@article{MTMT:34669504,
	title = {Exosomal small RNA profiling in first-trimester maternal blood explores early molecular pathways of preterm preeclampsia},
	url = {https://m2.mtmt.hu/api/publication/34669504},
	author = {Gál, Luca and Fóthi, Ábel and Orosz, Gergő and Nagy, Sándor and Than, Nándor Gábor and Orbán, Tamás I.},
	doi = {10.3389/fimmu.2024.1321191},
	journal-iso = {FRONT IMMUNOL},
	journal = {FRONTIERS IN IMMUNOLOGY},
	volume = {15},
	unique-id = {34669504},
	issn = {1664-3224},
	abstract = {Introduction: Preeclampsia (PE) is a severe obstetrical syndrome characterized by new-onset hypertension and proteinuria and it is often associated with fetal intrauterine growth restriction (IUGR). PE leads to long-term health complications, so early diagnosis would be crucial for timely prevention. There are multiple etiologies and subtypes of PE, and this heterogeneity has hindered accurate identification in the presymptomatic phase. Recent investigations have pointed to the potential role of small regulatory RNAs in PE, and these species, which travel in extracellular vesicles (EVs) in the circulation, have raised the possibility of non-invasive diagnostics. The aim of this study was to investigate the behavior of exosomal regulatory small RNAs in the most severe subtype of PE with IUGR.
		
		Methods: We isolated exosomal EVs from first-trimester peripheral blood plasma samples of women who later developed preterm PE with IUGR (n=6) and gestational age-matched healthy controls (n=14). The small RNA content of EVs and their differential expression were determined by next-generation sequencing and further validated by quantitative real-time PCR. We also applied the rigorous exceRpt bioinformatics pipeline for small RNA identification, followed by target verification and Gene Ontology analysis.
		
		Results: Overall, >2700 small RNAs were identified in all samples and, of interest, the majority belonged to the RNA interference (RNAi) pathways. Among the RNAi species, 16 differentially expressed microRNAs were up-regulated in PE, whereas up-regulated and down-regulated members were equally found among the six identified Piwi-associated RNAs. Gene ontology analysis of the predicted small RNA targets showed enrichment of genes in pathways related to immune processes involved in decidualization, placentation and embryonic development, indicating that dysregulation of the induced small RNAs is connected to the impairment of immune pathways in preeclampsia development. Finally, the subsequent validation experiments revealed that the hsa_piR_016658 piRNA is a promising biomarker candidate for preterm PE associated with IUGR.
		
		Discussion: Our rigorously designed study in a homogeneous group of patients unraveled small RNAs in circulating maternal exosomes that act on physiological pathways dysregulated in preterm PE with IUGR. Therefore, our small RNA hits are not only suitable biomarker candidates, but the revealed biological pathways may further inform us about the complex pathology of this severe PE subtype.},
	year = {2024},
	eissn = {1664-3224},
	orcid-numbers = {Orbán, Tamás I./0000-0002-3424-3428}
}

@article{MTMT:33697437,
	title = {One locus, several functional RNAs—emerging roles of the mechanisms responsible for the sequence variability of microRNAs},
	url = {https://m2.mtmt.hu/api/publication/33697437},
	author = {Orbán, Tamás I.},
	doi = {10.1007/s42977-023-00154-7},
	journal-iso = {BIOL FUTURA},
	journal = {BIOLOGIA FUTURA},
	volume = {74},
	unique-id = {33697437},
	issn = {2676-8615},
	abstract = {With the development of modern molecular genetics, the original “one gene-one enzyme” hypothesis has been outdated. For protein coding genes, the discovery of alternative splicing and RNA editing provided the biochemical background for the RNA repertoire of a single locus, which also serves as an important pillar for the enormous protein variability of the genomes. Non-protein coding RNA genes were also revealed to produce several RNA species with distinct functions. The loci of microRNAs (miRNAs), encoding for small endogenous regulatory RNAs, were also found to produce a population of small RNAs, rather than a single defined product. This review aims to present the mechanisms contributing to the astonishing variability of miRNAs revealed by the new sequencing technologies. One important source is the careful balance of arm selection, producing sequentially different 5p- or 3p-miRNAs from the same pre-miRNA, thereby broadening the number of regulated target RNAs and the phenotypic response. In addition, the formation of 5', 3' and polymorphic isomiRs, with variable end and internal sequences also leads to a higher number of targeted sequences, and increases the regulatory output. These miRNA maturation processes, together with other known mechanisms such as RNA editing, further increase the potential outcome of this small RNA pathway. By discussing the subtle mechanisms behind the sequence diversity of miRNAs, this review intends to reveal this engaging aspect of the inherited “RNA world”, how it contributes to the almost infinite molecular variability among living organisms, and how this variability can be exploited to treat human diseases. © 2023, The Author(s).},
	keywords = {RNA Interference; microRNA; RNAi; isomiR; Arm selection},
	year = {2023},
	eissn = {2676-8607},
	pages = {17-28},
	orcid-numbers = {Orbán, Tamás I./0000-0002-3424-3428}
}

@article{MTMT:33648095,
	title = {Nucleotide binding is the critical regulator of ABCG2 conformational transitions},
	url = {https://m2.mtmt.hu/api/publication/33648095},
	author = {Gyöngy, Zsuzsanna and Mocsár, Gábor and Hegedüs, Éva and Stockner, T. and Ritter, Z. and Homolya, László and Schamberger, Anita and Orbán, Tamás I. and Remenyik, J. and Szakács, Gergely and Kormosné, Goda Katalin},
	doi = {10.7554/eLife.83976},
	journal-iso = {ELIFE},
	journal = {ELIFE},
	volume = {12},
	unique-id = {33648095},
	issn = {2050-084X},
	abstract = {ABCG2 is an exporter-type ABC protein that can expel numerous chemically unrelated xeno- and endobiotics from cells. When expressed in tumor cells or tumor stem cells, ABCG2 confers multidrug resistance, contributing to the failure of chemotherapy. Molecular details orchestrating substrate translocation and ATP hydrolysis remain elusive. Here, we present methods to concomitantly investigate substrate and nucleotide binding by ABCG2 in cells. Using the conformation-sensitive antibody 5D3, we show that the switch from the inward-facing (IF) to the outward-facing (OF) conformation of ABCG2 is induced by nucleotide binding. IF-OF transition is facilitated by substrates, and hindered by the inhibitor Ko143. Direct measurements of 5D3 and substrate binding to ABCG2 indicate that the high-to-low affinity switch of the drug binding site coincides with the transition from the IF to the OF conformation. Low substrate binding persists in the post-hydrolysis state, supporting that dissociation of the ATP hydrolysis products is required to reset the high substrate affinity IF conformation of ABCG2. © 2023, Gyöngy et al.},
	keywords = {FLUORESCENCE CORRELATION SPECTROSCOPY; human; ABCG2; CELL BIOLOGY; confocal microscopy; Substrate binding; Catalytic cycle; Conformation changes},
	year = {2023},
	eissn = {2050-084X},
	orcid-numbers = {Gyöngy, Zsuzsanna/0000-0002-5886-398X; Homolya, László/0000-0003-1639-8140; Orbán, Tamás I./0000-0002-3424-3428}
}

@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:33133365,
	title = {Functional Characterization of the N-Terminal Disordered Region of the piggyBac Transposase},
	url = {https://m2.mtmt.hu/api/publication/33133365},
	author = {Wachtl, Gerda Gabriella and Schád, Éva and Huszár, Krisztina and Palazzo, A. and Ivics, Z. and Tantos, Ágnes and Orbán, Tamás I.},
	doi = {10.3390/ijms231810317},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {23},
	unique-id = {33133365},
	issn = {1661-6596},
	abstract = {The piggyBac DNA transposon is an active element initially isolated from the cabbage looper moth, but members of this superfamily are also present in most eukaryotic evolutionary lineages. The functionally important regions of the transposase are well described. There is an RNase H-like fold containing the DDD motif responsible for the catalytic DNA cleavage and joining reactions and a C-terminal cysteine-rich domain important for interaction with the transposon DNA. However, the protein also contains a ~100 amino acid long N-terminal disordered region (NTDR) whose function is currently unknown. Here we show that deletion of the NTDR significantly impairs piggyBac transposition, although the extent of decrease is strongly cell-type specific. Moreover, replacing the NTDR with scrambled but similarly disordered sequences did not rescue transposase activity, indicating the importance of sequence conservation. Cell-based transposon excision and integration assays reveal that the excision step is more severely affected by NTDR deletion. Finally, bioinformatic analyses indicated that the NTDR is specific for the piggyBac superfamily and is also present in domesticated, transposase-derived proteins incapable of catalyzing transposition. Our results indicate an essential role of the NTDR in the "fine-tuning" of transposition and its significance in the functions of piggyBac-originated co-opted genes.},
	keywords = {Intrinsically disordered protein; PIGGYBAC; DNA transposon; PGBD},
	year = {2022},
	eissn = {1422-0067},
	orcid-numbers = {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:32131519,
	title = {Posttranscriptional regulation of the human abcg2 multidrug transporter protein by artificial mirtrons},
	url = {https://m2.mtmt.hu/api/publication/32131519},
	author = {Schamberger, Anita and Várady, György and Fóthi, Ábel and Orbán, Tamás I.},
	doi = {10.3390/genes12071068},
	journal-iso = {GENES-BASEL},
	journal = {GENES},
	volume = {12},
	unique-id = {32131519},
	issn = {2073-4425},
	abstract = {ABCG2 is a membrane transporter protein that has been associated with multidrug resistance phenotype and tumor development. Additionally, it is expressed in various stem cells, providing cellular protection against endobiotics and xenobiotics. In this study, we designed artificial mirtrons to regulate ABCG2 expression posttranscriptionally. Applying EGFP as a host gene, we could achieve efficient silencing not only in luciferase reporter systems but also at the ABCG2 protein level. Moreover, we observed important new sequential‐functional features of the designed mirtrons. Mismatch at the first position of the mirtron‐derived small RNA resulted in better silencing than full complementarity, while the investigated middle and 3′ mismatches did not enhance silencing. These latter small RNAs operated most probably via non‐seed specific translational inhibition in luciferase assays. Additionally, we found that a mismatch in the first position has not, but a second mismatch in the third position has abolished target mRNA decay. Besides, one nucleotide mismatch in the seed region did not impair efficient silencing at the protein level, providing the possibility to silence targets carrying single nucleotide polymorphisms or mutations. Taken together, we believe that apart from establishing an efficient ABCG2 silencing system, our designing pipeline and results on sequential‐functional features are beneficial for developing artificial mirtrons for other targets. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},
	keywords = {MULTIDRUG TRANSPORTER; ABCG2; silencing; miRNA; Mirtron},
	year = {2021},
	eissn = {2073-4425},
	orcid-numbers = {Várady, György/0000-0003-2012-9680; Orbán, Tamás I./0000-0002-3424-3428}
}

@article{MTMT:31797112,
	title = {Establishing a human embryonic stem cell clone with a heterozygous mutation in the DGCR8 gene},
	url = {https://m2.mtmt.hu/api/publication/31797112},
	author = {Reé, Dóra and Borsy, Adrienn Éva and Fóthi, Ábel and Orbán, Tamás I. and Várady, György and Erdei, Zsuzsa and Sarkadi, Balázs and Réthelyi, János and Varga, Nóra and Apáti, Ágota},
	doi = {10.1016/j.scr.2020.102134},
	journal-iso = {STEM CELL RES},
	journal = {STEM CELL RESEARCH},
	volume = {50},
	unique-id = {31797112},
	issn = {1873-5061},
	abstract = {DiGeorge Syndrome (DGS) Critical Region 8 (DGCR8) is a primary candidate gene in they DGS. The DGCR8 microprocessor complex subunit is an essential cofactor in the canonical miRNA biogenesis which is involved in diverse cellular functions such as cell fate decisions, apoptosis and different signaling pathways. However, the role of DGCR8 in these processes or development of DGS is not fully understood. Here we present a heterozygous DGCR8 mutant human embryonic stem cell line (HuES9(DGcR8+/-)) created by the CRISPR/Cas9 system. The generated HuES9(DGCR8+/-) cells maintain normal karyotype, morphology, pluripotency and differentiation capacity into all three germ layers.},
	year = {2021},
	eissn = {1876-7753},
	orcid-numbers = {Reé, Dóra/0000-0003-1967-1288; Orbán, Tamás I./0000-0002-3424-3428; Várady, György/0000-0003-2012-9680; Sarkadi, Balázs/0000-0003-0592-4539; Réthelyi, János/0000-0002-3641-012X}
}

@article{MTMT:31662955,
	title = {Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human chromosome 19 MicroRNA cluster},
	url = {https://m2.mtmt.hu/api/publication/31662955},
	author = {Fóthi, Ábel and Biró, Orsolya and Erdei, Zsuzsa and Apáti, Ágota and Orbán, Tamás I.},
	doi = {10.1080/15476286.2020.1836457},
	journal-iso = {RNA BIOL},
	journal = {RNA BIOLOGY},
	volume = {18},
	unique-id = {31662955},
	issn = {1547-6286},
	abstract = {One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3ʹ end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that a difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional ‘fine-tuning’ can differentiate among miRNAs that are expressed simultaneously from a common precursor. © 2020 Informa UK Limited, trading as Taylor & Francis Group.},
	keywords = {ENHANCER; miRNA; Drosha; DGCR8; C19MC; ChIP-qPCR},
	year = {2021},
	eissn = {1555-8584},
	pages = {1170-1180},
	orcid-numbers = {Biró, Orsolya/0000-0002-4300-3602; Orbán, Tamás I./0000-0002-3424-3428}
}