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Longan ER, Fay JC. The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597243. [PMID: 38895255 PMCID: PMC11185594 DOI: 10.1101/2024.06.03.597243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Domesticated strains of Saccharomyces cerevisiae have adapted to resist copper and sulfite, two chemical stressors commonly used in winemaking. S. paradoxus, has not adapted to these chemicals despite being consistently present in sympatry with S. cerevisiae in vineyards. This contrast represents a case of apparent evolutionary constraints favoring greater adaptive capacity in S. cerevisiae. In this study, we used a comparative mutagenesis approach to test whether S. paradoxus is mutationally constrained with respect to acquiring greater copper and sulfite resistance. For both species, we assayed the rate, effect size, and pleiotropic costs of resistance mutations and sequenced a subset of 150 mutants isolated from our screen. We found that the distributions of mutational effects displayed by the two species were very similar and poorly explained the natural pattern. We also found that chromosome VIII aneuploidy and loss of function mutations in PMA1 confer copper resistance in both species, whereas loss of function mutations in REG1 were only a viable route to copper resistance in S. cerevisiae. We also observed a single de novo duplication of the CUP1 gene in S. paradoxus but none in S. cerevisiae. For sulfite, loss of function mutations in RTS1 and KSP1 confer resistance in both species, but mutations in RTS1 have larger average effects in S. paradoxus. Our results show that even when the distributions of mutational effects are largely similar, species can differ in the adaptive paths available to them. They also demonstrate that assays of the distribution of mutational effects may lack predictive insight concerning adaptive outcomes.
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Affiliation(s)
- Emery R. Longan
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
| | - Justin C. Fay
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
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2
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Gillet N, Dumont E, Bignon E. DNA damage and repair in the nucleosome: insights from computational methods. Biophys Rev 2024; 16:345-356. [PMID: 39099841 PMCID: PMC11297232 DOI: 10.1007/s12551-024-01183-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/05/2024] [Indexed: 08/06/2024] Open
Abstract
Cellular DNA is constantly exposed to endogenous or exogenous factors that can induce lesions. Several types of lesions have been described that can result from UV/ionizing irradiations, oxidative stress, or free radicals, among others. In order to overcome the deleterious effects of such damages, i.e., mutagenicity or cytotoxicity, cells possess a highly complex DNA repair machinery, involving repair enzymes targeting specific types of lesions through dedicated cellular pathways. In addition, DNA is highly compacted in the nucleus, the first level of compaction consisting of ~ 147 DNA base pairs wrapped around a core of histones, the so-called nucleosome core particle. In this complex environment, the DNA structure is highly constrained, and fine-tuned mechanisms involving remodeling processes are required to expose the DNA to repair enzymes and to facilitate the damage removal. However, these nucleosome-specific mechanisms remain poorly understood, and computational methods emerged only recently as powerful tools to investigate DNA damages in such complex systems as the nucleosome. In this mini-review, we summarize the latest advances brought out by computational approaches in the field, opening new exciting perspectives for the study of DNA damage and repair in the nucleosome context.
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Affiliation(s)
- Natacha Gillet
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, 69342 Lyon, France
| | - Elise Dumont
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, CNRS, 06108 Nice, France
- Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
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3
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Heffron J, Samsami M, Juedemann S, Lavin J, Tavakoli Nick S, Kieke BA, Mayer BK. Mitigation of viruses of concern and bacteriophage surrogates via common unit processes for water reuse: A meta-analysis. WATER RESEARCH 2024; 252:121242. [PMID: 38342066 DOI: 10.1016/j.watres.2024.121242] [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: 12/01/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
Water reuse is a growing global reality. In regulating water reuse, viruses have come to the fore as key pathogens due to high shedding rates, low infectious doses, and resilience to traditional wastewater treatments. To demonstrate the high log reductions required by emerging water reuse regulations, cost and practicality necessitate surrogates for viruses for use as challenge organisms in unit process evaluation and monitoring. Bacteriophage surrogates that are mitigated to the same or lesser extent than viruses of concern are routinely used for individual unit process testing. However, the behavior of these surrogates over a multi-barrier treatment train typical of water reuse has not been well-established. Toward this aim, we performed a meta-analysis of log reductions of common bacteriophage surrogates for five treatment processes typical of water reuse treatment trains: advanced oxidation processes, chlorination, membrane filtration, ozonation, and ultraviolet (UV) disinfection. Robust linear regression was applied to identify a range of doses consistent with a given log reduction of bacteriophages and viruses of concern for each treatment process. The results were used to determine relative conservatism of surrogates. We found that no one bacteriophage was a representative or conservative surrogate for viruses of concern across all multi-barrier treatments (encompassing multiple mechanisms of virus mitigation). Rather, a suite of bacteriophage surrogates provides both a representative range of inactivation and information about the effectiveness of individual processes within a treatment train. Based on the abundance of available data and diversity of virus treatability using these five key water reuse treatment processes, bacteriophages MS2, phiX174, and Qbeta were recommended as a core suite of surrogates for virus challenge testing.
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Affiliation(s)
- Joe Heffron
- U.S. Department of Agriculture-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Dr., Marshfield, WI 54449, USA.
| | - Maryam Samsami
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA
| | - Samantha Juedemann
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA
| | - Jennifer Lavin
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA
| | - Shadi Tavakoli Nick
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA
| | - Burney A Kieke
- Marshfield Clinic Research Institute, Center for Clinical Epidemiology and Population Health, 1000 N Oak Ave., Marshfield, WI 54449, USA
| | - Brooke K Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 West Wisconsin Avenue, Milwaukee, WI 53233, USA
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4
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Jiang D, Yang G, Huang LJ, Chen K, Tang Y, Pi X, Yang R, Peng X, Cui C, Li N. Unveiling the toxic effects, physiological responses and molecular mechanisms of tobacco (Nicotiana tabacum) in exposure to organic ultraviolet filters. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133060. [PMID: 38016314 DOI: 10.1016/j.jhazmat.2023.133060] [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: 08/22/2023] [Revised: 10/17/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023]
Abstract
Exposure to organic ultraviolet (UV) filters has raised concerns due to their potential adverse effects on environments. However, their toxic mechanisms on plants remain elusive. In this study, using integrative physiological and transcriptomic approaches we investigated the physiological and molecular responses to three representative UV filters, namely oxybenzone (OBZ), avobenzone (AVB), and octinoxate (OMC), in an agricultural model plant tobacco. The exposure to UV filters disrupts the functionality of photosystem reaction centers and the light-harvesting apparatus. Concurrently, UV filters exert a suppressive effect on the expression of genes encoding Rubisco and Calvin-Benson cycle enzymes, resulting in a decreased efficiency of the Calvin-Benson cycle and consequently hampering the process of photosynthesis. Exposure to UV filters leads to significant generation of reactive oxygen species within tobacco leaves and downregulation of oxidoreductase activities. Moreover, UV filters promote abscisic acid (ABA) accumulation by inducing the expression of ABA biosynthesis genes whereas repress indole-3-acetic acid (IAA) biosynthesis gene expression, which induce leaf yellowing and slow plant growth. In summary, the organic UV filters exert toxic effects on tobacco growth by inhibiting chlorophyll synthesis, photosynthesis, and the Calvin-Benson cycle, while generating excessive reactive oxygen species. This study sheds light on the toxic and tolerance mechanisms of UV filters in agricultural crops.
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Affiliation(s)
- Dong Jiang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Guoqun Yang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Li-Jun Huang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Kebin Chen
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Yangcan Tang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
| | - Xin Pi
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Runke Yang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Xia Peng
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Chuantong Cui
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China.
| | - Ning Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Central South University of Forestry and Technology, Changsha, China; Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China.
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5
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Fu I, Geacintov NE, Broyde S. Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase. Nucleic Acids Res 2023; 51:12261-12274. [PMID: 37933861 PMCID: PMC10711554 DOI: 10.1093/nar/gkad974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
Ultraviolet light generates cyclobutane pyrimidine dimer (CPD) and pyrimidine 6-4 pyrimidone (6-4PP) photoproducts that cause skin malignancies if not repaired by nucleotide excision repair (NER). While the faster repair of the more distorting 6-4PPs is attributed mainly to more efficient recognition by XPC, the XPD lesion verification helicase may play a role, as it directly scans the damaged DNA strand. With extensive molecular dynamics simulations of XPD-bound single-strand DNA containing each lesion outside the entry pore of XPD, we elucidate strikingly different verification processes for these two lesions that have very different topologies. The open book-like CPD thymines are sterically blocked from pore entry and preferably entrapped by sensors that are outside the pore; however, the near-perpendicular 6-4PP thymines can enter, accompanied by a displacement of the Arch domain toward the lesion, which is thereby tightly accommodated within the pore. This trapped 6-4PP may inhibit XPD helicase activity to foster lesion verification by locking the Arch to other domains. Furthermore, the movement of the Arch domain, only in the case of 6-4PP, may trigger signaling to the XPG nuclease for subsequent lesion incision by fostering direct contact between the Arch domain and XPG, and thereby facilitating repair of 6-4PP.
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Affiliation(s)
- Iwen Fu
- Department of Biology, New York University, 24 Waverly Place, 6th Floor, New York, NY 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- Department of Biology, New York University, 24 Waverly Place, 6th Floor, New York, NY 10003, USA
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6
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Smerdon MJ, Wyrick JJ, Delaney S. A half century of exploring DNA excision repair in chromatin. J Biol Chem 2023; 299:105118. [PMID: 37527775 PMCID: PMC10498010 DOI: 10.1016/j.jbc.2023.105118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
DNA in eukaryotic cells is packaged into the compact and dynamic structure of chromatin. This packaging is a double-edged sword for DNA repair and genomic stability. Chromatin restricts the access of repair proteins to DNA lesions embedded in nucleosomes and higher order chromatin structures. However, chromatin also serves as a signaling platform in which post-translational modifications of histones and other chromatin-bound proteins promote lesion recognition and repair. Similarly, chromatin modulates the formation of DNA damage, promoting or suppressing lesion formation depending on the chromatin context. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potentially mutagenic and carcinogenic lesions in DNA. Here, we survey many of the landmark findings on DNA damage and repair in chromatin over the last 50 years (i.e., since the beginning of this field), focusing on excision repair, the first repair mechanism studied in the chromatin landscape. For example, we highlight how the impact of chromatin on these processes explains the distinct patterns of somatic mutations observed in cancer genomes.
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Affiliation(s)
- Michael J Smerdon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - John J Wyrick
- Genetics and Cell Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
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MOLINA-CARRILLO L, Bassaglia Y, Schires G, BONNAUD-PONTICELLI L. Does the egg capsule protect against chronic UV-B radiation? A study based on encapsulated and decapsulated embryos of cuttlefish Sepia officinalis. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230602. [PMID: 37476507 PMCID: PMC10354468 DOI: 10.1098/rsos.230602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
Although the egg capsule plays a crucial role in the embryonic development of cephalopods, its ability to protect embryos from Ultraviolet (UV) radiation is unknown. Our study evaluated the photoprotection mechanisms of S. officinalis to UV-B radiation and estimated the ability of the black capsule to act as a physical shield against it. Embryos with and without capsule and juveniles were exposed to four experimental UVB conditions for 55 days. The effects of different UVB doses were evaluated in terms of morphological abnormalities and differences in gene expression between each group. We observed that the development might be severely impaired in embryos exposed to UVB without capsule protection, and these effects were time- and UVB-dose-dependent. In addition, we found variations in gene expression levels (light-sensitive, stress response and DNA repair) in different tissues as a function of UVB doses. We suggest a relationship between morphological abnormalities and the limit of molecular regulation. These results suggest that the quantitative differences in expression are essential for defining the survivability of the embryo face to UVB. Thus, we demonstrated that the egg capsule could ensure successful embryonic development of the cuttlefish S. officinalis even at high doses of UVB.
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Affiliation(s)
- Luis MOLINA-CARRILLO
- UMR Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d'Histoire Naturelle, CNRS 8067, Sorbonne Université, Paris, France
| | - Yann Bassaglia
- UMR Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d'Histoire Naturelle, CNRS 8067, Sorbonne Université, Paris, France
- Université Paris Est Créteil-Val de Marne (UPEC), France
| | - Gaëtan Schires
- Station Biologique de Roscoff, FR2424, CNRS-Sorbonne Université, Roscoff 29682, France
| | - Laure BONNAUD-PONTICELLI
- UMR Biologie des Organismes et Ecosystèmes Aquatiques, Muséum National d'Histoire Naturelle, CNRS 8067, Sorbonne Université, Paris, France
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8
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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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9
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George S, Cassidy RN, Saintilnord WN, Fondufe-Mittendorf Y. Epigenomic reprogramming in iAs-mediated carcinogenesis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 96:319-365. [PMID: 36858778 DOI: 10.1016/bs.apha.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Arsenic is a naturally occurring metal carcinogen found in the Earth's crust. Millions of people worldwide are chronically exposed to arsenic through drinking water and food. Exposure to inorganic arsenic has been implicated in many diseases ranging from acute toxicities to malignant transformations. Despite the well-known deleterious health effects of arsenic exposure, the molecular mechanisms in arsenic-mediated carcinogenesis are not fully understood. Since arsenic is non-mutagenic, the mechanism by which arsenic causes carcinogenesis is via alterations in epigenetic-regulated gene expression. There are two possible ways by which arsenic may modify the epigenome-indirectly through an arsenic-induced generation of reactive oxygen species which then impacts chromatin remodelers, or directly through interaction and modulation of chromatin remodelers. Whether directly or indirectly, arsenic modulates epigenetic gene regulation and our understanding of the direct effect of this modulation on chromatin structure is limited. In this chapter we will discuss the various ways by which inorganic arsenic affects the epigenome with consequences in health and disease.
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Affiliation(s)
- Smitha George
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Richard N Cassidy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Wesley N Saintilnord
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
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10
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BmNPV Orf 65 (Bm65) Is Identified as an Endonuclease Directly Facilitating UV-Induced DNA Damage Repair. J Virol 2022; 96:e0055722. [PMID: 35862702 PMCID: PMC9327686 DOI: 10.1128/jvi.00557-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Baculoviruses have been used as biopesticides for the control of Lepidoptera larvae. However, solar UV radiation reduces the activity of baculovirus. In this study, an UV endonuclease, Bm65, was found encoded in the genome of Bombyx mori nuclear polyhedrosis virus (BmNPV). Bm65 (the ortholog of AcMNPV orf79) was guided by a key nuclear localization signal to enter the nucleus and accumulated at UV-induced DNA damage sites. Subsequent results further showed that Bm65-mediated DNA damage repair was not the only UV damage repair pathway of BmNPV. BmNPV also used host DNA repair proteins to repair UV-induced DNA damage. In summary, these results revealed that Bm65 was very important in UV-induced DNA damage repair of BmNPV, and BmNPV repaired UV-damaged DNA through a variety of ways. IMPORTANCE Baculovirus biopesticides are environmentally friendly insecticides and specifically infect invertebrates. UV radiation from the sunlight greatly reduces the activity of baculovirus biopesticides. However, the molecular mechanisms of most baculoviruses to repair UV-induced DNA damage remain unclear. Nucleotide excision repair (NER) is a major DNA repair pathway that removes UV-induced DNA lesions. At present, there are few reports about the nucleotide excision repair pathway in viruses. Here, we showed for the first time that the baculovirus Bm65 endonuclease actually cleaved UV-damaged DNA. Meanwhile, we found that BmNPV used both viral-encoded enzymes and host DNA damage repair proteins to reverse UV-induced DNA damage. These results will provide a reference for the research of UV damage repair of other viruses.
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11
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Lin Y, Cao Z, Lyu T, Kong T, Zhang Q, Wu K, Wang Y, Zheng J. Single-cell RNA-seq of UVB-radiated skin reveals landscape of photoaging-related inflammation and protection by vitamin D. Gene 2022; 831:146563. [PMID: 35577040 DOI: 10.1016/j.gene.2022.146563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/14/2022] [Accepted: 05/06/2022] [Indexed: 12/20/2022]
Abstract
Ultraviolet rays are a potential threat to nature. It can accelerate skin aging by causing skin damage, cell infiltration, and inflammation. The present study investigated UV-irradiated mouse skin through single-cell sequencing. We observed that UV-irradiated mouse skin mainly induced inflammation of fibroblasts and demonstrated differential gene expression. Cell prediction revealed the significance of macrophages in tissue repair. Furthermore, cell culture studies substantiated vitamin D-induced inhibitory effect on skin inflammation. These findings thus indicate some references for skin photo-protection.
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Affiliation(s)
- Yuanbin Lin
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo 315300, PR China; School of Materials Science and Engineering, Shanghai University, Shanghai 200444, PR China
| | - Zhanglei Cao
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo 315300, PR China
| | - Tianqi Lyu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo 315300, PR China
| | - Tong Kong
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo 315300, PR China
| | - Qian Zhang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo 315300, PR China
| | - Kerong Wu
- Translational Research Laboratory for Urology, Department of Urology, Ningbo First Hospital, Ningbo, Zhejiang 315000, PR China.
| | - Yuhui Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo 315300, PR China.
| | - Jianping Zheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo 315300, PR China.
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12
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Fu I, Mu H, Geacintov NE, Broyde S. Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair. Nucleic Acids Res 2022; 50:6837-6853. [PMID: 35713557 PMCID: PMC9262607 DOI: 10.1093/nar/gkac496] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 01/19/2023] Open
Abstract
In nucleotide excision repair (NER), the xeroderma pigmentosum D helicase (XPD) scans DNA searching for bulky lesions, stalls when encountering such damage to verify its presence, and allows repair to proceed. Structural studies have shown XPD bound to its single-stranded DNA substrate, but molecular and dynamic characterization of how XPD translocates on undamaged DNA and how it stalls to verify lesions remains poorly understood. Here, we have performed extensive all-atom MD simulations of human XPD bound to undamaged and damaged ssDNA, containing a mutagenic pyrimidine (6-4) pyrimidone UV photoproduct (6-4PP), near the XPD pore entrance. We characterize how XPD responds to the presence of the DNA lesion, delineating the atomistic-scale mechanism that it utilizes to discriminate between damaged and undamaged nucleotides. We identify key amino acid residues, including FeS residues R112, R196, H135, K128, Arch residues E377 and R380, and ATPase lobe 1 residues 215-221, that are involved in damage verification and show how movements of Arch and ATPase lobe 1 domains relative to the FeS domain modulate these interactions. These structural and dynamic molecular depictions of XPD helicase activity with unmodified DNA and its inhibition by the lesion elucidate how the lesion is verified by inducing XPD stalling.
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Affiliation(s)
- Iwen Fu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Hong Mu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- To whom correspondence should be addressed. Tel: +1 212 998 8231;
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13
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Zhang X, Yin M, Hu J. Nucleotide excision repair: a versatile and smart toolkit. Acta Biochim Biophys Sin (Shanghai) 2022; 54:807-819. [PMID: 35975604 PMCID: PMC9828404 DOI: 10.3724/abbs.2022054] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nucleotide excision repair (NER) is a major pathway to deal with bulky adducts induced by various environmental toxins in all cellular organisms. The two sub-pathways of NER, global genome repair (GGR) and transcription-coupled repair (TCR), differ in the damage recognition modes. In this review, we describe the molecular mechanism of NER in mammalian cells, especially the details of damage recognition steps in both sub-pathways. We also introduce new sequencing methods for genome-wide mapping of NER, as well as recent advances about NER in chromatin by these methods. Finally, the roles of NER factors in repairing oxidative damages and resolving R-loops are discussed.
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Affiliation(s)
| | | | - Jinchuan Hu
- Correspondence address. Tel: +86-21-54237702; E-mail:
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14
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Li W, Jones K, Burke TJ, Hossain MA, Lariscy L. Epigenetic Regulation of Nucleotide Excision Repair. Front Cell Dev Biol 2022; 10:847051. [PMID: 35465333 PMCID: PMC9023881 DOI: 10.3389/fcell.2022.847051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.
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15
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González S, Aguilera J, Berman B, Calzavara-Pinton P, Gilaberte Y, Goh CL, Lim HW, Schalka S, Stengel F, Wolf P, Xiang F. Expert Recommendations on the Evaluation of Sunscreen Efficacy and the Beneficial Role of Non-filtering Ingredients. Front Med (Lausanne) 2022; 9:790207. [PMID: 35433750 PMCID: PMC9008233 DOI: 10.3389/fmed.2022.790207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
A variety of non-filtering agents have been introduced to enhance sunscreen photoprotection. Most of those agents have only weak erythema protective properties but may be valuable and beneficial in supporting protection against other effects of UV radiation, such as photoimmunosuppression, skin aging, and carcinogenesis, as well as photodermatoses. The question arises how to measure and evaluate this efficacy since standard SPF testing is not appropriate. In this perspective, we aim to provide a position statement regarding the actual value of SPF and UVA-PF to measure photoprotection. We argue whether new or additional parameters and scales can be used to better indicate the protection conferred by these products against the detrimental effects of natural/artificial, UV/visible light beyond sunburn, including DNA damage, photoimmunosuppression and pigmentation, and the potential benefits of the addition of other ingredients beyond traditional inorganic and organic filters to existing sunscreens. Also, we debate the overall usefulness of adding novel parameters that measure photoprotection to reach two tiers of users, that is, the general public and the medical community; and how this can be communicated to convey the presence of additional beneficial effects deriving from non-filtering agents, e.g., biological extracts. Finally, we provide a perspective on new challenges stemming from environmental factors, focusing on the role of the skin microbiome and the role of air pollutants and resulting needs for photoprotection.
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Affiliation(s)
- Salvador González
- Medicine and Medical Specialties Department, University of Alcalá de Henares, Madrid, Spain
- *Correspondence: Salvador González,
| | - José Aguilera
- Dermatological Photobiology Laboratory, Medical Research Center, School of Medicine, University of Málaga, Málaga, Spain
| | - Brian Berman
- Department of Dermatology and Cutaneous Surgery, University of Miami-Florida, Miami, FL, United States
| | | | - Yolanda Gilaberte
- Department of Dermatology, Hospital Universitario Miguel Servet, IIS Aragón, Zaragoza, Spain
| | | | - Henry W. Lim
- Department of Dermatology, Henry Ford Health System, Detroit, MI, United States
| | - Sergio Schalka
- Photoprotection Laboratory, Medicine Skin Research Center, São Paulo, Brazil
| | | | - Peter Wolf
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Flora Xiang
- Department of Dermatology, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
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16
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Jakhlal J, Denhez C, Coantic-Castex S, Martinez A, Harakat D, Douki T, Guillaume D, Clivio P. SN- and NS-puckered sugar conformers are precursors of the (6-4) photoproduct in thymine dinucleotide. Org Biomol Chem 2022; 20:2300-2307. [PMID: 35253821 DOI: 10.1039/d2ob00044j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some amount of furanose in a southern conformation, possibly in both, but certainly in one of the two adjacent nucleotides of a dipyrimidine site, is necessary for (6-4) photoproduct formation in oligonucleotides. To explore the necessity, role, and most favorable location of each South sugar conformer in the formation of the (6-4) adduct in the thymine dinucleotide TpT, the photochemical behavior of two synthetic analogues, in which the South sugar conformation is prohibited for one of their two sugars, has been examined. Herein, we experimentally demonstrate that the presence of one sugar presenting some amount of South puckering, at any of the extremities, is sufficient to trigger (6-4) adduct formation. Nonetheless, the photochemical behavior of the dinucleotide with a South-puckered conformation at the 5'-end, mimics more closely that of TpT. In addition, using the 5' North 3' South-dilocked dinucleotide, we demonstrate that the flexibility of the South pucker at the 3'-end has little influence on the (6-4) adduct formation.
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Affiliation(s)
- Jouda Jakhlal
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Clément Denhez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
- MaSCA, P3M, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Stéphanie Coantic-Castex
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Agathe Martinez
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Dominique Harakat
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR des Sciences Exactes et Naturelles, 51100 Reims, France
| | - Thierry Douki
- Université Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France
| | - Dominique Guillaume
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
| | - Pascale Clivio
- Université de Reims Champagne Ardenne, Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, UFR de Pharmacie, 51100 Reims, France.
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17
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Lu S, Liu J, Zhang X, Zhou J, Liu H, Liang J, Jiang L, Hu J, Zhang Y, Ma L, Luo L, Jia S, Yin Z. Protective effect of γ-glutamylcysteine against UVB radiation in NIH-3T3 cells. PHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE 2022; 38:522-530. [PMID: 35175655 DOI: 10.1111/phpp.12782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Ultraviolet (UV) radiation-induced oxidative stress is the main cause of photodamage to the skin. Glutathione (GSH) serves important physiological functions, including scavenging oxygen-free radicals and maintaining intracellular redox balance. γ-glutamylcysteine (γ-GC), as an immediate precursor of GSH and harboring antioxidant and anti-inflammatory properties, represents an unexplored option for skin photodamage treatment. PURPOSE The purpose of this study was to investigate whether γ-GC can reduce UVB-induced NIH-3T3 cell damage. METHODS The experimental groups were as follows: control, UVB radiation, UVB radiation after pretreatment with γ-GC. Cell counting kit-8 (CCK-8) assays were used to measure cell proliferation, flow cytometry, and immunoblotting to detect the apoptosis rate and apoptosis-associated proteins. The levels of Reactive Oxygen Species (ROS), Superoxide Dismutase (SOD), and GSH/GSSG (oxidized GSH) were measured to assess oxidative stress. Immunoblotting and immunofluorescence were used to detect DNA damage. The members of the MAPK signaling pathways were detected by immunoblotting. RESULTS UVB irradiation significantly reduced cell viability and destroyed the oxidative defense system. Pretreatment with γ-GC reduced UVB-induced cytotoxicity, restored the oxidation defense system, and inhibited activation of the MAPK pathway. It also reduced the apoptosis rate, downregulated the levels of cleaved caspase 3 and cleaved PARP. Furthermore, pretreatment with γ-GC reduced the accumulation of γH2AX after UVB radiation exposure, indicating that γ-GC could protect cells from DNA damage. CONCLUSION γ-GC protected NIH-3T3 from damage caused by UVB irradiation. The photoprotective effect of γ-GC is mediated via strengthening the endogenous antioxidant defense system, which prevents DNA damage and inhibits the activation of the MAPK pathway.
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Affiliation(s)
- Shuai Lu
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Jie Liu
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Xiaoxue Zhang
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Jinyi Zhou
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Huimin Liu
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Juanjuan Liang
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Longwei Jiang
- Department of Biotherapy, Nanjing Jinling Hospital, Nanjing, China
| | - Jianhua Hu
- Department of Biotherapy, Nanjing Jinling Hospital, Nanjing, China
| | - Yan Zhang
- Department of Biotherapy, Nanjing Jinling Hospital, Nanjing, China
| | - Lihua Ma
- Department of Biotherapy, Nanjing Jinling Hospital, Nanjing, China
| | - Lan Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shaochang Jia
- Department of Biotherapy, Nanjing Jinling Hospital, Nanjing, China
| | - Zhimin Yin
- Jiangsu Province Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
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18
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Stark B, Poon GM, Wyrick JJ. Molecular mechanism of UV damage modulation in nucleosomes. Comput Struct Biotechnol J 2022; 20:5393-5400. [PMID: 36212527 PMCID: PMC9529667 DOI: 10.1016/j.csbj.2022.08.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Exposure to ultraviolet (UV) light causes the formation of mutagenic cyclobutane pyrimidine dimers (CPDs) in cellular DNA. Previous studies have revealed that CPD formation in nucleosomes, the building blocks of chromatin, shows a striking ∼10 base pair (bp) periodic pattern. CPD formation is suppressed at positions where the DNA minor groove faces toward the histone octamer (minor-in) and elevated CPD formation at positions where the minor groove faces away from the histone octamer (minor-out). However, the molecular mechanism underlying this nucleosome photofootprint is unclear. Here, we analyzed ∼180 high-resolution nucleosome structures to characterize whether differences in DNA mobility or conformation are responsible for the CPD modulation in nucleosomes. Our results indicate that differences in DNA mobility cannot explain CPD modulation in nucleosome. Instead, we find that the sharp DNA bending around the histone octamer results in DNA conformations with structural parameters more susceptible to UV damage formation at minor-out positions and more resistant to CPD formation at minor-in positions. This analysis reveals the molecular mechanism responsible for periodic modulation of CPD formation and UV mutagenesis in nucleosomal DNA.
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19
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Paul D, Mu H, Tavakoli A, Dai Q, Chakraborty S, He C, Ansari A, Broyde S, Min JH. Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex. DNA Repair (Amst) 2021; 107:103194. [PMID: 34428697 PMCID: PMC8934541 DOI: 10.1016/j.dnarep.2021.103194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/14/2023]
Abstract
Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding ('opening') the damaged DNA site. Such 'opening' is also observed on a normal DNA sequence containing consecutive C/G's (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA 'opening' could occur on any DNA or if certain structures/sequences would resist being 'opened'. Here, we report that DNA containing alternating C/G's (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180°-reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote 'opening' contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being 'opened' even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion's mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.
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Affiliation(s)
- Debamita Paul
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Hong Mu
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Amirrasoul Tavakoli
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Sagnik Chakraborty
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA; Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Jung-Hyun Min
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA.
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20
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Manganelli M, Guida S, Ferretta A, Pellacani G, Porcelli L, Azzariti A, Guida G. Behind the Scene: Exploiting MC1R in Skin Cancer Risk and Prevention. Genes (Basel) 2021; 12:1093. [PMID: 34356109 PMCID: PMC8305013 DOI: 10.3390/genes12071093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Melanoma and non-melanoma skin cancers (NMSCs) are the most frequent cancers of the skin in white populations. An increased risk in the development of skin cancers has been associated with the combination of several environmental factors (i.e., ultraviolet exposure) and genetic background, including melanocortin-1 receptor (MC1R) status. In the last few years, advances in the diagnosis of skin cancers provided a great impact on clinical practice. Despite these advances, NMSCs are still the most common malignancy in humans and melanoma still shows a rising incidence and a poor prognosis when diagnosed at an advanced stage. Efforts are required to underlie the genetic and clinical heterogeneity of melanoma and NMSCs, leading to an optimization of the management of affected patients. The clinical implications of the impact of germline MC1R variants in melanoma and NMSCs' risk, together with the additional risk conferred by somatic mutations in other peculiar genes, as well as the role of MC1R screening in skin cancers' prevention will be addressed in the current review.
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Affiliation(s)
- Michele Manganelli
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari-“Aldo Moro”, 70125 Bari, Italy; (M.M.); (A.F.)
- DMMT-Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Stefania Guida
- Department of Surgical-Medical-Dental and Morphological Science with Interest Transplant-Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, 41124 Modena, Italy;
| | - Anna Ferretta
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari-“Aldo Moro”, 70125 Bari, Italy; (M.M.); (A.F.)
| | - Giovanni Pellacani
- Department of Clinical Internal, Anesthesiological and Cardiovascular Sciences, Dermatology Clinic, Sapienza University of Rome, 00161 Rome, Italy;
| | - Letizia Porcelli
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy; (L.P.); (A.A.)
| | - Amalia Azzariti
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy; (L.P.); (A.A.)
| | - Gabriella Guida
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari-“Aldo Moro”, 70125 Bari, Italy; (M.M.); (A.F.)
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21
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Perez BS, Wong KM, Schwartz EK, Herrera RE, King DA, García-Nieto PE, Morrison AJ. Genome-wide profiles of UV lesion susceptibility, repair, and mutagenic potential in melanoma. Mutat Res 2021; 823:111758. [PMID: 34333390 PMCID: PMC8671223 DOI: 10.1016/j.mrfmmm.2021.111758] [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: 06/14/2021] [Accepted: 07/14/2021] [Indexed: 10/20/2022]
Abstract
Exposure to the ultraviolet (UV) radiation in sunlight creates DNA lesions, which if left unrepaired can induce mutations and contribute to skin cancer. The two most common UV-induced DNA lesions are the cis-syn cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), both of which can initiate mutations. Interestingly, mutation frequency across the genomes of many cancers is heterogenous with significant increases in heterochromatin. Corresponding increases in UV lesion susceptibility and decreases in repair are observed in heterochromatin versus euchromatin. However, the individual contributions of CPDs and 6-4PPs to mutagenesis have not been systematically examined in specific genomic and epigenomic contexts. In this study, we compared genome-wide maps of 6-4PP and CPD lesion abundances in primary cells and conducted comprehensive analyses to determine the genetic and epigenetic features associated with susceptibility. Overall, we found a high degree of similarity between 6-4PP and CPD formation, with an enrichment of both in heterochromatin regions. However, when examining the relative levels of the two UV lesions, we found that bivalent and Polycomb-repressed chromatin states were uniquely more susceptible to 6-4PPs. Interestingly, when comparing UV susceptibility and repair with melanoma mutation frequency in these regions, disparate patterns were observed in that susceptibility was not always inversely associated with repair and mutation frequency. Functional enrichment analysis hint at mechanisms of negative selection for these regions that are essential for cell viability, immune function and induce cell death when mutated. Ultimately, these results reveal both the similarities and differences between UV-induced lesions that contribute to melanoma.
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Affiliation(s)
- Brian S Perez
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ka Man Wong
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Erin K Schwartz
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Devin A King
- Department of Biology, Stanford University, Stanford, CA, USA
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22
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Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes (Basel) 2021; 12:genes12060851. [PMID: 34205881 PMCID: PMC8228248 DOI: 10.3390/genes12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.
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Affiliation(s)
- Jérémy Barbier
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Cédric Vaillant
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Correspondence: (J.-N.V.); (B.A.)
| | - Frédéric G. Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
| | - Benjamin Audit
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
- Correspondence: (J.-N.V.); (B.A.)
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23
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Lu C, Gutierrez-Bayona NE, Taylor JS. The effect of flanking bases on direct and triplet sensitized cyclobutane pyrimidine dimer formation in DNA depends on the dipyrimidine, wavelength and the photosensitizer. Nucleic Acids Res 2021; 49:4266-4280. [PMID: 33849058 PMCID: PMC8096240 DOI: 10.1093/nar/gkab214] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/15/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the major products of DNA produced by direct absorption of UV light, and result in C to T mutations linked to human skin cancers. Most recently a new pathway to CPDs in melanocytes has been discovered that has been proposed to arise from a chemisensitized pathway involving a triplet sensitizer that increases mutagenesis by increasing the percentage of C-containing CPDs. To investigate how triplet sensitization may differ from direct UV irradiation, CPD formation was quantified in a 129-mer DNA designed to contain all 64 possible NYYN sequences. CPD formation with UVB light varied about 2-fold between dipyrimidines and 12-fold with flanking sequence and was most frequent at YYYR and least frequent for GYYN sites in accord with a charge transfer quenching mechanism. In contrast, photosensitized CPD formation greatly favored TT over C-containing sites, more so for norfloxacin (NFX) than acetone, in accord with their differing triplet energies. While the sequence dependence for photosensitized TT CPD formation was similar to UVB light, there were significant differences, especially between NFX and acetone that could be largely explained by the ability of NFX to intercalate into DNA.
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Affiliation(s)
- Chen Lu
- Department of Chemistry, Washington University, One Brookings Dr., St. Louis, MO 63130, USA
| | | | - John-Stephen Taylor
- Department of Chemistry, Washington University, One Brookings Dr., St. Louis, MO 63130, USA
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24
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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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25
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A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data. Nat Protoc 2021; 16:2190-2212. [PMID: 33731963 DOI: 10.1038/s41596-021-00496-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/06/2021] [Indexed: 01/13/2023]
Abstract
UV radiation may lead to melanoma and nonmelanoma skin cancers by causing helix-distorting DNA damage such as cyclobutane pyrimidine dimers (CPDs). These DNA lesions, if located in important genes and not repaired promptly, are mutagenic and may eventually result in carcinogenesis. Examining CPD formation and repair processes across the genome can shed light on the mutagenesis mechanisms associated with UV damage in relevant cancers. We recently developed CPD-Seq, a high-throughput and single-nucleotide resolution sequencing technique that can specifically capture UV-induced CPD lesions across the genome. This novel technique has been increasingly used in studies of UV damage and can be adapted to sequence other clinically relevant DNA lesions. Although the library preparation protocol has been established, a systematic protocol to analyze CPD-Seq data has not been described yet. To streamline the various general or specific analysis steps, we developed a protocol named CPDSeqer to assist researchers with CPD-Seq data processing. CPDSeqer can accommodate both a single- and multiple-sample experimental design, and it allows both genome-wide analyses and regional scrutiny (such as of suspected UV damage hotspots). The runtime of CPDSeqer scales with raw data size and takes roughly 4 h per sample with the possibility of acceleration by parallel computing. Various guiding graphics are generated to help diagnose the performance of the experiment and inform regional enrichment of CPD formation. UV damage comparison analyses are set forth in three analysis scenarios, and the resulting HTML pages report damage directional trends and statistical significance. CPDSeqer can be accessed at https://github.com/shengqh/cpdseqer .
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Hu X, Zhou L, Wang H, Gao Y, Gao Y. The Value of Photo Biological Regulation Based on Nano Semiconductor Laser Technology in the Treatment of Hypertension Fundus Disease. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2021; 21:1323-1330. [PMID: 33183479 DOI: 10.1166/jnn.2021.18698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
With the development of nanometer semiconductor laser technology, due to the wide range of photobiological regulation and non-invasive advantages, it is widely used in clinical research, including reducing pain, accelerating wound healing, nerve injury repair and regeneration. Increase tissue blood flow, improve anxiety and depression, and treat Parkinson's and retinal diseases. However, in many studies, the role of photobiological regulation is still controversial. There are two main problems, one is that the mechanism of photo biological regulation is not fully understood, and the other is that the specific parameters are not uniform in different treatments, such as wavelength density, power density, pulse, treatment timing, and number of treatments. In this paper, through the second question, the parameters of low-energy near-infrared light (810 nm semiconductor laser) in the treatment of fundus diseases are the main research objects. Based on understanding the parameters of low-energy lasers, cyan blue is irradiated with different energy near-infrared light. Data analysis of the actual energy obtained after the retina of the rabbit and observation and research on the cell morphology of each layer of the retina, to obtain relatively safe treatment parameters for the retina, provide theoretical data for near-infrared light in the treatment of clinical fundus disease, and make it safer to use in clinical treatment.
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Affiliation(s)
- Xingui Hu
- Department of Cardiovascular Medicine, Taiyuan Iron and Steel (Group) General Hospital, Taiyuan, 030008, Shanxi, China
| | - Linan Zhou
- Department of Cardiovascular Medicine, Taiyuan Iron and Steel (Group) General Hospital, Taiyuan, 030008, Shanxi, China
| | - Huifeng Wang
- Department of Intensive Care Unit, Shanxi Tumour Hospital, Taiyuan, 030000, Shanxi, China
| | - Yuanpeng Gao
- Department of Orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Yan Gao
- Department of Vitreoretinology, Shanxi Eye Hospital, Taiyuan, 030002, Shanxi, China
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27
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TGFβ Signaling in Photoaging and UV-Induced Skin Cancer. J Invest Dermatol 2021; 141:1104-1110. [PMID: 33358021 DOI: 10.1016/j.jid.2020.11.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 01/06/2023]
Abstract
UVR is a major etiology for premature skin aging that leads to photoaging and UV-induced skin cancers. In the skin, TGFβ signaling is a growth inhibitor for keratinocytes and a profibrotic factor in the dermis. It exerts context-dependent effects on tumor progression. Chronic UV exposure likely causes TGFβ1/SMAD3 signaling activation and contributes to metalloproteinase-induced collagen degradation and photoinflammation in photoaging. UV irradiation also causes gene mutations in key elements of the TGFβ pathway, including TGFβRI, TGFβRII, SMAD2, and SMAD4. These mutations enable tumor cells to escape from TGFβ-induced growth inhibition and induce genomic instability and cancer stem cells, leading to the initiation, progression, invasion, and metastasis of cutaneous squamous cell carcinoma (cSCC). Furthermore, UV-induced mutations cause TGFβ overexpression in the tumor microenvironment (TME) of cSCC, basal cell carcinoma (BCC), and cutaneous melanoma, resulting in inflammation, angiogenesis, cancer-associated fibroblasts, and immune inhibition, supporting cancer survival, immune evasion, and metastasis. The pleiotropic effects of TGFβ provide possible treatment options for photoaging and skin cancer. Given the high UV-induced mutational burden and immune-repressive TME seen in cSCC, BCC, and cutaneous melanoma, treatment with the combination of a TGFβ signaling inhibitor and immune checkpoint blockade could reverse immune evasion to reduce tumor growth.
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Jiang Y, Li W, Lindsey-Boltz LA, Yang Y, Li Y, Sancar A. Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome. J Biol Chem 2021; 296:100581. [PMID: 33771559 PMCID: PMC8081918 DOI: 10.1016/j.jbc.2021.100581] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
The formation of UV-induced DNA damage and its repair are influenced by many factors that modulate lesion formation and the accessibility of repair machinery. However, it remains unknown which genomic sites are prioritized for immediate repair after UV damage induction, and whether these prioritized sites overlap with hotspots of UV damage. We identified the super hotspots subject to the earliest repair for (6-4) pyrimidine-pyrimidone photoproduct by using the eXcision Repair-sequencing (XR-seq) method. We further identified super coldspots for (6-4) pyrimidine-pyrimidone photoproduct repair and super hotspots for cyclobutane pyrimidine dimer repair by analyzing available XR-seq time-course data. By integrating datasets of XR-seq, Damage-seq, adductSeq, and cyclobutane pyrimidine dimer-seq, we show that neither repair super hotspots nor repair super coldspots overlap hotspots of UV damage. Furthermore, we demonstrate that repair super hotspots are significantly enriched in frequently interacting regions and superenhancers. Finally, we report our discovery of an enrichment of cytosine in repair super hotspots and super coldspots. These findings suggest that local DNA features together with large-scale chromatin features contribute to the orders of magnitude variability in the rates of UV damage repair.
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Affiliation(s)
- Yuchao Jiang
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
| | - Wentao Li
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yuchen Yang
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yun Li
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Computer Science, College of Arts and Sciences, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Aziz Sancar
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA.
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Tissue-Specific DNA Repair Activity of ERCC-1/XPF-1. Cell Rep 2021; 34:108608. [PMID: 33440146 DOI: 10.1016/j.celrep.2020.108608] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/30/2020] [Accepted: 12/15/2020] [Indexed: 01/14/2023] Open
Abstract
Hereditary DNA repair defects affect tissues differently, suggesting that in vivo cells respond differently to DNA damage. Knowledge of the DNA damage response, however, is largely based on in vitro and cell culture studies, and it is currently unclear whether DNA repair changes depending on the cell type. Here, we use in vivo imaging of the nucleotide excision repair (NER) endonuclease ERCC-1/XPF-1 in C. elegans to demonstrate tissue-specific NER activity. In oocytes, XPF-1 functions as part of global genome NER (GG-NER) to ensure extremely rapid removal of DNA-helix-distorting lesions throughout the genome. In contrast, in post-mitotic neurons and muscles, XPF-1 participates in NER of transcribed genes only. Strikingly, muscle cells appear more resistant to the effects of DNA damage than neurons. These results suggest a tissue-specific organization of the DNA damage response and may help to better understand pleiotropic and tissue-specific consequences of accumulating DNA damage.
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Kciuk M, Marciniak B, Mojzych M, Kontek R. Focus on UV-Induced DNA Damage and Repair-Disease Relevance and Protective Strategies. Int J Mol Sci 2020; 21:ijms21197264. [PMID: 33019598 PMCID: PMC7582305 DOI: 10.3390/ijms21197264] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
The protective ozone layer is continually depleting due to the release of deteriorating environmental pollutants. The diminished ozone layer contributes to excessive exposure of cells to ultraviolet (UV) radiation. This leads to various cellular responses utilized to restore the homeostasis of exposed cells. DNA is the primary chromophore of the cells that absorbs sunlight energy. Exposure of genomic DNA to UV light leads to the formation of multitude of types of damage (depending on wavelength and exposure time) that are removed by effectively working repair pathways. The aim of this review is to summarize current knowledge considering cellular response to UV radiation with special focus on DNA damage and repair and to give a comprehensive insight for new researchers in this field. We also highlight most important future prospects considering application of the progressing knowledge of UV response for the clinical control of diverse pathologies.
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Affiliation(s)
- Mateusz Kciuk
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
- Correspondence:
| | - Beata Marciniak
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland;
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
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31
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Formation and Recognition of UV-Induced DNA Damage within Genome Complexity. Int J Mol Sci 2020; 21:ijms21186689. [PMID: 32932704 PMCID: PMC7555853 DOI: 10.3390/ijms21186689] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/18/2022] Open
Abstract
Ultraviolet (UV) light is a natural genotoxic agent leading to the formation of photolesions endangering the genomic integrity and thereby the survival of living organisms. To prevent the mutagenetic effect of UV, several specific DNA repair mechanisms are mobilized to accurately maintain genome integrity at photodamaged sites within the complexity of genome structures. However, a fundamental gap remains to be filled in the identification and characterization of factors at the nexus of UV-induced DNA damage, DNA repair, and epigenetics. This review brings together the impact of the epigenomic context on the susceptibility of genomic regions to form photodamage and focuses on the mechanisms of photolesions recognition through the different DNA repair pathways.
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Selvam K, Rahman SA, Forrester D, Bao A, Lieu M, Li S. Histone H4 LRS mutations can attenuate UV mutagenesis without affecting PCNA ubiquitination or sumoylation. DNA Repair (Amst) 2020; 95:102959. [PMID: 32927239 DOI: 10.1016/j.dnarep.2020.102959] [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: 06/14/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 11/18/2022]
Abstract
UV is a significant environmental agent that damages DNA. Translesion synthesis (TLS) is a DNA damage tolerance pathway that utilizes specialized DNA polymerases to replicate through the damaged DNA, often leading to mutagenesis. In eukaryotic cells, genomic DNA is organized into chromatin that is composed of nucleosomes. To date, if and/or how TLS is regulated by a specific nucleosome feature has been undocumented. We found that mutations of multiple histone H4 residues mostly or entirely embedded in the nucleosomal LRS (loss of ribosomal DNA-silencing) domain attenuate UV mutagenesis in Saccharomyces cerevisiae. The attenuation is not caused by an alteration of ubiquitination or sumoylation of PCNA (proliferating cell nuclear antigen), the modifications well-known to regulate TLS. Also, the attenuation is not caused by decreased chromatin accessibility, or by alterations of methylation of histone H3 K79, which is at the center of the LRS surface. The attenuation may result from compromised TLS by both DNA polymerases ζ and η, in which Rad6 and Rad5 are but Rad18 is not implicated. We propose that a feature of the LRS is recognized or accessed by the TLS machineries either during/after a nucleosome is disassembled in front of a lesion-stalled replication fork, or during/before a nucleosome is reassembled behind a lesion-stalled replication fork.
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Affiliation(s)
- Kathiresan Selvam
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Sheikh Arafatur Rahman
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Derek Forrester
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Adam Bao
- Department of Biological Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Michael Lieu
- School of Kinesiology, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, United States.
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Abstract
Ultraviolet (UV) irradiation causes various types of DNA damage, which leads to specific mutations and the emergence of skin cancer in humans, often decades after initial exposure. Different UV wavelengths cause the formation of prominent UV-induced DNA lesions. Most of these lesions are removed by the nucleotide excision repair pathway, which is defective in rare genetic skin disorders referred to as xeroderma pigmentosum. A major role in inducing sunlight-dependent skin cancer mutations is assigned to the cyclobutane pyrimidine dimers (CPDs). In this review, we discuss the mechanisms of UV damage induction, the genomic distribution of this damage, relevant DNA repair mechanisms, the proposed mechanisms of how UV-induced CPDs bring about DNA replication-dependent mutagenicity in mammalian cells, and the strong signature of UV damage and mutagenesis found in skin cancer genomes.
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34
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Ali SM, Ali U. An approach to design a wristwatch for the protection of the human skin damage induced by ultraviolet and infrared radiations. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2020; 36:278-289. [PMID: 32187717 DOI: 10.1111/phpp.12551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/24/2020] [Accepted: 03/13/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Ultraviolet radiations (UV) absorbed by the skin can drive photochemical reactions which range from sunburn to skin cancer. The repeated exposure to Infrared radiations (IR) induces the heat into the skin, which causes dehydration and erythema as an immediate effect. This heat activates the metalloproteinase enzyme that reduces the number of procollagen and collagen fibers in the dermal skin, which results premature skin aging. This work aims to design a protective measure in order to avoid these damages. METHOD The proposed protective measure is a wristwatch with an alert alarm which can sense UV and IR radiations. Whenever UV/IR radiation levels exceed beyond the defined limits, alarm will be activated that warns the user to apply protective measures. These radiations are detected by SI1145 digital UV Index/IR/visible light sensor and assigned, using Arduino, to an appropriate UV index and IR radiation levels. RESULTS The IR and UV readings were recorded several times and at four different hours through the day. The readings showed its highest value at 10 am and 2 pm, which are considered the highest sun intensity. The other readings were at 6 am and 5 pm and considered the least dangerous hours. CONCLUSION The data collected from the sensor are used to program the alarm. To combine all components, a PCB and a prototype were designed and printed. The UV/IR wristwatch is applicable to alert the user from the continuous and accumulated harmful effects of the radiations and enable them to seek protective measures.
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Affiliation(s)
- Syed Mehmood Ali
- Department of Biomedical Engineering, College of Engineering, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Uzma Ali
- Department of Public Health, College of Public Health, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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35
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Paul D, Mu H, Zhao H, Ouerfelli O, Jeffrey PD, Broyde S, Min JH. Structure and mechanism of pyrimidine-pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex. Nucleic Acids Res 2020; 47:6015-6028. [PMID: 31106376 PMCID: PMC6614856 DOI: 10.1093/nar/gkz359] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 12/31/2022] Open
Abstract
Failure in repairing ultraviolet radiation-induced DNA damage can lead to mutations and cancer. Among UV-lesions, the pyrimidine–pyrimidone (6-4) photoproduct (6-4PP) is removed from the genome much faster than the cyclobutane pyrimidine dimer (CPD), owing to the more efficient recognition of 6-4PP by XPC-RAD23B, a key initiator of global-genome nucleotide excision repair (NER). Here, we report a crystal structure of a Rad4–Rad23 (yeast XPC-Rad23B ortholog) bound to 6-4PP-containing DNA and 4-μs molecular dynamics (MD) simulations examining the initial binding of Rad4 to 6-4PP or CPD. This first structure of Rad4/XPC bound to a physiological substrate with matched DNA sequence shows that Rad4 flips out both 6-4PP-containing nucleotide pairs, forming an ‘open’ conformation. The MD trajectories detail how Rad4/XPC initiates ‘opening’ 6-4PP: Rad4 initially engages BHD2 to bend/untwist DNA from the minor groove, leading to unstacking and extrusion of the 6-4PP:AA nucleotide pairs towards the major groove. The 5′ partner adenine first flips out and is captured by a BHD2/3 groove, while the 3′ adenine extrudes episodically, facilitating ensuing insertion of the BHD3 β-hairpin to open DNA as in the crystal structure. However, CPD resists such Rad4-induced structural distortions. Untwisting/bending from the minor groove may be a common way to interrogate DNA in NER.
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Affiliation(s)
- Debamita Paul
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Hong Zhao
- Organic Synthesis Core, Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core, Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, NJ 08544, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
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36
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Sugiyama T, Chen Y. Biochemical reconstitution of UV-induced mutational processes. Nucleic Acids Res 2020; 47:6769-6782. [PMID: 31053851 PMCID: PMC6648339 DOI: 10.1093/nar/gkz335] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
We reconstituted two biochemical processes that may contribute to UV-induced mutagenesis in vitro and analysed the mutational profiles in the products. One process is translesion synthesis (TLS) by DNA polymerases (Pol) δ, η and ζ, which creates C>T transitions at pyrimidine dimers by incorporating two dAMPs opposite of the dimers. The other process involves spontaneous deamination of cytosine, producing uracil in pyrimidine dimers, followed by monomerization of the dimers by secondary UV irradiation, and DNA synthesis by Pol δ. The mutational spectrum resulting from deamination without translesion synthesis is similar to a mutational signature found in melanomas, suggesting that cytosine deamination encountered by the replicative polymerase has a prominent role in melanoma development. However, CC>TT dinucleotide substitution, which is also commonly observed in melanomas, was produced almost exclusively by TLS. We propose that both TLS-dependent and deamination-dependent mutational processes are likely involved in UV-induced melanoma development.
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Affiliation(s)
- Tomohiko Sugiyama
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Yizhang Chen
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
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37
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Abstract
Exposure to ultraviolet (UV) radiation is the major risk factor for skin cancers. UV induces helix-distorting DNA damage such as cyclobutane pyrimidine dimers (CPDs). If not repaired, CPDs can strongly block DNA and RNA polymerases and cause mutagenesis or cell death. Nucleotide excision repair (NER) is critical for the removal of UV-induced photolesions including CPDs in the cell. Investigating CPD formation and repair across the genome is important for understanding the mechanisms by which these lesions promote somatic mutations in skin cancers. Here we describe a high-throughput, single nucleotide-resolution damage mapping method named CPD sequencing (CPD-seq) for genome-wide analysis of UV-induced CPDs. Protocols for CPD-seq library preparation in yeast and human cells, as well as bioinformatics identification of the CPD damage site, are detailed below.
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Affiliation(s)
- Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA, 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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38
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Developmentally Regulated Oscillations in the Expression of UV Repair Genes in a Soilborne Plant Pathogen Dictate UV Repair Efficiency and Survival. mBio 2019; 10:mBio.02623-19. [PMID: 31796540 PMCID: PMC6890992 DOI: 10.1128/mbio.02623-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fusarium oxysporum infects plants through the roots and therefore is not exposed to the sun regularly. However, the ability to survive sun exposure expands the distribution of the population. UV from the sun is toxic and mutagenic, and to survive sun exposure, fungi encode several DNA repair mechanisms. We found that Fusarium oxysporum has a gene expression program that activates photolyase at the first hours of germination when the pathogen is not established in the plant tissue. Later on, the expression of photolyase decreases, and the expression of a light-independent UV repair mechanism increases. We suggest a novel point of view to a very fundamental question of how soilborne microorganisms defend themselves against sudden UV exposure. The ability to withstand UV damage shapes the ecology of microbes. While mechanisms of UV tolerance were extensively investigated in microorganisms regularly exposed to the sun, far less is known about UV repair of soilborne microorganisms. Fusarium oxysporum is a soilborne fungal plant pathogen that is resistant to UV light. We hypothesized that its UV repair capacity is induced to deal with irregular sun exposure. Unlike the SOS paradigm, our analysis revealed only sporadic increases and even decreases in UV repair gene expression following UVC irradiation or exposure to visible light. Strikingly, a major factor determining the expression of UV repair genes was the developmental status of the fungus. At the early stages of germination, the expression of photolyase increased while the expression of UV endonuclease decreased, and then the trend was reversed. These gene expression oscillations were dependent on cell cycle progression. Consequently, the contribution of photoreactivation to UV repair and survival was stronger at the beginning of germination than later when a filament was established. F. oxysporum germinates following cues from the host. Early on in germination, it is most vulnerable to UV; when the filament is established, the pathogen is protected from the sun because it is already within the host tissue.
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Ikehata H, Mori T, Kamei Y, Douki T, Cadet J, Yamamoto M. Wavelength- and Tissue-dependent Variations in the Mutagenicity of Cyclobutane Pyrimidine Dimers in Mouse Skin. Photochem Photobiol 2019; 96:94-104. [PMID: 31461538 DOI: 10.1111/php.13159] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/22/2019] [Indexed: 12/18/2022]
Abstract
The cyclobutane pyrimidine dimer (CPD) is a main mutagenic photolesion in DNA produced by UVR. We previously studied the wavelength-dependent kinetics of mutation induction efficiency using monochromatic UVR sources and transgenic mice developed for mutation assay and established the action spectra of UVR mutagenicity in the mouse epidermis and dermis. Here, we further established the action spectra of CPD and pyrimidine(6-4)pyrimidone photoproduct formation in the same tissues and in naked DNA using the same sources and mouse strain. Quantitative ELISA helped us estimate the photolesion formation efficiencies on a molecule-per-nucleotide basis. Using these action spectra, we confirmed that the UVR mutation mostly depends on CPD formation. Moreover, the mutagenicity of a CPD molecule (CPD mutagenicity) was found to vary by wavelength, peaking at approximately 313 nm in both the epidermis and dermis with similar wavelength-dependent patterns. Thus, the CPD formation efficiency is a main determinant of UVR mutagenicity in mouse skin, whereas a wavelength-dependent variation in the qualitative characteristics of CPD molecules also affects the mutagenic consequences of UVR insults. In addition, the CPD mutagenicity was always higher in the epidermis than in the dermis, suggesting different cellular responses to UVR between the two tissues irrespective of the wavelength.
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Affiliation(s)
- Hironobu Ikehata
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshio Mori
- Nara Medical University School of Medicine, Kashihara, Japan
| | - Yasuhiro Kamei
- Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Thierry Douki
- CEA, CNRS, INAC, SyMMES/CIBEST, Université Grenoble Alpes, Grenoble, France
| | - Jean Cadet
- University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
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40
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Tang Q, Chen F, Wu P, Qiu L, Chen H, Chen K, Li G. BmNPV infection correlates with the enhancement of the resistance of Bombyx mori cells to UV radiation. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 102:e21598. [PMID: 31290186 DOI: 10.1002/arch.21598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/31/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
At present, the effect of ultraviolet (UV) radiation on the interaction between Bombyx mori nucleopolyhedrovirus (BmNPV) and host remains unclear. In the current study, UV treatment significantly reduced the activity of BmNPV budded viruses (BVs), and UV-damaged BmN cells were not conducive to BmNPV proliferation. BmNPV infection significantly reduced the viability of host cells, but increased the viability of high-dose UV-treated host cells. Furthermore, the quantitative reverse-transcription PCR (qPCR) results suggested that BmNPV and Bombyx mori might mutually use the same DNA repair proteins for repairing UV-induced damage and BmNPV infection promote the ability of host cells to repair UV-induced damage.
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Affiliation(s)
- Qi Tang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Fangying Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Peng Wu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Lipeng Qiu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Huiqing Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Guohui Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
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41
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Mao P, Wyrick JJ. Organization of DNA damage, excision repair, and mutagenesis in chromatin: A genomic perspective. DNA Repair (Amst) 2019; 81:102645. [PMID: 31307926 DOI: 10.1016/j.dnarep.2019.102645] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genomic DNA is constantly assaulted by both endogenous and exogenous damaging agents. The resulting DNA damage, if left unrepaired, can interfere with DNA replication and be converted into mutations. Genomic DNA is packaged into a highly compact yet dynamic chromatin structure, in order to fit into the limited space available in the nucleus of eukaryotic cells. This hierarchical chromatin organization serves as both the target of DNA damaging agents and the context for DNA repair enzymes. Biochemical studies have suggested that both the formation and repair of DNA damage are significantly modulated by chromatin. Our understanding of the impact of chromatin on damage and repair has been significantly enhanced by recent studies. We focus on the nucleosome, the primary building block of chromatin, and discuss how the intrinsic structural properties of nucleosomes, and their associated epigenetic modifications, affect damage formation and DNA repair, as well as subsequent mutagenesis in cancer.
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Affiliation(s)
- Peng Mao
- 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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42
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Abstract
Nucleotide excision repair is a versatile mechanism to repair a variety of bulky DNA adducts. We developed excision repair sequencing (XR-seq) to study nucleotide excision repair of DNA adducts in humans, mice, Arabidopsis thaliana, yeast and Escherichia coli. In this protocol, the excised oligomers, generated in the nucleotide excision repair reaction, are isolated by cell lysis and fractionation, followed by immunoprecipitation with damage- or repair factor-specific antibodies from the non-chromatin fraction. The single-stranded excised oligomers are ligated to adapters and re-immunoprecipitated with damage-specific antibodies. The DNA damage in the excised oligomers is then reversed by enzymatic or chemical reactions before being converted into a sequencing library by PCR amplification. Alternatively, the excised oligomers containing DNA damage, especially those containing irreversible DNA damage such as benzo[a]pyrene-induced DNA adducts, can be converted to a double-stranded DNA (dsDNA) form by using appropriate translesion DNA synthesis (TLS) polymerases and then can be amplified by PCR. The current genome-wide approaches for studying repair measure the loss of damage signal with time, which limits their resolution. By contrast, an advantage of XR-seq is that the repair signal is directly detected above a background of zero. An XR-seq library using the protocol described here can be obtained in 7-9 d.
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Wróbel S, Przybyło M, Stępień E. The Clinical Trial Landscape for Melanoma Therapies. J Clin Med 2019; 8:E368. [PMID: 30884760 PMCID: PMC6463026 DOI: 10.3390/jcm8030368] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 12/28/2022] Open
Abstract
(1) Despite many years of research, melanoma still remains a big challenge for modern medicine. The purpose of this article is to review publicly available clinical trials to find trends regarding the number of trials, their location, and interventions including the most frequently studied drugs and their combinations. (2) We surveyed clinical trials registered in the International Clinical Trials Registry Platform (ICTRP), one of the largest databases on clinical trials. The search was performed on 30 November 2018 using the term "melanoma". Data have been supplemented with the information obtained from publicly available data repositories including PubMed, World Health Organization, National Cancer Institute, Centers for Disease Control and Prevention, European Cancer Information System, and many others to bring the historical context of this study. (3) Among the total of 2563 clinical trials included in the analysis, most have been registered in the USA (1487), which is 58% of the total. The most commonly studied drug in clinical trials was ipilimumab, described as applied intervention in 251 trials. (4) An increase in the number of melanoma clinical trials using immunomodulating monoclonal antibody therapies, small molecule-targeted therapies (inhibitors of BRAF, MEK, CDK4/6), and combination therapies is recognized. This illustrates the tendency towards precision medicine.
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Affiliation(s)
- Sonia Wróbel
- Department of Medical Physics, Marian Smoluchowski Institute of Physics, Jagiellonian University, 30-348 Krakow, Poland.
| | - Małgorzata Przybyło
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland.
| | - Ewa Stępień
- Department of Medical Physics, Marian Smoluchowski Institute of Physics, Jagiellonian University, 30-348 Krakow, Poland.
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45
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Roberts SA, Brown AJ, Wyrick JJ. Recurrent Noncoding Mutations in Skin Cancers: UV Damage Susceptibility or Repair Inhibition as Primary Driver? Bioessays 2019; 41:e1800152. [PMID: 30801747 PMCID: PMC6571124 DOI: 10.1002/bies.201800152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/05/2018] [Indexed: 12/14/2022]
Abstract
Somatic mutations arising in human skin cancers are heterogeneously distributed across the genome, meaning that certain genomic regions (e.g., heterochromatin or transcription factor binding sites) have much higher mutation densities than others. Regional variations in mutation rates are typically not a consequence of selection, as the vast majority of somatic mutations in skin cancers are passenger mutations that do not promote cell growth or transformation. Instead, variations in DNA repair activity, due to chromatin organization and transcription factor binding, have been proposed to be a primary driver of mutational heterogeneity in melanoma. However, as discussed in this review here, recent studies indicate that chromatin organization and transcription factor binding also significantly modulate the rate at which UV lesions form in DNA. The authors propose that local variations in lesion susceptibility may be an important driver of mutational hotspots in melanoma and other skin cancers, particularly at binding sites for ETS transcription factors.
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Affiliation(s)
- Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164
| | - Alexander J. Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164
| | - John J. Wyrick
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164
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46
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Brown AJ, Mao P, Smerdon MJ, Wyrick JJ, Roberts SA. Nucleosome positions establish an extended mutation signature in melanoma. PLoS Genet 2018; 14:e1007823. [PMID: 30485262 PMCID: PMC6287878 DOI: 10.1371/journal.pgen.1007823] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/10/2018] [Accepted: 11/09/2018] [Indexed: 12/24/2022] Open
Abstract
Ultraviolet (UV) light-induced mutations are unevenly distributed across skin cancer genomes, but the molecular mechanisms responsible for this heterogeneity are not fully understood. Here, we assessed how nucleosome structure impacts the positions of UV-induced mutations in human melanomas. Analysis of mutation positions from cutaneous melanomas within strongly positioned nucleosomes revealed a striking ~10 base pair (bp) oscillation in mutation density with peaks occurring at dinucleotides facing away from the histone octamer. Additionally, higher mutation density at the nucleosome dyad generated an overarching “translational curvature” across the 147 bp of DNA that constitutes the nucleosome core particle. This periodicity and curvature cannot be explained by sequence biases in nucleosomal DNA. Instead, our genome-wide map of UV-induced cyclobutane pyrimidine dimers (CPDs) indicates that CPD formation is elevated at outward facing dinucleotides, mirroring the oscillation of mutation density within nucleosome-bound DNA. Nucleotide excision repair (NER) activity, as measured by XR-seq, inversely correlated with the curvature of mutation density associated with the translational setting of the nucleosome. While the 10 bp periodicity of mutations is maintained across nucleosomes regardless of chromatin state, histone modifications, and transcription levels, overall mutation density and curvature across the core particle increased with lower transcription levels. Our observations suggest structural conformations of DNA promote CPD formation at specific sites within nucleosomes, and steric hindrance progressively limits lesion repair towards the nucleosome dyad. Both mechanisms create a unique extended mutation signature within strongly positioned nucleosomes across the human genome. UV-induced mutations are abundant and heterogeneously distributed across melanoma genomes. Understanding the mechanisms that produce this heterogeneity may help decipher which mutations drive the cancer phenotype. While it is known that mutation density correlates with chromatin compaction on a large scale, recent studies have suggested that local chromatin structure impacts mutation distribution in ways previously undetected. We therefore examined the distribution of melanoma mutations in strongly positioned nucleosomes where we observed a striking oscillatory and curvature pattern. UV lesion formation appeared to be responsible for mutation oscillation, despite active repair occurring in the nucleosome core particle. However, more CPD lesions are removed near the edges of nucleosomes, and thus generated an overall translational curvature in mutation density.
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Affiliation(s)
- Alexander J. Brown
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States of America
| | - Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States of America
| | - Michael J. Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States of America
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- * E-mail: (JJW); (SAR)
| | - Steven A. Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- * E-mail: (JJW); (SAR)
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47
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Mao P, Brown AJ, Esaki S, Lockwood S, Poon GMK, Smerdon MJ, Roberts SA, Wyrick JJ. ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma. Nat Commun 2018; 9:2626. [PMID: 29980679 PMCID: PMC6035183 DOI: 10.1038/s41467-018-05064-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/07/2018] [Indexed: 11/12/2022] Open
Abstract
Recurrent mutations are frequently associated with transcription factor (TF) binding sites (TFBS) in melanoma, but the mechanism driving mutagenesis at TFBS is unclear. Here, we use a method called CPD-seq to map the distribution of UV-induced cyclobutane pyrimidine dimers (CPDs) across the human genome at single nucleotide resolution. Our results indicate that CPD lesions are elevated at active TFBS, an effect that is primarily due to E26 transformation-specific (ETS) TFs. We show that ETS TFs induce a unique signature of CPD hotspots that are highly correlated with recurrent mutations in melanomas, despite high repair activity at these sites. ETS1 protein renders its DNA binding targets extremely susceptible to UV damage in vitro, due to binding-induced perturbations in the DNA structure that favor CPD formation. These findings define a mechanism responsible for recurrent mutations in melanoma and reveal that DNA binding by ETS TFs is inherently mutagenic in UV-exposed cells. Many factors contribute to mutation hotspots in cancer cells. Here the authors map UV damage at single-nucleotide resolution across the human genome and find that binding sites of ETS transcription factors are especially prone to forming UV lesions, leading to mutation hotspots in melanoma.
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Affiliation(s)
- Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Alexander J Brown
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Shingo Esaki
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Svetlana Lockwood
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Michael J Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, 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. .,Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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Ikehata H, Mori T, Douki T, Cadet J, Yamamoto M. Quantitative analysis of UV photolesions suggests that cyclobutane pyrimidine dimers produced in mouse skin by UVB are more mutagenic than those produced by UVC. Photochem Photobiol Sci 2018; 17:404-413. [PMID: 29464256 DOI: 10.1039/c7pp00348j] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The amount of photolesions produced in DNA after exposure to physiological doses of ultraviolet radiation (UVR) can be estimated with high sensitivity and at low cost through an immunological assay, ELISA, which, however, provides only a relative estimate that cannot be used for comparisons between different photolesions such as cyclobutane pyrimidine dimer (CPD) and pyrimidine(6-4)pyrimidone photoproduct (64PP) or for analysis of the genotoxicity of photolesions on a molecular basis. To solve this drawback of ELISA, we introduced a set of UVR-exposed, calibration DNA whose photolesion amounts were predetermined and estimated the absolute molecular amounts of CPDs and 64PPs produced in mouse skin exposed to UVC and UVB. We confirmed previously reported observations that UVC induced more photolesions in the skin than UVB at the same dose, and that both types of UVR produced more CPDs than 64PPs. The UVR protection abilities of the cornified and epidermal layers for the lower tissues were also evaluated quantitatively. We noticed that the values of absorbance obtained in ELISA were not always proportional to the molecular amounts of the lesion, especially for CPD, cautioning against the direct use of ELISA absorbance data for estimation of the photolesion amounts. We further estimated the mutagenicity of a CPD produced by UVC and UVB in the epidermis and dermis using the mutation data from our previous studies with mouse skin and found that CPDs produced in the epidermis by UVB were more than two-fold mutagenic than those by UVC, which suggests that the properties of CPDs produced by UVC and UVB might be different. The difference may originate from the wavelength-dependent methyl CpG preference of CPD formation. In addition, the mutagenicity of CPDs in the dermis was lower than that in the epidermis irrespective of the UVR source, suggesting a higher efficiency in the dermis to reduce the genotoxicity of CPDs produced within it. We also estimated the minimum amount of photolesions required to induce the mutation induction suppression (MIS) response in the epidermis to be around 15 64PPs or 100 CPDs per million bases in DNA as the mean estimate from UVC and UVB-induced MIS.
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Affiliation(s)
- Hironobu Ikehata
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Rodriguez Y, Duan M, Wyrick JJ, Smerdon MJ. A cassette of basic amino acids in histone H2B regulates nucleosome dynamics and access to DNA damage. J Biol Chem 2018; 293:7376-7386. [PMID: 29588367 PMCID: PMC5949990 DOI: 10.1074/jbc.ra117.000358] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/12/2018] [Indexed: 12/25/2022] Open
Abstract
Nucleosome dynamics, such as spontaneous DNA unwrapping, are postulated to have a critical role in regulating the access of DNA repair machinery to DNA lesions within nucleosomes. However, the specific histone domains that regulate nucleosome dynamics and the impact of such changes in intrinsic nucleosome dynamics on DNA repair are not well understood. Previous studies identified a highly conserved region in the N-terminal tail of histone H2B known as the histone H2Brepression (or HBR) domain, which has a significant influence on gene expression, chromatin assembly, and DNA damage formation and repair. However, the molecular mechanism(s) that may account for these observations are limited. In this study, we characterized the stability and dynamics of ΔHBR mutant nucleosome core particles (NCPs) in vitro by restriction enzyme accessibility (REA), FRET, and temperature-induced sliding of histone octamers. Our results indicate that ΔHBR-NCPs are more dynamic, with a larger steady-state fraction of the NCP population occupying the unwrapped state than for WT-NCPs. Additionally, ΔHBR-histone octamers are more susceptible to temperature-induced sliding on DNA than WT histone octamers. Furthermore, we show that the activity of base excision repair enzymes at uracil lesions and single nucleotide gaps is enhanced in a site-specific manner in ΔHBR-NCPs. This enhanced activity correlates well with regions exhibiting increased DNA unwrapping. Finally, removal of the HBR domain is not sufficient to completely alleviate the structural constraints imposed by histone octamers on the activity of base excision repair enzymes.
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Affiliation(s)
- Yesenia Rodriguez
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520
| | - Mingrui Duan
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520
| | - John J Wyrick
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520; Center for Reproductive Biology, Washington State University, Pullman, Washington 99164-7520
| | - Michael J Smerdon
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520.
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Single-nucleotide resolution dynamic repair maps of UV damage in Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A 2018; 115:E3408-E3415. [PMID: 29581276 DOI: 10.1073/pnas.1801687115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers and (6-4) pyrimidine-pyrimidone photoproducts in the Saccharomyces cerevisiae genome. We find that these photoproducts are removed from the genome primarily by incisions 13-18 nucleotides 5' and 6-7 nucleotides 3' to the UV damage that generate 21- to 27-nt-long excision products. Analyses of the excision repair kinetics both in single genes and at the genome-wide level reveal strong transcription-coupled repair of the transcribed strand at early time points followed by predominantly nontranscribed strand repair at later stages. We have also characterized the excision repair level as a function of the transcription level. The availability of high-resolution and dynamic repair maps should aid in future repair and mutagenesis studies in this model organism.
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