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Póti Á, Szüts D, Vermezovic J. Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa. Nucleic Acids Res 2024; 52:1779-1792. [PMID: 38180823 PMCID: PMC10899757 DOI: 10.1093/nar/gkad1250] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/07/2024] Open
Abstract
Planarians are organisms with a unique capacity to regenerate any part of their body. New tissues are generated in a process that requires many swift cell divisions. How costly is this process to an animal in terms of mutational load remains unknown. Using whole genome sequencing, we defined the mutational profile of the process of regeneration in the planarian species Schmidtea polychroa. We assembled de novo the genome of S. polychroa and analyzed mutations in animals that have undergone regeneration. We observed a threefold increase in the number of mutations and an altered mutational spectrum. High allele frequencies of subclonal mutations in regenerated animals suggested that most of the cells in the regenerated animal were descendants of a small number of stem cells with high expansion potential. We provide, for the first time, the draft genome assembly of S. polychroa, an estimation of the germline mutation rate for a planarian species and the mutational spectrum of the regeneration process of a living organism.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Jelena Vermezovic
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
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2
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Tordai C, Hathy E, Gyergyák H, Vincze K, Baradits M, Koller J, Póti Á, Jezsó B, Homolya L, Molnár MJ, Nagy L, Szüts D, Apáti Á, Réthelyi JM. Probing the biological consequences of a previously undescribed de novo mutation of ZMYND11 in a schizophrenia patient by CRISPR genome editing and induced pluripotent stem cell based in vitro disease-modeling. Schizophr Res 2024:S0920-9964(24)00024-0. [PMID: 38290943 DOI: 10.1016/j.schres.2024.01.024] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
BACKGROUND Schizophrenia (SCZ) is a severe neuropsychiatric disorder of complex, poorly understood etiology, associated with both genetic and environmental factors. De novo mutations (DNMs) represent a new source of genetic variation in SCZ, however, in most cases their biological significance remains unclear. We sought to investigate molecular disease pathways connected to DNMs in SCZ by combining human induced pluripotent stem cell (hiPSC) based disease modeling and CRISPR-based genome editing. METHODS We selected a SCZ case-parent trio with the case individual carrying a potentially disease causing 1495C > T nonsense DNM in the zinc finger MYND domain-containing protein 11 (ZMYND11), a gene implicated in biological processes relevant for SCZ. In the patient-derived hiPSC line the mutation was corrected using CRISPR, while monoallelic or biallelic frameshift mutations were introduced into a control hiPSC line. Isogenic cell lines were differentiated into hippocampal neuronal progenitor cells (NPCs) and functionally active dentate gyrus granule cells (DGGCs). Immunofluorescence microscopy and RNA sequencing were used to test for morphological and transcriptomic differences at NPC and DGCC stages. Functionality of neurons was investigated using calcium-imaging and multi-electrode array measurements. RESULTS Morphology in the mutant hippocampal NPCs and neurons was preserved, however, we detected significant transcriptomic and functional alterations. RNA sequencing showed massive upregulation of neuronal differentiation genes, and downregulation of cell adhesion genes. Decreased reactivity to glutamate was demonstrated by calcium-imaging. CONCLUSIONS Our findings lend support to the involvement of glutamatergic dysregulation in the pathogenesis of SCZ. This approach represents a powerful model system for precision psychiatry and pharmacological research.
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Affiliation(s)
- Csongor Tordai
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary; Molecular Psychiatry Research Group, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary
| | - Edit Hathy
- Molecular Psychiatry Research Group, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary
| | - Hella Gyergyák
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary
| | - Katalin Vincze
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary; Molecular Psychiatry Research Group, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary
| | - Máté Baradits
- Molecular Psychiatry Research Group, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary; Department of Psychiatry and Psychotherapy, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary
| | - Júlia Koller
- Molecular Psychiatry Research Group, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary; Institute of Genomic Medicine and Rare Disorders, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary
| | - Ádám Póti
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary
| | - Bálint Jezsó
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary; Doctoral School of Biology and Institute of Biology, Eötvös Loránd University, 1117 Budapest, Pázmány Péter sétány 1/c, Budapest, Hungary
| | - László Homolya
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary
| | - Mária Judit Molnár
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Egyetem tér 1, Debrecen, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary.
| | - Ágota Apáti
- Institute of Molecular Life Sciences, Research Center for Natural Sciences, 1117 Budapest, Magyar tudósok körútja 2, Budapest, Hungary.
| | - János M Réthelyi
- Molecular Psychiatry Research Group, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary; Department of Psychiatry and Psychotherapy, Semmelweis University, 1083 Budapest, Balassa utca 6, Budapest, Hungary.
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3
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Fekete F, Menus Á, Tóth K, Kiss ÁF, Minus A, Sirok D, Belič A, Póti Á, Csukly G, Monostory K. CYP1A2 expression rather than genotype is associated with olanzapine concentration in psychiatric patients. Sci Rep 2023; 13:18507. [PMID: 37898643 PMCID: PMC10613299 DOI: 10.1038/s41598-023-45752-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/23/2023] [Indexed: 10/30/2023] Open
Abstract
Olanzapine is a commonly prescribed atypical antipsychotic agent for treatment of patients with schizophrenia and bipolar disorders. Previous in vitro studies using human liver microsomes identified CYP1A2 and CYP2D6 enzymes being responsible for CYP-mediated metabolism of olanzapine. The present work focused on the impact of CYP1A2 and CYP2D6 genetic polymorphisms as well as of CYP1A2 metabolizing capacity influenced by non-genetic factors (sex, age, smoking) on olanzapine blood concentration in patients with psychiatric disorders (N = 139). CYP2D6 genotype-based phenotype appeared to have negligible contribution to olanzapine metabolism, whereas a dominant role of CYP1A2 in olanzapine exposure was confirmed. However, CYP1A2 expression rather than CYP1A2 genetic variability was demonstrated to be associated with olanzapine concentration in patients. Significant contribution of - 163C > A (rs762551), the most common SNP (single nucleotide polymorphism) in CYP1A2 gene, to enhanced inducibility was confirmed by an increase in CYP1A2 mRNA expression in smokers carrying - 163A, and smoking was found to have appreciable impact on olanzapine concentration normalized by the dose/bodyweight. Furthermore, patients' olanzapine exposure was in strong association with CYP1A2 expression; therefore, assaying CYP1A2 mRNA level in leukocytes can be an appropriate tool for the estimation of patients' olanzapine metabolizing capacity and may be relevant in optimizing olanzapine dosage.
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Affiliation(s)
- Ferenc Fekete
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
- Doctoral School of Biology and Institute of Biology, Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, 1117, Hungary
| | - Ádám Menus
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa 6, Budapest, 1082, Hungary
| | - Katalin Tóth
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Ádám Ferenc Kiss
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Annamária Minus
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Dávid Sirok
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
- Toxi-Coop Toxicological Research Center, Magyar jakobinusok 4/B, Budapest, 1122, Hungary
| | - Aleš Belič
- Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Menges, Slovenia
| | - Ádám Póti
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Gábor Csukly
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa 6, Budapest, 1082, Hungary
| | - Katalin Monostory
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary.
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Incze E, Mangó K, Fekete F, Kiss ÁF, Póti Á, Harkó T, Moldvay J, Szüts D, Monostory K. Potential Association of Cytochrome P450 Copy Number Alteration in Tumour with Chemotherapy Resistance in Lung Adenocarcinoma Patients. Int J Mol Sci 2023; 24:13380. [PMID: 37686184 PMCID: PMC10487787 DOI: 10.3390/ijms241713380] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
Resistance to anticancer agents is a major obstacle to efficacious tumour therapy and responsible for high cancer-related mortality rates. Some resistance mechanisms are associated with pharmacokinetic variability in anticancer drug exposure due to genetic polymorphisms of drug-metabolizing cytochrome P450 (CYP) enzymes, whereas variations in tumoural metabolism as a consequence of CYP copy number alterations are assumed to contribute to the selection of resistant cells. A high-throughput quantitative polymerase chain reaction (qPCR)-based method was developed for detection of CYP copy number alterations in tumours, and a scoring system improved the identification of inappropriate reference genes that underwent deletion/multiplication in tumours. The copy numbers of both the target (CYP2C8, CYP3A4) and the reference genes (ALB, B2M, BCKDHA, F5, CD36, MPO, TBP, RPPH1) established in primary lung adenocarcinoma by the qPCR-based method were congruent with those determined by next-generation sequencing (for 10 genes, slope = 0.9498, r2 = 0.72). In treatment naïve adenocarcinoma samples, the copy number multiplication of paclitaxel-metabolizing CYP2C8 and/or CYP3A4 was more prevalent in non-responder patients with progressive disease/exit than in responders with complete remission. The high-throughput qPCR-based method can become an alternative approach to next-generation sequencing in routine clinical practice, and identification of altered CYP copy numbers may provide a promising biomarker for therapy-resistant tumours.
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Affiliation(s)
- Evelyn Incze
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (E.I.); (K.M.); (F.F.); (Á.F.K.); (Á.P.); (D.S.)
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői 26, H-1085 Budapest, Hungary
| | - Katalin Mangó
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (E.I.); (K.M.); (F.F.); (Á.F.K.); (Á.P.); (D.S.)
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői 26, H-1085 Budapest, Hungary
| | - Ferenc Fekete
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (E.I.); (K.M.); (F.F.); (Á.F.K.); (Á.P.); (D.S.)
| | - Ádám Ferenc Kiss
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (E.I.); (K.M.); (F.F.); (Á.F.K.); (Á.P.); (D.S.)
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (E.I.); (K.M.); (F.F.); (Á.F.K.); (Á.P.); (D.S.)
| | - Tünde Harkó
- Department of Pathology, National Korányi Institute of Pulmonology, Pihenő 1, H-1121 Budapest, Hungary;
| | - Judit Moldvay
- 1st Department of Pulmonology, National Korányi Institute of Pulmonology, Pihenő 1, H-1121 Budapest, Hungary;
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (E.I.); (K.M.); (F.F.); (Á.F.K.); (Á.P.); (D.S.)
| | - Katalin Monostory
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (E.I.); (K.M.); (F.F.); (Á.F.K.); (Á.P.); (D.S.)
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5
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Gyüre Z, Póti Á, Németh E, Szikriszt B, Lózsa R, Krawczyk M, Richardson AL, Szüts D. Spontaneous mutagenesis in human cells is controlled by REV1-Polymerase ζ and PRIMPOL. Cell Rep 2023; 42:112887. [PMID: 37498746 DOI: 10.1016/j.celrep.2023.112887] [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: 03/17/2023] [Revised: 06/09/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Translesion DNA synthesis (TLS) facilitates replication over damaged or difficult-to-replicate templates by employing specialized DNA polymerases. We investigate the effect on spontaneous mutagenesis of three main TLS control mechanisms: REV1 and PCNA ubiquitylation that recruit TLS polymerases and PRIMPOL that creates post-replicative gaps. Using whole-genome sequencing of cultured human RPE-1 cell clones, we find that REV1 and Polymerase ζ are wholly responsible for one component of base substitution mutagenesis that resembles homologous recombination deficiency, whereas the remaining component that approximates oxidative mutagenesis is reduced in PRIMPOL-/- cells. Small deletions in short repeats appear in REV1-/-PCNAK164R/K164R double mutants, revealing an alternative TLS mechanism. Also, 500-5,000 bp deletions appear in REV1-/- and REV3L-/- mutants, and chromosomal instability is detectable in REV1-/-PRIMPOL-/- cells. Our results indicate that TLS protects the genome from deletions and large rearrangements at the expense of being responsible for the majority of spontaneous base substitutions.
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Affiliation(s)
- Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; Doctoral School of Molecular Medicine, Semmelweis University, 1085 Budapest, Hungary; Turbine Simulated Cell Technologies, 1027 Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Rita Lózsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Michał Krawczyk
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; National Laboratory for Drug Research and Development, 1117 Budapest, Hungary.
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6
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DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
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Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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7
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Póti Á, Szikriszt B, Gervai JZ, Chen D, Szüts D. Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis. PLoS Genet 2022; 18:e1010051. [PMID: 35130276 PMCID: PMC8870599 DOI: 10.1371/journal.pgen.1010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/06/2021] [Revised: 02/24/2022] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
Translesion DNA synthesis (TLS) is a fundamental damage bypass pathway that utilises specialised polymerases with relaxed template specificity to achieve replication through damaged DNA. Misinsertions by low fidelity TLS polymerases may introduce additional mutations on undamaged DNA near the original lesion site, which we termed collateral mutations. In this study, we used whole genome sequencing datasets of chicken DT40 and several human cell lines to obtain evidence for collateral mutagenesis in higher eukaryotes. We found that cisplatin and UVC radiation frequently induce close mutation pairs within 25 base pairs that consist of an adduct-associated primary and a downstream collateral mutation, and genetically linked their formation to TLS activity involving PCNA ubiquitylation and polymerase κ. PCNA ubiquitylation was also indispensable for close mutation pairs observed amongst spontaneously arising base substitutions in cell lines with disrupted homologous recombination. Collateral mutation pairs were also found in melanoma genomes with evidence of UV exposure. We showed that collateral mutations frequently copy the upstream base, and extracted a base substitution signature that describes collateral mutagenesis in the presented dataset regardless of the primary mutagenic process. Using this mutation signature, we showed that collateral mutagenesis creates approximately 10–20% of non-paired substitutions as well, underscoring the importance of the process. DNA base substitutions are the most common form of genomic mutations, formed both spontaneously and in response to environmental mutagens. One of the main mechanisms of base substitution mutagenesis is translesion synthesis, a process that relies on specialised DNA polymerases to replicate damaged DNA templates. In addition to incorrect base insertions at the site of lesions in the template, translesion polymerases may also generate ‘collateral’ mutations away from the lesion due to their lower accuracy in selecting the correct incoming nucleotide. In this study, we surveyed the whole genome sequence of experimental cell clones to examine the extent and genetic dependence of collateral mutagenesis in higher eukaryotes. Looking for close mutation pairs, we found that collateral mutations frequently occur near primary lesions generated by cisplatin or ultraviolet radiation in chicken and human cells, but are restricted to a short distance of approximately 25 base pairs. By analysing their sequence context, we showed that collateral mutations can also occur near correctly bypassed primary lesions and may be responsible for a considerable proportion of all base substitution mutations.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | | | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- * E-mail:
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8
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Chen D, Gervai JZ, Póti Á, Németh E, Szeltner Z, Szikriszt B, Gyüre Z, Zámborszky J, Ceccon M, d'Adda di Fagagna F, Szallasi Z, Richardson AL, Szüts D. BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1. Nat Commun 2022; 13:226. [PMID: 35017534 PMCID: PMC8752635 DOI: 10.1038/s41467-021-27872-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 04/15/2021] [Accepted: 12/15/2021] [Indexed: 12/25/2022] Open
Abstract
Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The inactivation of 53BP1 in BRCA1 mutant cells markedly reduces TLS-specific mutagenesis, and rescues the deficiency of template switch-mediated gene conversions in the immunoglobulin V locus of BRCA1 mutant chicken DT40 cells. 53BP1 also promotes TLS in human cellular extracts in vitro. Our results show that HR deficiency-specific mutagenesis is largely caused by TLS, and suggest a function for 53BP1 in regulating the choice between TLS and error-free template switching in replicative DNA damage bypass.
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Affiliation(s)
- Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Judit Z Gervai
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Zsolt Gyüre
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, Budapest, H-1085, Hungary
| | - Judit Zámborszky
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Marta Ceccon
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital and Harvard Medical School, Boston, MA, 02215, USA
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, H-1092, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, H-1117, Hungary.
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Pavani M, Bonaiuti P, Chiroli E, Gross F, Natali F, Macaluso F, Póti Á, Pasqualato S, Farkas Z, Pompei S, Cosentino Lagomarsino M, Rancati G, Szüts D, Ciliberto A. Epistasis, aneuploidy, and functional mutations underlie evolution of resistance to induced microtubule depolymerization. EMBO J 2021; 40:e108225. [PMID: 34605051 DOI: 10.15252/embj.2021108225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/10/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022] Open
Abstract
Cells with blocked microtubule polymerization are delayed in mitosis, but eventually manage to proliferate despite substantial chromosome missegregation. While several studies have analyzed the first cell division after microtubule depolymerization, we have asked how cells cope long-term with microtubule impairment. We allowed 24 clonal populations of yeast cells with beta-tubulin mutations preventing proper microtubule polymerization, to evolve for ˜150 generations. At the end of the laboratory evolution experiment, cells had regained the ability to form microtubules and were less sensitive to microtubule-depolymerizing drugs. Whole-genome sequencing identified recurrently mutated genes, in particular for tubulins and kinesins, as well as pervasive duplication of chromosome VIII. Recreating these mutations and chromosome VIII disomy prior to evolution confirmed that they allow cells to compensate for the original mutation in beta-tubulin. Most of the identified mutations did not abolish function, but rather restored microtubule functionality. Analysis of the temporal order of resistance development in independent populations repeatedly revealed the same series of events: disomy of chromosome VIII followed by a single additional adaptive mutation in either tubulins or kinesins. Since tubulins are highly conserved among eukaryotes, our results have implications for understanding resistance to microtubule-targeting drugs widely used in cancer therapy.
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Affiliation(s)
- Mattia Pavani
- IFOM, The Firc Institute of Molecular Oncology, Milano, Italy
| | - Paolo Bonaiuti
- IFOM, The Firc Institute of Molecular Oncology, Milano, Italy
| | - Elena Chiroli
- IFOM, The Firc Institute of Molecular Oncology, Milano, Italy
| | - Fridolin Gross
- IFOM, The Firc Institute of Molecular Oncology, Milano, Italy
| | - Federica Natali
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sebastiano Pasqualato
- IEO, European Institute of Oncology IRCCS, Milan, Italy.,Human Technopole, Milano, Italy
| | - Zoltán Farkas
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Simone Pompei
- IFOM, The Firc Institute of Molecular Oncology, Milano, Italy
| | | | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Andrea Ciliberto
- IFOM, The Firc Institute of Molecular Oncology, Milano, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy
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10
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Szikriszt B, Póti Á, Németh E, Kanu N, Swanton C, Szüts D. A comparative analysis of the mutagenicity of platinum-containing chemotherapeutic agents reveals direct and indirect mutagenic mechanisms. Mutagenesis 2021; 36:75-86. [PMID: 33502495 PMCID: PMC8081379 DOI: 10.1093/mutage/geab005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 10/20/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Platinum-based drugs are a mainstay of cancer chemotherapy. However, their mutagenic effect can increase tumour heterogeneity, contribute to the evolution of treatment resistance and also induce secondary malignancies. We coupled whole genome sequencing with phenotypic investigations on two cell line models to compare the magnitude and examine the mechanism of mutagenicity of cisplatin, carboplatin and oxaliplatin. Cisplatin induced significantly more base substitution mutations than carboplatin or oxaliplatin when used at equitoxic concentrations on human TK6 or chicken DT40 cells, and also induced the highest number of short insertions and deletions. The analysis of base substitution spectra revealed that all three tested platinum drugs elicit both a direct mutagenic effect at purine dinucleotides, and an indirect effect of accelerating endogenous mutagenic processes, whereas the direct mutagenic effect appeared to correlate with the level of DNA damage caused as assessed through histone H2AX phosphorylation and single-cell agarose gel electrophoresis, the indirect mutagenic effects were equal. The different mutagenicity and DNA-damaging effect of equitoxic platinum drug treatments suggest that DNA damage independent mechanisms significantly contribute to their cytotoxicity. Thus, the comparatively high mutagenicity of cisplatin should be taken into account in the design of chemotherapeutic regimens.
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Affiliation(s)
- Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nnennaya Kanu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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11
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Szeltner Z, Póti Á, Harami GM, Kovács M, Szüts D. Evaluation and modulation of DNA lesion bypass in an SV40 large T antigen-based in vitro replication system. FEBS Open Bio 2021; 11:1054-1075. [PMID: 33512058 PMCID: PMC8016126 DOI: 10.1002/2211-5463.13099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 11/09/2022] Open
Abstract
DNA damage removal by nucleotide excision repair (NER) and replicative bypass via translesion synthesis (TLS) and template switch (TSw) are important in ensuring genome stability. In this study, we tested the applicability of an SV40 large T antigen‐based replication system for the simultaneous examination of these damage tolerance processes. Using both Sanger and next‐generation sequencing combined with lesion‐specific qPCR and replication efficiency studies, we demonstrate that this system works well for studying NER and TLS, especially its one‐polymerase branch, while it is less suited to investigations of homology‐related repair processes, such as TSw. Cis‐syn cyclobutane pyrimidine dimer photoproducts were replicated with equal efficiency to lesion‐free plasmids in vitro, and the majority of TLS on this lesion could be inhibited by a peptide (PIR) specific for the polη‐PCNA interaction interface. TLS on 6–4 pyrimidine–pyrimidone photoproduct proved to be inefficient and was slightly facilitated by PIR as well as by a recombinant ubiquitin‐binding zinc finger domain of polη in HeLa extract, possibly by promoting polymerase exchange. Supplementation of the extract with recombinant PCNA variants indicated the dependence of TLS on PCNA ubiquitylation. In contrast to active TLS and NER, we found no evidence of successful TSw in cellular extracts. The established methods can promote in vitro investigations of replicative DNA damage bypass.
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Affiliation(s)
- Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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12
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Pálinkás HL, Békési A, Róna G, Pongor L, Papp G, Tihanyi G, Holub E, Póti Á, Gemma C, Ali S, Morten MJ, Rothenberg E, Pagano M, Szűts D, Győrffy B, Vértessy BG. Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments. eLife 2020; 9:e60498. [PMID: 32956035 PMCID: PMC7505663 DOI: 10.7554/elife.60498] [Citation(s) in RCA: 8] [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: 06/29/2020] [Accepted: 08/23/2020] [Indexed: 12/17/2022] Open
Abstract
Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell line models derived from HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards segments that are normally more active/functional. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can be applied to study the dynamic spatio-temporal nature of genomic uracil.
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Affiliation(s)
- Hajnalka L Pálinkás
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Doctoral School of Multidisciplinary Medical Science, University of SzegedSzegedHungary
| | - Angéla Békési
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Róna
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Lőrinc Pongor
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Gábor Papp
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Tihanyi
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Eszter Holub
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Ádám Póti
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Carolina Gemma
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Michael J Morten
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Dávid Szűts
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Balázs Győrffy
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Beáta G Vértessy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
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13
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Hámori L, Kudlik G, Szebényi K, Kucsma N, Szeder B, Póti Á, Uher F, Várady G, Szüts D, Tóvári J, Füredi A, Szakács G. Establishment and Characterization of a Brca1 -/-, p53 -/- Mouse Mammary Tumor Cell Line. Int J Mol Sci 2020; 21:ijms21041185. [PMID: 32053991 PMCID: PMC7072850 DOI: 10.3390/ijms21041185] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/25/2020] [Accepted: 02/01/2020] [Indexed: 12/15/2022] Open
Abstract
Breast cancer is the most commonly occurring cancer in women and the second most common cancer overall. By the age of 80, the estimated risk for breast cancer for women with germline BRCA1 or BRCA2 mutations is around 80%. Genetically engineered BRCA1-deficient mouse models offer a unique opportunity to study the pathogenesis and therapy of triple negative breast cancer. Here we present a newly established Brca1−/−, p53−/− mouse mammary tumor cell line, designated as CST. CST shows prominent features of BRCA1-mutated triple-negative breast cancers including increased motility, high proliferation rate, genome instability and sensitivity to platinum chemotherapy and PARP inhibitors (olaparib, veliparib, rucaparib and talazoparib). Genomic instability of CST cells was confirmed by whole genome sequencing, which also revealed the presence of COSMIC (Catalogue of Somatic Mutations in Cancer) mutation signatures 3 and 8 associated with homologous recombination (HR) deficiency. In vitro sensitivity of CST cells was tested against 11 chemotherapy agents. Tumors derived from orthotopically injected CST-mCherry cells in FVB-GFP mice showed sensitivity to cisplatin, providing a new model to study the cooperation of BRCA1-KO, mCherry-positive tumor cells and the GFP-expressing stromal compartment in therapy resistance and metastasis formation. In summary, we have established CST cells as a new model recapitulating major characteristics of BRCA1-negative breast cancers.
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Affiliation(s)
- Lilla Hámori
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
| | - Gyöngyi Kudlik
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
| | - Kornélia Szebényi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
- Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Nóra Kucsma
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
| | - Bálint Szeder
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
| | - Ferenc Uher
- Central Hospital of Southern Pest—National Institute of Hematology and Infectious Diseases, 1097 Budapest, Hungary;
| | - György Várady
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
| | - József Tóvári
- Department of Experimental Pharmacology, National Institute of Oncology, 1122, Budapest, Hungary;
| | - András Füredi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
- Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence: (A.F.); (G.S.)
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (L.H.); (G.K.); (K.S.); (N.K.); (B.S.); (Á.P.); (G.V.); (D.S.)
- Institute of Cancer Research, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence: (A.F.); (G.S.)
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14
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Póti Á, Gyergyák H, Németh E, Rusz O, Tóth S, Kovácsházi C, Chen D, Szikriszt B, Spisák S, Takeda S, Szakács G, Szallasi Z, Richardson AL, Szüts D. Correlation of homologous recombination deficiency induced mutational signatures with sensitivity to PARP inhibitors and cytotoxic agents. Genome Biol 2019; 20:240. [PMID: 31727117 PMCID: PMC6857305 DOI: 10.1186/s13059-019-1867-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [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: 05/07/2019] [Accepted: 10/28/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutations in further genes of the HR pathway or the DNA damage checkpoint also give rise to somatic mutation patterns that can be used for treatment prediction. RESULTS Using whole genome sequencing of an isogenic knockout cell line panel, we find a universal HR deficiency-specific base substitution signature that is similar to COSMIC signature 3. In contrast, we detect different deletion phenotypes corresponding to specific HR mutants. The inactivation of BRCA2 or PALB2 leads to larger deletions, typically with microhomology, when compared to the disruption of BRCA1, RAD51 paralogs, or RAD54. Comparison with the deletion spectrum of Cas9 cut sites suggests that most spontaneously arising genomic deletions are not the consequence of double-strand breaks. Surprisingly, the inactivation of checkpoint kinases ATM and CHK2 has no mutagenic consequences. Analysis of tumor exomes with biallelic inactivating mutations in the investigated genes confirms the validity of the cell line models. We present a comprehensive analysis of sensitivity of the investigated mutants to 13 therapeutic agents for the purpose of correlating genomic mutagenic phenotypes with drug sensitivity. CONCLUSION Our results suggest that no single genomic mutational class shows perfect correlation with sensitivity to common treatments, but the contribution of COSMIC signature 3 to base substitutions, or a combined measure of different features, may be reasonably good at predicting platinum and PARP inhibitor sensitivity.
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Affiliation(s)
- Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Hella Gyergyák
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Orsolya Rusz
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
- Department of Oncotherapy, University of Szeged, Szeged, Hungary
| | - Szilárd Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Csenger Kovácsházi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Dan Chen
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University Medical School, Kyoto, 606-8501, Japan
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary
- Institute of Cancer Research, Medical University Vienna, Vienna, Austria
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
- SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | | | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok krt 2, Budapest, H-1117, Hungary.
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15
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Pipek O, Ribli D, Molnár J, Póti Á, Krzystanek M, Bodor A, Tusnády GE, Szallasi Z, Csabai I, Szüts D. Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut. BMC Bioinformatics 2017; 18:73. [PMID: 28143617 PMCID: PMC5282906 DOI: 10.1186/s12859-017-1492-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 09/22/2016] [Accepted: 01/20/2017] [Indexed: 01/11/2023] Open
Abstract
Background Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. Methods Using 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. Results We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm. Conclusions IsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1492-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- O Pipek
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - D Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - J Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Á Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - M Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - A Bodor
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - G E Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Z Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark.,Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, MA, 02215, USA.,MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, H-1091, Budapest, Hungary
| | - I Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - D Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary.
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16
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Szikriszt B, Póti Á, Pipek O, Krzystanek M, Kanu N, Molnár J, Ribli D, Szeltner Z, Tusnády GE, Csabai I, Szallasi Z, Swanton C, Szüts D. A comprehensive survey of the mutagenic impact of common cancer cytotoxics. Genome Biol 2016; 17:99. [PMID: 27161042 PMCID: PMC4862131 DOI: 10.1186/s13059-016-0963-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [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: 12/02/2015] [Accepted: 04/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic mutations caused by cytotoxic agents used in cancer chemotherapy may cause secondary malignancies as well as contribute to the evolution of treatment-resistant tumour cells. The stable diploid genome of the chicken DT40 lymphoblast cell line, an established DNA repair model system, is well suited to accurately assay genomic mutations. RESULTS We use whole genome sequencing of multiple DT40 clones to determine the mutagenic effect of eight common cytotoxics used for the treatment of millions of patients worldwide. We determine the spontaneous mutagenesis rate at 2.3 × 10(-10) per base per cell division and find that cisplatin, cyclophosphamide and etoposide induce extra base substitutions with distinct spectra. After four cycles of exposure, cisplatin induces 0.8 mutations per Mb, equivalent to the median mutational burden in common leukaemias. Cisplatin-induced mutations, including short insertions and deletions, are mainly located at sites of putative intrastrand crosslinks. We find two of the newly defined cisplatin-specific mutation types as causes of the reversion of BRCA2 mutations in emerging cisplatin-resistant tumours or cell clones. Gemcitabine, 5-fluorouracil, hydroxyurea, doxorubicin and paclitaxel have no measurable mutagenic effect. The cisplatin-induced mutation spectrum shows good correlation with cancer mutation signatures attributed to smoking and other sources of guanine-directed base damage. CONCLUSION This study provides support for the use of cell line mutagenesis assays to validate or predict the mutagenic effect of environmental and iatrogenic exposures. Our results suggest genetic reversion due to cisplatin-induced mutations as a distinct mechanism for developing resistance.
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Affiliation(s)
- Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Orsolya Pipek
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Marcin Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Nnennaya Kanu
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - János Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Dezső Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Gábor E Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800, Lyngby, Denmark.
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, 02215, USA.
- MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, 1091, Budapest, Hungary.
| | - Charles Swanton
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK.
- Francis Crick Institute, 44 Lincoln's Inn Fields, London, WCA2 3PX, UK.
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary.
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Daru J, Benda Z, Póti Á, Novák Z, Stirling A. Mechanistic Study of Silver-Mediated Furan Formation by Oxidative Coupling. Chemistry 2014; 20:15395-400. [DOI: 10.1002/chem.201404302] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 01/25/2023]
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Molnár J, Póti Á, Pipek O, Krzystanek M, Kanu N, Swanton C, Tusnády GE, Szallasi Z, Csabai I, Szüts D. The genome of the chicken DT40 bursal lymphoma cell line. G3 (Bethesda) 2014; 4:2231-40. [PMID: 25227228 PMCID: PMC4232548 DOI: 10.1534/g3.114.013482] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/08/2014] [Indexed: 01/23/2023]
Abstract
The chicken DT40 cell line is a widely used model system in the study of multiple cellular processes due to the efficiency of homologous gene targeting. The cell line was derived from a bursal lymphoma induced by avian leukosis virus infection. In this study we characterized the genome of the cell line using whole genome shotgun sequencing and single nucleotide polymorphism array hybridization. The results indicate that wild-type DT40 has a relatively normal karyotype, except for whole chromosome copy number gains, and no karyotype variability within stocks. In a comparison to two domestic chicken genomes and the Gallus gallus reference genome, we found no unique mutational processes shaping the DT40 genome except for a mild increase in insertion and deletion events, particularly deletions at tandem repeats. We mapped coding sequence mutations that are unique to the DT40 genome; mutations inactivating the PIK3R1 and ATRX genes likely contributed to the oncogenic transformation. In addition to a known avian leukosis virus integration in the MYC gene, we detected further integration sites that are likely to de-regulate gene expression. The new findings support the hypothesis that DT40 is a typical transformed cell line with a relatively intact genome; therefore, it is well-suited to the role of a model system for DNA repair and related processes. The sequence data generated by this study, including a searchable de novo genome assembly and annotated lists of mutated genes, will support future research using this cell line.
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Affiliation(s)
- János Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Orsolya Pipek
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Marcin Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Nnennaya Kanu
- Cancer Research UK London Research Institute, London, WCA2 3PX, United Kingdom
| | - Charles Swanton
- Cancer Research UK London Research Institute, London, WCA2 3PX, United Kingdom
| | - Gábor E Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark Children's Hospital Informatics Program at the Harvard-Massachusetts Institutes of Technology Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, MA 02115
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
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