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A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage

Zou, Xueqing, Koh, Gene Ching Chiek, Nanda, Arjun Scott, Degasperi, Andrea, Urgo, Katie, Roumeliotis, Theodoros I., Agu, Chukwuma A., Badja, Cherif, Momen, Sophie, Young, Jamie, Amarante, Tauanne Dias, Side, Lucy, Brice, Glen, Perez-Alonso, Vanesa, Rueda, Daniel, Gomez, Celine, Bushell, Wendy, Harris, Rebecca, Choudhary, Jyoti S., Genomics England Research Consortium, Ambrose, John C., Arumugam, Prabhu, Baple, Emma L., Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Boustred, Christopher R., Brittain, Helen, Caulfield, Mark J., Chan, Georgia C., Craig, Clare E. H., Daugherty, Louise C., de Burca, Anna, Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Fowler, Tom, Furió-Tarí, Pedro, Giess, Adam, Hackett, Joanne M., Halai, Dina, Hamblin, Angela, Henderson, Shirley, Holman, James E., Hubbard, Tim J. P., ibáñez, Kristina, Jackson, Rob, Jones, Louise J., Kasperaviciute, Dalia, Kayikci, Melis, Kousathanas, Athanasios, Lahnstein, Lea, Lawson, Kay, Leigh, Sarah E. A., Leong, Ivonne U. S., Lopez, Javier F., Maleady-Crowe, Fiona, Mason, Joanne, McDonagh, Ellen M., Moutsianas, Loukas, Mueller, Michael, Murugaesu, Nirupa, Need, Anna C., O’Donovan, Pter, Odhams, Chris A., Orioli, Andrea, Patch, Christine, Pereira, Mariana Buongermino, Perez-Gil, Daniel, Polychronopoulos, Dimitris, Pullinger, John, Rahim, Tahrima, Rendon, Augusto, Riesgo-Ferreiro, Pablo, Rogers, Tim, Ryten, Mina, Savage, Kevin, Sawant, Kushmita, Scott, Richard H., Siddiq, Afshan, Sieghart, Alexander, Smedley, Damian, Smith, Katherine R., Smith, Samuel C., Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Tanguy, Mélanie, Thomas, Ellen R. A., Thompson, Simon R., Tregidgo, Carolyn, Tucci, Arianna, Walsh, Emma, Watters, Sarah A., Welland, Matthew J., Williams, Eleanor, Witkowska, Katarzyna, Wood, Suzanne M., Zarowiecki, Magdalena, Jiricny, Josef, Skarnes, William C., Nik-Zainal, Serena·2021·Nature Cancer
DOI 10.1038/s43018-021-00200-0PMC PMC7611045

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  1. Helleday, T., Eshtad, S. & Nik-Zainal, S. Mechanisms underlying mutational signatures in human cancers. Nat. Rev. Genet. 15, 585–598 (2014). · DOI
  2. Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013). · DOI · Paper page
  3. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012). · DOI · Paper page
  4. Haradhvala, N. J. et al. Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair. Nat. Commun. 9, 1746 (2018). · DOI
  5. Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020). · DOI · Paper page
  6. Kim, J. et al. Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat. Genet. 48, 600–606 (2016). · DOI
  7. Nik-Zainal, S. et al. The genome as a record of environmental exposure. Mutagenesis 30, 763–770 (2015).
  8. Zou, X. et al. Validating the concept of mutational signatures with isogenic cell models. Nat. Commun. 9, 1744 (2018). · DOI
  9. Christensen, S. et al. 5-Fluorouracil treatment induces characteristic T>G mutations in human cancer. Nat. Commun. 10, 4571 (2019). · DOI
  10. Kucab, J. E. et al. A compendium of mutational signatures of environmental agents. Cell 177, 821–836.e16 (2019). · DOI · Paper page
  11. Lindahl, T. & Nyberg, B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610–3618 (1972). · DOI
  12. Mardis, E. R.The impact of next-generation sequencing on cancer genomics: from discovery to clinic. Cold Spring Harb. Perspect. Med. 9, a036269 (2019). · DOI
  13. Berger, M. F. & Mardis, E. R. The emerging clinical relevance of genomics in cancer medicine. Nat. Rev. Clin. Oncol. 15, 353–365 (2018). · DOI
  14. Kunkel, T. A. & Erie, D. A. DNA mismatch repair. Annu. Rev. Biochem. 74, 681–710 (2005). · DOI
  15. Kottemann, M. C. & Smogorzewska, A. Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature 493, 356–363 (2013). · DOI
  16. Wood, R. D., Mitchell, M., Sgouros, J. & Lindahl, T. Human DNA repair genes. Science 291, 1284–1289 (2001). · DOI
  17. Ceccaldi, R., Rondinelli, B. & D’Andrea, A. D. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 26, 52–64 (2016). · DOI · Paper page
  18. Hanawalt, P. C. & Spivak, G. Transcription-coupled DNA repair: two decades of progress and surprises. Nat. Rev. Mol. Cell Biol. 9, 958–970 (2008). · DOI
  19. Abid, A., Zhang, M. J., Bagaria, V. K. & Zou, J. Exploring patterns enriched in a dataset with contrastive principal component analysis. Nat. Commun. 9, 2134 (2018). · DOI
  20. Van der Maaten, L. & Hinton, G. Visualizing data using t-SNE. J. Mach. Learn. Res. 9, 2579–2605 (2008).
  21. Degasperi, A. et al. A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies. Nat. Cancer 1, 249–263 (2020). · DOI · Paper page
  22. Radicella, J. P., Dherin, C., Desmaze, C., Fox, M. S. & Boiteux, S. Cloning and characterization of hOGG1, a human homolog of the OGG1 gene of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 94, 8010–8015 (1997). · DOI
  23. Lee, Y. A., Durandin, A., Dedon, P. C., Geacintov, N. E. & Shafirovich, V. Oxidation of guanine in G, GG, and GGG sequence contexts by aromatic pyrenyl radical cations and carbonate radical anions: relationship between kinetics and distribution of alkali-labile lesions. J. Phys. Chem. B 112, 1834–1844 (2008). · DOI
  24. Sugiyama, H. & Saito, I. Theoretical studies of GG-specific photocleavage of DNA via electron transfer: significant lowering of ionization potential and 5′-localization of HOMO of stacked GG bases in B-form DNA. J. Am. Chem. Soc. 118, 7063–7068 (1996). · DOI
  25. Allgayer, J., Kitsera, N., von der Lippen, C., Epe, B. & Khobta, A. Modulation of base excision repair of 8-oxoguanine by the nucleotide sequence. Nucleic Acids Res. 41, 8559–8571 (2013). · DOI
  26. Friedman, J. I. & Stivers, J. T. Detection of damaged DNA bases by DNA glycosylase enzymes. Biochemistry 49, 4957–4967 (2010). · DOI
  27. Lutsenko, E. & Bhagwat, A. S. Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells. A model, its experimental support and implications. Mutat. Res. 437, 11–20 (1999). · DOI
  28. Shen, J. C., Rideout, W. M. 3rd & Jones, P. A. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 22, 972–976 (1994). · DOI
  29. Waters, T. R. & Swann, P. F. Thymine-DNA glycosylase and G to A transition mutations at CpG sites. Mutat Res. 462, 137–147 (2000). · DOI
  30. Sanders, M. A. et al. MBD4 guards against methylation damage and germ line deficiency predisposes to clonal hematopoiesis and early-onset AML. Blood 132, 1526–1534 (2018). · DOI
  31. Mol, C. D. et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell 80, 869–878 (1995). · DOI
  32. Grolleman, J. E. et al. Mutational signature analysis reveals NTHL1 deficiency to cause a multi-tumor phenotype. Cancer Cell 35, 256–266.e5 (2019). · DOI
  33. Genschel, J. & Modrich, P. Mechanism of 5′-directed excision in human mismatch repair. Mol. Cell 12, 1077–1086 (2003). · DOI
  34. Bolderson, E. et al. Phosphorylation of Exo1 modulates homologous recombination repair of DNA double-strand breaks. Nucleic Acids Res. 38, 1821–1831 (2010). · DOI
  35. Mattiroli, F. et al. RNF168 ubiquitinates K13–15 on H2A/H2AX to drive DNA damage signaling. Cell 150, 1182–1195 (2012). · DOI
  36. Bohgaki, M. et al. RNF168 ubiquitylates 53BP1 and controls its response to DNA double-strand breaks. Proc. Natl Acad. Sci. USA 110, 20982 (2013). · DOI
  37. Doil, C. et al. RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell 136, 435–446 (2009). · DOI
  38. Stewart, G. S. et al. The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 136, 420–434 (2009). · DOI
  39. Gupta, S., Gellert, M. & Yang, W. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops. Nat. Struct. Mol. Biol. 19, 72–78 (2012). · DOI
  40. Palombo, F. et al. GTBP, a 160-kilodalton protein essential for mismatch-binding activity in human cells. Science 268, 1912–1914 (1995). · DOI
  41. Warren, J. J. et al. Structure of the human MutSα DNA lesion recognition complex. Mol. Cell 26, 579–592 (2007). · DOI
  42. Andrianova, M. A., Bazykin, G. A., Nikolaev, S. I. & Seplyarskiy, V. B. Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand. Genome Res. 27, 1336–1343 (2017). · DOI
  43. Lujan, S. A. et al. Mismatch repair balances leading and lagging strand DNA replication fidelity. PLoS Genet. 8, e1003016 (2012). · DOI
  44. Morganella, S. et al. The topography of mutational processes in breast cancer genomes. Nat. Commun. 7, 11383 (2016). · DOI
  45. Aboul-ela, F., Koh, D., Tinoco, I. Jr. & Martin, F. H. Base–base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res. 13, 4811–4824 (1985). · DOI
  46. Mazurek, A., Berardini, M. & Fishel, R. Activation of human MutS homologs by 8-oxo-guanine DNA damage. J. Biol. Chem. 277, 8260–8266 (2002). · DOI
  47. Morikawa, M. et al. Analysis of guanine oxidation products in double-stranded DNA and proposed guanine oxidation pathways in single-stranded, double-stranded or quadruplex DNA. Biomolecules 4, 140–159 (2014). · DOI
  48. Pavlov, Y. I., Newlon, C. S. & Kunkel, T. A. Yeast origins establish a strand bias for replicational mutagenesis. Mol. Cell 10, 207–213 (2002). · DOI
  49. Mudrak, S. V., Welz-Voegele, C. & Jinks-Robertson, S.The polymerase η translesion synthesis DNA polymerase acts independently of the mismatch repair system to limit mutagenesis caused by 7,8-dihydro-8-oxoguanine in yeast. Mol. Cell. Biol. 29, 5316–5326 (2009). · DOI
  50. Meier, B. et al. Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers. Genome Res. 28, 666–675 (2018). · DOI
  51. Drummond, J. T., Li, G. M., Longley, M. J. & Modrich, P.Isolation of an hMSH2-p160 heterodimer that restores DNA mismatch repair to tumor cells. Science 268, 1909–1912 (1995). · DOI
  52. Palombo, F. et al. hMutSβ, a heterodimer of hMSH2 and hMSH3, binds to insertion/deletion loops in DNA. Curr. Biol. 6, 1181–1184 (1996). · DOI
  53. Wind, Nd et al. HNPCC-like cancer predisposition in mice through simultaneous loss of Msh3 and Msh6 mismatch-repair protein functions. Nat. Genet. 23, 359–362 (1999). · DOI
  54. Poulogiannis, G., Frayling, I. M. & Arends, M. J. DNA mismatch repair deficiency in sporadic colorectal cancer and Lynch syndrome. Histopathology 56, 167–179 (2010). · DOI
  55. Heinen, C. D. Mismatch repair defects and Lynch syndrome: the role of the basic scientist in the battle against cancer. DNA Repair 38, 127–134 (2016). · DOI
  56. Agu, C. A. et al. Successful generation of human induced pluripotent stem cell lines from blood samples held at room temperature for up to 48 hr. Stem Cell Rep. 5, 660–671 (2015). · DOI
  57. Ni Huang, M. et al. MSIseq: software for assessing microsatellite instability from catalogs of somatic mutations. Sci. Rep. 5, 13321 (2015). · DOI
  58. Niu, B. et al. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics 30, 1015–1016 (2013). · DOI
  59. Wang, C. & Liang, C. MSIpred: a python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine. Sci. Rep. 8, 17546 (2018). · DOI
  60. Cortes-Ciriano, I., Lee, S., Park, W.-Y., Kim, T.-M. & Park, P. J. A molecular portrait of microsatellite instability across multiple cancers. Nat. Commun. 8, 15180 (2017). · DOI
  61. Salipante, S. J., Scroggins, S. M., Hampel, H. L., Turner, E. H. & Pritchard, C. C. Microsatellite instability detection by next generation sequencing. Clin. Chem. 60, 1192–1199 (2014). · DOI
  62. Hause, R. J., Pritchard, C. C., Shendure, J. & Salipante, S. J.Classification and characterization of microsatellite instability across 18 cancer types. Nat. Med. 22, 1342–1350 (2016). · DOI
  63. Fujimoto, A. et al. Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types. Genome Res. 30, 334–346 (2020). · DOI
  64. Campbell, B. B. et al. Comprehensive analysis of hypermutation in human cancer. Cell 171, 1042–1056.e10 (2017). · DOI
  65. Bressan, R. B. et al. Efficient CRISPR/Cas9-assisted gene targeting enables rapid and precise genetic manipulation of mammalian neural stem cells. Development 144, 635–648 (2017). · DOI
  66. Tate, P. H. & Skarnes, W. C. Bi-allelic gene targeting in mouse embryonic stem cells. Methods 53, 331–338 (2011). · DOI
  67. Hodgkins, A. et al. WGE: a CRISPR database for genome engineering. Bioinformatics 31, 3078–3080 (2015). · DOI
  68. Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013). · arXiv
  69. Jones, D. et al. cgpCaVEManWrapper: simple execution of CaVEMan in order to detect somatic single nucleotide variants in NGS data. Curr. Protoc. Bioinformatics 56, 15.10.1–15.10.18 (2016). · DOI
  70. Raine, K. M. et al. cgpPindel: identifying somatically acquired insertion and deletion events from paired end sequencing. Curr. Protoc. Bioinformatics 52, 15.7.1–15.7.12 (2015). · DOI
  71. Cradick, T. J., Qiu, P., Lee, C. M., Fine, E. J. & Bao, G. COSMID: a web-based tool for identifying and validating CRISPR/Cas off-target sites. Mol. Ther. Nucleic Acids 3, e214 (2014). · DOI · Paper page
  72. The Encode Project Consortium et al.An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012). · DOI · Paper page
  73. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010). · DOI · Paper page
  74. Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009). · DOI · Paper page

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Metadata

Authors
Zou, X., Koh, G. C. C., Nanda, A. S., Degasperi, A., Urgo, K., Roumeliotis, T. I., Agu, C. A., Badja, C., Momen, S., Young, J., Amarante, T. D., Side, L., Brice, G., Perez-Alonso, V., Rueda, D., Gomez, C., Bushell, W., Harris, R., Choudhary, J. S., Genomics England Research Consortium, Ambrose, J. C., Arumugam, P., Baple, E. L., Bleda, M., Boardman-Pretty, F., Boissiere, J. M., Boustred, C. R., Brittain, H., Caulfield, M. J., Chan, G. C., Craig, C. E. H., Daugherty, L. C., de Burca, A., Devereau, A., Elgar, G., Foulger, R. E., Fowler, T., Furió-Tarí, P., Giess, A., Hackett, J. M., Halai, D., Hamblin, A., Henderson, S., Holman, J. E., Hubbard, T. J. P., ibáñez, K., Jackson, R., Jones, L. J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Lawson, K., Leigh, S. E. A., Leong, I. U. S., Lopez, J. F., Maleady-Crowe, F., Mason, J., McDonagh, E. M., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A. C., O’Donovan, P., Odhams, C. A., Orioli, A., Patch, C., Pereira, M. B., Perez-Gil, D., Polychronopoulos, D., Pullinger, J., Rahim, T., Rendon, A., Riesgo-Ferreiro, P., Rogers, T., Ryten, M., Savage, K., Sawant, K., Scott, R. H., Siddiq, A., Sieghart, A., Smedley, D., Smith, K. R., Smith, S. C., Sosinsky, A., Spooner, W., Stevens, H. E., Stuckey, A., Sultana, R., Tanguy, M., Thomas, E. R. A., Thompson, S. R., Tregidgo, C., Tucci, A., Walsh, E., Watters, S. A., Welland, M. J., Williams, E., Witkowska, K., Wood, S. M., Zarowiecki, M., Jiricny, J., Skarnes, W. C., & Nik-Zainal, S.
Venue
Nature Cancer
Publisher
Springer Science and Business Media LLC
Published
2021-04-26
Volume
2
Issue
6
Pages
643-657
ISSN
2662-1347
DOI
10.1038/s43018-021-00200-0
PMC
PMC7611045
Cited by
164
References
13
Language
en
Licence
Funders
  • Cancer Research UK (C60100/A23916, C309/A25144)
  • Wellcome Trust (Wellcome Sanger Institute 4-year PhD Fellowships, WT101126)
  • DH | National Institute for Health Research
  • NHS England
  • Dr Josef Steiner Cancer Research Award 2019 Medical Research Council (MRC) Grant-in-Aid to the MRC Cancer unit CRUK Pioneer Award NIHR-BRC Cambridge core grant

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