REFERENCES
2. Holohan C, Van Schaeybroeck S, Longley DB, Johnston PG. Cancer drug resistance: an evolving paradigm. Nat Rev Cancer 2013;13:714-26.
3. Wang X, Zhang H, Chen X. Drug resistance and combating drug resistance in cancer. Cancer Drug Resist 2019;2:141-60.
4. Lippert TH, Ruoff HJ, Volm M. Intrinsic and acquired drug resistance in malignant tumors. The main reason for therapeutic failure. Arzneimittelforschung 2008;58:261-4.
5. Kelderman S, Schumacher TNN, Haanen JBAG. Acquired and intrinsic resistance in cancer immunotherapy. Mol Oncol 2014;8:1132-9.
7. Barretina J, Caponigro G, Stransky N, et al. The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012;483:603-7.
8. Basu A, Bodycombe NE, Cheah JH, et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell 2013;154:1151-61.
9. Iorio F, Knijnenburg TA, Vis DJ, et al. A landscape of pharmacogenomic interactions in cancer. Cell 2016;166:740-54.
10. Ghandi M, Huang FW, Jané-Valbuena J, et al. Next-generation characterization of the cancer cell line encyclopedia. Nature 2019;569:503-8.
11. Michaelis M, Wass MN, Cinatl J. Drug-adapted cancer cell lines as preclinical models of acquired resistance. Cancer Drug Resist 2019;2:447-56.
12. Rothenburger T, Thomas D, Schreiber Y, et al. Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells. J Exp Clin Cancer Res 2021;40:317.
13. Wang W, Itaka K, Ohba S, et al. 3D spheroid culture system on micropatterned substrates for improved differentiation efficiency of multipotent mesenchymal stem cells. Biomaterials 2009;30:2705-15.
14. Hirschhaeuser F, Menne H, Dittfeld C, West J, Mueller-Klieser W, Kunz-Schughart LA. Multicellular tumor spheroids: an underestimated tool is catching up again. J Biotechnol 2010;148:3-15.
15. Lee J, Cuddihy MJ, Kotov NA. Three-dimensional cell culture matrices: state of the art. Tissue Eng Part B Rev 2008;14:61-86.
17. Kim JB. Three-dimensional tissue culture models in cancer biology. Semin Cancer Biol 2005;15:365-77.
18. Fatehullah A, Tan SH, Barker N. Organoids as an in vitro model of human development and disease. Nat Cell Biol 2016;18:246-54.
19. Jensen C, Teng Y. Is it time to start transitioning from 2D to 3D cell culture? Front Mol Biosci 2020;7:33.
20. Takebe T, Zhang B, Radisic M. Synergistic engineering: organoids meet organs-on-a-chip. Cell Stem Cell 2017;21:297-300.
21. Ravi M, Paramesh V, Kaviya SR, Anuradha E, Solomon FDP. 3D cell culture systems: advantages and applications. J Cell Physiol 2015;230:16-26.
22. Antoni D, Burckel H, Josset E, Noel G. Three-dimensional cell culture: a breakthrough in vivo. Int J Mol Sci 2015;16:5517-27.
23. Huh D, Matthews BD, Mammoto A, Montoya-Zavala M, Hsin HY, Ingber DE. Reconstituting organ-level lung functions on a chip. Science 2010;328:1662-8.
24. Sambale F, Lavrentieva A, Stahl F, et al. Three dimensional spheroid cell culture for nanoparticle safety testing. J Biotechnol 2015;205:120-9.
25. Stoker AW, Streuli CH, Martins-Green M, Bissell MJ. Designer microenvironments for the analysis of cell and tissue function. Curr Opin Cell Biol 1990;2:864-74.
26. Fennema E, Rivron N, Rouwkema J, van Blitterswijk C, de Boer J. Spheroid culture as a tool for creating 3D complex tissues. Trends Biotechnol 2013;31:108-15.
27. Song HHG, Park KM, Gerecht S. Hydrogels to model 3D in vitro microenvironment of tumor vascularization. Adv Drug Deliv Rev 2014;79-80:19-29.
28. Friedl P, Gilmour D. Collective cell migration in morphogenesis, regeneration and cancer. Nat Rev Mol Cell Biol 2009;10:445-57.
29. Discher DE, Janmey P, Wang YL. Tissue cells feel and respond to the stiffness of their substrate. Science 2005;310:1139-43.
30. De Pieri A, Rochev Y, Zeugolis DI. Scaffold-free cell-based tissue engineering therapies: advances, shortfalls and forecast. NPJ Regen Med 2021;6:18.
31. Han L, Diao L, Yu S, et al. The genomic landscape and clinical relevance of A-to-I RNA editing in human cancers. Cancer Cell 2015;28:515-28.
32. Langhans SA. Three-dimensional in vitro cell culture models in drug discovery and drug repositioning. Front Pharmacol 2018;9:6.
33. Orso F, Quirico L, Dettori D, et al. Role of miRNAs in tumor and endothelial cell interactions during tumor progression. Semin Cancer Biol 2020;60:214-24.
34. Rizzolio S, Giordano S, Corso S. The importance of being CAFs (in cancer resistance to targeted therapies). J Exp Clin Cancer Res 2022;41:319.
35. Kaur S, Kaur I, Rawal P, Tripathi DM, Vasudevan A. Non-matrigel scaffolds for organoid cultures. Cancer Lett 2021;504:58-66.
36. Bock N, Forouz F, Hipwood L, et al. GelMA, click-chemistry gelatin and bioprinted polyethylene glycol-based hydrogels as 3D ex vivo drug testing platforms for patient-derived breast cancer organoids. Pharmaceutics 2023;15:261.
39. Sztankovics D, Moldvai D, Petővári G, et al. 3D bioprinting and the revolution in experimental cancer model systems - A review of developing new models and experiences with in vitro 3D bioprinted breast cancer tissue-mimetic structures. Pathol Oncol Res 2023;29:1610996.
40. Silvestri VL, Henriet E, Linville RM, Wong AD, Searson PC, Ewald AJ. A tissue-engineered 3D microvessel model reveals the dynamics of mosaic vessel formation in breast cancer. Cancer Res 2020;80:4288-301.
41. Groll J, Burdick JA, Cho DW, et al. A definition of bioinks and their distinction from biomaterial inks. Biofabrication 2018;11:013001.
42. Nunes AS, Barros AS, Costa EC, Moreira AF, Correia IJ. 3D tumor spheroids as in vitro models to mimic in vivo human solid tumors resistance to therapeutic drugs. Biotechnol Bioeng 2019;116:206-26.
43. Costa EC, Moreira AF, de Melo-Diogo D, Gaspar VM, Carvalho MP, Correia IJ. 3D tumor spheroids: an overview on the tools and techniques used for their analysis. Biotechnol Adv 2016;34:1427-41.
44. Däster S, Amatruda N, Calabrese D, et al. Induction of hypoxia and necrosis in multicellular tumor spheroids is associated with resistance to chemotherapy treatment. Oncotarget 2017;8:1725-36.
45. Nath S, Devi GR. Three-dimensional culture systems in cancer research: focus on tumor spheroid model. Pharmacol Ther 2016;163:94-108.
46. Lee KH, Kim TH. Recent advances in multicellular tumor spheroid generation for drug screening. Biosensors 2021;11:445.
47. Colombo E, Cattaneo MG. Multicellular 3D models to study tumour-stroma interactions. Int J Mol Sci 2021;22:1633.
48. Firuzi O, Che PP, El Hassouni B, et al. Role of c-MET inhibitors in overcoming drug resistance in spheroid models of primary human pancreatic cancer and stellate cells. Cancers 2019;11:638.
50. Qu J, Kalyani FS, Liu L, Cheng T, Chen L. Tumor organoids: synergistic applications, current challenges, and future prospects in cancer therapy. Cancer Commun 2021;41:1331-53.
51. Ooft SN, Weeber F, Dijkstra KK, et al. Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients. Sci Transl Med 2019;11:eaay2574.
52. Öhlund D, Handly-Santana A, Biffi G, et al. Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer. J Exp Med 2017;214:579-96.
53. Wen J, Liu F, Cheng Q, et al. Applications of organoid technology to brain tumors. CNS Neurosci Ther 2023;29:2725-43.
55. Vinci M, Gowan S, Boxall F, et al. Advances in establishment and analysis of three-dimensional tumor spheroid-based functional assays for target validation and drug evaluation. BMC Biol 2012;10:29.
56. Wakefield L, Agarwal S, Tanner K. Preclinical models for drug discovery for metastatic disease. Cell 2023;186:1792-813.
57. Coppo R, Kondo J, Iida K, et al. Distinct but interchangeable subpopulations of colorectal cancer cells with different growth fates and drug sensitivity. iScience 2023;26:105962.
58. Hsu PL, Chien CW, Tang YA, et al. Targeting BRD3 eradicates nuclear TYRO3-induced colorectal cancer metastasis. Sci Adv 2023;9:eade3422.
59. van de Haar J, Ma X, Ooft SN, et al. Codon-specific KRAS mutations predict survival benefit of trifluridine/tipiracil in metastatic colorectal cancer. Nat Med 2023;29:605-14.
60. Sui Q, Zhang X, Chen C, et al. Inflammation promotes resistance to immune checkpoint inhibitors in high microsatellite instability colorectal cancer. Nat Commun 2022;13:7316.
61. Küçükköse E, Heesters BA, Villaudy J, et al. Modeling resistance of colorectal peritoneal metastases to immune checkpoint blockade in humanized mice. J Immunother Cancer 2022;10:e005345.
62. Sun Y, Revach O, Anderson S, et al. Targeting TBK1 to overcome resistance to cancer immunotherapy. Nature 2023;615:158-67.
63. Wong TL, Loh JJ, Lu S, et al. ADAR1-mediated RNA editing of SCD1 drives drug resistance and self-renewal in gastric cancer. Nat Commun 2023;14:2861.
64. Yoon BK, Kim H, Oh TG, et al. PHGDH preserves one-carbon cycle to confer metabolic plasticity in chemoresistant gastric cancer during nutrient stress. Proc Natl Acad Sci U S A 2023;120:e2217826120.
65. Zhou T, Xie Y, Hou X, et al. Irbesartan overcomes gemcitabine resistance in pancreatic cancer by suppressing stemness and iron metabolism via inhibition of the Hippo/YAP1/c-Jun axis. J Exp Clin Cancer Res 2023;42:111.
66. Goodwin CM, Waters AM, Klomp JE, et al. Combination therapies with CDK4/6 inhibitors to treat KRAS-mutant pancreatic cancer. Cancer Res 2023;83:141-57.
67. Hennig A, Baenke F, Klimova A, et al. Detecting drug resistance in pancreatic cancer organoids guides optimized chemotherapy treatment. J Pathol 2022;257:607-19.
68. Schuth S, Le Blanc S, Krieger TG, et al. Patient-specific modeling of stroma-mediated chemoresistance of pancreatic cancer using a three-dimensional organoid-fibroblast co-culture system. J Exp Clin Cancer Res 2022;41:312.
69. Li L, Zhou Y, Zhang Y, Hu H, Mao HQ, Selaru FM. A combination therapy of bortezomib, CXCR4 inhibitor, and checkpoint inhibitor is effective in cholangiocarcinoma in vivo. iScience 2023;26:106095.
70. Su L, Chen Y, Huang C, et al. Targeting src reactivates pyroptosis to reverse chemoresistance in lung and pancreatic cancer models. Sci Transl Med 2023;15:eabl7895.
71. Heid J, Affolter A, Jakob Y, et al. 3D cell culture alters signal transduction and drug response in head and neck squamous cell carcinoma. Oncol Lett 2022;23:177.
72. Fabro F, Kannegieter NM, de Graaf EL, et al. Novel kinome profiling technology reveals drug treatment is patient and 2D/3D model dependent in glioblastoma. Front Oncol 2022;12:1012236.
73. Jia W, Zhu H, Zhao M, et al. Potential mechanisms underlying the promoting effects of 3D collagen scaffold culture on stemness and drug resistance of glioma cells. Biochim Biophys Acta Mol Basis Dis 2022;1868:166522.
74. Chaicharoenaudomrung N, Kunhorm P, Promjantuek W, et al. Transcriptomic profiling of 3D glioblastoma tumoroids for the identification of mechanisms involved in anticancer drug resistance. In Vivo 2020;34:199-211.
75. Liverani C, De Vita A, Spadazzi C, et al. Lineage-specific mechanisms and drivers of breast cancer chemoresistance revealed by 3D biomimetic culture. Mol Oncol 2022;16:921-39.
76. Liu Y, Gan Y, AiErken N, et al. Combining organoid models with next-generation sequencing to reveal tumor heterogeneity and predict therapeutic response in breast cancer. J Oncol 2022;2022:9390912.
77. Ng ASN, Zhang S, Mak VCY, et al. AKTIP loss is enriched in ERα-positive breast cancer for tumorigenesis and confers endocrine resistance. Cell Rep 2022;41:111821.
78. Anderle N, Koch A, Gierke B, et al. A platform of patient-derived microtumors identifies individual treatment responses and therapeutic vulnerabilities in ovarian cancer. Cancers 2022;14:2895.
79. Senkowski W, Gall-Mas L, Falco MM, et al. A platform for efficient establishment and drug-response profiling of high-grade serous ovarian cancer organoids. Dev Cell 2023;58:1106-21.e7.
80. Peterziel H, Jamaladdin N, ElHarouni D, et al. Drug sensitivity profiling of 3D tumor tissue cultures in the pediatric precision oncology program INFORM. NPJ Precis Oncol 2022;6:94.
81. Lee DW, Choi SY, Kim SY, et al. A novel 3D pillar/well array platform using patient-derived head and neck tumor to predict the individual radioresponse. Transl Oncol 2022;24:101483.
82. Millen R, De Kort WWB, Koomen M, et al. Patient-derived head and neck cancer organoids allow treatment stratification and serve as a tool for biomarker validation and identification. Med 2023;4:290-310.e12.
83. Jensen LH, Rogatto SR, Lindebjerg J, et al. Precision medicine applied to metastatic colorectal cancer using tumor-derived organoids and in-vitro sensitivity testing: a phase 2, single-center, open-label, and non-comparative study. J Exp Clin Cancer Res 2023;42:115.
84. Martini G, Belli V, Napolitano S, et al. Establishment of patient-derived tumor organoids to functionally inform treatment decisions in metastatic colorectal cancer. ESMO Open 2023;8:101198.
85. Papaccio F, García-Mico B, Gimeno-Valiente F, et al. "Proteotranscriptomic analysis of advanced colorectal cancer patient derived organoids for drug sensitivity prediction". J Exp Clin Cancer Res 2023;42:8.
86. Cromwell EF, Sirenko O, Nikolov E, et al. Multifunctional profiling of triple-negative breast cancer patient-derived tumoroids for disease modeling. SLAS Discov 2022;27:191-200.
87. Shu D, Shen M, Li K, et al. Organoids from patient biopsy samples can predict the response of BC patients to neoadjuvant chemotherapy. Ann Med 2022;54:2581-97.
88. Wang HM, Zhang CY, Peng KC, et al. Using patient-derived organoids to predict locally advanced or metastatic lung cancer tumor response: a real-world study. Cell Rep Med 2023;4:100911.
89. Mazzocchi A, Dominijanni A, Soker S. Pleural effusion aspirate for use in 3D lung cancer modeling and chemotherapy screening. Methods Mol Biol 2022;2394:471-83.
90. Brown JMC, Zaben M, Ormonde C, et al. A high-density 3-dimensional culture model of human glioblastoma for rapid screening of therapeutic resistance. Biochem Pharmacol 2023;208:115410.
91. Morelli M, Lessi F, Barachini S, et al. Metabolic-imaging of human glioblastoma live tumors: a new precision-medicine approach to predict tumor treatment response early. Front Oncol 2022;12:969812.
92. Demyan L, Habowski AN, Plenker D, et al. Pancreatic cancer patient-derived organoids can predict response to neoadjuvant chemotherapy. Ann Surg 2022;276:450-62.
93. Breslin S, O’Driscoll L. Three-dimensional cell culture: the missing link in drug discovery. Drug Discov Today 2013;18:240-9.