Multiplexed bioluminescence-mediated tracking of DNA double-strand break repairs in vitro and in vivo

Jasper Che-Yung Chien, Christian E. Badr, Charles Pin-Kuang Lai

Published: 2021-06-22 DOI: 10.1038/s41596-021-00564-8

genome editing

bioluminescence

DNA repair

homology-directed repair

nonhomologous end joining

AI 解读

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The dynamics of DNA double-strand break (DSB) repairs including homology-directed repair and nonhomologous end joining play an important role in diseases and therapies. However, investigating DSB repair is typically a low-throughput and cross-sectional pr
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
- Reporting Summary
- References
References
ACKNOWLEDGMENTS
ACKNOWLEDGMENTS

Maynard, S., Fang, E. F., Scheibye-Knudsen, M., Croteau, D. L. & Bohr, V. A. DNA damage, DNA repair, aging, and neurodegeneration. Cold Spring Harb. Perspect. Med. https://doi.org/10.1101/cshperspect.a025130 (2015).
Gomez-Herreros, F. DNA Double strand breaks and chromosomal translocations induced by DNA topoisomerase II. Front. Mol. Biosci. 6, 141 (2019).
Lieber, M. R. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 79, 181–211 (2010).
Chang, H. H. Y., Pannunzio, N. R., Adachi, N. & Lieber, M. R. Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat. Rev. Mol. Cell Biol. 18, 495–506 (2017).
Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020).
Toulany, M. Targeting DNA double-strand break repair pathways to improve radiotherapy response. Genes (Basel) https://doi.org/10.3390/genes10010025 (2019).
Kesari, S. et al. DNA damage response and repair: insights into strategies for radiation sensitization of gliomas. Future Oncol. 7, 1335–1346 (2011).
Gil Del Alcazar, C. R., Todorova, P. K., Habib, A. A., Mukherjee, B. & Burma, S. Augmented HR repair mediates acquired temozolomide resistance in glioblastoma. Mol. Cancer Res. 14, 928–940 (2016).
Welsh, J. W. et al. Rad51 protein expression and survival in patients with glioblastoma multiforme. Int. J. Radiat. Oncol. Biol. Phys. 74, 1251–1255 (2009).
King, H. O. et al. RAD51 is a selective DNA repair target to radiosensitize glioma stem cells. Stem Cell Rep. 8, 125–139 (2017).
Mashal, R. D., Koontz, J. & Sklar, J. Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nat. Genet. 9, 177–183 (1995).
Germini, D. et al. A comparison of techniques to evaluate the effectiveness of genome editing. Trends Biotechnol. 36, 147–159 (2018).
Chien, J. C. et al. A multiplexed bioluminescent reporter for sensitive and non-invasive tracking of DNA double strand break repair dynamics in vitro and in vivo. Nucleic Acids Res. 48, e100 (2020).
Haddock, S. H., Moline, M. A. & Case, J. F. Bioluminescence in the sea. Ann. Rev. Mar. Sci. 2, 443–493 (2010).
Lin, S., Staahl, B. T., Alla, R. K. & Doudna, J. A. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. eLife 3, e04766 (2014).
Bovenberg, M. S. et al. Multiplex blood reporters for simultaneous monitoring of cellular processes. Anal. Chem. 85, 10205–10210 (2013).
Nakajima, Y., Kobayashi, K., Yamagishi, K., Enomoto, T. & Ohmiya, Y. cDNA cloning and characterization of a secreted luciferase from the luminous Japanese ostracod, Cypridina noctiluca. Biosci. Biotechnol. Biochem. 68, 565–570 (2004).
Wurdinger, T. et al. A secreted luciferase for ex vivo monitoring of in vivo processes. Nat. Methods 5, 171–173 (2008).
Hendel, A. et al. Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep. 7, 293–305 (2014).
Brinkman, E. K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014).
Cox, D. B., Platt, R. J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med. 21, 121–131 (2015).
Certo, M. T. et al. Tracking genome engineering outcome at individual DNA breakpoints. Nat. Methods 8, 671–676 (2011).
Yang, Z. et al. Fast and sensitive detection of indels induced by precise gene targeting. Nucleic Acids Res. 43, e59 (2015).
Ramakrishna, S. et al. Surrogate reporter-based enrichment of cells containing RNA-guided Cas9 nuclease-induced mutations. Nat. Commun. 5, 3378 (2014).
Cornu, T. I., Mussolino, C. & Cathomen, T. Refining strategies to translate genome editing to the clinic. Nat. Med. 23, 415–423 (2017).
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Makarova, K. S. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015).
Yeh, C. D., Richardson, C. D. & Corn, J. E. Advances in genome editing through control of DNA repair pathways. Nat. Cell Biol. 21, 1468–1478 (2019).
Beckta, J. M., Bindra, R. S. & Chalmers, A. J. Targeting DNA repair in gliomas. Curr. Opin. Neurol. 32, 878–885 (2019).
Huang, R. X. & Zhou, P. K. DNA damage response signaling pathways and targets for radiotherapy sensitization in cancer. Signal Transduct. Target Ther. 5, 60 (2020).
Peng, Y. et al. The deubiquitylating enzyme USP15 regulates homologous recombination repair and cancer cell response to PARP inhibitors. Nat. Commun. 10, 1224 (2019).
Hendel, A., Fine, E. J., Bao, G. & Porteus, M. H. Quantifying on- and off-target genome editing. Trends Biotechnol. 33, 132–140 (2015).
Qiu, P. et al. Mutation detection using Surveyor nuclease. Biotechniques 36, 702–707 (2004).
Brinkman, E. K. et al. Easy quantification of template-directed CRISPR/Cas9 editing. Nucleic Acids Res. 46, e58 (2018).
Pinello, L. et al. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat. Biotechnol. 34, 695–697 (2016).
Porteus, M. H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in human cells. Science 300, 763 (2003).
Szczepek, M. et al. Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat. Biotechnol. 25, 786–793 (2007).
Wang, H. et al. CRISPR-mediated live imaging of genome editing and transcription. Science 365, 1301–1305 (2019).
Liu, Y. et al. Very fast CRISPR on demand. Science 368, 1265–1269 (2020).
Li, A. et al. AAV-CRISPR gene editing is negated by pre-existing immunity to Cas9. Mol. Ther. 28, 1432–1441 (2020).
Charlesworth, C. T. et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat. Med. 25, 249–254 (2019).
Wagner, D. L. et al. High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population. Nat. Med. 25, 242–248 (2019).
Bindra, R. S., Goglia, A. G., Jasin, M. & Powell, S. N. Development of an assay to measure mutagenic non-homologous end-joining repair activity in mammalian cells. Nucleic Acids Res. 41, e115–e115 (2013).
Lin, Y., Lukacsovich, T. & Waldman, A. S. Multiple pathways for repair of DNA double-strand breaks in mammalian chromosomes. Mol. Cell. Biol. 19, 8353–8360 (1999).
Gaj, T., Gersbach, C. A. & Barbas, C. F. 3rd ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31, 397–405 (2013).
van Haasteren, J., Li, J., Scheideler, O. J., Murthy, N. & Schaffer, D. V. The delivery challenge: fulfilling the promise of therapeutic genome editing. Nat. Biotechnol. 38, 845–855 (2020).
Yin, H., Kauffman, K. J. & Anderson, D. G. Delivery technologies for genome editing. Nat. Rev. Drug Discov. 16, 387–399 (2017).
Pinkham, K. et al. Stearoyl CoA desaturase is essential for regulation of endoplasmic reticulum homeostasis and tumor growth in glioblastoma cancer stem cells. Stem Cell Rep. 12, 712–727 (2019).
Huang, F., Mazina, O. M., Zentner, I. J., Cocklin, S. & Mazin, A. V. Inhibition of homologous recombination in human cells by targeting RAD51 recombinase. J. Med. Chem. 55, 3011–3020 (2012).
Leahy, J. J. et al. Identification of a highly potent and selective DNA-dependent protein kinase (DNA-PK) inhibitor (NU7441) by screening of chromenone libraries. Bioorg. Med. Chem. Lett. 14, 6083–6087 (2004).
Verhaegent, M. & Christopoulos, T. K. Recombinant Gaussia luciferase. Overexpression, purification, and analytical application of a bioluminescent reporter for DNA hybridization. Anal. Chem. 74, 4378–4385 (2002).
Thompson, E. M., Nagata, S. & Tsuji, F. I. Vargula hilgendorfii luciferase: a secreted reporter enzyme for monitoring gene expression in mammalian cells. Gene 96, 257–262 (1990).
Vouillot, L., Thelie, A. & Pollet, N. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 (Bethesda) 5, 407–415 (2015).
Guell, M., Yang, L. & Church, G. M. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 30, 2968–2970 (2014).
Degeling, M. H., Maguire, C. A., Bovenberg, M. S. & Tannous, B. A. Sensitive assay for mycoplasma detection in mammalian cell culture. Anal. Chem. 84, 4227–4232 (2012).
Shimomura, O. & Johnson, F. H. Mechanisms in the quantum yield of Cypridina bioluminescence. Photochem. Photobiol. 12, 291–295 (1970).
Lundholt, B. K., Scudder, K. M. & Pagliaro, L. A simple technique for reducing edge effect in cell-based assays. J. Biomol. Screen. 8, 566–570 (2003).
Szymczak, A. L. et al. Correction of multi-gene deficiency in vivo using a single ‘self-cleaving’ 2A peptide-based retroviral vector. Nat. Biotechnol. 22, 589–594 (2004).
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).

Multiplexed bioluminescence-mediated tracking of DNA double-strand break repairs in vitro and in vivo

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