maintain immune system homeostasis. Exposure of cells to TP triggered an innate immune response (IIR), documented particularly by elevated expression of pro-inflammatory interleukin 8. The results of mass spectrometry showed a higher abundance of proteins associated with IIR activation due to the regulation of complement cascade in cells cultivated with TP. These expression profiles provide evidence that the presence of cfDNA and its clearance in plasma of healthy individuals regulate fundamental mechanisms of the inflammation process and tissue homeostasis. The detailed understanding how neutrophil extracellular traps and their naturally occurring degradation products affect the performance of immune system is of crucial interest for future medical applications.

The use of Human Inflammatory Response and Autoimmunity RT2 lncRNA PCR Array for plasma examination in breast cancer patients prior to therapy.

Long non-coding RNAs (lncRNAs) are defined as RNA molecules longer than 200 nucleotides with poor protein-coding capacity and key functions in regulation of gene expression. Dysregulations of lncRNAs (e.g. HOTAIR and MALAT I) were detected in plasma of breast cancer (BC) patients. Plasma samples are examined as liquid biopsies for purposes of non-invasive diagnostics therefore the research of plasma lncRNAs as potential plasma biomarkers became highly topical. 84 lncRNAs were profiled in 18 plasma samples - 9 BC patients and 9 age-matched healthy - using Human Inflammatory Response & Autoimmunity RT2 lncRNA PCR Array. Total RNA from plasma samples was isolated using miRNeasy Serum/Plasma Kit. Although a pre-amplification recommended for quantification from small starting RNA amounts was used, only 3 lncRNAs (A2ML1-AS1, GAS5 and SNHG5) were detected in all plasma samples. A total of 72 lncRNAs (e.g. HOTAIR or MALAT I) were detected only in some samples and 9 lncRNAs were not detected in any samples. No significant differences were observed in levels of plasma lncRNAs between the BC patients and healthy controls despite the fact that our panel contained also the lncRNAs whose levels were previously reported as significantly different in plasma or cancer tissues (e.g. GAS5, HOTAIR, MALAT I) in BC patients. Detection of lncRNAs in plasma is due to their low concentrations quite difficult as compared with tissues. Our findings suggest that analysis of plasma lncRNAs using this technology is not suitable for use as non-invasive diagnostic tool in BC patients.

The potential roles of vesicle-enclosed miRNAs in communication between macrophages and cancer cells in tumor microenvironment.

Functional microRNA (miRNA) molecules are transported in extracellular vesicles among tumor cells and cells of the immune system. Macrophages as integral components of tumor microenvironment are known as potential contributors to tumor growth and progression. We searched for studies which could provide a direct link between the particular miRNAs transported between cancer cells and macrophages and experimental evidence of subsequent alterations in biological functions of target cells. The validated targets of such microRNAs were found using miRWalk database. These targets were further subjected to analysis by DAVID (Database for Annotation, Visualization and Integrated Discovery) to find the most prominent cellular events that could be potentially regulated in macrophages by miRNAs originated from cancer cells and vice versa. We found that the 5 miRNAs (let-7b, miR-21, miR-29a, miR-222-3p, miR-451) derived from cancer cells may together regulate 2304 target genes in macrophages. The genes involved in regulation of apoptosis, regulation of gene expression and protein transport were significantly overrepresented in this set. Four of the five sets of target genes for these individual miRNAs overlap in MYC oncogene. MYC dependent transcriptional program is responsible for cell cycle entry and regulates the inflammatory response in macrophages.Both miRNAs for which the functional transports from macrophages to cancer cells were experimental proven (miR-223, miR-142-3p) target total 684 genes including some well-known tumor suppressors like TP53 or APC. Suppression of tumor suppressor genes by miRNAs derived from macrophages may eventually contribute to cancer cell proliferation.Due to the complexity of tumor microenvironment, the altered expression profiles of its components affected by miRNA uptake from extracellular vesicles could contribute to the outcome of carcinogenesis therefore the vesicular transport of miRNAs should be studied more extensively in this context.

MicroRNAs in urine supernatant as potential non-invasive markers for bladder cancer detection.

Urinary bladder carcinoma contributes to 4% of newly diagnosed oncological diseases in the Czech Republic. Biomarkers for its early non-invasive detection are therefore highly desirable. Urine seems to be an ideal source of such biomarkers due to the content of cell-free nucleic acids, especially microRNAs (miRNAs).To find potential biomarkers among miRNAs in urine supernatant, we examined in total 109 individuals (36 controls and 73 bladder cancer patients) in three phases. In the first - discovery - phase, microarray cards with 381 miRNAs were used for miRNA analysis of 13 controls and 46 bladder cancer patients. In the second - verification - phase, the results of this first phase were verified on the same groups of subjects by single-target qPCR assays for the selected miRNAs. For the third - validation - phase, new independent samples of urine supernatant (23 controls and 27 bladder cancer patients) were analyzed using single-target qPCR assays for 13 verified in the previous phase. The results of all phases were normalized to miR-191, miR-28-3p, and miR-200b, which were selected as suitable for our study by the qBase+®.We found that miR-125b, miR-30b, miR-204, miR-99a, and miR-532-3p are significantly down-regulated in patients' urine supernatant. In our experiments, the analysis of miR-125 levels provided the highest AUC (0.801) with 95.65% specificity and 59.26% sensitivity, the analysis of miR-99a lead to AUC (0.738) with 82.61% specificity and 74.07% sensitivity. We demonstrate that levels of these miRNAs could potentially serve as promising diagnostic markers for the non-invasive diagnostics of bladder cancer.

DNA from microdissected tissues may be extracted and stored on microscopic slides.

With regard to complex structure of tissues, laser capture microdissection represents an important step in analytical workflow streaming to proper molecular characterization of different cell types in examined samples. Therefore the simple method for simultaneous processing of higher numbers of microdissected tissues leading not only to rapid and efficient DNA isolation but allowing also the repeated sampling and easy storage may be useful in the practice of histopathological laboratories. We elaborated such a methodology applicable downstream after the microdissection from formalin-fixed paraffin embedded tissues.The tissues for examination are microdissected directly into the circular areas having the diameter 2 mm and marked on the microscopic slide. In this way, one slide is able to accommodate multiple samples. The DNA extraction is performed in low volume of buffer with Proteinase K in a droplet covered by mineral oil just on the slide. Mineral oil in the quality for molecular biology not only avoids evaporation during DNA extraction, but it helps to position the microdisssected tissue, to control the level of cell lysis microscopically and to protect the DNA sample during subsequent manipulations. We provided the evidence that DNA isolated by our methodology remains in the positions on microscopic slide for months without any changes in the lengths of available fragments and that it may be removed from each position repetitively for different kinds of analysis. The new methodological approach presented by us can be practically applied in broad spectrum of laboratories performing routinely genetic analysis on microdissected tissues.

Genome-wide methylation analysis of tubulocystic and papillary renal cell carcinomas.

Tubulocystic renal cell carcinoma (TRCC) represents a rare tumor with incidence lower than 1 % of all renal carcinomas. This study was undertaken to contribute to characterization of molecular signatures associated with TRCC and to compare them with the features of papillary renal cell carcinoma (PRCC) at the level of genome wide methylation analysis.We performed methylated DNA immunoprecipitation (MeDIP) coupled with microarray analysis (Roche NimbleGen). Using the CHARM package, we compared the levels of gene methylation between paired samples of tumors and control renal tissues of each examined individual. We found significant global demethylation in all tumor samples in comparison with adjacent kidney tissues of normal histological appearance but no significant differences in gene methylation between the both compared tumor entities. Therefore we focused on characterization of differentially methylated regions between both tumors and control tissues. We found 42 differentially methylated genes.Hypermethylated genes for protocadherins (PCDHG) and genes coding for products associated with functions of plasma membrane were evaluated as significantly overrepresented among hypermethylated genes detected in both types of renal cell carcinomas.In our pilot study, we provide the first evidence that identical features in the process of carcinogenesis leading to TRCC and/or to PRCC may be found at the gene methylation level.

Quantification of plasminogen activator inhibitor type 1 in the aortic wall.

AIM: Plasminogen activator inhibitor type 1 (PAI-1) plays a key role in regulation of fibrinolytic system, cell-associated proteolysis and migration of smooth muscle cells (SMC). This study is focused on the types of PAI-1 expressing cells, quantification of PAI-1 expression in the walls of aneurysmatic abdominal aortas (AAA) and correlation between histological and clinical findings. METHODS: A group of nine patients who underwent surgery for AAA: asymptomatic (aAAA), symptomatic (sAAA) and ruptured (rAAA) and one control specimen (CA) were included in the study. Samples underwent histological processing and immunohistochemistry in comparison with in situ hybridisation. In order to assess the PAI-1 area fraction in histological sections through the aortic wall the Line System module of Ellipse software was used. PAI-1 expressing cells were measured in CA and AAA: endothelium, SMC, and foam cells. Photomicrographs with a total area of 0.7 mm(2) for each specimen were analysed by two independent observers. Mean values of PAI-1 positive components per section area were calculated as average values. RESULTS: The results of both observers are as follows: 28.6% in CA; 18.1% in aAAA; 10.9% in sAAA; 11.0% in rAAA. During the progression of AAA, the SMC (PAI-1 expression was found mainly in them) became less abundant in agreement with the values of PAI-1 area fraction. In rAAA immunohistochemistry detected PAI-1 in necrotic centres of atheromathous plaques. CONCLUSIONS: AAA may be evaluated as the result of gradual changes in regulation of fibrinolysis that is observed as redistribution of cells expressing PAI-1. The area fraction of PAI-1 positive components correlates with clinical classification of AAA.

[Tumorous stem cells--a novel view in oncology?]. / Nádorová kmenová bunka--nový pohled v onkologii?

Authors present contemporary knowledges, arguments and hypothesis about cancer STEM cells and their relations to current concepts of oncology and surgical oncology. The aim is to introduce new view of carcinogenesis and origin of metastatical process as a diseas of STEM cells to general surgical public that deal with surgical oncology and is confronted with new trends in modern oncological pharmacology. The presented theory of tumour origin by cancer STEM cells is confronted critically with all current theories.

Primers ITS1, ITS2 and ITS4 detect the intraspecies variability in the internal transcribed spacers and 5.8S rRNA gene region in clinical isolates of fungi.

Restriction fragment length polymorphism analysis of the 5.8S rRNA gene and the internal transcribed spacers (ITS1 and ITS2) was used for examination of 66 isolates belonging to 19 species. Intraspecies variability was found in the examined region of 11 species (Candida albicans, C. catenulata, C. colliculosa, C. glabrata, C. kefyr, C. melinii, C. parapsilosis, C. guillermondii, C. solanii, C. tropicalis, Saccharomyces cerevisiae). Region of ITS-5.8S rDNA was amplified using the primers ITS1 and ITS4. The amplicons were digested by HaeIII, HinfI and CfoI. The recognized intraspecies variability was confirmed in the second step, in which the shorter fragments of this region were amplified using primers ITS1 and ITS2 and analyzed by capillary electrophoresis. Considerable intraspecific variability renders this method unsuitable for species identification, whereas it can be useful for epidemiological tracing of isolates.

Molecular diagnosis of Epstein-Barr virus in paraffin-embedded tissues of tumors with abundant lymphoid infiltration.

To evaluate the significance of Epstein-Barr virus (EBV) infection in tumorogenesis, we examined ten archival samples of acinic cell carcinomas of salivary glands with lymphoid-rich stroma, four archival samples of lymphoepithelioma-like carcinomas (LELC) of the urinary bladder, ten samples of oncocytic papillary carcinoma of the thyroid (Warthin-like tumors) and one sample of lymphoepithelioma-like carcinoma of the cervix, together 25 paraffin-embedded tumor tissues. Polymerase chain reaction (PCR) and in situ hybridization (ISH) assays were used. The EBV genome was detected by PCR using primers targeting the IR region. ISH was performed using EBER oligonucleotide probes. Each examination was repeated two times. Positive PCR result was obtained in 12% of samples only. However, this result was not confirmed by the subsequent second PCR examination. ISH revealed negative signals in all samples. Our results demonstrate the importance of the diagnostic strategy based on combination at least two independent methods. PCR due to its sensitivity may produce false positive results depending on the degree of infiltration the tumor sample by EBV carrying lymphocytes.

[Molecular genetics methods in medical mycology]. / Moznosti aplikace molekulárne genetických metod v lékarské mykologii.

Molecular genetic methods that use the polymerase chain reaction (PCR) are due their speed widely employed in diagnostic approaches in microbiology. In this report, the possibilities of application of these methods in medical mycology are discussed with regard not only to species identification, but also for genotyping of strains for epidemiological purposes. Recently, a tendency to exploit molecular genetic methods rather for epidemiological studies than for routine species identification may be observed. With regard to the high inter-species variability, careful standardization using samples of isolates of the tested species from corresponding geographical origin is necessary. Perspectives of future development associated with the explanation of molecular biological relations between human tissues and the pathogen, with the recognition of mechanisms of virulence and resistance to antifungal drugs are discussed.

Oncocytic papillary carcinoma with lymphoid stroma (Warthin-like tumour) of the thyroid: a distinct entity with favourable prognosis.

AIMS: We report the clinicopathological and immunohistochemical characteristics of 12 cases of a recently recognized entity, oncocytic papillary thyroid carcinoma (PC) with lymphoid stroma (Warthin-like tumour). METHODS AND RESULTS: The cases were retrieved from the surgical pathology files of our departments. There were 11 female patients and one male patient; they ranged in age from 45 to 85 years (mean 64.2 years). The immunohistochemical profile demonstrated positivity of tumour cells for cytokeratins, thyroglobulin, Leu-M1 and anti-mitochondrial antigen. S100 protein-positive stromal dendritic/Langerhans cells were uniformly present. Polymerase chain reaction, in situ hybridization, and immunohistochemistry for Epstein-Barr virus (EBV) detection revealed no significant positive signal. MIB-1 labelling index was low, compatible with that of 'classical' PC. CONCLUSIONS: Warthin-like tumour is a rare variant of PC, occurring predominantly in elderly women. Its histological features are distinct and well recognizable, differentiating this tumour from a more aggressive tall-cell variant of PC. The apparent indolent behaviour seems to be consistent with the presence of dendritic/Langerhans cells and with low proliferative activity. A possible role of EBV in pathogenesis of this lesion was not proven. Further studies are necessary to determine the prognosis and metastatic potential of this neoplasm.

[The method of DNA isolation can affect the rate of preferential amplification of alleles by the polymerase chain reaction]. / Metoda izolace DNA muze ovlivnit stupen preferencní amplifikace alel polymerázovou retezovou reakcí.

Today, polymerase chain reaction is a common part of approaches serving for identification of individuals in legal medicine. This method is easily practicable, however attention must be paid to the optimization of reaction conditions and to the interpretation of results. From the literature, such cases are known, in which during amplification of extremely small amount of DNA (e.g. from one cell) the polymerase chain reaction preferably amplifies only one of two in the template DNA present alleles. If the amplified fragments differ in length, the shorter one is amplified preferably, and it may be cause of false results. In the presented study, DNA from 23 stains of male blood on different fabrics was isolated by two different methods (by treatment with proteinase K and boiling and by treatment with Chelex 100). The obtained DNA samples were amplified using primers, they are complementary to the amelogenin gene sequences. The system is suitable for sex determination, because amplification of the X-chromosomal sequence provides a fragment in length of 632 bp, amplification of the Y-chromosomal one a fragment in length of 443 bp. The isolation method based on proteinase K led in 17.38% of samples to the very intensive preferential amplification of the longer allele, and therefore to a false result. The isolation method based on Chelex 100 provided in all cases correct results with clearly recognizable preferential amplification of the shorter allele. The reported results accentuate the meaning of choice of the appropriate isolation method, the need of accurate PCR optimization, and the careful interpretations of its outputs.

[Paraffin-embedded tissues as a source of control DNA]. / Tkáne zalité v parafínu jako zdroj kontrolní DNA.

During elucidation of crime cases, the need of a sample of DNA of the victim of the violent attack appears very often. Regarding to the obligatory archiving of histopathological preparations from sectioned persons, the paraffin-embedded tissues are easily achievable material suitable for the given purpose. Such a modification of an isolation method was elaborated which allows the yield of the sufficient amount of DNA from one histological section, and its usefulness was tested on tissues of different types and from different persons. The method was used successfully during solving of concrete cases.

[Determination of the presence of traces of biological material using molecular genetics]. / Moznosti molekulárne genetického urcení druhové príslusnosti biologických stop.

Polymerase chain reaction is often used for molecular genetic human identification in forensic medicine today. In this study, the possibilities are demonstrated, which are provided by the method in such cases, where it is necessary to determine, if the biological traces are of animal or human origin. The method is rapid and well performed in a molecular genetic laboratory with standard equipment. Eleven samples of DNA isolated from different animals and birds were examined. In all cases, it was possible to distinguish these samples according to the results of reaction from simultaneously examined human DNA.