Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing.

Tytuł:: Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing.
Autorzy:: Leibowitz ML; Howard Hughes Medical Institute, Chevy Chase, MD, USA.; Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Papathanasiou S; Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Doerfler PA; Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Blaine LJ; Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Sun L; Single-Cell Sequencing Program, Dana-Farber Cancer Institute, Boston, MA, USA.
Yao Y; Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Zhang CZ; Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Weiss MJ; Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA. .
Pellman D; Howard Hughes Medical Institute, Chevy Chase, MD, USA. david_.; Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. david_.; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. david_.
Źródło:: Nature genetics [Nat Genet] 2021 Jun; Vol. 53 (6), pp. 895-905. Date of Electronic Publication: 2021 Apr 12.
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
Język:: English
Imprint Name(s):: Original Publication: New York, NY : Nature Pub. Co., c1992-
MeSH Terms:: Chromothripsis*
Gene Editing*
CRISPR-Cas Systems/*genetics
Anemia, Sickle Cell/genetics ; Antigens, CD34/metabolism ; CRISPR-Associated Protein 9/metabolism ; Cell Division ; Chromosomes, Human/genetics ; DNA Cleavage ; Genome, Human ; Humans ; Micronucleus, Germline/genetics ; Tumor Suppressor Protein p53/metabolism
References:: Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR–Cas9 for genome engineering. Cell 157, 1262–1278 (2014). (PMID: 249061464343198)
Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020). (PMID: 3205159810.1038/s41586-020-1978-58992613)
Xu, J. et al. Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science 334, 993–996 (2011). (PMID: 21998251374654510.1126/science.1211053)
Orkin, S. H. & Bauer, D. E. Emerging genetic therapy for sickle cell disease. Annu. Rev. Med. 70, 257–271 (2019). (PMID: 3035526310.1146/annurev-med-041817-125507)
Wu, Y. et al. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat. Med. 25, 776–783 (2019). (PMID: 30911135651298610.1038/s41591-019-0401-y)
Frangoul, H. et al. CRISPR–Cas9 gene editing for sickle cell disease and β-thalassemia. N. Engl. J. Med. 384, 252–260 (2021). (PMID: 3328398910.1056/NEJMoa2031054)
Dever, D. P. et al. CRISPR/Cas9 β-globin gene targeting in human haematopoietic stem cells. Nature 539, 384–389 (2016). (PMID: 27820943589860710.1038/nature20134)
DeWitt, M. A. et al. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci. Transl. Med. 8, 360ra134 (2016). (PMID: 27733558550030310.1126/scitranslmed.aaf9336)
Richardson, C. D. et al. CRISPR–Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nat. Genet. 50, 1132–1139 (2018). (PMID: 3005459510.1038/s41588-018-0174-0)
Romero, Z. et al. Editing the sickle cell disease mutation in human hematopoietic stem cells: comparison of endonucleases and homologous donor templates. Mol. Ther. 27, 1389–1406 (2019). (PMID: 31178391669740810.1016/j.ymthe.2019.05.014)
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016). (PMID: 27096365487337110.1038/nature17946)
Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017). (PMID: 29160308572655510.1038/nature24644)
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019). (PMID: 31634902690707410.1038/s41586-019-1711-4)
Kim, D., Luk, K., Wolfe, S. A. & Kim, J. S. Evaluating and enhancing target specificity of gene-editing nucleases and deaminases. Annu. Rev. Biochem. 88, 191–220 (2019). (PMID: 3088319610.1146/annurev-biochem-013118-111730)
Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. & Taipale, J. CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response. Nat. Med. 24, 927–930 (2018). (PMID: 2989206710.1038/s41591-018-0049-z)
Ihry, R. J. et al. p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells. Nat. Med. 24, 939–946 (2018). (PMID: 2989206210.1038/s41591-018-0050-6)
van den Berg, J. et al. A limited number of double-strand DNA breaks is sufficient to delay cell cycle progression. Nucleic Acids Res. 46, 10132–10144 (2018). (PMID: 30184135621279310.1093/nar/gky786)
Enache, O. M. et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat. Genet. 52, 662–668 (2020).
Whitworth, K. M. et al. Use of the CRISPR/Cas9 system to produce genetically engineered pigs from in vitro-derived oocytes and embryos. Biol. Reprod. 91, 78 (2014). (PMID: 25100712443506310.1095/biolreprod.114.121723)
Shin, H. Y. et al. CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Nat. Commun. 8, 15464 (2017). (PMID: 28561021546002110.1038/ncomms15464)
Adikusuma, F. et al. Large deletions induced by Cas9 cleavage. Nature 560, E8–E9 (2018). (PMID: 3008992210.1038/s41586-018-0380-z)
Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Nat. Biotechnol. 36, 765–771 (2018). (PMID: 30010673639093810.1038/nbt.4192)
Zuccaro, M. V. et al. Allele-specific chromosome removal after Cas9 cleavage in human embryos. Cell 183, 1650–1664 (2020).
Weisheit, I. et al. Detection of deleterious on-target effects after HDR-mediated CRISPR editing. Cell Rep. 31, 107689 (2020). (PMID: 3246002110.1016/j.celrep.2020.107689)
Alanis-Lobato, G. et al. Frequent loss-of-heterozygosity in CRISPR–Cas9-edited early human embryos. Preprint at bioRxiv https://doi.org/10.1101/2020.06.05.135913 (2020).
Cullot, G. et al. CRISPR–Cas9 genome editing induces megabase-scale chromosomal truncations. Nat. Commun. 10, 1136 (2019). (PMID: 30850590640849310.1038/s41467-019-09006-2)
Stadtmauer, E. A. et al. CRISPR-engineered T cells in patients with refractory cancer. Science 367, eaba7365 (2020). (PMID: 3202968710.1126/science.aba7365)
Zhang, C. Z. et al. Chromothripsis from DNA damage in micronuclei. Nature 522, 179–184 (2015). (PMID: 26017310474223710.1038/nature14493)
Umbreit, N. T. et al. Mechanisms generating cancer genome complexity from a single cell division error. Science 368, eaba0712 (2020). (PMID: 32299917734710810.1126/science.aba0712)
Liu, P. et al. Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146, 889–903 (2011). (PMID: 21925314324245110.1016/j.cell.2011.07.042)
Kloosterman, W. P. & Cuppen, E. Chromothripsis in congenital disorders and cancer: similarities and differences. Curr. Opin. Cell Biol. 25, 341–348 (2013). (PMID: 2347821610.1016/j.ceb.2013.02.008)
Stephens, P. J. et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144, 27–40 (2011). (PMID: 21215367306530710.1016/j.cell.2010.11.055)
Rausch, T. et al. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell 148, 59–71 (2012). (PMID: 22265402333221610.1016/j.cell.2011.12.013)
Ly, P. et al. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat. Genet. 51, 705–715 (2019). (PMID: 30833795644139010.1038/s41588-019-0360-8)
Consortium, I. T. P.-C. Ao. W. G. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020). (PMID: 10.1038/s41586-020-1969-6)
Cortes-Ciriano, I. et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat. Genet. 52, 331–341 (2020). (PMID: 32025003705853410.1038/s41588-019-0576-7)
Leibowitz, M. L., Zhang, C. Z. & Pellman, D. Chromothripsis: a new mechanism for rapid karyotype evolution. Annu. Rev. Genet. 49, 183–211 (2015). (PMID: 2644284810.1146/annurev-genet-120213-092228)
Ly, P. & Cleveland, D. W. Rebuilding chromosomes after catastrophe: emerging mechanisms of chromothripsis. Trends Cell Biol. 27, 917–930 (2017). (PMID: 28899600569604910.1016/j.tcb.2017.08.005)
Soto, M., Garcia-Santisteban, I., Krenning, L., Medema, R. H. & Raaijmakers, J. A. Chromosomes trapped in micronuclei are liable to segregation errors. J. Cell Sci. 131, jcs214742 (2018). (PMID: 29930083605134410.1242/jcs.214742)
Canver, M. C. et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527, 192–197 (2015). (PMID: 26375006464410110.1038/nature15521)
McKinley, K. L. & Cheeseman, I. M. Large-scale analysis of CRISPR/Cas9 cell-cycle knockouts reveals the diversity of p53-dependent responses to cell-cycle defects. Dev. Cell 40, 405–420 (2017). (PMID: 28216383534512410.1016/j.devcel.2017.01.012)
Brinkman, E. K. et al. Kinetics and fidelity of the repair of Cas9-induced double-strand DNA breaks. Mol. Cell 70, 801–813 (2018). (PMID: 29804829599387310.1016/j.molcel.2018.04.016)
Wu, J., Tang, B. & Tang, Y. Allele-specific genome targeting in the development of precision medicine. Theranostics 10, 3118–3137 (2020). (PMID: 32194858705319210.7150/thno.43298)
Stark, J. M. & Jasin, M. Extensive loss of heterozygosity is suppressed during homologous repair of chromosomal breaks. Mol. Cell Biol. 23, 733–743 (2003). (PMID: 1250947015154810.1128/MCB.23.2.733-743.2003)
Rao, P. N., Johnson, R. T. & Sperling, K. Premature Chromosome Condensation: Application in Basic, Clinical, and Mutation Research xvi (Academic Press, 1982). (PMID: 10.1016/B978-0-12-580450-9.50006-1)
Hoffelder, D. R. et al. Resolution of anaphase bridges in cancer cells. Chromosoma 112, 389–397 (2004). (PMID: 1515632710.1007/s00412-004-0284-6)
Terradas, M., Martin, M., Tusell, L. & Genesca, A. DNA lesions sequestered in micronuclei induce a local defective-damage response. DNA Repair 8, 1225–1234 (2009). (PMID: 1968347810.1016/j.dnarep.2009.07.004)
Crasta, K. et al. DNA breaks and chromosome pulverization from errors in mitosis. Nature 482, 53–58 (2012). (PMID: 22258507327113710.1038/nature10802)
Hatch, E. M., Fischer, A. H., Deerinck, T. J. & Hetzer, M. W. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell 154, 47–60 (2013). (PMID: 23827674374977810.1016/j.cell.2013.06.007)
Ly, P. et al. Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. Nat. Cell Biol. 19, 68–75 (2017). (PMID: 2791855010.1038/ncb3450)
Liu, S. et al. Nuclear envelope assembly defects link mitotic errors to chromothripsis. Nature 561, 551–555 (2018). (PMID: 30232450659962510.1038/s41586-018-0534-z)
Kneissig, M. et al. Micronuclei-based model system reveals functional consequences of chromothripsis in human cells. eLife 8, e50292 (2019). (PMID: 31778112691082710.7554/eLife.50292)
Priestley, P. et al. Pan-cancer whole-genome analyses of metastatic solid tumours. Nature 575, 210–216 (2019). (PMID: 31645765687249110.1038/s41586-019-1689-y)
Ikeda, K. et al. Efficient scarless genome editing in human pluripotent stem cells. Nat. Methods 15, 1045–1047 (2018). (PMID: 3050487210.1038/s41592-018-0212-y)
Liang, D. et al. Frequent gene conversion in human embryos induced by double strand breaks. Preprint at bioRxiv https://doi.org/10.1101/2020.06.19.162214 (2020).
Korbel, J. O. & Campbell, P. J. Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226–1236 (2013). (PMID: 2349893310.1016/j.cell.2013.02.023)
Vazquez-Diez, C., Yamagata, K., Trivedi, S., Haverfield, J. & FitzHarris, G. Micronucleus formation causes perpetual unilateral chromosome inheritance in mouse embryos. Proc. Natl Acad. Sci. USA 113, 626–631 (2016). (PMID: 2672987210.1073/pnas.15176281124725495)
Minocherhomji, S. et al. Replication stress activates DNA repair synthesis in mitosis. Nature 528, 286–290 (2015). (PMID: 2663363210.1038/nature16139)
Cleal, K., Jones, R. E., Grimstead, J. W., Hendrickson, E. A. & Baird, D. M. Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin. Genome Res. 29, 737–749 (2019). (PMID: 30872351649931210.1101/gr.240705.118)
Maciejowski, J., Li, Y., Bosco, N., Campbell, P. J. & de Lange, T. Chromothripsis and kataegis induced by telomere crisis. Cell 163, 1641–1654 (2015). (PMID: 26687355468702510.1016/j.cell.2015.11.054)
Maciejowski, J. et al. APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis. Nat. Genet. 52, 884–890 (2020). (PMID: 32719516748422810.1038/s41588-020-0667-5)
Ribeyre, C. & Shore, D. Regulation of telomere addition at DNA double-strand breaks. Chromosoma 122, 159–173 (2013). (PMID: 2350403510.1007/s00412-013-0404-2)
Maciejowski, J. & de Lange, T. Telomeres in cancer: tumour suppression and genome instability. Nat. Rev. Mol. Cell Biol. 18, 175–186 (2017). (PMID: 28096526558919110.1038/nrm.2016.171)
Canela, A. et al. DNA breaks and end resection measured genome-wide by end sequencing. Mol. Cell 63, 898–911 (2016). (PMID: 27477910629983410.1016/j.molcel.2016.06.034)
McClintock, B. The stability of broken ends of chromosomes in Zea mays. Genetics 26, 234–282 (1941). (PMID: 17247004120912710.1093/genetics/26.2.234)
Campbell, P. J. et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467, 1109–1113 (2010). (PMID: 20981101313736910.1038/nature09460)
Li, Y. et al. Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 508, 98–102 (2014). (PMID: 24670643397627210.1038/nature13115)
Ma, H. et al. Correction of a pathogenic gene mutation in human embryos. Nature 548, 413–419 (2017). (PMID: 2878372810.1038/nature23305)
Egli, D. et al. Inter-homologue repair in fertilized human eggs? Nature 560, E5–E7 (2018). (PMID: 3008992410.1038/s41586-018-0379-5)
Finn, J. D. et al. A single administration of CRISPR/Cas9 lipid nanoparticles achieves robust and persistent in vivo genome editing. Cell Rep. 22, 2227–2235 (2018). (PMID: 2949026210.1016/j.celrep.2018.02.014)
Humbert, O., Peterson, C. W., Norgaard, Z. K., Radtke, S. & Kiem, H. P. A nonhuman primate transplantation model to evaluate hematopoietic stem cell gene editing strategies for β-hemoglobinopathies. Mol. Ther. Methods Clin. Dev. 8, 75–86 (2018). (PMID: 2927671810.1016/j.omtm.2017.11.005)
Humbert, O. et al. Therapeutically relevant engraftment of a CRISPR–Cas9-edited HSC-enriched population with HbF reactivation in nonhuman primates. Sci. Transl. Med. 11, eaaw3768 (2019). (PMID: 3136658010.1126/scitranslmed.aaw37688407476)
Demirci, S. et al. BCL11A enhancer-edited hematopoietic stem cells persist in rhesus monkeys without toxicity. J. Clin. Invest. 130, 6677–6687 (2020).
Lu, Y. et al. Safety and feasibility of CRISPR-edited T cells in patients with refractory non-small-cell lung cancer. Nat. Med. 26, 732–740 (2020). (PMID: 3234157810.1038/s41591-020-0840-5)
Luc, S. et al. Bcl11a deficiency leads to hematopoietic stem cell defects with an aging-like phenotype. Cell Rep. 16, 3181–3194 (2016). (PMID: 27653684505471910.1016/j.celrep.2016.08.064)
Sanders, A. D. et al. Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat. Biotechnol. 38, 343–354 (2020). (PMID: 3187321310.1038/s41587-019-0366-x)
McDermott, D. H. et al. Chromothriptic cure of WHIM syndrome. Cell 160, 686–699 (2015). (PMID: 25662009432907110.1016/j.cell.2015.01.014)
Maeder, M. L. et al. Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10. Nat. Med. 25, 229–233 (2019). (PMID: 3066478510.1038/s41591-018-0327-9)
Lomova, A. et al. Improving gene editing outcomes in human hematopoietic stem and progenitor cells by temporal control of DNA repair. Stem Cells 37, 284–294 (2019). (PMID: 3037255510.1002/stem.2935)
Metais, J. Y. et al. Genome editing of HBG1 and HBG2 to induce fetal hemoglobin. Blood Adv. 3, 3379–3392 (2019). (PMID: 31698466685512710.1182/bloodadvances.2019000820)
Weber, L. et al. Editing a γ-globin repressor binding site restores fetal hemoglobin synthesis and corrects the sickle cell disease phenotype. Sci. Adv. 6, eaay9392 (2020). (PMID: 32917636701569410.1126/sciadv.aay9392)
Howden, S. E. et al. A Cas9 variant for efficient generation of indel-free knockin or gene-corrected human pluripotent stem cells. Stem Cell Rep. 7, 508–517 (2016). (PMID: 10.1016/j.stemcr.2016.07.001)
Rees, H. A. & Liu, D. R. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 19, 770–788 (2018). (PMID: 30323312653518110.1038/s41576-018-0059-1)
Connelly, J. P. & Pruett-Miller, S. M. CRIS.py: a versatile and high-throughput analysis program for CRISPR-based genome editing. Sci. Rep. 9, 4194 (2019). (PMID: 30862905641449610.1038/s41598-019-40896-w)
Grant Information:: F32 DK118822 United States DK NIDDK NIH HHS; 2020154 United States DDCF_ Doris Duke Charitable Foundation; P01 HL053749 United States HL NHLBI NIH HHS; P30 CA021765 United States CA NCI NIH HHS; R01 CA213404 United States CA NCI NIH HHS; K22 CA216319 United States CA NCI NIH HHS; 2017093 United States DDCF_ Doris Duke Charitable Foundation; United States HHMI_ Howard Hughes Medical Institute
Substance Nomenclature:: 0 (Antigens, CD34)
0 (Tumor Suppressor Protein p53)
EC 3.1.- (CRISPR-Associated Protein 9)
Entry Date(s):: Date Created: 20210413 Date Completed: 20210720 Latest Revision: 20220419
Update Code:: 20240104
PubMed Central ID:: PMC8192433
DOI:: 10.1038/s41588-021-00838-7
PMID:: 33846636
: Czasopismo naukowe

Genome editing has therapeutic potential for treating genetic diseases and cancer. However, the currently most practicable approaches rely on the generation of DNA double-strand breaks (DSBs), which can give rise to a poorly characterized spectrum of chromosome structural abnormalities. Here, using model cells and single-cell whole-genome sequencing, as well as by editing at a clinically relevant locus in clinically relevant cells, we show that CRISPR-Cas9 editing generates structural defects of the nucleus, micronuclei and chromosome bridges, which initiate a mutational process called chromothripsis. Chromothripsis is extensive chromosome rearrangement restricted to one or a few chromosomes that can cause human congenital disease and cancer. These results demonstrate that chromothripsis is a previously unappreciated on-target consequence of CRISPR-Cas9-generated DSBs. As genome editing is implemented in the clinic, the potential for extensive chromosomal rearrangements should be considered and monitored.

Comment in: Nat Genet. 2021 Jun;53(6):768-769. (PMID: 34103715)

Informacja