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Mediterranean Journal of Medical Research
https://mrj.org.ly/article/doi/10.5281/zenodo.19373711

Mediterranean Journal of Medical Research

Review Molecular biology

CRISPR-Cas9-based functional analysis of PARP inhibitor response in BRCA-mutated breast cancer and its implications for precision pharmacogenomics

Fathima, Nousheen, Karunakar Hegde

http://dx.doi.org/10.5281/zenodo.19373711 Mediterr J Med Res, vol.3, n2, p.137-146, 2026
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Abstract

BRCA1 and BRCA2 are tumour suppressor genes that play an essential role in homologous recombination and repair damaged DNA, maintaining genomic stability. Mutations in these genes can lead to inaccurate DNA repair, increasing the risk of breast cancer, and can be effectively targeted by PARP inhibitors. This review summarises the role of CRISPR-Cas9-based genome-wide screening to identify genetic determinants of PARP inhibitor response and resistance in BRCA-mutated breast cancer. These PARP inhibitors block the activity of the PARP protein, causing the single-strand DNA break to double-strand DNA break during replication due to replication fork collapse. Thus, the cancer cell DNA impairs DNA repair through defective homologous recombination. However, BRCA-mutated cells may endure resistance to PARP inhibitors due to BRCA reversion mutations, restoration of homologous recombination, 53BP1 pathway alterations, replication fork protection, drug efflux mechanisms, and the tumour microenvironment. CRISPR-Cas9 technology is an emerging genome-editing tool designed to identify the gene causing drug resistance and response. It systematically identifies determinants, synthetic lethal partners, and DNA damage response regulators using sgRNA libraries and next-generation sequencing. These findings support the development of combination therapy, PARP inhibitors with ATR or other DNA-damage response inhibitors, involved in biomarker discovery, personalised treatment, and improving precision medicine in breast cancer.

Keywords

BRCA1/BRCA2 mutations, PARP inhibitor resistance, precision therapy, synthetic lethality

References

  1. Sun YS, Zhao Z, Yang ZN, Xu F, Lu HJ, Zhu ZY, et al. Risk factors and prevention of breast cancer. International Journal of Biological Sciences. 2017; 13(11): 1387. doi: 10.7150/ijbs.21635
  2. Alssageer MA, Omar AM, Ghyte MW, Mohamed EH. Cancer burden and clinical presentation at Sebha Oncology Centre, Libya: A comparative study of urban and rural patient populations. Mediterranean Journal of Medical Research. 2026; 3(1): 105-113. doi: 10.5281/zenodo.19074828
  3. Alhadi AM, Alhadi AM, Mame ME, Mohammed AA, Ali AA. Evaluation of genetic engineering tools in anticancer drug discovery: Evidence-based insights for Libyan Pharmacology Departments. Mediterranean Journal of Pharmacy and Pharmaceutical Sciences. 2025; 5(4): 21-28. doi: 10.5281/zenodo.17334913
  4. Sherif FM. Vitamin D and therapy of breast cancer. Libyan Journal of Medical Research. 2014; 8(1): 116-125. doi: Nil.
  5. Cavanagh H, Rogers KM. The role of BRCA1 and BRCA2 mutations in prostate, pancreatic, and stomach cancers. Hereditary Cancer in Clinical Practice. 2015; 13(1): 16. doi: 10.1186/s13053-015-0038-x
  6. Sokolova A, Johnstone KJ, McCart Reed AE, Simpson PT, Lakhani SR. Hereditary breast cancer: syndromes, tumour pathology and molecular testing. Histopathology. 2023; 82(1): 70-82. doi: 10.1111/his.14808
  7. Zheng F, Zhang Y, Chen S, Weng X, Rao Y, Fang H. Mechanism and current progress of PARP inhibitors in ovarian cancer. Biomedicine and Pharmacotherapy. 2020; 123(1): 109661. doi: 10.1016/j.biopha.2019.109661
  8. Dilmac S, Ozpolat B. Mechanisms of PARP-inhibitor resistance in BRCA-mutated breast cancer and new therapeutic approaches. Cancers (Basel). 2023; 15(14): 3642. doi: 10.3390/cancers15143642
  9. Lee S, Kim K, Jeong HJ, Choi S, Cheng H, Kim D, et al. Combining multiplexed CRISPR/Cas9-nickase and PARP inhibitors efficiently and precisely targets cancer cells. Cancer Research. 2025; 85(15): 2890-2904. doi: 10.1158/0008-5472.CAN-24-2938
  10. Zhao W, Wiese C, Kwon Y, Hromas R, Sung P. The BRCA tumor suppressor network in chromosome damage repair by homologous recombination. Annual Review of Biochemistry. 2019; 88(1): 221-245. doi: 10.1146/ annurev-biochem-013118-111058
  11. Varol U, Kucukzeybek Y, Alacacioglu A, Somali I, Altun Z, Aktas S, et al. BRCA genes: BRCA1 and BRCA2. Apoptosis. 2018; 23(1): 862-866. PMID: 30358186.
  12. Arcieri M, Tius V, Andreetta C, Restaino S, Biasioli A, Poletto E, et al. How BRCA and homologous recombination deficiency change therapeutic strategies in ovarian cancer: a review of the literature. Frontiers in Oncology. 2024; 14(1): 1335196. doi: 10.3389/fonc.2024.1335196
  13. Shao C, Wan J, Lam FC, Tang H, Marley AR, Song Y, et al. A comprehensive literature review and meta‐analysis of the prevalence of pan-cancer BRCA mutations and HR deficiencies. Environmental and Molecular Mutagenesis. 2022; 63(6): 308-316. doi: 10.1002/em.22505
  14. Vogt A, He Y. Structure and mechanism in non-homologous end joining. DNA Repair (Amst). 2023; 130(1): 103547. doi: 10.1016/j.dnarep.2023.103547
  15. Yang K, Guo R, Xu D. Non-homologous end joining: advances and frontiers. Acta Biochimica et Biophysica Sinica (Shanghai). 2016; 48(7): 632-640. doi: 10.1093/abbs/gmw046
  16. Gorodetska I, Kozeretska I, Dubrovska A. BRCA genes: Role in genome stability and therapy resistance. Journal of Cancer. 2019; 10(9): 2109. doi: 10.7150/jca.30410
  17. Lord CJ, Ashworth A. PARP inhibitors: Synthetic lethality in the clinic. Science. 2017; 355(6330): 1152-1158. doi: 10.1126/science.aam7344
  18. Mateo J, Lord CJ, Serra V, Tutt A, Balmaña J, Castroviejo-Bermejo M, et al. A decade of clinical development of PARP inhibitors. Annals of Oncology. 2019; 30(9): 1437-1447. doi: 10.1093/annonc/mdz192
  19. Venkitaraman AR. How do mutations affecting the breast cancer genes BRCA1 and BRCA2 cause cancer susceptibility? DNA Repair (Amst). 2019; 81(1): 102668. doi: 10.1016/j.dnarep.2019.102668
  20. Frandsen SK, McNeil AK, Novak I, McNeil PL, Gehl J. Difference in membrane repair capacity between cancer cell lines and a normal cell line. The Journal of Membrane Biology. 2016;249(4):569-76. doi: 10.1007/s00232-016-9910-5
  21. Keung MY, Wu Y, Badar F, Vadgama JV. Response of breast cancer cells to PARP inhibitors independent of BRCA status. Journal of Clinical Medicine. 2020; 9(4): 940. doi: 10.3390/jcm9040940
  22. Robson M, Im SA, Senkus E, Xu B, Domchek SM, Masuda N, et al. Olaparib for metastatic breast cancer in patients with a germline BRCA mutation. The New England Journal of Medicine. 2017; 377(6): 523-533. doi: 10.1056/NEJMoa1706450
  23. Boussios S, Abson C, Moschetta M, Rassy E, Karathanasi A, Bhat T, et al. Poly (ADP-Ribose) polymerase inhibitors: Talazoparib in ovarian cancer and beyond. Drugs in R & D. 2020; 20(2): 55-73. doi: 10.1007/s40268-020-00301-8
  24. Ison G, Howie LJ, Amiri-Kordestani L, Zhang L, Tang S, Sridhara R, et al. FDA approval summary: Niraparib for the maintenance treatment of patients with recurrent ovarian cancer in response to platinum-based chemotherapy. Clinical Cancer Research. 2018; 24(17): 4066-40671. doi: 10.1158/1078-0432.CCR-18-0042
  25. Balasubramaniam S, Beaver JA, Horton S, Fernandes LL, Tang S, Horne HN, et al. FDA approval summary: Rucaparib for the treatment of patients with deleterious BRCA mutation–associated advanced ovarian cancer. Clinical Cancer Research. 2017; 23(23): 7165-7170. doi: 10.1158/1078-0432.ccr-17-1337 
  26. Diéras V, Han HS, Kaufman B, Wildiers H, Friedlander M, Ayoub JP, et al. Veliparib with carboplatin and paclitaxel in BRCA-mutated advanced breast cancer (BROCADE3): A randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncology. 2020; 21(10): 1269-1282. doi: 10.1016/S1470-2045(20)30447-2 
  27. Stradella A, Johnson M, Goel S, Park H, Lakhani N, Arkenau HT, et al. Phase 1b study to assess the safety, tolerability, and clinical activity of pamiparib in combination with temozolomide in patients with locally advanced or metastatic solid tumors. Cancer Medicine. 2024; 13(13): e7385. doi: 10.1002/cam4.7385
  28. Piombino C, Cortesi L. Insights into the possible molecular mechanisms of resistance to PARP inhibitors. Cancers (Basel). 2022; 14(11): 2804. doi: 10.3390/cancers14112804
  29. Karn V, Sandhya S, Hsu W, Parashar D, Singh HN, Jha NK, et al. CRISPR/Cas9 system in breast cancer therapy: advancement, limitations and future scope. Cancer Cell International. 2022; 22(1): 234. doi: 10.1186/s 12935-022-02654-3
  30. Tobalina L, Armenia J, Irving E, O'Connor MJ, Forment JV. A meta-analysis of reversion mutations in BRCA genes identifies signatures of DNA end-joining repair mechanisms driving therapy resistance. Annals of Oncology. 2021; 32(1): 103-112. doi: 10.1016/j.annonc.2020.10.470
  31. Paulet L, Trecourt A, Leary A, Peron J, Descotes F, Devouassoux-Shisheboran M, et al. Cracking the homologous recombination deficiency code: how to identify responders to PARP inhibitors. European Journal of Cancer. 2022; 166(1): 87-99. doi: 10.1016/j.ejca.2022.01.037
  32. Rass E, Willaume S, Bertrand P. 53BP1: Keeping it under control, even at a distance from DNA damage. Genes (Basel). 2022; 13(12): 2390. doi: 10.3390/genes13122390
  33. Moro RN, Biswas U, Kharat SS, Duzanic FD, Das P, Stavrou M, et al. Interferon restores replication fork stability and cell viability in BRCA-defective cells via ISG15. Nature Communications. 2023; 14(1): 6140. doi: 10.1101/2023.03.16.533020
  34. Li Y, Xu G, Zhang L, Zhao K, Zhao Y, Han D. Multiple drug resistance caused by germline mutation of exon 27 of BRCA2 gene in triple-negative breast cancer: a case report and literature review. Frontiers in Oncology. 2025; 15(1): 1602870. doi: 10.3389/fonc.2025.1602870
  35. Tay JY, Ho JX, Cheo FF, Iqbal J. The tumour microenvironment and epigenetic regulation in BRCA1 pathogenic variant-associated breast cancers. Cancers (Basel). 2024; 16(23): 3910. doi: 10.3390/cancers 16233910
  36. Jiang F, Doudna JA. CRISPR–Cas9 structures and mechanisms. Annual Review of Biophysics. 2017; 46(1): 505-529. doi: 10.1146/annurev-biophys-062215-010822
  37. Asmamaw M, Zawdie B. Mechanism and applications of CRISPR/Cas-9-mediated genome editing. Biologics. 2021; 15(1): 353-361. doi: 10.2147/BTT.S326422
  38. Wang T, Lander ES, Sabatini DM. Large-scale single guide RNA library construction and use for CRISPR–Cas9-based genetic screens. Cold Spring Harbor Protocols. 2016; 2016(3): pdb-top086892. doi: 10.1101/pdb. top086892
  39. Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nature Protocols. 2017; 12(4): 828-863. doi: 10.1038/ nprot.2017.016
  40. Villegas NK, Gaudreault YR, Keller A, Kearns P, Stapleton JA, Plesa C. Optimizing in vitro transcribed CRISPR-Cas9 single-guide RNA libraries for improved uniformity and affordability. BioRxiv. 2025; 644170. doi: 10.1101/2025.03.24.644170
  41. Otten AB, Sun BK. Research techniques made simple: CRISPR genetic screens. Journal of Investigative Dermatology. 2020; 140(4): 723-718. doi: 10.1016/j.jid.2020.01.018
  42. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014; 343(6166): 84-87. doi: 10.1126/science.1247005
  43. Barrangou R, Birmingham A, Wiemann S, Beijersbergen RL, Hornung V, Smith AV. Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Research. 2015; 43(7): 3407-7419. doi: 10.1093/nar/gkv226
  44. El-Ashouri AA, Smeo MNM, Sabei LT, Aldwebi HA, Abubaker NM, Abu-khatwa MS, Madi QF. Breast cancer delay presentation among Libyan patients: demographic and clinical features. Mediterranean Journal of Pharmacy and Pharmaceutical Sciences. 2024; 4(2): 30-36. 10.5281/zenodo.11224367
  45. Srivastava K, Pandit B. Genome-wide CRISPR screens and their applications in infectious disease. Frontiers in Genome Editing. 2023; 5(1): 1243731. doi: 10.3389/fgeed.2023.1243731
  46. Tang M, Pei G, Su D, Wang C, Feng X, Srivastava M, et al. Genome-wide CRISPR screens reveal cyclin C as synthetic survival target of BRCA2. Nucleic Acids Research. 2021; 49(13): 7476-7491. doi: 10.1093/nar/gkab 540
  47. Zhang Z, Wang H, Yan Q, Cui J, Chen Y, Ruan S, et al. Genome-wide CRISPR/Cas9 screening for drug resistance in tumors. Frontiers in Pharmacology. 2023; 14(1): 1284610. doi: 10.3389/fphar.2023.1284610
  48. Tsujino T, Takai T, Hinohara K, Gui F, Tsutsumi T, Bai X, et al. CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer. Nature Communications. 2023; 14(1): 252. doi: 10.1038/s41467-023-35880-y
  49. Noordermeer SM, van Attikum H. PARP inhibitor resistance: a tug-of-war in BRCA-mutated cells. Trends in Cell Biology. 2019; 29(10): 820-834. doi: 10.1016/j.tcb.2019.07.008
  50. Shao S, Li S, Tang S, Fan K, Li L. CRISPR double knockout library reveals synthetic lethal gene pairs in triple-negative breast cancer. bioRxiv. 2024; 594157. doi: 10.1101/2024.05.14.594157
  51. Samuels M, Besta S, Betrán AL, Nia RS, Xie X, Gu X, et al. CRISPR screening approaches in breast cancer research. Cancer and Metastasis Reviews. 2025; 44(3): 59. doi: .1007/s10555-025-10275-1
  52. Noordermeer SM, Adam S, Setiaputra D, Barazas M, Pettitt SJ, Ling AK, et al. Shieldin complex mediates 53BP1-dependent DNA repair. Nature. 2018; 560(7716): 117-121. doi: 10.1038/s41586-018-0340-7
  53. Breuer GA, Bezney J, Fons NR, Sundaram RK, Feng W, Gupta GP, et al. CRISPR screening identifies novel PARP inhibitor classification based on distinct base excision repair pathway dependencies. BioRxiv. 2020; 2020-10. doi: 10.1101/2020.10.18.333070
  54. Qiu Z, Oleinick NL, Zhang J. ATR/CHK1 inhibitors in cancer therapy. Radiotherapy and Oncology. 2018; 126(3): 450-464. doi: 10.20892/j.issn.2095-3941.2023.0260
  55. Clements KE, Hale A, Tolman NJ, Nicolae CM, Sharma A, Thakar T, et al. Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens. BioRxiv. 2019; 871970. doi: 10.1101/871970
  56. Yang H, Wei Y, Zhang Q, Yang Y, Bi X, Yang L, et al. CRISPR/Cas9‑induced saturated mutagenesis identifies Rad51 haplotype as a marker of PARP inhibitor sensitivity in breast cancer. Molecular Medicine Reports. 2022; 26(2): 1-2. doi: 10.3892/mmr.2022.12774
  57. Zhang T, Zhang Y, Wang X, Hu H, Lin CG, Xu Y, et al. Genome-wide CRISPR activation screen identifies ARL11 as a sensitivity determinant of PARP inhibitor therapy. Cancer Gene Therapy. 2025; 32(5): 521-537. doi: 10.1038/s41417-025-00893-w
  58. Fang P, De Souza C, Minn K, Chien J. Genome-scale CRISPR knockout screen identifies TIGAR as a modifier of PARP inhibitor sensitivity. Communications Biology. 2019; 2(1): 335. doi: 10.1038/s42003-019-0580-6
  59. Xie Y, Xiao D, Li D, Peng M, Peng W, Duan H, et al. Combined strategies with PARP inhibitors for the treatment of BRCA wide type cancer. Frontiers in Oncology. 2024; 14(1): 1441222. doi: 10.1186/s12943-021-01487-4
  60. Rasul MF, Hussen BM, Salihi A, Ismael BS, Jalal PJ, Zanichelli A, et al. Strategies to overcome the main challenges of the use of CRISPR/Cas9 as a replacement for cancer therapy. Molecular Cancer. 2022; 21(1): 1-30. doi: 10.1159/000547334

Submitted date:
01/19/2026

Reviewed date:
03/12/2026

Accepted date:
03/25/2026

Publication date:
04/01/2026

69cd71b1a953954e54611465 mjpe Articles
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