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Trsova I, Hrustincova A, Krejcik Z, Kundrat D, Holoubek A, Staflova K, Janstova L, Vanikova S, Szikszai K, Klema J, Rysavy P, Belickova M, Kaisrlikova M, Vesela J, Cermak J, Jonasova A, Dostal J, Fric J, Musil J, Dostalova Merkerova M. Expression of circular RNAs in myelodysplastic neoplasms and their association with mutations in the splicing factor gene SF3B1. Mol Oncol 2023; 17:2565-2583. [PMID: 37408496 DOI: 10.1002/1878-0261.13486] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/27/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Mutations in the splicing factor 3b subunit 1 (SF3B1) gene are frequent in myelodysplastic neoplasms (MDS). Because the splicing process is involved in the production of circular RNAs (circRNAs), we investigated the impact of SF3B1 mutations on circRNA processing. Using RNA sequencing, we measured circRNA expression in CD34+ bone marrow MDS cells. We defined circRNAs deregulated in a heterogeneous group of MDS patients and described increased circRNA formation in higher-risk MDS. We showed that the presence of SF3B1 mutations did not affect the global production of circRNAs; however, deregulation of specific circRNAs was observed. Particularly, we demonstrated that strong upregulation of circRNAs processed from the zinc finger E-box binding homeobox 1 (ZEB1) transcription factor; this upregulation was exclusive to SF3B1-mutated patients and was not observed in those with mutations in other splicing factors or other recurrently mutated genes, or with other clinical variables. Furthermore, we focused on the most upregulated ZEB1-circRNA, hsa_circ_0000228, and, by its knockdown, we demonstrated that its expression is related to mitochondrial activity. Using microRNA analyses, we proposed miR-1248 as a direct target of hsa_circ_0000228. To conclude, we demonstrated that mutated SF3B1 leads to deregulation of ZEB1-circRNAs, potentially contributing to the defects in mitochondrial metabolism observed in SF3B1-mutated MDS.
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Affiliation(s)
- Iva Trsova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Andrea Hrustincova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Zdenek Krejcik
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - David Kundrat
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Aleš Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Karolina Staflova
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucie Janstova
- Department of Modern Immunotherapy, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sarka Vanikova
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Katarina Szikszai
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Czech Technical University, Prague, Czech Republic
| | - Petr Rysavy
- Department of Computer Science, Czech Technical University, Prague, Czech Republic
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Monika Kaisrlikova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jitka Vesela
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jaroslav Cermak
- Laboratory of Anemias, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Anna Jonasova
- First Department of Medicine, General University Hospital, Prague, Czech Republic
| | - Jiri Dostal
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Fric
- Department of Modern Immunotherapy, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- International Clinical Research Center of St. Anne's University Hospital (FNUSA-ICRC), Brno, Czech Republic
| | - Jan Musil
- Department of Immunomonitoring and Flow Cytometry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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Saveleva L, Sima M, Klema J, Krejčík Z, Vartiainen P, Sitnikova V, Belaya I, Malm T, Jalava PI, Rössner P, Kanninen KM. Transcriptomic alterations in the olfactory bulb induced by exposure to air pollution: Identification of potential biomarkers and insights into olfactory system function. Environ Toxicol Pharmacol 2023; 104:104316. [PMID: 37981204 DOI: 10.1016/j.etap.2023.104316] [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] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
This study evaluated how exposure to the ubiquitous air pollution component, ultrafine particles (UFPs), alters the olfactory bulb (OB) transcriptome. The study utilised a whole-body inhalation chamber to simulate real-life conditions and focused on UFPs due to their high translocation and deposition ability in OBs as well as their prevalence in ambient air. Female C57BL/6J mice were exposed to clean air or to freshly generated combustion derived UFPs for two weeks, after which OBs were dissected and mRNA transcripts were investigated using RNA sequencing analysis. For the first time, transcriptomics was applied to determine changes in mRNA expression levels occurring after subacute exposure to UFPs in the OBs. We found forty-five newly described mRNAs to be involved in air pollution-induced responses, including genes involved in odorant binding, synaptic regulation, and myelination signalling pathway, providing new gene candidates for future research. This study provides new insights for the environmental science and neuroscience fields and nominates future research directions.
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Affiliation(s)
- Liudmila Saveleva
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Michal Sima
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Jugoslávských partyzánů 1580/3, Prague 160 00, Czech Republic
| | - Zdeněk Krejčík
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Petra Vartiainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Valeriia Sitnikova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Irina Belaya
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pasi I Jalava
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pavel Rössner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Vídeňská 1083, Prague 142 20, Czech Republic
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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Hruba P, Klema J, Le AV, Girmanova E, Mrazova P, Massart A, Maixnerova D, Voska L, Piredda GB, Biancone L, Puga AR, Seyahi N, Sever MS, Weekers L, Muhfeld A, Budde K, Watschinger B, Miglinas M, Zahradka I, Abramowicz M, Abramowicz D, Viklicky O. Novel transcriptomic signatures associated with premature kidney allograft failure. EBioMedicine 2023; 96:104782. [PMID: 37660534 PMCID: PMC10480056 DOI: 10.1016/j.ebiom.2023.104782] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND The power to predict kidney allograft outcomes based on non-invasive assays is limited. Assessment of operational tolerance (OT) patients allows us to identify transcriptomic signatures of true non-responders for construction of predictive models. METHODS In this observational retrospective study, RNA sequencing of peripheral blood was used in a derivation cohort to identify a protective set of transcripts by comparing 15 OT patients (40% females), from the TOMOGRAM Study (NCT05124444), 14 chronic active antibody-mediated rejection (CABMR) and 23 stable graft function patients ≥15 years (STA). The selected differentially expressed transcripts between OT and CABMR were used in a validation cohort (n = 396) to predict 3-year kidney allograft loss at 3 time-points using RT-qPCR. FINDINGS Archetypal analysis and classifier performance of RNA sequencing data showed that OT is clearly distinguishable from CABMR, but similar to STA. Based on significant transcripts from the validation cohort in univariable analysis, 2 multivariable Cox models were created. A 3-transcript (ADGRG3, ATG2A, and GNLY) model from POD 7 predicted graft loss with C-statistics (C) 0.727 (95% CI, 0.638-0.820). Another 3-transcript (IGHM, CD5, GNLY) model from M3 predicted graft loss with C 0.786 (95% CI, 0.785-0.865). Combining 3-transcripts models with eGFR at POD 7 and M3 improved C-statistics to 0.860 (95% CI, 0.778-0.944) and 0.868 (95% CI, 0.790-0.944), respectively. INTERPRETATION Identification of transcripts distinguishing OT from CABMR allowed us to construct models predicting premature graft loss. Identified transcripts reflect mechanisms of injury/repair and alloimmune response when assessed at day 7 or with a loss of protective phenotype when assessed at month 3. FUNDING Supported by the Ministry of Health of the Czech Republic under grant NV19-06-00031.
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Affiliation(s)
- Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Czech Technical University, Prague, Czech Republic
| | - Anh Vu Le
- Department of Computer Science, Czech Technical University, Prague, Czech Republic
| | - Eva Girmanova
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Petra Mrazova
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Annick Massart
- Antwerp University Hospital and Antwerp University, Antwerp, Belgium
| | - Dita Maixnerova
- Department of Nephrology, 1st Faculty of Medicine and General Faculty Hospital, Prague, Czech Republic
| | - Ludek Voska
- Department of Clinical and Transplant Pathology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Gian Benedetto Piredda
- Department of Kidney Disease Medicine of Renal Transplantation, G.Brotzu Hospital Cagliari, Italy
| | - Luigi Biancone
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Ana Ramirez Puga
- Hospital Universitario Insular de Gran Canaria, Servicio de nefrología, Spain
| | - Nurhan Seyahi
- Istanbul University, Cerrahpasa Medical Faculty, Nephrology, Istanbul, Turkey
| | - Mehmet Sukru Sever
- Istanbul University, Istanbul School of Medicine, Internal Medicine, Nephrology, Istanbul, Turkey
| | | | - Anja Muhfeld
- Department of Nephrology, Uniklinik RWTH Aachen, Aachen, Germany
| | - Klemens Budde
- Charité - Universitätsmedizin Berlin, Medizinische Klinik mit Schwerpunkt Nephrologie und Internistische Intensivmedizin, Berlin, Germany
| | - Bruno Watschinger
- Department of Internal Medicine III, Nephrology, Medical University Vienna / AKH Wien, Vienna, Austria
| | - Marius Miglinas
- Faculty of Medicine, Nephrology Center, Vilnius University Hospital Santaros Klinikos, Vilnius University, Vilnius, Lithuania
| | - Ivan Zahradka
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Marc Abramowicz
- Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1206 Geneva, Switzerland
| | - Daniel Abramowicz
- Antwerp University Hospital and Antwerp University, Antwerp, Belgium
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic; Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic.
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Hruba P, Klema J, Wu Le A, Girmanova E, Mrazova P, Massart A, Abramowitz D, Abramowicz M, Viklicky O. MO941: Novel Peripheral Molecular Markers Predict Premature Graft Loss: Lessons Learned from Operational Tolerance Assessment. Nephrol Dial Transplant 2022. [DOI: 10.1093/ndt/gfac086.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND AND AIMS
TOMOGRAM, a European multicenter study, recently identified a new cohort of kidney transplant recipients (KTR) with operational tolerance (OT) with the aim to identify new transcriptomic signatures of OT.
METHOD
RNA sequencing of peripheral blood was evaluated in 15 OT KTR identified by TOMOGRAM, 23 stable KTR (≥15 years, STA), 14 KTR with transplant glomerulopathy (≥1 year, CR), 14 CyA-treated primary GN patients and 14 healthy controls (HC). The ability to discriminate OT from others was analyzed using three classifiers (GLMNET, voomNSC and SVM-RFE) with 10-fold cross-validation and visualized by principal component analysis (PCA) of molecular archetypes.
RESULTS
Peripheral blood transcriptome of OT patients is similar to the STA group (AUC < 0.6) and different from the CR group (AUC > 0.8). Also, in PCA of molecular archetypes, direction of correlation suggested similarity between STA and OT and their anti-correlation to CR (Figure 1). Top 10 transcripts differentiated OT from CR were assessed in prospective independent cohort (n = 396) to predict premature graft loss. Multivariable Cox regression model based on the expression of 5 of those transcripts at 3 time-points was associated with graft loss at 3 years with an AUC = 0.815.
CONCLUSION
Identification of the OT peripheral molecular signature among stable KTR is not feasible. Instead, novel peripheral molecular markers associated with premature graft loss were identified.
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Affiliation(s)
- Petra Hruba
- Institute for Clinical and Experimental Medicine, Prague, Transplant Laboratory, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic
| | - Anh Wu Le
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic
| | - Eva Girmanova
- Institute for Clinical and Experimental Medicine, Prague, Transplant Laboratory, Prague, Czech Republic
| | - Petra Mrazova
- Institute for Clinical and Experimental Medicine, Prague, Transplant Laboratory, Prague, Czech Republic
| | | | | | | | - Ondrej Viklicky
- Institute for Clinical and Experimental Medicine, Prague, Transplant Laboratory, Prague, Czech Republic
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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5
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Kaisrlikova M, Vesela J, Kundrat D, Votavova H, Dostalova Merkerova M, Krejcik Z, Divoky V, Jedlicka M, Fric J, Klema J, Mikulenkova D, Stastna Markova M, Lauermannova M, Mertova J, Soukupova Maaloufova J, Jonasova A, Cermak J, Belickova M. RUNX1 mutations contribute to the progression of MDS due to disruption of antitumor cellular defense: a study on patients with lower-risk MDS. Leukemia 2022; 36:1898-1906. [PMID: 35505182 PMCID: PMC9252911 DOI: 10.1038/s41375-022-01584-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022]
Abstract
Patients with lower-risk myelodysplastic syndromes (LR-MDS) have a generally favorable prognosis; however, a small proportion of cases progress rapidly. This study aimed to define molecular biomarkers predictive of LR-MDS progression and to uncover cellular pathways contributing to malignant transformation. The mutational landscape was analyzed in 214 LR-MDS patients, and at least one mutation was detected in 137 patients (64%). Mutated RUNX1 was identified as the main molecular predictor of rapid progression by statistics and machine learning. To study the effect of mutated RUNX1 on pathway regulation, the expression profiles of CD34 + cells from LR-MDS patients with RUNX1 mutations were compared to those from patients without RUNX1 mutations. The data suggest that RUNX1-unmutated LR-MDS cells are protected by DNA damage response (DDR) mechanisms and cellular senescence as an antitumor cellular barrier, while RUNX1 mutations may be one of the triggers of malignant transformation. Dysregulated DDR and cellular senescence were also observed at the functional level by detecting γH2AX expression and β-galactosidase activity. Notably, the expression profiles of RUNX1-mutated LR-MDS resembled those of higher-risk MDS at diagnosis. This study demonstrates that incorporating molecular data improves LR-MDS risk stratification and that mutated RUNX1 is associated with a suppressed defense against LR-MDS progression.
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Affiliation(s)
- Monika Kaisrlikova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jitka Vesela
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - David Kundrat
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Votavova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Vladimir Divoky
- Department of Biology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Marek Jedlicka
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Fric
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Jiri Klema
- Czech Technical University, Prague, Czech Republic
| | - Dana Mikulenkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | | | - Jolana Mertova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Anna Jonasova
- First Department of Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic. .,First Faculty of Medicine, Charles University, Prague, Czech Republic.
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Iatsiuk V, Malinka F, Pickova M, Tureckova J, Klema J, Spoutil F, Novosadova V, Prochazka J, Sedlacek R. Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes ontology clusters with tissue expression patterns. BMC Gastroenterol 2022; 22:186. [PMID: 35413796 PMCID: PMC9006408 DOI: 10.1186/s12876-022-02265-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
Background Ubiquitin ligases (Ub-ligases) are essential intracellular enzymes responsible for the regulation of proteome homeostasis, signaling pathway crosstalk, cell differentiation and stress responses. Individual Ub-ligases exhibit their unique functions based on the nature of their substrates. They create a complex regulatory network with alternative and feedback pathways to maintain cell homeostasis, being thus important players in many physiological and pathological conditions. However, the functional classification of Ub-ligases needs to be revised and extended. Methods In the current study, we used a novel semantic biclustering technique for expression profiling of Ub-ligases and ubiquitination-related genes in the murine gastrointestinal tract (GIT). We accommodated a general framework of the algorithm for finding tissue-specific gene expression clusters in GIT. In order to test identified clusters in a biological system, we used a model of epithelial regeneration. For this purpose, a dextran sulfate sodium (DSS) mouse model, following with in situ hybridization, was used to expose genes with possible compensatory features. To determine cell-type specific distribution of Ub-ligases and ubiquitination-related genes, principal component analysis (PCA) and Uniform Manifold Approximation and Projection technique (UMAP) were used to analyze the Tabula Muris scRNA-seq data of murine colon followed by comparison with our clustering results. Results Our established clustering protocol, that incorporates the semantic biclustering algorithm, demonstrated the potential to reveal interesting expression patterns. In this manner, we statistically defined gene clusters consisting of the same genes involved in distinct regulatory pathways vs distinct genes playing roles in functionally similar signaling pathways. This allowed us to uncover the potentially redundant features of GIT-specific Ub-ligases and ubiquitination-related genes. Testing the statistically obtained results on the mouse model showed that genes clustered to the same ontology group simultaneously alter their expression pattern after induced epithelial damage, illustrating their complementary role during tissue regeneration. Conclusions An optimized semantic clustering protocol demonstrates the potential to reveal a readable and unique pattern in the expression profiling of GIT-specific Ub-ligases, exposing ontologically relevant gene clusters with potentially redundant features. This extends our knowledge of ontological relationships among Ub-ligases and ubiquitination-related genes, providing an alternative and more functional gene classification. In a similar way, semantic cluster analysis could be used for studding of other enzyme families, tissues and systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-022-02265-2.
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Affiliation(s)
- Veronika Iatsiuk
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Frantisek Malinka
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Computer Science, Czech Technical University in Prague, Prague, Czech Republic
| | - Marketa Pickova
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jolana Tureckova
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, Prague, Czech Republic
| | - Frantisek Spoutil
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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7
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Ambroz A, Rossner P, Rossnerova A, Honkova K, Milcova A, Pastorkova A, Klema J, Pulkrabova J, Parizek O, Vondraskova V, Zelenka J, Vrzáčková N, Schmuczerova J, Topinka J, Sram RJ. Oxidative Stress and Antioxidant Response in Populations of the Czech Republic Exposed to Various Levels of Environmental Pollutants. Int J Environ Res Public Health 2022; 19:ijerph19063609. [PMID: 35329296 PMCID: PMC8955578 DOI: 10.3390/ijerph19063609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/25/2022]
Abstract
We aimed to identify the variables that modify levels of oxidatively damaged DNA and lipid peroxidation in subjects living in diverse localities of the Czech Republic (a rural area, a metropolitan locality, and an industrial region). The sampling of a total of 126 policemen was conducted twice in two sampling seasons. Personal characteristics, concentrations of particulate matter of aerodynamic diameter <2.5 µm and benzo[a]pyrene in the ambient air, activities of antioxidant mechanisms (superoxide dismutase, catalase, glutathione peroxidase, and antioxidant capacity), levels of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6), concentrations of persistent organic pollutants in blood plasma, and urinary levels of polycyclic aromatic hydrocarbon metabolites were investigated as parameters potentially affecting the markers of DNA oxidation (8-oxo-7,8-dihydro-2′-deoxyguanosine) and lipid peroxidation (15-F2t-isoprostane). The levels of oxidative stress markers mostly differed between the localities in the individual sampling seasons. Multivariate linear regression analysis revealed IL-6, a pro-inflammatory cytokine, as a factor with the most pronounced effects on oxidative stress parameters. The role of other variables, including environmental pollutants, was minor. In conclusion, our study showed that oxidative damage to macromolecules was affected by processes related to inflammation; however, we did not identify a specific environmental factor responsible for the pro-inflammatory response in the organism.
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Affiliation(s)
- Antonin Ambroz
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic;
- Correspondence: (A.A.); (P.R.J.); Tel.: +420-720-045-780 (P.R.J.)
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic;
- Correspondence: (A.A.); (P.R.J.); Tel.: +420-720-045-780 (P.R.J.)
| | - Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (A.R.); (K.H.); (A.M.); (J.T.); (R.J.S.)
| | - Katerina Honkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (A.R.); (K.H.); (A.M.); (J.T.); (R.J.S.)
| | - Alena Milcova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (A.R.); (K.H.); (A.M.); (J.T.); (R.J.S.)
| | - Anna Pastorkova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic;
| | - Jiri Klema
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Karlovo Namesti 13, 121 35 Prague, Czech Republic;
| | - Jana Pulkrabova
- Department of Food Analysis and Nutrition, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague, Czech Republic; (J.P.); (O.P.); (V.V.)
| | - Ondrej Parizek
- Department of Food Analysis and Nutrition, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague, Czech Republic; (J.P.); (O.P.); (V.V.)
| | - Veronika Vondraskova
- Department of Food Analysis and Nutrition, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague, Czech Republic; (J.P.); (O.P.); (V.V.)
| | - Jaroslav Zelenka
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague, Czech Republic; (J.Z.); (N.V.)
| | - Nikola Vrzáčková
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague, Czech Republic; (J.Z.); (N.V.)
| | - Jana Schmuczerova
- Department of Medical Genetics, L. Pasteur University Hospital, Trieda SNP 1, 040 11 Kosice, Slovakia;
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (A.R.); (K.H.); (A.M.); (J.T.); (R.J.S.)
| | - Radim J. Sram
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (A.R.); (K.H.); (A.M.); (J.T.); (R.J.S.)
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8
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Merkerova MD, Klema J, Kundrat D, Szikszai K, Krejcik Z, Hrustincova A, Trsova I, LE AV, Cermak J, Jonasova A, Belickova M. Noncoding RNAs and Their Response Predictive Value in Azacitidine-treated Patients With Myelodysplastic Syndrome and Acute Myeloid Leukemia With Myelodysplasia-related Changes. Cancer Genomics Proteomics 2022; 19:205-228. [PMID: 35181589 DOI: 10.21873/cgp.20315] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/09/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Prediction of response to azacitidine (AZA) treatment is an important challenge in hematooncology. In addition to protein coding genes (PCGs), AZA efficiency is influenced by various noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular RNAs (circRNAs), and transposable elements (TEs). MATERIALS AND METHODS RNA sequencing was performed in patients with myelodysplastic syndromes or acute myeloid leukemia before AZA treatment to assess contribution of ncRNAs to AZA mechanisms and propose novel disease prediction biomarkers. RESULTS Our analyses showed that lncRNAs had the strongest predictive potential. The combined set of the best predictors included 14 lncRNAs, and only four PCGs, one circRNA, and no TEs. Epigenetic regulation and recombinational repair were suggested as crucial for AZA response, and network modeling defined three deregulated lncRNAs (CTC-482H14.5, RP11-419K12.2, and RP11-736I24.4) associated with these processes. CONCLUSION The expression of various ncRNAs can influence the effect of AZA and new ncRNA-based predictive biomarkers can be defined.
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Affiliation(s)
| | - Jiri Klema
- Department of Computer Sciences, Czech Technical University, Prague, Czech Republic
| | - David Kundrat
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Katarina Szikszai
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Zdenek Krejcik
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Andrea Hrustincova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Iva Trsova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Anh Vu LE
- Department of Computer Sciences, Czech Technical University, Prague, Czech Republic
| | - Jaroslav Cermak
- Laboratory of Anemias, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Anna Jonasova
- First Department of Medicine, General University Hospital, Prague, Czech Republic
| | - Monika Belickova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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9
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Osickova K, Hruba P, Kabrtova K, Klema J, Maluskova J, Slavcev A, Slatinska J, Marada T, Böhmig GA, Viklicky O. Predictive Potential of Flow Cytometry Crossmatching in Deceased Donor Kidney Transplant Recipients Subjected to Peritransplant Desensitization. Front Med (Lausanne) 2022; 8:780636. [PMID: 34970564 PMCID: PMC8712553 DOI: 10.3389/fmed.2021.780636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/21/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022] Open
Abstract
Recipient sensitization is a major risk factor of antibody-mediated rejection (ABMR) and inferior graft survival. The predictive effect of solid-phase human leukocyte antigen antibody testing and flow cytometry crossmatch (FCXM) in the era of peritransplant desensitization remains poorly understood. This observational retrospective single-center study with 108 donor-specific antibody (DSA)-positive deceased donor kidney allograft recipients who had undergone peritransplant desensitization aimed to analyze variables affecting graft outcome. ABMR rates were highest among patients with positive pretransplant FCXM vs. FCXM-negative (76 vs. 18.7%, p < 0.001) and with donor-specific antibody mean fluorescence intensity (DSA MFI) > 5,000 vs. <5,000 (54.5 vs. 28%, p = 0.01) despite desensitization. In univariable Cox regression, FCXM positivity, retransplantation, recipient gender, immunodominant DSA MFI, DSA number, and peak panel reactive antibodies were found to be associated with ABMR occurrence. In multivariable Cox regression adjusted for desensitization treatment (AUC = 0.810), only FCXM positivity (HR = 4.6, p = 0.001) and DSA number (HR = 1.47, p = 0.039) remained significant. In conclusion, our data suggest that pretransplant FCXM and DSA number, but not DSA MFI, are independent predictors of ABMR in patients who received peritransplant desensitization.
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Affiliation(s)
- Klara Osickova
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Katerina Kabrtova
- Department of Immunogenetics, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Jiri Klema
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University, Prague, Czechia
| | - Jana Maluskova
- Department of Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia.,Aesculab Pathology, Prague, Czechia
| | - Antonij Slavcev
- Department of Immunogenetics, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Janka Slatinska
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Tomas Marada
- Department of Transplant Surgery, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University Vienna, Vienna, Austria
| | - Ondrej Viklicky
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
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10
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Merkerova M, Klema J, Kundrat D, Krejcik Z, Hrustincova A, Trsova I, Cermak J, Jonasova A, Belickova M. Topic: AS04-MDS Biology and Pathogenesis/AS04f-Gene expression profiling. Leuk Res 2021. [DOI: 10.1016/j.leukres.2021.106681.25] [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: 11/16/2022]
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11
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Cervena T, Vojtisek-Lom M, Vrbova K, Ambroz A, Novakova Z, Elzeinova F, Sima M, Beranek V, Pechout M, Macoun D, Klema J, Rossnerova A, Ciganek M, Topinka J, Rossner P. Ordinary Gasoline Emissions Induce a Toxic Response in Bronchial Cells Grown at Air-Liquid Interface. Int J Mol Sci 2020; 22:E79. [PMID: 33374749 PMCID: PMC7801947 DOI: 10.3390/ijms22010079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/05/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Gasoline engine emissions have been classified as possibly carcinogenic to humans and represent a significant health risk. In this study, we used MucilAir™, a three-dimensional (3D) model of the human airway, and BEAS-2B, cells originating from the human bronchial epithelium, grown at the air-liquid interface to assess the toxicity of ordinary gasoline exhaust produced by a direct injection spark ignition engine. The transepithelial electrical resistance (TEER), production of mucin, and lactate dehydrogenase (LDH) and adenylate kinase (AK) activities were analyzed after one day and five days of exposure. The induction of double-stranded DNA breaks was measured by the detection of histone H2AX phosphorylation. Next-generation sequencing was used to analyze the modulation of expression of the relevant 370 genes. The exposure to gasoline emissions affected the integrity, as well as LDH and AK leakage in the 3D model, particularly after longer exposure periods. Mucin production was mostly decreased with the exception of longer BEAS-2B treatment, for which a significant increase was detected. DNA damage was detected after five days of exposure in the 3D model, but not in BEAS-2B cells. The expression of CYP1A1 and GSTA3 was modulated in MucilAir™ tissues after 5 days of treatment. In BEAS-2B cells, the expression of 39 mRNAs was affected after short exposure, most of them were upregulated. The five days of exposure modulated the expression of 11 genes in this cell line. In conclusion, the ordinary gasoline emissions induced a toxic response in MucilAir™. In BEAS-2B cells, the biological response was less pronounced, mostly limited to gene expression changes.
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Affiliation(s)
- Tereza Cervena
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (M.S.)
- Department of Physiology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Michal Vojtisek-Lom
- Centre of Vehicles for Sustainable Mobility, Faculty of Mechanical Engineering, Czech Technical University in Prague, Technicka 4, 160 00 Prague, Czech Republic; (M.V.-L.); (V.B.)
| | - Kristyna Vrbova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (M.S.)
| | - Antonin Ambroz
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (M.S.)
| | - Zuzana Novakova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (M.S.)
| | - Fatima Elzeinova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (M.S.)
| | - Michal Sima
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (M.S.)
| | - Vit Beranek
- Centre of Vehicles for Sustainable Mobility, Faculty of Mechanical Engineering, Czech Technical University in Prague, Technicka 4, 160 00 Prague, Czech Republic; (M.V.-L.); (V.B.)
| | - Martin Pechout
- Department of Vehicles and Ground Transport, Czech University of Life Sciences in Prague, Kamycka 129, 165 21 Prague, Czech Republic; (M.P.); (D.M.)
| | - David Macoun
- Department of Vehicles and Ground Transport, Czech University of Life Sciences in Prague, Kamycka 129, 165 21 Prague, Czech Republic; (M.P.); (D.M.)
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, 121 35 Prague, Czech Republic;
| | - Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (A.R.); (J.T.)
| | - Miroslav Ciganek
- Department of Chemistry and Toxicology, Veterinary Research Institute, 621 00 Brno, Czech Republic;
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (A.R.); (J.T.)
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (M.S.)
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12
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Sima M, Vrbova K, Zavodna T, Honkova K, Chvojkova I, Ambroz A, Klema J, Rossnerova A, Polakova K, Malina T, Belza J, Topinka J, Rossner P. The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and Dose. Int J Mol Sci 2020; 21:E4763. [PMID: 32635498 PMCID: PMC7369946 DOI: 10.3390/ijms21134763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 05/28/2020] [Revised: 06/18/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
This study presents a toxicological evaluation of two types of carbon dots (CD), similar in size (<10 nm) but differing in surface charge. Whole-genome mRNA and miRNA expression (RNAseq), as well as gene-specific DNA methylation changes, were analyzed in human embryonic lung fibroblasts (HEL 12469) after 4 h and 24 h exposure to concentrations of 10 and 50 µg/mL (for positive charged CD; pCD) or 10 and 100 µg/mL (for negative charged CD, nCD). The results showed a distinct response for the tested nanomaterials (NMs). The exposure to pCD induced the expression of a substantially lower number of mRNAs than those to nCD, with few commonly differentially expressed genes between the two CDs. For both CDs, the number of deregulated mRNAs increased with the dose and exposure time. The pathway analysis revealed a deregulation of processes associated with immune response, tumorigenesis and cell cycle regulation, after exposure to pCD. For nCD treatment, pathways relating to cell proliferation, apoptosis, oxidative stress, gene expression, and cycle regulation were detected. The expression of miRNAs followed a similar pattern: more pronounced changes after nCD exposure and few commonly differentially expressed miRNAs between the two CDs. For both CDs the pathway analysis based on miRNA-mRNA interactions, showed a deregulation of cancer-related pathways, immune processes and processes involved in extracellular matrix interactions. DNA methylation was not affected by exposure to any of the two CDs. In summary, although the tested CDs induced distinct responses on the level of mRNA and miRNA expression, pathway analyses revealed a potential common biological impact of both NMs independent of their surface charge.
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Affiliation(s)
- Michal Sima
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (M.S.); (K.V.); (A.A.)
| | - Kristyna Vrbova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (M.S.); (K.V.); (A.A.)
| | - Tana Zavodna
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (T.Z.); (K.H.); (I.C.); (A.R.); (J.T.)
| | - Katerina Honkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (T.Z.); (K.H.); (I.C.); (A.R.); (J.T.)
| | - Irena Chvojkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (T.Z.); (K.H.); (I.C.); (A.R.); (J.T.)
| | - Antonin Ambroz
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (M.S.); (K.V.); (A.A.)
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, 12135 Prague, Czech Republic;
| | - Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (T.Z.); (K.H.); (I.C.); (A.R.); (J.T.)
| | - Katerina Polakova
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, 77146 Olomouc, Czech Republic; (K.P.); (T.M.); (J.B.)
| | - Tomas Malina
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, 77146 Olomouc, Czech Republic; (K.P.); (T.M.); (J.B.)
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 77146 Olomouc, Czech Republic
| | - Jan Belza
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, 77146 Olomouc, Czech Republic; (K.P.); (T.M.); (J.B.)
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 77146 Olomouc, Czech Republic
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (T.Z.); (K.H.); (I.C.); (A.R.); (J.T.)
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, 14220 Prague, Czech Republic; (M.S.); (K.V.); (A.A.)
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13
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Viklicky O, Klema J, Mrazova P, Abramowicz D, Abramowicz M, Massart A, Hruba P, Study Group TOMOGRAM. TO005OPERATIONAL TOLERANCE IN KIDNEY TRANSPLANT RECIPIENTS: TOMOGRAM TRANSCRIPTOMIC STUDY. Nephrol Dial Transplant 2020. [DOI: 10.1093/ndt/gfaa141.to005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background and Aims
TOMOGRAM, multicenter study founded by DESCARTES ERA/EDTA WG, aims to identify transcriptomic and genomic signatures of operational tolerance (OT) in recently identified cohort of OT kidney transplant recipients.
Method
RNA sequencing of peripheral blood was evaluated in 15 OT patients recently identified by TOMOGRAM consortium in 8 European countries, 23 stable patients (≥ 15 years on immunosuppression, STA), 14 CABMR patients (≥ 1 year, CR), 14 non-transplant CNI-treated patients and 14 healthy controls (HC). Differential expression was performed using DESEq2 and gene annotation analysis using Enrichr. Besides immunosuppression unadjusted model, robust negative-binomial regression model was created to adjust for immunosuppression intake. The models was trained on homogeneous group of STA patients.
Results
Using model unadjusted for immunosuppression, no differences in transcriptomic profiles between OT, STA and HC groups were identified. Nine transcripts were upregulated and 2 downregulated in OT compared CR group. The number of deregulated transcripts substantially increased when the model was adjusted for immunosuppression. Gene annotation analysis of top ranked deregulated 1109 transcripts (FC>2, adjusted p value <0.0001) showed deregulation of biological processes related to interferon-γ-mediated signaling pathway (p=1.4*10-5), response to cytokine (p=1.5*10-5), type I interferon signaling pathway (p=0.00036), regulation of I-kappaB kinase/NF-kappaB signaling (p=0.0021), cytokine-mediated signaling pathway (p=0.019) and neutrophil mediated immunity (p=0.033). While interferon-γ-mediated and type I interferon signaling were related to transcripts increased in CR, neutrophils associated transcripts were increased in OT. Analysis of cell types transcripts showed enrichment of CD19 B cells (p=1.6*10-9) in CR, while CD56NK cells (p=2.5*10-11) and CD8 T cells (p=1.6*10-11) transcripts predominated in OT. To reveal probability of operational tolerance inside STA group, 13 transcripts able to discriminate OT and CR cohorts with high AUC (>0.89) were used in PCA analysis (ADGRG3, ATG2A, GDPD5, IL16, MX2, SLA2, PRKD2, SLIRP, GNLY, SRCAP, ARGHAP9, IGHM, CD5). The high probability of OT signature was found in a single STA patient.
Conclusion
Contrary to previous reports which pointed out towards naïve B cell signatures, unique OT patients exhibit other specific immunosuppression-independent transcriptomic profiles.
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Affiliation(s)
- Ondrej Viklicky
- Institute for Clinical and Experimental Medicine, Dept. of Nephrology, Prague
| | - Jiri Klema
- Czech Technical University, Department of Computer Science, Prague, Czech Republic
| | - Petra Mrazova
- Institute for Clinical and Experimental Medicine, Transplant Laboratory, Prague, Czech Republic
| | - Daniel Abramowicz
- Antwerp University Hospital and Antwerp University, Antwerp, Belgium
| | - Marc Abramowicz
- Université Libre de Bruxelles, Department of Medical Genetics, Hôpital Erasme, Brussels, Belgium
| | - Annick Massart
- Antwerp University Hospital and Antwerp University, Antwerp, Belgium
| | - Petra Hruba
- Institute for Clinical and Experimental Medicine, Transplant Laboratory, Prague, Czech Republic
| | - TOMOGRAM Study Group
- Institute for Clinical and Experimental Medicine, Transplant Laboratory, Prague, Czech Republic
- Antwerp University Hospital and Antwerp University, Antwerp, Belgium
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14
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Rossnerova A, Honkova K, Pelclova D, Zdimal V, Hubacek JA, Chvojkova I, Vrbova K, Rossner P, Topinka J, Vlckova S, Fenclova Z, Lischkova L, Klusackova P, Schwarz J, Ondracek J, Ondrackova L, Kostejn M, Klema J, Dvorackova S. DNA Methylation Profiles in a Group of Workers Occupationally Exposed to Nanoparticles. Int J Mol Sci 2020; 21:E2420. [PMID: 32244494 PMCID: PMC7177382 DOI: 10.3390/ijms21072420] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 03/17/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
The risk of exposure to nanoparticles (NPs) has rapidly increased during the last decade due to the vast use of nanomaterials (NMs) in many areas of human life. Despite this fact, human biomonitoring studies focused on the effect of NP exposure on DNA alterations are still rare. Furthermore, there are virtually no epigenetic data available. In this study, we investigated global and gene-specific DNA methylation profiles in a group of 20 long-term (mean 14.5 years) exposed, nanocomposite, research workers and in 20 controls. Both groups were sampled twice/day (pre-shift and post-shift) in September 2018. We applied Infinium Methylation Assay, using the Infinium MethylationEPIC BeadChips with more than 850,000 CpG loci, for identification of the DNA methylation pattern in the studied groups. Aerosol exposure monitoring, including two nanosized fractions, was also performed as proof of acute NP exposure. The obtained array data showed significant differences in methylation between the exposed and control groups related to long-term exposure, specifically 341 CpG loci were hypomethylated and 364 hypermethylated. The most significant CpG differences were mainly detected in genes involved in lipid metabolism, the immune system, lung functions, signaling pathways, cancer development and xenobiotic detoxification. In contrast, short-term acute NP exposure was not accompanied by DNA methylation changes. In summary, long-term (years) exposure to NP is associated with DNA epigenetic alterations.
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Affiliation(s)
- Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Katerina Honkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Daniela Pelclova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Vladimir Zdimal
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jaroslav A. Hubacek
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21 Prague 4, Czech Republic;
| | - Irena Chvojkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Kristyna Vrbova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.V.); (P.R.)
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.V.); (P.R.)
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Stepanka Vlckova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Zdenka Fenclova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Lucie Lischkova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Pavlina Klusackova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Jaroslav Schwarz
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jakub Ondracek
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Lucie Ondrackova
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Martin Kostejn
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, Karlovo namesti 13, 121 35 Prague 2, Czech Republic;
| | - Stepanka Dvorackova
- Department of Machining and Assembly, Department of Engineering Technology, Department of Material Science, Faculty of Mechanical Engineering, Technical University in Liberec, Studentska 1402/2 Liberec, Czech Republic;
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15
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Hruba P, Krejcik Z, Dostalova Merkerova M, Klema J, Stranecky V, Slatinska J, Maluskova J, Honsova E, Viklicky O. Molecular Fingerprints of Borderline Changes in Kidney Allografts Are Influenced by Donor Category. Front Immunol 2020; 11:423. [PMID: 32269565 PMCID: PMC7109293 DOI: 10.3389/fimmu.2020.00423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/20/2019] [Accepted: 02/24/2020] [Indexed: 11/13/2022] Open
Abstract
The fate of transplanted kidneys is substantially influenced by graft quality, with transplantation of kidneys from elderly and expanded criteria donors (ECDs) associated with higher occurrence of delayed graft function, rejection, and inferior long-term outcomes. However, little is known about early molecular fingerprints of these events in different donor categories. Borderline changes represent the most frequent histological finding early after kidney transplantation. Therefore, we examined outcomes and transcriptomic profiles of early-case biopsies diagnosed as borderline changes in different donor categories. In this single-center, retrospective, observational study, we compared midterm outcomes of kidney transplant recipients with early borderline changes as a first pathology between ECD (n = 109), standard criteria donor (SCDs, n = 109), and living donor (LD, n = 51) cohorts. Intragraft gene expression profiling by microarray was performed in part of these ECD, SCD, and LD cohorts. Although 5 year graft survival in patients with borderline changes in early-case biopsies was not influenced by donor category (log-rank P = 0.293), impaired kidney graft function (estimated glomerular filtration rate by Chronic Kidney Disease Epidemiology Collaboration equation) at M3, 1, 2, and 3 years was observed in the ECD cohort (P < 0.001). Graft biopsies from ECD donors had higher vascular intimal fibrosis and arteriolar hyalinosis compared to SCD and LD (P < 0.001), suggesting chronic vascular changes. Increased transcripts typical for ECD, as compared to both LD and SCD, showed enrichment of the inflammatory, defense, and wounding responses and the ECM-receptor interaction pathway. Additionally, increased transcripts in ECD vs. LD showed activation of complement and coagulation and cytokine-cytokine receptor pathways along with platelet activation and cell cycle regulation. Comparative gene expression overlaps of ECD, SCD, and LD using Venn diagrams found 64 up- and 16 down-regulated genes in ECD compared to both LD and SCD. Shared increased transcripts in ECD vs. both SCD and LD included thrombospondin-2 (THBS2), angiopoietin-like 4 (ANGPTL4), collagens (COL6A3, COL1A1), chemokine CCL13, and interleukin IL11, and most significantly, down-regulated transcripts included proline-rich 35 (PRR35) and fibroblast growth factor 9. Early borderline changes in ECD kidney transplantation are characterized by increased regulation of inflammation, extracellular matrix remodeling, and acute kidney injury transcripts in comparison with both LD and SCD grafts.
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Affiliation(s)
- Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Zdenek Krejcik
- Department of Genomics, Institute of Haematology and Blood Transfusion, Prague, Czechia
| | | | - Jiri Klema
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University, Prague, Czechia
| | - Viktor Stranecky
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Janka Slatinska
- Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Jana Maluskova
- Department of Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Eva Honsova
- Department of Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia.,Department of Nephrology, Institute for Clinical and Experimental Medicine, Prague, Czechia
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Rossner P, Cervena T, Vojtisek-Lom M, Vrbova K, Ambroz A, Novakova Z, Elzeinova F, Margaryan H, Beranek V, Pechout M, Macoun D, Klema J, Rossnerova A, Ciganek M, Topinka J. The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAir TM) and in Human Bronchial Epithelial Cells (BEAS-2B). Int J Mol Sci 2019; 20:E5710. [PMID: 31739528 PMCID: PMC6888625 DOI: 10.3390/ijms20225710] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 10/02/2019] [Revised: 10/30/2019] [Accepted: 11/12/2019] [Indexed: 01/31/2023] Open
Abstract
The biological effects induced by complete engine emissions in a 3D model of the human airway (MucilAirTM) and in human bronchial epithelial cells (BEAS-2B) grown at the air-liquid interface were compared. The cells were exposed for one or five days to emissions generated by a Euro 5 direct injection spark ignition engine. The general condition of the cells was assessed by the measurement of transepithelial electrical resistance and mucin production. The cytotoxic effects were evaluated by adenylate kinase (AK) and lactate dehydrogenase (LDH) activity. Phosphorylation of histone H2AX was used to detect double-stranded DNA breaks. The expression of the selected 370 relevant genes was analyzed using next-generation sequencing. The exposure had minimal effects on integrity and AK leakage in both cell models. LDH activity and mucin production in BEAS-2B cells significantly increased after longer exposures; DNA breaks were also detected. The exposure affected CYP1A1 and HSPA5 expression in MucilAirTM. There were no effects of this kind observed in BEAS-2B cells; in this system gene expression was rather affected by the time of treatment. The type of cell model was the most important factor modulating gene expression. In summary, the biological effects of complete emissions exposure were weak. In the specific conditions used in this study, the effects observed in BEAS-2B cells were induced by the exposure protocol rather than by emissions and thus this cell line seems to be less suitable for analyses of longer treatment than the 3D model.
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Affiliation(s)
- Pavel Rossner
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
| | - Tereza Cervena
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
- Department of Physiology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Michal Vojtisek-Lom
- Center of Vehicles for Sustainable Mobility, Faculty of Mechanical Engineering, Czech Technical University in Prague, Technicka 4, 160 00 Prague, Czech Republic; (M.V.-L.); (V.B.)
| | - Kristyna Vrbova
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
| | - Antonin Ambroz
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
| | - Zuzana Novakova
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
| | - Fatima Elzeinova
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
| | - Hasmik Margaryan
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
| | - Vit Beranek
- Center of Vehicles for Sustainable Mobility, Faculty of Mechanical Engineering, Czech Technical University in Prague, Technicka 4, 160 00 Prague, Czech Republic; (M.V.-L.); (V.B.)
| | - Martin Pechout
- Department of Vehicles and Ground Transport, Czech University of Life Sciences in Prague, Kamycka 129, 165 21 Prague, Czech Republic; (M.P.); (D.M.)
| | - David Macoun
- Department of Vehicles and Ground Transport, Czech University of Life Sciences in Prague, Kamycka 129, 165 21 Prague, Czech Republic; (M.P.); (D.M.)
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, 12135 Prague, Czech Republic;
| | - Andrea Rossnerova
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
| | - Miroslav Ciganek
- Department of Chemistry and Toxicology, Veterinary Research Institute, 621 00 Brno, Czech Republic;
| | - Jan Topinka
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the CAS, Videnska 1083, 142 20 Prague, Czech Republic; (T.C.); (K.V.); (A.A.); (Z.N.); (F.E.); (H.M.); (A.R.); (J.T.)
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Brzicova T, Sikorova J, Milcova A, Vrbova K, Klema J, Pikal P, Lubovska Z, Philimonenko V, Franco F, Topinka J, Rossner P. Nano-TiO2 stability in medium and size as important factors of toxicity in macrophage-like cells. Toxicol In Vitro 2019; 54:178-188. [DOI: 10.1016/j.tiv.2018.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
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18
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Rynning I, Arlt VM, Vrbova K, Neča J, Rossner Jr P, Klema J, Ulvestad B, Petersen E, Skare Ø, Haugen A, Phillips DH, Machala M, Topinka J, Mollerup S. Bulky DNA adducts, microRNA profiles, and lipid biomarkers in Norwegian tunnel finishing workers occupationally exposed to diesel exhaust. Occup Environ Med 2019; 76:10-16. [PMID: 30425118 PMCID: PMC6327869 DOI: 10.1136/oemed-2018-105445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 08/21/2018] [Revised: 10/04/2018] [Accepted: 10/21/2018] [Indexed: 01/27/2023]
Abstract
OBJECTIVES This study aimed to assess the biological impact of occupational exposure to diesel exhaust (DE) including DE particles (DEP) from heavy-duty diesel-powered equipment in Norwegian tunnel finishing workers (TFW). METHODS TFW (n=69) and referents (n=69) were investigated for bulky DNA adducts (by 32P-postlabelling) and expression of microRNAs (miRNAs) (by small RNA sequencing) in peripheral blood mononuclear cells (PBMC), as well as circulating free arachidonic acid (AA) and eicosanoid profiles in plasma (by liquid chromatography-tandem mass spectrometry). RESULTS PBMC from TFW showed significantly higher levels of DNA adducts compared with referents. Levels of DNA adducts were also related to smoking habits. Seventeen miRNAs were significantly deregulated in TFW. Several of these miRNAs are related to carcinogenesis, apoptosis and antioxidant effects. Analysis of putative miRNA-gene targets revealed deregulation of pathways associated with cancer, alterations in lipid molecules, steroid biosynthesis and cell cycle. Plasma profiles showed higher levels of free AA and 15-hydroxyeicosatetraenoic acid, and lower levels of prostaglandin D2 and 9-hydroxyoctadecadienoic acid in TFW compared with referents. CONCLUSION Occupational exposure to DE/DEP is associated with biological alterations in TFW potentially affecting lung homoeostasis, carcinogenesis, inflammation status and the cardiovascular system. Of particular importance is the finding that tunnel finishing work is associated with an increased level of DNA adducts formation in PBMC.
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Affiliation(s)
- Iselin Rynning
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, Oslo, Norway
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King’s College London, London, UK
- NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King’s College London in Partnership with Public Health England and Imperial College London, London, UK
| | - Kristyna Vrbova
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Neča
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Pavel Rossner Jr
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, Prague, Czech Republic
| | - Bente Ulvestad
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Elisabeth Petersen
- Department of Work Psychology and Physiology, National Institute of Occupational Health, Oslo, Norway
| | - Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Aage Haugen
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, Oslo, Norway
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King’s College London, London, UK
- NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King’s College London in Partnership with Public Health England and Imperial College London, London, UK
| | - Miroslav Machala
- Department of Chemistry and Toxicology, Veterinary Research Institute, Brno, Czech Republic
| | - Jan Topinka
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Steen Mollerup
- Section for Toxicology and Biological Work Environment, Department of Chemical and Biological Work Environment, National Institute of Occupational Health, Oslo, Norway
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Rössner P, Brzicova T, Libalova H, Vrbova K, Sikorova J, Philimonenko V, Klema J, Topinka J. Whole-genome expression analysis in THP-1 macrophage-like cells exposed to diverse metal-containing nanomaterials. Toxicol Lett 2018. [DOI: 10.1016/j.toxlet.2018.06.908] [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: 11/16/2022]
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Honkova K, Rossnerova A, Pavlikova J, Svecova V, Klema J, Topinka J, Milcova A, Libalova H, Choi H, Veleminsky M, Sram RJ, Rossner P. Gene expression profiling in healthy newborns from diverse localities of the Czech Republic. Environ Mol Mutagen 2018; 59:401-415. [PMID: 29602183 DOI: 10.1002/em.22184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 06/08/2023]
Abstract
Prenatal exposure to air pollution is associated with intrauterine growth restriction and low birth weight. Gene expression changes in newborns in relation to air pollution have not been sufficiently studied. We analyzed whole genome expression in cord blood leukocytes of 202 newborns from diverse localities of the Czech Republic, differing among other factors in levels of air pollution: the district of Karvina (characterized by higher concentration of air pollutants) and Ceske Budejovice (lower air pollution levels). We aimed to identify differentially expressed genes (DEGs) and pathways in relation to locality and concentration of air pollutants. We applied the linear model to identify the specific DEGs and the correlation analysis, to investigate the relationship between the concentrations of air pollutants and gene expression data. An analysis of biochemical pathways and gene set enrichment was also performed. In general, we observed modest changes of gene expression, mostly attributed to the effect of the locality. The highest number of DEGs was found in samples from the district of Karvina. A pathway analysis revealed a deregulation of processes associated with cell growth, apoptosis or cellular homeostasis, immune response-related processes or oxidative stress response. The association between concentrations of air pollutants and gene expression changes was weak, particularly for samples collected in Karvina. In summary, as we did not find a direct effect of exposure to air pollutants, we assume that the general differences in the environment, rather than actual concentrations of individual pollutants, represent a key factor affecting gene expression changes at delivery. Environ. Mol. Mutagen. 59:401-415, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Katerina Honkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrea Rossnerova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jitka Pavlikova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vlasta Svecova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Klema
- Czech Technical University, Prague, Czech Republic
| | - Jan Topinka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alena Milcova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Helena Libalova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hyunok Choi
- School of Public Health, University at Albany, Rensselaer, New York
| | - Milos Veleminsky
- Faculty of Health and Social Studies, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Radim J Sram
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Rossner
- Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
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Wohlfahrtova M, Hruba P, Novotny M, Klema J, Krejcik Z, Stranecky V, Honsova E, Vichova P, Viklicky O. FP696ISOLATED V-LESION EARLY AFTER KIDNEY TRANSPLANTATION MAY NOT TRULY REPRESENT A REJECTION. Nephrol Dial Transplant 2018. [DOI: 10.1093/ndt/gfy104.fp696] [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] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Petra Hruba
- Transplant Laboratory, IKEM, Prague, Czech Republic
| | | | - Jiri Klema
- Dept. of Computer Science, Czech Technical University, Prague, Czech Republic
| | - Zdenek Krejcik
- UHKT, Institute of Haematology and Blood Transfusion, Prague, Czech Republic
| | - Viktor Stranecky
- Inst. of Inherited Metabolic Disorders, 1st Faculty of Medicine Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Eva Honsova
- Dept. of Clinical and Transplant Pathology, IKEM, Prague, Czech Republic
| | - Petra Vichova
- Dept. of Immunogenetics, IKEM, Prague, Czech Republic
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Topinka J, Vojtisek-Lom M, Klema J, Machala M, Libalova H. Mechanisms of toxicity of particulate engine emissions from diesel and alternative fuels under realistic traffic conditions. Toxicol Lett 2017. [DOI: 10.1016/j.toxlet.2017.07.088] [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: 11/15/2022]
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Prochazkova J, Hyzdalova M, Strapacova S, Svrzkova L, Hruba E, Masek J, Libalova H, Klema J, Topinka J, Vondracek J, Machala M. Global changes in expression and functional profile of lung adenocarcinoma cells exposed to various toxic AhR ligands. Toxicol Lett 2017. [DOI: 10.1016/j.toxlet.2017.07.234] [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: 11/30/2022]
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Liskova P, Dudakova L, Krepelova A, Klema J, Hysi PG. Replication of SNP associations with keratoconus in a Czech cohort. PLoS One 2017; 12:e0172365. [PMID: 28207827 PMCID: PMC5313182 DOI: 10.1371/journal.pone.0172365] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/04/2017] [Indexed: 11/19/2022] Open
Abstract
Introduction Keratoconus is a relatively frequent disease leading to severe visual impairment. Existing therapies are imperfect and clinical management may benefit from improved understanding of mechanisms leading to this disease. We aim to investigate the replication of 11 single nucleotide polymorphisms (SNPs) with keratoconus. Methods SNPs from loci previously found in association with keratoconus were genotyped in 165 keratoconus cases of Caucasian Czech origin (108 males and 57 females) and 193 population and gender-matched controls. They included rs1536482 (COL5A1), rs4839200 (KCND3), rs757219 and rs214884 (IMMP2L), rs1328083 and rs1328089 (DAOA), rs2721051 (FOXO1), rs4894535 (FNDC3B), rs4954218 (MAP3K19, RAB3GAP1), rs9938149 (ZNF469) and rs1324183 (MPDZ). A case-control association analysis was assessed using Fisher’s exact tests. Results The strongest association was found for rs1324183 (allelic test OR = 1.58; 95% CI, 1.10–2.24, p = 0.01). Statistically significant values were also obtained for rs2721051 (allelic test OR = 1.72; 95% CI, 1.07–2.77, p = 0.025) and rs4954218 (allelic test OR = 1.53; 95% CI, 1.01–2.34; p = 0.047) which showed an opposite effect direction compared to previously reported one. Conclusion Independent replication of association between two SNPs and keratoconus supports the association of these loci with the risks for the disease development, while the effect of rs4954218 warrants further investigation. Understanding the role of the genetic factors involved in keratoconus etiopathogenesis may facilitate development of novel therapies and an early detection.
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Affiliation(s)
- Petra Liskova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- * E-mail:
| | - Lubica Dudakova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Anna Krepelova
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, Prague, Czech Republic
| | - Pirro G. Hysi
- KCL Department of Ophthalmology, King’s College London and Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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Monika Belickova M, Merkerova MD, Votavova H, Valka J, Vesela J, Pejsova B, Hajkova H, Klema J, Cermak J, Jonasova A. Up-regulation of ribosomal genes is associated with a poor response to azacitidine in myelodysplasia and related neoplasms. Int J Hematol 2016; 104:566-573. [DOI: 10.1007/s12185-016-2058-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 10/21/2022]
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Merkerova MD, Krejcik Z, Belickova M, Hrustincova A, Klema J, Stara E, Zemanova Z, Michalova K, Cermak J, Jonasova A. Genome‐wide mi
RNA
profiling in myelodysplastic syndrome with del(5q) treated with lenalidomide. Eur J Haematol 2014; 95:35-43. [DOI: 10.1111/ejh.12458] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2014] [Indexed: 12/14/2022]
Affiliation(s)
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion Prague Czech Republic
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion Prague Czech Republic
| | | | - Jiri Klema
- Department of Cybernetics Faculty of Electrical Engineering Czech Technical University Prague Czech Republic
| | - Eliška Stara
- Institute of Hematology and Blood Transfusion Prague Czech Republic
| | - Zuzana Zemanova
- Center of Oncocytogenetics General University Hospital and First Faculty of Medicine Charles University Prague Czech Republic
| | - Kyra Michalova
- Institute of Hematology and Blood Transfusion Prague Czech Republic
- Center of Oncocytogenetics General University Hospital and First Faculty of Medicine Charles University Prague Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion Prague Czech Republic
| | - Anna Jonasova
- First Department of Medicine General University Hospital Prague Czech Republic
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Hrdlicka J, Klema J. Schizophrenia prediction with the adaboost algorithm. Stud Health Technol Inform 2011; 169:574-578. [PMID: 21893814] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper presents an adaBoost approach for schizophrenia relapse prediction. The data for the adaBoost are extracted from patients answers to Early Warning Signs questionnaires sent regularly via mobile phone messages. The performance of the adaBoost algorithm is confronted with current ITAREPS system with sensitivity 0.65 and specificity 0.73. AdaBoost has the same sensitivity 0.65 but higher specificity 0.84 and is then ready to became the part of the ITAREPS care program.
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Affiliation(s)
- Jan Hrdlicka
- Department of Cybernetics, Czech Technical University in Prague, The Czech Republic
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Plantevit M, Charnois T, Klema J, Rigotti C, Cremilleux B. Combining sequence and itemset mining to discover named entities in biomedical texts: a new type of pattern. IJDMMM 2009. [DOI: 10.1504/ijdmmm.2009.026073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Klema J, Novakova L, Karel F, Stepankova O, Zelezny F. Sequential Data Mining: A Comparative Case Study in Development of Atherosclerosis Risk Factors. ACTA ACUST UNITED AC 2008. [DOI: 10.1109/tsmcc.2007.906055] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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