@article{MTMT:33282552,
	title = {Partial Disturbance of Microprocessor Function in Human Stem Cells Carrying a Heterozygous Mutation in the DGCR8 Gene},
	url = {https://m2.mtmt.hu/api/publication/33282552},
	author = {Reé, Dóra and Fóthi, Ábel and Varga, Nóra and Kolacsek, Orsolya and Orbán, Tamás I. and Apáti, Ágota},
	doi = {10.3390/genes13111925},
	journal-iso = {GENES-BASEL},
	journal = {GENES},
	volume = {13},
	unique-id = {33282552},
	issn = {2073-4425},
	abstract = {Maturation of microRNAs (miRNAs) begins by the "Microprocessor" complex, containing the Drosha endonuclease and its partner protein, "DiGeorge Syndrome Critical Region 8" (DGCR8). Although the main function of the two proteins is to coordinate the first step of precursor miRNAs formation, several studies revealed their miRNA-independent functions in other RNA-related pathways (e.g., in snoRNA decay) or, for the DGCR8, the role in tissue development. To investigate the specific roles of DGCR8 in various cellular pathways, we previously established a human embryonic stem-cell (hESC) line carrying a monoallelic DGCR8 mutation by using the CRISPR-Cas9 system. In this study, we genetically characterized single-cell originated progenies of the cell line and showed that DGCR8 heterozygous mutation results in only a modest effect on the mRNA level but a significant decrease at the protein level. Self-renewal and trilineage differentiation capacity of these hESCs were not affected by the mutation. However, partial disturbance of the Microprocessor function could be revealed in pri-miRNA processing along the human chromosome 19 miRNA cluster in several clones. With all these studies, we can demonstrate that the mutant hESC line is a good model to study not only miRNA-related but also other "noncanonical" functions of the DGCR8 protein.},
	year = {2022},
	eissn = {2073-4425},
	orcid-numbers = {Reé, Dóra/0000-0003-1967-1288; Orbán, Tamás I./0000-0002-3424-3428}
}

@article{MTMT:33133117,
	title = {A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles},
	url = {https://m2.mtmt.hu/api/publication/33133117},
	author = {Raskó, Tamás and Pande, Amit and Radscheit, Kathrin and Zink, Annika and Singh, Manvendra and Sommer, Christian and Wachtl, Gerda Gabriella and Kolacsek, Orsolya and Inak, Gizem and Szvetnik, Attila and Petrakis, Spyros and Bunse, Mario and Bansal, Vikas and Selbach, Matthias and Orbán, Tamás I. and Prigione, Alessandro and Hurst, Laurence D and Izsvák, Zsuzsanna},
	doi = {10.1093/molbev/msac175},
	journal-iso = {MOL BIOL EVOL},
	journal = {MOLECULAR BIOLOGY AND EVOLUTION},
	volume = {39},
	unique-id = {33133117},
	issn = {0737-4038},
	abstract = {Although new genes can arrive from modes other than duplication, few examples are well characterized. Given high expression in some human brain subregions and a putative link to psychological disorders [e.g., schizophrenia (SCZ)], suggestive of brain functionality, here we characterize piggyBac transposable element-derived 1 (PGBD1). PGBD1 is nonmonotreme mammal-specific and under purifying selection, consistent with functionality. The gene body of human PGBD1 retains much of the original DNA transposon but has additionally captured SCAN and KRAB domains. Despite gene body retention, PGBD1 has lost transposition abilities, thus transposase functionality is absent. PGBD1 no longer recognizes piggyBac transposon-like inverted repeats, nonetheless PGBD1 has DNA binding activity. Genome scale analysis identifies enrichment of binding sites in and around genes involved in neuronal development, with association with both histone activating and repressing marks. We focus on one of the repressed genes, the long noncoding RNA NEAT1, also dysregulated in SCZ, the core structural RNA of paraspeckles. DNA binding assays confirm specific binding of PGBD1 both in the NEAT1 promoter and in the gene body. Depletion of PGBD1 in neuronal progenitor cells (NPCs) results in increased NEAT1/paraspeckles and differentiation. We conclude that PGBD1 has evolved core regulatory functionality for the maintenance of NPCs. As paraspeckles are a mammal-specific structure, the results presented here show a rare example of the evolution of a novel gene coupled to the evolution of a contemporaneous new structure.},
	year = {2022},
	eissn = {1537-1719},
	orcid-numbers = {Singh, Manvendra/0000-0002-8626-5418; Orbán, Tamás I./0000-0002-3424-3428; Hurst, Laurence D/0000-0002-1002-1054}
}

@article{MTMT:32873583,
	title = {Functional indications for transposase domestications – Characterization of the human piggyBac transposase derived (PGBD) activities},
	url = {https://m2.mtmt.hu/api/publication/32873583},
	author = {Kolacsek, Orsolya and Wachtl, Gerda Gabriella and Fóthi, Ábel and Schamberger, Anita and Sándor, Sára Anna and Pergel, Enikő and Varga, Nóra and Raskó, Tamás and Izsvák, Zsuzsa and Apáti, Ágota and Orbán, Tamás I.},
	doi = {10.1016/j.gene.2022.146609},
	journal-iso = {GENE},
	journal = {GENE},
	volume = {834},
	unique-id = {32873583},
	issn = {0378-1119},
	abstract = {Transposable elements are widespread in all living organisms. In addition to self-reproduction, they are a major source of genetic variation that drives genome evolution but our knowledge of the functions of human genes derived from transposases is limited. There are examples of transposon-derived, domesticated human genes that lost (SETMAR) or retained (THAP9) their transposase activity, however, several remnants in the human genome have not been thoroughly investigated yet. These include the five human piggyBac-derived sequences (PGBD1-5) which share ancestry with the Trichoplusia ni originated piggyBac (PB) transposase. Since PB is widely used in gene delivery applications, the potential activities of endogenous PGBDs are important to address. However, previous data is controversial, especially with the claimed transposition activity of PGBD5, it awaits further investigations. Here, we aimed to systematically analyze all five human PGBD proteins from several aspects, including phylogenetic conservation, potential transposase activity, expression pattern and their regulation in different stress conditions. Among PGBDs, PGBD5 is under the highest purifying selection, and exhibits the most cell type specific expression pattern. In a two-component vector system, none of the human PGBDs could mobilize either the insect PB transposon or the endogenous human PB-like MER75 and MER85 elements with intact terminal sequences. When cells were exposed to various stress conditions, including hypoxia, oxidative or UV stress, the expression profiles of all PGBDs showed different, often cell type specific responses; however, the pattern of PGBD5 in most cases had the opposite tendency than that of the other piggyBac-derived elements. Taken together, our results indicate that human PGBD elements did not retain their mobilizing activity, but their cell type specific, and cellular stress related expression profiles point toward distinct domesticated functions that require further characterization.},
	year = {2022},
	eissn = {1879-0038},
	orcid-numbers = {Sándor, Sára Anna/0000-0002-2945-8379; Orbán, Tamás I./0000-0002-3424-3428}
}

@article{MTMT:3399410,
	title = {Transcription activity of transposon sequence limits Sleeping Beauty transposition},
	url = {https://m2.mtmt.hu/api/publication/3399410},
	author = {Kolacsek, Orsolya and Orbán, Tamás I.},
	doi = {10.1016/j.gene.2018.07.045},
	journal-iso = {GENE},
	journal = {GENE},
	volume = {676},
	unique-id = {3399410},
	issn = {0378-1119},
	abstract = {Sleeping Beauty (SB) transposon based technology has been extensively applied in basic research and biotechnology for routine cell culture gene delivery and vertebrate transgenesis, and it is also investigated in various gene therapy applications. Cell tolerance for the transgene is a key factor during transgenesis and is modulated not only through the type but by the dose of expression. Our experimental results exemplify that transgenes regulated with high activity promoters can reduce the overall success of gene delivery. Observations connected to transposon donors regulated by different promoters have also revealed inverse correlation between transcription activity and the hyperactive variant SB100X excision efficiency. This competition between transcription and transposition was independent of the transgene coding sequence and did not alter the transgenic efficiency in general. However, promoters applied in the transgene cassette can produce different average copy numbers depending on the transcriptional activity of the transposon. Unlike the piggyBac (PB) transposon system, this phenomenon allows a fine balance of expression using the high copy potential SB system that adjusts the copy number of lower activity promoter driven transgenes to a higher expression level. All this contributes to a well-tolerated and satisfactory transgenesis, and would be important to consider in gene therapy applications.},
	year = {2018},
	eissn = {1879-0038},
	pages = {184-188},
	orcid-numbers = {Orbán, Tamás I./0000-0002-3424-3428}
}

@mastersthesis{MTMT:3322146,
	title = {DNS transzpozon alapú génbeviteli eljárások vizsgálata emlős rendszerekben},
	url = {https://m2.mtmt.hu/api/publication/3322146},
	author = {Kolacsek, Orsolya},
	doi = {10.15476/ELTE.2016.170},
	publisher = {Eötvös Loránd University},
	unique-id = {3322146},
	keywords = {Doktori disszertáció; DNS transzpozonok},
	year = {2017}
}

@article{MTMT:3251043,
	title = {Extensive astrocyte synchronization advances neuronal coupling in slow wave activity in vivo},
	url = {https://m2.mtmt.hu/api/publication/3251043},
	author = {Szabó, Zsolt and Héja, László and Szalay, Gergely and Kékesi, Orsolya Sára and Füredi, András and Szebényi, Kornélia and Dobolyi, Árpád and Orbán, Tamás I. and Kolacsek, Orsolya and Tompa, Tamás and Miskolczy, Zsombor and Biczók, László and Rózsa J., Balázs and Sarkadi, Balázs and Kardos, Julianna},
	doi = {10.1038/s41598-017-06073-7},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {7},
	unique-id = {3251043},
	issn = {2045-2322},
	abstract = {Slow wave activity (SWA) is a characteristic brain oscillation in sleep and quiet wakefulness. Although the cell types contributing to SWA genesis are not yet identified, the principal role of neurons in the emergence of this essential cognitive mechanism has not been questioned. To address the possibility of astrocytic involvement in SWA, we used a transgenic rat line expressing a calcium sensitive fluorescent protein in both astrocytes and interneurons and simultaneously imaged astrocytic and neuronal activity in vivo. Here we demonstrate, for the first time, that the astrocyte network display synchronized recurrent activity in vivo coupled to UP states measured by field recording and neuronal calcium imaging. Furthermore, we present evidence that extensive synchronization of the astrocytic network precedes the spatial build-up of neuronal synchronization. The earlier extensive recruitment of astrocytes in the synchronized activity is reinforced by the observation that neurons surrounded by active astrocytes are more likely to join SWA, suggesting causality. Further supporting this notion, we demonstrate that blockade of astrocytic gap junctional communication or inhibition of astrocytic Ca2+ transients reduces the ratio of both astrocytes and neurons involved in SWA. These in vivo findings conclusively suggest a causal role of the astrocytic syncytium in SWA generation.},
	keywords = {HUMAN BRAIN; CEREBRAL-CORTEX; sleep; tonic inhibition; NETWORK MECHANISMS; LESS-THAN-1 HZ; GABA RELEASE; Calcium dynamics; GAP-JUNCTION; interneurons},
	year = {2017},
	eissn = {2045-2322},
	orcid-numbers = {Szabó, Zsolt/0000-0002-2902-743X; Füredi, András/0000-0002-7883-9901; Szebényi, Kornélia/0000-0003-1558-8372; Dobolyi, Árpád/0000-0003-0397-2991; Orbán, Tamás I./0000-0002-3424-3428; Biczók, László/0000-0003-2568-5942; Sarkadi, Balázs/0000-0003-0592-4539}
}

@article{MTMT:3148390,
	title = {Ct shift: A novel and accurate real-time PCR quantification model for direct comparison of different nucleic acid sequences and its application for transposon quantifications},
	url = {https://m2.mtmt.hu/api/publication/3148390},
	author = {Kolacsek, Orsolya and Pergel, Enikő and Varga, Nóra and Apáti, Ágota and Orbán, Tamás I.},
	doi = {10.1016/j.gene.2016.10.035},
	journal-iso = {GENE},
	journal = {GENE},
	volume = {598},
	unique-id = {3148390},
	issn = {0378-1119},
	abstract = {There are numerous applications of quantitative PCR for both diagnostic and basic research. As in many other techniques the basis of quantification is that comparisons are made between different (unknown and known or reference) specimens of the same entity. When the aim is to compare real quantities of different species in samples, one cannot escape their separate precise absolute quantification. We have established a simple and reliable method for this purpose (Ct shift method) which combines the absolute and the relative approach. It requires a plasmid standard containing both sequences of amplicons to be compared (e.g. the target of interest and the endogenous control). It can serve as a reference sample with equal copies of templates for both targets. Using the DeltaDeltaCt formula we can quantify the exact ratio of the two templates in each unknown sample. The Ct shift method has been successfully applied for transposon gene copy measurements, as well as for comparison of different mRNAs in cDNA samples. This study provides the proof of concept and introduces some potential applications of the method; the absolute nature of results even without the need for real reference samples can contribute to the universality of the method and comparability of different studies.},
	year = {2017},
	eissn = {1879-0038},
	pages = {43-49},
	orcid-numbers = {Orbán, Tamás I./0000-0002-3424-3428}
}

@article{MTMT:3148042,
	title = {A transgenic rat hepatocyte - Kupffer cell co-culture model for evaluation of direct and macrophage-related effect of poly(amidoamine) dendrimers},
	url = {https://m2.mtmt.hu/api/publication/3148042},
	author = {Jemnitz, Katalin and Batai-Konczos, A and Szabó, Mónika and Ioja, Enikő and Kolacsek, Orsolya and Orbán, Tamás I. and Török, György and Homolya, László and Kovacs, E and Jablonkai, István and Veres, Zsuzsa},
	doi = {10.1016/j.tiv.2016.09.016},
	journal-iso = {TOXICOL IN VITRO},
	journal = {TOXICOLOGY IN VITRO},
	volume = {38},
	unique-id = {3148042},
	issn = {0887-2333},
	abstract = {Increasing number of papers demonstrate that Kupffer cells (KCs) play a role in the development of drug induced liver injury (DILI). Furthermore, elevated intracellular Ca2+ level of hepatocytes is considered as a common marker of DILI. Here we applied an in vitro model based on hepatocyte mono- and hepatocyte/KC co-cultures (H/KC) isolated from transgenic rats stably expressing the GCaMP2 fluorescent Ca2+ sensor protein to investigate the effects of polycationic (G5), polyanionic (G4.5) and polyethylene-glycol coated neutral (G5 Peg) dendrimers known to accumulate in the liver, primarily in KCs. Following dendrimer exposure, hepatocyte homeostasis was measured by MTT cytotoxicity assay and by Ca2+ imaging, while hepatocyte functions were studied by CYP2B1/2 inducibility, and bilirubin and taurocholate transport. G5 was significantly more cytotoxic than G4.5 for hepatocytes and induced Ca2+ oscillation and sustained Ca2+ signals at 1muM and10 muM, respectively both in hepatocytes and KCs. Dendrimer-induced Ca2+ signals in hepatocytes were attenuated by macrophages. Activation of KCs by lipopolysaccharide and G5 decreased the inducibility of CYP2B1/2, which was restored by depleting the KCs with gadolinium-chloride and pentoxyphylline, suggesting a role of macrophages in the hindrance of CYP2B1/2 induction by G5 and lipopolysaccharide. In the H/KC, but not in the hepatocyte mono-culture, G5 reduced the canalicular efflux of bilirubin and stimulated the uptake and canalicular efflux of taurocholate. In conclusion, H/KC provides a good model for the prediction of hepatotoxic potential of drugs, especially of nanomaterials known to be trapped by macrophages, activation of which presumably contributes to DILI.},
	year = {2017},
	eissn = {1879-3177},
	pages = {159-169},
	orcid-numbers = {Orbán, Tamás I./0000-0002-3424-3428; Török, György/0000-0001-7616-5782; Homolya, László/0000-0003-1639-8140}
}

@article{MTMT:2938283,
	title = {Generation of a Homozygous Transgenic Rat Strain Stably Expressing a Calcium Sensor Protein for Direct Examination of Calcium Signaling},
	url = {https://m2.mtmt.hu/api/publication/2938283},
	author = {Szebényi, Kornélia and Füredi, András and Kolacsek, Orsolya and Pergel, Enikő and Bősze, Zsuzsanna and Bender, B and Vajdovich, Péter and Tóvári, József and Homolya, László and Szakács, Gergely and Héja, László and Enyedi, Ágnes and Sarkadi, Balázs and Apáti, Ágota and Orbán, Tamás I.},
	doi = {10.1038/srep12645},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {5},
	unique-id = {2938283},
	issn = {2045-2322},
	abstract = {In drug discovery, prediction of selectivity and toxicity require the evaluation of cellular calcium homeostasis. The rat is a preferred laboratory animal for pharmacology and toxicology studies, while currently no calcium indicator protein expressing rat model is available. We established a transgenic rat strain stably expressing the GCaMP2 fluorescent calcium sensor by a transposon-based methodology. Zygotes were co-injected with mRNA of transposase and a CAG-GCaMP2 expressing construct and animals with one transgene copy were pre-selected by measuring fluorescence in blood cells. A homozygous rat strain was generated with high sensor protein expression in the heart, kidney, liver and blood cells. No pathological alterations were found in these animals and fluorescence measurements in cardiac tissue slices and primary cultures demonstrated the applicability of this system for studying calcium signaling. We show here that the GCaMP2 expressing rat cardiomyocytes allow the prediction of cardiotoxic drug side-effects and provide evidence for the role of Na+/Ca2+ exchanger and its beneficial pharmacological modulation in cardiac reperfusion. Our data indicate that drug-induced alterations and pathological processes can be followed by using this rat model, suggesting that transgenic rats expressing a calcium-sensitive protein provide a valuable system for pharmacological and toxicological studies.},
	year = {2015},
	eissn = {2045-2322},
	orcid-numbers = {Szebényi, Kornélia/0000-0003-1558-8372; Füredi, András/0000-0002-7883-9901; Tóvári, József/0000-0002-5543-3204; Homolya, László/0000-0003-1639-8140; Enyedi, Ágnes/0000-0002-7366-9376; Sarkadi, Balázs/0000-0003-0592-4539; Orbán, Tamás I./0000-0002-3424-3428}
}

@article{MTMT:2886263,
	title = {GENETICALLY ENCODED INDICATOR PROTEIN IN RAT ENABLES THE VISUALIZATION OF CALCIUM DYNAMICS OF ISCHEMIA/REPERFUSION INJURY IN PROXIMAL TUBULES},
	url = {https://m2.mtmt.hu/api/publication/2886263},
	author = {Csohány, Rózsa and Prókai, Ágnes and Szebényi, Kornélia and Füredi, András and Kolacsek, Orsolya and Orbán, Tamás I. and Apáti, Ágota and Kis-Petik, Katalin and Szabó, Attila and Sarkadi, Balázs},
	journal-iso = {PEDIATR TRANSPLANT},
	journal = {PEDIATRIC TRANSPLANTATION},
	volume = {19},
	unique-id = {2886263},
	issn = {1397-3142},
	year = {2015},
	eissn = {1399-3046},
	pages = {141-141},
	orcid-numbers = {Csohány, Rózsa/0000-0002-0784-0040; Prókai, Ágnes/0000-0003-1646-7599; Szebényi, Kornélia/0000-0003-1558-8372; Füredi, András/0000-0002-7883-9901; Orbán, Tamás I./0000-0002-3424-3428; Kis-Petik, Katalin/0000-0003-3271-5468; Szabó, Attila/0000-0001-7321-9861; Sarkadi, Balázs/0000-0003-0592-4539}
}