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Acquired resistance in cancer: towards targeted therapeutic strategies

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Abstract

Development of acquired therapeutic resistance limits the efficacy of cancer treatments and accounts for therapeutic failure in most patients. How resistance arises, varies across cancer types and differs depending on therapeutic modalities is incompletely understood. Novel strategies that address and overcome the various and complex resistance mechanisms necessitate a deep understanding of the underlying dynamics. We are at a crucial time when innovative technologies applied to patient-relevant tumour models have the potential to bridge the gap between fundamental research into mechanisms and timing of acquired resistance and clinical applications that translate these findings into actionable strategies to extend therapy efficacy. Unprecedented spatial and time-resolved high-throughput platforms generate vast amounts of data, from which increasingly complex information can be extracted and analysed through artificial intelligence and machine learning-based approaches. This Roadmap outlines key mechanisms that underlie the acquisition of therapeutic resistance in cancer and explores diverse modelling strategies. Clinically relevant, tractable models of disease and biomarker-driven precision approaches are poised to transform the landscape of acquired therapy resistance in cancer and its clinical management. Here, we propose an integrated strategy that leverages next-generation technologies to dissect the complexities of therapy resistance, shifting the paradigm from reactive management to predictive and proactive prevention.

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Fig. 1: Genetic and phenotypic heterogeneity in tumours drives the development of acquired resistance.
Fig. 2: Acquired resistance mechanisms arising from dynamic evolutionary processes under different therapeutic strategies.
Fig. 3: A dynamic framework for intercepting and rationally targeting acquired therapy resistance in cancer.

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Change history

  • 13 June 2025

    In the version of the article initially published, the Fig. 1 legend inadvertently omitted to state that the figure is adapted from Laisné, M., Lupien, M. & Vallot, C. Epigenomic heterogeneity as a source of tumour evolution. Nat. Rev. Cancer 25, 7–26 (2025). This has now been corrected in the HTML and PDF versions of the article.

References

  1. Siegel, R. L., Giaquinto, A. N. & Jemal, A. Cancer statistics, 2024. CA Cancer J. Clin. 74, 12–49 (2024).

    PubMed  Google Scholar 

  2. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).

    Article  Google Scholar 

  5. Klein, C. A. Selection and adaptation during metastatic cancer progression. Nature 501, 365–372 (2013).

    Article  CAS  PubMed  Google Scholar 

  6. Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239–2254.e39 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bhandari, V. et al. Molecular landmarks of tumor hypoxia across cancer types. Nat. Genet. 51, 308–318 (2019).

    Article  CAS  PubMed  Google Scholar 

  8. Bhandari, V., Li, C. H., Bristow, R. G. & Boutros, P. C. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat. Commun. 11, 737 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. De Palma, M., Biziato, D. & Petrova, T. V. Microenvironmental regulation of tumour angiogenesis. Nat. Rev. Cancer 17, 457–474 (2017).

    Article  PubMed  Google Scholar 

  10. Olive, K. P. et al. Inhibition of Hedgehog signaling enhances delivery of chemotherapy in a mouse model of pancreatic cancer. Science 324, 1457–1461 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Emert, B. L. et al. Variability within rare cell states enables multiple paths toward drug resistance. Nat. Biotechnol. 39, 865–876 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Taplin, M. E. et al. Mutation of the androgen-receptor gene in metastatic androgen-independent prostate cancer. N. Engl. J. Med. 332, 1393–1398 (1995).

    Article  CAS  PubMed  Google Scholar 

  13. Cahill, D. P. et al. Mutations of mitotic checkpoint genes in human cancers. Nature 392, 300–303 (1998).

    Article  CAS  PubMed  Google Scholar 

  14. Watanabe, T. et al. Molecular predictors of survival after adjuvant chemotherapy for colon cancer. N. Engl. J. Med. 344, 1196–1206 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Robey, R. W. et al. Revisiting the role of ABC transporters in multidrug-resistant cancer. Nat. Rev. Cancer 18, 452–464 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Dhanyamraju, P. K., Schell, T. D., Amin, S. & Robertson, G. P. Drug-tolerant persister cells in cancer therapy resistance. Cancer Res. 82, 2503–2514 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Morin, P. J. Drug resistance and the microenvironment: nature and nurture. Drug Resist. Updat. 6, 169–172 (2003).

    Article  CAS  PubMed  Google Scholar 

  18. Winkler, J., Abisoye-Ogunniyan, A., Metcalf, K. J. & Werb, Z. Concepts of extracellular matrix remodelling in tumour progression and metastasis. Nat. Commun. 11, 5120 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Almeida, F. V., Douglass, S. M., Fane, M. E. & Weeraratna, A. T. Bad company: microenvironmentally mediated resistance to targeted therapy in melanoma. Pigment Cell Melanoma Res. 32, 237–247 (2019).

    Article  PubMed  Google Scholar 

  20. National Cancer Institute. Cancer Moonshot Blue Ribbon Panel Report 2016 https://www.cancer.gov/research/key-initiatives/moonshot-cancer-initiative/history/blue-ribbon-panel-report-2016.pdf (2025).

  21. West, J. et al. Towards Multidrug Adaptive Therapy. Cancer Res. 80, 1578–1589 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Marine, J.-C., Dawson, S.-J. & Dawson, M. A. Non-genetic mechanisms of therapeutic resistance in cancer. Nat. Rev. Cancer 20, 743–756 (2020).

    Article  CAS  PubMed  Google Scholar 

  23. Whiting, F. J. H., Househam, J., Baker, A. M., Sottoriva, A. & Graham, T. A. Phenotypic noise and plasticity in cancer evolution. Trends Cell Biology. 34, 451–464 (2024).

    Article  CAS  Google Scholar 

  24. Terekhanova, N. V. et al. Epigenetic regulation during cancer transitions across 11 tumour types. Nature 623, 432–441 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Hagenbeek, T. J. et al. An allosteric pan-TEAD inhibitor blocks oncogenic YAP/TAZ signaling and overcomes KRAS G12C inhibitor resistance. Nat. Cancer 4, 812–828 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zhang, Y. et al. Metabolic switch regulates lineage plasticity and induces synthetic lethality in triple-negative breast cancer. Cell Metab. 36, 193–208.e8 (2024).

    Article  CAS  PubMed  Google Scholar 

  27. Hu, Q. et al. Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nat. Immunol. 20, 835–851 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Sharma, S. V. et al. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 141, 69–80 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Wang, H. et al. Antiandrogen treatment induces stromal cell reprogramming to promote castration resistance in prostate cancer. Cancer Cell 41, 1345–1362.e9 (2023).

    Article  CAS  PubMed  Google Scholar 

  30. Denmeade, S. R. et al. TRANSFORMER: a randomized phase II study comparing bipolar androgen therapy versus enzalutamide in asymptomatic men with castration-resistant metastatic prostate cancer. J. Clin. Oncol. 39, 1371–1382 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sena, L. A. et al. Bipolar androgen therapy sensitizes castration-resistant prostate cancer to subsequent androgen receptor ablative therapy. Eur. J. Cancer 144, 302–309 (2021).

    Article  CAS  PubMed  Google Scholar 

  32. Gao, A. & Guo, M. Epigenetic based synthetic lethal strategies in human cancers. Biomark. Res. 8, 44 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Boudreau, A. et al. Metabolic plasticity underpins innate and acquired resistance to LDHA inhibition. Nat. Chem. Biol. 12, 779–786 (2016).

    Article  CAS  PubMed  Google Scholar 

  34. Stine, Z. E., Schug, Z. T., Salvino, J. M. & Dang, C. V. Targeting cancer metabolism in the era of precision oncology. Nat. Rev. Drug Discov. 21, 141–162 (2022).

    Article  CAS  PubMed  Google Scholar 

  35. Viswanathan, V. S. et al. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature 547, 453–457 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Olou, A. A., King, R. J., Yu, F. & Singh, P. K. MUC1 oncoprotein mitigates ER stress via CDA-mediated reprogramming of pyrimidine metabolism. Oncogene 39, 3381–3395 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Cheung, E. C. & Vousden, K. H. The role of ROS in tumour development and progression. Nat. Rev. Cancer 22, 280–297 (2022).

    Article  CAS  PubMed  Google Scholar 

  38. Osman, A. A. et al. Dysregulation and epigenetic reprogramming of NRF2 signaling axis promote acquisition of cisplatin resistance and metastasis in head and neck squamous cell carcinoma. Clin. Cancer Res. 29, 1344–1359 (2023). This study identifies that acquired cisplatin resistance in head and neck squamous cell carcinoma is driven by dysregulation of the KEAP1–NRF2 signalling axis, where epigenetic reprogramming and mutations in KEAP1 lead to enhanced NRF2 activation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Yu, W. et al. Evolution of cisplatin resistance through coordinated metabolic reprogramming of the cellular reductive state. Br. J. Cancer 128, 2013–2024 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Tadros, S. et al. De novo lipid synthesis facilitates gemcitabine resistance through endoplasmic reticulum stress in pancreatic cancer. Cancer Res. 77, 5503–5517 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Shukla, S. K. et al. MUC1 and HIF-1alpha signaling crosstalk induces anabolic glucose metabolism to impart gemcitabine resistance to pancreatic cancer. Cancer Cell 32, 392 (2017).

    Article  CAS  PubMed  Google Scholar 

  42. Mullen, N. J. & Singh, P. K. Nucleotide metabolism: a pan-cancer metabolic dependency. Nat. Rev. Cancer 23, 275–294 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Murthy, D. et al. Cancer-associated fibroblast-derived acetate promotes pancreatic cancer development by altering polyamine metabolism via the ACSS2-SP1-SAT1 axis. Nat. Cell Biol. 26, 613–627 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Murthy, D. et al. The MUC1-HIF-1α signaling axis regulates pancreatic cancer pathogenesis through polyamine metabolism remodeling. Proc. Natl Acad. Sci. USA 121, e2315509121 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. King, R. J. et al. CD73 induces GM-CSF/MDSC-mediated suppression of T cells to accelerate pancreatic cancer pathogenesis. Oncogene 41, 971–982 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. He, C. et al. Vitamin B6 competition in the tumor microenvironment hampers antitumor functions of NK cells. Cancer Discov. 14, 176–193 (2024).

    Article  CAS  PubMed  Google Scholar 

  47. Mehta, A. & Stanger, B. Z. Lineage plasticity: the new cancer hallmark on the block Cancer Res. 84, 184–191 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Beltran, H. et al. The role of lineage plasticity in prostate cancer therapy resistance. Clin. Cancer Res. 25, 6916–6924 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Cannell, I. G. et al. FOXC2 promotes vasculogenic mimicry and resistance to anti-angiogenic therapy. Cell Rep. 42, 112791 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. He, J. et al. Drug tolerant persister cell plasticity in cancer: a revolutionary strategy for more effective anticancer therapies. Signal Transduct. Target. Ther. 9, 209 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Mancini, C., Lori, G., Pranzini, E. & Taddei, M. L. Metabolic challengers selecting tumor-persistent cells. Trends Endocrinol. Metab. 35, 263–276 (2024).

    Article  CAS  PubMed  Google Scholar 

  52. Russo, M. et al. Cancer drug-tolerant persister cells: from biological questions to clinical opportunities. Nat. Rev. Cancer 24, 694–717 (2024).

    Article  CAS  PubMed  Google Scholar 

  53. Marsolier, J. et al. H3K27me3 conditions chemotolerance in triple-negative breast cancer. Nat. Genet. 54, 459–468 (2022). By identifying how chromatin landscapes influence drug-resistant persister cells in triple-negative breast cancer, this study highlights H3K27me3 as a therapeutic target to delay acquired resistance and tumour recurrence.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. França, G. S. et al. Cellular adaptation to cancer therapy along a resistance continuum. Nature 631, 876–883 (2024). This study introduces the concept of resistance continuum, whereby cancer cells undergo multiple state transitions encompassing mutational, epigenetic and transcriptional changes.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Guler, G. D. et al. Repression of stress-Induced LINE-1 expression protects cancer cell subpopulations from lethal drug exposure. Cancer Cell 32, 221–237.e13 (2017).

    Article  CAS  PubMed  Google Scholar 

  56. National Comprehensive Cancer Network. Treatment by cancer type. nccn.org https://www.nccn.org/guidelines/category_1 (2025).

  57. Vasan, N., Baselga, J. & Hyman, D. M. A view on drug resistance in cancer. Nature 575, 299–309 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Misale, S. et al. Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature 486, 532–536 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. André Fabrice, et al. Alpelisib for PIK3CA-mutated, hormone receptor–positive advanced breast cancer. N. Engl. J. Med. 380, 1929–1940 (2019).

    Article  PubMed  Google Scholar 

  60. Braun, T. P., Eide, C. A. & Druker, B. J. Response and resistance to BCR-ABL1-targeted therapies. Cancer Cell 37, 530–542 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Matulonis, U. A. et al. Ovarian cancer. Nat. Rev. Dis. Prim. 2, 16061 (2016).

    Article  PubMed  Google Scholar 

  62. Christie, E. L. & Bowtell, D. D. L. Acquired chemotherapy resistance in ovarian cancer. Ann. Oncol. 28, viii13–viii15 (2017).

    Article  CAS  PubMed  Google Scholar 

  63. Osman, A. A. et al. Evolutionary action score of TP53 coding variants is predictive of platinum response in head and neck cancer patients. Cancer Res. 75, 1205–1215 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Pal Choudhuri, S. et al. Acquired cross-resistance in small cell lung cancer due to extrachromosomal DNA amplification of MYC paralogs. Cancer Discov. 14, 804–827 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  65. Prasanna, P. G. et al. Therapy-induced senescence: opportunities to improve anticancer therapy. J. Natl Cancer Inst. 113, 1285–1298 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Schmitt, C. A., Wang, B. & Demaria, M. Senescence and cancer — role and therapeutic opportunities. Nat. Rev. Clin. Oncol. 19, 619–636 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  67. Vander Velde, R. et al. Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures. Nat. Commun. 11, 2393 (2020).

    Article  Google Scholar 

  68. O’Dwyer, P. J. et al. The NCI-MATCH trial: lessons for precision oncology. Nat. Med. 29, 1349–1357 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  69. Sicklick, J. K. et al. Molecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study. Nat. Med. 25, 744–750 (2019). The I-PREDICT study demonstrates that personalized, multi-drug regimens based on molecular profiling can improve disease control in patients with advanced cancers, highlighting the potential for personalized combination therapies over single-agent approaches.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Flaherty, K. T. et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N. Engl. J. Med. 363, 809–819 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Tyner, J. W. et al. Understanding drug sensitivity and tackling resistance in cancer. Cancer Res. 82, 1448–1460 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Chapman, P. B. et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N. Engl. J. Med. 364, 2507–2516 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Gouda, M. A. & Subbiah, V. Precision oncology for BRAF-mutant cancers with BRAF and MEK inhibitors: from melanoma to tissue-agnostic therapy. ESMO Open 8, 100788 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Hanrahan, A. J., Chen, Z., Rosen, N. & Solit, D. B. BRAF - a tumour-agnostic drug target with lineage-specific dependencies. Nat. Rev. Clin. Oncol. 21, 224–247 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Knudsen, E. S., Witkiewicz, A. K. & Rubin, S. M. Cancer takes many paths through G1/S. Trends Cell Biol. 34, 636–645 (2024).

    Article  CAS  PubMed  Google Scholar 

  76. Gerosa, R. et al. Cyclin-dependent kinase 2 (CDK2) inhibitors and others novel CDK inhibitors (CDKi) in breast cancer: clinical trials, current impact, and future directions. Crit. Rev. Oncol. Hematol. 196, 104324 (2024).

    Article  PubMed  Google Scholar 

  77. Kollmann, K. et al. A kinase-independent function of CDK6 links the cell cycle to tumor angiogenesis. Cancer Cell 24, 167–181 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Singhal, A., Li, B. T. & O’Reilly, E. M. Targeting KRAS in cancer. Nat. Med. 30, 969–983 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Awad, M. M. et al. Acquired resistance to KRAS(G12C) inhibition in cancer. N. Engl. J. Med. 384, 2382–2393 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Schoenfeld, A. J. & Hellmann, M. D. Acquired resistance to immune checkpoint inhibitors. Cancer Cell 37, 443–455 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Zaretsky, J. M. et al. Mutations associated with acquired resistance to PD-1 blockade in melanoma. N. Engl. J. Med. 375, 819–829 (2016). This study shows that acquired resistance to PD1 blockade in melanoma is driven by mutations affecting interferon-receptor signalling (JAK1 and JAK2) and antigen presentation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Chowell, D. et al. Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science 359, 582–587 (2018).

    Article  CAS  PubMed  Google Scholar 

  83. Sade-Feldman, M. et al. Resistance to checkpoint blockade therapy through inactivation of antigen presentation. Nat. Commun. 8, 1136 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  84. Sharma, P., Hu-Lieskovan, S., Wargo, J. A. & Ribas, A. Primary, adaptive and acquired resistance to cancer immunotherapy. Cell 168, 707–723 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Gao, J. et al. Loss of IFN-γ pathway genes in tumor cells as a mechanism of resistance to anti-CTLA-4 therapy. Cell 167, 397–404.e9 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Shin, D. S. et al. Primary resistance to PD-1 blockade mediated by JAK1/2 mutations. Cancer Discov. 7, 188–201 (2017).

    Article  CAS  PubMed  Google Scholar 

  87. Pulanco, M. C., Madsen, A. T., Tanwar, A., Corrigan, D. T. & Zang, X. Recent advancements in the B7/CD28 immune checkpoint families: new biology and clinical therapeutic strategies. Cell Mol. Immunol. 20, 694–713 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Hugo, W. et al. Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma. Cell 168, 542 (2017).

    Article  CAS  PubMed  Google Scholar 

  89. Lee, J. H. et al. Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition. Nat. Commun. 11, 1897 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Wang, L. et al. EMT- and stroma-related gene expression and resistance to PD-1 blockade in urothelial cancer. Nat. Commun. 9, 3503 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  91. O’Hare, T. et al. AP24534, a pan-BCR-ABL inhibitor for chronic myeloid leukemia, potently inhibits the T315I mutant and overcomes mutation-based resistance. Cancer Cell 16, 401–412 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  92. Khorashad, J. S. et al. BCR-ABL1 compound mutations in tyrosine kinase inhibitor-resistant CML: frequency and clonal relationships. Blood 121, 489–498 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Joshi, S. K. et al. The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance. Cancer Cell 39, 999–1014.e8 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Intlekofer, A. M. et al. Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations. Nature 559, 125–129 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Perner, F. et al. MEN1 mutations mediate clinical resistance to menin inhibition. Nature 615, 913–919 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Furman, R. R. et al. Ibrutinib resistance in chronic lymphocytic leukemia. N. Engl. J. Med. 370, 2352–2354 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Blombery, P. et al. Acquisition of the recurrent Gly101Val mutation in BCL2 confers resistance to venetoclax in patients with progressive chronic lymphocytic leukemia. Cancer Discov. 9, 342–353 (2019).

    Article  CAS  PubMed  Google Scholar 

  98. McMahon, C. M. et al. Clonal selection with RAS pathway activation mediates secondary clinical resistance to selective FLT3 inhibition in acute myeloid leukemia. Cancer Discov. 9, 1050–1063 (2019). Emergence of gilteritinib resistance, a FLT3 inhibitor, in FLT3-mutated AML is driven by diverse clonal adaptations and evolution, highlighting the need for combination therapies to overcome complex resistance patterns upon FLT3 kinase inhibition.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Zhang, H. et al. Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms. Nat. Commun. 10, 244 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  100. Woyach, J. A. et al. Resistance mechanisms for the Bruton’s tyrosine kinase inhibitor ibrutinib. N. Engl. J. Med. 370, 2286–2294 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  101. Harding, J. J. et al. Isoform switching as a mechanism of acquired resistance to mutant isocitrate dehydrogenase inhibition. Cancer Discov. 8, 1540–1547 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Bonnet, D. & Dick, J. E. Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat. Med. 3, 730–737 (1997).

    Article  CAS  PubMed  Google Scholar 

  103. Sachs, K. et al. Single-cell gene expression analyses reveal distinct self-renewing and proliferating subsets in the leukemia stem cell compartment in acute myeloid leukemia. Cancer Res. 80, 458–470 (2020).

    Article  CAS  PubMed  Google Scholar 

  104. Hope, K. J., Jin, L. & Dick, J. E. Acute myeloid leukemia originates from a hierarchy of leukemic stem cell classes that differ in self-renewal capacity. Nat. Immunol. 5, 738–743 (2004).

    Article  CAS  PubMed  Google Scholar 

  105. Kuusanmäki, H. et al. Erythroid/megakaryocytic differentiation confers BCL-XL dependency and venetoclax resistance in acute myeloid leukemia. Blood 141, 1610–1625 (2023).

    Article  PubMed  Google Scholar 

  106. Kuusanmäki, H. et al. Phenotype-based drug screening reveals association between venetoclax response and differentiation stage in acute myeloid leukemia. Haematologica 105, 708–720 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  107. Majumder, M. M. et al. Multi-parametric single cell evaluation defines distinct drug responses in healthy hematologic cells that are retained in corresponding malignant cell types. Haematologica 105, 1527–1538 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Pei, S. et al. Monocytic subclones confer resistance to venetoclax-based therapy in patients with acute myeloid leukemia. Cancer Discov. 10, 536–551 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Zhang, H. et al. Integrated analysis of patient samples identifies biomarkers for venetoclax efficacy and combination strategies in acute myeloid leukemia. Nat. Cancer 1, 826–839 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Nuno, K. et al. Convergent epigenetic evolution drives relapse in acute myeloid leukemia. eLife 13, e93019 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Zeng, A. G. X. et al. A cellular hierarchy framework for understanding heterogeneity and predicting drug response in acute myeloid leukemia. Nat. Med. 28, 1212–1223 (2022).

    Article  CAS  PubMed  Google Scholar 

  112. Bottomly, D. et al. Integrative analysis of drug response and clinical outcome in acute myeloid leukemia. Cancer Cell 40, 850–864.e9 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Kopper, O. et al. An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity. Nat. Med. 25, 838–849 (2019).

    Article  CAS  PubMed  Google Scholar 

  114. Vlachogiannis, G. et al. Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science 359, 920–926 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Phan, N. et al. A simple high-throughput approach identifies actionable drug sensitivities in patient-derived tumor organoids. Commun. Biol. 2, 78 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  116. Wang, H.-M. et al. Using patient-derived organoids to predict locally advanced or metastatic lung cancer tumor response: A real-world study. Cell Rep. Med. 4, 100911 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Al Shihabi, A. et al. The landscape of drug sensitivity and resistance in sarcoma. Cell Stem Cell 31, 1524–1542.e4 (2024). This paper demonstrates feasibility of establishing PDOs from serially collected samples of rare cancers and performing large-scale drug screenings within a clinically actionable timeframe.

    Article  CAS  PubMed  Google Scholar 

  118. Zhao, Z. et al. Organoids. Nat. Rev. Methods Prim. 2, 94 (2022).

    Article  CAS  Google Scholar 

  119. Drost, J. & Clevers, H. Organoids in cancer research. Nat. Rev. Cancer 18, 407–418 (2018).

    Article  CAS  PubMed  Google Scholar 

  120. Pine, A. R. et al. Tumor microenvironment is critical for the maintenance of cellular states found in primary glioblastomas. Cancer Discov. 10, 964–979 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Nguyen, H. T. L. et al. A platform for rapid patient-derived cutaneous neurofibroma organoid establishment and screening. Cell Rep. Methods 4, 100772 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Tuveson, D. & Clevers, H. Cancer modeling meets human organoid technology. Science 364, 952–955 (2019).

    Article  CAS  PubMed  Google Scholar 

  123. Öhlund, D. et al. Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer. J. Exp. Med. 214, 579–596 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  124. Langer, E. M. et al. Modeling tumor phenotypes in vitro with three-dimensional bioprinting. Cell Rep. 26, 608–623.e6 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Tebon, P. J. et al. Drug screening at single-organoid resolution via bioprinting and interferometry. Nat. Commun. 14, 3168 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Polak, R., Zhang, E. T. & Kuo, C. J. Cancer organoids 2.0: modelling the complexity of the tumour immune microenvironment. Nat. Rev. Cancer 24, 523–539 (2024).

    Article  CAS  PubMed  Google Scholar 

  127. Zhou, Z. et al. Harnessing 3D in vitro systems to model immune responses to solid tumours: a step towards improving and creating personalized immunotherapies. Nat. Rev. Immunol. 24, 18–32 (2024).

    Article  CAS  PubMed  Google Scholar 

  128. Ding, S. et al. Patient-derived micro-organospheres enable clinical precision oncology. Cell Stem Cell 29, 905–917.e6 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Dekkers, J. F. et al. Uncovering the mode of action of engineered T cells in patient cancer organoids. Nat. Biotechnol. 41, 60–69 (2023).

    Article  CAS  PubMed  Google Scholar 

  130. Alieva, M. et al. BEHAV3D: a 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response. Nat. Protoc. 19, 2052–2084 (2024).

    Article  CAS  PubMed  Google Scholar 

  131. Dekkers, J. F. et al. High-resolution 3D imaging of fixed and cleared organoids. Nat. Protoc. 14, 1756–1771 (2019).

    Article  CAS  PubMed  Google Scholar 

  132. Sufi, J. et al. Multiplexed single-cell analysis of organoid signaling networks. Nat. Protoc. 16, 4897–4918 (2021).

    Article  CAS  PubMed  Google Scholar 

  133. Qin, X. et al. Cell-type-specific signaling networks in heterocellular organoids. Nat. Methods 17, 335–342 (2020). This study presents a multiplexed mass cytometry protocol enabling single-cell analysis of PTMs within organoids co-cultured with stromal cells, illustrating how cellular signalling networks and cell states adapt to therapeutic resistance.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Song, H. et al. Epitranscriptomics and epiproteomics in cancer drug resistance: therapeutic implications. Signal Transduct. Target. Ther. 5, 193 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  135. Steiner, S. et al. Ex vivo modeling of acquired drug resistance in BRAF - mutated pancreatic cancer organoids uncovers individual therapeutic vulnerabilities. Cancer Lett. 584, 216650 (2024).

    Article  CAS  PubMed  Google Scholar 

  136. Tang, M. et al. Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions. Cell Res. 30, 833–853 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Paek, J. et al. Microphysiological engineering of self-assembled and perfusable microvascular beds for the production of vascularized three-dimensional human microtissues. ACS Nano 13, 7627–7643 (2019).

    Article  CAS  PubMed  Google Scholar 

  138. Jing, X. et al. Role of hypoxia in cancer therapy by regulating the tumor microenvironment. Mol. Cancer 18, 157 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  139. Ingber, D. E. Human organs-on-chips for disease modelling, drug development and personalized medicine. Nat. Rev. Genet. 23, 467–491 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/study/NCT06064682 (2025).

  141. US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/study/NCT05890781 (2023).

  142. US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/study/NCT03890614 (2025).

  143. US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/study/NCT06406608 (2024).

  144. Wang, H. et al. Pharmacogenomic profiling of pediatric acute myeloid leukemia to identify therapeutic vulnerabilities and inform functional precision medicine Blood Cancer Discov. 3, 516–535 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Pemovska, T. et al. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov. 3, 1416–1429 (2013). Leveraging clinical specimens, this paper uses a personalized functional testing approach to identify effective regimens and predict disease evolution.

    Article  CAS  PubMed  Google Scholar 

  146. Tognon, C. E., Sears, R. C., Mills, G. B., Gray, J. W. & Tyner, J. W. Ex vivo analysis of primary tumor specimens for evaluation of cancer therapeutics. Annu. Rev. Cancer Biol. 5, 39–57 (2021).

    Article  PubMed  Google Scholar 

  147. Tyner, J. W. et al. Kinase pathway dependence in primary human leukemias determined by rapid inhibitor screening. Cancer Res. 73, 285–296 (2013).

    Article  CAS  PubMed  Google Scholar 

  148. Barbaglio, F. et al. Three-dimensional co-culture model of chronic lymphocytic leukemia bone marrow microenvironment predicts patient-specific response to mobilizing agents. Haematologica 106, 2334–2344 (2021).

    Article  CAS  PubMed  Google Scholar 

  149. Kurtz, S. E. et al. Dual inhibition of JAK1/2 kinases and BCL2: a promising therapeutic strategy for acute myeloid leukemia. Leukemia 32, 2025–2028 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  150. Eide, C. A. et al. Simultaneous kinase inhibition with ibrutinib and BCL2 inhibition with venetoclax offers a therapeutic strategy for acute myeloid leukemia. Leukemia 34, 2342–2353 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Eldfors, S. et al. Monosomy 7/del(7q) cause sensitivity to inhibitors of nicotinamide phosphoribosyltransferase in acute myeloid leukemia. Blood Adv. 8, 1621–1633 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Nechiporuk, T. et al. The TP53 apoptotic network is a primary mediator of resistance to BCL2 inhibition in AML cells. Cancer Discov. 9, 910–925 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Jafari, M. et al. Bipartite network models to design combination therapies in acute myeloid leukaemia. Nat. Commun. 13, 2128 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Mirzaie, M. et al. Designing patient-oriented combination therapies for acute myeloid leukemia based on efficacy/toxicity integration and bipartite network modeling. Oncogenesis 13, 11 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  155. Kytölä, S. et al. Ex vivo venetoclax sensitivity predicts clinical response in acute myeloid leukemia in the prospective VenEx trial. Blood 145, 409–421 (2025).

    Article  PubMed  Google Scholar 

  156. Kuusanmäki, H. et al. Ex vivo venetoclax sensitivity testing predicts treatment response in acute myeloid leukemia. Haematologica 108, 1768–1781 (2023).

    Article  PubMed  Google Scholar 

  157. Bray, L. J. et al. A three-dimensional ex vivo tri-culture model mimics cell-cell interactions between acute myeloid leukemia and the vascular niche. Haematologica 102, 1215–1226 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. de Janon, A., Mantalaris, A. & Panoskaltsis, N. Three-dimensional human bone marrow organoids for the study and application of normal and abnormal hematoimmunopoiesis. J. Immunol. 210, 895–904 (2023).

    Article  PubMed  Google Scholar 

  159. Khan, A. O. et al. Human bone marrow organoids for disease modeling, discovery, and validation of therapeutic targets in hematologic malignancies Cancer Discov. 13, 364–385 (2023).

    Article  CAS  PubMed  Google Scholar 

  160. Olijnik, A. A. et al. Generating human bone marrow organoids for disease modeling and drug discovery. Nat. Protoc. 19, 2117–2146 (2024).

    Article  CAS  PubMed  Google Scholar 

  161. Sommerkamp, P., Mercier, F. E., Wilkinson, A. C., Bonnet, D. & Bourgine, P. E. Engineering human hematopoietic environments through ossicle and bioreactor technologies exploitation. Exp. Hematol. 94, 20–25 (2021).

    Article  CAS  PubMed  Google Scholar 

  162. Bourgine, P. E. et al. In vitro biomimetic engineering of a human hematopoietic niche with functional properties. Proc. Natl Acad. Sci. USA 115, E5688–e5695 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Dozzo, A. et al. Modelling acute myeloid leukemia (AML): What’s new? A transition from the classical to the modern. Drug Deliv. Transl. Res. 13, 2110–2141 (2023).

    Article  PubMed  Google Scholar 

  164. García-García, A. et al. Culturing patient-derived malignant hematopoietic stem cells in engineered and fully humanized 3D niches. Proc. Natl Acad. Sci. USA 118, e2114227118 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  165. Borella, G. et al. Targeting the plasticity of mesenchymal stromal cells to reroute the course of acute myeloid leukemia. Blood 138, 557–570 (2021).

    CAS  PubMed  Google Scholar 

  166. Giallongo, S. et al. Engagement of mesenchymal stromal cells in the remodeling of the bone marrow microenvironment in hematological cancers. Biomolecules 13, 1701 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Barozzi, D. & Scielzo, C. Emerging strategies in 3D culture models for hematological cancers. Hemasphere 7, e932 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Koc, S. et al. PDXNet portal: patient-derived xenograft model, data, workflow and tool discovery. NAR Cancer 4, zcac014 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  169. Liu, Y. et al. Patient-derived xenograft models in cancer therapy: technologies and applications. Signal Transduct. Target. Ther. 8, 160 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  170. Meric-Bernstam, F. et al. Assessment of patient-derived xenograft growth and antitumor activity: the NCI PDXNet consensus recommendations. Mol. Cancer Ther. 23, 924–938 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Guillen, K. P. et al. A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nat. Cancer 3, 232–250 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  172. Knudsen, E. S. et al. Pancreatic cancer cell lines as patient-derived avatars: genetic characterisation and functional utility. Gut 67, 508–520 (2018).

    Article  CAS  PubMed  Google Scholar 

  173. Sun, H. et al. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nat. Commun. 12, 5086 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Yao, Y. et al. Clinical utility of PDX cohorts to reveal biomarkers of intrinsic resistance and clonal architecture changes underlying acquired resistance to cetuximab in HNSCC. Signal Transduct. Target. Ther. 7, 73 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Zanella, E. R., Grassi, E. & Trusolino, L. Towards precision oncology with patient-derived xenografts. Nat. Rev. Clin. Oncol. 19, 719–732 (2022).

    Article  PubMed  Google Scholar 

  176. Kahounová, Z. et al. Circulating tumor cell-derived preclinical models: current status and future perspectives. Cell Death Dis. 14, 530 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  177. Dietrich, C. et al. INX-315, a selective CDK2 inhibitor, induces cell cycle arrest and senescence in solid tumors. Cancer Discov. 14, 446–467 (2024).

    Article  CAS  PubMed  Google Scholar 

  178. Gao, H. et al. High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response. Nat. Med. 21, 1318–1325 (2015).

    Article  CAS  PubMed  Google Scholar 

  179. Knudsen, E. S. et al. Targeting dual signalling pathways in concert with immune checkpoints for the treatment of pancreatic cancer. Gut 70, 127–138 (2021).

    Article  CAS  PubMed  Google Scholar 

  180. Witkiewicz, A. K. et al. Integrated patient-derived models delineate individualized therapeutic vulnerabilities of pancreatic cancer. Cell Rep. 16, 2017–2031 (2016). This study finds that PDX models can recapitulate unique drug sensitivities in pancreatic cancer that cannot be predicted by genetic analysis alone, highlighting the potential of functional drug sensitivity testing to guide individualized therapies.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Chuprin, J. et al. Humanized mouse models for immuno-oncology research. Nat. Rev. Clin. Oncol. 20, 192–206 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  182. Jeon, S. H. et al. Anti-4-1BB×PD-L1 bispecific antibody reinvigorates tumor-specific exhausted CD8+ T cells and enhances the efficacy of anti-PD-1 blockade. Clin. Cancer Res. 30, 4155–4166 (2024).

    Article  CAS  PubMed  Google Scholar 

  183. Knorr, D. A. et al. FcγRIIB Is an immune checkpoint limiting the activity of Treg-targeting antibodies in the tumor microenvironment. Cancer Immunol. Res. 12, 322–333 (2024).

    Article  CAS  PubMed  Google Scholar 

  184. Brentjens, R. J. et al. Eradication of systemic B-cell tumors by genetically targeted human T lymphocytes co-stimulated by CD80 and interleukin-15. Nat. Med. 9, 279–286 (2003).

    Article  CAS  PubMed  Google Scholar 

  185. Kochenderfer, J. N. & Rosenberg, S. A. Treating B-cell cancer with T cells expressing anti-CD19 chimeric antigen receptors. Nat. Rev. Clin. Oncol. 10, 267–276 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Wei, Y. et al. KIR3DL3-HHLA2 is a human immunosuppressive pathway and a therapeutic target. Sci. Immunol. 6, eabf9792 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Ren, X. et al. Blockade of the immunosuppressive KIR2DL5/PVR pathway elicits potent human NK cell-mediated antitumor immunity. J. Clin. Invest. 132, e163620 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Ren, X., Corrigan, D. T. & Zang, X. Protocol for evaluating antitumor activity of KIR3DL3 blockade in an NK cell-based xenogeneic lung tumor model. STAR Protoc. 3, 101818 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/study/NCT05958199 (2025).

  190. Odunsi, A. et al. Fidelity of human ovarian cancer patient-derived xenografts in a partially humanized mouse model for preclinical testing of immunotherapies. J. Immunother. Cancer 8, e001237 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  191. Ashizawa, T. et al. Antitumor effect of programmed death-1 (PD-1) blockade in humanized the NOG-MHC double knockout mouse. Clin. Cancer Res. 23, 149–158 (2017).

    Article  CAS  PubMed  Google Scholar 

  192. Jia, Q., Chu, H., Jin, Z., Long, H. & Zhu, B. High-throughput single-сell sequencing in cancer research. Signal Transduct. Target. Ther. 7, 145 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  193. Tan, Y., Lin, H. & Cheng, J. X. Profiling single cancer cell metabolism via high-content SRS imaging with chemical sparsity. Sci. Adv. 9, eadg6061 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Blakely, C. M. et al. Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers. Nat. Genet. 49, 1693–1704 (2017). This study uncovers the intrinsic and acquired heterogeneity of the gene alteration landscapes in advanced-stage non-small-cell lung cancers.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Cao, L. et al. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell 184, 5031–5052.e26 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Zhang, K. et al. Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer. Sci. Adv. 8, eabm1831 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Kim, C. et al. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell 173, 879–893.e13 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Zaidi, S. et al. Single-cell analysis of treatment-resistant prostate cancer: implications of cell state changes for cell surface antigen–targeted therapies. Proc. Natl Acad. Sci. USA 121, e2322203121 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Maynard, A. et al. Therapy-induced evolution of human lung cancer revealed by single-cell RNA sequencing. Cell 182, 1232–1251.e22 (2020). In this study, the authors apply scRNA-seq to longitudinally collected lung cancer biopsies and identify key transcriptional signatures distinctive of the residual disease and resistant tumours.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Bleijs, M., van de Wetering, M., Clevers, H. & Drost, J. Xenograft and organoid model systems in cancer research. EMBO J. 38, e101654 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  201. Wang, E., Xiang, K., Zhang, Y. & Wang, X.-F. Patient-derived organoids (PDOs) and PDO-derived xenografts (PDOXs): new opportunities in establishing faithful pre-clinical cancer models. J. Natl Cancer Cent. 2, 263–276 (2022).

    PubMed  PubMed Central  Google Scholar 

  202. Zhang, Y. et al. Sample-multiplexing approaches for single-cell sequencing. Cell Mol. Life Sci. 79, 466 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Adil, A., Kumar, V., Jan, A. T. & Asger, M. Single-cell transcriptomics: current methods and challenges in data acquisition and analysis. Front. Neurosci. 15, 591122 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  204. Sinha, S. et al. PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. Nat. Cancer 5, 938–952 (2024). This study develops a machine learning platform based on scRNA-seq data that can help predict acquired resistance to therapy and identifying novel sensitivities.

    Article  PubMed  Google Scholar 

  205. Zhu, Y. et al. Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets. Mol. Cell Proteom. 17, 1864–1874 (2018).

    Article  CAS  Google Scholar 

  206. Espina, V. et al. Laser-capture microdissection. Nat. Protoc. 1, 586–603 (2006).

    Article  CAS  PubMed  Google Scholar 

  207. Ctortecka, C. et al. An automated nanowell-array workflow for quantitative multiplexed single-cell proteomics sample preparation at high sensitivity. Mol. Cell Proteom. 22, 100665 (2023).

    Article  CAS  Google Scholar 

  208. Zhu, Y. et al. Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells. Nat. Commun. 9, 882 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  209. van Galen, P. et al. Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity. Cell 176, 1265–1281.e24 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  210. Eckert, S. et al. Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics. Nat. Biotechnol. 43, 406–415 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  211. Bandyopadhyay, S. et al. Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging. Cell 187, 3120–3140.e29 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Bosc, C. et al. Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia. Nat. Cancer 2, 1204–1223 (2021). This article shows how in AML, adaptive resistance to combination therapy is linked to mitochondrial adaptations, particularly oxidative phosphorylation, which can be targeted to delay relapse.

    Article  CAS  PubMed  Google Scholar 

  213. Hoyt, C. C. Multiplex immunofluorescence and multispectral imaging: forming the basis of a clinical test platform for immuno-oncology. Front. Mol. Biosci. 8, 674747 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Proietto, M. et al. Tumor heterogeneity: preclinical models, emerging technologies, and future applications. Front. Oncol. 13, 1164535 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  215. Gaglia, G. et al. Temporal and spatial topography of cell proliferation in cancer. Nat. Cell Biol. 24, 316–326 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Pearson, J. D. et al. Binary pan-cancer classes with distinct vulnerabilities defined by pro- or anti-cancer YAP/TEAD activity. Cancer Cell 39, 1115–1134.e12 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Black, S. et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat. Protoc. 16, 3802–3835 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. Kuett, L. et al. Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. Nat. Cancer 3, 122–133 (2022).

    Article  CAS  PubMed  Google Scholar 

  219. Marx, V. Method of the Year: spatially resolved transcriptomics. Nat. Methods 18, 9–14 (2021).

    Article  CAS  PubMed  Google Scholar 

  220. Sans, M. et al. Spatial transcriptomics of intraductal papillary mucinous neoplasms of the pancreas identifies NKX6-2 as a driver of gastric differentiation and indolent biological potential. Cancer Discov. 13, 1844–1861 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Denisenko, E. et al. Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones. Nat. Commun. 15, 2860 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  222. Izumi, M. et al. Integrative single-cell RNA-seq and spatial transcriptomics analyses reveal diverse apoptosis-related gene expression profiles in EGFR-mutated lung cancer. Cell Death Dis. 15, 580 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  223. Kumarasamy, V., Vail, P., Nambiar, R., Witkiewicz, A. K. & Knudsen, E. S. Functional determinants of cell cycle plasticity and sensitivity to CDK4/6 inhibition. Cancer Res. 81, 1347–1360 (2021).

    Article  CAS  PubMed  Google Scholar 

  224. Witkiewicz, A. K. et al. Determinants of response to CDK4/6 inhibitors in the real-world setting. npj Precis. Oncol. 7, 90 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  225. Kumarasamy, V. et al. The extracellular niche and tumor microenvironment enhance KRAS inhibitor efficacy in pancreatic cancer. Cancer Res. 84, 1115–1132 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. Hickey, J. W. et al. T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. Cell Rep. 42, 113494 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Hickey, J. W. et al. Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy. Cell Syst. 15, 322–338.e5 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  228. Phillips, D. et al. Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma. Nat. Commun. 12, 6726 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  229. Wang, X. Q. et al. Spatial predictors of immunotherapy response in triple-negative breast cancer. Nature 621, 868–876 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  230. Quek, C. et al. Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy. Cell Rep. 43, 114392 (2024).

    Article  CAS  PubMed  Google Scholar 

  231. Taube, J. M. et al. Multi-institutional TSA-amplified multiplexed immunofluorescence reproducibility evaluation (MITRE) study. J. Immunother. Cancer 9, e002197 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  232. Lord, C. J., Quinn, N. & Ryan, C. J. Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions. eLife 9, e58925 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  233. McFarland, J. M. et al. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nat. Commun. 9, 4610 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  234. Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  235. Kampmann, M. CRISPRi and CRISPRa screens in mammalian cells for precision biology and medicine. ACS Chem. Biol. 13, 406–416 (2018).

    Article  CAS  PubMed  Google Scholar 

  236. Li, S. et al. Gain-of-function genetic screening identifies the antiviral function of TMEM120A via STING activation. Nat. Commun. 13, 105 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  237. Schmidt, R. et al. CRISPR activation and interference screens decode stimulation responses in primary human T cells. Science 375, eabj4008 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  238. Liu, S. J. et al. In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma. Genome Biol. 25, 256 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  239. Han, K. et al. CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities. Nature 580, 136–141 (2020). CRISPR screens in 3D cancer spheroids reveal vulnerabilities specific to the 3D growth environment, highlighting the importance of using physiologically accurate models for therapy prediction.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  240. McLean, B. et al. A CRISPR path to finding vulnerabilities and solving drug resistance: targeting the diverse cancer landscape and its ecosystem. Adv. Genet. Hoboken 3, 2200014 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  241. Coelho, M. A. et al. Base editing screens define the genetic landscape of cancer drug resistance mechanisms. Nat. Genet. 56, 2479–2492 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  242. Gallo, D. et al. CCNE1 amplification is synthetic lethal with PKMYT1 kinase inhibition. Nature 604, 749–756 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  243. Pfeifer, M. et al. Genome-wide CRISPR screens identify the YAP/TEAD axis as a driver of persister cells in EGFR mutant lung cancer. Commun. Biol. 7, 497 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  244. Jost, M. et al. Combined CRISPRi/a-based chemical genetic screens reveal that rigosertib is a microtubule-destabilizing agent. Mol. Cell 68, 210–223.e6 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  245. Wei, L. et al. Genome-wide CRISPR/Cas9 library screening identified PHGDH as a critical driver for sorafenib resistance in HCC. Nat. Commun. 10, 4681 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  246. Zeng, H. et al. Genome-wide CRISPR screening reveals genetic modifiers of mutant EGFR dependence in human NSCLC. eLife 8, e50223 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  247. US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/study/NCT05147272 (2024).

  248. Hustedt, N. et al. A consensus set of genetic vulnerabilities to ATR inhibition. Open Biol. 9, 190156 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  249. Benada, J. et al. Synthetic lethal interaction between WEE1 and PKMYT1 is a target for multiple low-dose treatment of high-grade serous ovarian carcinoma. NAR Cancer 5, zcad029 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  250. Shirani-Bidabadi, S. et al. CRISPR technology: a versatile tool to model, screen, and reverse drug resistance in cancer. Eur. J. Cell Biol. 102, 151299 (2023).

    Article  CAS  PubMed  Google Scholar 

  251. Quintanal-Villalonga, A. et al. Multiomic analysis of lung tumors defines pathways activated in neuroendocrine transformation. Cancer Discov. 11, 3028–3047 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  252. Chan, J. M. et al. Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling. Science 377, 1180–1191 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  253. Lewis, S. M. et al. Spatial omics and multiplexed imaging to explore cancer biology. Nat. Methods 18, 997–1012 (2021).

    Article  CAS  PubMed  Google Scholar 

  254. Jones, M. G., Yang, D. & Weissman, J. S. New tools for lineage tracing in cancer in vivo. Annu. Rev. Cancer Biol. 7, 111–129 (2023).

    Article  Google Scholar 

  255. Quinn, J. J. et al. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science 371, eabc1944 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  256. Simeonov, K. P. et al. Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states. Cancer Cell 39, 1150–1162.e9 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  257. Erickson, A. et al. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature 608, 360–367 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  258. Miller, T. E. et al. Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nat. Biotechnol. 40, 1030–1034 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  259. Cotton, J. L. et al. Expressed barcoding enables high-resolution tracking of the evolution of drug tolerance. Cancer Res. 83, 3611–3623 (2023).

    Article  CAS  PubMed  Google Scholar 

  260. Kester, L. & van Oudenaarden, A. Single-cell transcriptomics meets lineage tracing. Cell Stem Cell 23, 166–179 (2018).

    Article  CAS  PubMed  Google Scholar 

  261. Yang, D. et al. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell 185, 1905–1923.e25 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  262. Fazzari, E. et al. Stem-22. Single-cell lineage tracing in primary glioblastoma reveals distinct progenitor subtypes driving intratumoral heterogeneity. Neuro Oncol. 25, v37 (2023).

    Article  PubMed Central  Google Scholar 

  263. De Las Rivas, J. et al. Cancer drug resistance induced by EMT: novel therapeutic strategies. Arch. Toxicol. 95, 2279–2297 (2021).

    Article  PubMed Central  Google Scholar 

  264. Lin, L. et al. The Hippo effector YAP promotes resistance to RAF- and MEK-targeted cancer therapies. Nat. Genet. 47, 250–256 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  265. Sommer, E. R., Napoli, G. C., Chau, C. H., Price, D. K. & Figg, W. D. Targeting the metastatic niche: single-cell lineage tracing in prime time. iScience 26, 106174 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  266. Genovese, G. et al. Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer. Nature 542, 362–366 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  267. Kim, D. H., Kim, W. D., Kim, S. K., Moon, D. H. & Lee, S. J. TGF-β1-mediated repression of SLC7A11 drives vulnerability to GPX4 inhibition in hepatocellular carcinoma cells. Cell Death Dis. 11, 406 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  268. Haderk, F. et al. Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer. Nat. Commun. 15, 3741 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  269. Chen, H. Y. et al. Regulation of neuroendocrine plasticity by the RNA-binding protein ZFP36L1. Nat. Commun. 13, 4998 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  270. Davies, A. et al. An androgen receptor switch underlies lineage infidelity in treatment-resistant prostate cancer. Nat. Cell Biol. 23, 1023–1034 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  271. Ku, S. Y. et al. Rb1 and Trp53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance. Science 355, 78–83 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  272. Alix-Panabières, C. & Pantel, K. Liquid biopsy: from discovery to clinical application. Cancer Discov. 11, 858–873 (2021).

    Article  PubMed  Google Scholar 

  273. Ignatiadis, M., Sledge, G. W. & Jeffrey, S. S. Liquid biopsy enters the clinic — implementation issues and future challenges. Nat. Rev. Clin. Oncol. 18, 297–312 (2021).

    Article  PubMed  Google Scholar 

  274. Goossens, N., Nakagawa, S., Sun, X. & Hoshida, Y. Cancer biomarker discovery and validation. Transl. Cancer Res. 4, 256–269 (2015).

    CAS  PubMed  Google Scholar 

  275. Passaro, A. et al. Cancer biomarkers: emerging trends and clinical implications for personalized treatment. Cell 187, 1617–1635 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  276. Khleif, S. N., Doroshow, J. H., Hait, W. N. & AACR-FDA-NCI Cancer Biomarkers Collaborative. AACR-FDA-NCI Cancer Biomarkers Collaborative consensus report: advancing the use of biomarkers in cancer drug development. Clin. Cancer Res. 16, 3299–3318 (2010).

    Article  CAS  PubMed  Google Scholar 

  277. Duffy, M. J. et al. Clinical use of biomarkers in breast cancer: Updated guidelines from the European Group on Tumor Markers (EGTM). Eur. J. Cancer 75, 284–298 (2017).

    Article  CAS  PubMed  Google Scholar 

  278. Albain, K. S., Paik, S. & Van’t Veer, L. Prediction of adjuvant chemotherapy benefit in endocrine responsive, early breast cancer using multigene assays. Breast 18, S141–S145 (2009).

    Article  PubMed  Google Scholar 

  279. Tarabichi, M. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat. Methods 18, 144–155 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  280. Salcedo, A. et al. A community effort to create standards for evaluating tumor subclonal reconstruction. Nat. Biotechnol. 38, 97–107 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  281. Al Bakir, M. et al. The evolution of non-small cell lung cancer metastases in TRACERx. Nature 616, 534–542 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  282. Caputo, V. et al. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. Explor. Target. Antitumor Ther. 4, 102–138 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  283. Amirouchene-Angelozzi, N., Swanton, C. & Bardelli, A. Tumor evolution as a therapeutic target. Cancer Discov. 7, 805–817 (2017).

    Article  Google Scholar 

  284. Jamshidi, A. et al. Evaluation of cell-free DNA approaches for multi-cancer early detection. Cancer Cell 40, 1537–1549.e12 (2022).

    Article  CAS  PubMed  Google Scholar 

  285. Liu, M. C. et al. Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA. Ann. Oncol. 31, 745–759 (2020).

    Article  CAS  PubMed  Google Scholar 

  286. Bergqvist, M. et al. Thymidine kinase activity levels in serum can identify HR+ metastatic breast cancer patients with a low risk of early progression (SWOG S0226). Biomarkers 28, 313–322 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  287. McCartney, A. et al. Plasma thymidine kinase activity as a biomarker in patients with luminal metastatic breast cancer treated with palbociclib within the TREnd trial. Clin. Cancer Res. 26, 2131–2139 (2020).

    Article  CAS  PubMed  Google Scholar 

  288. Nanni, C., Farolfi, A., Castellucci, P. & Fanti, S. Total body positron emission tomography/computed tomography: current status in oncology. Semin. Nucl. Med. 55, 31–40 (2025).

    Article  PubMed  Google Scholar 

  289. Pai, S. et al. Foundation model for cancer imaging biomarkers. Nat. Mach. Intell. 6, 354–367 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  290. Prelaj, A. et al. Artificial intelligence for predictive biomarker discovery in immuno-oncology: a systematic review. Ann. Oncol. 35, 29–65 (2024).

    Article  CAS  PubMed  Google Scholar 

  291. Vazquez-Levin, M. H., Reventos, J. & Zaki, G. Editorial: Artificial intelligence: a step forward in biomarker discovery and integration towards improved cancer diagnosis and treatment. Front. Oncol. 13, 1161118 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  292. Danielli, S. G. et al. Single cell transcriptomic profiling identifies tumor-acquired and therapy-resistant cell states in pediatric rhabdomyosarcoma. Nat. Commun. 15, 6307 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  293. Wegmann, R. et al. Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia. Nat. Commun. 15, 9402 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  294. Caswell, D. R. et al. The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance. Nat. Genet. 56, 60–73 (2024).

    Article  CAS  PubMed  Google Scholar 

  295. Lipkova, J. et al. Artificial intelligence for multimodal data integration in oncology. Cancer Cell 40, 1095–1110 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  296. Morris, S. R. & Carey, L. A. Gene expression profiling in breast cancer. Curr. Opin. Oncol. 19, 547–551 (2007).

    Article  CAS  PubMed  Google Scholar 

  297. Kim, C. & Paik, S. Gene-expression-based prognostic assays for breast cancer. Nat. Rev. Clin. Oncol. 7, 340–347 (2010).

    Article  CAS  PubMed  Google Scholar 

  298. US National Library of Medicine. ClinicalTrials.gov https://clinicaltrials.gov/study/NCT03460977 (2025).

  299. Gini, B., Thomas, N. & Blakely, C. M. Impact of concurrent genomic alterations in epidermal growth factor receptor (EGFR)-mutated lung cancer. J. Thorac. Dis. 12, 2883–2895 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  300. Johnson, B. E. et al. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep. Med. 3, 100525 (2022). This publication showcases analysis of serial biopsy samples taken from a patient with breast cancer and serves as an example of how integrative data analysis can reveal potential mechanisms of response and resistance and suggest novel therapeutic vulnerabilities.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  301. Labrie, M. et al. Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. NPJ Precis. Oncol. 5, 92 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  302. Wirth, A.-K. et al. In vivo PDX CRISPR/Cas9 screens reveal mutual therapeutic targets to overcome heterogeneous acquired chemo-resistance. Leukemia 36, 2863–2874 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  303. Kim, M. et al. Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening. Nat. Commun. 10, 3991 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  304. Al Shihabi, A. et al. Personalized chordoma organoids for drug discovery studies. Sci. Adv. 8, eabl3674 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  305. Gutmann, D. H. et al. Precision preclinical modeling to advance cancer treatment. J. Natl Cancer Inst. 117, 586–594 (2025).

    Article  PubMed  Google Scholar 

  306. Meric-Bernstam, F. et al. National Cancer Institute Combination Therapy Platform Trial with Molecular Analysis for Therapy Choice (ComboMATCH). Clin. Cancer Res. 29, 1412–1422 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  307. O’Donnell, P. H. & Dolan, M. E. Cancer pharmacoethnicity: ethnic differences in susceptibility to the effects of chemotherapy. Clin. Cancer Res. 15, 4806–4814 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  308. Marcu, L. G. & Marcu, D. C. Pharmacogenomics and Big Data in medical oncology: developments and challenges. Ther. Adv. Med. Oncol. 16, 17588359241287658 (2024).

    PubMed  PubMed Central  Google Scholar 

  309. American Association for Cancer Research. AACR Cancer Disparities Progress Report 2024. https://cancerprogressreport.aacr.org/disparities/cdpr24-contents/cdpr24-disparities-in-clinical-research-and-cancer-treatment/ (2024).

  310. Habibzadeh, F. Disparity in the selection of patients in clinical trials. Lancet 399, 1048 (2022).

    Article  PubMed  Google Scholar 

  311. Letai, A. Functional precision cancer medicine-moving beyond pure genomics. Nat. Med. 23, 1028–1035 (2017).

    Article  CAS  PubMed  Google Scholar 

  312. Han, J. J. FDA Modernization Act 2.0 allows for alternatives to animal testing. Artif. Organs 47, 449–450 (2023).

    Article  PubMed  Google Scholar 

  313. Chang, T. G. et al. LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features. Nat. Cancer 5, 1158–1175 (2024).

    Article  PubMed  PubMed Central  Google Scholar 

  314. Laisné, M., Lupien, M. & Vallot, C. Epigenomic heterogeneity as a source of tumour evolution. Nat. Rev. Cancer 25, 7–26 (2025).

    Article  PubMed  Google Scholar 

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Acknowledgements

The authors thank M. Espey and J. Hildesheim for helpful discussions. They acknowledge the following grant support: R01CA244729 and R01CA244729-03S (to A.S. and P.C.B.); R01CA240718 and R01CA264248 (to A.S.); P30CA016042, U2CCA271894, U24CA248265 and DOD W81XWH2210751 (to P.C.B.); U01CA223976 and U01CA223976-03S1 (to C.D.W.); R01CA247362 and R01CA267467 (to E.S.K. and A.K.W.); U24CA274159, R01CA234162 and PCF 22CHAL13 (to D.W.G.); U54CA274220 (to D.J. and S.T.G.); U54CA224019 (to C.E.T. and J.W.T.); U01CA271412 (to C.E.T.); U54CA224081 (to T.G.B.); R01CA175495 (to X.Z.); U54CA274321 (to V.C.S., A.A.O. and J.N.M.); R01CA280980 (to V.C.S.); R01CA270234, R01CA163649, R01CA256911 and U54CA274329 (to P.K.S.); R37CA276924 (to K.M.); and R01CA175397-07S1 (to K.S.C.).

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E.S.K., T.N.O., A.K.W. and A.S. researched data for the article. E.S.K., T.N.O., C.E.T., J.W.T., B.G., T.G.B., D.W.G., P.K.S., K.S.C., H.M. and A.S. contributed substantially to discussion of the content. E.S.K., C.E.T., J.W.T., B.G., T.G.B., X.Z., A.K.W., D.W.G., D.J., S.T.G., C.D.W., P.C.B., V.C.S., A.A.O., J.N.M., P.K.S., D.K., K.S.C. and A.S. wrote the article. E.S.K., T.N.O., B.G., T.G.B., X.Z., C.D.W., V.C.S., A.A.O. and A.S. reviewed and/or edited the manuscript before submission.

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Correspondence to Alice Soragni or Erik S. Knudsen.

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The authors declare no direct competing interests. For full disclosure, C.D.W. has received research funding from Varian Medical Systems, AACR-Novocure and OMS Foundation, clinical trial support from MuReva and Tactile Medical, and consultancy/honoraria from LifeNet Health, Guidepoint Global and EMD Serono; A.S. sits on the Board of the Society for Functional Precision Medicine; P.C.B. sits on the Scientific Advisory Boards of Intersect Diagnostics Inc., BioSymetrics Inc. and previously sat on the board of Sage Bionetworks; E.S.K. has sponsored research funded by Blueprint Medicines and Bristol Myers Squibb and is a member of the Cancer Cell Cyclse–LLC consulting enterprise; A.K.W. has sponsored research funded by Blueprint Medicines and Bristol Myers Squibb; C.E.T. has received funding from AstraZeneca; J.W.T. has received research support from Acerta, Agios, Aptose, Array, AstraZeneca, Constellation, Genentech, Gilead, Incyte, Janssen, Kronos, Meryx, Petra, Schrodinger, Seattle Genetics, Syros, Takeda and Tolero and serves on the advisory board for Recludix Pharm, AmMax Bio and Ellipses Pharma; V.C.S. is a consultant for and equity holder in Femtovox Inc.

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Soragni, A., Knudsen, E.S., O’Connor, T.N. et al. Acquired resistance in cancer: towards targeted therapeutic strategies. Nat Rev Cancer 25, 613–633 (2025). https://doi.org/10.1038/s41568-025-00824-9

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