CRISPR-Cas9 in Precision Oncology: Unraveling Resistance Mechanisms and Redefining Molecular Targeted Cancer Therapy

Authors

  • Muhammad Osama Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
  • Ayesha Ghafoor Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
  • Toheed Fatima Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
  • Muhammad Shaharyar Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
  • Khadija Javed Department of Natural Sciences, University of Chester, Chester, England
  • Zainab Bibi Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
  • Bisma Department of Computer Science, University of Agriculture, Faisalabad, Pakistan
  • Farwa Shafique Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
  • Maryam Jameel Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan

DOI:

https://doi.org/10.62382/jcbt.v3i2.109

Keywords:

CRISPR-Cas9 genome editing, Molecular targeted cancer therapy, Drug resistance, Functional genomics, Precision oncology, Gene editing

Abstract

Cancer therapeutics have evolved from standard cytotoxic chemotherapy to specialized molecular targeted therapies, which scientists now develop using purposeful design methods. The treatments function by targeting molecular changes that lead to cancer development through epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER2), B-Raf proto-oncogene, serine/threonine kinase (BRAF) pathway mutations. Targeted therapies have achieved outstanding results, but drug resistance development creates a major obstacle that restricts their treatment success in medical practice. Scientists now understand genetic networks that control treatment outcomes and drug resistance because of major developments in Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9 (CRISPR-Cas9) genome-editing technology. This review provides a full examination of molecular targeted cancer therapy development and resistance mechanisms, and CRISPR-Cas9 applications for discovering new cancer cell weaknesses. It explains CRISPR-based functional genomic screens, which identify genes and pathways responsible for drug resistance, to develop new treatment approaches and explore the ethical aspects and technical obstacles, and future development possibilities for combining artificial intelligence with omics data and CRISPR precision oncology. The scientific breakthroughs create a new era for personalized cancer treatment, which unites genetic discoveries with medical practice. Beyond identifying oncogenic drivers, CRISPR-based functional genomics expands the therapeutic paradigm toward systematic interrogation of resistance circuits and synthetic lethal interactions. This shift redefines molecular targeted therapy from static inhibition of single driver mutations to dynamic targeting of adaptive survival networks that sustain tumor progression under therapeutic pressure. The medical field is experiencing a new period of individualized cancer treatment through these technological developments, which connect genetic discoveries to their clinical applications.

Downloads

Download data is not yet available.

References

Bode AM, Dong ZG. Recent advances in precision oncology research. NPJ Precision Oncology. 2018, 2, 11. DOI: 10.1038/s41698-018-0055-0

Bhat AA, Nisar S, Mukherjee S, Saha N, Yarravarapu N, Lone SN, et al. Integration of CRISPR/Cas9 with artificial intelligence for improved cancer therapeutics. Journal of Translational Medicine. 2022, 20(1), 534. DOI: 10.1186/s12967-022-03765-1

You LT, Tong RZ, Li MQ, Liu YC, Xue JX, Lu Y. Advancements and obstacles of CRISPR-Cas9 technology in translational research. Molecular Therapy Methods & Clinical Development. 2019, 13, 359-370. DOI: 10.1016/j.omtm.2019.02.008

Chanchal DK, Chaudhary JS, Kumar P, Agnihotri N, Porwal P. CRISPR-based therapies: Revolutionizing drug development and precision medicine. Current Gene Therapy. 2024, 24(3), 193-207. DOI: 10.2174/0115665232275754231204072320

Biswash MAR, Siddique MAB, Shabuj MMH, Aunni SAA, Rahman MM, Das DC. Advancing personalized cancer care: Integrating CRISPR/Cas9 with next-generation sequencing technologies. Journal of Precision Biosciences. 2024, 6(1), 1-14. DOI: 10.25163/biosciences.6110004

Khan Z, Mumtaz, Gupta S, Mehan S, Sharma T, Kumar M, et al. CRISPR-Cas9: Transforming functional genomics, precision medicine, and drug development – opportunities, challenges, and future directions. Current Gene Therapy. 2025. DOI: 10.2174/0115665232376648250312050239

Nussinov R, Jang H, Tsai CJ, Cheng FX. Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Computational Biology. 2019, 15(3), e1006658. DOI: 10.1371/journal.pcbi.1006658

Youssef E, Fletcher B, Palmer D. Enhancing precision in cancer treatment: The role of gene therapy and immune modulation in oncology. Frontiers in Medicine. 2025, 11, 1527600. DOI: 10.3389/fmed.2024.1527600

Mochizuki AY, Frost IM, Mastrodimos MB, Plant AS, Wang AC, Moore TB, et al. Precision medicine in pediatric neurooncology: A review. ACS Chemical Neuroscience. 2018, 9(1), 11-28. DOI: 10.1021/acschemneuro.7b00388

Menon AV, Song B, Chao LM, Sriram D, Chansky P, Bakshi I, et al. Unraveling the future of genomics: CRISPR, single-cell omics, and the applications in cancer and immunology. Frontiers in Genome Editing. 2025, 7, 1565387. DOI: 10.3389/fgeed.2025.1565387

Dujardin P, Baginska AK, Urban S, Grüner BM. Unraveling tumor heterogeneity by using DNA barcoding technologies to develop personalized treatment strategies in advanced-stage PDAC. Cancers. 2021, 13(16), 4187. DOI: 10.3390/cancers13164187

Pradhan A, Pattnaik G, Das S, Acharya B, Patra CN. Advancements in lung cancer: Molecular insights, innovative therapies, and future prospects. Medical Oncology. 2025, 42(9), 383. DOI: 10.1007/s12032-025-02725-1

Granata I, Manzo M, Kusumastuti A, Guarracino MR. Learning from metabolic networks: Current trends and future directions for precision medicine. Current Medicinal Chemistry. 2021, 28(32), 6619-6653. DOI: 10.2174/0929867328666201217103148

Paffenholz SV, Salvagno C, Ho YJ, Limjoco M, Baslan T, Tian S, et al. Senescence induction dictates response to chemo and immunotherapy in preclinical models of ovarian cancer. Proceedings of the National Academy of Sciences of the United States of America. 2022, 119(5), e2117754119. DOI: 10.1073/pnas.2117754119

Gamal H, Shoeib EM, Hajjaj A, Abdullah HEA, Elramy EH, Abd Ellah DA, et al. Incorporating AI, in silico, and CRISPR technologies to uncover the potential of repurposed drugs in cancer therapy. RSC Pharmaceutics. 2025, 2, 1019-1033. DOI: 10.1039/D5PM00158G

Castells-Roca L, Tejero E, Rodriguez-Santiago B, Surralles J. CRISPR screens in synthetic lethality and combinatorial therapies for cancer. Cancers. 2021, 13(7), 1591. DOI: 10.3390/cancers13071591

Balasubramanian B, Venkatraman S, Myint KZ, Janvilisri T, Wongprasert K, Kumkate S, et al. Co-clinical trials: An innovative drug development platform for cholangiocarcinoma. Pharmaceuticals. 2021, 14(1), 51. DOI: 10.3390/ph14020051

Mir GJ, Ali A, ul Ashraf N, Bhat JIA, Ganie SA, Ahmad SB, et al. CRISPR-Cas systems in cancer biology and therapeutics. In: Gene Editing by CRISPR-Cas. 1st ed. Boca Raton: CRC Press. 2025.

Claringbould A, Zaugg JB. Enhancers in disease: Molecular basis and emerging treatment strategies. Trends in Molecular Medicine. 2021, 27(11), 1060-1073. DOI: 10.1016/j.molmed.2021.07.012

Irfan M, Majeed H, Iftikhar T, Ravi PK. A review on molecular scissoring with CRISPR/Cas9 genome editing technology. Toxicology Research. 2024, 13(4), 105. DOI: 10.1093/toxres/tfae105

Siddique U. Biotechnology innovations: Shaping the future of medicine. Journal of Technological Information, Management & Engineering Sciences. 2020, 1, 28-35.

Hou J, He ZS, Liu T, Chen DF, Wang B, Wen QL, et al. Evolution of molecular targeted cancer therapy: Mechanisms of drug resistance and novel opportunities identified by CRISPR-Cas9 screening. Frontiers in Oncology. 2022, 12, 755053. DOI: 10.3389/fonc.2022.755053

Stulpinas A, Imbrasaitė A, Krestnikova N, Kalvelytė AV. Recent approaches encompassing the phenotypic cell heterogeneity for anticancer drug efficacy. Tumor Progression and Metastasis. 2020, 147. DOI: 10.5772/intechopen.89395

Xu CC. CRISPR/Cas9-mediated knockout strategies for enhancing immunotherapy in breast cancer. Naunyn-Schmiedeberg's Archives of Pharmacology. 2024, 397(11), 8561-8601. DOI: 10.1007/s00210-024-03208-2

Li TY, Li SQ, Kang Y, Zhou WJ, Yi M. Harnessing the evolving CRISPR/Cas9 for precision oncology. Journal of Translational Medicine. 2024, 22(1), 749. DOI: 10.1186/s12967-024-05570-4

Scandolara TB, Barreto Pires BR, Vacario B, de Amorim ISS, Siqueira PB, Serpeloni JM, et al. An overview regarding pharmacogenomics and biomarkers discovery: Focus on breast cancer. Current Topics in Medicinal Chemistry. 2022, 22(20), 1654-1673. DOI: 10.2174/1568026622666220801115040

Xing H, Meng LH. CRISPR-Cas9: A powerful tool towards precision medicine in cancer treatment. Acta Pharmacologica Sinica. 2020, 41(5), 583-587. DOI: 10.1038/s41401-019-0354-0

Huang L, Liao Z, Liu ZX, Chen Y, Huang T, Xiao HT. Application and prospect of CRISPR/Cas9 technology in reversing drug resistance of non-small cell lung cancer. Frontiers in Pharmacology. 2022, 13, 900825. DOI: 10.3389/fphar.2022.900825

Brooks IR, Garrone CM, Kerins C, Kiar CS, Syntaka S, Xu JZ, et al. Functional genomics and the future of iPSCs in disease modeling. Stem Cell Reports. 2022, 17(5), 1033-1047. DOI: 10.1016/j.stemcr.2022.03.019

Balon K, Sheriff A, Jacków J, Łaczmański Ł. Targeting cancer with CRISPR/Cas9-based therapy. International Journal of Molecular Sciences. 2022, 23(1), 573. DOI: 10.3390/ijms23020573

Vaghari-Tabari M, Hassanpour P, Sadeghsoltani F, Malakoti F, Alemi F, Qujeq D, et al. CRISPR/Cas9 gene editing: A new approach for overcoming drug resistance in cancer. Cellular and Molecular Biology Letters. 2022, 27(1), 49. DOI: 10.1186/s11658-022-00356-7

Massa A, Varamo C, Vita F, Tavolari S, Peraldo-Neia C, Brandi G, et al. Evolution of the experimental models of cholangiocarcinoma. Cancers. 2020, 12(8), 2308. DOI: 10.3390/cancers12082308

Akimov Y, Aittokallio T. Re-defining synthetic lethality by phenotypic profiling for precision oncology. Cell Chemical Biology. 2021, 28(3), 246-256. DOI: 10.1016/j.chembiol.2021.01.026

Lan B, Zeng SY, Zhang SM, Ren XF, Xing YM, Kutschick I, et al. CRISPR-Cas9 screen identifies DYRK1A as a target for radiotherapy sensitization in pancreatic cancer. Cancers. 2022, 14(2), 326. DOI: 10.3390/cancers14020326

Gee S, Nelson N, Bornot A, Carter N, Cuomo ME, Dovedi SJ, et al. Developing an arrayed CRISPR-Cas9 co-culture screen for immuno-oncology target ID. SLAS DISCOVERY: Advancing the Science of Drug Discovery. 2020, 25(6), 581-590. DOI: 10.1177/2472555220901760

Stine ZE, Schug ZT, Salvino JM, Dang CV. Targeting cancer metabolism in the era of precision oncology. Nature Reviews Drug Discovery. 2022, 21(2), 141-162. DOI: 10.1038/s41573-021-00353-2

Terraneo N, Jacob F, Dubrovska A, Grünberg J. Novel therapeutic strategies for ovarian cancer stem cells. Frontiers in Oncology. 2020, 10, 319. DOI: 10.3389/fonc.2020.00319

Uddin F, Rudin CM, Sen T. CRISPR gene therapy: Applications, limitations, and implications for the future. Frontiers in Oncology. 2020, 10, 1387. DOI: 10.3389/fonc.2020.01387

Alhasso B, Shareef A, Baldaniya L, Oweis R, Jyothi R, Singh U, et al. CRISPR/Cas9 in colorectal cancer: Revolutionizing precision oncology through genome editing and targeted therapeutics. Iranian Journal of Basic Medical Sciences. 2025, 28(10), 1279-1300. DOI: 10.22038/ijbms.2025.87531.18902

Kumar N. Genome editing in gynecological oncology: The emerging role of CRISPR/Cas9 in precision cancer therapy. Therapeutic Innovation & Regulatory Science. 2025, 59(5), 937-948. DOI: 10.1007/s43441-025-00807-w

Yang Y, Xu J, Ge SY, Lai LQ. CRISPR/Cas: Advances, limitations, and applications for precision cancer research. Frontiers in Medicine. 2021, 8, 649896. DOI: 10.3389/fmed.2021.649896

Das S, Bano S, Kapse P, Kundu GC. CRISPR based therapeutics: A new paradigm in cancer precision medicine. Molecular Cancer. 2022, 21(1), 85. DOI: 10.1186/s12943-022-01552-6

Wu YM, Sun RW, Ren S, Zengin G, Li MY. Neuronal reshaping of the tumor microenvironment in tumorigenesis and metastasis: Bench to clinic. Medicine Advances. 2025, 3, 364-371. DOI: 10.1002/med4.70044

Abdul-Hussin IF, Alkhalidi MHO, Al-Musawi S, Alshalah LAM, Sheykhhasan M. CRISPR-Cas9 in functional genomics: Implications for target validation in precision oncology. Trends in Pharmaceutical Biotechnology. 2025, 3, 36-48. DOI: 10.57238/tpb.2025.153196.1026

Noor A, Bilal A, Ali U. Towards personalized cancer care: A report of CRISPR-Cas9 applications in targeted therapies and precision medicine. Journal of Health and Rehabilitation Research. 2024, 4(2), 1375-1380. DOI: 10.61919/jhrr.v4i2.1028

Khoshandam M, Soltaninejad H, Mousazadeh M, Hamidieh AA, Hosseinkhani S. Clinical applications of the CRISPR/Cas9 genome-editing system: Delivery options and challenges in precision medicine. Genes & Diseases. 2023, 11(1), 268-282. DOI: 10.1016/j.gendis.2023.02.027

Selvakumar SC, Preethi KA, Ross K, Tusubira D, Khan MWA, Mani P, et al. CRISPR/Cas9 and next generation sequencing in the personalized treatment of Cancer. Molecular Cancer. 2022, 21(1), 83. DOI: 10.1186/s12943-022-01565-1

Mahato RK, Bhattacharya S, Khullar N, Sidhu IS, Reddy PH, Bhatti GK, et al. Targeting long non-coding RNAs in cancer therapy using CRISPR-Cas9 technology: A novel paradigm for precision oncology. Journal of Biotechnology. 2024, 379, 98-119. DOI: 10.1016/j.jbiotec.2023.12.003

Kanbar K, El Darzi R, Jaalouk DE. Precision oncology revolution: CRISPR-Cas9 and PROTAC technologies unleashed. Frontiers in Genetics. 2024, 15, 1434002. DOI: 10.3389/fgene.2024.1434002

Jameel ZI. CRISPR-Cas9 technology: A breakthrough in cancer gene therapy. Egyptian Journal of Medical Human Genetics. 27, 4 (2026). DOI: 10.1186/s43042-025-00833-1

Tian XL, Gu TX, Patel S, Bode AM, Lee MH, Dong ZG. CRISPR/Cas9–An evolving biological tool kit for cancer biology and oncology. NPJ Precision Oncology. 2019, 3, 8. DOI: 10.1038/s41698-019-0080-7

Li JT, Gu A, Tang NN, Zengin G, Li MY, Liu YB. Patient‐derived xenograft models in pan‐cancer: From bench to clinic. Interdisciplinary Medicine. 2025, 3(5), e20250016. DOI: 10.1002/INMD.20250016

Sharma AK, Giri AK. Engineering CRISPR/Cas9 therapeutics for cancer precision medicine. Frontiers in Genetics. 2024, 15, 1309175. DOI: 10.3389/fgene.2024.1309175

Khalil A. Precision oncology in the era of CRISPR-Cas9 technology. Frontiers in Genetics. 2024, 15, 1506627. DOI: 10.3389/fgene.2024.1506627

Wu YM, Sun RW, Zengin G, Ren S, Li MY. Tumor organoids: Breakthroughs in clinical decision making, drug development, and translational advances beyond conventional models. Med Research. 2025. DOI: 10.1002/mdr2.70048

Ravichandran M, Maddalo D. Applications of CRISPR-Cas9 for advancing precision medicine in oncology: From target discovery to disease modeling. Frontiers in Genetics. 2023, 14, 1273994. DOI: 10.3389/fgene.2023.1273994

Downloads

Published

2026-04-08

How to Cite

Muhammad Osama, Ayesha Ghafoor, Toheed Fatima, Muhammad Shaharyar, Khadija Javed, Zainab Bibi, … Maryam Jameel. (2026). CRISPR-Cas9 in Precision Oncology: Unraveling Resistance Mechanisms and Redefining Molecular Targeted Cancer Therapy. Journal of Cancer Biomoleculars and Therapeutics, 3(2), 1–12. https://doi.org/10.62382/jcbt.v3i2.109