CRISPR-Based Approaches for Diagnosing and Treating Infectious Diseases
Nabil Deb Nath1*, Md Abdur Rahman Biswash2, Tufael3, Asim Debnath4, Md Abu Bakar Siddique5
Journal of Primeasia 5(1) 1-8 https://doi.org/10.25163/primeasia.5110166
Submitted: 04 July 2024 Revised: 09 September 2024 Published: 14 September 2024
Abstract
Background: CRISPR gene-editing technology has the potential to change how we diagnose and treat infectious diseases significantly, yet many clinicians aren’t fully aware of its wide-ranging applications. This technology stems from a natural defense mechanism found in microbes, and it's often referred to as “molecular scissors” because of its ability to make precise edits in DNA with minimal errors. Beyond just gene editing, CRISPR can also target the DNA or RNA of pathogens, and researchers are actively exploring innovative ways to deliver this technology for new treatments. Methods: To gather information, we looked through PubMed and Google Scholar for studies on CRISPR-related methods for tackling infectious diseases. We also reviewed reference lists to compile a comprehensive overview. Results: The findings indicate that CRISPR-based strategies could offer groundbreaking solutions for several difficult infectious diseases. For instance, CRISPR can be utilized to develop rapid and affordable diagnostic tools, as well as to pinpoint genes associated with drug resistance. There are promising therapeutic strategies in the works, including the use of CRISPR to cut viral genomes or to take down drug-resistant bacteria. Additionally, ideas for using CRISPR to tackle emerging viruses like SARS-CoV-2 have also been suggested. Moreover, researchers are exploring how to reprogram human B cells to produce antibodies that can neutralize infections. However, it’s important to acknowledge that there are risks associated with CRISPR therapies, such as unintended changes to the genome. Researchers are currently working on strategies to mitigate these risks, and phase 1 clinical trials for CRISPR therapies targeting cancer and genetic disorders are already underway. Conclusions: Overall, CRISPR technology holds great promise in the realm of infectious diseases, potentially providing solutions to some of the most pressing health challenges we face today.
Keywords: CRISPR gene editing, Infectious diseases, Viral infections, Resistant bacteria, Pandemic viruses
References
Abbott, T. R., Dhamdhere, G., Liu, Y., Lin, X., Goudy, L., Zeng, L., et al. (2020). Development of CRISPR as an antiviral strategy to combat SARS-CoV-2 and influenza. Cell, 181(4), 865–876.
Barrangou, R., & Marraffini, L. A. (2014). CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Molecular Cell, 54, 234–244.
Bella, R., Kaminski, R., Mancuso, P., Young, W.-B., Chen, C., Sariyer, R., et al. (2018). Removal of HIV DNA by CRISPR from patient blood engrafts in humanized mice. Molecular Therapy - Nucleic Acids, 12, 275–282.
Bikard, D., Euler, C. W., Jiang, W., Nussenzweig, P. M., Goldberg, G. W., Duportet, X., et al. (2014). Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nature Biotechnology, 32(11), 1146–1150.
Brown, A., Woods, W. S., & Perez-Pinera, P. (2017). Targeted gene activation using RNA-guided nucleases. Methods in Molecular Biology, 1468, 235–250.
c V. V., Vlassov, V. V., & Tikunova, N. V. (2018). Applications of bacteriophages in the treatment of localized infections in humans. Frontiers in Microbiology, 9, 1696.
Chen, J. S., Ma, E., Harrington, L. B., Da Costa, M., Tian, X., Palefsky, J. M., et al. (2018). CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science, 360, 436–439.
Chertow, D. S. (2018). Next-generation diagnostics with CRISPR. Science, 360, 381–382.
Chou, Y.-Y., Krupp, A., Kaynor, C., Gaudin, R., Ma, M., Cahir-McFarland, E., et al. (2016). Inhibition of JCPyV infection mediated by targeted viral genome editing using CRISPR/Cas9. Scientific Reports, 6, 36921.
Citorik, R. J., Mimee, M., & Lu, T. K. (2014). Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nature Biotechnology, 32(11), 1141–1145.
Cobb, L. H., Park, J., Swanson, E. A., Beard, M. C., McCabe, E. M., Rourke, A. S., et al. (2019). CRISPR-Cas9 modified bacteriophage for treatment of Staphylococcus aureus-induced osteomyelitis and soft tissue infection. PLoS ONE, 14(8), e0220421.
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819–823.
Dash, P. K., Kaminski, R., Bella, R., Su, H., Mathews, S., Ahooyi, T. M., et al. (2019). Sequential LASER ART and CRISPR treatments eliminate HIV-1 in a subset of infected humanized mice. Nature Communications, 10, 2753.
Fish, R., Kutter, E., Bryan, D., Wheat, G., & Kuhl, S. (2018). Resolving digital staphylococcal osteomyelitis using bacteriophage: A case report. Antibiotics, 7(4), 87.
Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., & Joung, J. K. (2014). Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nature Biotechnology, 32(3), 279–284.
Gibson, S. B., Green, S. I., Liu, C. G., Salazar, K. C., Clark, J. R., Terwilliger, A. L., et al. (2019). Constructing and characterizing bacteriophage libraries for phage therapy of human infections. Frontiers in Microbiology, 10, 2537.
Gilbert, S. C. (2012). T-cell-inducing vaccines: What’s the future? Immunology, 135(1), 19–26.
Gootenberg, J. S., Abudayyeh, O. O., Lee, J. W., Essletzbichler, P., Dy, A. J., Joung, J., et al. (2017). Nucleic acid detection with CRISPR-Cas13a/C2c2. Science, 356, 438–442.
Gu, W., Crawford, E. D., O’Donovan, B. D., Wilson, M. R., Chow, E. D., Retallack, H., et al. (2016). Depletion of abundant sequences by hybridization (DASH): Using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biology, 17, 41.
Hartweger, H., McGuire, A. T., Horning, M., Taylor, J. J., Dosenovic, P., Yost, D., et al. (2019). HIV-specific humoral immune responses by CRISPR/Cas9-edited B cells. Journal of Experimental Medicine, 216(6), 1301–1310.
Hirakawa, M. P., Krishnakumar, R., Timlin, J. A., Carney, J. P., & Butler, K. S. (2020). Gene editing and CRISPR in the clinic: Current and future perspectives. Bioscience Reports, 40(4), BSR20200127.
Hsu, J. L., & Glaser, S. L. (2000). Epstein-Barr virus-associated malignancies: Epidemiologic patterns and etiologic implications. Critical Reviews in Oncology/Hematology, 34(1), 27–53.
Hu, Z., Yu, L., Zhu, D., Ding, W., Wang, X., Zhang, C., et al. (2014). Disruption of HPV16-E7 by CRISPR/Cas system induces apoptosis and growth inhibition in HPV16 positive human cervical cancer cells. BioMed Research International, 2014, 612823.
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–821.
Joint United Nations Programme on HIV/AIDS. (2019). Fact sheet—Latest global and regional statistics on the status of the AIDS epidemic. Geneva: Joint United Nations Programme on HIV/AIDS.
Kaminski, R., Chen, Y., Fischer, T., Tedaldi, E., Napoli, A., Zhang, Y., et al. (2016). Elimination of HIV-1 genomes from human T-lymphoid cells by CRISPR/Cas9 gene editing. Scientific Reports, 6, 22555.
Kanda, T., Furuse, Y., Oshitani, H., & Kiyono, T. (2016). Highly efficient CRISPR/Cas9-mediated cloning and functional characterization of gastric cancer-derived Epstein-Barr virus strains. Journal of Virology, 90(9), 4383–4393.
Kang, J. G., Park, J. S., Ko, J.-H., & Kim, Y.-S. (2019). Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system. Scientific Reports, 9, 11960.
Kennedy, E. M., Kornepati, A. V. R., Goldstein, M., Bogerd, H. P., Poling, B. C., Whisnant, A. W., et al. (2014). Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells by using a bacterial CRISPR/Cas RNA-guided endonuclease. Journal of Virology, 88(20), 11965–11972.
Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H. R., et al. (2015). Digenome-seq: Genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nature Methods, 12(3), 237–243.
Kimberland, M. L., Hou, W., Alfonso-Pecchio, A., Wilson, S., Rao, Y., Zhang, S., et al. (2018). Strategies for controlling CRISPR/Cas9 off-target effects and biological variations in mammalian genome editing experiments. Journal of Biotechnology, 284, 91–101.
Kleinstiver, B. P., Pattanayak, V., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Zheng, Z., et al. (2016). High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature, 529(7587), 490–495.
Konermann, S., Lotfy, P., Brideau, N. J., Oki, J., Shokhirev, M. N., & Hsu, P. D. (2018). Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell, 173(3), 665–676.e14.
Lander, E. S. (2016). The heroes of CRISPR. Cell, 164, 18–28.
Lebbink, R. J., de Jong, D. C. M., Wolters, F., Kruse, E. M., van Ham, P. M., Wiertz, E. J. H. J., et al. (2017). A combinational CRISPR/Cas9 gene-editing approach can halt HIV replication and prevent viral escape. Scientific Reports, 7, 41968.
Li, C., Guan, X., Du, T., Jin, W., Wu, B., Liu, Y., et al. (2015). Inhibition of HIV-1 infection of primary CD4+ T-cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. Journal of General Virology, 96(9), 2381–2393.
Lieberman, P. M. (2016). Epigenetics and genetics of viral latency. Cell Host & Microbe, 19(5), 619–628.
Lin, C., Li, H., Hao, M., Xiong, D., Luo, Y., Huang, C., et al. (2016). Increasing the efficiency of CRISPR/Cas9-mediated precise genome editing of HSV-1 virus in human cells. Scientific Reports, 6, 34531.
Liu, J., Gaj, T., Yang, Y., Wang, N., Shui, S., Kim, S., et al. (2015). Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells. Nature Protocols, 10, 1842–1859.
Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2013). Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Research, 41, 4360–4377.
Mojica, F. J. M., Díez-Villaseñor, C., García-Martínez, J., & Soria, E. (2005). Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of Molecular Evolution, 60(2), 174–182.
Myhrvold, C., Freije, C. A., Gootenberg, J. S., Abudayyeh, O. O., Metsky, H. C., Durbin, A. F., et al. (2018). Field-deployable viral diagnostics using CRISPR-Cas13. Science, 360, 444–448.
Newport, M. J., Goetghebuer, T., Weiss, H. A., Whittle, H., Siegrist, C.-A., Marchant, A., et al. (2004). Genetic regulation of immune responses to vaccines in early life. Genes & Immunity, 5(2), 122–129.
Nguyen, T. M., Zhang, Y., & Pandolfi, P. P. (2020). Virus against virus: A potential treatment for 2019-nCoV (SARS-CoV-2) and other RNA viruses. Cell Research, 30(3), 189–190.
Niu, D., Wei, H.-J., Lin, L., George, H., Wang, T., Lee, I.-H., et al. (2017). Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science, 357, 1303–1307.
O’Connell, M. R., Oakes, B. L., Sternberg, S. H., East-Seletsky, A., Kaplan, M., & Doudna, J. A. (2014). Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature, 516(7530), 263–266.
Park, J. Y., Moon, B. Y., Park, J. W., Thornton, J. A., Park, Y. H., & Seo, K. S. (2017). Genetic engineering of a temperate phage-based delivery system for CRISPR/Cas9 antimicrobials against Staphylococcus aureus. Scientific Reports, 7, 44929.
Quan, J., Langelier, C., Kuchta, A., Batson, J., Teyssier, N., Lyden, A., et al. (2019). FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic Acids Research, 47, e83.
Ramanan, V., Shlomai, A., Cox, D. B. T., Schwartz, R. E., Michailidis, E., Bhatta, A., et al. (2015). CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus. Scientific Reports, 5, 10833.
Rees, H. A., & Liu, D. R. (2018). Base editing: Precision chemistry on the genome and transcriptome of living cells. Nature Reviews Genetics, 19, 770–788.
Romero-Calle, D., Guimarães Benevides, R., Góes-Neto, A., & Billington, C. (2019). Bacteriophages as alternatives to antibiotics in clinical care. Antibiotics, 8(3), 138.
Savic, N., & Schwank, G. (2016). Advances in therapeutic CRISPR/Cas9 genome editing. Translational Research, 168, 15–21.
Schiffer, J. T., Aubert, M., Weber, N. D., Mintzer, E., Stone, D., & Jerome, K. R. (2012). Targeted DNA mutagenesis for the cure of chronic viral infections. Journal of Virology, 86(16), 8920–8936.
Schooley, R. T., Biswas, B., Gill, J. J., Hernandez-Morales, A., Lancaster, J., Lessor, L., et al. (2017). Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrobial Agents and Chemotherapy, 61(10), e00954-17.
Schweitzer, A., Horn, J., Mikolajczyk, R. T., Krause, G., & Ott, J. J. (2015). Estimations of worldwide prevalence of chronic hepatitis B virus infection: A systematic review of data published between 1965 and 2013. The Lancet, 386(10003), 1546–1555.
Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., et al. (2015). Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Molecular Cell, 60, 385–397.
Stadtmauer, E. A., Fraietta, J. A., Davis, M. M., Cohen, A. D., Weber, K. L., Lancaster, E., et al. (2020). T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Science, 367, eaba7365.
Traylen, C. M., Patel, H. R., Fondaw, W., Mahatme, S., Williams, J. F., Walker, L. R., et al. (2011). Virus reactivation: A panoramic view in human infections. Future Virology, 6(5), 451–463.
van Diemen, F. R., Kruse, E. M., Hooykaas, M. J. G., Bruggeling, C. E., Schürch, A. C., van Ham, P. M., et al. (2016). CRISPR/Cas9-mediated genome editing of herpesviruses limits productive and latent infections. PLOS Pathogens, 12(6), e1005701.
Virgin, H. W., Wherry, E. J., & Ahmed, R. (2009). Redefining chronic viral infection. Cell, 138(1), 30–50.
Wang, Z., Pan, Q., Gendron, P., Zhu, W., Guo, F., Cen, S., et al. (2016). CRISPR/Cas9-derived mutations both inhibit HIV-1 replication and accelerate viral escape. Cell Reports, 15(3), 481–489.
Westra, E. R., Buckling, A., & Fineran, P. C. (2014). CRISPR-Cas systems: Beyond adaptive immunity. Nature Reviews Microbiology, 12, 317–326.
Yang, Y.-C., Chen, Y.-H., Kao, J.-H., Ching, C., Liu, I.-J., Wang, C.-C., et al. (2020). Permanent inactivation of HBV genomes by CRISPR/Cas9-mediated non-cleavage base editing. Molecular Therapy - Nucleic Acids, 20, 1–47.
Yuen, K.-S., Wang, Z.-M., Wong, N.-H. M., Zhang, Z.-Q., Cheng, T.-F., Lui, W.-Y., et al. (2018). Suppression of Epstein-Barr virus DNA load in latently infected nasopharyngeal carcinoma cells by CRISPR/Cas9. Virus Research, 244, 296–303.
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015). Off-target effects in CRISPR/Cas9-mediated genome engineering. Molecular Therapy Nucleic Acids, 4, e264.
Zhen, S., Hua, L., Takahashi, Y., Narita, S., Liu, Y.-H., & Li, Y. (2014). In vitro and in vivo growth suppression of human papillomavirus 16-positive cervical cancer cells by CRISPR/Cas9. Biochemical and Biophysical Research Communications, 450(4), 1422–1426.
View Dimensions
View Altmetric
Save
Citation
View
Share