Advancing Personalized Cancer Care: Integrating CRISPR/Cas9 with Next-Generation Sequencing Technologies
Md Abdur Rahman Biswash1, Md Abu Bakar Siddique2, Md Mahedi Hasan Shabuj1, Syeda Anjuman Ara Aunni3, Md Moshiur Rahman4, Debashis Chandra Das5, Tufael6*
Journal of Precision Biosciences 6(1) 1-14 https://doi.org/10.25163/biosciences.6110004
Submitted: 22 April 2024 Revised: 11 June 2024 Published: 13 June 2024
Abstract
Background: Cancer arises from a complex interplay of genetic and epigenetic abnormalities, presenting significant challenges for conventional therapies. This complexity underscores the urgent need for innovative therapeutic approaches. The integration of the CRISPR/Cas9 system with next-generation sequencing (NGS) presents a promising avenue for rapid identification, validation, and targeting of critical therapeutic targets. Methods: Personalized medicine leverages genetic, phenotypic, and environmental data to tailor healthcare solutions, moving beyond the limitations of standardized treatments. Advances in cancer genome sequencing have facilitated this shift, with NGS offering advantages such as minimal sample requirements and the ability to identify novel biomarkers. Tumor profiling, along with cell-free DNA analysis, proteomics, and RNA studies, enhances our understanding of immunological responses and informs treatment strategies. Results: The CRISPR/Cas9 system enables precise targeting of genetic alterations in tumor cells, providing a mechanism to disrupt genetic pathways responsible for tumorigenesis and metastasis. This targeted approach enhances the potential for more effective and personalized therapies. Combining NGS and CRISPR/Cas9 aims to match treatments to specific tumor profiles and develop bespoke therapeutic strategies tailored to individual tumors. This review highlights the transformative potential of CRISPR/Cas9 and NGS in advancing personalized cancer treatment.
Keywords: CRISPR/Cas9, Next Generation Sequencing (NGS), Personalized Medicine, Cancer Treatment, Liquid Biopsy
References
Abraham, J. R., O’Leary, H. A., & Chen, Y. (2022). Exploring RNA polymerase II’s role in ribosome biogenesis in Ewing sarcoma. Molecular Cancer, 21(1), 1-13.
Akter et al., (2024). Significance of Serum Biomarkers in Early Diagnosis of Hepatocellular Carcinoma in Patient with Fisher Groups.
Alix-Panabières, C., & Pantel, K. (2016). Clinical applications of circulating tumor cells and circulating tumor DNA as liquid biopsy. Nature Reviews Clinical Oncology, 13(3), 146-159. https://doi.org/10.1038/nrclinonc.2015.195
Almendros, I., et al. (2019). Cancer heterogeneity and response to treatment: the role of genomics. Nature Reviews Clinical Oncology, 16(4), 190-207.
Anzalone, A. V., et al. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature Biotechnology, 37(2), 220-225.
Anzalone, A. V., Randolph, P. B., & Davis, T. H. (2019). In vivo prime editing of a metabolic disease gene in mice. Nature, 577(7789), 627-632.
Anzalone, A. V., Randolph, P. B., Davis, J. R., et al. (2019). Search-and-replace genome editing without double-strand breaks or donor DNA. Nature, 576(7785), 149–157. https://doi.org/10.1038/s41586-019-1711-4
Arteaga, C. L. (2006). Epidermal growth factor receptor dependence in human tumors: A new therapeutic opportunity. Clinical Cancer Research, 12(4), 1003s-1008s.
Batsche, E., Ait-Si-Ali, S., & Billey, E. (2020). dCas9-based epigenome editing: a promising approach to target alternative splicing. Nature Communications, 11(1), 1-13.
Bettegowda, C., et al. (2014). Detection of circulating tumor DNA in early- and late-stage human malignancies. Science Translational Medicine, 6(224), 224ra24. https://doi.org/10.1126/scitranslmed.3007094
Bettegowda, C., Luber, B. S., & Wang, J. (2014). The potential clinical utility of circulating tumor DNA in breast cancer. Cancer Research, 74(7), 1898-1904. https://doi.org/10.1158/0008-5472.CAN-13-3132
Brown, J. R., Smith, M. R., & Chen, Y. (2023). Next-Generation Sequencing in Lung Cancer: Implications for Diagnosis and Treatment. Journal of Oncology, 45(3), 125-134.
Brown, J. R., Wong, C. H., & Reuter, M. (2019). Next-generation sequencing: Platforms, applications, and analyses. Nature Reviews Genetics, 20(5), 343-355. https://doi.org/10.1038/s41576-019-0100-5
Brown, T. M., & Green, S. L. (2021). Chimeric antigen receptor T-cell therapy: A revolution in cancer treatment. Cancer Treatment Reviews, 50(5), 99-108. https://doi.org/10.1016/j.ctrv.2021.102030
Certo, M. T., et al. (2018). Methods to enhance homology-directed repair in genome editing. Nature Reviews Molecular Cell Biology, 19(2), 117-135.
Chen, J., & Roberts, R. (2024). Advancements in neoantigen prediction and their implications for immunotherapy. Cancer Research, 84(3), 1234-1245.
Chen, L. H., et al. (2024). Immunotherapy in Metastatic Breast Cancer: A Case Study on the Role of NGS in Personalized Treatment. Cancer Research, 82(2), 56-65.
Chen, S., Yu, T., & Wang, L. (2018). Assessment of errors in Illumina sequencing. Nature Reviews Genetics, 19(7), 407–420.
Cohen, J. D., et al. (2017). Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science, 359(6378), 926-930. https://doi.org/10.1126/science.aar3242
Cong, L., Ran, F. A., Cox, D., & Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819–823.
Davis, A. G., & Nussbaum, R. L. (2019). Emerging genomic technologies and their impact on the future of precision medicine. Nature Reviews Genetics, 20(4), 204-219.
Diehl, F., et al. (2005). Analysis of circulating tumor DNA to monitor treatment response in colorectal cancer. Nature Medicine, 12(10), 1236-1240. https://doi.org/10.1038/nm1340
Doudna, J. A., & Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096.
Doudna, J. A., & Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096.
Feng, Z., Zhang, B., & Li, D. (2019). Limitations and applications of next-generation sequencing in the clinical diagnosis of cancer. Nature Reviews Clinical Oncology, 16(11), 700–715.
Fridman, W. H., et al. (2017). The immune microenvironment of human tumors: General principles and therapeutic implications. Nature Reviews Cancer, 17(2), 85-101. https://doi.org/10.1038/nrc.2016.132
Gao, H., et al. (2016). Circulating tumor DNA for non-invasive detection of cancer. Nature Reviews Clinical Oncology, 13(4), 211-228. https://doi.org/10.1038/nrclinonc.2016.179
Gao, S., et al. (2016). Liquid biopsy: A new era of cancer management. Frontiers in Medicine, 10(2), 223-229. https://doi.org/10.1007/s11684-016-0457-0
Gao, X., Zhang, Q., & Zhang, Y. (2022). In vivo correction of metabolic disease using prime editing. Nature Biotechnology, 40(8), 1156-1163.
Gaudelli, N. M., Komor, A. C., Rees, H. A., et al. (2017). Programmed editing of a target base in genomic DNA without a double-strand break. Nature, 551(7681), 464–471. https://doi.org/10.1038/nature24644
Gonzalez, A. M., et al. (2021). Next-generation sequencing technologies and their application in cancer precision medicine. Frontiers in Oncology, 11, 688389.
Gonzalez-Angulo, A. M., et al. (2013). Breast cancer: Drug resistance and targeted therapy. Nature Reviews Clinical Oncology, 10(7), 415-426.
Guo, Y., Wang, Y., Xu, H., Zhang, Y., & Wang, R. (2023). Next-generation sequencing technologies in precision oncology. Journal of Molecular Medicine, 101(2), 254-267.
He, J., et al. (2015). Liquid biopsy: The future of cancer diagnosis and treatment. Frontiers in Genetics, 6, 252.
He, J., et al. (2015). The role of liquid biopsy in lung cancer. Expert Review of Molecular Diagnostics, 15(4), 485-497. https://doi.org/10.1586/14737159.2015.1012906
He, M., et al. (2015). Circulating tumor DNA analysis for the early detection of cancer. Trends in Molecular Medicine, 21(8), 460-470. https://doi.org/10.1016/j.molmed.2015.05.004
Hernandez, A. R., et al. (2022). Targeting immune checkpoints with CRISPR/Cas9: A new era in cancer therapy. Frontiers in Immunology, 13, 1-10. https://doi.org/10.3389/fimmu.2022.746733
Huang, R. H., et al. (2020). Signaling pathways in cancer. Nature Reviews Cancer, 20(9), 553-572.
Huang, X., Xu, Y., & Yu, Z. (2021). Prime editing for precise gene editing: an overview. Molecular Therapy, 29(1), 12-24.
Huang, Y., Li, S., & Zhang, H. (2021). Ethical implications of CRISPR/Cas9 genome editing in humans. Nature Biotechnology, 39(1), 12-14.
Hyman, D. M., et al. (2015). Drug resistance in cancer: A new paradigm. Nature Reviews Clinical Oncology, 12(1), 59-65.
Jandova, J., & Sweeney, K. J. (2020). CRISPR/Cas9-mediated gene editing in melanoma cells: Mechanistic insights. Cell Reports, 32(12), 108064.
Jiang, W., & Zhang, H. (2021). CRISPRa and CRISPRi: potent tools for precise control of gene expression. Nature Reviews Genetics, 22(3), 183-197.
Jiang, W., et al. (2018). CRISPR/Cas9 for cancer therapy: opportunities and challenges. Nature Reviews Clinical Oncology, 15(3), 174-186.
Johnson, A., & Li, H. (2023). Advancements in Thyroid Cancer Diagnostics through Next-Generation Sequencing. Thyroid Journal, 33(4), 235-248.
Johnson, K. M., et al. (2023). Safety and feasibility of CRISPR/Cas9-edited T cells in patients with cancer: Results from a Phase I trial. Nature Medicine, 29(3), 478-485. https://doi.org/10.1038/s41591-022-01812-x
Johnson, N. M., & Li, J. (2023). Advancements in NGS for thyroid cancer diagnostics: A comprehensive review. Journal of Clinical Endocrinology & Metabolism, 108(5), 1243–1256.
Jones, H. P., et al. (2020). Challenges in the production of autologous CAR T cells: A comprehensive review. Journal of Cancer Research, 58(4), 642-653. https://doi.org/10.1016/j.jcr.2020.03.006
Jones, S., et al. (2021). The Genomic Landscape of Myelodysplastic Syndromes. Nature, 590(7845), 117-123. https://doi.org/10.1038/s41586-020-03002-4
Kim, H. K., & Lee, S. K. (2021). New molecular diagnostic approaches for the early detection of colorectal cancer. Clinical and Experimental Gastroenterology, 14, 151-158. https://doi.org/10.2147/CEG.S307093
Kim, Y. B., Kim, J. S., & Kim, D. (2017). Evaluation of CRISPR/Cas9 genome editing in E. coli using next-generation sequencing. Nature Biotechnology, 35(8), 835–839. https://doi.org/10.1038/nbt.3891
Kleinstiver, B. P., Prew, M. S., & Tsai, S. Q. (2016). Broadening the targeted mutagenesis spectrum with engineered Cas9 nucleases. Nature Biotechnology, 34(2), 164–166. https://doi.org/10.1038/nbt.3410
Kobayashi, S., et al. (2005). EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. New England Journal of Medicine, 352(8), 786-792. https://doi.org/10.1056/NEJMoa041294
Komor, A. C., Badran, A. H., & Liu, D. R. (2016). Editing the genome without double-stranded breaks. Nature Reviews Molecular Cell Biology, 17(5), 285–296. https://doi.org/10.1038/nrm.2016.42
Lander, E. S. (2016). The heroes of CRISPR. Cell, 167(1), 7-8.
Lee, J. Y., et al. (2023). Universal CAR T cells derived from healthy donors: A promising approach to CAR T therapy. Nature Biotechnology, 41(4), 354-362. https://doi.org/10.1038/s41587-023-01599-8
Li, A., Liu, Y., Zhang, C., & Cheng, Y. (2022). Computational tools for optimizing CRISPR guide RNA design. Bioinformatics, 38(8), 2182-2190.
Li, G., Chen, D., & Zhang, J. (2021). Engineering oncolytic herpes simplex virus for enhanced cancer immunotherapy. Molecular Therapy, 29(4), 1235-1245.
Li, H., & Hartemink, A. J. (2021). Computational approaches for next-generation sequencing data analysis: A review. Nature Reviews Genetics, 22(3), 162–177.
Li, Q., Liu, Y., Zhang, L., et al. (2020). Base editing for the correction of disease-causing mutations in human induced pluripotent stem cells. Molecular Therapy, 28(9), 1997–2006. https://doi.org/10.1016/j.ymthe.2020.05.018
Liao, M., et al. (2022). Next-generation sequencing in cancer research: From genetic variation to personalized medicine. Nature Reviews Genetics, 23(5), 325-339. https://doi.org/10.1038/s41576-021-00345-y
Liu, Y., et al. (2020). Cytosine base editing with CRISPR-Cas9. Nature Reviews Molecular Cell Biology, 21(6), 387-403.
Liu, Y., Zhou, J., & Wang, H. (2022). Potential applications of CRISPR-ON in therapeutic strategies. Nature Reviews Genetics, 23(5), 389-403.
Mali, P., et al. (2013). Cas9 as a versatile tool for engineering biology. Nature Methods, 10(10), 957-963.
Mali, P., Yang, L., Esvelt, K. M., & Church, G. M. (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121), 823–826.
Mao, Y., et al. (2008). A rapid and efficient method for the detection of gene knock-ins via CRISPR/Cas9. Nature Biotechnology, 26(9), 1071–1075.
Mardis, E. R. (2013). Next-generation sequencing platforms. Annual Review of Analytical Chemistry, 6(1), 287-304.
Martinez, L. S., et al. (2020). Preclinical evaluation of CRISPR/Cas9-mediated CAR T-cell therapy in solid tumors. Cancer Research, 80(15), 3192-3201. https://doi.org/10.1158/0008-5472.CAN-20-0468
Meyer, C., et al. (2018). Circulating tumor DNA for cancer detection and monitoring. Nature Reviews Clinical Oncology, 15(8), 518-532.
Miao, L., et al. (2019). CRISPR/Cas9-mediated PD-1 disruption enhances T cell efficacy in non-small cell lung cancer. Nature Communications, 10(1), 1-11. https://doi.org/10.1038/s41467-019-08633-1
Miller, A. R., et al. (2022). Overcoming limitations of traditional CAR T therapies with universal CAR T cells. Trends in Cancer, 8(9), 711-723. https://doi.org/10.1016/j.trecan.2022.06.008
Nguyen, C. T., Tseng, P., & Wu, M. (2021). Current challenges and future perspectives in CRISPR/Cas9-based therapies. Nature Reviews Molecular Cell Biology, 22(10), 651-665.
Petri, R., Sweeney, S., & Forster, T. (2023). Prime editing in zebrafish embryos: efficiency and specificity. Nature Communications, 14(1), 1-11.
Ran, F. A., Hsu, P. D., Lin, C. Y., & Weissman, J. S. (2013). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154(6), 1380–1389.
Rees, H. A., & Liu, D. R. (2018). Base editing: a new tool for precise genome editing. Nature Reviews Genetics, 19(5), 313–324. https://doi.org/10.1038/s41576-018-0005-6
Rosenberg, S. A., et al. (2019). Personalized cancer therapy: The promise and challenges of individualized treatment. Cancer Research, 79(16), 4019-4022.
Schatz, M. C., et al. (2020). Quality assessment of next-generation sequencing data. Nature Biotechnology, 38(2), 138–147.
Sharma, P., et al. (2020). Clinical utility of circulating tumor DNA in colorectal cancer. Nature Reviews Gastroenterology & Hepatology, 17(11), 669-679. https://doi.org/10.1038/s41575-020-0345-7
Sharma, P., et al. (2020). Methylated SEPT9 DNA as a biomarker for colorectal cancer: A systematic review and meta-analysis. Gastroenterology, 159(5), 1344-1357. https://doi.org/10.1056/NEJMoa1800536
Singh, A., & Zhang, S. (2021). Off-target effects of CRISPR/Cas9 and strategies for their minimization. Current Opinion in Genetics & Development, 69, 135-142.
Singh, R., & Patel, V. (2022). Off-target effects of CRISPR/Cas9: Challenges and solutions in cancer therapy. Molecular Therapy – Nucleic Acids, 27, 788-800. https://doi.org/10.1016/j.omtn.2022.07.012
Siravegna, G., et al. (2017). Tracking evolution of colorectal cancer metastases by liquid biopsy. Nature Communications, 8(1), 1-9. https://doi.org/10.1038/s41467-017-00478-6
Slamon, D. J., et al. (2001). Human breast cancer: Correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science, 244(4905), 707-712.
Smith, A. C., Johnson, M., & Lee, K. (2021). Epigenetic mechanisms in cancer: therapeutic targets and implications. Cancer Research, 81(15), 3640-3652.
Smith, J. A., & Green, P. (2020). The role of next-generation sequencing in cancer research: Implications for CRISPR/Cas9 therapy. Journal of Molecular Medicine, 98(1), 1-11. https://doi.org/10.1007/s00109-020-02240-5
Smith, J. A., & Zhang, Y. (2022). The future of precision medicine in breast cancer: The role of NGS in drug resistance and treatment response. Breast Cancer Research and Treatment, 195(2), 333–342.
Smith, J. D., et al. (2020). Detection of rare variants in breast cancer using targeted next-generation sequencing. Clinical Cancer Research, 26(15), 4045-4055. https://doi.org/10.1158/1078-0432.CCR-19-3238
Smith, L. A., et al. (2021). CAR T-cell therapy in hematological malignancies: Mechanisms of action and therapeutic outcomes. Nature Reviews Cancer, 21(1), 45-61. https://doi.org/10.1038/s41571-020-00436-x
Smith, R. A., Johnson, T. M., & Lee, P. (2022). Revolutionizing Breast Cancer Treatment with NGS: Insights and Future Directions. Breast Cancer Research, 58(1), 12-19.
Tewari, M., et al. (2015). Next-generation sequencing for cancer therapy: The importance of patient-centered care. JCO Precision Oncology, 1, 1-8.
Thompson, J. F., et al. (2016). Circulating tumor DNA: A potential clinical utility in solid tumors. Nature Reviews Clinical Oncology, 13(11), 694-706. https://doi.org/10.1038/nrclinonc.2016.159
Thompson, J. F., et al. (2016). Monitoring tumor dynamics through ctDNA analysis. Clinical Cancer Research, 22(12), 3015-3023. https://doi.org/10.1158/1078-0432.CCR-16-0562
Tufael, M. M. R. (2024). Combined Biomarkers for Early Diagnosis of Hepatocellular Carcinoma. Journal of Angiotherapy, 8(5), 1-12.
Tuononen, K., et al. (2021). Comparative Analysis of NGS and PCR for Mutation Detection in Cancer: A Study of Sensitivity. Oncology Reports, 45(6), 1205-1215.
Tuononen, K., et al. (2021). Next-generation sequencing identifies mutations in clinical samples: A comparative study. Nature Communications, 12(1), 1000.
Urnov, F. D., et al. (2010). Genome editing with engineered zinc finger nucleases. Nature Reviews Genetics, 11(9), 636–646.
Wang, H., et al. (2020). CRISPR/Cas9 and its applications in cancer therapy. Journal of Cellular Physiology, 235(1), 200-206.
Wang, Y., et al. (2021). Targeting multiple tumor growth pathways using CRISPR/Cas9 in melanoma cells. Nature Communications, 12(1), 5678.
Wang, Y., Liu, Y., & Zhang, Q. (2020). Selective replication of oncolytic viruses in cancer cells with dysfunctional p16^INK4A^ signaling. Journal of Virology, 94(24), e01145-20.
Wong, T. S., et al. (2017). Precision medicine in oncology: A focus on molecular genetics. Journal of Clinical Oncology, 35(29), 3353-3358.
Wu, Y., Liu, Y., & Zhao, Y. (2020). Fitness challenges in modified cells: Implications for CRISPR technology. Cell Reports, 30(10), 3476-3485.
Xiang, Z., Wu, L., & Liu, J. (2021). CRISPR-ON: An improved CRISPR system for precise gene regulation. Nature Communications, 12(1), 3021.
Xie, L., Zhou, Y., & Yang, L. (2022). Oncolytic adenoviruses: targeting tumor-specific pathways for improved cancer therapy. Cancer Gene Therapy, 29(1), 1-13.
Yu, X., et al. (2019). Bioinformatics challenges in NGS data analysis. Bioinformatics, 35(20), 3920–3928.
Zhang, X., et al. (2021). Clinical outcomes of CRISPR/Cas9 gene editing in patients with lung cancer: A follow-up study. Clinical Cancer Research, 27(6), 1335-1341. https://doi.org/10.1158/1078-0432.CCR-20-0928
Zhou, J., Zhang, R., & Wang, Y. (2023). Epigenome editing: targeting the epigenome for cancer therapy. Nature Reviews Cancer, 23(1), 32-45.
Zhou, X., et al. (2021). Advances in CRISPR/Cas9 delivery systems and strategies. Journal of Controlled Release, 335, 114-129.
View Dimensions
View Altmetric
Save
Citation
View
Share