TY - JOUR AU - Mórocz, Mónika AU - Qorri, Erda AU - Pekker, Emese AU - Tick, Gabriella AU - Haracska, Lajos TI - Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools JF - JOURNAL OF BIOTECHNOLOGY J2 - J BIOTECHNOL VL - 380 PY - 2024 SP - 1 EP - 19 PG - 19 SN - 0168-1656 DO - 10.1016/j.jbiotec.2023.12.001 UR - https://m2.mtmt.hu/api/publication/34489854 ID - 34489854 N1 - Funding Agency and Grant Number: European Union [739593, RRF-2.3.1-21-2022-00015]; National Research, Development, and Innovation Office [TKP-31-8/PALY-2021, 2020-1.1.2-PIACI-KFI-2021-00304]; (European Union) Funding text: This project received Funding from the European Union ' s Horizon 2020 research and innovation program under grant agreement No. 739593. This work was also supported by the National Research, Development, and Innovation Office (TKP-31-8/PALY-2021 and 2020-1.1.2-PIACI-KFI-2021-00304) . Project no. RRF-2.3.1-21-2022-00015 has been implemented with the support provided by the European Union) . AB - DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and doublestranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors. LA - English DB - MTMT ER - TY - JOUR AU - Pekker, Emese AU - Priskin, Katalin AU - Szabo-Kriston, Eva AU - Csanyi, Bernadett AU - Buzas-Bereczki, Orsolya AU - Adorjan, Lili AU - Szukacsov, Valéria AU - Pinter, Lajos AU - Rusvai, Miklos AU - Cooper, Paul AU - Kiss-Toth, Endre AU - Haracska, Lajos TI - Development of a Large-Scale Pathogen Screening Test for the Biosafety Evaluation of Canine Mesenchymal Stem Cells JF - BIOLOGICAL PROCEDURES ONLINE J2 - BIOL PROCED ONLINE VL - 25 PY - 2023 IS - 1 PG - 14 SN - 1480-9222 DO - 10.1186/s12575-023-00226-x UR - https://m2.mtmt.hu/api/publication/34473962 ID - 34473962 N1 - Funding Agency and Grant Number: European Union [739593]; National Research, Development, and Innovation Office [RRF-2.3.1-21-2022-00015, TKP-31-8/PALY-2021] Funding text: This project received funding from the European Union ' s Horizon 2020 research and innovation program under grant agreement No. 739593. This work was also supported by the National Research, Development, and Innovation Office (PharmaLab, RRF-2.3.1-21-2022-00015 and TKP-31-8/PALY-2021). AB - BackgroundThe action of mesenchymal stem cells (MSCs) is the subject of intense research in the field of regenerative medicine, including their potential use in companion animals, such as dogs. To ensure the safety of canine MSC batches for their application in regenerative medicine, a quality control test must be conducted in accordance with Good Manufacturing Practices (GMP). Based on guidance provided by the European Medicines Agency, this study aimed to develop and validate a highly sensitive and robust, nucleic acid-based test panel for the detection of various canine pathogens. Analytical sensitivity, specificity, amplification efficiency, and linearity were evaluated to ensure robust assessment. Additionally, viable spike-in controls were used to control for optimal nucleic acid extraction. The conventional PCR-based and real-time PCR-based pathogen assays were evaluated in a real-life setting, by direct testing MSC batches.ResultsThe established nucleic acid-based assays displayed remarkable sensitivity, detecting 100-1 copies/reaction of template DNA. They also exhibited high specificity and efficiency. Moreover, highly effective nucleic acid isolation was confirmed by the sensitive detection of spike-in controls. The detection capacity of our optimized and validated methods was determined by direct pathogen testing of nine MSC batches that displayed unusual phenotypes, such as reduced cell division or other deviating characteristics. Among these MCS batches of uncertain purity, only one tested negative for all pathogens. The direct testing of these samples yielded positive results for important canine pathogens, including tick-borne disease-associated species and viral members of the canine infectious respiratory disease complex (CIRDC). Notably, samples positive for the etiological agents responsible for enteritis (CPV), leptospirosis (Leptospira interrogans), and neosporosis (Neospora caninum) were also identified. Furthermore, we conducted biosafety evaluation of 12 MSC batches intended for therapeutic application. Eleven MSC batches were found to be free of extraneous agents, and only one tested positive for a specific pathogen, namely, canine parvovirus.ConclusionIn this study, we established and validated reliable, highly sensitive, and accurate nucleic acid-based testing methods for a broad spectrum of canine pathogens. LA - English DB - MTMT ER - TY - GEN AU - Mamar, Hasan AU - Fajka-Boja, Roberta AU - Mórocz, Mónika AU - Pinto, Eva AU - Siham, Zentout AU - Mihut, Alexandra AU - Kopasz, Anna Georgina AU - Mérey, Mihály AU - Rebecca, Smith AU - Haracska, Lajos AU - Sébastien, Huet AU - Timinszky, Gyula TI - The loss of DNA polymerase epsilon accessory subunits POLE3-POLE4 leads to BRCA1-independent PARP inhibitor sensitivity PY - 2023 UR - https://m2.mtmt.hu/api/publication/34169536 ID - 34169536 LA - English DB - MTMT ER - TY - JOUR AU - Imre, Gergely AU - Takács, Bertalan Vilmos AU - Czipa, Erik AU - Drubi, Andrea AU - Jaksa, Gábor AU - Latinovics, Dóra AU - Nagy, Andrea AU - Karkas, Réka AU - Hudoba, Liza AU - Vásárhelyi, Bálint Márk AU - Pankotai-Bodó, Gabriella AU - Blastyák, András AU - Hegedűs, Zoltán AU - Germán, Péter AU - Bálint, Balázs AU - Ahmed Abdullah, Khaldoon Sadiq AU - Kopasz, Anna Georgina AU - Kovács, Anita Kármen AU - Nagy, László AU - Sükösd, Farkas AU - Pintér, Lajos AU - Rülicke, Thomas AU - Barta, Endre AU - Nagy, István AU - Haracska, Lajos AU - Mátés, Lajos TI - Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy JF - MOLECULAR THERAPY-METHODS AND CLINICAL DEVELOPMENT J2 - MOL THER-METH CLIN D VL - 29 PY - 2023 SP - 145 EP - 159 PG - 15 SN - 2329-0501 DO - 10.1016/j.omtm.2023.03.003 UR - https://m2.mtmt.hu/api/publication/33708483 ID - 33708483 LA - English DB - MTMT ER - TY - JOUR AU - Sükösd, Farkas AU - Priskin, Katalin AU - Giricz, Zsófia AU - Mező, Béla AU - Pintér, Lajos AU - Pankotai, Tibor AU - Haracska, Lajos TI - Az újgenerációs szekvenáláson innen és túl: a tumorpanelek elemzéséből leszűrhető információk JF - KLINIKAI ONKOLÓGIA J2 - KLINIKAI ONKOLÓGIA VL - 9 PY - 2022 IS - Suppl.2 SP - 16 EP - 16 PG - 1 SN - 2064-5058 UR - https://m2.mtmt.hu/api/publication/33253071 ID - 33253071 LA - Hungarian DB - MTMT ER - TY - CHAP AU - Takács, Bertalan Vilmos AU - Gyuris, Zoltán AU - Pintér, Lajos AU - Visnyovszki, Ádám AU - Enyedi, Márton Zsolt AU - Hajdú, Edit AU - Haracska, Lajos ED - Bánfalvi, Zsófia ED - Gócza, Elen ED - Olasz, Ferenc ED - Pál, Magda ED - Posta, Katalin ED - Várallyay, Éva TI - UNDERSTANDING THE EFFECTS OF COVID-19 ON THE MICROBIOME USING BIOINFORMATICS AND MACHINE LEARNING T2 - „FIBOK 2022” : Fiatal Biotechnológusok V. Országos Konferenciája PB - Magyar Agrár- és Élettudományi Egyetem, Genetika és Biotechnológia Intézet CY - Gödöllő SN - 9789632699998 PY - 2022 UR - https://m2.mtmt.hu/api/publication/33089595 ID - 33089595 LA - English DB - MTMT ER - TY - JOUR AU - Qorri, Erda AU - Takács, Bertalan Vilmos AU - Gráf, Alexandra AU - Enyedi, Márton Zsolt AU - Pintér, Lajos AU - Kiss, Ernő AU - Haracska, Lajos TI - A Comprehensive Evaluation of the Performance of Prediction Algorithms on Clinically Relevant Missense Variants JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 23 PY - 2022 IS - 14 SN - 1661-6596 DO - 10.3390/ijms23147946 UR - https://m2.mtmt.hu/api/publication/33029933 ID - 33029933 N1 - Funding Agency and Grant Number: European Union [739593]; National Research, Development, and Innovation Office [TKP2021-EGA-09, RRF-2.3.1-21-2022-00015] Funding text: This project received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 739593. This work was also supported by the National Research, Development, and Innovation Office (TKP2021-EGA-09 and RRF-2.3.1-21-2022-00015). LA - English DB - MTMT ER - TY - JOUR AU - Fenteany, Gabriel AU - Sharma, Gaurav AU - Gaur, Paras AU - Borics, Attila AU - Wéber, Edit AU - Kiss, Ernő AU - Haracska, Lajos TI - A series of xanthenes inhibiting Rad6 function and Rad6–Rad18 interaction in the PCNA ubiquitination cascade JF - ISCIENCE J2 - ISCIENCE VL - 25 PY - 2022 IS - 4 PG - 23 SN - 2589-0042 DO - 10.1016/j.isci.2022.104053 UR - https://m2.mtmt.hu/api/publication/32746161 ID - 32746161 N1 - Funding Agency and Grant Number: E '.1-15-2017-00072; National Research, Development and Innovation OfficeNational Research, Development & Innovation Office (NRDIO) - Hungary [GINOP-2.3.2-15-2016-00024, GINOP-2.2.1-15-2017-00072]; European UnionEuropean Commission [739593] Funding text: We wish to acknowledge Tama ' sMartinek for sharing his expertise, as well as Katalin Kovacs, Katalin Konta ' r, and E ' va Hunyadi-Gulyas for their technical assistance and Gabriella Tick for proofreading the manuscript. We thank the US National Cancer Institute's Developmental Therapeutics Program for providing chemical libraries and individual compounds. This work was supported by the National Research, Development and Innovation Office (GINOP-2.3.2-15-2016-00024 and GINOP-2.2.1-15-2017-00072). This project has also received funding from the European Union's Horizon 2020 Research And Innovation Program under grant agreement No. 739593. AB - Ubiquitination of proliferating cell nuclear antigen (PCNA) triggers pathways of DNA damage tolerance, including mutagenic translesion DNA synthesis, and comprises a cascade of reactions involving the E1 ubiquitin-activating enzyme Uba1, the E2 ubiquitin-conjugating enzyme Rad6, and the E3 ubiquitin ligase Rad18. We report here the discovery of a series of xanthenes that inhibit PCNA ubiquitination, Rad6-ubiquitin thioester formation, and the Rad6-Rad18 interaction. Structure-activity relationship experiments across multiple assays reveal chemical and structural features important for different activities along the pathway to PCNA ubiquitination. The compounds that inhibit these processes are all a subset of the xanthen-3-ones we tested. These small molecules thus represent first-in-class probes of Rad6 function and the association of Rad6 and Rad18, the latter being a new inhibitory activity discovered for a small molecule, in the PCNA ubiquitination cascade and potential therapeutic agents to contain cancer progression. LA - English DB - MTMT ER - TY - JOUR AU - Tóth, Róbert AU - Balogh, Dávid AU - Pintér, Lajos AU - Jaksa, G. AU - Szeplaki, B. AU - Gráf, Alexandra AU - Győrfy, Zsuzsanna AU - Enyedi, Márton Zsolt AU - Kiss, Ernő AU - Haracska, Lajos AU - Unk, Ildikó TI - The Rad5 Helicase and RING Domains Contribute to Genome Stability through their Independent Catalytic Activities JF - JOURNAL OF MOLECULAR BIOLOGY J2 - J MOL BIOL VL - 434 PY - 2022 IS - 5 SN - 0022-2836 DO - 10.1016/j.jmb.2021.167437 UR - https://m2.mtmt.hu/api/publication/32606165 ID - 32606165 N1 - DNA Repair Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, H-6726, Hungary University of Szeged, Doctoral School of Biology, Hungary HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, H-6726, Hungary Delta Bio 2000 Ltd., Szeged, H-6726, Hungary Export Date: 21 January 2022 CODEN: JMOBA Correspondence Address: Unk, I.; Biological Research Centre, Temesvari krt. 62., Hungary; email: unk.ildiko@brc.hu AB - Genomic stability is compromised by DNA damage that obstructs replication. Rad5 plays a prominent role in DNA damage bypass processes that evolved to ensure the continuation of stalled replication. Like its human orthologs, the HLTF and SHPRH tumor suppressors, yeast Rad5 has a RING domain that supports ubiquitin ligase activity promoting PCNA polyubiquitylation and a helicase domain that in the case of HLTF and Rad5 was shown to exhibit an ATPase-linked replication fork reversal activity. The RING domain is embedded in the helicase domain, confusing their separate investigation and the understanding of the exact role of Rad5 in DNA damage bypass. Particularly, it is still debated whether the helicase domain plays a catalytic or a non-enzymatic role during error-free damage bypass and whether it facilitates a function separately from the RING domain. In this study, through in vivo and in vitro characterization of domain-specific mutants, we delineate the contributions of the two domains to Rad5 function. Yeast genetic experiments and whole-genome sequencing complemented with biochemical assays demonstrate that the ubiquitin ligase and the ATPase-linked activities of Rad5 exhibit independent catalytic activities in facilitating separate pathways during error-free lesion bypass. Our results also provide important insights into the mutagenic role of Rad5 and indicate its tripartite contribution to DNA damage tolerance. © 2021 The Author(s) LA - English DB - MTMT ER - TY - JOUR AU - Majoros, Hajnalka AU - Borsos, Barbara Nikolett AU - Újfaludi, Zsuzsanna AU - Páhi, Zoltán Gábor AU - Mórocz, Mónika AU - Haracska, Lajos AU - Boros, Imre Miklós AU - Pankotai, Tibor TI - SerpinB10, a Serine Protease Inhibitor, Is Implicated in UV-Induced Cellular Response JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 22 PY - 2021 IS - 16 PG - 13 SN - 1661-6596 DO - 10.3390/ijms22168500 UR - https://m2.mtmt.hu/api/publication/32164980 ID - 32164980 N1 - Institute of Pathology, Faculty of Medicine, University of Szeged, 1 Állomás utca, Szeged, H-6725, Hungary HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, H-6726, Hungary Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary Institute of Biochemistry, Biological Research Centre, Szeged, H-6726, Hungary Export Date: 31 August 2021 Correspondence Address: Pankotai, T.; Institute of Pathology, 1 Állomás utca, Hungary; email: pankotai.tibor@szte.hu Institute of Pathology, Faculty of Medicine, University of Szeged, 1 Állomás utca, Szeged, H-6725, Hungary HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, H-6726, Hungary Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary Institute of Biochemistry, Biological Research Centre, Szeged, H-6726, Hungary Export Date: 2 September 2021 Correspondence Address: Pankotai, T.; Institute of Pathology, 1 Állomás utca, Hungary; email: pankotai.tibor@szte.hu Funding Agency and Grant Number: National Research, Development and Innovation OfficeNational Research, Development & Innovation Office (NRDIO) - Hungary [GINOP-2.2.1-15-2017-00052, GINOP-2.3.2-15-2016-00024, GINOP-2.3.2-15-2016-00026, NKFI-FK 132080]; Janos Bolyai Research Scholarship of the Hungarian Academy of SciencesHungarian Academy of Sciences [BO/27/20, uNKP-20-5-SZTE-265]; EMBO short-term fellowshipEuropean Molecular Biology Organization (EMBO) [8513]; European UnionEuropean Commission [739593]; [NTP-NFTo-20-B-400] Funding text: We are grateful Vilmos Tubak for providing the Hker E6SFM cell line. This research was funded by National Research, Development and Innovation Office grant GINOP-2.2.1-15-2017-00052, GINOP-2.3.2-15-2016-00024, GINOP-2.3.2-15-2016-00026 and NKFI-FK 132080. T.P. was funded by National Research, Development and Innovation Office grant GINOP-2.2.1-15-2017-00052, the Janos Bolyai Research Scholarship of the Hungarian Academy of Sciences BO/27/20, uNKP-20-5-SZTE-265. H.M. was funded by NTP-NFTo-20-B-400. B.N.B. was funded by NKFI-FK 132080 and EMBO short-term fellowship 8513. H.L. was funded by European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No.: 739593. LA - English DB - MTMT ER -