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Barbour JA, Ou T, Yang H, Fang H, Yue NC, Zhu X, Wong-Brown MW, Wong YT, Bowden NA, Wu S, Wong JWH. ERCC2 mutations alter the genomic distribution pattern of somatic mutations and are independently prognostic in bladder cancer. CELL GENOMICS 2024; 4:100627. [PMID: 39096913 DOI: 10.1016/j.xgen.2024.100627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/17/2024] [Accepted: 07/10/2024] [Indexed: 08/05/2024]
Abstract
Excision repair cross-complementation group 2 (ERCC2) encodes the DNA helicase xeroderma pigmentosum group D, which functions in transcription and nucleotide excision repair. Point mutations in ERCC2 are putative drivers in around 10% of bladder cancers (BLCAs) and a potential positive biomarker for cisplatin therapy response. Nevertheless, the prognostic significance directly attributed to ERCC2 mutations and its pathogenic role in genome instability remain poorly understood. We first demonstrated that mutant ERCC2 is an independent predictor of prognosis in BLCA. We then examined its impact on the somatic mutational landscape using a cohort of ERCC2 wild-type (n = 343) and mutant (n = 39) BLCA whole genomes. The genome-wide distribution of somatic mutations is significantly altered in ERCC2 mutants, including T[C>T]N enrichment, altered replication time correlations, and CTCF-cohesin binding site mutation hotspots. We leverage these alterations to develop a machine learning model for predicting pathogenic ERCC2 mutations, which may be useful to inform treatment of patients with BLCA.
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Affiliation(s)
- Jayne A Barbour
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Ou
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Haocheng Yang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hu Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Institute of Biomedical Data, South China Hospital, Medical School, Shenzhen University, Shenzhen, China
| | - Noel C Yue
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoqiang Zhu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Michelle W Wong-Brown
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Yuen T Wong
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Nikola A Bowden
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Song Wu
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China; Department of Urology, South China Hospital, Medical School, Shenzhen University, Shenzhen, China.
| | - Jason W H Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China; Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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2
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The activity of yeast Apn2 AP endonuclease at uracil-derived AP sites is dependent on the major carbon source. Curr Genet 2021; 67:283-294. [PMID: 33386486 DOI: 10.1007/s00294-020-01141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/16/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Yeast Apn2 is an AP endonuclease and DNA 3'-diesterase that belongs to the Exo III family with homology to the E. coli exonuclease III, Schizosaccharomyces pombe eth1, and human AP endonucleases APEX1 and APEX2. In the absence of Apn1, the major AP endonuclease in yeast, Apn2 can cleave the DNA backbone at an AP lesion initiating the base excision repair pathway. To study the role and relative contribution of Apn2, we took advantage of a reporter system that was previously used to delineate how uracil-derived AP sites are repaired. At this reporter, disruption of the Apn1-initiated base excision repair pathway led to a significant elevation of A:T to C:G transversions. Here we show that such highly elevated A:T to C:G transversion mutations associated with uracil residues in DNA are abolished when apn1∆ yeast cells are grown in glucose as the primary carbon source. We also show that the disruption of Apn2, either by the complete gene deletion or by the mutation of a catalytic residue, results in a similarly reduced rate of the uracil-associated mutations. Overall, our results indicate that Apn2 activity is regulated by the glucose repression pathway in yeast.
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Singh S, Berroyer A, Kim M, Kim N. Yeast Nucleolin Nsr1 Impedes Replication and Elevates Genome Instability at an Actively Transcribed Guanine-Rich G4 DNA-Forming Sequence. Genetics 2020; 216:1023-1037. [PMID: 33106247 PMCID: PMC7768239 DOI: 10.1534/genetics.120.303736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/21/2020] [Indexed: 12/01/2022] Open
Abstract
A significant increase in genome instability is associated with the conformational shift of a guanine-run-containing DNA strand into the four-stranded G-quadruplex (G4) DNA. The mechanism underlying the recombination and genome rearrangements following the formation of G4 DNA in vivo has been difficult to elucidate but has become better clarified by the identification and functional characterization of several key G4 DNA-binding proteins. Mammalian nucleolin (NCL) is a highly specific G4 DNA-binding protein with a well-defined role in the transcriptional regulation of genes with associated G4 DNA-forming sequence motifs at their promoters. The consequence of the in vivo interaction between G4 DNA and nucleolin in respect to the genome instability has not been previously investigated. We show here that the yeast nucleolin Nsr1 is enriched at a G4 DNA-forming sequence in vivo and is a major factor in inducing the genome instability associated with the cotranscriptionally formed G4 DNA in the yeast genome. We also show that Nsr1 results in impeding replication past such a G4 DNA-forming sequence. The G4-associated genome instability and the G4 DNA-binding in vivo require the arginine-glycine-glycine (RGG) repeats located at the C-terminus of the Nsr1 protein. Nsr1 with the deletion of RGG domain supports normal cell growth and is sufficient for its pre-rRNA processing function. However, the truncation of the RGG domain of Nsr1 significantly weakens its interaction with G4 DNA in vivo and restores unhindered replication, overall resulting in a sharp reduction in the genome instability associated with a guanine-rich G4 DNA-forming sequence. Our data suggest that the interaction between Nsr1 with the intact RGG repeats and G4 DNA impairs genome stability by precluding the access of G4-resolving proteins and impeding replication.
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Affiliation(s)
- Shivani Singh
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Alexandra Berroyer
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Minseon Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030
- University of Texas (UT) Health MD Anderson Cancer Center Graduate School of Biomedical Sciences, Houston, Texas 77030
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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] [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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Cerritelli SM, El Hage A. RNases H1 and H2: guardians of the stability of the nuclear genome when supply of dNTPs is limiting for DNA synthesis. Curr Genet 2020; 66:1073-1084. [PMID: 32886170 DOI: 10.1007/s00294-020-01086-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 11/29/2022]
Abstract
RNA/DNA hybrids are processed by RNases H1 and H2, while single ribonucleoside-monophosphates (rNMPs) embedded in genomic DNA are removed by the error-free, RNase H2-dependent ribonucleotide excision repair (RER) pathway. In the absence of RER, however, topoisomerase 1 (Top1) can cleave single genomic rNMPs in a mutagenic manner. In RNase H2-deficient mice, the accumulation of genomic rNMPs above a threshold of tolerance leads to catastrophic genomic instability that causes embryonic lethality. In humans, deficiencies in RNase H2 induce the autoimmune disorders Aicardi-Goutières syndrome and systemic lupus erythematosus, and cause skin and intestinal cancers. Recently, we reported that in Saccharomyces cerevisiae, the depletion of Rnr1, the major catalytic subunit of ribonucleotide reductase (RNR), which converts ribonucleotides to deoxyribonucleotides, leads to cell lethality in absence of RNases H1 and H2. We hypothesized that under replicative stress and compromised DNA repair that are elicited by an insufficient supply of deoxyribonucleoside-triphosphates (dNTPs), cells cannot survive the accumulation of persistent RNA/DNA hybrids. Remarkably, we found that cells lacking RNase H2 accumulate ~ 5-fold more genomic rNMPs in absence than in presence of Rnr1. When the load of genomic rNMPs is further increased in the presence of a replicative DNA polymerase variant that over-incorporates rNMPs in leading or lagging strand, cells missing both Rnr1 and RNase H2 suffer from severe growth defects. These are reversed in absence of Top1. Thus, in cells lacking RNase H2 and containing a limiting supply of dNTPs, there is a threshold of tolerance for the accumulation of genomic ribonucleotides that is tightly associated with Top1-mediated DNA damage. In this mini-review, we describe the implications of the loss of RNase H2, or RNases H1 and H2, on the integrity of the nuclear genome and viability of budding yeast cells that are challenged with a critically low supply of dNTPs. We further propose that our findings in budding yeast could pave the way for the study of the potential role of mammalian RNR in RNase H2-related diseases.
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Affiliation(s)
- Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Aziz El Hage
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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Hulke ML, Massey DJ, Koren A. Genomic methods for measuring DNA replication dynamics. Chromosome Res 2020; 28:49-67. [PMID: 31848781 PMCID: PMC7131883 DOI: 10.1007/s10577-019-09624-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
Abstract
Genomic DNA replicates according to a defined temporal program in which early-replicating loci are associated with open chromatin, higher gene density, and increased gene expression levels, while late-replicating loci tend to be heterochromatic and show higher rates of genomic instability. The ability to measure DNA replication dynamics at genome scale has proven crucial for understanding the mechanisms and cellular consequences of DNA replication timing. Several methods, such as quantification of nucleotide analog incorporation and DNA copy number analyses, can accurately reconstruct the genomic replication timing profiles of various species and cell types. More recent developments have expanded the DNA replication genomic toolkit to assays that directly measure the activity of replication origins, while single-cell replication timing assays are beginning to reveal a new level of replication timing regulation. The combination of these methods, applied on a genomic scale and in multiple biological systems, promises to resolve many open questions and lead to a holistic understanding of how eukaryotic cells replicate their genomes accurately and efficiently.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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7
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Chon J, Field MS, Stover PJ. Deoxyuracil in DNA and disease: Genomic signal or managed situation? DNA Repair (Amst) 2019; 77:36-44. [PMID: 30875637 DOI: 10.1016/j.dnarep.2019.02.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 12/21/2022]
Abstract
Genomic instability is implicated in the etiology of several deleterious health outcomes including megaloblastic anemia, neural tube defects, and neurodegeneration. Uracil misincorporation and its repair are known to cause genomic instability by inducing DNA strand breaks leading to apoptosis, but there is emerging evidence that uracil incorporation may also result in broader modifications of gene expression, including: changes in transcriptional stalling, strand break-mediated transcriptional upregulation, and direct promoter inhibition. The factors that influence uracil levels in DNA are cytosine deamination, de novo thymidylate (dTMP) biosynthesis, salvage dTMP biosynthesis, dUTPase, and DNA repair. There is evidence that the nuclear localization of the enzymes in these pathways in mammalian cells may modify and/or control the levels of uracil accumulation into nuclear DNA. Uracil sequencing technologies demonstrate that uracil in DNA is not distributed stochastically across the genome, but instead shows patterns of enrichment. Nuclear localization of the enzymes that modify uracil in DNA may serve to change these patterns of enrichment in a tissue-specific manner, and thereby signal the genome in response to metabolic and/or nutritional state of the cell.
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Affiliation(s)
- James Chon
- Graduate Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Martha S Field
- Division of Nutritional Sciences, Cornell University, 127 Savage Hall, Ithaca, NY, 14853, USA
| | - Patrick J Stover
- Graduate Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, NY, 14853, USA; Division of Nutritional Sciences, Cornell University, 127 Savage Hall, Ithaca, NY, 14853, USA.
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The etiology of uracil residues in the Saccharomyces cerevisiae genomic DNA. Curr Genet 2018; 65:393-399. [PMID: 30328489 PMCID: PMC6420880 DOI: 10.1007/s00294-018-0895-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/11/2018] [Accepted: 10/13/2018] [Indexed: 11/29/2022]
Abstract
Non-canonical residue in DNA is a major and conserved source of genome instability. The appearance of uracil residues in DNA accompanies a significant mutagenic consequence and is regulated at multiple levels, from the concentration of available dUTP in the nucleotide pool to the excision repair for removal from DNA. Recently, an interesting phenomenon of transcription-associated elevation in uracil-derived mutations was described in Saccharomyces cerevisiae genome. While trying to understand the variability in mutagenesis, we uncovered that the frequency of uracil incorporation into DNA can vary depending on the transcription rate and that the non-replicative, repair-associated DNA synthesis underlies the higher uracil density of the actively transcribed genomic loci. This novel mechanism brings together the chemical vulnerability of DNA under transcription and the uracil-associated mutagenesis, and has the potential to apply to other non-canonical residues of mutagenic importance.
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