Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Protocol
  • Published:

CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver

Abstract

Genetically engineered mouse models (GEMMs) transformed the study of organismal disease phenotypes but are limited by their lengthy generation in embryonic stem cells. Here, we describe methods for rapid and scalable genome engineering in somatic cells of the liver and pancreas through delivery of CRISPR components into living mice. We introduce the spectrum of genetic tools, delineate viral and nonviral CRISPR delivery strategies and describe a series of applications, ranging from gene editing and cancer modeling to chromosome engineering or CRISPR multiplexing and its spatio-temporal control. Beyond experimental design and execution, the protocol describes quantification of genetic and functional editing outcomes, including sequencing approaches, data analysis and interpretation. Compared to traditional knockout mice, somatic GEMMs face an increased risk for mouse-to-mouse variability because of the higher experimental demands of the procedures. The robust protocols described here will help unleash the full potential of somatic genome manipulation. Depending on the delivery method and envisaged application, the protocol takes 3–5 weeks.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Overview of workflows for somatic genome editing in the mouse liver and pancreas.
Fig. 2: Overview of CRISPR delivery approaches to the pancreas or liver and schemes of Cas9 GEMMs for somatic CRISPR engineering.
Fig. 3: Overview of CRISPR systems and applications.
Fig. 4: Efficacy of viral and nonviral nucleic acid delivery methods for the pancreas and liver of mice.
Fig. 5: Quantification of CRISPR editing efficiencies in the liver and pancreas upon scAAV8-based sgRNA delivery.
Fig. 6: Induction of pancreatic ductal adenocarcinoma (PDAC) through somatic genome engineering in mice.
Fig. 7: Intrachromosomal rearrangements induced by somatic CRISPR–Cas9 multiplexing in the mouse liver by using HTVI.
Fig. 8: Interchromosomal rearrangements induced by CRISPR–Cas9 multiplexing in the pancreas.
Fig. 9: Mutational analysis of CRISPR-edited tumors and corresponding cell lines.

Similar content being viewed by others

Data availability

All data generated or analyzed during this study are included in either this paper or our original research study5,6. Source data are provided with this paper.

References

  1. Bradley, A., Evans, M., Kaufman, M. H. & Robertson, E. Formation of germ-line chimaeras from embryo-derived teratocarcinoma cell lines. Nature 309, 255–256 (1984).

    Article  CAS  PubMed  Google Scholar 

  2. Doetschman, T. et al. Targetted correction of a mutant HPRT gene in mouse embryonic stem cells. Nature 330, 576–578 (1987).

    Article  CAS  PubMed  Google Scholar 

  3. Kersten, K., de Visser, K. E., van Miltenburg, M. H. & Jonkers, J. Genetically engineered mouse models in oncology research and cancer medicine. EMBO Mol. Med. 9, 137–153 (2017).

    Article  CAS  PubMed  Google Scholar 

  4. Weber, J. & Rad, R. Engineering CRISPR mouse models of cancer. Curr. Opin. Genet. Dev. 54, 88–96 (2019).

    Article  CAS  PubMed  Google Scholar 

  5. Weber, J. et al. CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice. Proc. Natl Acad. Sci. USA 112, 13982–13987 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Maresch, R. et al. Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice. Nat. Commun. 7, 10770 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Mueller, S. et al. Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes. Nature 554, 62–68 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Pickar-Oliver, A. & Gersbach, C. A. The next generation of CRISPR-Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 20, 490–507 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Zhang, G., Budker, V. & Wolff, J. A. High levels of foreign gene expression in hepatocytes after tail vein injections of naked plasmid DNA. Hum. Gene Ther. 10, 1735–1737 (1999).

    Article  CAS  PubMed  Google Scholar 

  10. Zhang, G. et al. Hydroporation as the mechanism of hydrodynamic delivery. Gene Ther. 11, 675–682 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Suda, T., Gao, X., Stolz, D. B. & Liu, D. Structural impact of hydrodynamic injection on mouse liver. Gene Ther. 14, 129–137 (2007).

    Article  CAS  PubMed  Google Scholar 

  12. Kim, M. J. & Ahituv, N. The hydrodynamic tail vein assay as a tool for the study of liver promoters and enhancers. Methods Mol. Biol. 1015, 279–289 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Liu, F., Song, Y. & Liu, D. Hydrodynamics-based transfection in animals by systemic administration of plasmid DNA. Gene Ther. 6, 1258–1266 (1999).

    Article  CAS  PubMed  Google Scholar 

  14. Hubner, E. K. et al. Constitutive and inducible systems for genetic in vivo modification of mouse hepatocytes using hydrodynamic tail vein injection. J. Vis. Exp 2018, 56613 (2018).

    Google Scholar 

  15. Xue, W. et al. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature 514, 380–384 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Sato, M. et al. Site-targeted non-viral gene delivery by direct DNA injection into the pancreatic parenchyma and subsequent in vivo electroporation in mice. Biotechnol. J. 8, 1355–1361 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Suzuki, T., Shin, B.-C., Fujikura, K., Matsuzaki, T. & Takata, K. Direct gene transfer into rat liver cells by in vivo electroporation. FEBS Lett. 425, 436–440 (1998).

    Article  CAS  PubMed  Google Scholar 

  18. Gürlevik, E. et al. Administration of gemcitabine after pancreatic tumor resection in mice induces an antitumor immune response mediated by natural killer cells. Gastroenterology 151, 338–350.e7 (2016).

    Article  PubMed  Google Scholar 

  19. Seehawer, M. et al. Necroptosis microenvironment directs lineage commitment in liver cancer. Nature 562, 69–75 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Rosenfeld, M. A. et al. Adenovirus-mediated transfer of a recombinant α1-antitrypsin gene to the lung epithelium in vivo. Science 252, 431–434 (1991).

    Article  CAS  PubMed  Google Scholar 

  21. Shirley, J. L., Jong, Y. P., de, Terhorst, C. & Herzog, R. W. Immune responses to viral gene therapy vectors. Mol. Ther. 28, 709–722 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Somanathan, S., Breous, E., Bell, P. & Wilson, J. M. AAV vectors avoid inflammatory signals necessary to render transduced hepatocyte targets for destructive T cells. Mol. Ther. 18, 977–982 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Snyder, R. O. et al. Correction of hemophilia B in canine and murine models using recombinant adeno-associated viral vectors. Nat. Med. 5, 64–70 (1999).

    Article  CAS  PubMed  Google Scholar 

  24. Cunningham, S. C., Dane, A. P., Spinoulas, A. & Alexander, I. E. Gene delivery to the juvenile mouse liver using AAV2/8 vectors. Mol. Ther. 16, 1081–1088 (2008).

    Article  CAS  PubMed  Google Scholar 

  25. Fitzpatrick, Z. et al. Influence of pre-existing anti-capsid neutralizing and binding antibodies on AAV vector transduction. Mol. Ther. Methods Clin. Dev. 9, 119–129 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Grimm, D. et al. Preclinical in vivo evaluation of pseudotyped adeno-associated virus vectors for liver gene therapy. Blood 102, 2412–2419 (2003).

    Article  CAS  PubMed  Google Scholar 

  27. Wu, Z., Asokan, A. & Samulski, R. J. Adeno-associated virus serotypes: vector toolkit for human gene therapy. Mol. Ther. 14, 316–327 (2006).

    Article  CAS  PubMed  Google Scholar 

  28. Gao, G.-P. et al. Novel adeno-associated viruses from rhesus monkeys as vectors for human gene therapy. Proc. Natl Acad. Sci. USA 99, 11854–11859 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Inagaki, K. et al. Robust systemic transduction with AAV9 vectors in mice: efficient global cardiac gene transfer superior to that of AAV8. Mol. Ther. 14, 45–53 (2006).

    Article  CAS  PubMed  Google Scholar 

  30. Jimenez, V. et al. In vivo genetic engineering of murine pancreatic beta cells mediated by single-stranded adeno-associated viral vectors of serotypes 6, 8 and 9. Diabetologia 54, 1075–1086 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Quirin, K. A. et al. Safety and efficacy of AAV retrograde pancreatic ductal gene delivery in normal and pancreatic cancer mice. Mol. Ther. Methods Clin. Dev. 8, 8–20 (2018).

    Article  CAS  PubMed  Google Scholar 

  32. Penaud-Budloo, M. et al. Adeno-associated virus vector genomes persist as episomal chromatin in primate muscle. J. Virol. 82, 7875–7885 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Fisher, K. J. et al. Transduction with recombinant adeno-associated virus for gene therapy is limited by leading-strand synthesis. J. Virol. 70, 520–532 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Ferrari, F. K., Samulski, T., Shenk, T. & Samulski, R. J. Second-strand synthesis is a rate-limiting step for efficient transduction by recombinant adeno-associated virus vectors. J. Virol. 70, 3227–3234 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Miao, C. H. et al. Nonrandom transduction of recombinant adeno-associated virus vectors in mouse hepatocytes in vivo: cell cycling does not influence hepatocyte transduction. J. Virol. 74, 3793–3803 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. McCarty, D. M. et al. Adeno-associated virus terminal repeat (TR) mutant generates self-complementary vectors to overcome the rate-limiting step to transduction in vivo. Gene Ther. 10, 2112–2118 (2003).

    Article  CAS  PubMed  Google Scholar 

  37. Wang, Z. et al. Widespread and stable pancreatic gene transfer by adeno-associated virus vectors via different routes. Diabetes 55, 875–884 (2006).

    Article  CAS  PubMed  Google Scholar 

  38. McCarty, D. M. Self-complementary AAV vectors; advances and applications. Mol. Ther. 16, 1648–1656 (2008).

    Article  CAS  PubMed  Google Scholar 

  39. Ideno, N. et al. A pipeline for rapidly generating genetically engineered mouse models of pancreatic cancer using in vivo CRISPR-Cas9-mediated somatic recombination. Lab. Invest. 99, 1233–1244 (2019).

    Article  CAS  PubMed  Google Scholar 

  40. Muzumdar, M. D., Tasic, B., Miyamichi, K., Li, L. & Luo, L. A global double-fluorescent Cre reporter mouse. Genesis 45, 593–605 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Bell, P. et al. Inverse zonation of hepatocyte transduction with AAV vectors between mice and non-human primates. Mol. Genet. Metab. 104, 395–403 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Weber, J. et al. PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice. Nat. Commun. 10, 1415 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Platt, R. J. et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440–455 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Chiou, S.-H. et al. Pancreatic cancer modeling using retrograde viral vector delivery and in vivo CRISPR/Cas9-mediated somatic genome editing. Genes Dev. 29, 1576–1585 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Dow, L. E. et al. Inducible in vivo genome editing with CRISPR-Cas9. Nat. Biotechnol. 33, 390–394 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Bowling, S. et al. An engineered CRISPR-Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells. Cell 181, 1410–1422.e27 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Katigbak, A., Robert, F., Paquet, M. & Pelletier, J. Inducible genome editing with conditional CRISPR/Cas9 Mice. G3 (Bethesda) 8, 1627–1635 (2018).

    Article  CAS  Google Scholar 

  48. Lundin, A. et al. Development of an ObLiGaRe Doxycycline Inducible Cas9 system for pre-clinical cancer drug discovery. Nat. Commun. 11, 4903 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Premsrirut, P. K. et al. A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell 145, 145–158 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Bardeesy, N. et al. Both p16(Ink4a) and the p19(Arf)-p53 pathway constrain progression of pancreatic adenocarcinoma in the mouse. Proc. Natl Acad. Sci. USA 103, 5947–5952 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Wang, G. et al. Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening. Sci. Adv. 4, eaao5508 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Wei, T., Cheng, Q., Min, Y.-L., Olson, E. N. & Siegwart, D. J. Systemic nanoparticle delivery of CRISPR-Cas9 ribonucleoproteins for effective tissue specific genome editing. Nat. Commun. 11, 3232 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Blasco, R. B. et al. Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology. Cell Rep. 9, 1219–1227 (2014).

    Article  CAS  PubMed  Google Scholar 

  54. Maddalo, D. et al. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system. Nature 516, 423–427 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Rowley, M. et al. Inactivation of Brca2 promotes Trp53-associated but inhibits KrasG12D-dependent pancreatic cancer development in mice. Gastroenterology 140, 1303–1313.e1-3 (2011).

    Article  CAS  PubMed  Google Scholar 

  56. Xu, C. et al. piggyBac mediates efficient in vivo CRISPR library screening for tumorigenesis in mice. Proc. Natl Acad. Sci. USA 114, 722–727 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Xu, Y., Liu, R. & Dai, Z. Key considerations in designing CRISPR/Cas9-carrying nanoparticles for therapeutic genome editing. Nanoscale 12, 21001–21014 (2020).

    Article  CAS  PubMed  Google Scholar 

  58. Cheng, Q. et al. Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR-Cas gene editing. Nat. Nanotechnol. 15, 313–320 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Mitchell, M. J. et al. Engineering precision nanoparticles for drug delivery. Nat. Rev. Drug Discov 20, 101–124 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Sanità, G., Carrese, B. & Lamberti, A. Nanoparticle surface functionalization: how to improve biocompatibility and cellular internalization. Front. Mol. Biosci. 7, 587012 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  61. 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).

    Article  CAS  PubMed  Google Scholar 

  62. Yin, H. et al. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat. Biotechnol. 35, 1179–1187 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Zhang, Y.-N., Poon, W., Tavares, A. J., McGilvray, I. D. & Chan, W. C. W. Nanoparticle-liver interactions: cellular uptake and hepatobiliary elimination. J. Control. Release 240, 332–348 (2016).

    Article  CAS  PubMed  Google Scholar 

  64. Yang, Y. et al. Cellular immunity to viral antigens limits E1-deleted adenoviruses for gene therapy. Proc. Natl Acad. Sci. USA 91, 4407–4411 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Worgall, S., Wolff, G., Falck-Pedersen, E. & Crystal, R. G. Innate immune mechanisms dominate elimination of adenoviral vectors following in vivo administration. Hum. Gene Ther. 8, 37–44 (1997).

    Article  CAS  PubMed  Google Scholar 

  66. Muruve, D. A. et al. Helper-dependent adenovirus vectors elicit intact innate but attenuated adaptive host immune responses in vivo. J. Virol. 78, 5966–5972 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Alba, R., Bosch, A. & Chillon, M. Gutless adenovirus: last-generation adenovirus for gene therapy. Gene Ther. 12(Suppl 1), S18–S27 (2005).

    Article  CAS  PubMed  Google Scholar 

  68. Morró, M. et al. Pancreatic transduction by helper-dependent adenoviral vectors via intraductal delivery. Hum. Gene Ther. 25, 824–836 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  69. Gallaher, S. D., Gil, J. S., Dorigo, O. & Berk, A. J. Robust in vivo transduction of a genetically stable Epstein-Barr virus episome to hepatocytes in mice by a hybrid viral vector. J. Virol. 83, 3249–3257 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Cronin, J., Zhang, X.-Y. & Reiser, J. Altering the tropism of lentiviral vectors through pseudotyping. Curr. Gene Ther. 5, 387–398 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Pan, D. et al. Biodistribution and toxicity studies of VSVG-pseudotyped lentiviral vector after intravenous administration in mice with the observation of in vivo transduction of bone marrow. Mol. Ther. 6, 19–29 (2002).

    Article  CAS  PubMed  Google Scholar 

  72. Pfeifer, A. et al. Transduction of liver cells by lentiviral vectors: analysis in living animals by fluorescence imaging. Mol. Ther. 3, 319–322 (2001).

    Article  CAS  PubMed  Google Scholar 

  73. van Til, N. P. et al. Kupffer cells and not liver sinusoidal endothelial cells prevent lentiviral transduction of hepatocytes. Mol. Ther. 11, 26–34 (2005).

    Article  PubMed  Google Scholar 

  74. Ranzani, M. et al. Lentiviral vector-based insertional mutagenesis identifies genes associated with liver cancer. Nat. Methods 10, 155–161 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Dalsgaard, T. et al. Improved lentiviral gene delivery to mouse liver by hydrodynamic vector injection through tail vein. Mol. Ther. Nucleic Acids 12, 672–683 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Brown, B. D. et al. In vivo administration of lentiviral vectors triggers a type I interferon response that restricts hepatocyte gene transfer and promotes vector clearance. Blood 109, 2797–2805 (2007).

    Article  CAS  PubMed  Google Scholar 

  77. Follenzi, A. et al. Targeting lentiviral vector expression to hepatocytes limits transgene-specific immune response and establishes long-term expression of human antihemophilic factor IX in mice. Blood 103, 3700–3709 (2004).

    Article  CAS  PubMed  Google Scholar 

  78. Annunziato, S. et al. Modeling invasive lobular breast carcinoma by CRISPR/Cas9-mediated somatic genome editing of the mammary gland. Genes Dev. 30, 1470–1480 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Brown, B. D. et al. A microRNA-regulated lentiviral vector mediates stable correction of hemophilia B mice. Blood 110, 4144–4152 (2007).

    Article  CAS  PubMed  Google Scholar 

  80. Yin, H. et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat. Biotechnol. 32, 551–553 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Winters, I. P. et al. Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity. Nat. Commun. 8, 2053 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  82. Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).

    Article  CAS  PubMed  Google Scholar 

  83. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Kurt, I. C. et al. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nat. Biotechnol. 39, 41–46 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  85. Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Chadwick, A. C., Wang, X. & Musunuru, K. In vivo base editing of PCSK9 (proprotein convertase subtilisin/kexin type 9) as a therapeutic alternative to genome editing. Arterioscler. Thromb. Vasc. Biol. 37, 1741–1747 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Villiger, L. et al. Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nat. Med. 24, 1519–1525 (2018).

    Article  CAS  PubMed  Google Scholar 

  88. Liu, P. et al. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat. Commun. 12, 2121 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Gilbert, L. A. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442–451 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Gemberling, M. P. et al. Transgenic mice for in vivo epigenome editing with CRISPR-based systems. Nat. Methods 18, 965–974 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Tanenbaum, M. E., Gilbert, L. A., Qi, L. S., Weissman, J. S. & Vale, R. D. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159, 635–646 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583–588 (2015).

    Article  CAS  PubMed  Google Scholar 

  93. Chavez, A. et al. Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12, 326–328 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Zhou, H. et al. In vivo simultaneous transcriptional activation of multiple genes in the brain using CRISPR-dCas9-activator transgenic mice. Nat. Neurosci. 21, 440–446 (2018).

    Article  CAS  PubMed  Google Scholar 

  95. Wangensteen, K. J. et al. Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform. Hepatology 68, 663–676 (2018).

    Article  CAS  PubMed  Google Scholar 

  96. Liao, H.-K. et al. In vivo target gene activation via CRISPR/Cas9-mediated trans-epigenetic modulation. Cell 171, 1495–1507.e15 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Chew, W. L. et al. A multifunctional AAV-CRISPR-Cas9 and its host response. Nat. Methods 13, 868–874 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Moreno, A. M. et al. In situ gene therapy via AAV-CRISPR-Cas9-mediated targeted gene regulation. Mol. Ther. 26, 1818–1827 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hilton, I. B. et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33, 510–517 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Liu, X. S. et al. Editing DNA methylation in the mammalian genome. Cell 167, 233–247.e17 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019–1027 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Abudayyeh, O. O. et al. A cytosine deaminase for programmable single-base RNA editing. Science 365, 382–386 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Konermann, S. et al. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173, 665–676.e14 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Du, M., Jillette, N., Zhu, J. J., Li, S. & Cheng, A. W. CRISPR artificial splicing factors. Nat. Commun. 11, 2973 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Wilson, C., Chen, P. J., Miao, Z. & Liu, D. R. Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase. Nat. Biotechnol. 38, 1431–1440 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. He, B. et al. Modulation of metabolic functions through Cas13d-mediated gene knockdown in liver. Protein Cell 11, 518–524 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Jiang, W. et al. Precise and efficient silencing of mutant KrasG12D by CRISPR-CasRx controls pancreatic cancer progression. Theranostics 10, 11507–11519 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Wang, D. et al. Adenovirus-mediated somatic genome editing of Pten by CRISPR/Cas9 in mouse liver in spite of Cas9-specific immune responses. Hum. Gene Ther. 26, 432–442 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Enache, O. M. et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat. Genet. 52, 662–668 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Akcakaya, P. et al. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature 561, 416–419 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Chen, J. S. et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature 550, 407–410 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Wong, N., Liu, W. & Wang, X. WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol. 16, 218 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  115. Yarrington, R. M., Verma, S., Schwartz, S., Trautman, J. K. & Carroll, D. Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo. Proc. Natl Acad. Sci. USA 115, 9351–9358 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Hanna, R. E. & Doench, J. G. Design and analysis of CRISPR-Cas experiments. Nat. Biotechnol. 38, 813–823 (2020).

    Article  CAS  PubMed  Google Scholar 

  117. Montague, T. G., Cruz, J. M., Gagnon, J. A., Church, G. M. & Valen, E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42, W401–W407 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Heigwer, F., Kerr, G. & Boutros, M. E-CRISP: fast CRISPR target site identification. Nat. Methods 11, 122–123 (2014).

    Article  CAS  PubMed  Google Scholar 

  119. Concordet, J.-P. & Haeussler, M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res. 46, W242–W245 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Meier, J. A., Zhang, F. & Sanjana, N. E. GUIDES: sgRNA design for loss-of-function screens. Nat. Methods 14, 831–832 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Park, J., Lim, K., Kim, J.-S. & Bae, S. Cas-analyzer: an online tool for assessing genome editing results using NGS data. Bioinformatics 33, 286–288 (2017).

    Article  CAS  PubMed  Google Scholar 

  123. Güell, M., Yang, L. & Church, G. M. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 30, 2968–2970 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  124. Sledzinski, P., Nowaczyk, M. & Olejniczak, M. Computational tools and resources supporting CRISPR-Cas experiments. Cells 9, 1288 (2020).

    Article  CAS  PubMed Central  Google Scholar 

  125. Hess, J. et al. Gain of chromosome band 7q11 in papillary thyroid carcinomas of young patients is associated with exposure to low-dose irradiation. Proc. Natl Acad. Sci. USA 108, 9595–9600 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  126. Lange, S. et al. Analysis pipelines for cancer genome sequencing in mice. Nat. Protoc. 15, 266–315 (2020).

    Article  CAS  PubMed  Google Scholar 

  127. Jentsch, I., Adler, I. D., Carter, N. P. & Speicher, M. R. Karyotyping mouse chromosomes by multiplex-FISH (M-FISH). Chromosome Res. 9, 211–214 (2001).

    Article  CAS  PubMed  Google Scholar 

  128. Espina, V. et al. Laser-capture microdissection. Nat. Protoc. 1, 586–603 (2006).

    Article  CAS  PubMed  Google Scholar 

  129. Bell, J. B. et al. Preferential delivery of the Sleeping Beauty transposon system to livers of mice by hydrodynamic injection. Nat. Protoc. 2, 3153–3165 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Sakai, M., Nishikawa, M., Thanaketpaisarn, O., Yamashita, F. & Hashida, M. Hepatocyte-targeted gene transfer by combination of vascularly delivered plasmid DNA and in vivo electroporation. Gene Ther. 12, 607–616 (2005).

    Article  CAS  PubMed  Google Scholar 

  131. Rizvi, F. et al. Murine liver repair via transient activation of regenerative pathways in hepatocytes using lipid nanoparticle-complexed nucleoside-modified mRNA. Nat. Commun. 12, 613 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Li, Q., Kay, M. A., Finegold, M., Stratford-Perricaudet, L. D. & Woo, S. L. Assessment of recombinant adenoviral vectors for hepatic gene therapy. Hum. Gene Ther. 4, 403–409 (1993).

    Article  CAS  PubMed  Google Scholar 

  133. Ryu, S.-M. et al. Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy. Nat. Biotechnol. 36, 536–539 (2018).

    Article  CAS  PubMed  Google Scholar 

  134. Thakore, P. I. et al. RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. Nat. Commun. 9, 1674 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

D.S. is supported by the European Research Council (Consolidator Grant 648521) and the Deutsche Forschungsgemeinschaft (SA1374/4-2; SFB 1321 Project-ID 329628492, SFB 1371 Project-ID 395357507). R.R. is supported by the European Research Council (Consolidator Grants PACA-MET (819642) and MSCA-ITN-ETN (861196)), the Deutsche Forschungsgemeinschaft (DFG RA1629/2-1; SFB1321), the German Cancer Consortium and the Deutsche Krebshilfe (70114314).

Author information

Authors and Affiliations

Authors

Contributions

T.K., J.L., R.M., J.W., S.M., R.O. and R.R. conceptualized, designed or developed workflows, tools or procedures. U.E. provided resources and critical input to HTVI experiments. P.A., D.R., S. Brummer and S.E produced and purified AAV. T.K., J.L., R.M., J.W., S.M., R.O., N.G. and J.G. performed wet-lab experiments. N.A.K. performed computational analysis. A.A., J.M., M.S.-S., M.R., G.S. and D.S. provided biological resources. T.K, J.L. and R.R. wrote the manuscript with input from R.M., J.W., S.A.W., S. Bärthel, C.F., A.P. and C.J.B.

Corresponding author

Correspondence to Roland Rad.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Protocols thanks Takahiro Kodama and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related links

Key references using this protocol

Maresch, R. et al. Nat. Commun. 7, 10770 (2016): https://doi.org/10.1038/ncomms10770

Weber, J. et al. Proc. Natl Acad. Sci. USA 112, 13982–13987 (2015): https://doi.org/10.1073/pnas.1512392112

Mueller, S. et al. Nature 554, 62–68 (2018): https://doi.org/10.1038/nature25459

Supplementary information

Source data

Source Data Fig. 4c

Quantification of transduction efficiencies of scAAV8 in the pancreas and the liver in Rosa26mT/mG reporter mice.

Source Data Fig. 5b

Quantification of CRISPR editing efficiencies in the liver and pancreas upon scAAV8-based sgRNA delivery.

Source Data Fig. 6

Statistical data.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kaltenbacher, T., Löprich, J., Maresch, R. et al. CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver. Nat Protoc 17, 1142–1188 (2022). https://doi.org/10.1038/s41596-021-00677-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41596-021-00677-0

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer