Publications

@article{Maronek2021,

title = {Extracellular DNA Correlates with Intestinal Inflammation in Chemically Induced Colitis in Mice},

author = {M Maronek and B Gromova and R Liptak and B Konecna and M Pastorek and B Cechova and M Harsanyova and J Budis and D Smolak and J Radvanszky and T Szemes and J Harsanyiova and A Kralova Trancikova and R Gardlik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099721641&doi=10.3390%2fcells10010081&partnerID=40&md5=e2a2d57bcd02c36a1091367862022bb1},

doi = {10.3390/cells10010081},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {1},

publisher = {NLM (Medline)},

abstract = {Circulating extracellular DNA (ecDNA) is known to worsen the outcome of many diseases. ecDNA released from neutrophils during infection or inflammation is present in the form of neutrophil extracellular traps (NETs). It has been shown that higher ecDNA concentration occurs in a number of inflammatory diseases including inflammatory bowel disease (IBD). Enzymes such as peptidyl arginine deiminases (PADs) are crucial for NET formation. We sought to describe the dynamics of ecDNA concentrations and fragmentation, along with NETosis during a mouse model of chemically induced colitis. Plasma ecDNA concentration was highest on day seven of dextran sulfate sodium (DSS) intake and the increase was time-dependent. This increase correlated with the percentage of cells undergoing NETosis and other markers of disease activity. Relative proportion of nuclear ecDNA increased towards more severe colitis; however, absolute amount decreased. In colon explant medium, the highest concentration of ecDNA was on day three of DSS consumption. Early administration of PAD4 inhibitors did not alleviate disease activity, but lowered the ecDNA concentration. These results uncover the biological characteristics of ecDNA in IBD and support the role of ecDNA in intestinal inflammation. The therapeutic intervention aimed at NETs and/or nuclear ecDNA has yet to be fully investigated.},

keywords = {Body fluids, Cell-free nucleic acids},

pubstate = {published},

tppubtype = {article}

}

@article{Pös20201,

title = {Technical and methodological aspects of cell‐free nucleic acids analyzes},

author = {Z Pös and O Pös and J Styk and A Mocova and L Strieskova and J Budis and L Kadasi and J Radvanszky and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096148893&doi=10.3390%2fijms21228634&partnerID=40&md5=826434c64ac9dbe5f81fc0ee5b62eaa3},

doi = {10.3390/ijms21228634},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {22},

pages = {1-43},

publisher = {MDPI AG},

abstract = {Analyzes of cell‐free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Body fluids, Cell-free nucleic acids, Liquid biopsy, Non-invasive prenatal testing, Review},

pubstate = {published},

tppubtype = {article}

}

@article{Soltysova20201,

title = {Monosomy 3 influences epithelial-mesenchymal transition gene expression in uveal melanoma patients; consequences for liquid biopsy},

author = {A Soltysova and T Sedlackova and D Dvorska and K Jasek and P C Baradaran and V H Kajabova and L Demkova and V Buocikova and T Kurucova and D Lyskova and A Furdova and G Minarik and P Babal and Z Dankova and B Smolkova},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097833518&doi=10.3390%2fijms21249651&partnerID=40&md5=133b8d5d56ebac3bf7a09024f007273e},

doi = {10.3390/ijms21249651},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {24},

pages = {1-24},

publisher = {MDPI AG},

abstract = {Despite outstanding advances in diagnosis and the treatment of primary uveal melanoma (UM), nearly 50% of UM patients develop metastases via hematogenous dissemination, driven by the epithelial-mesenchymal transition (EMT). Despite the failure in UM to date, a liquid biopsy may offer a feasible non-invasive approach for monitoring metastatic disease progression and addressing protracted dormancy. To detect circulating tumor cells (CTCs) in UM patients, we evaluated the mRNA expression of EMT-associated transcription factors in CD45-depleted blood fraction, using qRT-PCR. ddPCR was employed to assess UM-specific GNA11, GNAQ, PLCβ4, and CYSLTR2 mutations in plasma DNA. Moreover, microarray analysis was performed on total RNA isolated from tumor tissues to estimate the prognostic value of EMT-associated gene expression. In total, 42 primary UM and 11 metastatic patients were enrolled. All CD45-depleted samples were negative for CTC when compared to the peripheral blood fraction of 60 healthy controls. Tumor-specific mutations were detected in the plasma of 21.4% patients, merely, in 9.4% of primary UM, while 54.5% in metastatic patients. Unsupervised hierarchical clustering of differentially expressed EMT genes showed significant differences between monosomy 3 and disomy 3 tumors. Newly identified genes can serve as non-invasive prognostic biomarkers that can support therapeutic decisions. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Aneuploidy, Body fluids, Circulating tumor cells, Liquid biopsy, Oncology},

pubstate = {published},

tppubtype = {article}

}

@article{Smolkova20201,

title = {Increased stromal infiltrating lymphocytes are associated with the risk of disease progression in mesenchymal circulating tumor cell-positive primary breast cancer patients},

author = {B Smolkova and Z Cierna and K Kalavska and S Miklikova and J Plava and G Minarik and T Sedlackova and D Cholujova and P Gronesova and M Cihova and K Majerova and M Karaba and J Benca and D Pindak and J Mardiak and M Mego},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097678410&doi=10.3390%2fijms21249460&partnerID=40&md5=8dd0aa352be241f64188de23774ac3c4},

doi = {10.3390/ijms21249460},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {24},

pages = {1-16},

publisher = {MDPI AG},

abstract = {Circulating tumor cells (CTCs) and the immune infiltration of tumors are closely related to clinical outcomes. This study aimed to verify the influence of stromal lymphocyte infiltration and the immune context of tumor microenvironment on the hematogenous spread and prognosis of 282 chemotherapy naïve primary BC patients. To detect the presence of mesenchymal CTCs, RNA extracted from CD45-depleted peripheral blood was interrogated for the expression of mesenchymal gene transcripts. Tumor-infiltrating lymphocytes (TILs) were detected in the stromal areas by immunohistochemistry, using CD3, CD8, and CD45RO antibodies. The concentrations of 51 plasma cytokines were measured by multiplex bead arrays. TILs infiltration in mesenchymal CTC-positive patients significantly decreased their progression-free survival (HR = 4.88, 95% CI 2.30–10.37, p < 0.001 for CD3high; HR = 6.17, 95% CI 2.75–13.80, p < 0.001 for CD8high; HR = 6.93, 95% CI 2.86–16.81, p < 0.001 for CD45ROhigh). Moreover, the combination of elevated plasma concentrations of transforming growth factor beta-3 (cut-off 662 pg/mL), decreased monocyte chemotactic protein-3 (cut-off 52.5 pg/mL) and interleukin-15 (cut-off 17.1 pg/mL) significantly increased the risk of disease recurrence (HR = 4.838, 95% CI 2.048–11.427, p < 0.001). Our results suggest a strong impact of the immune tumor microenvironment on BC progression, especially through influencing the dissemination and survival of more aggressive, mesenchymal CTC subtypes. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Body fluids, Circulating tumor cells, Liquid biopsy, Oncology},

pubstate = {published},

tppubtype = {article}

}

@article{Kamodyová2013124,

title = {Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing},

author = {N Kamodyová and J Durdiaková and P Celec and T Sedláčková and G Repiská and B Sviežená and G Minárik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84869494452&doi=10.1016%2fj.fsigen.2012.07.007&partnerID=40&md5=f8e720ec77c4cb403c6ae43168224959},

doi = {10.1016/j.fsigen.2012.07.007},

issn = {18724973},

year  = {2013},

date = {2013-01-01},

journal = {Forensic Science International: Genetics},

volume = {7},

number = {1},

pages = {124-128},

abstract = {Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60 min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30 min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence. © 2012 Elsevier Ireland Ltd.},

keywords = {Body fluids, Short tandem repeats},

pubstate = {published},

tppubtype = {article}

}

@article{Vlková2010258,

title = {Does maternal saliva contain fetal DNA usable for prenatal diagnostics?},

author = {B Vlková and T Szemes and G Minárik and J Turňa and P Celec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-72449174721&doi=10.1016%2fj.mehy.2009.09.022&partnerID=40&md5=e4a8ec14001f99b11fadd011098f2c5d},

doi = {10.1016/j.mehy.2009.09.022},

issn = {03069877},

year  = {2010},

date = {2010-01-01},

journal = {Medical Hypotheses},

volume = {74},

number = {2},

pages = {258-260},

abstract = {Non-invasive molecular analysis of fetal DNA is the diagnostic goal of prenatal medicine. Circulating fetal DNA can be detected in maternal plasma. Recently, it has been detected in the urine of pregnant women. We hypothesize that fetal DNA is present also in maternal saliva and that advances in stabilization and isolation of nucleic acids from saliva enable non-invasive and repeated sampling for prenatal diagnostics. The hypothesis is testable using saliva samples of pregnant women with confirmed male fetuses. Y-specific sequences should be detectable in salivary DNA. Caution must be given to the prevention of contamination. If proved in large studies, the presence of fetal DNA fragments in maternal saliva would enable a wide range of applications in prenatal medicine. © 2009 Elsevier Ltd. All rights reserved.},

keywords = {Body fluids, Cell-free nucleic acids, Non-invasive prenatal testing, Prenatal diagnosis},

pubstate = {published},

tppubtype = {article}

}