1
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Zhang Y, Ostrowski SM, Fisher DE. Nevi and Melanoma. Hematol Oncol Clin North Am 2024; 38:939-952. [PMID: 38880666 PMCID: PMC11368644 DOI: 10.1016/j.hoc.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Cutaneous melanoma is an aggressive form of skin cancer derived from skin melanocytes and is associated with significant morbidity and mortality. A significant fraction of melanomas are associated with precursor lesions, benign clonal proliferations of melanocytes called nevi. Nevi can be either congenital or acquired later in life. Identical oncogenic driver mutations are found in benign nevi and melanoma. While much progress has been made in our understanding of nevus formation and the molecular steps required for transformation of nevi into melanoma, the clinical diagnosis of benign versus malignant lesions remains challenging.
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Affiliation(s)
- Yifan Zhang
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA; Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephen M Ostrowski
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA; Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David E Fisher
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA; Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA.
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2
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Pfeifer GP, Jin SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet 2024:10.1038/s41576-024-00748-4. [PMID: 38918545 DOI: 10.1038/s41576-024-00748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
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3
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Laughery MF, Wilson HE, Sewell A, Stevison S, Wyrick JJ. The Surprising Diversity of UV-Induced Mutations. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300205. [PMID: 38884048 PMCID: PMC11170076 DOI: 10.1002/ggn2.202300205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/22/2024] [Indexed: 06/18/2024]
Abstract
Ultraviolet (UV) light is the most pervasive environmental mutagen and the primary cause of skin cancer. Genome sequencing of melanomas and other skin cancers has revealed that the vast majority of somatic mutations in these tumors are cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which, together with tandem CC>TT substitutions, comprise the canonical UV mutation "signature". These mutation classes are caused by DNA damage directly induced by UV absorption, namely cyclobutane pyrimidine dimers (CPDs) or 6-4 pyrimidine-pyrimidone photoproducts (6-4PP), which form between neighboring pyrimidine bases. However, many of the key driver mutations in melanoma do not fit this mutation signature, but instead are caused by T>A, T>C, C>A, or AC>TT substitutions, frequently occurring in non-dipyrimidine sequence contexts. This article describes recent studies indicating that UV light causes a more diverse spectrum of mutations than previously appreciated, including many of the mutation classes observed in melanoma driver mutations. Potential mechanisms for these diverse mutation signatures are discussed, including UV-induced pyrimidine-purine photoproducts and indirect DNA damage induced by UVA light. Finally, the article reviews recent findings indicating that human DNA polymerase eta normally suppresses these non-canonical UV mutation classes, which can potentially explain why canonical C>T substitutions predominate in human skin cancers.
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Affiliation(s)
- Marian F Laughery
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - Hannah E Wilson
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - Allysa Sewell
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - Scott Stevison
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
| | - John J Wyrick
- School of Molecular Biosciences Washington State University Pullman WA 99164 USA
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4
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Ginno PA, Borgers H, Ernst C, Schneider A, Behm M, Aitken SJ, Taylor MS, Odom DT. Single-mitosis dissection of acute and chronic DNA mutagenesis and repair. Nat Genet 2024; 56:913-924. [PMID: 38627597 PMCID: PMC11096113 DOI: 10.1038/s41588-024-01712-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 03/08/2024] [Indexed: 04/24/2024]
Abstract
How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, during single mitoses and at single-strand resolution. To distinguish between chronic (reactive oxygen species (ROS)) and acute (ultraviolet light (UV)) mutagenesis, we microfluidically separate pairs of sister cells from the first mitosis following burst UV damage. Strikingly, UV mutations manifest as sister-specific events, revealing mirror-image mutation phasing genome-wide. In contrast, ROS mutagenesis in transcribed regions is reduced strand agnostically. Successive rounds of genome replication over persisting UV damage drives multiallelic variation at CC dinucleotides. Finally, we show that mutation phasing can be resolved to single strands across the entire genome of liver tumors from F1 mice. This strategy can be broadly used to distinguish the contributions of overlapping cancer relevant mutational processes.
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Affiliation(s)
- Paul Adrian Ginno
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Helena Borgers
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Christina Ernst
- Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anja Schneider
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Mikaela Behm
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | - Sarah J Aitken
- Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Duncan T Odom
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany.
- Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK.
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5
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Menck CFM, Galhardo RS, Quinet A. The accurate bypass of pyrimidine dimers by DNA polymerase eta contributes to ultraviolet-induced mutagenesis. Mutat Res 2024; 828:111840. [PMID: 37984186 DOI: 10.1016/j.mrfmmm.2023.111840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023]
Abstract
Human xeroderma pigmentosum variant (XP-V) patients are mutated in the POLH gene, responsible for encoding the translesion synthesis (TLS) DNA polymerase eta (Pol eta). These patients suffer from a high frequency of skin tumors. Despite several decades of research, studies on Pol eta still offer an intriguing paradox: How does this error-prone polymerase suppress mutations? This review examines recent evidence suggesting that cyclobutane pyrimidine dimers (CPDs) are instructional for Pol eta. Consequently, it can accurately replicate these lesions, and the mutagenic effects induced by UV radiation stem from the deamination of C-containing CPDs. In this model, the deamination of C (forming a U) within CPDs leads to the correct insertion of an A opposite to the deaminated C (or U)-containing dimers. This intricate process results in C>T transitions, which represent the most prevalent mutations detected in skin cancers. Finally, the delayed replication in XP-V cells amplifies the process of C-deamination in CPDs and increases the burden of C>T mutations prevalent in XP-V tumors through the activity of backup TLS polymerases.
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Affiliation(s)
- C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil.
| | - R S Galhardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - A Quinet
- Université Paris Cité, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France; Université Paris-Saclay, Inserm, CEA, Stabilité Génétique Cellules Souches et Radiations, LRS/iRCM/IBFJ, F-92265 Fontenay-aux-Roses, France
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6
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Cohen Y, Adar S. Novel insights into bulky DNA damage formation and nucleotide excision repair from high-resolution genomics. DNA Repair (Amst) 2023; 130:103549. [PMID: 37566959 DOI: 10.1016/j.dnarep.2023.103549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
DNA damages compromise cell function and fate. Cells of all organisms activate a global DNA damage response that includes a signaling stress response, activation of checkpoints, and recruitment of repair enzymes. Especially deleterious are bulky, helix-distorting damages that block transcription and replication. Due to their miscoding nature, these damages lead to mutations and cancer. In human cells, bulky DNA damages are repaired by nucleotide excision repair (NER). To date, the basic mechanism of NER in naked DNA is well defined. Still, there is a fundamental gap in our understanding of how repair is orchestrated despite the packaging of DNA in chromatin, and how it is coordinated with active transcription and replication. The last decade has brought forth huge advances in our ability to detect and assay bulky DNA damages and their repair at single nucleotide resolution across the human genome. Here we review recent findings on the effect of chromatin and DNA-binding proteins on the formation of bulky DNA damages, and novel insights on NER, provided by the recent application of genomic methods.
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Affiliation(s)
- Yuval Cohen
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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7
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Laughery MF, Plummer DA, Wilson HE, Vandenberg BN, Mitchell D, Mieczkowski PA, Roberts SA, Wyrick JJ. Genome-wide maps of UVA and UVB mutagenesis in yeast reveal distinct causative lesions and mutational strand asymmetries. Genetics 2023; 224:iyad086. [PMID: 37170598 PMCID: PMC10324949 DOI: 10.1093/genetics/iyad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
Ultraviolet (UV) light primarily causes C > T substitutions in lesion-forming dipyrimidine sequences. However, many of the key driver mutations in melanoma do not fit this canonical UV signature, but are instead caused by T > A, T > C, or C > A substitutions. To what extent exposure to the UVB or UVA spectrum of sunlight can induce these noncanonical mutation classes, and the molecular mechanism involved is unclear. Here, we repeatedly exposed wild-type or repair-deficient yeast (Saccharomyces cerevisiae) to UVB or UVA light and characterized the resulting mutations by whole genome sequencing. Our data indicate that UVB induces C > T and T > C substitutions in dipyrimidines, and T > A substitutions that are often associated with thymine-adenine (TA) sequences. All of these mutation classes are induced in nucleotide excision repair-deficient cells and show transcriptional strand asymmetry, suggesting they are caused by helix-distorting UV photoproducts. In contrast, UVA exposure induces orders of magnitude fewer mutations with a distinct mutation spectrum. UVA-induced mutations are elevated in Ogg1-deficient cells, and the resulting spectrum consists almost entirely of C > A/G > T mutations, indicating they are likely derived from oxidative guanine lesions. These mutations show replication asymmetry, with elevated G > T mutations on the leading strand, suggesting there is a strand bias in the removal or bypass of guanine lesions during replication. Finally, we develop a mutation reporter to show that UVA induces a G > T reversion mutation in yeast that mimics the oncogenic NRAS Q61K mutation in melanoma. Taken together, these findings indicate that UVA and UVB exposure can induce many of the noncanonical mutation classes that cause driver mutations in melanoma.
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Affiliation(s)
- Marian F Laughery
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Hannah E Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Brittany N Vandenberg
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Debra Mitchell
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
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8
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Yurchenko AA, Rajabi F, Braz-Petta T, Fassihi H, Lehmann A, Nishigori C, Wang J, Padioleau I, Gunbin K, Panunzi L, Morice-Picard F, Laplante P, Robert C, Kannouche PL, Menck CFM, Sarasin A, Nikolaev SI. Genomic mutation landscape of skin cancers from DNA repair-deficient xeroderma pigmentosum patients. Nat Commun 2023; 14:2561. [PMID: 37142601 PMCID: PMC10160032 DOI: 10.1038/s41467-023-38311-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Xeroderma pigmentosum (XP) is a genetic disorder caused by mutations in genes of the Nucleotide Excision Repair (NER) pathway (groups A-G) or in Translesion Synthesis DNA polymerase η (V). XP is associated with an increased skin cancer risk, reaching, for some groups, several thousand-fold compared to the general population. Here, we analyze 38 skin cancer genomes from five XP groups. We find that the activity of NER determines heterogeneity of the mutation rates across skin cancer genomes and that transcription-coupled NER extends beyond the gene boundaries reducing the intergenic mutation rate. Mutational profile in XP-V tumors and experiments with POLH knockout cell line reveal the role of polymerase η in the error-free bypass of (i) rare TpG and TpA DNA lesions, (ii) 3' nucleotides in pyrimidine dimers, and (iii) TpT photodimers. Our study unravels the genetic basis of skin cancer risk in XP and provides insights into the mechanisms reducing UV-induced mutagenesis in the general population.
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Affiliation(s)
- Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Fatemeh Rajabi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Tirzah Braz-Petta
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, s/n, Natal, 59078-970, Brazil
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, Department of Photodermatology, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London, SE1 7EH, UK
| | - Alan Lehmann
- National Xeroderma Pigmentosum Service, Department of Photodermatology, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London, SE1 7EH, UK
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Jinxin Wang
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Ismael Padioleau
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Konstantin Gunbin
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Leonardo Panunzi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | | | - Pierre Laplante
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
- Department of Medical Oncology, Gustave Roussy and Paris-Saclay University, Villejuif, France
| | - Patricia L Kannouche
- CNRS UMR9019 Genome Integrity and Cancers, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Carlos F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Alain Sarasin
- CNRS UMR9019 Genome Integrity and Cancers, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Sergey I Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France.
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9
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Vandenberg BN, Laughery MF, Cordero C, Plummer D, Mitchell D, Kreyenhagen J, Albaqshi F, Brown AJ, Mieczkowski PA, Wyrick JJ, Roberts SA. Contributions of replicative and translesion DNA polymerases to mutagenic bypass of canonical and atypical UV photoproducts. Nat Commun 2023; 14:2576. [PMID: 37142570 PMCID: PMC10160025 DOI: 10.1038/s41467-023-38255-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
UV exposure induces a mutation signature of C > T substitutions at dipyrimidines in skin cancers. We recently identified additional UV-induced AC > TT and A > T substitutions that could respectively cause BRAF V600K and V600E oncogenic mutations. The mutagenic bypass mechanism past these atypical lesions, however, is unknown. Here, we whole genome sequenced UV-irradiated yeast and used reversion reporters to delineate the roles of replicative and translesion DNA polymerases in mutagenic bypass of UV-lesions. Our data indicates that yeast DNA polymerase eta (pol η) has varied impact on UV-induced mutations: protecting against C > T substitutions, promoting T > C and AC > TT substitutions, and not impacting A > T substitutions. Surprisingly, deletion rad30Δ increased novel UV-induced C > A substitutions at CA dinucleotides. In contrast, DNA polymerases zeta (pol ζ) and epsilon (pol ε) participated in AC > TT and A > T mutations. These results uncover lesion-specific accurate and mutagenic bypass of UV lesions, which likely contribute to key driver mutations in melanoma.
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Affiliation(s)
- Brittany N Vandenberg
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Marian F Laughery
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Cameron Cordero
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Dalton Plummer
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Debra Mitchell
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Jordan Kreyenhagen
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Fatimah Albaqshi
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Alexander J Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - John J Wyrick
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
| | - Steven A Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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10
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Bohm KA, Morledge-Hampton B, Stevison S, Mao P, Roberts SA, Wyrick JJ. Genome-wide maps of rare and atypical UV photoproducts reveal distinct patterns of damage formation and mutagenesis in yeast chromatin. Proc Natl Acad Sci U S A 2023; 120:e2216907120. [PMID: 36853943 PMCID: PMC10013872 DOI: 10.1073/pnas.2216907120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
Ultraviolet (UV) light induces different classes of mutagenic photoproducts in DNA, namely cyclobutane pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and atypical thymine-adenine photoproducts (TA-PPs). CPD formation is modulated by nucleosomes and transcription factors (TFs), which has important ramifications for Ultraviolet (UV) mutagenesis. How chromatin affects the formation of 6-4PPs and TA-PPs is unclear. Here, we use UV damage endonuclease-sequencing (UVDE-seq) to map these UV photoproducts across the yeast genome. Our results indicate that nucleosomes, the fundamental building block of chromatin, have opposing effects on photoproduct formation. Nucleosomes induce CPDs and 6-4PPs at outward rotational settings in nucleosomal DNA but suppress TA-PPs at these settings. Our data also indicate that DNA binding by different classes of yeast TFs causes lesion-specific hotspots of 6-4PPs or TA-PPs. For example, DNA binding by the TF Rap1 generally suppresses CPD and 6-4PP formation but induces a TA-PP hotspot. Finally, we show that 6-4PP formation is strongly induced at the binding sites of TATA-binding protein (TBP), which is correlated with higher mutation rates in UV-exposed yeast. These results indicate that the formation of 6-4PPs and TA-PPs is modulated by chromatin differently than CPDs and that this may have important implications for UV mutagenesis.
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Affiliation(s)
- Kaitlynne A. Bohm
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
| | | | - Scott Stevison
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM87131
| | - Steven A. Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
- Center for Reproductive Biology, Washington State University, Pullman, WA99164
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
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11
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Bohm KA, Wyrick JJ. Damage mapping techniques and the light they have shed on canonical and atypical UV photoproducts. Front Genet 2023; 13:1102593. [PMID: 36704334 PMCID: PMC9871259 DOI: 10.3389/fgene.2022.1102593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Ultraviolet (UV) light is a pervasive threat to the DNA of terrestrial organisms. UV light induces helix-distorting DNA lesions, primarily cyclobutane pyrimidine dimers (CPDs) that form between neighboring pyrimidine bases. Unrepaired CPD lesions cause cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which is the predominant mutation class in skin cancer genomes. However, many driver mutations in melanoma (e.g., in the BRAF and NRAS oncogenes) do not fit this UV mutation signature. Recent studies have brought to light the intriguing hypothesis that these driver mutations may be induced by infrequent or atypical UV photoproducts, including pyrimidine 6-4 pyrimidone photoproducts (6-4PP) and thymine-adenine (TA) photoproducts. Here, we review innovative methods for mapping both canonical and atypical UV-induced photoproducts across the genome.
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Affiliation(s)
- Kaitlynne A. Bohm
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
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12
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Pecorelli A, Valacchi G. Oxidative-Stress-Sensitive microRNAs in UV-Promoted Development of Melanoma. Cancers (Basel) 2022; 14:3224. [PMID: 35804995 PMCID: PMC9265047 DOI: 10.3390/cancers14133224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/23/2022] Open
Abstract
Melanoma is the most aggressive and life-threatening form of skin cancer. Key molecular events underlying the melanocytic transformation into malignant melanoma mainly involve gene mutations in which exposure to ultraviolet (UV) radiation plays a prominent role. However, several aspects of UV-induced melanomagenesis remain to be explored. Interestingly, redox-mediated signaling and perturbed microRNA (miRNA) profiles appear to be interconnected contributing factors able to act synergistically in melanoma initiation and progression. Since UV radiation can promote both redox imbalance and miRNA dysregulation, a harmful crosstalk between these two key cellular networks, with UV as central hub among them, is likely to occur in skin tissue. Therefore, decoding the complex circuits that orchestrate the interaction of UV exposure, oxidative stress, and dysregulated miRNA profiling can provide a deep understanding of the molecular basis of the melanomagenesis process. Furthermore, these mechanistic insights into the reciprocal regulation between these systems could have relevant implications for future therapeutic approaches aimed at counteracting UV-induced redox and miRNome imbalances for the prevention and treatment of malignant melanoma. In this review, we illustrate current information on the intricate connection between UV-induced dysregulation of redox-sensitive miRNAs and well-known signaling pathways involved in the malignant transformation of normal melanocytes to malignant melanoma.
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Affiliation(s)
- Alessandra Pecorelli
- Department of Animal Science, N.C. Research Campus, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA;
| | - Giuseppe Valacchi
- Department of Animal Science, N.C. Research Campus, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA;
- Department of Environment and Prevention, University of Ferrara, 44121 Ferrara, Italy
- Department of Food and Nutrition, Kyung Hee University, Seoul 02447, Korea
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13
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Bohm KA, Sivapragasam S, Wyrick JJ. Mapping atypical UV photoproducts in vitro and across the S. cerevisiae genome. STAR Protoc 2022; 3:101059. [PMID: 35005641 PMCID: PMC8715331 DOI: 10.1016/j.xpro.2021.101059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Exposure to ultraviolet (UV) light induces DNA damage, predominantly cyclobutane pyrimidine dimers (CPD) and 6,4-photoproducts (6,4-PP), as well as rare, atypical photoproducts at thymidine-adenine (TA) sequences. We have recently shown 'TA' photoproducts are induced in UV-irradiated oligonucleotides and across the budding yeast genome. Here, we describe a protocol for mapping atypical 'TA' photoproducts in vitro and in vivo. This protocol overcomes the technical challenges involved in accurately mapping such rare photoproducts by using ultraviolet damage endonuclease (UVDE) enzymes. For complete details on the use and execution of this protocol, please refer to Laughery et al. (2020).
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Affiliation(s)
- Kaitlynne A Bohm
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.,Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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14
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Sivapragasam S, Stark B, Albrecht AV, Bohm KA, Mao P, Emehiser RG, Roberts SA, Hrdlicka PJ, Poon GMK, Wyrick JJ. CTCF binding modulates UV damage formation to promote mutation hot spots in melanoma. EMBO J 2021; 40:e107795. [PMID: 34487363 DOI: 10.15252/embj.2021107795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 12/29/2022] Open
Abstract
Somatic mutations in DNA-binding sites for CCCTC-binding factor (CTCF) are significantly elevated in many cancers. Prior analysis has suggested that elevated mutation rates at CTCF-binding sites in skin cancers are a consequence of the CTCF-cohesin complex inhibiting repair of UV damage. Here, we show that CTCF binding modulates the formation of UV damage to induce mutation hot spots. Analysis of genome-wide CPD-seq data in UV-irradiated human cells indicates that formation of UV-induced cyclobutane pyrimidine dimers (CPDs) is primarily suppressed by CTCF binding but elevated at specific locations within the CTCF motif. Locations of CPD hot spots in the CTCF-binding motif coincide with mutation hot spots in melanoma. A similar pattern of damage formation is observed at CTCF-binding sites in vitro, indicating that UV damage modulation is a direct consequence of CTCF binding. We show that CTCF interacts with binding sites containing UV damage and inhibits repair by a model repair enzyme in vitro. Structural analysis and molecular dynamic simulations reveal the molecular mechanism for how CTCF binding modulates CPD formation.
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Affiliation(s)
- Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Bastian Stark
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | | | - Kaitlynne A Bohm
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA.,Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA
| | | | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | | | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA.,Center for Reproductive Biology, Washington State University, Pullman, WA, USA
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15
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Jin SG, Pettinga D, Johnson J, Li P, Pfeifer GP. The major mechanism of melanoma mutations is based on deamination of cytosine in pyrimidine dimers as determined by circle damage sequencing. SCIENCE ADVANCES 2021; 7:eabi6508. [PMID: 34330711 PMCID: PMC8324051 DOI: 10.1126/sciadv.abi6508] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/14/2021] [Indexed: 05/22/2023]
Abstract
Sunlight-associated melanomas carry a unique C-to-T mutation signature. UVB radiation induces cyclobutane pyrimidine dimers (CPDs) as the major form of DNA damage, but the mechanism of how CPDs cause mutations is unclear. To map CPDs at single-base resolution genome wide, we developed the circle damage sequencing (circle-damage-seq) method. In human cells, CPDs form preferentially in a tetranucleotide sequence context (5'-Py-T<>Py-T/A), but this alone does not explain the tumor mutation patterns. To test whether mutations arise at CPDs by cytosine deamination, we specifically mapped UVB-induced cytosine-deaminated CPDs. Transcription start sites (TSSs) were protected from CPDs and deaminated CPDs, but both lesions were enriched immediately upstream of the TSS, suggesting a mutation-promoting role of bound transcription factors. Most importantly, the genomic dinucleotide and trinucleotide sequence specificity of deaminated CPDs matched the prominent mutation signature of melanomas. Our data identify the cytosine-deaminated CPD as the leading premutagenic lesion responsible for mutations in melanomas.
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Affiliation(s)
- Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Dean Pettinga
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peipei Li
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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16
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Duan M, Speer RM, Ulibarri J, Liu KJ, Mao P. Transcription-coupled nucleotide excision repair: New insights revealed by genomic approaches. DNA Repair (Amst) 2021; 103:103126. [PMID: 33894524 DOI: 10.1016/j.dnarep.2021.103126] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/29/2021] [Accepted: 04/12/2021] [Indexed: 01/13/2023]
Abstract
Elongation of RNA polymerase II (Pol II) is affected by many factors including DNA damage. Bulky damage, such as lesions caused by ultraviolet (UV) radiation, arrests Pol II and inhibits gene transcription, and may lead to genome instability and cell death. Cells activate transcription-coupled nucleotide excision repair (TC-NER) to remove Pol II-impeding damage and allow transcription resumption. TC-NER initiation in humans is mediated by Cockayne syndrome group B (CSB) protein, which binds to the stalled Pol II and promotes assembly of the repair machinery. Given the complex nature of the TC-NER pathway and its unique function at the interface between transcription and repair, new approaches are required to gain in-depth understanding of the mechanism. Advances in genomic approaches provide an important opportunity to investigate how TC-NER is initiated upon damage-induced Pol II stalling and what factors are involved in this process. In this Review, we discuss new mechanisms of TC-NER revealed by genome-wide DNA damage mapping and new TC-NER factors identified by high-throughput screening. As TC-NER conducts strand-specific repair of mutagenic damage, we also discuss how this repair pathway causes mutational strand asymmetry in the cancer genome.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Rachel M Speer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jenna Ulibarri
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA.
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