TY - JOUR AU - Lózsa, Rita Bernadett AU - Németh, Eszter AU - Gervai, Judit Zsuzsanna AU - Márkus, Bence Gábor AU - Kollarics, Sándor AU - Gyüre, Zsolt Tamás AU - Tóth, Judit AU - Simon, Ferenc AU - Szüts, Dávid TI - DNA mismatch repair protects the genome from oxygen-induced replicative mutagenesis JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 51 PY - 2023 IS - 20 SP - 11040 EP - 11055 PG - 16 SN - 0305-1048 DO - 10.1093/nar/gkad775 UR - https://m2.mtmt.hu/api/publication/34192915 ID - 34192915 AB - DNA mismatch repair (MMR) corrects mismatched DNA bases arising from multiple sources including polymerase errors and base damage. By detecting spontaneous mutagenesis using whole genome sequencing of cultured MMR deficient human cell lines, we show that a primary role of MMR is the repair of oxygen-induced mismatches. We found an approximately twofold higher mutation rate in MSH6 deficient DLD-1 cells or MHL1 deficient HCT116 cells exposed to atmospheric conditions as opposed to mild hypoxia, which correlated with oxidant levels measured using electron paramagnetic resonance spectroscopy. The oxygen-induced mutations were dominated by T to C base substitutions and single T deletions found primarily on the lagging strand. A broad sequence context preference, dependence on replication timing and a lack of transcriptional strand bias further suggested that oxygen-induced mutations arise from polymerase errors rather than oxidative base damage. We defined separate low and high oxygen-specific MMR deficiency mutation signatures common to the two cell lines and showed that the effect of oxygen is observable in MMR deficient cancer genomes, where it best correlates with the contribution of mutation signature SBS21. Our results imply that MMR corrects oxygen-induced genomic mismatches introduced by a replicative process in proliferating cells. Graphical Abstract LA - English DB - MTMT ER - TY - JOUR AU - Póti, Ádám AU - Szikriszt, Bernadett AU - Gervai, Judit Zsuzsanna AU - Chen, Dan AU - Szüts, Dávid TI - Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis JF - PLOS GENETICS J2 - PLOS GENET VL - 18 PY - 2022 IS - 2 SN - 1553-7390 DO - 10.1371/journal.pgen.1010051 UR - https://m2.mtmt.hu/api/publication/32679015 ID - 32679015 N1 - Export Date: 30 March 2022 Correspondence Address: Szüts, D.; Institute of Enzymology, Hungary; email: szuts.david@ttk.hu Funding details: FIEK_16-1-2016-0005, K_134779, PD_121381, VEKOP-2.3.3-15-2017-00014 Funding details: Magyar Tudományos Akadémia, MTA, LP2011-015 Funding text 1: This work was supported by the Hungarian Academy of Sciences (https://mta.hu) [Momentum Grant LP2011-015 to DS] and the National Research, Technology and Innovation Fund of Hungary (https://nkfih.gov.hu) [K_124881, K_134779, FIEK_16-1-2016-0005 and VEKOP-2.3.3-15-2017-00014 to DS, PD_121381 to BS and DS]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. LA - English DB - MTMT ER - TY - JOUR AU - Chen, Dan AU - Gervai, Judit Zsuzsanna AU - Póti, Ádám AU - Németh, Eszter AU - Szeltner, Zoltán AU - Szikriszt, Bernadett AU - Gyüre, Zsolt Tamás AU - Zámborszky, Judit AU - Ceccon, Marta AU - d’Adda di Fagagna, Fabrizio AU - Szállási, Zoltán AU - Richardson, Andrea L. AU - Szüts, Dávid TI - BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1 JF - NATURE COMMUNICATIONS J2 - NAT COMMUN VL - 13 PY - 2022 IS - 1 PG - 13 SN - 2041-1723 DO - 10.1038/s41467-021-27872-7 UR - https://m2.mtmt.hu/api/publication/32586615 ID - 32586615 N1 - These authors contributed equally: Dan Chen, Judit Z. Gervai. LA - English DB - MTMT ER - TY - JOUR AU - Németh, Eszter AU - Lovrics, Anna AU - Gervai, Judit Zsuzsanna AU - Seki, M. AU - Rospo, G. AU - Bardelli, A. AU - Szüts, Dávid TI - Two main mutational processes operate in the absence of DNA mismatch repair JF - DNA REPAIR J2 - DNA REPAIR VL - 89 PY - 2020 SN - 1568-7864 DO - 10.1016/j.dnarep.2020.102827 UR - https://m2.mtmt.hu/api/publication/31240665 ID - 31240665 N1 - Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary Department of Biochemistry, Tohoku Medical & Pharmaceutical University, Miyagi, 981-8558, Japan Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO 10060, Italy Department of Oncology, University of Turin, Candiolo, TO 10060, Italy Export Date: 13 March 2020 CODEN: DRNEA Correspondence Address: Szüts, D.; Research Centre for Natural Sciences, Magyar tudosok krt 2, Hungary; email: szuts.david@ttk.hu Funding details: 21091 Funding details: PD_124467, K_124881, FIEK_16-1-2016-0005 Funding details: Fondazione per la Ricerca Biomedica, FORB Funding details: 22795 Funding details: Ministero della Salute Funding details: Associazione Italiana per la Ricerca sul Cancro, AIRC, 21923 Funding text 1: This work was supported by the National Research, Development and Innovation Office of Hungary (FIEK_16-1-2016-0005 and K_124881 to DS, PD_124467 to AL). The research leading to these results has received funding from Fondazione AIRC under 5 per Mille 2018 - ID. 21091 program ? P.I. Bardelli Alberto, AIRC IG 2018 - ID. 21923 project - PI Bardelli Alberto; Progetto NET-2011-02352137 Ministero della Salute (AB); AIRC-CRUK-FC AECC Accelerator Award contract 22795 (AB); Fondazione Piemontese per la Ricerca sul Cancro-ONLUS 5 per mille 2014 e 2015 Ministero della Salute (AB); Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary Department of Biochemistry, Tohoku Medical & Pharmaceutical University, Miyagi, 981-8558, Japan Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO 10060, Italy Department of Oncology, University of Turin, Candiolo, TO 10060, Italy Export Date: 8 April 2020 CODEN: DRNEA Correspondence Address: Szüts, D.; Research Centre for Natural Sciences, Magyar tudosok krt 2, Hungary; email: szuts.david@ttk.hu Chemicals/CAS: DNA mismatch repair protein MSH2, 153700-72-2; MutL protein homolog 1, 155577-96-1 Funding details: PD_124467, K_124881, FIEK_16-1-2016-0005 Funding text 1: This work was supported by the National Research, Development and Innovation Office of Hungary ( FIEK_16-1-2016-0005 and K_124881 to DS, PD_124467 to AL). The research leading to these results has received funding from Fondazione AIRC under 5 per Mille 2018 - ID. 21091 program – P.I. Bardelli Alberto, AIRC IG 2018 - ID. 21923 project - PI Bardelli Alberto; Progetto NET-2011-02352137 Ministero della Salute (AB); AIRC-CRUK-FC AECC Accelerator Award contract 22795 (AB); Fondazione Piemontese per la Ricerca sul Cancro-ONLUS 5 per mille 2014 e 2015 Ministero della Salute (AB); Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary Department of Biochemistry, Tohoku Medical & Pharmaceutical University, Miyagi, 981-8558, Japan Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO 10060, Italy Department of Oncology, University of Turin, Candiolo, TO 10060, Italy Cited By :1 Export Date: 10 June 2020 CODEN: DRNEA Correspondence Address: Szüts, D.; Research Centre for Natural Sciences, Magyar tudosok krt 2, Hungary; email: szuts.david@ttk.hu Chemicals/CAS: DNA mismatch repair protein MSH2, 153700-72-2; MutL protein homolog 1, 155577-96-1 Funding details: PD_124467, K_124881, FIEK_16-1-2016-0005 Funding text 1: This work was supported by the National Research, Development and Innovation Office of Hungary ( FIEK_16-1-2016-0005 and K_124881 to DS, PD_124467 to AL). The research leading to these results has received funding from Fondazione AIRC under 5 per Mille 2018 - ID. 21091 program – P.I. Bardelli Alberto, AIRC IG 2018 - ID. 21923 project - PI Bardelli Alberto; Progetto NET-2011-02352137 Ministero della Salute (AB); AIRC-CRUK-FC AECC Accelerator Award contract 22795 (AB); Fondazione Piemontese per la Ricerca sul Cancro-ONLUS 5 per mille 2014 e 2015 Ministero della Salute (AB); AB - The analysis of tumour genome sequences has demonstrated high rates of base substitution mutagenesis upon the inactivation of DNA mismatch repair (MMR), and the resulting somatic mutations in MMR deficient tumours appear to significantly enhance the response to immune therapy. A handful of different algorithmically derived base substitution mutation signatures have been attributed to MMR deficiency in tumour somatic mutation datasets. In contrast, mutation data obtained from whole genome sequences of isogenic wild type and MMR deficient cell lines in this study, as well as from published sources, show a more uniform experimental mutation spectrum of MMR deficiency. In order to resolve this discrepancy, we reanalysed mutation data from MMR deficient tumour whole exome and whole genome sequences. We derived two base substitution signatures using non-negative matrix factorisation, which together adequately describe mutagenesis in all tumour and cell line samples. The two new signatures broadly resemble COSMIC signatures 6 and 20, but perform better than existing COSMIC signatures at identifying MMR deficient tumours in mutation signature deconstruction. We show that the contribution of the two identified signatures, one of which is dominated by C to T mutations at CpG sites, is biased by the different sequence composition of the exome and the whole genome. We further show that the identity of the inactivated MMR gene, the tissue type, the mutational burden or the patient's age does not influence the mutation spectrum, but that a tendency for a greater contribution by the CpG mutational process is observed in tumours as compared to cultured cells. Our analysis suggest that two separable mutational processes operate in the genomes of MMR deficient cells. © 2020 The Author(s) LA - English DB - MTMT ER - TY - THES AU - Gervai, Judit Zsuzsanna TI - A DNS-hibaelkerülő útvonalak szabályozásának genetikai vizsgálata PB - Eötvös Loránd Tudományegyetem (ELTE) PY - 2018 SP - 104 DO - 10.15476/ELTE.2017.136 UR - https://m2.mtmt.hu/api/publication/30414241 ID - 30414241 LA - Hungarian DB - MTMT ER - TY - JOUR AU - Gervai, Judit Zsuzsanna AU - Gálicza, J AU - Szeltner, Zoltán AU - Zámborszky, Judit AU - Szüts, Dávid TI - A genetic study based on PCNA-ubiquitin fusions reveals no requirement for PCNA polyubiquitylation in DNA damage tolerance JF - DNA REPAIR J2 - DNA REPAIR VL - 54 PY - 2017 SP - 46 EP - 54 PG - 9 SN - 1568-7864 DO - 10.1016/j.dnarep.2017.04.003 UR - https://m2.mtmt.hu/api/publication/3238612 ID - 3238612 N1 - Megjegyzés-26650701 N1 Funding details: LP2011-015, MTA, Magyar Tudományos Akadémia N1 Funding text: We thank Ádám Póti for his assistance in data processing, György Várady for help with flow cytometry, and Lajos Haracska for the HLTF cDNA. This study was supported by Momentum Grant LP2011-015 of the Hungarian Academy of Sciences. Megjegyzés-26650713 N1 Funding details: LP2011-015, MTA, Magyar Tudományos Akadémia N1 Funding text: We thank Ádám Póti for his assistance in data processing, György Várady for help with flow cytometry, and Lajos Haracska for the HLTF cDNA. This study was supported by Momentum Grant LP2011-015 of the Hungarian Academy of Sciences. Megjegyzés-26650736 N1 Funding details: LP2011-015, MTA, Magyar Tudományos Akadémia N1 Funding text: We thank Ádám Póti for his assistance in data processing, György Várady for help with flow cytometry, and Lajos Haracska for the HLTF cDNA. This study was supported by Momentum Grant LP2011-015 of the Hungarian Academy of Sciences. Megjegyzés-26650765 N1 Funding details: LP2011-015, MTA, Magyar Tudományos Akadémia N1 Funding text: We thank Ádám Póti for his assistance in data processing, György Várady for help with flow cytometry, and Lajos Haracska for the HLTF cDNA. This study was supported by Momentum Grant LP2011-015 of the Hungarian Academy of Sciences. AB - Post-translational modifications of Proliferating Cell Nuclear Antigen (PCNA) play a key role in regulating the bypass of DNA lesions during DNA replication. PCNA can be monoubiquitylated at lysine 164 by the RAD6-RAD18 ubiquitin ligase complex. Through this modification, PCNA can interact with low fidelity Y family DNA polymerases to promote translesion synthesis. Monoubiquitylated PCNA can be polyubiquitylated on lysine 63 of ubiquitin by a further ubiquitin-conjugating complex. This modification promotes a template switching bypass process in yeast, while its role in higher eukaryotes is less clear. We investigated the function of PCNA ubiquitylation using a PCNAK164R mutant DT40 chicken B lymphoblastoma cell line, which is hypersensitive to DNA damaging agents such as methyl methanesulfonate (MMS), cisplatin or ultraviolet radiation (UV) due to the loss of PCNA modifications. In the PCNAK164R mutant we also detected cell cycle arrest following UV treatment, a reduced rate of damage bypass through translesion DNA synthesis on synthetic UV photoproducts, and an increased rate of genomic mutagenesis following MMS treatment. PCNA-ubiquitin fusion proteins have been reported to mimic endogenous PCNA ubiquitylation. We found that the stable expression of a PCNAK164R-ubiquitin fusion protein fully or partially rescued the observed defects of the PCNAK164R mutant. The expression of a PCNAK164R-ubiquitinK63R fusion protein, on which the formation of lysine 63-linked polyubiquitin chains is not possible, similarly rescued the cell cycle arrest, DNA damage sensitivity, reduction of translesion synthesis and increase of MMS-induced genomic mutagenesis. Template switching bypass was not affected by the genetic elimination of PCNA polyubiquitylation, but it was reduced in the absence of the recombination proteins BRCA1 or XRCC3. Our study found no requirement for PCNA polyubiquitylation to protect cells from replication-stalling DNA damage. © 2017 Elsevier B.V. LA - English DB - MTMT ER - TY - JOUR AU - Zámborszky, Judit AU - Szikriszt, Bernadett AU - Gervai, Judit Zsuzsanna AU - Pipek, Orsolya Anna AU - Póti, Ádám AU - Krzystanek, M AU - Ribli, Dezső AU - Szalai-Gindl, János Márk AU - Csabai, István AU - Szállási, Zoltán AU - Swanton, C AU - Richardson, AL AU - Szüts, Dávid TI - Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions JF - ONCOGENE J2 - ONCOGENE VL - 36 PY - 2017 IS - 6 SP - 746 EP - 755 PG - 10 SN - 0950-9232 DO - 10.1038/onc.2016.243 UR - https://m2.mtmt.hu/api/publication/3118171 ID - 3118171 AB - Loss-of-function mutations in the BRCA1 and BRCA2 genes increase the risk of cancer. Owing to their function in homologous recombination repair, much research has focused on the unstable genomic phenotype of BRCA1/2 mutant cells manifest mainly as large-scale rearrangements. We used whole-genome sequencing of multiple isogenic chicken DT40 cell clones to precisely determine the consequences of BRCA1/2 loss on all types of genomic mutagenesis. Spontaneous base substitution mutation rates increased sevenfold upon the disruption of either BRCA1 or BRCA2, and the arising mutation spectra showed strong and specific correlation with a mutation signature associated with BRCA1/2 mutant tumours. To model endogenous alkylating damage, we determined the mutation spectrum caused by methyl methanesulfonate (MMS), and showed that MMS also induces more base substitution mutations in BRCA1/2-deficient cells. Spontaneously arising and MMS-induced insertion/deletion mutations and large rearrangements were also more common in BRCA1/2 mutant cells compared with the wild-type control. A difference in the short deletion phenotypes of BRCA1 and BRCA2 suggested distinct roles for the two proteins in the processing of DNA lesions, as BRCA2 mutants contained more short deletions, with a wider size distribution, which frequently showed microhomology near the breakpoints resembling repair by non-homologous end joining. An increased and prolonged gamma-H2AX signal in MMS-treated BRCA1/2 cells suggested an aberrant processing of stalled replication forks as the cause of increased mutagenesis. The high rate of base substitution mutagenesis demonstrated by our experiments is likely to significantly contribute to the oncogenic effect of the inactivation of BRCA1 or BRCA2.Oncogene advance online publication, 25 July 2016; doi:10.1038/onc.2016.243. © 2016 The Author(s) LA - English DB - MTMT ER - TY - JOUR AU - Calcutt, MJ AU - Szikriszt, Bernadett AU - Póti, Ádám AU - Molnár, János AU - Gervai, Judit Zsuzsanna AU - Tusnády, Gábor AU - Foecking, MF AU - Szüts, Dávid TI - Genome Sequence Analysis of Mycoplasma sp. HU2014, Isolated from Tissue Culture. JF - GENOME ANNOUNCEMENTS J2 - GENOME ANNOUNC VL - 3 PY - 2015 IS - 5 PG - 2 SN - 2169-8287 DO - 10.1128/genomeA.01086-15 UR - https://m2.mtmt.hu/api/publication/2944718 ID - 2944718 AB - The draft genome sequence of a novel Mycoplasma strain, designated Mycoplasma sp. HU2014, has been determined. The genome comprises 1,084,927 nucleotides and was obtained from a mycoplasma-infected culture of chicken DT40 cells. Phylogenetic analysis places this taxon in a group comprising the closely related species Mycoplasma yeatsii and Mycoplasma cottewii. LA - English DB - MTMT ER -