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Abstract
Triple-negative breast cancer (TNBC) remains a challenging malignancy due to its immunosuppressive microenvironment. Here, we employed CRISPR-Cas9 to knockout PD-L1 in TNBC cell lines and evaluated changes in immune recognition and T cell activation. PD-L1 ablation resulted in increased expression of antigen-presenting machinery and enhanced sensitivity to T cell-mediated cytotoxicity. Our findings suggest that CRISPR-mediated PD-L1 disruption could potentiate immunotherapy efficacy in TNBC.
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Copyright (c) 2025 Ashwaq MS Al-Jbouri, Asmaa Sami Jawad, Zainab Adil Ghani Chabuck, Saad Mardi Muhammad (Author)

This work is licensed under a Creative Commons Attribution 4.0 International License.
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References
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- Singh DD, Han I, Choi EH, Yadav DK. CRISPR/Cas9-based genome editing for targeted transcriptional control in triple-negative breast cancer. Front Genet. 2021;12:1–10.
- Chen X, Feng L, Huang Y, Wu Y, et al. Mechanisms and strategies to overcome PD-1/PD-L1 blockade resistance in triple-negative breast cancer. Front Immunol. 2022;13:1–12.
- Khanfir A, Lahiani F, Bouzguenda R, Ayedi I, Daoud J, Frikha M. Prognostic factors and survival in metastatic breast cancer: a single institution experience. Rep Pract Oncol Radiother. 2013;18(3):127–32. https://doi.org/10.1016/j.rpor.2013.01.001.
- Li R, Li Y, Wang H, Qin T, Yin X, Ma X. Therapeutic progress and challenges for triple-negative breast cancer. Signal Transduct Target Ther. 2022;7:8.
- Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T, et al. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell. 2018;173(4):879–93.e13. https://doi.org/10.1016/j.cell.2018.03.041.
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- Emens LA. Breast cancer immunotherapy: facts and hopes. Clin Cancer Res. 2018;24(3):511–20. https://doi.org/10.1158/1078-0432.CCR-16-3001.
- Alkaabi D, Arafat K, Sulaiman S, Al-Azawi AM, Attoub S. PD-1 independent role of PD-L1 in triple-negative breast cancer progression. Int J Mol Sci. 2023;24(7):6420. https://doi.org/10.3390/ijms24076420.
- Tung N, Garber JE, Hacker MR, Torous V, et al. Prevalence and predictors of androgen receptor and programmed death-ligand 1 in BRCA1-associated and sporadic triple-negative breast cancer. Breast Cancer Res Treat. 2016;160(2):253–62.
- Yu Y, Jin X, Zhu X, Xu Y, Si W, Zhao J. PD-1/PD-L1 immune checkpoint inhibitors in metastatic triple-negative breast cancer: a systematic review and meta-analysis. Front Immunol. 2023;14:1206689. https://doi.org/10.3389/fimmu.2023.1206689.
- Xiong N, Wu H, Yu Z. Advancements and challenges in triple-negative breast cancer: a comprehensive review of therapeutic and diagnostic strategies. Front Oncol. 2024;14:1405491. https://doi.org/10.3389/fonc.2024.1405491.
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- Lehmann BD, Abramson VG, Dees EC, Shah PD, Ballinger TJ, Isaacs C, et al. Atezolizumab in combination with carboplatin and survival outcomes in patients with metastatic triple-negative breast cancer: The TBCRC 043 phase 2 randomized clinical trial. JAMA Oncol. 2023;10(2):193–201. https://doi.org/10.1001/jamaoncol.2023.5424.
- Lin X, Kang K, Chen P, Zeng Z, Li G, Xiong W, et al. Regulatory mechanisms of PD-1/PD-L1 in cancers. Mol Cancer. 2024;23:108. https://doi.org/10.1186/s12943-024-02023-w.
- Dai X, Gao Y, Wei W. Post-translational regulations of PD-L1/PD-1: mechanisms and opportunities for combined immunotherapy. Semin Cancer Biol. 2021;85:246–52. https://doi.org/10.1016/j.semcancer.2021.04.002.
- Pilon-Thomas S, Mackay A, Vohra N, Mulé JJ. Blockade of PD-L1 enhances the therapeutic efficacy of combination immunotherapy against melanoma. J Immunol. 2010;184(7):3442–9. https://doi.org/10.4049/jimmunol.0904114.
- Zhang F, Wang SS. Narrative review on advancing breast cancer treatment: harnessing the power of PD-1/PD-L1 inhibitors for improved patient outcomes. Front Oncol. 2023;13:1–12.
- Guo Y, Wang Z, Zhou H, Pan H, Han W, Deng Y, et al. First-in-human study of GFH018, a small molecule inhibitor of transforming growth factor-β receptor I, in patients with advanced solid tumors. BMC Cancer. 2024;24:444. https://doi.org/10.1186/s12885-024-12121-4.
- Dong E, Yue XZ, Shui L, Liu BR, Li QQ, Yang Y, et al. IFN-γ surmounts PD-L1/PD-1 inhibition to CAR-T cell therapy by upregulating ICAM-1 on tumor cells. Signal Transduct Target Ther. 2021;6:20. https://doi.org/10.1038/s41392-020-00452-5.
- Annunziato S, Kas SM, Nethe M, Yücel H, Del Bravo J, Pritchard C, et al. Modeling invasive lobular breast carcinoma by CRISPR/Cas9-mediated somatic genome editing of the mammary gland. Genes Dev. 2016;30(12):1470–80. https://doi.org/10.1101/gad.279190.116.
- Chow RD, Chen S. Cancer CRISPR screens in vivo. Trends Cancer. 2018;4(5):349–58. https://doi.org/10.1016/j.trecan.2018.03.002.
- Rosenblum D, Gutkin A, Kedmi R, Ramishetti S, Veiga N, Jacobi AM, et al. CRISPR-Cas9 genome editing using targeted lipid nanoparticles for cancer therapy. Sci Adv. 2020;6(47):eabc9450. https://doi.org/10.1126/sciadv.abc9450.
- Wang Y, Shelton SE, Kastrunes G, Barbie DA, Freeman GJ, Marasco WA. Preclinical models for development of immune-oncology therapies. Immuno-Oncol Insights. 2022;3(8):379–98. https://doi.org/10.18609/ioi.2022.41.
- Allison KH, Hammond MEH, Dowsett M, McKernin SE, Carey LA, Fitzgibbons PL, et al. Estrogen and progesterone receptor testing in breast cancer: ASCO/CAP guideline update. J Clin Oncol. 2020;38(12):1346–66. https://doi.org/10.1200/JCO.19.02309.
- Sreevalsan S, Döring M, Paszkowski-Rogacz M, Brux M, et al. MLLT6 maintains PD-L1 expression and mediates tumor immune resistance. EMBO Rep. 2020;21(12):e51397. https://doi.org/10.15252/embr.202051397.
- Wei SC, Duffy CR, Allison JP. Fundamental mechanisms of immune checkpoint blockade therapy. Cancer Discov. 2018;8(9):1069–86. https://doi.org/10.1158/2159-8290.CD-18-0367.
- Zhao Z, Shi L, Zhang W, Han J, Zhang S, Fu Z, et al. CRISPR knockout of programmed cell death protein 1 enhances anti-tumor activity of cytotoxic T lymphocytes. Oncotarget. 2017;9(4):5208–15. https://doi.org/10.18632/oncotarget.23730.
- Zhang B. CRISPR/Cas9: a robust genome-editing tool with versatile functions and endless application. Int J Mol Sci. 2020;21(14):5111. https://doi.org/10.3390/ijms21145111.
- Chen S, Sun H, Miao K, Deng CX. CRISPR-Cas9: from genome editing to cancer research. Int J Biol Sci. 2016;12(12):1427–36. https://doi.org/10.7150/ijbs.17421.
- Lu Y, Xue J, Deng T, Zhou X, Yu K, Huang M, et al. A phase I trial of PD-1 deficient engineered T cells with CRISPR/Cas9 in patients with advanced non-small cell lung cancer. J Clin Oncol. 2018;36(15_suppl):3050. https://doi.org/10.1200/JCO.2018.36.15_suppl.3050.
- Le Naour A, Rossary A, Vasson MP. EO771: is it a well-characterized cell line for mouse mammary cancer model? Limit and uncertainty. Cancer Med. 2020;9(21):8074–85. https://doi.org/10.1002/cam4.3295.
- Karn T. High-throughput gene expression and mutation profiling: current methods and future perspectives. Breast Care (Basel). 2013;8(6):401–6. https://doi.org/10.1159/000357461.
- He C, Han S, Chang Y, Wu M, Zhao Y, Chen C, et al. CRISPR screen in cancer: status quo and future perspectives. Am J Cancer Res. 2021;11(4):1031–50.
- Laurent M, Geoffroy M, Pavani G, Guiraud S. CRISPR-based gene therapies: from preclinical to clinical treatments. Cells. 2024;13(10):800. https://doi.org/10.3390/cells13100800.
- Mout R, Ray M, Lee YW, Scaletti F, Rotello VM. In vivo delivery of CRISPR/Cas9 for therapeutic gene editing: progress and challenges. Bioconjug Chem. 2017;28(4):880–4. https://doi.org/10.1021/acs.bioconjchem.7b00057.
- Davidson AR, Lu WT, Stanley SY, Wang J, Mejdani M, Trost CN, et al. Anti-CRISPRs: protein inhibitors of CRISPR-Cas systems. Annu Rev Biochem. 2020;89:309–32. https://doi.org/10.1146/annurev-biochem-011420-111224.
- Zheng Y, Li S, Tang H, Meng X, Zheng Q. Molecular mechanisms of immunotherapy resistance in triple-negative breast cancer. Front Immunol. 2023;14:1153990. https://doi.org/10.3389/fimmu.2023.1153990.
- Flörcken A, Kopp J, van Lessen A, Movassaghi K, Takvorian A, Jöhrens K, et al. Allogeneic partially HLA-matched dendritic cells pulsed with autologous tumor cell lysate as a vaccine in metastatic renal cell cancer: a clinical phase I/II study. Hum Vaccin Immunother. 2013;9(6):1217–27. https://doi.org/10.4161/hv.24149.
References
Zhao Z, Shi L, Zhang W, Han J, et al. CRISPR knockout of programmed cell death protein 1 enhances anti-tumor activity of cytotoxic T lymphocytes. Oncotarget. 2017;9(4):5208–15. https://doi.org/10.18632/oncotarget.23730.
Li JP, Zhang XM, Zhang ZZ, Zheng LH, Jindal S, Liu YJ. Association of p53 expression with poor prognosis in patients with triple-negative breast invasive ductal carcinoma. Medicine (Baltimore). 2019;98(18):e15449. https://doi.org/10.1097/MD.0000000000015449.
Amir E, Cescon DW. Pembrolizumab monotherapy in metastatic triple-negative breast cancer. Lancet Oncol. 2021;22(4):415–7. https://doi.org/10.1016/S1470-2045(21)00019-X.
Farheen J, Hosmane NS, Zhao R, Zhao Q, Iqbal MZ, Kong X. Nanomaterial-assisted CRISPR gene-engineering: a hallmark for triple-negative breast cancer therapeutics advancement. Mater Today Bio. 2022;16:100450. https://doi.org/10.1016/j.mtbio.2022.100450.
Fierro J Jr, DiPasquale J, Perez J, Chin B, Chokpapone Y, Tran AM, et al. Dual sgRNA CRISPR/Cas9 knockout of PD-L1 in human U87 glioblastoma tumor cells inhibits proliferation, invasion, and tumor-associated macrophage polarization. Sci Rep. 2022;12:1–13.
Singh DD, Han I, Choi EH, Yadav DK. CRISPR/Cas9-based genome editing for targeted transcriptional control in triple-negative breast cancer. Front Genet. 2021;12:1–10.
Chen X, Feng L, Huang Y, Wu Y, et al. Mechanisms and strategies to overcome PD-1/PD-L1 blockade resistance in triple-negative breast cancer. Front Immunol. 2022;13:1–12.
Khanfir A, Lahiani F, Bouzguenda R, Ayedi I, Daoud J, Frikha M. Prognostic factors and survival in metastatic breast cancer: a single institution experience. Rep Pract Oncol Radiother. 2013;18(3):127–32. https://doi.org/10.1016/j.rpor.2013.01.001.
Li R, Li Y, Wang H, Qin T, Yin X, Ma X. Therapeutic progress and challenges for triple-negative breast cancer. Signal Transduct Target Ther. 2022;7:8.
Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T, et al. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell. 2018;173(4):879–93.e13. https://doi.org/10.1016/j.cell.2018.03.041.
Papadimitriou M, Liakouli Z, Papadimitriou CA. The role of immune checkpoint inhibitors in triple-negative breast cancer: recent developments and future perspectives. J Cancer Metastasis Treat. 2021;7:63. https://doi.org/10.20517/2394-4722.2021.127.
Emens LA. Breast cancer immunotherapy: facts and hopes. Clin Cancer Res. 2018;24(3):511–20. https://doi.org/10.1158/1078-0432.CCR-16-3001.
Alkaabi D, Arafat K, Sulaiman S, Al-Azawi AM, Attoub S. PD-1 independent role of PD-L1 in triple-negative breast cancer progression. Int J Mol Sci. 2023;24(7):6420. https://doi.org/10.3390/ijms24076420.
Tung N, Garber JE, Hacker MR, Torous V, et al. Prevalence and predictors of androgen receptor and programmed death-ligand 1 in BRCA1-associated and sporadic triple-negative breast cancer. Breast Cancer Res Treat. 2016;160(2):253–62.
Yu Y, Jin X, Zhu X, Xu Y, Si W, Zhao J. PD-1/PD-L1 immune checkpoint inhibitors in metastatic triple-negative breast cancer: a systematic review and meta-analysis. Front Immunol. 2023;14:1206689. https://doi.org/10.3389/fimmu.2023.1206689.
Xiong N, Wu H, Yu Z. Advancements and challenges in triple-negative breast cancer: a comprehensive review of therapeutic and diagnostic strategies. Front Oncol. 2024;14:1405491. https://doi.org/10.3389/fonc.2024.1405491.
Li H, Chang Y, Jin T, Zhang M. Progress of PD-1/PD-L1 immune checkpoint inhibitors in the treatment of triple-negative breast cancer. Cancer Cell Int. 2025;25:139. https://doi.org/10.1186/s12935-025-03769-z.
Lin X, Kang K, Chen P, Zeng Z, Li G, Xiong W, et al. Regulatory mechanisms of PD-1/PD-L1 in cancers. Mol Cancer. 2024;23:108. https://doi.org/10.1186/s12943-024-02023-w.
Papakyriacou I, Kutkaite G, Rúbies Bedós M, Nagarajan D, et al. Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer. Nat Commun. 2024;15:1–12.
Zheng Y, Li S, Tang H, Meng X, Zheng Q. Molecular mechanisms of immunotherapy resistance in triple-negative breast cancer. Front Immunol. 2023;14:1153990. https://doi.org/10.3389/fimmu.2023.1153990.
Chariou PL, Minnar CM, Tandon M, Guest MR, et al. Generation of murine tumor models refractory to αPD-1/-L1 therapies due to defects in antigen processing/presentation or IFNγ signaling using CRISPR/Cas9. PLoS One. 2024;19(3):e0287733. https://doi.org/10.1371/journal.pone.0287733.
Lehmann BD, Abramson VG, Dees EC, Shah PD, Ballinger TJ, Isaacs C, et al. Atezolizumab in combination with carboplatin and survival outcomes in patients with metastatic triple-negative breast cancer: The TBCRC 043 phase 2 randomized clinical trial. JAMA Oncol. 2023;10(2):193–201. https://doi.org/10.1001/jamaoncol.2023.5424.
Lin X, Kang K, Chen P, Zeng Z, Li G, Xiong W, et al. Regulatory mechanisms of PD-1/PD-L1 in cancers. Mol Cancer. 2024;23:108. https://doi.org/10.1186/s12943-024-02023-w.
Dai X, Gao Y, Wei W. Post-translational regulations of PD-L1/PD-1: mechanisms and opportunities for combined immunotherapy. Semin Cancer Biol. 2021;85:246–52. https://doi.org/10.1016/j.semcancer.2021.04.002.
Pilon-Thomas S, Mackay A, Vohra N, Mulé JJ. Blockade of PD-L1 enhances the therapeutic efficacy of combination immunotherapy against melanoma. J Immunol. 2010;184(7):3442–9. https://doi.org/10.4049/jimmunol.0904114.
Zhang F, Wang SS. Narrative review on advancing breast cancer treatment: harnessing the power of PD-1/PD-L1 inhibitors for improved patient outcomes. Front Oncol. 2023;13:1–12.
Guo Y, Wang Z, Zhou H, Pan H, Han W, Deng Y, et al. First-in-human study of GFH018, a small molecule inhibitor of transforming growth factor-β receptor I, in patients with advanced solid tumors. BMC Cancer. 2024;24:444. https://doi.org/10.1186/s12885-024-12121-4.
Dong E, Yue XZ, Shui L, Liu BR, Li QQ, Yang Y, et al. IFN-γ surmounts PD-L1/PD-1 inhibition to CAR-T cell therapy by upregulating ICAM-1 on tumor cells. Signal Transduct Target Ther. 2021;6:20. https://doi.org/10.1038/s41392-020-00452-5.
Annunziato S, Kas SM, Nethe M, Yücel H, Del Bravo J, Pritchard C, et al. Modeling invasive lobular breast carcinoma by CRISPR/Cas9-mediated somatic genome editing of the mammary gland. Genes Dev. 2016;30(12):1470–80. https://doi.org/10.1101/gad.279190.116.
Chow RD, Chen S. Cancer CRISPR screens in vivo. Trends Cancer. 2018;4(5):349–58. https://doi.org/10.1016/j.trecan.2018.03.002.
Rosenblum D, Gutkin A, Kedmi R, Ramishetti S, Veiga N, Jacobi AM, et al. CRISPR-Cas9 genome editing using targeted lipid nanoparticles for cancer therapy. Sci Adv. 2020;6(47):eabc9450. https://doi.org/10.1126/sciadv.abc9450.
Wang Y, Shelton SE, Kastrunes G, Barbie DA, Freeman GJ, Marasco WA. Preclinical models for development of immune-oncology therapies. Immuno-Oncol Insights. 2022;3(8):379–98. https://doi.org/10.18609/ioi.2022.41.
Allison KH, Hammond MEH, Dowsett M, McKernin SE, Carey LA, Fitzgibbons PL, et al. Estrogen and progesterone receptor testing in breast cancer: ASCO/CAP guideline update. J Clin Oncol. 2020;38(12):1346–66. https://doi.org/10.1200/JCO.19.02309.
Sreevalsan S, Döring M, Paszkowski-Rogacz M, Brux M, et al. MLLT6 maintains PD-L1 expression and mediates tumor immune resistance. EMBO Rep. 2020;21(12):e51397. https://doi.org/10.15252/embr.202051397.
Wei SC, Duffy CR, Allison JP. Fundamental mechanisms of immune checkpoint blockade therapy. Cancer Discov. 2018;8(9):1069–86. https://doi.org/10.1158/2159-8290.CD-18-0367.
Zhao Z, Shi L, Zhang W, Han J, Zhang S, Fu Z, et al. CRISPR knockout of programmed cell death protein 1 enhances anti-tumor activity of cytotoxic T lymphocytes. Oncotarget. 2017;9(4):5208–15. https://doi.org/10.18632/oncotarget.23730.
Zhang B. CRISPR/Cas9: a robust genome-editing tool with versatile functions and endless application. Int J Mol Sci. 2020;21(14):5111. https://doi.org/10.3390/ijms21145111.
Chen S, Sun H, Miao K, Deng CX. CRISPR-Cas9: from genome editing to cancer research. Int J Biol Sci. 2016;12(12):1427–36. https://doi.org/10.7150/ijbs.17421.
Lu Y, Xue J, Deng T, Zhou X, Yu K, Huang M, et al. A phase I trial of PD-1 deficient engineered T cells with CRISPR/Cas9 in patients with advanced non-small cell lung cancer. J Clin Oncol. 2018;36(15_suppl):3050. https://doi.org/10.1200/JCO.2018.36.15_suppl.3050.
Le Naour A, Rossary A, Vasson MP. EO771: is it a well-characterized cell line for mouse mammary cancer model? Limit and uncertainty. Cancer Med. 2020;9(21):8074–85. https://doi.org/10.1002/cam4.3295.
Karn T. High-throughput gene expression and mutation profiling: current methods and future perspectives. Breast Care (Basel). 2013;8(6):401–6. https://doi.org/10.1159/000357461.
He C, Han S, Chang Y, Wu M, Zhao Y, Chen C, et al. CRISPR screen in cancer: status quo and future perspectives. Am J Cancer Res. 2021;11(4):1031–50.
Laurent M, Geoffroy M, Pavani G, Guiraud S. CRISPR-based gene therapies: from preclinical to clinical treatments. Cells. 2024;13(10):800. https://doi.org/10.3390/cells13100800.
Mout R, Ray M, Lee YW, Scaletti F, Rotello VM. In vivo delivery of CRISPR/Cas9 for therapeutic gene editing: progress and challenges. Bioconjug Chem. 2017;28(4):880–4. https://doi.org/10.1021/acs.bioconjchem.7b00057.
Davidson AR, Lu WT, Stanley SY, Wang J, Mejdani M, Trost CN, et al. Anti-CRISPRs: protein inhibitors of CRISPR-Cas systems. Annu Rev Biochem. 2020;89:309–32. https://doi.org/10.1146/annurev-biochem-011420-111224.
Zheng Y, Li S, Tang H, Meng X, Zheng Q. Molecular mechanisms of immunotherapy resistance in triple-negative breast cancer. Front Immunol. 2023;14:1153990. https://doi.org/10.3389/fimmu.2023.1153990.
Flörcken A, Kopp J, van Lessen A, Movassaghi K, Takvorian A, Jöhrens K, et al. Allogeneic partially HLA-matched dendritic cells pulsed with autologous tumor cell lysate as a vaccine in metastatic renal cell cancer: a clinical phase I/II study. Hum Vaccin Immunother. 2013;9(6):1217–27. https://doi.org/10.4161/hv.24149.
