Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

No excessive mutations in transcription activator-like effector nuclease-mediated α-1,3-galactosyltransferase knockout Yucatan miniature pigs

  • Received : 2019.06.11
  • Accepted : 2019.07.29
  • Published : 2020.02.01
Download PDF
⟨ Previous Next ⟩

Abstract

Objective: Specific genomic sites can be recognized and permanently modified by genome editing. The discovery of endonucleases has advanced genome editing in pigs, attenuating xenograft rejection and cross-species disease transmission. However, off-target mutagenesis caused by these nucleases is a major barrier to putative clinical applications. Furthermore, off-target mutagenesis by genome editing has not yet been addressed in pigs. Methods: Here, we generated genetically inheritable α-1,3-galactosyltransferase (GGTA1) knockout Yucatan miniature pigs by combining transcription activator-like effector nuclease (TALEN) and nuclear transfer. For precise estimation of genomic mutations induced by TALEN in GGTA1 knockout pigs, we obtained the whole-genome sequence of the donor cells for use as an internal control genome. Results: In-depth whole-genome sequencing analysis demonstrated that TALEN-mediated GGTA1 knockout pigs had a comparable mutation rate to homologous recombination-treated pigs and wild-type strain controls. RNA sequencing analysis associated with genomic mutations revealed that TALEN-induced off-target mutations had no discernable effect on RNA transcript abundance. Conclusion: Therefore, TALEN appears to be a precise and safe tool for generating genomeedited pigs, and the TALEN-mediated GGTA1 knockout Yucatan miniature pigs produced in this study can serve as a safe and effective organ and tissue resource for clinical applications.

Keywords

References

  1. Hoshijima K, Jurynec MJ, Grunwald DJ. Precise genome editing by homologous recombination. Methods Cell Biol 2016;135:121-47. https://doi.org/10.1016/bs.mcb.2016.04.008
  2. Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 1996;93:1156-60. https://doi.org/10.1073/pnas.93.3.1156
  3. Christian M, Cermak T, Doyle EL, et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 2010; 186:757-61. https://doi.org/10.1534/genetics.110.120717
  4. Mali P, Yang L, Esvelt KM, et al. RNA-guided human genome engineering via Cas9. Science 2013;339:823-6. https://doi.org/10.1126/science.1232033
  5. Ramalingam S, Kandavelou K, Rajenderan R, Chandrasegaran S. Creating designed zinc-finger nucleases with minimal cytotoxicity. J Mol Biol 2011;405:630-41. https://doi.org/10.1016/j.jmb.2010.10.043
  6. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 2014;32:279-84. https://doi.org/10.1038/nbt. 2808
  7. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 2014;32:677-83. https://doi.org/10.1038/nbt.2916
  8. Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 2013;154:1370-9. https://doi.org/10.1016/j.cell.2013.08.022
  9. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science 2014; 343:80-4. https://doi.org/10.1126/science.1246981
  10. Park CY, Kim J, Kweon J, et al. Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci USA 2014;111:9253-8. https://doi.org/10.1073/pnas.1323941111
  11. Yang H, Wu Z. Genome editing of pigs for agriculture and biomedicine. Front Genet 2018;9:360. https://doi.org/10.3389/fgene.2018.00360
  12. Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 2014;42:W401-7. https://doi.org/10.1093/nar/gku410
  13. Choi K, Shim J, Ko N, et al. Production of heterozygous alpha 1,3-galactosyltransferase (GGTA1) knock-out transgenic miniature pigs expressing human CD39. Transgenic Res 2017;26: 209-24. https://doi.org/10.1007/s11248-016-9996-7
  14. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60. https://doi.org/10.1093/bioinformatics/btp324
  15. Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25:2078-9. https://doi.org/10.1093/bioinformatics/btp352
  16. DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011;43:491-8. https://doi.org/10.1038/ng.806
  17. Cingolani P, Platts A, Wang le L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012;6:80-92. https://doi.org/10.4161/fly.19695
  18. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26:841-2. https://doi.org/10.1093/bioinformatics/btq033
  19. Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011;29:644-52. https://doi.org/10.1038/nbt.1883
  20. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012;28:3150-2. https://doi.org/10.1093/bioinformatics/bts565
  21. Yang Y, Smith SA. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics 2013;14: 328. https://doi.org/10.1186/1471-2164-14-328
  22. Becker KG, Hosack DA, Dennis G, Jr., et al. PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics 2003;4:61. https://doi.org/10.1186/1471-2105-4-61
  23. Nakabayashi K, Trujillo AM, Tayama C, et al. Methylation screening of reciprocal genome-wide UPDs identifies novel human-specific imprinted genes. Hum Mol Genet 2011;20: 3188-97. https://doi.org/10.1093/hmg/ddr224
  24. Mostafavi N, Vermeulen R, Ghantous A, et al. Acute changes in DNA methylation in relation to 24h personal air pollution exposure measurements: A panel study in four European countries. Environ Int 2018;120:11-21. https://doi.org/10.1016/ j.envint.2018.07.026
  25. Altmann S, Murani E, Schwerin M, Metges CC, Wimmers K, Ponsuksili S. Somatic cytochrome c (CYCS) gene expression and promoter-specific DNA methylation in a porcine model of prenatal exposure to maternal dietary protein excess and restriction. Br J Nutr 2012;107:791-9. https://doi.org/10.1017/S0007114511003667
  26. Oner D, Ghosh M, Bove H, et al. Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition. Part Fibre Toxicol 2018;15:11. https://doi.org/10.1186/s12989-018-0244-6
  27. Mullapudi N, Ye B, Suzuki M, et al. Genome wide methylome alterations in lung cancer. PLoS One 2015;10:e0143826. https://doi.org/10.1371/journal.pone.0143826
  28. Grasse S, Lienhard M, Frese S, et al. Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance. Genome Med 2018;10:55. https://doi.org/10.1186/s13073-018-0562-1
  29. de Miguel FJ, Sharma RD, Pajares MJ, Montuenga LM, Rubio A, Pio R. Identification of alternative splicing events regulated by the oncogenic factor SRSF1 in lung cancer. Cancer Res 2014;74:1105-15. https://doi.org/10.1158/0008-5472.CAN-13-1481
  30. Han Q, Lin X, Zhang X, et al. WWC3 regulates the Wnt and Hippo pathways via Dishevelled proteins and large tumour suppressor 1, to suppress lung cancer invasion and metastasis. J Pathol 2017;242:435-47. https://doi.org/10.1002/path.4919
  31. Ou C, Li X, Li G, Ma J. WWC3: the bridge linking Hippo and Wnt pathways in lung cancer. J Thorac Dis 2017;9:2315-6. https://doi.org/10.21037/jtd.2017.08.35
  32. Han Q, Kremerskothen J, Lin X, et al. WWC3 inhibits epithelial-mesenchymal transition of lung cancer by activating Hippo-YAP signaling. Onco Targets Ther 2018;11:2581-91. https://doi.org/10.2147/OTT.S162387
  33. Li N, Li S. RASAL2 promotes lung cancer metastasis through epithelial-mesenchymal transition. Biochem Biophys Res Commun 2014;455:358-62. https://doi.org/10.1016/j.bbrc. 2014.11.020
  34. Chen CH, Chuang SM, Yang MF, Liao JW, Yu SL, Chen JJ. A novel function of YWHAZ/beta-catenin axis in promoting epithelial-mesenchymal transition and lung cancer metastasis. Mol Cancer Res 2012;10:1319-31. https://doi.org/10.1158/1541-7786.MCR-12-0189
  35. Guo Z, Han C, Du J, et al. Proteomic study of differential protein expression in mouse lung tissues after aerosolized ricin poisoning. Int J Mol Sci 2014;15:7281-92. https://doi.org/10.3390/ijms15057281
  36. Park J, Lai L, Samuel M, et al. Altered gene expression profiles in the brain, kidney, and lung of one-month-old cloned pigs. Cell Reprogram 2011;13:215-23. https://doi.org/10.1089/cell.2010.0088
  37. Kim H, Song KD, Kim HJ, et al. Exploring the genetic signature of body size in Yucatan miniature pig. PLoS One 2015;10: e0121732. https://doi.org/10.1371/journal.pone.0121732
  38. Wilson CJ, Fennell T, Bothmer A, et al. Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods 2018;15:236-7. https://doi.org/10.1038/nmeth.4552
  39. Kim ST, Park J, Kim D, et al. Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods 2018; 15:239-40. https://doi.org/10.1038/nmeth.4554
  40. Nutter LMJ, Heaney JD, Lloyd KCK, et al. Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods 2018;15:235-6. https://doi.org/10.1038/nmeth.4559
  41. Alexandrov LB, Jones PH, Wedge DC, et al. Clock-like mutational processes in human somatic cells. Nat Genet 2015;47: 1402-7. https://doi.org/10.1038/ng.3441
  42. Boesen JJ, Niericker MJ, Dieteren N, Simons JW. How variable is a spontaneous mutation rate in cultured mammalian cells? Mutat Res 1994;307:121-9. https://doi.org/10.1016/0027-5107(94)90284-4
  43. Veres A, Gosis BS, Ding Q, et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 2014;15:27-30. https://doi.org/10.1016/j.stem. 2014.04.020
  44. Cornu TI, Mussolino C, Cathomen T. Refining strategies to translate genome editing to the clinic. Nat Med 2017;23:415-23. https://doi.org/10.1038/nm.4313
  45. Fu Y, Foden JA, Khayter C, et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 2013;31:822-6. https://doi.org/10.1038/nbt.2623
  46. Hsu PD, Scott DA, Weinstein JA, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013; 31:827-32. https://doi.org/10.1038/nbt.2647
  47. Kosicki M, Tomberg K, Bradley A. Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol 2018;36:765-71. https://doi.org/10.1038/nbt.4192
  48. Deschamps JY, Roux FA, Sai P, Gouin E. History of xenotransplantation. Xenotransplantation 2005;12:91-109. https://doi.org/10.1111/j.1399-3089.2004.00199.x
  49. Galili U. Interaction of the natural anti-Gal antibody with alpha-galactosyl epitopes: a major obstacle for xenotransplantation in humans. Immunol Today 1993;14:480-2. https://doi.org/10.1016/0167-5699(93)90261-I
  50. Lai L, Kolber-Simonds D, Park KW, et al. Production of alpha-1,3-galactosyltransferase knockout pigs by nuclear transfer cloning. Science 2002;295:1089-92. https://doi.org/10.1126/science.1068228
  51. Phelps CJ, Koike C, Vaught TD, et al. Production of alpha 1,3-galactosyltransferase-deficient pigs. Science 2003;299: 411-4. https://doi.org/10.1126/science.1078942
  52. Xin J, Yang H, Fan N, et al. Highly efficient generation of GGTA1 biallelic knockout inbred mini-pigs with TALENs. PLoS One 2013;8:e84250. https://doi.org/10.1371/journal.pone.0084250
  53. Petersen B, Frenzel A, Lucas-Hahn A, et al. Efficient production of biallelic GGTA1 knockout pigs by cytoplasmic microinjection of CRISPR/Cas9 into zygotes. Xenotransplantation 2016;23:338-46. https://doi.org/10.1111/xen.12258
  54. Tseng YL, Kuwaki K, Dor FJ, et al. alpha1,3-Galactosyltransferase gene-knockout pig heart transplantation in baboons with survival approaching 6 months. Transplantation 2005;80:1493-500. https://doi.org/10.1097/01.tp.0000181397.41143.fa
  55. Yamada K, Yazawa K, Shimizu A, et al. Marked prolongation of porcine renal xenograft survival in baboons through the use of alpha1,3-galactosyltransferase gene-knockout donors and the cotransplantation of vascularized thymic tissue. Nat Med 2005;11:32-4. https://doi.org/10.1038/nm1172
  56. Patience C, Takeuchi Y, Weiss RA. Infection of human cells by an endogenous retrovirus of pigs. Nat Med 1997;3:282-6. https://doi.org/10.1038/nm0397-282
  57. Niu D, Wei HJ, Lin L, et al. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 2017;357:1303-7. https://doi.org/10.1126/science.aan4187

Cited by

  1. Current status of the application of gene editing in pigs vol.67, pp.3, 2020, https://doi.org/10.1262/jrd.2021-025