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Chien JCY, Badr CE, Lai CP. Multiplexed bioluminescence-mediated tracking of DNA double-strand break repairs in vitro and in vivo. Nat Protoc 2021; 16:3933-3953. [PMID: 34163064 PMCID: PMC9124064 DOI: 10.1038/s41596-021-00564-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/27/2021] [Indexed: 02/06/2023]
Abstract
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 process, requiring disruption of cells and organisms for subsequent nuclease-, sequencing- or reporter-based assays. In this protocol, we provide instructions for establishing a bioluminescent repair reporter system using engineered Gaussia and Vargula luciferases for noninvasive tracking of homology-directed repair and nonhomologous end joining, respectively, induced by SceI meganuclease, SpCas9 or SpCas9 D10A nickase-mediated editing. We also describe complementation with orthogonal DSB repair assays and omics analyses to validate the reporter readouts. The bioluminescent repair reporter system provides longitudinal and rapid readout (~seconds per sample) to accurately and efficiently measure the efficacy of genome-editing tools and small-molecule modulators on DSB repair. This protocol takes ~2-4 weeks to establish, and as little as 2 h to complete the assay. The entire bioluminescent repair reporter procedure can be performed by one person with standard molecular biology expertise and equipment. However, orthogonal DNA repair assays would require a specialized facility that performs Sanger sequencing or next-generation sequencing.
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Affiliation(s)
| | - Christian E. Badr
- Department of Neurology, Massachusetts General Hospital, Boston MA, United States,Neuroscience Program, Harvard Medical School, Boston MA, United States,To whom correspondence should be addressed: Christian E. Badr, Tel: 1-617-643-3485; Fax: 1-617-724-1537; ; Charles P. Lai, Tel: 886-2-2366-8204; Fax: 886-2-2362-0200; . C.E.B and C.P.L contributed equally to this work
| | - Charles P. Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan,To whom correspondence should be addressed: Christian E. Badr, Tel: 1-617-643-3485; Fax: 1-617-724-1537; ; Charles P. Lai, Tel: 886-2-2366-8204; Fax: 886-2-2362-0200; . C.E.B and C.P.L contributed equally to this work
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Chien JCY, Tabet E, Pinkham K, da Hora CC, Chang JCY, Lin S, Badr CE, Lai CPK. 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 2020; 48:e100. [PMID: 32797168 PMCID: PMC7515717 DOI: 10.1093/nar/gkaa669] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022] Open
Abstract
Tracking DNA double strand break (DSB) repair is paramount for the understanding and therapeutic development of various diseases including cancers. Herein, we describe a multiplexed bioluminescent repair reporter (BLRR) for non-invasive monitoring of DSB repair pathways in living cells and animals. The BLRR approach employs secreted Gaussia and Vargula luciferases to simultaneously detect homology-directed repair (HDR) and non-homologous end joining (NHEJ), respectively. BLRR data are consistent with next-generation sequencing results for reporting HDR (R2 = 0.9722) and NHEJ (R2 = 0.919) events. Moreover, BLRR analysis allows longitudinal tracking of HDR and NHEJ activities in cells, and enables detection of DSB repairs in xenografted tumours in vivo. Using the BLRR system, we observed a significant difference in the efficiency of CRISPR/Cas9-mediated editing with guide RNAs only 1-10 bp apart. Moreover, BLRR analysis detected altered dynamics for DSB repair induced by small-molecule modulators. Finally, we discovered HDR-suppressing functions of anticancer cardiac glycosides in human glioblastomas and glioma cancer stem-like cells via inhibition of DNA repair protein RAD51 homolog 1 (RAD51). The BLRR method provides a highly sensitive platform to simultaneously and longitudinally track HDR and NHEJ dynamics that is sufficiently versatile for elucidating the physiology and therapeutic development of DSB repair.
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Affiliation(s)
| | - Elie Tabet
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.,Department of Biomedical Engineering, University of South Dakota, 4800 N. Career Ave, Suite 221, Sioux Falls, Vermillion, SD 57069, USA
| | - Kelsey Pinkham
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Cintia Carla da Hora
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.,Neuroscience Program, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Cheng-Yu Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Steven Lin
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Christian E Badr
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.,Neuroscience Program, Harvard Medical School, Boston, MA 02115, USA
| | - Charles Pin-Kuang Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan.,Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
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Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed nanoparticles released by cells. They range from 30 nm to several micrometers in diameter, and ferry biological cargos such as proteins, lipids, RNAs and DNAs for local and distant intercellular communications. EVs have since been found to play a role in development, as well as in diseases including cancers. To elucidate the roles of EVs, researchers have established different methods to visualize and study their spatiotemporal properties. However, since EV are nanometer-sized, imaging them demands a full understanding of each labeling strategy to ensure accurate monitoring. This review covers current and emerging strategies for EV imaging for prospective studies.
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Affiliation(s)
- Steven Ting-Yu Chuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617 Taiwan
| | - Jasper Che-Yung Chien
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617 Taiwan
| | - Charles Pin-Kuang Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617 Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
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