1
|
Kvapilova K, Misenko P, Radvanszky J, Brzon O, Budis J, Gazdarica J, Pos O, Korabecna M, Kasny M, Szemes T, Kvapil P, Paces J, Kozmik Z. Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses. BMC Genomics 2024; 25:187. [PMID: 38365587 PMCID: PMC10873937 DOI: 10.1186/s12864-024-10080-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols. METHODS The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results. RESULTS The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol. CONCLUSION Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.
Collapse
Affiliation(s)
- Katerina Kvapilova
- Faculty of Science, Charles University, Albertov 6, Prague, 128 00, Czech Republic.
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic.
| | - Pavol Misenko
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
| | - Jan Radvanszky
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, Bratislava, 845 05, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Ondrej Brzon
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jaroslav Budis
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Juraj Gazdarica
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Ondrej Pos
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, Prague, 128 00, Czech Republic
| | - Martin Kasny
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Tomas Szemes
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Petr Kvapil
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jan Paces
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
| |
Collapse
|
2
|
Tomasova K, Kroupa M, Zinkova A, Korabecna M, Vymetalkova V, Skrobanek P, Sojka L, Levy M, Hemminki K, Liska V, Hosek P, Kumar R, Vodickova L, Vodicka P. Monitoring of telomere dynamics in peripheral blood leukocytes in relation to colorectal cancer patients’ outcomes. Front Oncol 2022; 12:962929. [PMID: 36203452 PMCID: PMC9530927 DOI: 10.3389/fonc.2022.962929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2022] Open
Abstract
We investigated the possible associations between leukocyte telomere length, therapy outcomes, and clinicopathological features in patients with colorectal cancer. Additionally, telomerase reverse transcriptase (TERT) expression was evaluated. Telomere length was measured using singleplex qPCR in 478 consecutive leukocyte DNA samples from 198 patients. Blood was drawn at diagnosis prior to any therapy and then at 6-month intervals for 18 months. Following diagnosis, the telomeres gradually shortened during the course of the treatment regardless of the patient’s age. The most pronounced decrease was observed 12 months after the diagnosis (p < 0.0001). Based on tumor localization, the decrease in telomere length one year after the diagnosis followed different trajectories (p = 0.03). In patients treated with adjuvant therapy, telomere length correlated with the time elapsed after completion of therapy (p = 0.03). TERT expression did not correlate with the telomere length; however, it was higher in women than men (1.35-fold, 95% CI 1.11–1.65, p = 0.003) and in smokers than non-smokers (1.27-fold, 95% CI 1.01–1.61, p = 0.04). Leukocyte telomere length declines naturally during aging, but the accelerated shortening observed in our patients was age-independent. Telomere length manifestly reflected chemotherapy impact and could be linked to therapy toxicity.
Collapse
Affiliation(s)
- Kristyna Tomasova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- *Correspondence: Kristyna Tomasova,
| | - Michal Kroupa
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Alzbeta Zinkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Veronika Vymetalkova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Pavel Skrobanek
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czechia
| | - Ladislav Sojka
- Department of Surgery, First Faculty of Medicine, Charles Univesity and Thomayer Hospital, Prague, Czechia
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles Univesity and Thomayer Hospital, Prague, Czechia
| | - Kari Hemminki
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Vaclav Liska
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Department of Surgery, Medical Faculty in Pilsen, Charles University, Pilsen, Czechia
| | - Petr Hosek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Rajiv Kumar
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- German Cancer Research Center, Heidelberg, Germany
| | - Ludmila Vodickova
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Pavel Vodicka
- Department of the Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czechia
| |
Collapse
|
3
|
Zhang H, Laššáková S, Yan Z, Wang X, Šenkyřík P, Gaňová M, Chang H, Korabecna M, Neuzil P. Digital polymerase chain reaction duplexing method in a single fluorescence channel. Anal Chim Acta 2022; 1238:340243. [DOI: 10.1016/j.aca.2022.340243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022]
|
4
|
Frydlova J, Zednikova I, Satrapova V, Pazourkova E, Santorova S, Hruskova Z, Tesar V, Vokurka M, Prikryl P, Korabecna M. Analysis of microRNAs in Small Urinary Extracellular Vesicles and Their Potential Roles in Pathogenesis of Renal ANCA-Associated Vasculitis. Int J Mol Sci 2022; 23:ijms23084344. [PMID: 35457163 PMCID: PMC9028884 DOI: 10.3390/ijms23084344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
Antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis (AAV) represents an autoimmunity disease characterized by high mortality. For successful treatment, the detailed knowledge of its complex pathogenesis and the set of biomarkers for differential diagnostics are desired. Analysis of molecular content of small urinary extracellular vesicles (uEV) offers the possibility to find markers in the form of microRNAs (miRNAs) and study the pathways involved in pathogenesis. We used next-generation sequencing in the first preliminary study to detect the miRNAs with altered expression in uEVs of patients with AAV in comparison with age-matched controls. We confirmed the results using single-target quantitative polymerase chain reaction tests on different sets of samples and found five miRNAs (miR-30a-5p, miR-31-3p, miR-99a-5p, miR-106b-5p, miR-182-5p) with highly elevated levels in uEVs of patients. We performed the comparison of their targets with the differentially expressed proteins in uEVs of patients included in the first phase. We realized that upregulated miRNAs and proteins in uEVs in AAV patients target different biological pathways. The only overlap was detected in pathways regulating the actin cytoskeleton assembly and thus potentially affecting the glomerular functions. The associations of upregulated miRNAs with pathways that were neglected as components of complex AAV pathogenesis, e.g., the epidermal growth factor receptor signaling pathway, were found.
Collapse
Affiliation(s)
- Jana Frydlova
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, U Nemocnice 5, 128 53 Prague, Czech Republic; (J.F.); (M.V.)
| | - Iveta Zednikova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Albertov 4, 128 00 Prague, Czech Republic; (I.Z.); (E.P.); (S.S.)
| | - Veronika Satrapova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 128 08 Prague, Czech Republic; (V.S.); (Z.H.); (V.T.)
| | - Eva Pazourkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Albertov 4, 128 00 Prague, Czech Republic; (I.Z.); (E.P.); (S.S.)
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 128 08 Prague, Czech Republic; (V.S.); (Z.H.); (V.T.)
| | - Sarka Santorova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Albertov 4, 128 00 Prague, Czech Republic; (I.Z.); (E.P.); (S.S.)
| | - Zdenka Hruskova
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 128 08 Prague, Czech Republic; (V.S.); (Z.H.); (V.T.)
| | - Vladimir Tesar
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 128 08 Prague, Czech Republic; (V.S.); (Z.H.); (V.T.)
| | - Martin Vokurka
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, U Nemocnice 5, 128 53 Prague, Czech Republic; (J.F.); (M.V.)
| | - Petr Prikryl
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, U Nemocnice 5, 128 53 Prague, Czech Republic; (J.F.); (M.V.)
- Correspondence: (P.P.); (M.K.)
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Albertov 4, 128 00 Prague, Czech Republic; (I.Z.); (E.P.); (S.S.)
- Correspondence: (P.P.); (M.K.)
| |
Collapse
|
5
|
Geryk J, Zinkova A, Zedníková I, Simková H, Stenzl V, Korabecna M. Improving structural variant clustering to reduce the negative effect of the breakpoint uncertainty problem. BMC Bioinformatics 2021; 22:464. [PMID: 34579642 PMCID: PMC8474851 DOI: 10.1186/s12859-021-04374-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/15/2021] [Indexed: 11/12/2022] Open
Abstract
Background Structural variants (SVs) represent an important source of genetic variation. One of the most critical problems in their detection is breakpoint uncertainty associated with the inability to determine their exact genomic position. Breakpoint uncertainty is a characteristic issue of structural variants detected via short-read sequencing methods and complicates subsequent population analyses. The commonly used heuristic strategy reduces this issue by clustering/merging nearby structural variants of the same type before the data from individual samples are merged. Results We compared the two most used dissimilarity measures for SV clustering in terms of Mendelian inheritance errors (MIE), kinship prediction, and deviation from Hardy–Weinberg equilibrium. We analyzed the occurrence of Mendelian-inconsistent SV clusters that can be collapsed into one Mendelian-consistent SV as a new measure of dataset consistency. We also developed a new method based on constrained clustering that explicitly identifies these types of clusters. Conclusions We found that the dissimilarity measure based on the distance between SVs breakpoints produces slightly better results than the measure based on SVs overlap. This difference is evident in trivial and corrected clustering strategy, but not in constrained clustering strategy. However, constrained clustering strategy provided the best results in all aspects, regardless of the dissimilarity measure used. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04374-3.
Collapse
Affiliation(s)
- Jan Geryk
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, V Úvalu 84, 15006, Prague, Czech Republic. .,Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
| | - Alzbeta Zinkova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Iveta Zedníková
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Halina Simková
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Vlastimil Stenzl
- Department of Forensic Genetics, Institute of Criminalistics, Strojnická 27, 170 89, Prague, Czech Republic
| | - Marie Korabecna
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| |
Collapse
|
6
|
Zhang H, Yan Z, Wang X, Gaňová M, Chang H, Laššáková S, Korabecna M, Neuzil P. Determination of Advantages and Limitations of qPCR Duplexing in a Single Fluorescent Channel. ACS Omega 2021; 6:22292-22300. [PMID: 34497918 PMCID: PMC8412922 DOI: 10.1021/acsomega.1c02971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Real-time (quantitative) polymerase chain reaction (qPCR) has been widely applied in molecular diagnostics due to its immense sensitivity and specificity. qPCR multiplexing, based either on fluorescent probes or intercalating dyes, greatly expanded PCR capability due to the concurrent amplification of several deoxyribonucleic acid sequences. However, probe-based multiplexing requires multiple fluorescent channels, while intercalating dye-based multiplexing needs primers to be designed for amplicons having different melting temperatures. Here, we report a single fluorescent channel-based qPCR duplexing method on a model containing the sequence of chromosomes 21 (Chr21) and 18 (Chr18). We combined nonspecific intercalating dye EvaGreen with a 6-carboxyfluorescein (FAM) probe specific to either Chr21 or Chr18. The copy number (cn) of the target linked to the FAM probe could be determined in the entire tested range from the denaturation curve, while the cn of the other one was determined from the difference between the denaturation and elongation curves. We recorded the amplitude of fluorescence at the end of denaturation and elongation steps, thus getting statistical data set to determine the limit of the proposed method in detail in terms of detectable concentration ratios of both targets. The proposed method eliminated the fluorescence overspilling that happened in probe-based qPCR multiplexing and determined the specificity of the PCR product via melting curve analysis. Additionally, we performed and verified our method using a commercial thermal cycler instead of a self-developed system, making it more generally applicable for researchers. This quantitative single-channel duplexing method is an economical substitute for a conventional rather expensive probe-based qPCR requiring different color probes and hardware capable of processing these fluorescent signals.
Collapse
Affiliation(s)
- Haoqing Zhang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Zhiqiang Yan
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Xinlu Wang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Martina Gaňová
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
| | - Honglong Chang
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
| | - Soňa Laššáková
- Institute
of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital
in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Marie Korabecna
- Institute
of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital
in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Pavel Neuzil
- School
of Mechanical Engineering, Department of Microsystem Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072, P. R. China
- Central
European Institute of Technology, Brno University
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- School
of Electrical Engineering and Computer Technology, Brno University of Technology, Technická 10, 612 00 Brno, Czech Republic
| |
Collapse
|
7
|
Pazourkova E, Zednikova I, Korabecna M, Kralova J, Pisacka M, Novotna M, Calda P, Horinek A. Optimization of diagnostic strategy for non-invasive cell-free foetal RHD determination from maternal plasma. Vox Sang 2021; 116:1012-1019. [PMID: 33761162 DOI: 10.1111/vox.13099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/20/2020] [Accepted: 03/01/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND OBJECTIVES The aim of the study was to optimize routine non-invasive prenatal detection of fetal RHD gene from plasma of RhD-negative pregnant women (the median of gestational age was 25 weeks, range 10-38) to detect RhD materno-fetal incompatibility and to avoid the redundant immunoprophylaxis. MATERIALS AND METHODS Initially only one exon of RHD gene (exon 10) was investigated in 281 plasma samples (144 verified after delivery), in the second phase three RHD exons (5, 7, 10) were analyzed in 246 samples of plasma and maternal genomic DNA (204 verified) by real-time PCR method. Detection of Y-chromosomal sequence DYS-14 and five X-chromosomal insertion/deletion polymorphisms was used to confirm the fetal cfDNA detectability in plasma. Specific polymorphisms in RHD gene were detected by sequence-specific primer PCR in nine samples. RESULTS When only the RHD exon 10 was tested, 2·8% of verified samples were false positive and 3·5% false negative. With three RHD exons (5, 7, 10) and maternal genomic DNA testing, only one case was false negative (0·5%). Nine samples were inconclusive due to RHD-positive results in maternal genomic DNA. These samples were analyzed for specific mutations in RHD gene. Combination of both methods for fetal cfDNA verification succeeded in 75% of tested group. CONCLUSION Implementation of analysis of three RHD exons and maternal genomic DNA to routine practice lowers dramatically the ratio of false positive and negative results. This method enables more accurate determination of fetal RHD status with the reduction of unnecessary medical care and RhD immunoprophylaxis.
Collapse
Affiliation(s)
- Eva Pazourkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic.,Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic
| | - Iveta Zednikova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic
| | - Jana Kralova
- Department of Immunohematology, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Martin Pisacka
- Department of Immunohematology, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Michaela Novotna
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic
| | - Pavel Calda
- Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic
| | - Ales Horinek
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic.,3rd Department of Medicine, Department of Endocrinology and Metabolism, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic
| |
Collapse
|
8
|
Zednikova I, Pazourkova E, Lassakova S, Vesela B, Korabecna M. Detection of cell-free foetal DNA fraction in female-foetus bearing pregnancies using X-chromosomal insertion/deletion polymorphisms examined by digital droplet PCR. Sci Rep 2020; 10:20036. [PMID: 33208834 PMCID: PMC7676229 DOI: 10.1038/s41598-020-77084-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 10/23/2020] [Indexed: 12/03/2022] Open
Abstract
In families with X-linked recessive diseases, foetal sex is determined prenatally by detection of Y-chromosomal sequences in cell-free foetal DNA (cffDNA) in maternal plasma. The same procedure is used to confirm the cffDNA presence during non-invasive prenatal RhD incompatibility testing but there are no generally accepted markers for the detection of cffDNA fraction in female-foetus bearing pregnancies. We present a methodology allowing the detection of paternal X-chromosomal alleles on maternal background and the confirmation of female sex of the foetus by positive amplification signals. Using digital droplet PCR (ddPCR) we examined X-chromosomal INDEL (insertion/deletion) polymorphisms: rs2307932, rs16397, rs16637, rs3048996, rs16680 in buccal swabs of 50 females to obtain the population data. For all INDELs, we determined the limits of detection for each ddPCR assay. We examined the cffDNA from 63 pregnant women bearing Y-chromosome negative foetuses. The analysis with this set of INDELs led to informative results in 66.67% of examined female-foetus bearing pregnancies. Although the population data predicted higher informativity (74%) we provided the proof of principle of this methodology. We successfully applied this methodology in prenatal diagnostics in a family with Wiscott-Aldrich syndrome and in pregnancies tested for the risk of RhD incompatibility.
Collapse
Affiliation(s)
- Iveta Zednikova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Eva Pazourkova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U nemocnice 2, 128 08, Prague, Czech Republic
| | - Sona Lassakova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Barbora Vesela
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Marie Korabecna
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
| |
Collapse
|
9
|
Korabecna M, Zinkova A, Brynychova I, Chylikova B, Prikryl P, Sedova L, Neuzil P, Seda O. Cell-free DNA in plasma as an essential immune system regulator. Sci Rep 2020; 10:17478. [PMID: 33060738 PMCID: PMC7566599 DOI: 10.1038/s41598-020-74288-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/04/2020] [Indexed: 02/08/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- M Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
| | - A Zinkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - I Brynychova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - B Chylikova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - P Prikryl
- First Faculty of Medicine, Institute of Pathological Physiology, Charles University, Prague, Czech Republic
| | - L Sedova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - P Neuzil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, People's Republic of China
- CEITEC, Brno University of Technology, Brno, Czech Republic
| | - O Seda
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| |
Collapse
|
10
|
Sterbova M, Pazourkova E, Santorova-Pospisilova S, Zednikova I, Tesarova P, Korabecna M. The use of Human Inflammatory Response and Autoimmunity RT2 lncRNA PCR Array for plasma examination in breast cancer patients prior to therapy. Neoplasma 2019; 66:641-646. [PMID: 30943749 DOI: 10.4149/neo_2018_180907n679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/20/2019] [Indexed: 11/08/2022]
Abstract
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.
Collapse
Affiliation(s)
- M Sterbova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Prague, Czech Republic
| | - E Pazourkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Prague, Czech Republic
| | - S Santorova-Pospisilova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Prague, Czech Republic
| | - I Zednikova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Prague, Czech Republic
| | - P Tesarova
- Department of Oncology, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Prague, Czech Republic
| | - M Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Prague, Czech Republic
| |
Collapse
|
11
|
Brynychova I, Zinkova A, Hoffmanova I, Korabecna M, Dankova P. Immunoregulatory properties of cell-free DNA in plasma of celiac disease patients - A pilot study. Autoimmunity 2019; 52:88-94. [PMID: 31056951 DOI: 10.1080/08916934.2019.1608965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The elevated plasma cell-free DNA (cfDNA) concentrations were repeatedly reported in association with the process of inflammation. The qualitative and quantitative characteristics of plasma cfDNA in active (newly diagnosed) celiac disease patients (CD) have not yet been studied despite the fact that cfDNA of healthy individuals is able to regulate immune response. We determined the total cfDNA concentration and relative content of telomeric sequences in plasma cfDNA in CD (n = 10) and healthy age- and sex-matched controls (HC, n = 10) by quantitative PCR. To obtain the evidence that the observed biological effects are caused solely by cfDNA molecules, we applied the treatment of paired plasma samples with DNase. Using paired samples of plasma (non-treated/native and treated by DNase), we analyzed the contribution of cfDNA to the activation of TLR9 and TNF-α mRNA expression in THP1 monocytic cell line. There were no significant differences in the quantities of plasma cfDNA and relative contents of telomeric sequences in their pools. When we compared the levels of TNF-α mRNA expression in THP1 cells achieved after stimulation with native CD and HC plasma samples, we found significantly (p = .031) higher expression after stimulation with CD samples. We documented also the ability of cfDNA contained in CD plasma samples to stimulate the production of TLR9 mRNA. The TLR9 mRNA expression levels were significantly (p = .014) lowered after cfDNA removal from CD plasma samples. The design of our experiments allowed us to study the effects of cfDNA without its isolation from plasma. cfDNA contained in CD plasma samples differs significantly in its immunoregulatory capacity from cfDNA in HC plasma. The differences are caused neither by different concentrations of cfDNA in plasma samples nor by different relative abundance of telomeric sequences. Further studies are needed to elucidate the role of plasma cfDNA in celiac disease pathogenesis.
Collapse
Affiliation(s)
- Iva Brynychova
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic
| | - Alzbeta Zinkova
- b Department of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Prague , Czech Republic
| | - Iva Hoffmanova
- c Second Department of Internal Medicine, Third Faculty of Medicine , Charles University , Prague , Czech Republic
| | - Marie Korabecna
- b Department of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Prague , Czech Republic
| | - Pavlina Dankova
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic
| |
Collapse
|
12
|
Pospisilova S, Pazourkova E, Horinek A, Brisuda A, Svobodova I, Soukup V, Hrbacek J, Capoun O, Hanus T, Mares J, Korabecna M, Babjuk M. MicroRNAs in urine supernatant as potential non-invasive markers for bladder cancer detection. Neoplasma 2019; 63:799-808. [PMID: 27468885 DOI: 10.4149/neo_2016_518] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
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.
Collapse
|
13
|
Abstract
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.
Collapse
|
14
|
Korabecna M, Geryk J, Hora M, Steiner P, Seda O, Tesar V. Genome-wide methylation analysis of tubulocystic and papillary renal cell carcinomas. Neoplasma 2019; 63:402-10. [PMID: 26925785 DOI: 10.4149/309_151102n559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
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.
Collapse
|
15
|
Zinkova A, Brynychova I, Svacina A, Jirkovska M, Korabecna M. Cell-free DNA from human plasma and serum differs in content of telomeric sequences and its ability to promote immune response. Sci Rep 2017; 7:2591. [PMID: 28572683 PMCID: PMC5453964 DOI: 10.1038/s41598-017-02905-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/20/2017] [Indexed: 12/23/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) may be involved in immune response regulation. We studied the variations in abundance of telomeric sequences in plasma and serum in young healthy volunteers and the ability of cfDNA contained in these samples to co-activate the TNF-α m RNA expression in monocytes. We performed qPCR to determine relative telomere length (T/S ratios) in plasma, serum and whole blood of 36 volunteers. Using paired samples of plasma and serum and DNase treatment, we analysed the contribution of cfDNA to the co-activation of TNF-α mRNA expression in THP1 monocytic cell line. We found significant differences between paired plasma and serum samples in relative T/S ratios (median 1.38 ± 1.1 vs. 0.86 ± 0.25, respectively) and in total amounts of cfDNA and in estimated total amounts of telomeres which were significantly higher in serum than in plasma. TNF-α mRNA expression in THP1 cells increased significantly after DNase treatment of all samples used for stimulation. The highest TNF-α mRNA expressions were observed after stimulation with DNase treated serum samples. Our results suggest that the different content of telomeric sequences in plasma and serum may contribute to the tuning of immune response. Further studies of this interesting phenomenon are needed.
Collapse
Affiliation(s)
- Alzbeta Zinkova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General Faculty Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Iva Brynychova
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Vinicna 7, 128 43, Prague, Czech Republic
| | - Alexander Svacina
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General Faculty Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Marie Jirkovska
- Department of Histology and Embryology, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Marie Korabecna
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General Faculty Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
| |
Collapse
|
16
|
Korabecna M, Koutova L, Tesarova P. The potential roles of vesicle-enclosed miRNAs in communication between macrophages and cancer cells in tumor microenvironment. Neoplasma 2017; 64:406-411. [DOI: 10.4149/neo_2017_311] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
17
|
Korabecna M, Tesar V. NETosis provides the link between activation of neutrophils on hemodialysis membrane and comorbidities in dialyzed patients. Inflamm Res 2016; 66:369-378. [PMID: 27885378 PMCID: PMC5380691 DOI: 10.1007/s00011-016-1010-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Neutrophil extracellular traps (NETs) are formed by activated neutrophils during the process of NETosis in which the nuclear material is released into extracellular space, including DNA molecules, citrullinated histones, and neutrophil granule enzymes, such as elastase. This material forms networks that are able not only to physically entrap bacteria but also to provide elevated concentration of bactericidal components. Over the last years, it has become clear that NETs can also be formed under numerous sterile inflammatory conditions, i.e., thrombosis, cancer, SLE, atherosclerosis, and diabetes. METHOD We reviewed studies published until July 2016 to find possible associations between elevated cell-free DNA levels in dialyzed patients and the process of NETosis and its consequences. RESULTS The process of NETosis, its elevated activation, or impaired clearance provides the link between clinical conditions and elevated levels of cell-free DNA found in plasma after the hemodialytic procedure which itself is able to activate neutrophils via platelets and ROS formation. NETs stimulate thrombosis and endothelial damage, and their formation may contribute to the development of spectrum of comorbidities described in dialyzed patients. CONCLUSION The study of plasma cell-free DNA levels together with markers of NETosis could contribute to the evaluation of the influence of hemodialysis on the immune system of patients.
Collapse
Affiliation(s)
- Marie Korabecna
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
| | - Vladimir Tesar
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U Nemocnice 2, 128 08, Prague, Czech Republic
| |
Collapse
|
18
|
Koutova L, Sterbova M, Pazourkova E, Pospisilova S, Svobodova I, Horinek A, Lysak D, Korabecna M. The impact of standard chemotherapy on miRNA signature in plasma in AML patients. Leuk Res 2015; 39:1389-95. [PMID: 26340914 DOI: 10.1016/j.leukres.2015.08.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 07/22/2015] [Accepted: 08/15/2015] [Indexed: 12/20/2022]
Abstract
AIM In our pilot study, we used plasma samples as liquid biopsy to search for miRNA signatures in patients with acute myeloid leukemia (AML) at diagnosis and in remission achieved after standard chemotherapy before planned transplantation. MATERIAL AND METHODS We examined 10 plasma samples from healthy volunteers and 8 paired samples from patients with AML at diagnosis and in remission using TaqMan MicroRNA Arrays. The results were validated using single-target qPCR reactions run in triplicates. RESULTS We selected 6 miRNAs with expressions significantly sensitive to therapy: miR-199b-5p, miR-301b, miR-326, miR-361-5p, miR-625 and miR-655. All selected miRNAs were not or very weakly expressed in healthy individuals. They were abundant in plasma in patients at diagnosis but their levels decreased after chemotherapy. CONCLUSION We detected a therapy sensitive miRNA signature in plasma of patients with AML.
Collapse
MESH Headings
- Adult
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Consolidation Chemotherapy
- Cytarabine/administration & dosage
- Female
- Gene Expression Regulation, Leukemic/drug effects
- Humans
- Idarubicin/administration & dosage
- Leukemia, Myeloid, Acute/blood
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Male
- MicroRNAs/biosynthesis
- MicroRNAs/blood
- MicroRNAs/genetics
- Middle Aged
- Mitoxantrone/administration & dosage
- Pilot Projects
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/blood
- RNA, Neoplasm/genetics
- Real-Time Polymerase Chain Reaction
- Remission Induction
- Transcriptome
Collapse
Affiliation(s)
- Linda Koutova
- Department of Hematoonocology, Charles University Hospital in Pilsen, Alej Svobody 80, 304 60 Pilsen, Czech Republic
| | - Monika Sterbova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Eva Pazourkova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Sarka Pospisilova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Iveta Svobodova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Ales Horinek
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic
| | - Daniel Lysak
- Department of Hematoonocology, Charles University Hospital in Pilsen, Alej Svobody 80, 304 60 Pilsen, Czech Republic
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General Faculty Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic; Medical Faculty in Pilsen, Charles University in Prague, Husova 3, 306 05 Pilsen, Czech Republic.
| |
Collapse
|
19
|
Brisuda A, Pazourkova E, Soukup V, Horinek A, Hrbáček J, Capoun O, Svobodova I, Pospisilova S, Korabecna M, Mares J, Hanuš T, Babjuk M. Urinary Cell-Free DNA Quantification as Non-Invasive Biomarker in Patients with Bladder Cancer. Urol Int 2015; 96:25-31. [PMID: 26338254 DOI: 10.1159/000438828] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/16/2015] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Concentration of urinary cell-free DNA (ucfDNA) belongs to potential bladder cancer markers, but the reported results are inconsistent due to the use of various non-standardised methodologies. The aim of the study was to standardise the methodology for ucfDNA quantification as a potential non-invasive tumour biomarker. MATERIAL AND METHODS In total, 66 patients and 34 controls were enrolled into the study. Volumes of each urine portion (V) were recorded and ucfDNA concentrations (c) were measured using real-time PCR. Total amounts (TA) of ucfDNA were calculated and compared between patients and controls. Diagnostic accuracy of the TA of ucfDNA was determined. RESULTS The calculation of TA of ucfDNA in the second urine portion was the most appropriate approach to ucfDNA quantification, as there was logarithmic dependence between the volume and the concentration of a urine portion (p = 0.0001). Using this methodology, we were able to discriminate between bladder cancer patients and subjects without bladder tumours (p = 0.0002) with area under the ROC curve of 0.725. Positive and negative predictive value of the test was 90 and 45%, respectively. CONCLUSION Quantification of ucf DNA according to our modified method could provide a potential non-invasive biomarker for diagnosis of patients with bladder cancer.
Collapse
Affiliation(s)
- Antonin Brisuda
- Department of Urology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Korabecna M, Jirkovska M. How to Characterize Fetal Cells from the Maternal Circulation? Fetal Diagn Ther 2015; 39:238-40. [PMID: 25677942 DOI: 10.1159/000368830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/02/2014] [Indexed: 11/19/2022]
Affiliation(s)
- Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | |
Collapse
|
21
|
Korabecna M, Ulcova-Gallova Z, Horinek A, Pazourková E, Calda P. Quantification of circulating fetal DNA as a tool for potential monitoring of pregnant patients with antiphospholipid antibodies. Autoimmunity 2014; 47:473-7. [PMID: 24829103 DOI: 10.3109/08916934.2014.917372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Apoptosis of tissues of fetal origin is thought to be one of the main sources of cell-free fetal DNA (cffDNA) in maternal circulation, impaired apoptosis is also involved in the mechanisms contributing to recurrent spontaneous miscarriages (RSM) associated with antiphospholipid syndrome (APS). The APS increases the risk for preeclampsia nine times. In preeclampsia, the elevated levels of cffDNA were described by different authors. To our knowledge, cffDNA in pregnant patients with APS was never studied. In our pilot study, we focused on the levels of cffDNA in four pregnant patients with treated primary APS and compared them with values obtained in twenty-one healthy subjects of comparable gestation age (the third trimester of pregnancy). We supposed that the increase of cffDNA concentration in our treated patients would signalize the elevated apoptosis of fetal tissues as in other pathological changes of placentation. The aim of our pilot study was to determine cffDNA concentrations in patients with treated APS and to compare them with values detected in healthy pregnant women of comparable gestation age in order to discover potential non-physiological elevations in patients. The elevated values of cffDNA were not observed in our patients (p value = 0.4363, Mann-Whitney test). All patients delivered healthy children. The measurement of concentrations of cffDNA seems to be a promising tool for monitoring of therapy effectiveness in pregnant women with APS but evaluation of randomized controlled trials would be necessary to determine the specificity and the sensitivity of this test.
Collapse
Affiliation(s)
- Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine , Prague , Czech Republic
| | | | | | | | | |
Collapse
|
22
|
Korabecna M, Pazourkova E, Horinek A, Mokrejsova M, Tesar V. Methylation status of immune response genes promoters in cell-free DNA differs in hemodialyzed patients with diabetic nephropathy according to the intensity of anemia therapy. Blood Purif 2013; 36:280-6. [PMID: 24496200 DOI: 10.1159/000356094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 10/01/2013] [Indexed: 01/15/2023]
Abstract
BACKGROUND Anemia is a major complication of end-stage renal disease. Hemodialysis itself is regarded as a stimulus activating inflammation. Pro-inflammatory cytokines are able to suppress erythropoiesis. In this pilot study, we analyzed the changes in methylation status of promoters of immune response genes in cell-free DNA to detect the differences between diabetic subjects (n = 18) with different therapeutic doses of recombinant erythropoietin. METHODS The extent of promoter methylation of 24 genes in plasma cell-free DNA was examined before and after hemodialysis using EpiTect Methyl qPCR Array Inflammatory Response and Autoimmunity (Qiagen). RESULTS The patients with higher methylation status of gene sequences IL13RA1, IL15, EDG3 and INHA in interdialytic interval were significantly overrepresented in the group with none or mild anemia therapy. CONCLUSION The results are in agreement with the fact that IL13 and IL15 are known inhibitors of erythropoiesis and with considered immunomodulatory role of cell-free DNA.
Collapse
Affiliation(s)
- Marie Korabecna
- Institute of Biology and Medical Genetics and Institute of Medical Biochemistry and Laboratory Medicine, Charles University in Prague, Prague, Czech Republic
| | | | | | | | | |
Collapse
|
23
|
Steiner P, Hora M, Stehlik J, Martinek P, Vanecek T, Petersson F, Michal M, Korabecna M, Travnicek I, Hes O. Tubulocystic renal cell carcinoma: is there a rational reason for targeted therapy using angiogenic inhibition? Analysis of seven cases. Virchows Arch 2013; 462:183-92. [PMID: 23296808 DOI: 10.1007/s00428-012-1367-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/11/2012] [Accepted: 12/21/2012] [Indexed: 11/26/2022]
Abstract
Generally, patients with renal cell carcinoma (RCC) are viewed as potential candidates for antiangiogenic targeted therapy. Tubulocystic RCC (TCRC) is a recently described entity which may behave aggressively, and the rationale for antiangiogenic therapy in this group of renal tumors has yet to be determined. Seven TCRCs and five non-tumor tissue samples from seven patients were subjected to relative expression analysis of mRNA levels of 16 genes involved in three angiogenic signal pathways: (1) VHL/HIF, (2) RTK/mitogen-activated protein kinase (MAPK), and (3) PI3K/Akt/mTOR. Two of them, pathways (2) and (3), are often targeted by antiangiogenic agents. We also determined the mutation and methylation status of the VHL gene. Finally, the levels of vascular endothelial growth factor A (VEGFA), HIF-1α, HIF-2α proteins, and phosphorylated mTOR protein were also determined. The comparison of tumor and control samples revealed no changes of mRNA levels of the following genes: VHL, HIF-1α, HIF-2α, PTEN, Akt2, Akt3, mTOR, VEGFA, KDR, HRas, C-Jun, EGFR, and FGF2. Significantly elevated mRNA level of TP53 was found, while the mRNA levels of FLT1 and C-FOS were reduced in tumor samples. No mutations or methylation in the VHL gene were found. Changes in levels of studied proteins VEGFA, HIF-1α, HIF-2α, and increased phosphorylation of mTOR protein were not found. Three studied angiogenic pathways (VHL/HIF, RTK/MAPK, and PI3K/Akt/mTOR) seem not to be upregulated in TCRC samples, so there appears to be no rationale for a general recommendation of antiangiogenic targeted therapeutic protocols for patients with these tumors.
Collapse
Affiliation(s)
- Petr Steiner
- Department of Pathology, Faculty of Medicine Plzen, Charles University Prague, Alej Svobody 80, 304 60 Pilsen, Czech Republic
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Zidkova A, Horinek A, Stenzl V, Korabecna M. Application of multifactor dimensionality reduction analysis and Bayesian networks for eye color and ancestry prediction for forensic purposes in the Czech Republic. Forensic Science International: Genetics Supplement Series 2013. [DOI: 10.1016/j.fsigss.2013.10.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
25
|
Korabecna M, Pazourkova E, Horinek A, Mokrejsova M, Tesar V. Alterations in methylation status of immune response genes promoters in cell-free DNA during a hemodialysis procedure. Expert Opin Biol Ther 2012; 12 Suppl 1:S27-33. [DOI: 10.1517/14712598.2012.676034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
26
|
Zidkova A, Horinek A, Kebrdlova V, Korabecna M. Application of the new insertion-deletion polymorphism kit for forensic identification and parentage testing on the Czech population. Int J Legal Med 2011; 127:7-10. [PMID: 22124616 PMCID: PMC3538009 DOI: 10.1007/s00414-011-0649-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 11/11/2011] [Indexed: 12/05/2022]
Abstract
Insertion-deletion polymorphisms (INDELs) are diallelic markers derived from a single mutation event. Their low mutation frequency makes them suitable for forensic and parentage testing. The examination of INDELs thus combines advantages of both short tandem repeats (STR) and single nucleotide polymorphisms (SNP). This type of polymorphisms may be examined using as small amplicon size as SNP (about 100 bp) but could be analyzed by techniques used for routine STR analysis. For our population study, we genotyped 55 unrelated Czech individuals. We also genotyped 11 trios to analyze DIPplex Kit (QIAGEN, Germany) suitability for parentage testing. DIPplex Kit contains 30 diallelic autosomal markers. INDELs in DIPplex Kit were tested with linkage disequilibrium test, which showed that they could be treated as independent markers. All 30 loci fulfill Hardy–Weinberg equilibrium. There were several significant differences between Czech and African populations, but no significant ones within European population. Probability of a match in the Czech population was 1 in 6.8 × 1012; combined power of discrimination was 99.9999999999%. Average paternity index was 1.13–1.77 for each locus; combined paternity index reached about 27,000 for a set of 30 loci. We can conclude that DIPplex kit is useful as an additional panel of markers in paternity cases when mutations in STR polymorphisms are present. For application on degraded or inhibited samples, further optimization of buffer and primer concentrations is needed.
Collapse
Affiliation(s)
- Anastassiya Zidkova
- First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | | | | |
Collapse
|
27
|
Kang YS, Cha JJ, Hyun YY, Lee MH, Song HK, Cha DR, Bang K, Jeong J, Shin JH, Kang JH, Yang J, Ahn C, Kim JH, Toledo K, Merino A, GonzaLez-Burdiel L, Perez-Saez MJ, Aguera M, Ramirez R, Del Castillo D, Aljama P, Kahveci A, Tugtepe H, Asicioglu E, Nalcaci S, Birdal G, Arikan H, Koc M, Tuglular S, Kaya H, Ozener C, Kocak G, Azak A, Huddam B, Astarci HM, Can M, Duranay M, Tayama Y, Hasegawa H, Takayanagi K, Matsuda A, Shimizu T, Asakura J, Iwashita T, Okazaki S, Hatano M, Kiba T, Ogawa T, Mitarai T, Sanchez JE, Nunez M, Gonzalez I, Fernandez-Vina A, Pelaez B, Quintana A, Rodriguez C, Park KA, Kim EJ, Choi SJ, Kim NR, Park MY, Kim JK, Hwang SD, Cotovio P, Rocha A, Carvalho MJ, Teixeira L, Mendonca D, Rodrigues A, Cabrita A, Ito M, Wu HY, Peng YS, Huang JW, Hu FC, Hung KY, Tsai TJ, Wu KD, Temiz G, Sahin G, Degirmenci N, Ozkurt S, Yalcin AU, Rufino M, Garcia C, Vega N, Macia M, Rodriguez A, Maceira B, Hernandez D, Lorenzo V, Levallois J, Nadeau-Fredette AC, Labbe AC, Laverdiere M, Ouimet D, Vallee M, Matsuda A, Katou H, Tayama Y, Iwanaga M, Ogawa T, Shimizu T, Asakura J, Noiri C, Kanouzawa K, Hasegawa H, Mitarai T, Karakan S, Sezer S, Ozdemir Acar N, Haberal M, Ueda A, Nagai K, Morimoto M, Hirayama A, Yoh K, Saito C, Yamagata K, Parikova A, Vlijm A, deGraaff M, Brabcova I, Viklicky O, Krediet R, Nagamine N, Katoh KI, Yoshitake O, Cho KH, Jung SY, Do JY, Park JW, Yoon KW, Hwang SD, Kim NR, Kim EJ, Chung CH, Park MY, Choi SJ, Kim JK, Mravljak M, Karas B, Pajek J, Pintar T, Benedik M, Gucek A, Tomo T, Kadota JI, Tsuchida K, Minakuchi J, Yamanaka M, Numata A, Masakane I, Fujimori A, Kawanishi H, Naito H, Bordignon J, Manonelles A, Andujar A, Gonzalez-Segura C, Gonzalez MT, Glavas-Boras S, Zlopasa G, Boras S, Smalcelj R, Slavicek J, Knezevic N, Puretic Z, Prasad N, Gupta A, Sinha A, Saxena A, Sharma RK, Kaul A, Ramos R, Gonzalez MT, Vera M, Garcia I, Barbosa F, Teixido J, Garcia C, Cuxart M, Gonzalez C, de la Cruz JJ, Fukuoka K, Sinozaki M, Kato N, Oba I, Harada K, Kanai H, Ota K, Do JY, Kang SW, Cho KH, Park JW, Shin KL, Kim YH, Yoon KW, Prasad N, Gupta A, Sinha A, Sharma RK, Kaul A, Saxena A, Schneider K, Huszar T, Bator B, Di Napoli A, Franco F, Salvatori MF, Di Lallo D, Guasticchi G, Hassan S, Kristal B, Khazim K, Hassan F, Hassan K, Korabecna M, Krizkova V, Kocova J, Tonar Z, Opatrna S, Gaiao S, Beco A, Oliveira A, Santos-Araujo C, Pestana M, Denizot A, Milliard B, Kahveci A, Asicioglu E, Arikan H, Tuglular S, Ozener C, Hsu BG, Lai YH, Wang CH, Fang TC, Yesil H, Paydas S, Balal M, Cinkir U, Sertdemir Y, Santos-Araujo C, Oliveira A, Beco A, Sousa J, Silva N, Santos D, Pestana M, Oliveira A, Beco A, Santos C, Pestana M, Vera M, Fontsere N, Maduell F, Arias M, Bergada E, Cases A, Campistol JM, Grzelak T, Czyzewska K, Mortazavi M, Seirafian S, Halabian M, Emami Naini A, Farajzadegan Z, Moinzade F, Golabchi K, Portoles J, Moreno F, Lopez-Sanchez P, Gomez M, Corchete E, del Peso G, Bajo MA, Rivera M, Arribas G, Ferreira AC, Fernandes V, Sousa J, Vila Lobos A, Nolasco F, Martino F, di Loreto P, Rodighiero MP, Crepaldi C, Ronco C, Asicioglu E, Kahveci A, Nalcaci S, Arikan H, Tuglular S, Ozener C, Cavallini M, Centi A, Broccoli ML, Rocca AR, Testorio M, Borzacca B, Pugliese F, Russo GE, Tokgoz B, Ucar C, Kocyigit I, Somdas MA, Unal A, Vural A, Sipahioglu MH, Oymak O, Utas C, Teixeira L, Rodrigues A, Carvalho MJ, Cabrita A, Mendonca D, Micha T, Takouli L, Karaitianou A, Koupari G, Trompouki S, Arvanitis D, Vlassopoulos D, Ferreira AC, Fernandes V, Vila Lobos A, Nolasco F, Kahveci A, Nalcaci S, Asicioglu E, Birdal G, Arikan H, Tuglular S, Ozener C, Carvalho C, Beco A, Oliveira A, Santos C, Pestana M, Hiramatsu M, Ishida M, Tonozuka Y, Mikami H, Yamanari T, Momoki N, Onishi A, Maruyama K, Ito M, Masakane I, Takahashi T, Chung SH, Han DC, Noh H, Jeon JS, Kwon SH, Lindholm B, Lee HB, Tekeli L, Inal S, Derici U, Celik N, Kiran G, Derin O, Durunay M, Erten Y, Cho JH, Do JY, Park SH, Kim CD, Choi JY, Ryu HM, Kim YL, Kawahara K, Ishihara Y, Iwadou H, Uemura N, Kinashi M, Oobayashi S, Pilcevic D, Tadic-Pilcevic J, Kovacevic Z, Maksic D, Paunic Z, Mitrovic M, Mijuskovic M, Petrovic M. Peritoneal dialysis. Clin Kidney J 2011. [DOI: 10.1093/ndtplus/4.s2.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
28
|
|
29
|
Skálová A, Sima R, Vanecek T, Muller S, Korabecna M, Nemcova J, Elmberger G, Leivo I, Passador-Santos F, Walter J, Rousarova M, Jedlickova K, Curik R, Geierova M, Michal M. Acinic Cell Carcinoma With High-grade Transformation. Am J Surg Pathol 2009; 33:1137-45. [DOI: 10.1097/pas.0b013e3181a38e1c] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
30
|
Korabecna M, Opatrna S, Wirth J, Rulcova K, Eiselt J, Sefrna F, Horinek A. Cell-free plasma DNA during peritoneal dialysis and hemodialysis and in patients with chronic kidney disease. Ann N Y Acad Sci 2008; 1137:296-301. [PMID: 18837963 DOI: 10.1196/annals.1448.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The mechanisms of clearance of circulating plasma DNA are not fully understood, and so we aimed to examine it in patients with impaired renal function compared with healthy individuals. We also assessed the effect of peritoneal dialysis and hemodialysis on circulating plasma cell-free DNA (cfDNA) in our treated patients. Overall, 20 healthy volunteers, 20 patients with chronic kidney disease (CKD), 18 patients undergoing peritoneal dialysis (PD), and 17 patients on hemodialysis (HD; high-flux polysulfone membrane) were examined. Cell-free DNA levels were determined using real-time GADPH gene sequence amplification. The levels of cfDNA in all groups of our patients did not differ significantly from those of healthy volunteers. In HD patients, cfDNA levels were significantly increased compared with those of CKD patients (P < 0.05) and PD-treated patients (P < 0.01). In PD-treated patients, cfDNA was detectable in overnight effluent, with its levels correlating inversely with the duration of PD treatment (r=-0.619, Spearman's coefficient, P= 0.008). Factors contributing to these differences may include changes in the quality and quantity of the cell population of the peritoneum, highlighting the need for additional studies clarifying the dynamics of cfDNA during PD. The plasma levels of cfDNA do not seem to be dramatically altered even in CKD patients or those on PD or HD (as long as they are measured prior to the procedure in the latter two). Our data suggest renal elimination is not the main mechanism of circulating cfDNA clearance.
Collapse
Affiliation(s)
- Marie Korabecna
- Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic.
| | | | | | | | | | | | | |
Collapse
|
31
|
Horinek A, Korabecna M, Panczak A, Gallova ZU, Nouzova K, Calda P, Hancarova M. Cell-Free Fetal DNA in Maternal Plasma during Physiological Single Male Pregnancies: Methodology Issues and Kinetics. Fetal Diagn Ther 2008; 24:15-21. [DOI: 10.1159/000132400] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 02/09/2007] [Indexed: 11/19/2022]
|