Deciphering Treatment Resistance in NSCLC with Single-Cell Sequencing Technology

Main Article Content

Na Li

Keywords

single-cell RNA sequencing, tumor heterogeneity, drug resistance, tumor microenvironment, NSCLC

Abstract

Acquired resistance to targeted and immune therapies severely limits the success of non-small cell lung cancer (NSCLC) treatment. Single-cell sequencing technologies now empower researchers to dissect this resistance at unprecedented resolution, moving beyond the averaging limitations of bulk genomics. This review highlights how single-cell and spatial multiomics approaches reveal key mechanisms of NSCLC resistance, from rare drug-tolerant subpopulations and cellular plasticity to immunosuppressive niches and metabolic adaptation within the TME. We also discuss emerging strategies-such as liquid biopsy and AI-driven data integration-that hold promise for translating these insights into more effective therapeutic interventions.

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References

  • [1] Sung, H., Ferlay, J., Siegel, R. L., Laversanne, M., Soerjomataram, I., Jemal, A. and Bray, F. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA: A Cancer Journal for Clinicians. 2021, 71(3), pp. 209-249. https://doi.org/https://doi.org/10.3322/caac.21660.
  • [2] Soria, J.-C., Ohe, Y., Vansteenkiste, J., Reungwetwattana, T., Chewaskulyong, B., Lee, K. H., Dechaphunkul, A., Imamura, F., Nogami, N. and Kurata, T. Osimertinib in untreated EGFR-mutated advanced non–small-cell lung cancer. New England Journal of Medicine. 2018, 378(2), pp. 113-125. https://doi.org/10.1056/NEJMoa1713137.
  • [3] Brahmer, J. R., Lee, J.-S., Ciuleanu, T.-E., Bernabe Caro, R., Nishio, M., Urban, L., Audigier-Valette, C., Lupinacci, L., Sangha, R. and Pluzanski, A. Five-year survival outcomes with nivolumab plus ipilimumab versus chemotherapy as first-line treatment for metastatic non–small-cell lung cancer in CheckMate 227. Journal of Clinical Oncology. 2023, 41(6), pp. 1200-1212. https://doi.org/10.1200/JCO.22.01503.
  • [4] Maynard, A., McCoach, C. E., Rotow, J. K., Harris, L., Haderk, F., Kerr, D. L., Yu, E. A., Schenk, E. L., Tan, W., Zee, A., et al. Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing. Cell. 2020, 182(5), pp. 1232-1251.e22. https://doi.org/10.1016/j.cell.2020.07.017.
  • [5] Stuart, T. and Satija, R. Integrative single-cell analysis-ProQuest. Available from: https://wvpn.ahu.edu.cn/https/77726476706e69737468656265737421e7e056d2372267416b0d9ab8d6562c38/docview/2210427092?pq-origsite=wos&accountid=31106&sourcetype=Scholarly%20Journals (accessed 8 January 2026).
  • [6] Hu, J., Chen, Z., Bao, L., Zhou, L., Hou, Y., Liu, L., Xiong, M., Zhang, Y., Wang, B. and Tao, Z. Single-cell transcriptome analysis reveals intratumoral heterogeneity in ccRCC, which results in different clinical outcomes. Molecular Therapy. 2020, 28(7), pp. 1658-1672. https://doi.org/10.1016/j.ymthe.2020.04.023.
  • [7] Kim, N., Kim, H. K., Lee, K., Hong, Y., Cho, J. H., Choi, J. W., Lee, J.-I., Suh, Y.-L., Ku, B. M. and Eum, H. H. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nature communications. 2020, 11(1), p. 2285. https://doi.org/10.1038/s41467-020-16164-1.
  • [8] Kolodziejczyk, A. A., Kim, J. K., Svensson, V., Marioni, J. C. and Teichmann, S. A. The technology and biology of single-cell RNA sequencing. Molecular cell. 2015, 58(4), pp. 610-620. https://doi.org/10.1016/j.molcel.2015.04.005.
  • [9] Kashima, Y., Shibahara, D., Suzuki, A., Muto, K., Kobayashi, I. S., Plotnick, D., Udagawa, H., Izumi, H., Shibata, Y. and Tanaka, K. Single-cell analyses reveal diverse mechanisms of resistance to EGFR tyrosine kinase inhibitors in lung cancer. Cancer research. 2021, 81(18), pp. 4835-4848. https://doi.org/10.1158/0008-5472.CAN-20-2811.
  • [10] Gu, C., Liu, S., Wu, Q., Zhang, L. and Guo, F. Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes. Cell research. 2019, 29(2), pp. 110-123. https://doi.org/10.1038/s41422-018-0125-4.
  • [11] Sathe, A., Grimes, S. M., Lau, B. T., Chen, J., Suarez, C., Huang, R. J., Poultsides, G. and Ji, H. P. Single-cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment. Clinical Cancer Research. 2020, 26(11), pp. 2640-2653. https://doi.org/10.1158/1078-0432.CCR-19-3231.
  • [12] Ji, A. L., Rubin, A. J., Thrane, K., Jiang, S., Reynolds, D. L., Meyers, R. M., Guo, M. G., George, B. M., Mollbrink, A. and Bergenstråhle, J. Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma. cell. 2020, 182(2), pp. 497-514. e22. https://doi.org/10.1016/j.cell.2020.05.039.
  • [13] Lomakin, A., Svedlund, J., Strell, C., Gataric, M., Shmatko, A., Rukhovich, G., Park, J. S., Ju, Y. S., Dentro, S. and Kleshchevnikov, V. Spatial genomics maps the structure, nature and evolution of cancer clones. Nature. 2022, 611(7936), pp. 594-602. https://doi.org/10.1038/s41586-022-05425-2.
  • [14] Haque, A., Engel, J., Teichmann, S. A. and Lönnberg, T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome medicine. 2017, 9(1), p. 75. https://doi.org/10.1186/s13073-017-0467-4.
  • [15] Liang, J., Cai, W. and Sun, Z. Single-cell sequencing technologies: current and future. Journal of Genetics and Genomics. 2014, 41(10), pp. 513-528. https://doi.org/10.1016/j.jgg.2014.09.005.
  • [16] Azizi, E., Carr, A. J., Plitas, G., Cornish, A. E., Konopacki, C., Prabhakaran, S., Nainys, J., Wu, K., Kiseliovas, V. and Setty, M. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell. 2018, 174(5), pp. 1293-1308. e36. https://doi.org/16.10.1016/j.cell.2018.05.060.
  • [17] Jackson, H. W., Fischer, J. R., Zanotelli, V. R., Ali, H. R., Mechera, R., Soysal, S. D., Moch, H., Muenst, S., Varga, Z. and Weber, W. P. The single-cell pathology landscape of breast cancer. Nature. 2020, 578(7796), pp. 615-620. https://doi.org/10.1038/s41586-019-1876-x.
  • [18] Li, J. J., Tsang, J. Y. and Tse, G. M. Tumor microenvironment in breast cancer-updates on therapeutic implications and pathologic assessment. Cancers. 2021, 13(16), p. 4233. https://doi.org/10.3390/cancers13164233.
  • [19] Müller, S., Cho, A., Liu, S. J., Lim, D. A. and Diaz, A. CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones. Bioinformatics. 2018, 34(18), pp. 3217-3219. https://doi.org/10.1093/bioinformatics/bty316.
  • [20] Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P. and Aerts, J. SCENIC: single-cell regulatory network inference and clustering. Nature methods. 2017, 14(11), pp. 1083-1086. https://doi.org/10.1038/nmeth.4463.
  • [21] Wu, S. Z., Roden, D. L., Wang, C., Holliday, H., Harvey, K., Cazet, A. S., Murphy, K. J., Pereira, B., Al‐Eryani, G. and Bartonicek, N. Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer. The EMBO journal. 2020, 39(19), p. e104063. https://doi.org/10.15252/embj.2019104063.
  • [22] Barker, H. E., Paget, J. T., Khan, A. A. and Harrington, K. J. The tumour microenvironment after radiotherapy: mechanisms of resistance and recurrence. Nature Reviews Cancer. 2015, 15(7), pp. 409-425. https://doi.org/10.1038/nrc3958.
  • [23] Park, Y. H., Lal, S., Lee, J. E., Choi, Y.-L., Wen, J., Ram, S., Ding, Y., Lee, S.-H., Powell, E. and Lee, S. K. Chemotherapy induces dynamic immune responses in breast cancers that impact treatment outcome. Nature communications. 2020, 11(1), p. 6175. https://doi.org/10.1038/s41467-020-19933-0.

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