1
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Wu Y, Adeel MM, Xia D, Sancar A, Li W. Nucleotide excision repair of aflatoxin-induced DNA damage within the 3D human genome organization. Nucleic Acids Res 2024:gkae755. [PMID: 39258558 DOI: 10.1093/nar/gkae755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 08/13/2024] [Accepted: 08/20/2024] [Indexed: 09/12/2024] Open
Abstract
Aflatoxin B1 (AFB1), a potent mycotoxin, is one of the environmental risk factors that cause liver cancer. In the liver, the bioactivated AFB1 intercalates into the DNA double helix to form a bulky DNA adduct which will lead to mutation if left unrepaired. Here, we adapted the tXR-seq method to measure the nucleotide excision repair of AFB1-induced DNA adducts at single-nucleotide resolution on a genome-wide scale, and compared it with repair data obtained from conventional UV-damage XR-seq. Our results showed that transcription-coupled repair plays a major role in the damage removal process. We further analyzed the distribution of nucleotide excision repair sites for AFB1-induced DNA adducts within the 3D human genome organization. Our analysis revealed a heterogeneous AFB1-dG repair across four different organization levels, including chromosome territories, A/B compartments, TADs, and chromatin loops. We found that chromosomes positioned closer to the nuclear center and regions within A compartments have higher levels of nucleotide excision repair. Notably, we observed high repair activity around both TAD boundaries and loop anchors. These findings provide insights into the complex interplay between AFB1-induced DNA damage repair, transcription, and 3D genome organization, shedding light on the mechanisms underlying AFB1-induced mutagenesis.
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Affiliation(s)
- Yiran Wu
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Muhammad Muzammal Adeel
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Dian Xia
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Wentao Li
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA
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2
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Barbour JA, Ou T, Yang H, Fang H, Yue NC, Zhu X, Wong-Brown MW, Wong YT, Bowden NA, Wu S, Wong JWH. ERCC2 mutations alter the genomic distribution pattern of somatic mutations and are independently prognostic in bladder cancer. CELL GENOMICS 2024; 4:100627. [PMID: 39096913 PMCID: PMC11406173 DOI: 10.1016/j.xgen.2024.100627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/17/2024] [Accepted: 07/10/2024] [Indexed: 08/05/2024]
Abstract
Excision repair cross-complementation group 2 (ERCC2) encodes the DNA helicase xeroderma pigmentosum group D, which functions in transcription and nucleotide excision repair. Point mutations in ERCC2 are putative drivers in around 10% of bladder cancers (BLCAs) and a potential positive biomarker for cisplatin therapy response. Nevertheless, the prognostic significance directly attributed to ERCC2 mutations and its pathogenic role in genome instability remain poorly understood. We first demonstrated that mutant ERCC2 is an independent predictor of prognosis in BLCA. We then examined its impact on the somatic mutational landscape using a cohort of ERCC2 wild-type (n = 343) and mutant (n = 39) BLCA whole genomes. The genome-wide distribution of somatic mutations is significantly altered in ERCC2 mutants, including T[C>T]N enrichment, altered replication time correlations, and CTCF-cohesin binding site mutation hotspots. We leverage these alterations to develop a machine learning model for predicting pathogenic ERCC2 mutations, which may be useful to inform treatment of patients with BLCA.
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Affiliation(s)
- Jayne A Barbour
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Ou
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China
| | - Haocheng Yang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hu Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Institute of Biomedical Data, South China Hospital, Medical School, Shenzhen University, Shenzhen, China
| | - Noel C Yue
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaoqiang Zhu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Michelle W Wong-Brown
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Yuen T Wong
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Nikola A Bowden
- Centre for Drug Repurposing and Medicines Research, University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Song Wu
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, China; Department of Urology, South China Hospital, Medical School, Shenzhen University, Shenzhen, China.
| | - Jason W H Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China; Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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3
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Yao YM, Miodownik I, O'Hagan MP, Jbara M, Afek A. Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome. Transcription 2024:1-25. [PMID: 39033307 DOI: 10.1080/21541264.2024.2379161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Transcription factors (TFs) intricately navigate the vast genomic landscape to locate and bind specific DNA sequences for the regulation of gene expression programs. These interactions occur within a dynamic cellular environment, where both DNA and TF proteins experience continual chemical and structural perturbations, including epigenetic modifications, DNA damage, mechanical stress, and post-translational modifications (PTMs). While many of these factors impact TF-DNA binding interactions, understanding their effects remains challenging and incomplete. This review explores the existing literature on these dynamic changes and their potential impact on TF-DNA interactions.
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Affiliation(s)
- Yumi Minyi Yao
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Irina Miodownik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michael P O'Hagan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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4
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Pfeifer GP, Jin SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet 2024:10.1038/s41576-024-00748-4. [PMID: 38918545 DOI: 10.1038/s41576-024-00748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
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5
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Bergis-Ser C, Reji M, Latrasse D, Bergounioux C, Benhamed M, Raynaud C. Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity. NATURE PLANTS 2024; 10:857-873. [PMID: 38658791 DOI: 10.1038/s41477-024-01678-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Maintenance of genome integrity is an essential process in all organisms. Mechanisms avoiding the formation of DNA lesions or mutations are well described in animals because of their relevance to human health and cancer. In plants, they are of growing interest because DNA damage accumulation is increasingly recognized as one of the consequences of stress. Although the cellular response to DNA damage is mostly studied in response to genotoxic treatments, the main source of DNA lesions is cellular activity itself. This can occur through the production of reactive oxygen species as well as DNA processing mechanisms such as DNA replication or transcription and chromatin dynamics. In addition, how lesions are formed and repaired is greatly influenced by chromatin features and dynamics and by DNA and RNA metabolism. Notably, actively transcribed regions or replicating DNA, because they are less condensed and are sites of DNA processing, are more exposed to DNA damage. However, at the same time, a wealth of cellular mechanisms cooperate to favour DNA repair at these genomic loci. These intricate relationships that shape the distribution of mutations along the genome have been studied extensively in animals but much less in plants. In this Review, we summarize how chromatin dynamics influence lesion formation and DNA repair in plants, providing a comprehensive view of current knowledge and highlighting open questions with regard to what is known in other organisms.
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Affiliation(s)
- Clara Bergis-Ser
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Meega Reji
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, India
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
- Institut Universitaire de France, Orsay, France
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France.
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6
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Duan M, Leng S, Mao P. Cisplatin in the era of PARP inhibitors and immunotherapy. Pharmacol Ther 2024; 258:108642. [PMID: 38614254 DOI: 10.1016/j.pharmthera.2024.108642] [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: 01/02/2024] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/15/2024]
Abstract
Platinum compounds such as cisplatin, carboplatin and oxaliplatin are widely used in chemotherapy. Cisplatin induces cytotoxic DNA damage that blocks DNA replication and gene transcription, leading to arrest of cell proliferation. Although platinum therapy alone is effective against many tumors, cancer cells can adapt to the treatment and gain resistance. The mechanisms for cisplatin resistance are complex, including low DNA damage formation, high DNA repair capacity, changes in apoptosis signaling pathways, rewired cell metabolisms, and others. Drug resistance compromises the clinical efficacy and calls for new strategies by combining cisplatin with other therapies. Exciting progress in cancer treatment, particularly development of poly (ADP-ribose) polymerase (PARP) inhibitors and immune checkpoint inhibitors, opened a new chapter to combine cisplatin with these new cancer therapies. In this Review, we discuss how platinum synergizes with PARP inhibitors and immunotherapy to bring new hope to cancer patients.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Shuguang Leng
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA.
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA.
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7
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Mas-Ponte D, Supek F. Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation. Nucleic Acids Res 2024; 52:4393-4408. [PMID: 38587182 PMCID: PMC11077091 DOI: 10.1093/nar/gkae252] [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: 09/18/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Local mutation rates in human are highly heterogeneous, with known variability at the scale of megabase-sized chromosomal domains, and, on the other extreme, at the scale of oligonucleotides. The intermediate, kilobase-scale heterogeneity in mutation risk is less well characterized. Here, by analyzing thousands of somatic genomes, we studied mutation risk gradients along gene bodies, representing a genomic scale spanning roughly 1-10 kb, hypothesizing that different mutational mechanisms are differently distributed across gene segments. The main heterogeneity concerns several kilobases at the transcription start site and further downstream into 5' ends of gene bodies; these are commonly hypomutated with several mutational signatures, most prominently the ubiquitous C > T changes at CpG dinucleotides. The width and shape of this mutational coldspot at 5' gene ends is variable across genes, and corresponds to variable interval of lowered DNA methylation depending on gene activity level and regulation. Such hypomutated loci, at 5' gene ends or elsewhere, correspond to DNA hypomethylation that can associate with various landmarks, including intragenic enhancers, Polycomb-marked regions, or chromatin loop anchor points. Tissue-specific DNA hypomethylation begets tissue-specific local hypomutation. Of note, direction of mutation risk is inverted for AID/APOBEC3 cytosine deaminase activity, whose signatures are enriched in hypomethylated regions.
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Affiliation(s)
- David Mas-Ponte
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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8
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Ngo TTM, Liu B, Wang F, Basu A, Wu C, Ha T. Dependence of nucleosome mechanical stability on DNA mismatches. eLife 2024; 13:RP95514. [PMID: 38656237 DOI: 10.7554/elife.95514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.
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Affiliation(s)
- Thuy T M Ngo
- Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States
- Division of Oncological Sciences, Oregon Health and Science University, Portland, United States
| | - Bailey Liu
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Aakash Basu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, United States
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, United States
| | - Taekjip Ha
- Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States
- Department of Pediatrics, Harvard Medical School, Boston, United States
- Howard Hughes Medical Institute, Boston, United States
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9
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Kaur K, Ai R, Perry AG, Riley B, Roberts EL, Montano EN, Han J, Roacho J, Lopez BG, Skelsey MK, Childs MV, Childs JN, Dobak J, Ibarra C, Jansen B, Clarke LE, Stone S, Whitaker JW. Skin Cancer Risk Is Increased by Somatic Mutations Detected Noninvasively in Healthy-Appearing Sun-Exposed Skin. J Invest Dermatol 2024:S0022-202X(24)00176-3. [PMID: 38513819 DOI: 10.1016/j.jid.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 03/23/2024]
Abstract
Skin cancer risk is increased by exposure to ultraviolet radiation (UVR). Because UVR exposure accumulates over time and lighter skin is more susceptible to UVR, age and skin tone are risk factors for skin cancer. However, measurements of somatic mutations in healthy-appearing skin have not been used to calculate skin cancer risk. In this study, we developed a noninvasive test that quantifies somatic mutations in healthy-appearing sun-exposed skin and applied it to a 1038-subject cohort. Somatic mutations were combined with other known skin cancer risk factors to train a model to calculate risk. The final model (DNA-Skin Cancer Assessment of Risk) was trained to predict personal history of skin cancer from age, family history, skin tone, and mutation count. The addition of mutation count significantly improved model performance (OR = 1.3, 95% confidence interval = 1.14-1.48; P = 5.3 × 10-6) and made a more significant contribution than skin tone. Calculations of skin cancer risk matched the known United States population prevalence, indicating that DNA-Skin Cancer Assessment of Risk was well-calibrated. In conclusion, somatic mutations in healthy-appearing sun-exposed skin increase skin cancer risk, and mutations capture risk information that is not accounted for by other risk factors. Clinical utility is supported by the noninvasive nature of skin sample collection through adhesive patches.
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Affiliation(s)
| | - Rizi Ai
- DermTech, San Diego, California, USA
| | | | - Bae Riley
- DermTech, San Diego, California, USA
| | | | | | | | | | | | - Maral K Skelsey
- Department of Dermatology, School of Medicine, Georgetown University, Washington, District of Columbia, USA
| | - Maria V Childs
- Department of Dermatology, Texas A&M University College of Medicine, Temple, Texas, USA
| | - James N Childs
- Department of Dermatology, Texas A&M University College of Medicine, Temple, Texas, USA
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10
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Shen Y, Shi K, Li D, Wang Q, Wu K, Feng C. Prognostic analysis of mutated genes and insight into effects of DNA damage and repair on mutational strand asymmetries in gastric cancer. Biochem Biophys Rep 2024; 37:101597. [PMID: 38371526 PMCID: PMC10873876 DOI: 10.1016/j.bbrep.2023.101597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024] Open
Abstract
Gastric cancer (GACA) is a complex and multifaceted disease influenced by a variety of environmental and genetic factors. Somatic mutations play a major role in its development, and their characteristics, including the asymmetry between two DNA strands, are of great interest and appear as a signal of information and guidance, revealing mechanisms of DNA damage and repair. Here, we analyzed the impact of High-frequency mutated genes on patient prognosis and found that the effect of expression levels of tumor protein p53 (TP53) and lysine methyltransferase 2C (KMT2C) genes remained high throughout the development of GACA, with similar expression patterns. After investigating mutation asymmetry across mutagenic processes, we found that transcriptional asymmetry was dominated by T > G mutations under the influence of transcription couples repair and damage. The apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC) enzyme that induces mutations during DNA replication has been identified here and we identified a replicative asymmetry, which was dominated by C > A mutations in left-replicating. Strand bias in different mutation classes at transcription factor binding sites and enhancer regions were also confirmed, which implies the important role of non-coding regulatory elements in the occurrence of mutations. This work systematically describes mutational strand asymmetries in specific genomic regions, shedding light on the DNA damage and repair mechanisms underlying somatic mutations in cohorts of GACA patients with gastric cancer.
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Affiliation(s)
- Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Science, Jiangsu Academy of Agriculture Science, Nanjing, China
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qiang Wang
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Kangkang Wu
- Department of Infectious Disease, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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11
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Morledge-Hampton B, Kalyanaraman A, Wyrick JJ. Analysis of cytosine deamination events in excision repair sequencing reads reveals mechanisms of incision site selection in NER. Nucleic Acids Res 2024; 52:1720-1735. [PMID: 38109317 PMCID: PMC10899786 DOI: 10.1093/nar/gkad1195] [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: 05/17/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
Nucleotide excision repair (NER) removes helix-distorting DNA lesions and is therefore critical for genome stability. During NER, DNA is unwound on either side of the lesion and excised, but the rules governing incision site selection, particularly in eukaryotic cells, are unclear. Excision repair-sequencing (XR-seq) sequences excised NER fragments, but analysis has been limited because the lesion location is unknown. Here, we exploit accelerated cytosine deamination rates in UV-induced CPD (cyclobutane pyrimidine dimer) lesions to precisely map their locations at C to T mismatches in XR-seq reads, revealing general and species-specific patterns of incision site selection during NER. Our data indicate that the 5' incision site occurs preferentially in HYV (i.e. not G; C/T; not T) sequence motifs, a pattern that can be explained by sequence preferences of the XPF-ERCC1 endonuclease. In contrast, the 3' incision site does not show strong sequence preferences, once truncated reads arising from mispriming events are excluded. Instead, the 3' incision is partially determined by the 5' incision site distance, indicating that the two incision events are coupled. Finally, our data reveal unique and coupled NER incision patterns at nucleosome boundaries. These findings reveal key principles governing NER incision site selection in eukaryotic cells.
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Affiliation(s)
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
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12
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Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gordân R, He Y, Mao P. High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma. Proc Natl Acad Sci U S A 2024; 121:e2310854121. [PMID: 38241433 PMCID: PMC10823218 DOI: 10.1073/pnas.2310854121] [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: 06/27/2023] [Accepted: 11/20/2023] [Indexed: 01/21/2024] Open
Abstract
Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5' side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
| | - Shenghan Song
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM87131
| | - Hana Wasserman
- Program in Computational Biology and Bioinformatics, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC27708
| | - Po-Hsuen Lee
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
| | - Ke Jian Liu
- Department of Pathology, Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY11794-7263
| | - Raluca Gordân
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC27708
- Department of Computer Science, Duke University, Durham, NC27708
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC27708
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM87131
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
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13
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Otlu B, Alexandrov LB. Evaluating topography of mutational signatures with SigProfilerTopography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574683. [PMID: 38260507 PMCID: PMC10802511 DOI: 10.1101/2024.01.08.574683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The mutations found in a cancer genome are shaped by diverse processes, each displaying a characteristic mutational signature that may be influenced by the genome's architecture. While prior analyses have evaluated the effect of topographical genomic features on mutational signatures, there has been no computational tool that can comprehensively examine this interplay. Here, we present SigProfilerTopography, a Python package that allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures, unveiling their underlying biological and molecular mechanisms.
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Affiliation(s)
- Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA 92037
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14
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Arnedo-Pac C, Muiños F, Gonzalez-Perez A, Lopez-Bigas N. Hotspot propensity across mutational processes. Mol Syst Biol 2024; 20:6-27. [PMID: 38177930 PMCID: PMC10883281 DOI: 10.1038/s44320-023-00001-w] [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: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024] Open
Abstract
The sparsity of mutations observed across tumours hinders our ability to study mutation rate variability at nucleotide resolution. To circumvent this, here we investigated the propensity of mutational processes to form mutational hotspots as a readout of their mutation rate variability at single base resolution. Mutational signatures 1 and 17 have the highest hotspot propensity (5-78 times higher than other processes). After accounting for trinucleotide mutational probabilities, sequence composition and mutational heterogeneity at 10 Kbp, most (94-95%) signature 17 hotspots remain unexplained, suggesting a significant role of local genomic features. For signature 1, the inclusion of genome-wide distribution of methylated CpG sites into models can explain most (80-100%) of the hotspot propensity. There is an increased hotspot propensity of signature 1 in normal tissues and de novo germline mutations. We demonstrate that hotspot propensity is a useful readout to assess the accuracy of mutation rate models at nucleotide resolution. This new approach and the findings derived from it open up new avenues for a range of somatic and germline studies investigating and modelling mutagenesis.
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Affiliation(s)
- Claudia Arnedo-Pac
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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15
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Seplyarskiy V, Koch EM, Lee DJ, Lichtman JS, Luan HH, Sunyaev SR. A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription. Nat Genet 2023; 55:2235-2242. [PMID: 38036792 PMCID: PMC11348951 DOI: 10.1038/s41588-023-01562-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 10/06/2023] [Indexed: 12/02/2023]
Abstract
De novo mutations occur at substantially different rates depending on genomic location, sequence context and DNA strand. The success of methods to estimate selection intensity, infer demographic history and map rare disease genes, depends strongly on assumptions about the local mutation rate. Here we present Roulette, a genome-wide mutation rate model at basepair resolution that incorporates known determinants of local mutation rate. Roulette is shown to be more accurate than existing models. We use Roulette to refine the estimates of population growth within Europe by incorporating the full range of human mutation rates. The analysis of significant deviations from the model predictions revealed a tenfold increase in mutation rate in nearly all genes transcribed by polymerase III (Pol III), suggesting a new mutagenic mechanism. We also detected an elevated mutation rate within transcription factor binding sites restricted to sites actively used in testis and residing in promoters.
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Affiliation(s)
- Vladimir Seplyarskiy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Evan M Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Daniel J Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua S Lichtman
- NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
- Soleil Labs, South San Francisco, CA, USA
| | - Harding H Luan
- NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
- Soleil Labs, South San Francisco, CA, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA.
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16
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Cohen Y, Adar S. Novel insights into bulky DNA damage formation and nucleotide excision repair from high-resolution genomics. DNA Repair (Amst) 2023; 130:103549. [PMID: 37566959 DOI: 10.1016/j.dnarep.2023.103549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
DNA damages compromise cell function and fate. Cells of all organisms activate a global DNA damage response that includes a signaling stress response, activation of checkpoints, and recruitment of repair enzymes. Especially deleterious are bulky, helix-distorting damages that block transcription and replication. Due to their miscoding nature, these damages lead to mutations and cancer. In human cells, bulky DNA damages are repaired by nucleotide excision repair (NER). To date, the basic mechanism of NER in naked DNA is well defined. Still, there is a fundamental gap in our understanding of how repair is orchestrated despite the packaging of DNA in chromatin, and how it is coordinated with active transcription and replication. The last decade has brought forth huge advances in our ability to detect and assay bulky DNA damages and their repair at single nucleotide resolution across the human genome. Here we review recent findings on the effect of chromatin and DNA-binding proteins on the formation of bulky DNA damages, and novel insights on NER, provided by the recent application of genomic methods.
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Affiliation(s)
- Yuval Cohen
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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17
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Yuan C, Tang L, Lopdell T, Petrov VA, Oget-Ebrad C, Moreira GCM, Gualdrón Duarte JL, Sartelet A, Cheng Z, Salavati M, Wathes DC, Crowe MA, Coppieters W, Littlejohn M, Charlier C, Druet T, Georges M, Takeda H. An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants. Genome Res 2023; 33:1848-1864. [PMID: 37751945 PMCID: PMC10691486 DOI: 10.1101/gr.277947.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023]
Abstract
We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.
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Affiliation(s)
- Can Yuan
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Lijing Tang
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Thomas Lopdell
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - Vyacheslav A Petrov
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Claire Oget-Ebrad
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | | | - José Luis Gualdrón Duarte
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Arnaud Sartelet
- Clinical Department of Ruminant, University of Liège, 4000 Liège, Belgium
| | - Zhangrui Cheng
- Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
| | - Mazdak Salavati
- Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
| | - D Claire Wathes
- Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
| | - Mark A Crowe
- School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
| | - Wouter Coppieters
- GIGA Genomics platform, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Mathew Littlejohn
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium;
| | - Haruko Takeda
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
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18
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Liu C, Wang Z, Wang J, Liu C, Wang M, Ngo V, Wang W. Predicting regional somatic mutation rates using DNA motifs. PLoS Comput Biol 2023; 19:e1011536. [PMID: 37782656 PMCID: PMC10569533 DOI: 10.1371/journal.pcbi.1011536] [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: 04/02/2023] [Revised: 10/12/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
How the locus-specificity of epigenetic modifications is regulated remains an unanswered question. A contributing mechanism is that epigenetic enzymes are recruited to specific loci by DNA binding factors recognizing particular sequence motifs (referred to as epi-motifs). Using these motifs to predict biological outputs depending on local epigenetic state such as somatic mutation rates would confirm their functionality. Here, we used DNA motifs including known TF motifs and epi-motifs as a surrogate of epigenetic signals to predict somatic mutation rates in 13 cancers at an average 23kbp resolution. We implemented an interpretable neural network model, called contextual regression, to successfully learn the universal relationship between mutations and DNA motifs, and uncovered motifs that are most impactful on the regional mutation rates such as TP53 and epi-motifs associated with H3K9me3. Furthermore, we identified genomic regions with significantly higher mutation rates than the expected values in each individual tumor and demonstrated that such cancer-related regions can accurately predict cancer types. Interestingly, we found that the same mutation signatures often have different contributions to cancer-related and cancer-independent regions, and we also identified the motifs with the most contribution to each mutation signature.
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Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Jun Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Chengyu Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Vu Ngo
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
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19
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Liu Z, Samee M. Structural underpinnings of mutation rate variations in the human genome. Nucleic Acids Res 2023; 51:7184-7197. [PMID: 37395403 PMCID: PMC10415140 DOI: 10.1093/nar/gkad551] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
Single nucleotide mutation rates have critical implications for human evolution and genetic diseases. Importantly, the rates vary substantially across the genome and the principles underlying such variations remain poorly understood. A recent model explained much of this variation by considering higher-order nucleotide interactions in the 7-mer sequence context around mutated nucleotides. This model's success implicates a connection between DNA shape and mutation rates. DNA shape, i.e. structural properties like helical twist and tilt, is known to capture interactions between nucleotides within a local context. Thus, we hypothesized that changes in DNA shape features at and around mutated positions can explain mutation rate variations in the human genome. Indeed, DNA shape-based models of mutation rates showed similar or improved performance over current nucleotide sequence-based models. These models accurately characterized mutation hotspots in the human genome and revealed the shape features whose interactions underlie mutation rate variations. DNA shape also impacts mutation rates within putative functional regions like transcription factor binding sites where we find a strong association between DNA shape and position-specific mutation rates. This work demonstrates the structural underpinnings of nucleotide mutations in the human genome and lays the groundwork for future models of genetic variations to incorporate DNA shape.
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Affiliation(s)
- Zian Liu
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Md Abul Hassan Samee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
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20
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Elliott K, Singh VK, Boström M, Larsson E. Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins. Nat Commun 2023; 14:2701. [PMID: 37169761 PMCID: PMC10175305 DOI: 10.1038/s41467-023-38266-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/30/2023] [Indexed: 05/13/2023] Open
Abstract
Decades ago, it was shown that proteins binding to DNA can quantitatively alter the formation of DNA damage by UV light. This established the principle of UV footprinting for non-intrusive study of protein-DNA contacts in living cells, albeit at limited scale and precision. Here, we perform deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing. Several transcription factors exhibited distinctive and repeatable damage signatures indicative of site occupancy, involving strong (up to 17-fold) position-specific elevations and reductions in CPD formation frequency relative to naked DNA. Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions.
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Affiliation(s)
- Kerryn Elliott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Vinod Kumar Singh
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Martin Boström
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden.
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21
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Selvam K, Sivapragasam S, Poon GMK, Wyrick JJ. Detecting recurrent passenger mutations in melanoma by targeted UV damage sequencing. Nat Commun 2023; 14:2702. [PMID: 37169747 PMCID: PMC10175485 DOI: 10.1038/s41467-023-38265-3] [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: 09/21/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Sequencing of melanomas has identified hundreds of recurrent mutations in both coding and non-coding DNA. These include a number of well-characterized oncogenic driver mutations, such as coding mutations in the BRAF and NRAS oncogenes, and non-coding mutations in the promoter of telomerase reverse transcriptase (TERT). However, the molecular etiology and significance of most of these mutations is unknown. Here, we use a new method known as CPD-capture-seq to map UV-induced cyclobutane pyrimidine dimers (CPDs) with high sequencing depth and single nucleotide resolution at sites of recurrent mutations in melanoma. Our data reveal that many previously identified drivers and other recurrent mutations in melanoma occur at CPD hotspots in UV-irradiated melanocytes, often associated with an overlapping binding site of an E26 transformation-specific (ETS) transcription factor. In contrast, recurrent mutations in the promoters of a number of known or suspected cancer genes are not associated with elevated CPD levels. Our data indicate that a subset of recurrent protein-coding mutations are also likely caused by ETS-induced CPD hotspots. This analysis indicates that ETS proteins profoundly shape the mutation landscape of melanoma and reveals a method for distinguishing potential driver mutations from passenger mutations whose recurrence is due to elevated UV damage.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, 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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22
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Adeyemi RO. Transcription and DNA repair collide after UV exposure. Proc Natl Acad Sci U S A 2023; 120:e2303201120. [PMID: 37036973 PMCID: PMC10120015 DOI: 10.1073/pnas.2303201120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Affiliation(s)
- Richard O. Adeyemi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
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23
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Mielko Z, Zhang Y, Sahay H, Liu Y, Schaich MA, Schnable B, Morrison AM, Burdinski D, Adar S, Pufall M, Van Houten B, Gordân R, Afek A. UV irradiation remodels the specificity landscape of transcription factors. Proc Natl Acad Sci U S A 2023; 120:e2217422120. [PMID: 36888663 PMCID: PMC10089200 DOI: 10.1073/pnas.2217422120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
Somatic mutations are highly enriched at transcription factor (TF) binding sites, with the strongest trend being observed for ultraviolet light (UV)-induced mutations in melanomas. One of the main mechanisms proposed for this hypermutation pattern is the inefficient repair of UV lesions within TF-binding sites, caused by competition between TFs bound to these lesions and the DNA repair proteins that must recognize the lesions to initiate repair. However, TF binding to UV-irradiated DNA is poorly characterized, and it is unclear whether TFs maintain specificity for their DNA sites after UV exposure. We developed UV-Bind, a high-throughput approach to investigate the impact of UV irradiation on protein-DNA binding specificity. We applied UV-Bind to ten TFs from eight structural families, and found that UV lesions significantly altered the DNA-binding preferences of all the TFs tested. The main effect was a decrease in binding specificity, but the precise effects and their magnitude differ across factors. Importantly, we found that despite the overall reduction in DNA-binding specificity in the presence of UV lesions, TFs can still compete with repair proteins for lesion recognition, in a manner consistent with their specificity for UV-irradiated DNA. In addition, for a subset of TFs, we identified a surprising but reproducible effect at certain nonconsensus DNA sequences, where UV irradiation leads to a high increase in the level of TF binding. These changes in DNA-binding specificity after UV irradiation, at both consensus and nonconsensus sites, have important implications for the regulatory and mutagenic roles of TFs in the cell.
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Affiliation(s)
- Zachery Mielko
- Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27708
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Department of Computer Science, Duke University, Durham, NC 27708
| | - Yuning Zhang
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
| | - Harshit Sahay
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham NC 27708
| | - Yiling Liu
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27708
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham NC 27708
| | - Matthew A Schaich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- UPMC-Hillman Cancer Center, Pittsburgh, PA 15213
| | - Brittani Schnable
- UPMC-Hillman Cancer Center, Pittsburgh, PA 15213
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Abigail M Morrison
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Debbie Burdinski
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Miles Pufall
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242
| | - Bennett Van Houten
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham NC 27708
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- UPMC-Hillman Cancer Center, Pittsburgh, PA 15213
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA 15213
| | - Raluca Gordân
- Department of Computer Science, Duke University, Durham, NC 27708
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27708
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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24
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Carrasco Pro S, Hook H, Bray D, Berenzy D, Moyer D, Yin M, Labadorf AT, Tewhey R, Siggers T, Fuxman Bass JI. Widespread perturbation of ETS factor binding sites in cancer. Nat Commun 2023; 14:913. [PMID: 36808133 PMCID: PMC9938127 DOI: 10.1038/s41467-023-36535-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/03/2023] [Indexed: 02/19/2023] Open
Abstract
Although >90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a transcription factor (TF)-aware burden test based on a model of coherent TF function in promoters. We apply this test to NCVs from the Pan-Cancer Analysis of Whole Genomes cohort and predict 2555 driver NCVs in the promoters of 813 genes across 20 cancer types. These genes are enriched in cancer-related gene ontologies, essential genes, and genes associated with cancer prognosis. We find that 765 candidate driver NCVs alter transcriptional activity, 510 lead to differential binding of TF-cofactor regulatory complexes, and that they primarily impact the binding of ETS factors. Finally, we show that different NCVs within a promoter often affect transcriptional activity through shared mechanisms. Our integrated computational and experimental approach shows that cancer NCVs are widespread and that ETS factors are commonly disrupted.
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Affiliation(s)
| | - Heather Hook
- Department of Biology, Boston University, Boston, MA, USA
| | - David Bray
- Bioinformatics Program, Boston University, Boston, MA, USA
| | | | - Devlin Moyer
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meimei Yin
- Department of Biology, Boston University, Boston, MA, USA
| | - Adam Thomas Labadorf
- Bioinformatics Hub, Boston University, Boston, MA, USA
- Boston University School of Medicine, Department of Neurology, Boston, MA, USA
| | | | - Trevor Siggers
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
| | - Juan Ignacio Fuxman Bass
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
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25
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Bohm KA, Wyrick JJ. Damage mapping techniques and the light they have shed on canonical and atypical UV photoproducts. Front Genet 2023; 13:1102593. [PMID: 36704334 PMCID: PMC9871259 DOI: 10.3389/fgene.2022.1102593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Ultraviolet (UV) light is a pervasive threat to the DNA of terrestrial organisms. UV light induces helix-distorting DNA lesions, primarily cyclobutane pyrimidine dimers (CPDs) that form between neighboring pyrimidine bases. Unrepaired CPD lesions cause cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which is the predominant mutation class in skin cancer genomes. However, many driver mutations in melanoma (e.g., in the BRAF and NRAS oncogenes) do not fit this UV mutation signature. Recent studies have brought to light the intriguing hypothesis that these driver mutations may be induced by infrequent or atypical UV photoproducts, including pyrimidine 6-4 pyrimidone photoproducts (6-4PP) and thymine-adenine (TA) photoproducts. Here, we review innovative methods for mapping both canonical and atypical UV-induced photoproducts across the genome.
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Affiliation(s)
- Kaitlynne A. Bohm
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
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26
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Draetta EL, Lazarević D, Provero P, Cittaro D. The frequency of somatic mutations in cancer predicts the phenotypic relevance of germline mutations. Front Genet 2023; 13:1045301. [PMID: 36699457 PMCID: PMC9868957 DOI: 10.3389/fgene.2022.1045301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Genomic sequence mutations can be pathogenic in both germline and somatic cells. Several authors have observed that often the same genes are involved in cancer when mutated in somatic cells and in genetic diseases when mutated in the germline. Recent advances in high-throughput sequencing techniques have provided us with large databases of both types of mutations, allowing us to investigate this issue in a systematic way. Hence, we applied a machine learning based framework to this problem, comparing multiple models. The models achieved significant predictive power as shown by both cross-validation and their application to recently discovered gene/phenotype associations not used for training. We found that genes characterized by high frequency of somatic mutations in the most common cancers and ancient evolutionary age are most likely to be involved in abnormal phenotypes and diseases. These results suggest that the combination of tolerance for mutations at the cell viability level (measured by the frequency of somatic mutations in cancer) and functional relevance (demonstrated by evolutionary conservation) are the main predictors of disease genes. Our results thus confirm the deep relationship between pathogenic mutations in somatic and germline cells, provide new insight into the common origin of cancer and genetic diseases, and can be used to improve the identification of new disease genes.
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Affiliation(s)
- Edoardo Luigi Draetta
- University of Milan, Milan, Italy,Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dejan Lazarević
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Provero
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy,Department of Neurosciences “Rita Levi Montalcini”, University of Turin, Turin, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy,*Correspondence: Davide Cittaro ,
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27
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Castro-Mondragon JA, Aure M, Lingjærde O, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen V, Mathelier A. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers. Nucleic Acids Res 2022; 50:12131-12148. [PMID: 36477895 PMCID: PMC9757053 DOI: 10.1093/nar/gkac1143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/03/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Most cancer alterations occur in the noncoding portion of the human genome, where regulatory regions control gene expression. The discovery of noncoding mutations altering the cells' regulatory programs has been limited to few examples with high recurrence or high functional impact. Here, we show that transcription factor binding sites (TFBSs) have similar mutation loads to those in protein-coding exons. By combining cancer somatic mutations in TFBSs and expression data for protein-coding and miRNA genes, we evaluate the combined effects of transcriptional and post-transcriptional alterations on the regulatory programs in cancers. The analysis of seven TCGA cohorts culminates with the identification of protein-coding and miRNA genes linked to mutations at TFBSs that are associated with a cascading trans-effect deregulation on the cells' regulatory programs. Our analyses of cis-regulatory mutations associated with miRNAs recurrently predict 12 mature miRNAs (derived from 7 precursors) associated with the deregulation of their target gene networks. The predictions are enriched for cancer-associated protein-coding and miRNA genes and highlight cis-regulatory mutations associated with the dysregulation of key pathways associated with carcinogenesis. By combining transcriptional and post-transcriptional regulation of gene expression, our method predicts cis-regulatory mutations related to the dysregulation of key gene regulatory networks in cancer patients.
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Affiliation(s)
- Jaime A Castro-Mondragon
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Gaustadalléen 23 B, N-0373 Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Ullernchausseen 70, N-0372 Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
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28
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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29
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Murat P, Perez C, Crisp A, van Eijk P, Reed SH, Guilbaud G, Sale JE. DNA replication initiation shapes the mutational landscape and expression of the human genome. SCIENCE ADVANCES 2022; 8:eadd3686. [PMID: 36351018 PMCID: PMC9645720 DOI: 10.1126/sciadv.add3686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with two distinct mechanisms, reflecting the two-step process of origin activation, triggering the formation of DNA breaks at the center of origins and local error-prone DNA synthesis in their immediate vicinity. We demonstrate that these replication initiation-dependent mutational processes exert an influence on phenotypic diversity in humans that is disproportionate to the origins' genomic size: By increasing mutational loads at gene promoters and splice junctions, the presence of an origin significantly influences both gene expression and mRNA isoform usage. Last, we show that mutagenesis at origins not only drives the evolution of origin sequences but also contributes to sculpting regulatory domains of the human genome.
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Affiliation(s)
- Pierre Murat
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alastair Crisp
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patrick van Eijk
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Simon H. Reed
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Guillaume Guilbaud
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julian E. Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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30
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Heide T, Househam J, Cresswell GD, Spiteri I, Lynn C, Mossner M, Kimberley C, Fernandez-Mateos J, Chen B, Zapata L, James C, Barozzi I, Chkhaidze K, Nichol D, Gunasri V, Berner A, Schmidt M, Lakatos E, Baker AM, Costa H, Mitchinson M, Piazza R, Jansen M, Caravagna G, Ramazzotti D, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Graham TA, Sottoriva A. The co-evolution of the genome and epigenome in colorectal cancer. Nature 2022; 611:733-743. [PMID: 36289335 PMCID: PMC9684080 DOI: 10.1038/s41586-022-05202-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/05/2022] [Indexed: 12/13/2022]
Abstract
Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
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Affiliation(s)
- Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chris Kimberley
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
- Centre for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Ketevan Chkhaidze
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Vinaya Gunasri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alison Berner
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Schmidt
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helena Costa
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Miriam Mitchinson
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Marnix Jansen
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Mathematics and Geosciences, University of Triest, Triest, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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31
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Effects of replication domains on genome-wide UV-induced DNA damage and repair. PLoS Genet 2022; 18:e1010426. [PMID: 36155646 PMCID: PMC9536635 DOI: 10.1371/journal.pgen.1010426] [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: 04/21/2022] [Revised: 10/06/2022] [Accepted: 09/12/2022] [Indexed: 11/19/2022] Open
Abstract
Nucleotide excision repair is the primary repair mechanism that removes UV-induced DNA lesions in placentals. Unrepaired UV-induced lesions could result in mutations during DNA replication. Although the mutagenesis of pyrimidine dimers is reasonably well understood, the direct effects of replication fork progression on nucleotide excision repair are yet to be clarified. Here, we applied Damage-seq and XR-seq techniques and generated replication maps in synchronized UV-treated HeLa cells. The results suggest that ongoing replication stimulates local repair in both early and late replication domains. Additionally, it was revealed that lesions on lagging strand templates are repaired slower in late replication domains, which is probably due to the imbalanced sequence context. Asymmetric relative repair is in line with the strand bias of melanoma mutations, suggesting a role of exogenous damage, repair, and replication in mutational strand asymmetry.
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32
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Garcia-Ruiz A, Kornacker K, Brash DE. Cyclobutane Pyrimidine Dimer Hyperhotspots as Sensitive Indicators of Keratinocyte UV Exposure †. Photochem Photobiol 2022; 98:987-997. [PMID: 35944237 PMCID: PMC9802031 DOI: 10.1111/php.13683] [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: 05/26/2022] [Accepted: 07/25/2022] [Indexed: 01/03/2023]
Abstract
The dominant DNA damage generated by UV exposure is the cyclobutane pyrimidine dimer (CPD), which alters skin cell physiology and induces cell death and mutation. Genome-wide nucleotide-resolution analysis of CPDs in melanocytes and fibroblasts has identified "CPD hyperhotspots", pyrimidine-pyrimidine sites hundreds of fold more susceptible to the generation of CPDs than the genomic average. Identifying hyperhotspots in keratinocytes could enable measuring individual past UV exposure in small skin samples and predicting future skin cancer risk. We therefore exposed neonatal human epidermal keratinocytes to narrowband UVB and quantified CPDs using the adductSeq high-throughput DNA sequencing method. Keratinocytes contained thousands of CPD hyperhotspots, with a UVB-sensitivity up to 550 fold greater than the genomic average. As with melanocytes, the most sensitive sites were located in promoter regions at ETS-family transcription factor binding sequence motifs, near RNA processing genes. Moreover, they lay at sequence motifs bound to ETS1 in CpG islands. These genes were specifically upregulated in skin and the CPD hyperhotspots were mutated in a fraction of keratinocyte cancers. Crucially for their biological importance and practical application, CPD hyperhotspot locations and UV-sensitivity ranking demonstrated high reproducibility across experiments and across skin donors. CPD hyperhotspots are therefore sensitive indicators of UV exposure.
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Affiliation(s)
- Alejandro Garcia-Ruiz
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA
| | | | - Douglas E. Brash
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520-8040, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520-8059, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520-8028, USA
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33
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Rouhani FJ, Zou X, Danecek P, Badja C, Amarante TD, Koh G, Wu Q, Memari Y, Durbin R, Martincorena I, Bassett AR, Gaffney D, Nik-Zainal S. Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells. Nat Genet 2022; 54:1406-1416. [PMID: 35953586 PMCID: PMC9470532 DOI: 10.1038/s41588-022-01147-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/24/2022] [Indexed: 12/27/2022]
Abstract
We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide resolution. We used genome sequencing data from two large hiPSC repositories involving 696 hiPSCs and daughter subclones. We find ultraviolet light (UV)-related damage in ~72% of skin fibroblast-derived hiPSCs (F-hiPSCs), occasionally resulting in substantial mutagenesis (up to 15 mutations per megabase). We demonstrate remarkable genomic heterogeneity between independent F-hiPSC clones derived during the same round of reprogramming due to oligoclonal fibroblast populations. In contrast, blood-derived hiPSCs (B-hiPSCs) had fewer mutations and no UV damage but a high prevalence of acquired BCOR mutations (26.9% of lines). We reveal strong selection pressure for BCOR mutations in F-hiPSCs and B-hiPSCs and provide evidence that they arise in vitro. Directed differentiation of hiPSCs and RNA sequencing showed that BCOR mutations have functional consequences. Our work strongly suggests that detailed nucleotide-resolution characterization is essential before using hiPSCs.
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Affiliation(s)
- Foad J Rouhani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Xueqing Zou
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cherif Badja
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Tauanne Dias Amarante
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Gene Koh
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Qianxin Wu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yasin Memari
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Inigo Martincorena
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniel Gaffney
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genomics plc, King Charles House, Oxford, UK
| | - Serena Nik-Zainal
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
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34
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Ocsenas O, Reimand J. Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin. PLoS Comput Biol 2022; 18:e1010393. [PMID: 35947558 PMCID: PMC9365152 DOI: 10.1371/journal.pcbi.1010393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/15/2022] [Indexed: 11/19/2022] Open
Abstract
Somatic mutations in cancer genomes are associated with DNA replication timing (RT) and chromatin accessibility (CA), however these observations are based on normal tissues and cell lines while primary cancer epigenomes remain uncharacterised. Here we use machine learning to model megabase-scale mutation burden in 2,500 whole cancer genomes and 17 cancer types via a compendium of 900 CA and RT profiles covering primary cancers, normal tissues, and cell lines. CA profiles of primary cancers, rather than those of normal tissues, are most predictive of regional mutagenesis in most cancer types. Feature prioritisation shows that the epigenomes of matching cancer types and organ systems are often the strongest predictors of regional mutation burden, highlighting disease-specific associations of mutational processes. The genomic distributions of mutational signatures are also shaped by the epigenomes of matched cancer and tissue types, with SBS5/40, carcinogenic and unknown signatures most accurately predicted by our models. In contrast, fewer associations of RT and regional mutagenesis are found. Lastly, the models highlight genomic regions with overrepresented mutations that dramatically exceed epigenome-derived expectations and show a pan-cancer convergence to genes and pathways involved in development and oncogenesis, indicating the potential of this approach for coding and non-coding driver discovery. The association of regional mutational processes with the epigenomes of primary cancers suggests that the landscape of passenger mutations is predominantly shaped by the epigenomes of cancer cells after oncogenic transformation.
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Affiliation(s)
- Oliver Ocsenas
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- * E-mail:
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35
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Thind AS, Ashford B, Strbenac D, Mitchell J, Lee J, Mueller SA, Minaei E, Perry JR, Ch’ng S, Iyer NG, Clark JR, Gupta R, Ranson M. Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma. Front Oncol 2022; 12:919118. [PMID: 35982973 PMCID: PMC9379253 DOI: 10.3389/fonc.2022.919118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Metastatic cutaneous squamous cell carcinoma (CSCC) is a highly morbid disease requiring radical surgery and adjuvant therapy, which is associated with a poor prognosis. Yet, compared to other advanced malignancies, relatively little is known of the genomic landscape of metastatic CSCC. We have previously reported the mutational signatures and mutational patterns of CCCTC-binding factor (CTCF) regions in metastatic CSCC. However, many other genomic components (indel signatures, non-coding drivers, and structural variants) of metastatic CSCC have not been reported. To this end, we performed whole genome sequencing on lymph node metastases and blood DNA from 25 CSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic CSCC. In the non-coding genome, 3′ untranslated region (3′UTR) regions of EVC (48% of specimens), PPP1R1A (48% of specimens), and ABCA4 (20% of specimens) along with the tumor-suppressing long non-coding RNA (lncRNA) LINC01003 (64% of specimens) were significantly functionally altered (Q-value < 0.05) and represent potential non-coding biomarkers of CSCC. Recurrent copy number loss in the tumor suppressor gene PTPRD was observed. Gene amplification was much less frequent, and few genes were recurrently amplified. Single nucleotide variants driver analyses from three tools confirmed TP53 and CDKN2A as recurrently mutated genes but also identified C9 as a potential novel driver in this disease. Furthermore, indel signature analysis highlighted the dominance of ID signature 13 (ID13) followed by ID8 and ID9. ID9 has previously been shown to have no association with skin melanoma, unlike ID13 and ID8, suggesting a novel pattern of indel variation in metastatic CSCC. The enrichment analysis of various genetically altered candidates shows enrichment of “TGF-beta regulation of extracellular matrix” and “cell cycle G1 to S check points.” These enriched terms are associated with genetic instability, cell proliferation, and migration as mechanisms of genomic drivers of metastatic CSCC.
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Affiliation(s)
- Amarinder Singh Thind
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Bruce Ashford
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
- *Correspondence: Bruce Ashford,
| | - Dario Strbenac
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Jenny Mitchell
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
| | - Jenny Lee
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Simon A. Mueller
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Otorhinolaryngology, Head and Neck Surgery, Zurich University Hospital and University of Zurich, Zurich, Switzerland
| | - Elahe Minaei
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jay R. Perry
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Sydney Ch’ng
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
| | - N. Gopalakrishna Iyer
- Department of Head and Neck Surgery, National Cancer Center, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Jonathan R. Clark
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Sydney, NSW, Australia
| | - Ruta Gupta
- Anatomical Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Marie Ranson
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
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Veitia RA. Who ever thought genetic mutations were random? TRENDS IN PLANT SCIENCE 2022; 27:733-735. [PMID: 35307269 DOI: 10.1016/j.tplants.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
In a recent study of de novo mutations in arabidopsis (Arabidopsis thaliana), Monroe et al. found a lower mutation frequency inside gene bodies and certain essential genes, shattering the long-standing idea that mutations are entirely random across the genome. Here I highlight the molecular nonrandomness of mutations and the type of gene affected.
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Affiliation(s)
- Reiner A Veitia
- Université de Paris, Paris 752052, France; Institut Jacques Monod, CNRS UMR7592, Paris 75013, France; Université Paris Saclay, 91190 Gif-sur-Yvette, France; Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives/CEA, 92 265 Fontenay aux Roses, France.
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The shaping of cancer genomes with the regional impact of mutation processes. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1049-1060. [PMID: 35902761 PMCID: PMC9355972 DOI: 10.1038/s12276-022-00808-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/03/2022] [Accepted: 04/28/2022] [Indexed: 11/09/2022]
Abstract
Mutation signature analysis has been used to infer the contributions of various DNA mutagenic-repair events in individual cancer genomes. Here, we build a statistical framework using a multinomial distribution to assign individual mutations to their cognate mutation signatures. We applied it to 47 million somatic mutations in 1925 publicly available cancer genomes to obtain a mutation signature map at the resolution of individual somatic mutations. Based on mutation signature-level genetic-epigenetic correlative analyses, mutations with transcriptional and replicative strand asymmetries show different enrichment patterns across genomes, and “transcribed” chromatin states and gene boundaries are particularly vulnerable to transcription-coupled repair activities. While causative processes of cancer-driving mutations can be diverse, as shown for converging effects of multiple mutational processes on TP53 mutations, the substantial fraction of recurrently mutated amino acids points to specific mutational processes, e.g., age-related C-to-T transition for KRAS p.G12 mutations. Our investigation of evolutionary trajectories with respect to mutation signatures further revealed that candidate pairs of early- vs. late-operative mutation processes in cancer genomes represent evolutionary dynamics of multiple mutational processes in the shaping of cancer genomes. We also observed that the local mutation clusters of kataegis often include mutations arising from multiple mutational processes, suggestive of a locally synchronous impact of multiple mutational processes on cancer genomes. Taken together, our examination of the genome-wide landscape of mutation signatures at the resolution of individual somatic mutations shows the spatially and temporally distinct mutagenesis-repair-replication histories of various mutational processes and their effects on shaping cancer genomes. A statistical model that assigns non-hereditary DNA alterations known as somatic mutations to mutation “signatures” (groups of mutations arising from a specific biological process) on cancer genomes provides novel insights into disease evolution. Somatic mutations result from exposure to factors often linked to cancer development, such as tobacco or ultraviolet radiation. However, assigning a somatic mutation to a particular mutation “signature” remains challenging. The model created by Ruibin Xi (Peking University, China) and Tae-Min Kim (Catholic University of Korea, Seoul, South Korea) and co-workers grouped 47 million somatic mutations in 1925 cancer genomes into localized clusters before connecting them with mutation signatures. This strategy highlights the spatial and temporal patterns related to the origins of mutations, how the DNA strands are repaired and replicated, and how this influences the emerging cancer genome.
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Dukler N, Mughal MR, Ramani R, Huang YF, Siepel A. Extreme purifying selection against point mutations in the human genome. Nat Commun 2022; 13:4312. [PMID: 35879308 PMCID: PMC9314448 DOI: 10.1038/s41467-022-31872-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 07/07/2022] [Indexed: 12/13/2022] Open
Abstract
Large-scale genome sequencing has enabled the measurement of strong purifying selection in protein-coding genes. Here we describe a new method, called ExtRaINSIGHT, for measuring such selection in noncoding as well as coding regions of the human genome. ExtRaINSIGHT estimates the prevalence of "ultraselection" by the fractional depletion of rare single-nucleotide variants, after controlling for variation in mutation rates. Applying ExtRaINSIGHT to 71,702 whole genome sequences from gnomAD v3, we find abundant ultraselection in evolutionarily ancient miRNAs and neuronal protein-coding genes, as well as at splice sites. By contrast, we find much less ultraselection in other noncoding RNAs and transcription factor binding sites, and only modest levels in ultraconserved elements. We estimate that ~0.4-0.7% of the human genome is ultraselected, implying ~ 0.26-0.51 strongly deleterious mutations per generation. Overall, our study sheds new light on the genome-wide distribution of fitness effects by combining deep sequencing data and classical theory from population genetics.
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Affiliation(s)
- Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Mehreen R Mughal
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ritika Ramani
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yi-Fei Huang
- Department of Biology and Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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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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40
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Abstract
Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.
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41
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Yang J, Gupta E, Horton JR, Blumenthal RM, Zhang X, Cheng X. Differential ETS1 binding to T:G mismatches within a CpG dinucleotide contributes to C-to-T somatic mutation rate of the IDH2 hotspot at codon Arg140. DNA Repair (Amst) 2022; 113:103306. [PMID: 35255310 PMCID: PMC9411267 DOI: 10.1016/j.dnarep.2022.103306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/16/2022]
Abstract
Cytosine to thymine (C>T) somatic mutation is highly enriched in certain types of cancer, and most commonly occurs via deamination of a 5-methylcytosine (5mC) to thymine, in the context of a CpG dinucleotide. In theory, deamination should occur at equal rates to both 5mC nucleotides on opposite strands. In most cases, the resulting T:G or G:T mismatch can be repaired by thymine DNA glycosylase activities. However, while some hotspot-associated CpG mutations have approximately equal numbers of mutations that resulted either from C>T or G>A in a CpG dinucleotide, many showed strand bias, being skewed toward C>T of the first base pair or G>A of the second base pair. Using the IDH2 Arg140 codon as a case study, we show that the two possible T:G mismatches at the codon-specific CpG site have differing effects on transcription factor ETS1 binding affinity, differentially affecting access of a repair enzyme (MBD4) to the deamination-caused T:G mismatch. Our study thus provides a plausible mechanism for exclusion of repair enzymes by the differential binding of transcription factors affecting the rate at which the antecedent opposite-strand mutations occur.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Esha Gupta
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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42
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Kikutake C, Suyama M. Pan-cancer analysis of mutations in open chromatin regions and their possible association with cancer pathogenesis. Cancer Med 2022; 11:3902-3916. [PMID: 35416406 PMCID: PMC9582691 DOI: 10.1002/cam4.4749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Open chromatin is associated with gene transcription. Previous studies have shown that the density of mutations in open chromatin regions is lower than that in flanking regions because of the higher accessibility of DNA repair machinery. However, in several cancer types, open chromatin regions show an increased local density of mutations in activated regulatory regions. Although the mutation distribution within open chromatin regions in cancer cells has been investigated, only few studies have focused on their functional implications in cancer. To reveal the impact of highly mutated open chromatin regions on cancer, we investigated the association between mutations in open chromatin regions and their possible functions. METHODS Whole-genome sequencing data of 18 cancer types were downloaded from the PanCancer Analysis of Whole Genomes and Catalog of Somatic Mutations in Cancer. We quantified the mutations located in open chromatin regions defined by The Cancer Genome Atlas and classified open chromatin regions into three categories based on the number of mutations. Then, we investigated the chromatin state, amplification, and possible target genes of the open chromatin regions with a high number of mutations. We also analyzed the association between the number of mutations in open chromatin regions and patient prognosis. RESULTS In some cancer types, the proportion of promoter or enhancer chromatin state in open chromatin regions with a high number of mutations was significantly higher than that in the regions with a low number of mutations. The possible target genes of open chromatin regions with a high number of mutations were more strongly associated with cancer than those of other open chromatin regions. Moreover, a high number of mutations in open chromatin regions was significantly associated with a poor prognosis in some cancer types. CONCLUSIONS These results suggest that highly mutated open chromatin regions play an important role in cancer pathogenesis and can be effectively used to predict patient prognosis.
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Affiliation(s)
- Chie Kikutake
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mikita Suyama
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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43
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Wu S, Huang Y, Selby CP, Gao M, Sancar A, Hu J. A new technique for genome-wide mapping of nucleotide excision repair without immunopurification of damaged DNA. J Biol Chem 2022; 298:101863. [PMID: 35339490 PMCID: PMC9034098 DOI: 10.1016/j.jbc.2022.101863] [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: 02/09/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/03/2022] Open
Abstract
Nucleotide excision repair functions to protect genome integrity, and ongoing studies using excision repair sequencing (XR-seq) have contributed to our understanding of how cells prioritize repair across the genome. In this method, the products of excision repair bearing damaged DNA are captured, sequenced, and then mapped genome-wide at single-nucleotide resolution. However, reagent requirements and complex procedures have limited widespread usage of this technique. In addition to the expense of these reagents, it has been hypothesized that the immunoprecipitation step using antibodies directed against damaged DNA may introduce bias in different sequence contexts. Here, we describe a newly developed adaptation called dA-tailing and adaptor ligation (ATL)–XR-seq, a relatively simple XR-seq method that avoids the use of immunoprecipitation targeting damaged DNA. ATL-XR-seq captures repair products by 3′-dA-tailing and 5′-adapter ligation instead of the original 5′- and 3′-dual adapter ligation. This new approach avoids adapter dimer formation during subsequent PCR, omits inefficient and time-consuming purification steps, and is very sensitive. In addition, poly(dA) tail length heterogeneity can serve as a molecular identifier, allowing more repair hotspots to be mapped. Importantly, a comparison of both repair mapping methods showed that no major bias is introduced by the anti-UV damage antibodies used in the original XR-seq procedure. Finally, we also coupled the described dA-tailing approach with quantitative PCR in a new method to quantify repair products. These new methods provide powerful and user-friendly tools to qualitatively and quantitatively measure excision repair.
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Affiliation(s)
- Sizhong Wu
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yanchao Huang
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA
| | - Meng Gao
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA.
| | - Jinchuan Hu
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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44
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Duan M, Sivapragasam S, Antony JS, Ulibarri J, Hinz JM, Poon GMK, Wyrick JJ, Mao P. High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors. eLife 2022; 11:73943. [PMID: 35289750 PMCID: PMC8970589 DOI: 10.7554/elife.73943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
DNA base damage arises frequently in living cells and needs to be removed by base excision repair (BER) to prevent mutagenesis and genome instability. Both the formation and repair of base damage occur in chromatin and are conceivably affected by DNA-binding proteins such as transcription factors (TFs). However, to what extent TF binding affects base damage distribution and BER in cells is unclear. Here, we used a genome-wide damage mapping method, N-methylpurine-sequencing (NMP-seq), and characterized alkylation damage distribution and BER at TF binding sites in yeast cells treated with the alkylating agent methyl methanesulfonate (MMS). Our data show that alkylation damage formation was mainly suppressed at the binding sites of yeast TFs ARS binding factor 1 (Abf1) and rDNA enhancer binding protein 1 (Reb1), but individual hotspots with elevated damage levels were also found. Additionally, Abf1 and Reb1 binding strongly inhibits BER in vivo and in vitro, causing slow repair both within the core motif and its adjacent DNA. Repair of ultraviolet (UV) damage by nucleotide excision repair (NER) was also inhibited by TF binding. Interestingly, TF binding inhibits a larger DNA region for NER relative to BER. The observed effects are caused by the TF–DNA interaction, because damage formation and BER can be restored by depletion of Abf1 or Reb1 protein from the nucleus. Thus, our data reveal that TF binding significantly modulates alkylation base damage formation and inhibits repair by the BER pathway. The interplay between base damage formation and BER may play an important role in affecting mutation frequency in gene regulatory regions.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico, Albuquerque, United States
| | - Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Jacob S Antony
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Jenna Ulibarri
- Department of Internal Medicine, University of New Mexico, Albuquerque, United States
| | - John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, United States
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico, Albuquerque, United States
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Colebatch AJ, Paver EC, Vergara IA, Thompson JF, Long GV, Wilmott JS, Scolyer RA. Elevated non-coding promoter mutations are associated with malignant transformation of melanocytic naevi to melanoma. Pathology 2022; 54:533-540. [DOI: 10.1016/j.pathol.2021.12.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 10/19/2022]
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46
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Kogure Y, Kameda T, Koya J, Yoshimitsu M, Nosaka K, Yasunaga JI, Imaizumi Y, Watanabe M, Saito Y, Ito Y, McClure MB, Tabata M, Shingaki S, Yoshifuji K, Chiba K, Okada A, Kakiuchi N, Nannya Y, Kamiunten A, Tahira Y, Akizuki K, Sekine M, Shide K, Hidaka T, Kubuki Y, Kitanaka A, Hidaka M, Nakano N, Utsunomiya A, Sica RA, Acuna-Villaorduna A, Janakiram M, Shah U, Ramos JC, Shibata T, Takeuchi K, Takaori-Kondo A, Miyazaki Y, Matsuoka M, Ishitsuka K, Shiraishi Y, Miyano S, Ogawa S, Ye BH, Shimoda K, Kataoka K. Whole-genome landscape of adult T-cell leukemia/lymphoma. Blood 2022; 139:967-982. [PMID: 34695199 PMCID: PMC8854674 DOI: 10.1182/blood.2021013568] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022] Open
Abstract
Adult T-cell leukemia/lymphoma (ATL) is an aggressive neoplasm immunophenotypically resembling regulatory T cells, associated with human T-cell leukemia virus type-1. Here, we performed whole-genome sequencing (WGS) of 150 ATL cases to reveal the overarching landscape of genetic alterations in ATL. We discovered frequent (33%) loss-of-function alterations preferentially targeting the CIC long isoform, which were overlooked by previous exome-centric studies of various cancer types. Long but not short isoform-specific inactivation of Cic selectively increased CD4+CD25+Foxp3+ T cells in vivo. We also found recurrent (13%) 3'-truncations of REL, which induce transcriptional upregulation and generate gain-of-function proteins. More importantly, REL truncations are also common in diffuse large B-cell lymphoma, especially in germinal center B-cell-like subtype (12%). In the non-coding genome, we identified recurrent mutations in regulatory elements, particularly splice sites, of several driver genes. In addition, we characterized the different mutational processes operative in clustered hypermutation sites within and outside immunoglobulin/T-cell receptor genes and identified the mutational enrichment at the binding sites of host and viral transcription factors, suggesting their activities in ATL. By combining the analyses for coding and noncoding mutations, structural variations, and copy number alterations, we discovered 56 recurrently altered driver genes, including 11 novel ones. Finally, ATL cases were classified into 2 molecular groups with distinct clinical and genetic characteristics based on the driver alteration profile. Our findings not only help to improve diagnostic and therapeutic strategies in ATL, but also provide insights into T-cell biology and have implications for genome-wide cancer driver discovery.
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Affiliation(s)
- Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Takuro Kameda
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Makoto Yoshimitsu
- Department of Hematology and Rheumatology, Kagoshima University Hospital, Kagoshima, Japan
| | - Kisato Nosaka
- Department of Hematology, Rheumatology, and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun-Ichirou Yasunaga
- Department of Hematology, Rheumatology, and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshitaka Imaizumi
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Mizuki Watanabe
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Yuta Ito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Clinical Oncology and Hematology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Marni B McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kota Yoshifuji
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ayako Kamiunten
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yuki Tahira
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Keiichi Akizuki
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Masaaki Sekine
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kotaro Shide
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tomonori Hidaka
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoko Kubuki
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akira Kitanaka
- Department of Laboratory Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Michihiro Hidaka
- Department of Hematology, National Hospital Organization Kumamoto Medical Center, Kumamoto, Japan
| | - Nobuaki Nakano
- Department of Hematology, Imamura General Hospital, Kagoshima, Japan
| | - Atae Utsunomiya
- Department of Hematology, Imamura General Hospital, Kagoshima, Japan
| | - R Alejandro Sica
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Ana Acuna-Villaorduna
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Murali Janakiram
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Urvi Shah
- Department of Oncology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY
| | - Juan Carlos Ramos
- Division of Hematology/Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Masao Matsuoka
- Department of Hematology, Rheumatology, and Infectious Disease, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenji Ishitsuka
- Department of Hematology and Rheumatology, Kagoshima University Hospital, Kagoshima, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - B Hilda Ye
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY; and
| | - Kazuya Shimoda
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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47
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Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, Weng ML, Imbert E, Ågren J, Rutter MT, Fenster CB, Weigel D. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 2022; 602:101-105. [PMID: 35022609 PMCID: PMC8810380 DOI: 10.1038/s41586-021-04269-6] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome-mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.
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Affiliation(s)
- J Grey Monroe
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
- Department of Plant Sciences, University of California Davis, Davis, CA, USA.
| | - Thanvi Srikant
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | | | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Faculty of Biology, Ludwig Maximilian University, Martinsried, Germany
| | - Mariele Lensink
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Marie Klein
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Julia Hildebrandt
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Daniel Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Mao-Lun Weng
- Department of Biology, Westfield State University, Westfield, MA, USA
| | - Eric Imbert
- ISEM, University of Montpellier, Montpellier, France
| | - Jon Ågren
- Department of Ecology and Genetics, EBC, Uppsala University, Uppsala, Sweden
| | - Matthew T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Charles B Fenster
- Oak Lake Field Station, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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48
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Tang F, Yuan J, Yuan BF, Wang Y. DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol. J Am Chem Soc 2022; 144:454-462. [PMID: 34978433 PMCID: PMC8755629 DOI: 10.1021/jacs.1c10490] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesions in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2'-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol, and its subsequent deamination also yields Tg. However, Tg's distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach capitalizes on the specificity of a bifunctional DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in the human genome, where dual ablation of NTHL1 and NEIL1, the major DNA glycosylases responsible for Tg repair, led to pronounced increases in the number of Tg peaks. In addition, Tg is depleted in genomic regions associated with active transcription but enriched at nucleosome-binding sites, especially at heterochromatin sites marked with H3K9me2. Collectively, we developed a DPC-Seq method for highly efficient enrichment of Tg-containing DNA and for genome-wide mapping of Tg in human cells. Our work offers a robust tool for future functional studies of Tg in DNA, and we envision that the method can also be adapted for mapping other modified nucleosides in genomic DNA in the future.
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Affiliation(s)
- Feng Tang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jun Yuan
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
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49
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El Ghamrasni S, Quevedo R, Hawley J, Mazrooei P, Hanna Y, Cirlan I, Zhu H, Bruce JP, Oldfield LE, Yang SYC, Guilhamon P, Reimand J, Cescon DW, Done SJ, Lupien M, Pugh TJ. Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer. Mol Cancer Res 2022; 20:102-113. [PMID: 34556523 PMCID: PMC9398156 DOI: 10.1158/1541-7786.mcr-21-0471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/31/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023]
Abstract
Whole-genome sequencing of primary breast tumors enabled the identification of cancer driver genes and noncoding cancer driver plexuses from somatic mutations. However, differentiating driver from passenger events among noncoding genetic variants remains a challenge. Herein, we reveal cancer-driver cis-regulatory elements linked to transcription factors previously shown to be involved in development of luminal breast cancers by defining a tumor-enriched catalogue of approximately 100,000 unique cis-regulatory elements from 26 primary luminal estrogen receptor (ER)+ progesterone receptor (PR)+ breast tumors. Integrating this catalog with somatic mutations from 350 publicly available breast tumor whole genomes, we uncovered cancer driver cistromes, defined as the sum of binding sites for a transcription factor, for ten transcription factors in luminal breast cancer such as FOXA1 and ER, nine of which are essential for growth in breast cancer with four exclusive to the luminal subtype. Collectively, we present a strategy to find cancer driver cistromes relying on quantifying the enrichment of noncoding mutations over cis-regulatory elements concatenated into a functional unit. IMPLICATIONS: Mapping the accessible chromatin of luminal breast cancer led to discovery of an accumulation of mutations within cistromes of transcription factors essential to luminal breast cancer. This demonstrates coopting of regulatory networks to drive cancer and provides a framework to derive insight into the noncoding space of cancer.
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Affiliation(s)
- Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rene Quevedo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - James Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Genentech, South San Francisco, California
| | - Youstina Hanna
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Iulia Cirlan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Helen Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeff P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - S Y Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Paul Guilhamon
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jüri Reimand
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dave W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Susan J Done
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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50
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Stark B, Poon GMK, Wyrick JJ. CTCF puts a new twist on UV damage and repair in skin cancer. Mol Cell Oncol 2021; 8:2009424. [PMID: 35419468 PMCID: PMC8997251 DOI: 10.1080/23723556.2021.2009424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 05/26/2023]
Abstract
Somatic mutations in skin cancers are highly enriched at binding sites for CCCTC-binding factor (CTCF). We have discovered that CTCF binding alters the DNA structure to render it more susceptible to UV damage. Elevated UV damage formation at CTCF binding sites, in conjunction with subsequent repair inhibition, promotes UV mutagenesis.
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Affiliation(s)
- Bastian Stark
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Gregory M. K. Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA, USA
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