991
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

PlmCas12e (CasX2) cleavage of CCR5: impact of guide RNA spacer length and PAM sequence on cleavage activity

ORCID Icon, , , ORCID Icon, ORCID Icon & ORCID Icon
Pages 296-305 | Accepted 31 May 2023, Published online: 07 Jun 2023

References

  • Dragic T, Litwin V, Allaway GP, et al. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature. 1996;381(6584):667–673. doi:10.1038/381667a0.
  • Deng H, Liu R, Ellmeier W, et al. Identification of a major co-receptor for primary isolates of HIV-1. Nature. 1996;381(6584):661–666. doi:10.1038/381661a0.
  • Barmania F, Pepper MS. C-C chemokine receptor type five (CCR5): an emerging target for the control of HIV infection. Appl Transl Genom. 2013;2:3–16. doi:10.1016/j.atg.2013.05.004.
  • Joung JK, Sander JD. Talens: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol. 2013;14(1):49–55.
  • Carroll D. Genome engineering with zinc-finger nucleases. Genetics. 2011;188(4):773–782.
  • Hofer U, Henley JE, Exline CM, et al. Pre-clinical modeling of CCR5 knockout in human hematopoietic stem cells by zinc finger nucleases using humanized mice. Journal Of Infectious Diseasesquery. 2013;208(Suppl 2):S160–4. doi:10.1093/infdis/jit382.
  • Romito M, Juillerat A, Kok YL, et al. Preclinical evaluation of a novel TALEN targeting CCR5 confirms efficacy and safety in conferring resistance to HIV-1 infection. Biotechnol J. 2021;16(1):e2000023. doi:10.1002/biot.202000023.
  • Shi B, Li J, Shi X, et al. TALEN-Mediated knockout of CCR5 confers protection against infection of human immunodeficiency virus. J Acquir Immune Defic Syndr. 2017;74(2):229–241.
  • Tebas P, Stein D, Tang WW, et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med. 2014;370(10):901–910. doi:10.1056/NEJMoa1300662.
  • Cannon P, June C. Chemokine receptor 5 knockout strategies. Curr Opin HIV AIDS. 2011;6(1):74–79.
  • Maier DA, Brennan AL, Jiang S, et al. Efficient clinical scale gene modification via zinc finger nuclease-targeted disruption of the HIV co-receptor CCR5. Hum Gene Ther. 2013;24(3):245–258. doi:10.1089/hum.2012.172.
  • Knipping F, Newby GA, Eide CR, et al. Disruption of HIV-1 co-receptors CCR5 and CXCR4 in primary human T cells and hematopoietic stem and progenitor cells using base editing. Mol Ther. 2022;30(1):130–144. doi:10.1016/j.ymthe.2021.10.026.
  • Huang TP, Newby GA, Liu DR. Precision genome editing using cytosine and adenine base editors in mammalian cells. Nat Protoc. 2021;16(2):1089–1128. doi:10.1038/s41596-020-00450-9.
  • Jinek M, Chylinski K, Fonfara I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816–821. doi:10.1126/science.1225829.
  • Gilbert LA, Larson MH, Morsut L, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013;154(2):442–451.
  • Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–823.
  • Dash PK, Kaminski R, Bella R, et al. Sequential LASER ART and CRISPR treatments eliminate HIV-1 in a subset of infected humanized mice. Nat Commun. 2019;10(1):2753. doi:10.1038/s41467-019-10366-y.
  • Yang YC, Yang HC. Recent progress and future prospective in HBV cure by CRISPR/Cas. Viruses. 2021;14(1):4.
  • Stone D, Long KR, Loprieno MA, et al. CRISPR-Cas9 gene editing of hepatitis B virus in chronically infected humanized mice. Mol Ther Methods Clin Dev. 2021;20:258–275.
  • Lu Y, Xue J, Deng T, et al. Safety and feasibility of CRISPR-edited T cells in patients with refractory non-small-cell lung cancer. Nat Med. 2020;26(5):732–740. doi:10.1038/s41591-020-0840-5.
  • Vazquez-Salat N, Yuhki N, Beck T, et al. Gene conversion between mammalian CCR2 and CCR5 chemokine receptor genes: a potential mechanism for receptor dimerization. Genomics. 2007;90(2):213–224.
  • Xu L, Yang H, Gao Y, et al. Crispr/cas9-mediated CCR5 ablation in human hematopoietic stem/progenitor cells confers HIV-1 resistance in vivo. Mol Ther. 2017;25(8):1782–1789. doi:10.1016/j.ymthe.2017.04.027.
  • Gupta RK, Abdul-Jawad S, McCoy LE, et al. HIV-1 remission following CCR5Delta32/Delta32 haematopoietic stem-cell transplantation. Nature. 2019;568(7751):244–248. doi:10.1038/s41586-019-1027-4.
  • Hutter G, Nowak D, Mossner M, et al. Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation. N Engl J Med. 2009;360(7):692–698. doi:10.1056/NEJMoa0802905.
  • Ding J, Liu Y, Lai Y. Knowledge from London and Berlin: finding threads to a functional HIV cure. Front Immunol. 2021;12:688747.
  • Gupta RK, Peppa D, Hill AL, et al. Evidence for HIV-1 cure after CCR5Delta32/Delta32 allogeneic haemopoietic stem-cell transplantation 30 months post analytical treatment interruption: a case report. Lancet HIV. 2020;7(5):e340–e347. doi:10.1016/S2352-3018(20)30069-2.
  • Mehta A, Merkel OM. Immunogenicity of Cas9 protein. J Pharm Sci. 2020;109(1):62–67.
  • Crudele JM, Chamberlain JS. Cas9 immunity creates challenges for CRISPR gene editing therapies. Nat Commun. 2018;9(1):3497.
  • Charlesworth CT, Deshpande PS, Dever DP, et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat Med. 2019;25(2):249–254. doi:10.1038/s41591-018-0326-x.
  • Chen JS, Ma E, Harrington LB, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018;360(6387):436–439.
  • Zetsche B, Gootenberg JS, Abudayyeh OO, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163(3):759–771. doi:10.1016/j.cell.2015.09.038.
  • Strecker J, Jones S, Koopal B, et al. Engineering of CRISPR-Cas12b for human genome editing. Nat Commun. 2019;10(1):212.
  • Shmakov S, Abudayyeh OO, Makarova KS, et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas Systems. Mol Cell. 2015;60(3):385–397. doi:10.1016/j.molcel.2015.10.008.
  • Chen LX, Al-Shayeb B, Meheust R, et al. Candidate phyla radiation roizmanbacteria from hot springs have novel and unexpectedly abundant CRISPR-Cas systems. Front Microbiol. 2019;10:928.
  • Burstein D, Harrington LB, Strutt SC, et al. New CRISPR-Cas systems from uncultivated microbes. Nature. 2017;542(7640):237–241. doi:10.1038/nature21059.
  • Tsuchida CA, Zhang S, Doost MS, et al. Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Mol Cell. 2022;82(6):1199–1209 e6. doi:10.1016/j.molcel.2022.02.002.
  • Abudayyeh OO, Gootenberg JS, Konermann S, et al., C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science, 2016. 353(6299): p. aaf5573.
  • Liu J-J, Orlova N, Oakes BL, et al. CRISPR-Casx is an RNA-dominated enzyme active for human genome editing. Nature. 2019;566(7743):218–223. doi:10.1038/s41586-019-0908-x.
  • Mummidi S, Ahuja SS, McDaniel BL, et al. The human CC chemokine receptor 5 (CCR5) gene. Multiple transcripts with 5’-end heterogeneity, dual promoter usage, and evidence for polymorphisms within the regulatory regions and noncoding exons. J Biol Chem. 1997;272(49):30662–30671.
  • Liu R, Paxton WA, Choe S, et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell. 1996;86(3):367–377. doi:10.1016/S0092-8674(00)80110-5.
  • So CC, Martin A, Maizels N. DSB structure impacts DNA recombination leading to class switching and chromosomal translocations in human B cells. PLoS Genet. 2019;15(4):e1008101.
  • Moreno-Mateos MA, Fernandez JP, Rouet R, et al. CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat Commun. 2017;8(1):2024.
  • Keilwagen J, Wenk M, Erickson JL, et al. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 2016;44(9):e89.
  • Kato-Inui T, Takahashi G, Hsu S, et al. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair. Nucleic Acids Res. 2018;46(9):4677–4688.
  • Chauhan VP, Sharp PA, Langer R. Altered DNA repair pathway engagement by engineered CRISPR-Cas9 nucleases. Proc Natl Acad Sci U S A. 2023;120(11):e2300605120.
  • Selkova P, Vasileva A, Pobegalov G, et al. Position of Deltaproteobacteria Cas12e nuclease cleavage sites depends on spacer length of guide RNA. RNA Biol. 2020;17(10):1472–1479. doi:10.1080/15476286.2020.1777378.
  • Hsu PD, Scott DA, Weinstein JA, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31(9):827–832.
  • Heredia JD, Park J, Brubaker RJ, et al. Mapping interaction sites on human chemokine receptors by deep mutational scanning. J Immunol. 2018;200(11):3825–3839.
  • Ratti V, Nanda S, Eszterhas SK, et al. A mathematical model of HIV dynamics treated with a population of gene-edited haematopoietic progenitor cells exhibiting threshold phenomenon. Math Med Biol. 2020;37(2):212–242. doi:10.1093/imammb/dqz011.