Research Papers Relevant to CRISPR

CRISPR-based genome editing is a rapidly expanding domain and with extensive research and clinical studies, numerous articles and reviews are published regularly. Select peer-reviewed articles and in-depth reviews related to different aspects of the CRISPR/Cas system have been listed below:

1. Reference: Doudna, J. A. and Charpentier, E. (2014) ‘The new frontier of genome engineering with CRISPR-Cas9’, Science. American Association for the Advancement of Science, 346(6213), p. 1258096. doi: 10.1126/science.1258096.

Description: This article has been authored by Jennifer A. Doudna and Emmanuelle Charpentier, both of whom have been awarded the Nobel Prize in 2020 due to their pioneering efforts to use CRISPR/Cas9 as a genome editing tool in different animals, plants, microorganisms, tissues, and cell lines. The article reviews CRISPR from its discovery to the stage where CRISPR/Cas9 is extensively being used for genome editing in different cell lines and organisms with potential applications in diverse fields.

2. Reference: Adli, M. (2018) ‘The CRISPR tool kit for genome editing and beyond’, Nature Communications. Nature Publishing Group, pp. 1–13. doi: 10.1038/s41467-018-04252-2.

Description: The article reviews different genome editing technologies including CRISPR/Cas technique. It also discusses different CRISPR systems and Cas9 variants, and their application in genome editing.

3. Reference: Hsu, P. D., Lander, E. S. and Zhang, F. (2014) ‘Development and applications of CRISPR-Cas9 for genome engineering’, Cell. Cell Press, pp. 1262–1278. doi: 10.1016/j.cell.2014.05.010.

Description: This article has been authored by Feng Zhang from the Broad Institute of MIT and Harvard along with others. The article reviews the use of CRISPR/Cas9 for research or translational applications, and also discusses the challenges and prospects of the technique.

• Reference: Niccheri, F., Pecori, R. and Conticello, S. G. (2017) ‘An efficient method to enrich for knock-out and knock-in cellular clones using the CRISPR/Cas9 system’, Cellular and Molecular Life Sciences. Birkhauser Verlag AG, 74(18), pp. 3413–3423. doi: 10.1007/s00018-017-2524-y.

Description: In this study, the authors describe an experiment where CRISPR/Cas9 has been used to knock-in and knock-out Aicda genes in CH12F3 lymphoma cells.

• Reference: Asokan, A. (2019) ‘CRISPR genome editing in stem cells turns to gold’, Nature materials. NLM (Medline), pp. 1038–1039. doi: 10.1038/s41563-019-0491-4.

Description: This article discusses the use of the CRISPR technique in editing hematopoietic stem and progenitor cells and the use of gold nano-formulations for the in vivo delivery of the CRISPR components. This has immense therapeutic prospects including stem cell-based engraftment.

6. Reference: Broughton, J. P. et al. (2020) ‘CRISPR–Cas12-based detection of SARS-CoV-2’, Nature Biotechnology. Nature Research, pp. 1–5. doi: 10.1038/s41587-020-0513-4.

Description: This study describes the development of a rapid CRISPR/Cas12-based assay for the detection of SARS-CoV-2 in the swabs collected from the patients. The rapid technique requiring less than 40 minutes for the detection of SARS-CoV-2 is a potential alternative to the conventionally used RT-PCR assay.

7. Reference: Byrne, S. M., Mali, P. and Church, G. M. (2014) ‘Genome editing in human stem cells’, in Methods in Enzymology. Academic Press Inc., pp. 119–138. doi: 10.1016/B978-0-12-801185-0.00006-4.

Description: Although genome editing technologies are capable of cleaving DNA, introducing point mutations and gene insertions, human embryonic stem cells and induced pluripotent stem cells (iPSCs) are difficult to transfect and can easily undergo DNA damage compared to tumour cells. In this article, the authors describe a protocol for introducing genetic mutations in iPSCs using plasmids and single-stranded oligonucleotides for transfection.

• Reference: Corte, L. E. D. et al. (2019) ‘Development of improved fruit, vegetable, and ornamental crops using the CRISPR/cas9 genome editing technique’, Plants. MDPI AG. doi: 10.3390/plants8120601.

Description: The article systematically reviews the CRISPR/Cas9 system from its discovery in prokaryotic cells. Additionally, the review evaluates the potential application of the CRISPR/Cas9 system in biotechnology, particularly in the improvement of horticultural crops such as fruits, vegetables, and other ornamental plants.

9. Reference: Cui, Y. et al. (2018) ‘Review of CRISPR/Cas9 sgRNA Design Tools’, Interdisciplinary Sciences: Computational Life Sciences, 10, pp. 455–465. doi: 10.1007/s12539-018-0298-z.

Description: CRISPR beyond doubt is a powerful genome editing tool. However, the functioning of the CRISPR/Cas system depends upon the sgRNA design. Therefore by customising the sgRNA design, diverse genomic sequences can be targeted by the CRISPR system. The review discusses different sgRNA design tools based on their on-target and off-target efficiency.

10. Reference: Gao, Q. et al. (2019) ‘Therapeutic potential of CRISPR/Cas9 gene editing in engineered T‐cell therapy’, Cancer Medicine. Blackwell Publishing Ltd, 8(9), p. 4254‐4264. doi: 10.1002/cam4.2257.

Description: The review discusses the application of CRISPR/Cas9 in developing cancer immunotherapies such as immune checkpoint inhibitors, cancer vaccines, and adoptive T-cell therapy. It also discusses various gene delivery methods for CRISPR/Cas-based gene editing in immunotherapies, and the advantages and limitations of each method.

11. Reference: García-Tuñón, I. et al. (2019) ‘Splice donor site sgRNAs enhance CRISPR/Cas9-mediated knockout efficiency’, PLOS ONE. Edited by S. Maas. Public Library of Science, 14(5), p. e0216674. doi: 10.1371/journal.pone.0216674.

Description: CRISPR/Cas technique introduces double-stranded breaks in the target DNA, and can thereby generate cell lines with gene knock-out and null zygotes. Through an experiment, the study shows the strategy to increase this null effect by targeting the splice donor site of the target exon.

1. Reference: Jiang, F. and Doudna, J. A. (2017) ‘CRISPR–Cas9 Structures and Mechanisms’, Annual Review of Biophysics. Annual Reviews, 46(1), pp. 505–529. doi: 10.1146/annurev-biophys-062215-010822.

Description: Since the discovery of CRISPR technology, different CRISPR systems and Cas endonuclease variants have been identified. The review provides a detailed insight into the mechanism of CRISPR/Cas9 functioning and the structural changes that are associated at the molecular level.

1. Reference: Alok, A. et al. (2020) ‘The Rise of the CRISPR/Cpf1 System for Efficient Genome Editing in Plants’, Frontiers in Plant Science. Frontiers Media S.A., 11, p. 264. doi: 10.3389/fpls.2020.00264.

Description: This article reviews the use of CRISPR/Cpf1 in performing multiplexed genome editing in crops such as rice, wheat, soybean, etc. with few off-target effects.

1. Reference: Naeem, M. et al. (2020) ‘Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing’, Cells. NLM (Medline), 9(7). doi: 10.3390/cells9071608.

Description: The study discusses the potential off-target effects of the CRISPR technique that contribute to its limitation. The study also discusses the different approaches that can be adopted to minimise such off-target effects.

1. Reference: Zhang, X. H. et al. (2015) ‘Off-target effects in CRISPR/Cas9-mediated genome engineering’, Molecular Therapy – Nucleic Acids. Nature Publishing Group, 4(11), p. e264. doi: 10.1038/mtna.2015.37.

Description: The review discusses off-target effects observed in genome editing using the CRISPR technique. It investigates the mechanisms underlying the off-target effects, methods to detect such off-target effects, and approaches to minimise them.

1. Reference: Wang, Z. and Cui, W. (2020) ‘CRISPR‐Cas system for biomedical diagnostic platforms’, View. Wiley, 1(3), p. 20200008. doi: 10.1002/viw.20200008.

Description: This review provides an overview of the applications of the CRISPR technique in biomedical diagnostics, especially in the detection of pathogens. Furthermore, the review highlights the challenges and prospects of CRISPR-based diagnostic platforms.

1. Reference: Fellmann, C. et al. (2017) ‘Cornerstones of CRISPR-Cas in drug discovery and therapy’, Nature Reviews Drug Discovery. Nature Publishing Group, pp. 89–100. doi: 10.1038/nrd.2016.238.

Description: CRISPR/Cas technique has the potential of developing therapies that can cure complex heritable and other somatic disorders. Towards this end, CRISPR can accelerate the development of next-generation drugs through the identification of biomarkers, validation of therapeutic targets, and developing therapies.

1. Reference: Park, R. J. et al. (2017) ‘A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors’, Nature Genetics. Nature Publishing Group, 49(2), pp. 193–203. doi: 10.1038/ng.3741.

Description: The study uses CRISPR-based screens to identify host factors that mediate HIV infection. The study identifies five factors including host co-receptors such as CD4 and CCR5 that facilities the entry of the virus, its cellular proliferation and survival.

1. Reference: Raposo, V. L. (2019) ‘The first chinese edited babies: A leap of faith in science’, Jornal Brasileiro de Reproducao Assistida. Sociedade Brasileira de Reproducao Assistida, pp. 197–199. doi: 10.5935/1518-0557.20190042.

Description: This article discusses the first attempt to genetically modify embryos in humans by Dr. He Jiankin. It highlights the ethical issues associated with genome editing in germline cells and embryos and provides the author’s view on the topic.

• Reference: Taemaitree, L. et al. (2019) ‘An artificial triazole backbone linkage provides a split-and-click strategy to bioactive chemically modified CRISPR sgRNA’, Nature Communications. Nature Publishing Group, 10(1), pp. 1–8. doi: 10.1038/s41467-019-09600-4.

Description: The study highlights the growing requirement of customised sgRNA sequences with diverse applications of the CRISPR technique. The authors provide a rapid ‘split-and-click convergent synthetic route of synthesising sgRNAs as opposed to the enzymatic routes that are time-consuming.