Organoid-Guided Precision Medicine: From Bench to Bedside

Abstract

Organoid technology, as an emerging field within biotechnology, has demonstrated transformative potential in advancing precision medicine. This review systematically outlines the translational trajectory of organoids from bench to bedside, emphasizing their construction methodologies, key regulatory factors, and multifaceted applications in personalized healthcare. By recapitulating physiological architectures and disease phenotypes through three-dimensional culture systems, organoids leverage natural and synthetic scaffolds, stem cell sources, and spatiotemporal cytokine regulation to model tissue-specific microenvironments. Diverse organoid types—including skin, intestinal, lung, and tumor organoids—have facilitated breakthroughs in modeling tissue development, drug efficacy and toxicity screening, disease pathogenesis studies, and patient-tailored diagnostics. For instance, patient-derived tumor organoids preserve tumor heterogeneity and genomic profiles, serving as predictive platforms for individualized chemotherapy responses. In precision medicine, organoid-guided multiomics analyses identify actionable biomarkers and resistance mechanisms, while clustered regularly interspaced short palindromic repeats-based functional screens optimize therapeutic targeting. Despite preclinical successes, challenges persist in standardization, vascularization, and ethical considerations. Future integration of artificial intelligence, microfluidics, and spatial transcriptomics will enhance organoid scalability, reproducibility, and clinical relevance. By bridging molecular insights with patient-specific therapies, organoids are poised to revolutionize precision medicine, offering dynamic platforms for drug development, regenerative strategies, and individualized treatment paradigms.

Keywords

drug screening / organoids / precision medicine / regenerative medicine

References

[1] R. Xu, X. Zhou, S. Wang, and C. Trinkle, “Tumor organoid models in precision medicine and investigating cancer-stromal interactions,” Pharmacology & Therapeutics 218 (2021): 107668.

[2] K. P. Guillen, M. Fujita, A. J. Butterfield, et al., “A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology,” Nature Cancer 3, no. 2 (2022): 232-250.

[3] D. Gao, I. Vela, A. Sboner, et al., “Organoid cultures derived From patients With advanced prostate cancer,” Cell 159, no. 1 (2014): 176-187.

[4] M. van de Wetering, H. E. Francies, J. M. Francis, et al., “Prospective derivation of a living organoid biobank of colorectal cancer patients,” Cell 161, no. 4 (2015): 933-945.

[5] D. Dutta, I. Heo, and H. Clevers, “Disease Modeling in Stem Cell-Derived 3D Organoid Systems,” Trends in Molecular Medicine 23, no. 5 (2017): 393-410.

[6] A. I. Astashkina, B. K. Mann, G. D. Prestwich, and D. W. Grainger, “Comparing predictive drug nephrotoxicity biomarkers in kidney 3-D primary organoid culture and immortalized cell lines,” Biomaterials 33, no. 18 (2012): 4712-4721.

[7] H. V. Wilson, “A NEW METHOD BY WHICH SPONGES MAY BE ARTIFICIALLY REARED,” Science 25, no. 649 (1907): 912-915.

[8] W. Ni, S. Yao, Y. Zhou, et al., “Long noncoding RNA GAS5 inhibits progression of colorectal cancer by interacting With and triggering YAP phosphorylation and degradation and is negatively regulated by the m6A reader YTHDF3,” Molecular Cancer 18, no. 1 (2019): 143.

[9] H. Clevers, “Modeling Development and Disease With Organoids,” Cell 165, no. 7 (2016): 1586-1597.

[10] G. Rossi, A. Manfrin, and M. P. Lutolf, “Progress and potential in organoid research,” Nature Reviews Genetics 19, no. 11 (2018): 671-687.

[11] G. Richer, R. M. Hobbs, K. L. Loveland, E. Goossens, and Y. Baert, “Long-Term Maintenance and Meiotic Entry of Early Germ Cells in Murine Testicular Organoids Functionalized by 3D Printed Scaffolds and Air-Medium Interface Cultivation,” Frontiers in Physiology 12 (2021): 757565.

[12] D. Hendriks, B. Artegiani, H. Hu, S. Chuva de Sousa Lopes, and H. Clevers, “Establishment of human fetal hepatocyte organoids and CRISPR-Cas9-based gene knockin and knockout in organoid cultures From human liver,” Nature Protocols 16, no. 1 (2021): 182-217.

[13] B. Desoize, “Contribution of three-dimensional culture to cancer research,” Critical Reviews in Oncology/Hematology 36, no. 2-3 (2000): 59-60.

[14] M. T. Santini, G. Rainaldi, and P. L. Indovina, “Apoptosis, cell adhesion and the extracellular matrix in the three-dimensional growth of multicellular tumor spheroids,” Critical Reviews in Oncology/Hematology 36, no. 2-3 (2000): 75-87.

[15] N. Banu, M. Rosenzweig, H. Kim, J. Bagley, and M. Pykett, “Cytokine-augmented culture of haematopoietic progenitor cells in a novel three-dimensional cell growth matrix,” Cytokine 13, no. 6 (2001): 349-358.

[16] C. Jensen and Y. Teng, “Is It Time to Start Transitioning From 2D to 3D Cell Culture?,” Frontiers in Molecular Biosciences 7 (2020): 33.

[17] K. R. Koehler and E. Hashino, “3D mouse embryonic stem cell culture for generating inner ear organoids,” Nature Protocols 9, no. 6 (2014): 1229-1244.

[18] E. Garreta, R. D. Kamm, S. M. Chuva de Sousa Lopes, et al., “Rethinking organoid technology Through bioengineering,” Nature Materials 20, no. 2 (2021): 145-155.

[19] J. Lee, C. C. Rabbani, H. Gao, et al., “Hair-bearing human skin generated entirely From pluripotent stem cells,” Nature 582, no. 7812 (2020): 399-404.

[20] D. S. Park, T. Kozaki, S. K. Tiwari, et al., “iPS-cell-derived microglia promote brain organoid maturation via cholesterol transfer,” Nature 623, no. 7986 (2023): 397-405.

[21] D. Serra, U. Mayr, A. Boni, et al., “Self-organization and symmetry breaking in intestinal organoid development,” Nature 569, no. 7754 (2019): 66-72.

[22] K. T. Lawlor, J. M. Vanslambrouck, J. W. Higgins, et al., “Cellular extrusion bioprinting improves kidney organoid reproducibility and conformation,” Nature Materials 20, no. 2 (2021): 260-271.

[23] S. J. Aronson and H. L. Rehm, “Building the foundation for genomics in precision medicine,” Nature 526, no. 7573 (2015): 336-342.

[24] C. M. Rhee, Y. Obi, A. T. Mathew, and K. Kalantar-Zadeh, “Precision Medicine in the Transition to Dialysis and Personalized Renal Replacement Therapy,” Seminars in Nephrology 38, no. 4 (2018): 325-335.

[25] J. L. Tang and L. M. Li, “[Some reflections on evidenced-based medicine, precision medicine, and big data-based research],” Zhonghua Liu Xing Bing Xue Za Zhi = Zhonghua Liuxingbingxue Zazhi 39, no. 1 (2018): 1-7.

[26] H. Nakagawa and M. Fujita, “Whole genome sequencing analysis for cancer genomics and precision medicine,” Cancer Science 109, no. 3 (2018): 513-522.

[27] V. Dao, K. Yuki, Y.-H. Lo, M. Nakano, and C. J. Kuo, “Immune organoids: From tumor modeling to precision oncology,” Trends in Cancer 8, no. 10 (2022): 870-880.

[28] M. A. Lancaster, M. Renner, C.-A. Martin, et al., “Cerebral organoids model human brain development and microcephaly,” Nature 501, no. 7467 (2013): 373-379.

[29] L. Zhu, K. Liu, Q. Feng, and Y. Liao, “Cardiac Organoids: A 3D Technology for Modeling Heart Development and Disease,” Stem Cell Reviews and Reports 18, no. 8 (2022): 2593-2605.

[30] C. Zhang, Y. Zhou, J. Zheng, et al., “Inhibition of GABAA receptors in intestinal stem cells prevents chemoradiotherapy-induced intestinal toxicity,” Journal of Experimental Medicine 219, no. 12 (2022): e20220541.

[31] P. Li, S. T. Pachis, G. Xu, et al., “Mpox virus infection and drug treatment modelled in human skin organoids,” Nature Microbiology 8, no. 11 (2023): 2067-2079.

[32] D. A. Brenner, “Alternatives to animal testing to assess MASH drugs and hepatotoxicity,” Hepatology (2023).

[33] M. Devarasetty, A. R. Mazzocchi, and A. Skardal, “Applications of Bioengineered 3D Tissue and Tumor Organoids in Drug Development and Precision Medicine: Current and Future,” Biodrugs 32, no. 1 (2018): 53-68.

[34] N. Jalan-Sakrikar, T. Brevini, R. C. Huebert, and F. Sampaziotis, “Organoids and regenerative hepatology,” Hepatology 77, no. 1 (2023): 305-322.

[35] T. T. Puck, S. J. Cieciura, and H. W. Fisher, “Clonal growth in vitro of human cells With fibroblastic morphology; comparison of growth and genetic characteristics of single epithelioid and fibroblast-Like cells From a variety of human organs,” Journal of Experimental Medicine 106, no. 1 (1957): 145-158.

[36] A. D. Theocharis, S. S. Skandalis, C. Gialeli, and N. K. Karamanos, “Extracellular matrix structure,” Advanced Drug Delivery Reviews 97 (2016): 4-27.

[37] N. K. Karamanos, A. D. Theocharis, Z. Piperigkou, et al., “A guide to the composition and functions of the extracellular matrix,” The FEBS Journal 288, no. 24 (2021): 6850-6912.

[38] J. W. Kim, S. A. Nam, J. Yi, et al., “Kidney Decellularized Extracellular Matrix Enhanced the Vascularization and Maturation of Human Kidney Organoids,” Advanced Science (Weinh) 9, no. 15 (2022): e2103526.

[39] H. K. Kleinman and G. R. Martin, “Matrigel: Basement membrane matrix With biological activity,” Seminars in Cancer Biology 15, no. 5 (2005): 378-386.

[40] P. Ebner-Peking, L. Krisch, M. Wolf, et al., “Self-assembly of differentiated progenitor cells facilitates spheroid human skin organoid formation and planar skin regeneration,” Theranostics 11, no. 17 (2021): 8430-8447.

[41] J. Diao, J. Liu, S. Wang, et al., “Sweat gland organoids contribute to cutaneous wound healing and sweat gland regeneration,” Cell Death & Disease 10, no. 3 (2019): 238.

[42] S. Xie, L. Chen, M. Zhang, C. Zhang, and H. Li, “Self-assembled complete hair follicle organoids by coculture of neonatal mouse epidermal cells and dermal cells in Matrigel,” Annals of Translational Medicine 10, no. 14 (2022): 767.

[43] M. Castellote-Borrell, F. Merlina, A. R. Rodríguez, and J. Guasch, “Biohybrid Hydrogels for Tumoroid Culture,” Advanced Biology (Weinh) 7, no. 12 (2023): e2300118.

[44] L. Zhu, J. Yuhan, H. Yu, B. Zhang, K. Huang, and L. Zhu, “Decellularized Extracellular Matrix for Remodeling Bioengineering Organoid's Microenvironment,” Small (Weinheim an Der Bergstrasse, Germany) 19, no. 25 (2023): e2207752.

[45] C. Liu, M. Pei, Q. Li, and Y. Zhang, “Decellularized extracellular matrix mediates tissue construction and regeneration,” Frontiers in Medicine 16, no. 1 (2022): 56-82.

[46] G. G. Giobbe, C. Crowley, C. Luni, et al., “Extracellular matrix hydrogel derived From decellularized tissues enables endodermal organoid culture,” Nature Communications 10, no. 1 (2019): 5658.

[47] S. H. Kim, D. Kim, M. Cha, S. H. Kim, and Y. Jung, “The Regeneration of Large-Sized and Vascularized Adipose Tissue Using a Tailored Elastic Scaffold and dECM Hydrogels,” International Journal of Molecular Sciences 22, no. 22 (2021): 12560.

[48] M. K. Kim, W. Jeong, and H.-W. Kang, “Liver dECM-Gelatin Composite Bioink for Precise 3D Printing of Highly Functional Liver Tissues,” Journal of Functional Biomaterials 14, no. 8 (2023): 417.

[49] X. Zhu, Y. Li, Y. Yang, et al., “Ordered micropattern arrays fabricated by lung-derived dECM hydrogels for chemotherapeutic drug screening,” Materials Today Bio 15 (2022): 100274.

[50] F. Navaee, P. Renaud, A. Kleger, and T. Braschler, “Highly Efficient Cardiac Differentiation and Maintenance by Thrombin-Coagulated Fibrin Hydrogels Enriched With Decellularized Porcine Heart Extracellular Matrix,” International Journal of Molecular Sciences 24, no. 3 (2023): 2842.

[51] Z.-Y. Xu, J.-J. Huang, Y. Liu, et al., “Extracellular matrix bioink boosts stemness and facilitates transplantation of intestinal organoids as a biosafe Matrigel alternative,” Bioengineering & Translational Medicine 8, no. 1 (2023): e10327.

[52] Z. Wang, R. Liu, Y. Liu, et al., “Human Placenta Decellularized Extracellular Matrix Hydrogel Promotes the Generation of Human Spinal Cord Organoids With Dorsoventral Organization From Human Induced Pluripotent Stem Cells,” ACS Biomaterials Science & Engineering 10, no. 5 (2024): 3218-3231.

[53] J. S. Choi, J. D. Kim, H. S. Yoon, and Y. W. Cho, “Full-thickness skin wound healing using human placenta-derived extracellular matrix containing bioactive molecules,” Tissue Engineering Part A 19, no. 3-4 (2013): 329-339.

[54] Q. Zhang, J. A. Johnson, L. W. Dunne, et al., “Decellularized skin/adipose tissue flap matrix for engineering vascularized composite soft tissue flaps,” Acta Biomaterialia 35 (2016): 166-184.

[55] E. Kalabusheva, V. Terskikh, and E. Vorotelyak, “Hair Germ Model In Vitro via Human Postnatal Keratinocyte-Dermal Papilla Interactions: Impact of Hyaluronic Acid,” Stem Cells International 2017 (2017): 9271869.

[56] W. Zhang, B. Vazquez, D. Oreadi, and P. C. Yelick, “Decellularized Tooth Bud Scaffolds for Tooth Regeneration,” Journal of Dental Research 96, no. 5 (2017): 516-523.

[57] X. Yin, B. E. Mead, H. Safaee, R. Langer, J. M. Karp, and O. Levy, “Engineering Stem Cell Organoids,” Cell Stem Cell 18, no. 1 (2016): 25-38.

[58] E. Allaire, P. Bruneval, C. Mandet, J. P. Becquemin, and J. B. Michel, “The immunogenicity of the extracellular matrix in arterial xenografts,” Surgery 122, no. 1 (1997): 73-81.

[59] W. Ferraro, A. Civilleri, C. Gögele, et al., “The Phenotype of Mesenchymal Stromal Cell and Articular Chondrocyte Cocultures on Highly Porous Bilayer Poly-L-Lactic Acid Scaffolds Produced by Thermally Induced Phase Separation and Supplemented With Hydroxyapatite,” Polymers (Basel) 16, no. 3 (2024): 331.

[60] A. Ravindran Girija, V. Palaninathan, X. Strudwick, S. Balasubramanian, S. Dasappan Nair, and A. J. Cowin, “Collagen-functionalized electrospun smooth and porous polymeric scaffolds for the development of human skin-equivalent,” RSC Advances 10, no. 45 (2020): 26594-26603.

[61] D. M. Supp, J. M. Hahn, C. M. Lloyd, et al., “Light or Dark Pigmentation of Engineered Skin Substitutes Containing Melanocytes Protects Against Ultraviolet Light-Induced DNA Damage In Vivo,” Journal of Burn Care & Research 41, no. 4 (2020): 751-760.

[62] C. Quílez, E. Y. Jeon, A. Pappalardo, P. Pathak, and H. E. Abaci, “Efficient Generation of Skin Organoids From Pluripotent Cells via Defined Extracellular Matrix Cues and Morphogen Gradients in a Spindle-Shaped Microfluidic Device,” Advanced Healthcare Materials 13, no. 20 (2024): e2400405.

[63] S. G. Edalat, Y. Jang, J. Kim, and Y. Park, “Collagen Type I Containing Hybrid Hydrogel Enhances Cardiomyocyte Maturation in a 3D Cardiac Model,” Polymers (Basel) 11, no. 4 (2019): 687.

[64] J. Lee, A. Sutani, R. Kaneko, et al., “In vitro generation of functional murine heart organoids via FGF4 and extracellular matrix,” Nature Communications 11, no. 1 (2020): 4283.

[65] E. Garreta, D. Moya-Rull, A. Marco, et al., “Natural Hydrogels Support Kidney Organoid Generation and Promote In Vitro Angiogenesis,” Advanced Materials 36, no. 34 (2024): e2400306.

[66] M. Isik, B. O. Okesola, C. C. Eylem, et al., “Bioactive and chemically defined hydrogels With tunable stiffness guide cerebral organoid formation and modulate multi-omics plasticity in cerebral organoids,” Acta Biomaterialia 171 (2023): 223-238.

[67] A. Feldman, D. Mukha, I. I. Maor, et al., “Blimp1+ cells generate functional mouse sebaceous gland organoids in vitro,” Nature Communications 10, no. 1 (2019): 2348.

[68] Z. Liu, J. Huang, D. Kang, et al., “Microenvironmental reprogramming of human dermal papilla cells for hair follicle tissue engineering,” Acta Biomaterialia 165 (2023): 31-49.

[69] A. Ootani, X. Li, E. Sangiorgi, et al., “Sustained in vitro intestinal epithelial culture Within a Wnt-dependent stem cell niche,” Nature Medicine 15, no. 6 (2009): 701-706.

[70] F. Portier, R. Kania, C. Planès, et al., “Enhanced sodium absorption in middle ear epithelial cells cultured at air-liquid interface,” Acta Oto-Laryngologica 125, no. 1 (2005): 16-22.

[71] J. Graf, M. Trautmann-Rodriguez, S. Sabnis, A. M. Kloxin, and C. A. Fromen, “On the path to predicting immune responses in the lung: Modeling the pulmonary innate immune system at the air-liquid interface (ALI),” European Journal of Pharmaceutical Sciences 191 (2023): 106596.

[72] Y. Qiang, N. Yao, F. Zuo, S. Qiu, X. Cao, and W. Zheng, “Tumor Organoid Model and Its Pharmacological Applications in Tumorigenesis Prevention,” Current Molecular Pharmacology 16, no. 4 (2023): 435-447.

[73] G. Wilke, L. J. Funkhouser-Jones, Y. Wang, et al., “A Stem-Cell-Derived Platform Enables Complete Cryptosporidium Development In Vitro and Genetic Tractability,” Cell Host & Microbe 26, no. 1 (2019): 123-134.e8.

[74] B.-Y. Xie and A.-W. Wu, “Organoid Culture of Isolated Cells From Patient-derived Tissues With Colorectal Cancer,” Chinese Medical Journal 129, no. 20 (2016): 2469-2475.

[75] P. Acharya, P. Joshi, S. Shrestha, N. Y. Choi, S. Jeong, and M.-Y. Lee, “Uniform cerebral organoid culture on a pillar plate by simple and reproducible spheroid transfer From an ultralow attachment well plate,” Biofabrication 16, no. 2 (2024): 25005.

[76] A. C. Gupta, S. Chawla, A. Hegde, et al., “Establishment of an in vitro organoid model of dermal papilla of human hair follicle,” Journal of Cellular Physiology 233, no. 11 (2018): 9015-9030.

[77] A. Urciuolo, G. G. Giobbe, Y. Dong, et al., “Hydrogel-in-hydrogel live bioprinting for guidance and control of organoids and organotypic cultures,” Nature Communications 14, no. 1 (2023): 3128.

[78] G. Saorin, I. Caligiuri, and F. Rizzolio, “Microfluidic organoids-on-a-chip: The future of human models,” Seminars in Cell & Developmental Biology 144 (2023): 41-54.

[79] A. Sattari, P. Hanafizadeh, and M. Hoorfar, “Multiphase flow in microfluidics: From droplets and bubbles to the encapsulated structures,” Advances in Colloid and Interface Science 282 (2020): 102208.

[80] S.-Y. Teh, R. Lin, L.-H. Hung, and A. P. Lee, “Droplet microfluidics,” Lab on A Chip 8, no. 2 (2008): 198-220.

[81] D. Choi, A. M. Gonzalez-Suarez, M. G. Dumbrava, et al., “Microfluidic Organoid Cultures Derived From Pancreatic Cancer Biopsies for Personalized Testing of Chemotherapy and Immunotherapy,” Advanced Science (Weinh) 11, no. 5 (2024): e2303088.

[82] A. S. Caldwell, B. A. Aguado, and K. S. Anseth, “Designing Microgels for Cell Culture and Controlled Assembly of Tissue Microenvironments,” Advanced Functional Materials 30, no. 37 (2020): 1907670.

[83] F. Nativel, D. Renard, F. Hached, et al., “Application of Millifluidics to Encapsulate and Support Viable Human Mesenchymal Stem Cells in a Polysaccharide Hydrogel,” International Journal of Molecular Sciences 19, no. 7 (2018): 1952.

[84] S.-R. Lee, Y. Kim, S. Kim, et al., “U-IMPACT: A universal 3D microfluidic cell culture platform,” Microsystems & Nanoengineering 8 (2022): 126.

[85] B. Gabbin, V. Meraviglia, M. L. Angenent, et al., “Heart and kidney organoids maintain organ-specific function in a microfluidic system,” Materials Today Bio 23 (2023): 100818.

[86] B. Pain, “Organoids in domestic animals: With which stem cells?,” Veterinary Research 52, no. 1 (2021): 38.

[87] H. H. N. Yan, A. S. Chan, F. P.-L. Lai, and S. Y. Leung, “Organoid cultures for cancer modeling,” Cell Stem Cell 30, no. 7 (2023): 917-937.

[88] J. van der Vaart and H. Clevers, “Airway organoids as models of human disease,” Journal of Internal Medicine 289, no. 5 (2021): 604-613.

[89] A. A. Dayem, K. Kim, S. B. Lee, A. Kim, and S.-G. Cho, “Application of Adult and Pluripotent Stem Cells in Interstitial Cystitis/Bladder Pain Syndrome Therapy: Methods and Perspectives,” Journal of Clinical Medicine 9, no. 3 (2020): 766.

[90] S. Al-Ghadban and B. A. Bunnell, “Adipose Tissue-Derived Stem Cells: Immunomodulatory Effects and Therapeutic Potential,” Physiology (Bethesda, Md.) 35, no. 2 (2020): 125-133.

[91] Z. Si, X. Wang, C. Sun, et al., “Adipose-derived stem cells: Sources, potency, and implications for regenerative therapies,” Biomedicine & Pharmacotherapy 114 (2019): 108765.

[92] S. Rauth, S. Karmakar, S. K. Batra, and M. P. Ponnusamy, “Recent advances in organoid development and applications in disease modeling,” Biochim Biophys Acta Rev Cancer 1875, no. 2 (2021): 188527.

[93] L. Hemeryck, F. Hermans, J. Chappell, et al., “Organoids From human tooth showing epithelial stemness phenotype and differentiation potential,” Cellular and Molecular Life Sciences 79, no. 3 (2022): 153.

[94] K. Shin, “Stem cells, organoids and their applications for human diseases: Special issue of BMB Reports in 2023,” BMB Reports 56, no. 1 (2023): 1.

[95] M. Chang, M. S. Bogacheva, and Y.-R. Lou, “Challenges for the Applications of Human Pluripotent Stem Cell-Derived Liver Organoids,” Frontiers in Cell and Developmental Biology 9 (2021): 748576.

[96] M. Magni, B. Bossi, P. Conforti, et al., “Brain Regional Identity and Cell Type Specificity Landscape of Human Cortical Organoid Models,” International Journal of Molecular Sciences 23, no. 21 (2022): 13159.

[97] W. L. Thompson and T. Takebe, “Generation of multi-cellular human liver organoids From pluripotent stem cells,” Methods in Cell Biology 159 (2020): 47-68.

[98] R. Ouchi and H. Koike, “Modeling human liver organ development and diseases With pluripotent stem cell-derived organoids,” Frontiers in Cell and Developmental Biology 11 (2023): 1133534.

[99] Y. Zhang, S. Yan, Z. Mei, et al., “Exploring the Cocktail Factor Approach to Generate Salivary Gland Progenitors Through Co-Culture Techniques,” Tissue Engineering and Regenerative Medicine 21, no. 5 (2024): 749-759.

[100] I. Hautefort, M. Poletti, D. Papp, and T. Korcsmaros, “Everything You Always Wanted to Know About Organoid-Based Models (and Never Dared to Ask),” Cellular and Molecular Gastroenterology and Hepatology 14, no. 2 (2022): 311-331.

[101] K. Santerre, S. Cortez Ghio, and S. Proulx, “TGF-β-Mediated Modulation of Cell-Cell Interactions in Postconfluent Maturing Corneal Endothelial Cells,” Investigative Ophthalmology & Visual Science 63, no. 11 (2022): 3.

[102] M. Oft, J. Peli, C. Rudaz, H. Schwarz, H. Beug, and E. Reichmann, “TGF-beta1 and Ha-Ras collaborate in modulating the phenotypic plasticity and invasiveness of epithelial tumor cells,” Genes & Development 10, no. 19 (1996): 2462-2477.

[103] X. Li, R. Xie, Y. Luo, et al., “Cooperation of TGF-β and FGF signalling pathways in skin development,” Cell Proliferation 56, no. 11 (2023): e13489.

[104] X.-M. Meng, D. J. Nikolic-Paterson, and H. Y. Lan, “TGF-β: The master regulator of fibrosis,” Nature Reviews Nephrology 12, no. 6 (2016): 325-338.

[105] S. B. Telerman, E. Rognoni, I. Sequeira, et al., “Dermal Blimp1 Acts Downstream of Epidermal TGFβ and Wnt/β-Catenin to Regulate Hair Follicle Formation and Growth,” Journal of Investigative Dermatology 137, no. 11 (2017): 2270-2281.

[106] S. B. Hwang, H. J. Park, and B.-H. Lee, “Hair-Growth-Promoting Effects of the Fish Collagen Peptide in Human Dermal Papilla Cells and C57BL/6 Mice Modulating Wnt/β-Catenin and BMP Signaling Pathways,” International Journal of Molecular Sciences 23, no. 19 (2022): 11904.

[107] G. J. Fisher, B. Wang, Y. Cui, et al., “Skin aging From the perspective of dermal fibroblasts: The interplay Between the adaptation to the extracellular matrix microenvironment and cell autonomous processes,” Journal of Cell Communication and Signaling 17, no. 3 (2023): 523-529.

[108] M. K. Lichtman, M. Otero-Vinas, and V. Falanga, “Transforming growth factor beta (TGF-β) isoforms in wound healing and fibrosis,” Wound Repair and Regeneration 24, no. 2 (2016): 215-222.

[109] K. E. Boonekamp, K. Kretzschmar, D. J. Wiener, et al., “Long-term expansion and differentiation of adult murine epidermal stem cells in 3D organoid cultures,” Proceedings of the National Academy of Sciences of the United States of America 116, no. 29 (2019): 14630-14638.

[110] J.-P. Ng-Blichfeldt, T. de Jong, R. K. Kortekaas, et al., “TGF-β activation impairs fibroblast ability to support adult lung epithelial progenitor cell organoid formation,” American Journal of Physiology. Lung Cellular and Molecular Physiology 317, no. 1 (2019): L14-L28.

[111] T. Ringel, N. Frey, F. Ringnalda, et al., “Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance,” Cell Stem Cell 26, no. 3 (2020): 431-440.e8.

[112] S. Sahu, S. Sahoo, T. Sullivan, et al., “Spatiotemporal modulation of growth factors directs the generation of multilineage mouse embryonic stem cell-derived mammary organoids,” Developmental Cell 59, no. 2 (2024): 175-186.e8.

[113] X.-J. Zhu, Y. Liu, Z.-M. Dai, et al., “BMP-FGF signaling axis mediates Wnt-induced epidermal stratification in developing mammalian skin,” PLOS Genetics 10, no. 10 (2014): e1004687.

[114] J. R. Hens, P. Dann, J.-P. Zhang, S. Harris, G. W. Robinson, and J. Wysolmerski, “BMP4 and PTHrP interact to stimulate ductal outgrowth During embryonic mammary development and to inhibit hair follicle induction,” Development (Cambridge, England) 134, no. 6 (2007): 1221-1230.

[115] P. A. Wilson, G. Lagna, A. Suzuki, and A. Hemmati-Brivanlou, “Concentration-dependent patterning of the Xenopus ectoderm by BMP4 and its signal transducer Smad1,” Development (Cambridge, England) 124, no. 16 (1997): 3177-3184.

[116] M. Goswami, A. R. Uzgare, and A. K. Sater, “Regulation of MAP kinase by the BMP-4/TAK1 pathway in Xenopus ectoderm,” Developmental Biology 236, no. 2 (2001): 259-270.

[117] E. Pera, S. Stein, and M. Kessel, “Ectodermal patterning in the avian embryo: Epidermis versus neural plate,” Development (Cambridge, England) 126, no. 1 (1999): 63-73.

[118] M. H. Kwack, J. M. Yang, G. H. Won, M. K. Kim, J. C. Kim, and Y. K. Sung, “Establishment and characterization of five immortalized human scalp dermal papilla cell lines,” Biochemical and Biophysical Research Communications 496, no. 2 (2018): 346-351.

[119] K. R. Koehler, A. M. Mikosz, A. I. Molosh, D. Patel, and E. Hashino, “Generation of inner ear sensory epithelia From pluripotent stem cells in 3D culture,” Nature 500, no. 7461 (2013): 217-221.

[120] M.-I. Chung, M. Bujnis, C. E. Barkauskas, Y. Kobayashi, and B. L. M. Hogan, “Niche-mediated BMP/SMAD signaling regulates lung alveolar stem cell proliferation and differentiation,” Development (Cambridge, England) 145, no. 9 (2018): dev163014.

[121] X.-P. Liu, K. R. Koehler, A. M. Mikosz, E. Hashino, and J. R. Holt, “Functional development of mechanosensitive hair cells in stem cell-derived organoids parallels native vestibular hair cells,” Nature Communications 7 (2016): 11508.

[122] S. Yamasaki, A. Kuwahara, A. Kishino, T. Kimura, M. Takahashi, and M. Mandai, “Addition of Chk1 inhibitor and BMP4 cooperatively promotes retinal tissue formation in self-organizing human pluripotent stem cell differentiation culture,” Regenerative Therapy 19 (2022): 24-34.

[123] C. G. Mills, M. L. Lawrence, D. A. D. Munro, M. Elhendawi, J. J. Mullins, and J. A. Davies, “Asymmetric BMP4 signalling improves the realism of kidney organoids,” Scientific Reports 7, no. 1 (2017): 14824.

[124] J. Beumer, J. Puschhof, F. Y. Yengej, et al., “BMP gradient Along the intestinal villus axis controls zonated enterocyte and goblet cell states,” Cell Reports 38, no. 9 (2022): 110438.

[125] Y. Hu, X. Hu, J. Luo, et al., “Liver organoid culture methods,” Cell & Bioscience 13, no. 1 (2023): 197.

[126] M. Kawano, A. Komi-Kuramochi, M. Asada, et al., “Comprehensive analysis of FGF and FGFR expression in skin: FGF18 is highly expressed in hair follicles and capable of inducing anagen From telogen stage hair follicles,” Journal of Investigative Dermatology 124, no. 5 (2005): 877-885.

[127] J. G. Rheinwald and H. Green, “Epidermal growth factor and the multiplication of cultured human epidermal keratinocytes,” Nature 265, no. 5593 (1977): 421-424.

[128] Y. Hu, A. Mintz, S. R. Shah, A. Quinones-Hinojosa, and W. Hsu, “The FGFR/MEK/ERK/brachyury pathway is critical for chordoma cell growth and survival,” Carcinogenesis 35, no. 7 (2014): 1491-1499.

[129] M. Czyz, “Fibroblast Growth Factor Receptor Signaling in Skin Cancers,” Cells 8, no. 6 (2019): 540.

[130] X. Wang, Y. Zhu, C. Sun, et al., “Feedback Activation of Basic Fibroblast Growth Factor Signaling via the Wnt/β-Catenin Pathway in Skin Fibroblasts,” Frontiers in Pharmacology 8 (2017): 32.

[131] T. Horigome, S. Takumi, K. Shirai, et al., “Sulfated glycosaminoglycans and non-classically secreted proteins, basic FGF and epimorphin, coordinately regulate TGF-β-induced cell behaviors of human scar dermal fibroblasts,” Journal of Dermatological Science 86, no. 2 (2017): 132-141.

[132] J. Otte, L. Dizdar, B. Behrens, et al., “FGF Signalling in the Self-Renewal of Colon Cancer Organoids,” Scientific Reports 9, no. 1 (2019): 17365.

[133] A. Rabata, R. Fedr, K. Soucek, A. Hampl, and Z. Koledova, “3D Cell Culture Models Demonstrate a Role for FGF and WNT Signaling in Regulation of Lung Epithelial Cell Fate and Morphogenesis,” Frontiers in Cell and Developmental Biology 8 (2020): 574.

[134] M. Fujii, M. Matano, K. Toshimitsu, et al., “Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition,” Cell Stem Cell 23, no. 6 (2018): 787-793.e6.

[135] C.-H. Park and J. H. Chung, “Epidermal growth factor-induced matrix metalloproteinase-1 expression is negatively regulated by p38 MAPK in human skin fibroblasts,” Journal of Dermatological Science 64, no. 2 (2011): 134-141.

[136] D. L. du Cros, “Fibroblast growth factor and epidermal growth factor in hair development,” Journal of Investigative Dermatology 101, no. 1 Suppl (1993): 106S-113S.

[137] H. Zhang, W. Nan, S. Wang, et al., “Epidermal growth factor promotes proliferation of dermal papilla cells via Notch signaling pathway,” Biochimie 127 (2016): 10-18.

[138] H. E. Abud, W. H. Chan, and T. Jardé, “Source and Impact of the EGF Family of Ligands on Intestinal Stem Cells,” Frontiers in Cell and Developmental Biology 9 (2021): 685665.

[139] Y.-J. Yoon, D. Kim, K. Y. Tak, et al., “Salivary gland organoid culture maintains distinct glandular properties of murine and human major salivary glands,” Nature Communications 13, no. 1 (2022): 3291.

[140] T. Sato, J. H. van Es, H. J. Snippert, et al., “Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts,” Nature 469, no. 7330 (2011): 415-418.

[141] T. Jardé, B. Lloyd-Lewis, M. Thomas, et al., “Wnt and Neuregulin1/ErbB signalling extends 3D culture of hormone responsive mammary organoids,” Nature Communications 7 (2016): 13207.

[142] E. Suarez-Martinez, I. Suazo-Sanchez, M. Celis-Romero, and A. Carnero, “3D and organoid culture in research: Physiology, hereditary genetic diseases and cancer,” Cell & Bioscience 12, no. 1 (2022): 39.

[143] J. Lee, R. Böscke, P.-C. Tang, B. H. Hartman, S. Heller, and K. R. Koehler, “Hair Follicle Development in Mouse Pluripotent Stem Cell-Derived Skin Organoids,” Cell Reports 22, no. 1 (2018): 242-254.

[144] O. Arda, N. Göksügür, and Y. Tüzün, “Basic histological structure and functions of facial skin,” Clinics in Dermatology 32, no. 1 (2014): 3-13.

[145] M. I. Koster, “Making an epidermis,” Annals of the New York Academy of Sciences 1170 (2009): 7-10.

[146] M. I. Morasso and M. Tomic-Canic, “Epidermal stem cells: The cradle of epidermal determination, differentiation and wound healing,” Biologie Cellulaire 97, no. 3 (2005): 173-183.

[147] D. T. Woodley, “Distinct Fibroblasts in the Papillary and Reticular Dermis: Implications for Wound Healing,” Dermatologic Clinics 35, no. 1 (2017): 95-100.

[148] M. Wang, X. Zhou, S. Zhou, et al., “Mechanical force drives the initial mesenchymal-epithelial interaction During skin organoid development,” Theranostics 13, no. 9 (2023): 2930-2945.

[149] Y. Kim and J. H. Ju, “Generation of 3D Skin Organoid From Cord Blood-derived Induced Pluripotent Stem Cells,” Journal of Visualized Experiments: JoVE no. 146 (2019).

[150] Y. Kim, N. Park, Y. A. Rim, et al., “Establishment of a complex skin structure via layered co-culture of keratinocytes and fibroblasts derived From induced pluripotent stem cells,” Stem Cell Research & Therapy 9, no. 1 (2018): 217.

[151] F. Groeber, L. Engelhardt, J. Lange, et al., “A first vascularized skin equivalent as an alternative to animal experimentation,” Altex 33, no. 4 (2016): 415-422.

[152] T. H. Browning and J. S. Trier, “Organ culture of mucosal biopsies of human small intestine,” The Journal of Clinical Investigation 48, no. 8 (1969): 1423-1432.

[153] C. Booth and C. S. Potten, “Gut instincts: Thoughts on intestinal epithelial stem cells,” The Journal of Clinical Investigation 105, no. 11 (2000): 1493-1499.

[154] A. J. Miller, B. R. Dye, D. Ferrer-Torres, et al., “Generation of lung organoids From human pluripotent stem cells in vitro,” Nature Protocols 14, no. 2 (2019): 518-540.

[155] A. A. Salahudeen, S. S. Choi, A. Rustagi, et al., “Progenitor identification and SARS-CoV-2 infection in human distal lung organoids,” Nature 588, no. 7839 (2020): 670-675.

[156] X. Gao, A. S. Bali, S. H. Randell, and B. L. M. Hogan, “GRHL2 coordinates regeneration of a polarized mucociliary epithelium From basal stem cells,” Journal of Cell Biology 211, no. 3 (2015): 669-682.

[157] L. Drakhlis, S. Biswanath, C.-M. Farr, et al., “Human heart-forming organoids recapitulate early heart and foregut development,” Nature Biotechnology 39, no. 6 (2021): 737-746.

[158] E. Driehuis, K. Kretzschmar, and H. Clevers, “Establishment of patient-derived cancer organoids for drug-screening applications,” Nature Protocols 15, no. 10 (2020): 3380-3409.

[159] L. Huang, A. Holtzinger, I. Jagan, et al., “Ductal pancreatic cancer modeling and drug screening using human pluripotent stem cell- and patient-derived tumor organoids,” Nature Medicine 21, no. 11 (2015): 1364-1371.

[160] H. Zhao, E. Jiang, and Z. Shang, “3D Co-culture of Cancer-Associated Fibroblast With Oral Cancer Organoids,” Journal of Dental Research 100, no. 2 (2021): 201-208.

[161] Z. Zhou, K. Van der Jeught, Y. Fang, et al., “An organoid-based screen for epigenetic inhibitors that stimulate antigen presentation and potentiate T-cell-mediated cytotoxicity,” Nature Biomedical Engineering 5, no. 11 (2021): 1320-1335.

[162] S. Kwak, C. L. Song, J. Lee, et al., “Development of pluripotent stem cell-derived epidermal organoids that generate effective extracellular vesicles in skin regeneration,” Biomaterials 307 (2024): 122522.

[163] M.-J. Kim, H.-J. Ahn, D. Kong, S. Lee, D.-H. Kim, and K.-S. Kang, “Modeling of solar UV-induced photodamage on the hair follicles in human skin organoids,” Journal of Tissue Engineering 15 (2024): 20417314241248753.

[164] M. Kubista, J. M. Andrade, M. Bengtsson, et al., “The real-time polymerase chain reaction,” Molecular Aspects of Medicine 27, no. 2-3 (2006): 95-125.

[165] H. Begum, P. Murugesan, and A. D. Tangutur, “Western blotting: A powerful staple in scientific and biomedical research,” Biotechniques 73, no. 1 (2022): 58-69.

[166] J. Zhu, Y. Fan, Y. Xiong, et al., “Delineating the dynamic evolution From preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics,” Experimental & Molecular Medicine 54, no. 11 (2022): 2060-2076.

[167] C. Haase, K. Gustafsson, S. Mei, et al., “Image-seq: Spatially resolved single-cell sequencing guided by in situ and in vivo imaging,” Nature Methods 19, no. 12 (2022): 1622-1633.

[168] P. W. Harms, T. L. Frankel, M. Moutafi, et al., “Multiplex Immunohistochemistry and Immunofluorescence: A Practical Update for Pathologists,” Modern Pathology 36, no. 7 (2023): 100197.

[169] B. Yuan, X. Zhao, X. Wang, et al., “Patient-derived organoids for personalized gallbladder cancer modelling and drug screening,” Clinical and Translational Medicine 12, no. 1 (2022): e678.

[170] J. Lighten, C. van Oosterhout, and P. Bentzen, “Critical review of NGS analyses for de novo genotyping multigene families,” Molecular Ecology 23, no. 16 (2014): 3957-3972.

[171] D. Grün and A. van Oudenaarden, “Design and Analysis of Single-Cell Sequencing Experiments,” Cell 163, no. 4 (2015): 799-810.

[172] C. Zhang, J. Li, Y. Cheng, et al., “Single-cell RNA sequencing reveals intrahepatic and peripheral immune characteristics related to disease phases in HBV-infected patients,” Gut 72, no. 1 (2023): 153-167.

[173] L. Zhang, Z. Li, K. M. Skrzypczynska, et al., “Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer,” Cell 181, no. 2 (2020): 442-459.e29.

[174] S. Jain, J. W. Rick, R. S. Joshi, et al., “Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma With protumoral effects,” The Journal of Clinical Investigation 133, no. 5 (2023): e147087.

[175] J. Bues, M. Biočanin, J. Pezoldt, et al., “Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition,” Nature Methods 19, no. 3 (2022): 323-330.

[176] F. X. Galdos, C. Lee, S. Lee, et al., “Combined lineage tracing and scRNA-seq reveals unexpected first heart field predominance of human iPSC differentiation,” Elife 12 (2023): e80075.

[177] K. Chen, Y. Ma, X. Zhong, et al., “Single-cell transcriptome profiling of primary tumors and paired organoids of pancreatobiliary cancer,” Cancer Letters 582 (2024): 216586.

[178] J. Lu, A. Krepelova, S. M. M. Rasa, et al., “Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling,” Scientific Reports 11, no. 1 (2021): 16668.

[179] T. Denyer, X. Ma, S. Klesen, E. Scacchi, K. Nieselt, and M. C. P. Timmermans, “Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing,” Developmental Cell 48, no. 6 (2019): 840-852.e5.

[180] A. Cherubini, F. Rusconi, R. Piras, et al., “Exploring human pancreatic organoid modelling Through single-cell RNA sequencing analysis,” Communications Biology 7, no. 1 (2024): 1527.

[181] A. R. Stabell, G. E. Lee, Y. Jia, et al., “Single-cell transcriptomics of human-skin-equivalent organoids,” Cell Reports 42, no. 5 (2023): 112511.

[182] S. Guinn, B. Kinny-Köster, J. A. Tandurella, et al., “Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated With Epithelial-Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma,” Cancer Research 84, no. 9 (2024): 1517-1533.

[183] X. Wan, J. Xiao, S. S. T. Tam, et al., “Integrating spatial and single-cell transcriptomics data using deep generative models With SpatialScope,” Nature Communications 14, no. 1 (2023): 7848.

[184] I. Chiaradia, I. Imaz-Rosshandler, B. S. Nilges, et al., “Tissue morphology influences the temporal program of human brain organoid development,” Cell Stem Cell 30, no. 10 (2023): 1351-1367.e10.

[185] M. Wang, L. Zhang, S. W. Novak, et al., “Morphological diversification and functional maturation of human astrocytes in glia-enriched cortical organoid transplanted in mouse brain,” Nature Biotechnology 43, no. 1 (2025): 52-62.

[186] S. E. Kornguth and J. W. Anderson, “Localization of a basic protein in the myelin of various species With the aid of fluorescence and electron microscopy,” Journal of Cell Biology 26, no. 1 (1965): 157-166.

[187] C. Stadler, E. Rexhepaj, V. R. Singan, et al., “Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells,” Nature Methods 10, no. 4 (2013): 315-323.

[188] M. Cario-Andre, “Analysis of CCN Expression by Immunofluorescence on Skin Cells, Skin, and Reconstructed Epidermis,” Methods in Molecular Biology 1489 (2017): 63-76.

[189] S. Liu, H. Zhang, and E. Duan, “Epidermal development in mammals: Key regulators, signals From beneath, and stem cells,” International Journal of Molecular Sciences 14, no. 6 (2013): 10869-10895.

[190] E. Fuchs, “Scratching the surface of skin development,” Nature 445, no. 7130 (2007): 834-842.

[191] F. Oceguera-Yanez, A. Avila-Robinson, and K. Woltjen, “Differentiation of pluripotent stem cells for modeling human skin development and potential applications,” Frontiers in Cell and Developmental Biology 10 (2022): 1030339.

[192] A. L. Rippa, E. P. Kalabusheva, and E. A. Vorotelyak, “Regeneration of Dermis: Scarring and Cells Involved,” Cells 8, no. 6 (2019): 607.

[193] T. Tabib, C. Morse, T. Wang, W. Chen, and R. Lafyatis, “SFRP2/DPP4 and FMO1/LSP1 Define Major Fibroblast Populations in Human Skin,” Journal of Investigative Dermatology 138, no. 4 (2018): 802-810.

[194] H. J. Morgan, A. Benketah, C. Olivero, et al., “Hair follicle differentiation-specific keratin expression in human basal cell carcinoma,” Clinical and Experimental Dermatology 45, no. 4 (2020): 417-425.

[195] L. Van Hove, A. Toniolo, M. Ghiasloo, et al., “Autophagy critically controls skin inflammation and apoptosis-induced stem cell activation,” Autophagy 19, no. 11 (2023): 2958-2971.

[196] A. L. Mesler, N. A. Veniaminova, M. V. Lull, and S. Y. Wong, “Hair Follicle Terminal Differentiation Is Orchestrated by Distinct Early and Late Matrix Progenitors,” Cell Reports 19, no. 4 (2017): 809-821.

[197] D. D. Bikle, H. Elalieh, S. Chang, Z. Xie, and J. P. Sundberg, “Development and progression of alopecia in the vitamin D receptor null mouse,” Journal of Cellular Physiology 207, no. 2 (2006): 340-353.

[198] S. Xiong, W. Liu, Y. Song, et al., “Metformin Promotes Mechanical Stretch-Induced Skin Regeneration by Improving the Proliferative Activity of Skin-Derived Stem Cells,” Frontiers in Medicine (Lausanne) 9 (2022): 813917.

[199] S. Müller-Röver, Y. Tokura, P. Welker, et al., “E- and P-cadherin expression During murine hair follicle morphogenesis and cycling,” Experimental Dermatology 8, no. 4 (1999): 237-246.

[200] I. Lukonin, D. Serra, L. Challet Meylan, et al., “Phenotypic landscape of intestinal organoid regeneration,” Nature 586, no. 7828 (2020): 275-280.

[201] S. S. Jose, M. De Zuani, F. Tidu, et al., “Comparison of two human organoid models of lung and intestinal inflammation reveals Toll-Like receptor signalling activation and monocyte recruitment,” Clinical & Translational Immunology 9, no. 5 (2020): e1131.

[202] M. C. Basil, F. L. Cardenas-Diaz, J. J. Kathiriya, et al., “Human distal airways contain a multipotent secretory cell that can regenerate alveoli,” Nature 604, no. 7904 (2022): 120-126.

[203] T. Suezawa, S. Kanagaki, K. Moriguchi, et al., “Disease modeling of pulmonary fibrosis using human pluripotent stem cell-derived alveolar organoids,” Stem Cell Reports 16, no. 12 (2021): 2973-2987.

[204] E. Tran, T. Shi, X. Li, et al., “Development of human alveolar epithelial cell models to study distal lung biology and disease,” Iscience 25, no. 2 (2022): 103780.

[205] S. L. Leibel, A. Winquist, I. Tseu, et al., “Reversal of Surfactant Protein B Deficiency in Patient Specific Human Induced Pluripotent Stem Cell Derived Lung Organoids by Gene Therapy,” Scientific Reports 9, no. 1 (2019): 13450.

[206] K. Murata, U. Jadhav, S. Madha, et al., “Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells,” Cell Stem Cell 26, no. 3 (2020): 377-390.e6.

[207] J. E. van Timmeren, D. Cester, S. Tanadini-Lang, H. Alkadhi, and B. Baessler, “Radiomics in medical imaging-“how-to” guide and critical reflection,” Insights Imaging 11, no. 1 (2020): 91.

[208] R. Gupta, D. Srivastava, M. Sahu, S. Tiwari, R. K. Ambasta, and P. Kumar, “Artificial intelligence to deep learning: Machine intelligence approach for drug discovery,” Molecular Diversity 25, no. 3 (2021): 1315-1360.

[209] M. Bhat, M. Rabindranath, B. S. Chara, and D. A. Simonetto, “Artificial intelligence, machine learning, and deep learning in liver transplantation,” Journal of Hepatology 78, no. 6 (2023): 1216-1233.

[210] W. Caii, X. Wu, K. Guo, Y. Chen, Y. Shi, and J. Chen, “Integration of deep learning and habitat radiomics for predicting the response to immunotherapy in NSCLC patients,” Cancer Immunology, Immunotherapy 73, no. 8 (2024): 153.

[211] H. Espedal, K. E. Fasmer, H. F. Berg, et al., “MRI radiomics captures early treatment response in patient-derived organoid endometrial cancer mouse models,” Frontiers In Oncology 14 (2024): 1334541.

[212] M. P. Schwartz, Z. Hou, N. E. Propson, et al., “Human pluripotent stem cell-derived neural constructs for predicting neural toxicity,” Proceedings of the National Academy of Sciences of the United States of America 112, no. 40 (2015): 12516-12521.

[213] X. Pang, R. Xie, Z. Zhang, Q. Liu, S. Wu, and Y. Cui, “Identification of SPP1 as an Extracellular Matrix Signature for Metastatic Castration-Resistant Prostate Cancer,” Frontiers in Oncology 9 (2019): 924.

[214] H. Wu, K. Uchimura, E. L. Donnelly, Y. Kirita, S. A. Morris, and B. D. Humphreys, “Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation With Single-Cell Transcriptomics,” Cell Stem Cell 23, no. 6 (2018): 869-881.e8.

[215] S. Ji, L. Feng, Z. Fu, et al., “Pharmaco-proteogenomic characterization of liver cancer organoids for precision oncology,” Science Translational Medicine 15, no. 706 (2023): eadg3358.

[216] J. Qiu, X. Qu, Y. Wang, et al., “Single-Cell Landscape Highlights Heterogenous Microenvironment, Novel Immune Reaction Patterns, Potential Biomarkers and Unique Therapeutic Strategies of Cervical Squamous Carcinoma, Human Papillomavirus-Associated (HPVA) and Non-HPVA Adenocarcinoma,” Advanced Science (Weinh) 10, no. 10 (2023): e2204951.

[217] M. Nesbit, H. Schaider, C. Berking, et al., “Alpha5 and alpha2 integrin gene transfers mimic the PDGF-B-induced transformed phenotype of fibroblasts in human skin,” Laboratory Investigation 81, no. 9 (2001): 1263-1274.

[218] J. Lee, W. H. van der Valk, S. A. Serdy, et al., “Generation and characterization of hair-bearing skin organoids From human pluripotent stem cells,” Nature Protocols 17, no. 5 (2022): 1266-1305.

[219] J. Xu, X. Wang, J. Chen, et al., “Embryonic stem cell-derived mesenchymal stem cells promote colon epithelial integrity and regeneration by elevating circulating IGF-1 in colitis mice,” Theranostics 10, no. 26 (2020): 12204-12222.

[220] Y. Chen, Z. Fan, X. Wang, et al., “PI3K/Akt signaling pathway is essential for de novo hair follicle regeneration,” Stem Cell Research & Therapy 11, no. 1 (2020): 144.

[221] M. Lei, L. J. Schumacher, Y.-C. Lai, et al., “Self-organization process in newborn skin organoid formation inspires strategy to restore hair regeneration of adult cells,” Proceedings of the National Academy of Sciences of the United States of America 114, no. 34 (2017): E7101-E7110.

[222] M. Sadagurski, S. Yakar, G. Weingarten, et al., “Insulin-Like growth factor 1 receptor signaling regulates skin development and inhibits skin keratinocyte differentiation,” Molecular and Cellular Biology 26, no. 7 (2006): 2675-2687.

[223] R. Bai, Y. Guo, W. Liu, Y. Song, Z. Yu, and X. Ma, “The Roles of WNT Signaling Pathways in Skin Development and Mechanical-Stretch-Induced Skin Regeneration,” Biomolecules 13, no. 12 (2023): 1702.

[224] A. R. Jussila, B. Zhang, E. Caves, et al., “Skin Fibrosis and Recovery Is Dependent on Wnt Activation via DPP4,” Journal of Investigative Dermatology 142, no. 6 (2022): 1597-1606.e9.

[225] J. Fu and W. Hsu, “Epidermal Wnt controls hair follicle induction by orchestrating dynamic signaling crosstalk Between the epidermis and dermis,” Journal of Investigative Dermatology 133, no. 4 (2013): 890-898.

[226] M. Ito, Z. Yang, T. Andl, et al., “Wnt-dependent de novo hair follicle regeneration in adult mouse skin After wounding,” Nature 447, no. 7142 (2007): 316-320.

[227] C. Zhang, P. Chen, Y. Fei, et al., “Wnt/β-catenin signaling is critical for dedifferentiation of aged epidermal cells in vivo and in vitro,” Aging Cell 11, no. 1 (2012): 14-23.

[228] Y. Su, J. Wen, J. Zhu, et al., “Pre-aggregation of scalp progenitor dermal and epidermal stem cells activates the WNT pathway and promotes hair follicle formation in in vitro and in vivo systems,” Stem Cell Research & Therapy 10, no. 1 (2019): 403.

[229] L. Leng, J. Ma, L. Lv, et al., “Both Wnt signaling and epidermal stem cell-derived extracellular vesicles are involved in epidermal cell growth,” Stem Cell Research & Therapy 11, no. 1 (2020): 415.

[230] A. Veltri, C. Lang, and W.-H. Lien, “Concise Review: Wnt Signaling Pathways in Skin Development and Epidermal Stem Cells,” Stem Cells 36, no. 1 (2018): 22-35.

[231] W. Fan, K. M. Christian, H. Song, and G.-L. Ming, “Applications of Brain Organoids for Infectious Diseases,” Journal of Molecular Biology 434, no. 3 (2022): 167243.

[232] D. Rodrigues, L. Coyle, B. Füzi, et al., “Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids,” International Journal of Molecular Sciences 23, no. 3 (2022): 1286.

[233] A. L. Haber, M. Biton, N. Rogel, et al., “A single-cell survey of the small intestinal epithelium,” Nature 551, no. 7680 (2017): 333-339.

[234] A. Lowe, R. Harris, P. Bhansali, A. Cvekl, and W. Liu, “Intercellular Adhesion-Dependent Cell Survival and ROCK-Regulated Actomyosin-Driven Forces Mediate Self-Formation of a Retinal Organoid,” Stem Cell Reports 6, no. 5 (2016): 743-756.

[235] J. P. Alves-Lopes and J.-B. Stukenborg, “Testicular organoids: A new model to study the testicular microenvironment in vitro?,” Human Reproduction Update 24, no. 2 (2018): 176-191.

[236] P. Hofbauer, S. M. Jahnel, N. Papai, et al., “Cardioids reveal self-organizing principles of human cardiogenesis,” Cell 184, no. 12 (2021): 3299-3317.e22.

[237] Y. Zhao, S. Li, L. Zhu, et al., “Personalized drug screening using patient-derived organoid and its clinical relevance in gastric cancer,” Cell Reports Medicine 5, no. 7 (2024): 101627.

[238] Y. Mao, W. Wang, J. Yang, et al., “Drug repurposing screening and mechanism analysis based on human colorectal cancer organoids,” Protein Cell 15, no. 4 (2024): 285-304.

[239] T. Shinozawa, M. Kimura, Y. Cai, et al., “High-Fidelity Drug-Induced Liver Injury Screen Using Human Pluripotent Stem Cell-Derived Organoids,” Gastroenterology 160, no. 3 (2021): 831-846.e10.

[240] S.-Y. Jung, H. J. You, M.-J. Kim, G. Ko, S. Lee, and K.-S. Kang, “Wnt-activating human skin organoid model of atopic dermatitis induced by Staphylococcus aureus and its protective effects by Cutibacterium acnes,” Iscience 25, no. 10 (2022): 105150.

[241] J. Ma, J. Liu, D. Gao, et al., “Establishment of Human Pluripotent Stem Cell-Derived Skin Organoids Enabled Pathophysiological Model of SARS-CoV-2 Infection,” Advanced Science (Weinh) 9, no. 7 (2022): e2104192.

[242] J. Ma, W. Li, R. Cao, et al., “Application of an iPSC-Derived Organoid Model for Localized Scleroderma Therapy,” Advanced Science (Weinh) 9, no. 16 (2022): e2106075.

[243] J. W. Foster, K. Wahlin, S. M. Adams, D. E. Birk, D. J. Zack, and S. Chakravarti, “Cornea organoids From human induced pluripotent stem cells,” Scientific Reports 7 (2017): 41286.

[244] X. Wan, J. Gu, X. Zhou, et al., “Establishment of human corneal epithelial organoids for ex vivo modelling dry eye disease,” Cell Proliferation 57, no. 11 (2024): e13704.

[245] X. Ren, M. Huang, W. Weng, et al., “Personalized drug screening in patient-derived organoids of biliary tract cancer and its clinical application,” Cell Reports Medicine 4, no. 11 (2023): 101277.

[246] J. F. Dekkers, C. L. Wiegerinck, H. R. de Jonge, et al., “A functional CFTR assay using primary cystic fibrosis intestinal organoids,” Nature Medicine 19, no. 7 (2013): 939-945.

[247] D. Wang, J. Wang, L. Bai, et al., “Long-Term Expansion of Pancreatic Islet Organoids From Resident Procr+ Progenitors,” Cell 180, no. 6 (2020): 1198-1211.e19.

[248] A. Zeleniak, C. Wiegand, W. Liu, et al., “De novo construction of T cell compartment in humanized mice engrafted With iPSC-derived thymus organoids,” Nature Methods 19, no. 10 (2022): 1306-1319.

[249] A. Pappalardo, D. Alvarez Cespedes, S. Fang, et al., “Engineering edgeless human skin With enhanced biomechanical properties,” Science Advances 9, no. 4 (2023): eade2514.

[250] H. Wu, G. Wang, Y. Shang, et al., “Organoids and Their Research Progress in Plastic and Reconstructive Surgery,” Aesthetic Plastic Surgery 47, no. 2 (2023): 880-891.

[251] S. Choudhury, N. R. Dhoke, S. Chawla, and A. Das, “Bioengineered MSCCxcr2 transdifferentiated keratinocyte-Like cell-derived organoid potentiates skin regeneration Through ERK1/2 and STAT3 signaling in diabetic wound,” Cellular and Molecular Life Sciences 81, no. 1 (2024): 172.

[252] T. Zhang, S. Sheng, W. Cai, et al., “3-D bioprinted human-derived skin organoids accelerate full-thickness skin defects repair,” Bioactive Materials 42 (2024): 257-269.

[253] F. Sampaziotis, D. Muraro, O. C. Tysoe, et al., “Cholangiocyte organoids can repair bile ducts After transplantation in the human liver,” Science 371, no. 6531 (2021): 839-846.

[254] Q. Tan, K. M. Choi, D. Sicard, and D. J. Tschumperlin, “Human airway organoid engineering as a step Toward lung regeneration and disease modeling,” Biomaterials 113 (2017): 118-132.

[255] C. Mukhopadhyay and M. K. Paul, “Organoid-based 3D in vitro microphysiological systems as alternatives to animal experimentation for preclinical and clinical research,” Archives of Toxicology 97, no. 5 (2023): 1429-1431.

[256] E. M. Boisvert, R. E. Means, M. Michaud, J. A. Madri, and S. G. Katz, “Minocycline mitigates the effect of neonatal hypoxic insult on human brain organoids,” Cell Death & Disease 10, no. 4 (2019): 325.

[257] B. M. Clarke, S. Kireta, J. Johnston, et al., “In Vivo Formation of Adrenal Organoids in a Novel Porcine Model of Adrenocortical Cell Transplantation,” Endocrinology 165, no. 8 (2024): bqae086.

[258] L. Grassi, R. Alfonsi, F. Francescangeli, et al., “Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases,” Cell Death & Disease 10, no. 3 (2019): 201.

[259] S. Yan, Y. He, Y. Zhu, et al., “Human patient derived organoids: An emerging precision medicine model for gastrointestinal cancer research,” Frontiers in Cell and Developmental Biology 12 (2024): 1384450.

[260] A. Lavazza and M. Massimini, “Cerebral organoids: Ethical issues and consciousness assessment,” Journal of Medical Ethics 44, no. 9 (2018): 606-610.

[261] E. Kuijk, M. Jager, B. van der Roest, et al., “The mutational impact of culturing human pluripotent and adult stem cells,” Nature Communications 11, no. 1 (2020): 2493.

[262] Y. Zhao, Z.-X. Li, Y.-J. Zhu, et al., “Single-Cell Transcriptome Analysis Uncovers Intratumoral Heterogeneity and Underlying Mechanisms for Drug Resistance in Hepatobiliary Tumor Organoids,” Advanced Science (Weinh) 8, no. 11 (2021): e2003897.

[263] T. J. Borges, Y. Ganchiku, J. O. Aceves, et al., “Exploring immune response Toward transplanted human kidney tissues assembled From organoid building blocks,” Iscience 27, no. 10 (2024): 110957.

[264] K. C. Kasuba, A. P. Buccino, J. Bartram, et al., “Mechanical stimulation and electrophysiological monitoring at subcellular resolution reveals differential mechanosensation of neurons Within networks,” Nature Nanotechnology 19, no. 6 (2024): 825-833.

[265] C. Zhou, Y. Wu, Z. Wang, et al., “Standardization of organoid culture in cancer research,” Cancer Medicine 12, no. 13 (2023): 14375-14386.

[266] B. L. LeSavage, R. A. Suhar, N. Broguiere, M. P. Lutolf, and S. C. Heilshorn, “Next-generation cancer organoids,” Nature Materials 21, no. 2 (2022): 143-159.

[267] B. Schuster, M. Junkin, S. S. Kashaf, et al., “Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids,” Nature Communications 11, no. 1 (2020): 5271.

[268] S. T. Seiler, G. L. Mantalas, J. Selberg, et al., “Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids,” Scientific Reports 12, no. 1 (2022): 20173.

[269] K. Takayama, “In Vitro and Animal Models for SARS-CoV-2 research,” Trends in Pharmacological Sciences 41, no. 8 (2020): 513-517.

[270] G. Kanuri and I. Bergheim, “In vitro and in vivo models of non-alcoholic fatty liver disease (NAFLD),” International Journal of Molecular Sciences 14, no. 6 (2013): 11963-11980.

[271] I. R. Dunay, K. Gajurel, R. Dhakal, O. Liesenfeld, and J. G. Montoya, “Treatment of Toxoplasmosis: Historical Perspective, Animal Models, and Current Clinical Practice,” Clinical Microbiology Reviews 31, no. 4 (2018): e00057-17.

[272] J. P. Garner, “The significance of meaning: Why do Over 90% of behavioral neuroscience results fail to translate to humans, and what can we do to fix it?,” ILAR Journal 55, no. 3 (2014): 438-456.

[273] T. Takahashi, “Organoids for Drug Discovery and Personalized Medicine,” Annual Review of Pharmacology and Toxicology 59 (2019): 447-462.

[274] C. Pauli, B. D. Hopkins, D. Prandi, et al., “Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine,” Cancer Discovery 7, no. 5 (2017): 462-477.

[275] K. Kawasaki, K. Toshimitsu, M. Matano, et al., “An Organoid Biobank of Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping,” Cell 183, no. 5 (2020): 1420-1435.e21.

[276] Y.-D. T. Tzeng, J.-H. Hsiao, L.-M. Tseng, M.-F. Hou, and C.-J. Li, “Breast cancer organoids derived From patients: A platform for tailored drug screening,” Biochemical Pharmacology 217 (2023): 115803.

[277] K. K. Dijkstra, J. G. van den Berg, F. Weeber, et al., “Patient-Derived Organoid Models of Human Neuroendocrine Carcinoma,” Frontiers In Endocrinology 12 (2021): 627819.

[278] A. Shafiee, J. Sun, I. A. Ahmed, et al., “Development of Physiologically Relevant Skin Organoids From Human Induced Pluripotent Stem Cells,” Small (Weinheim an Der Bergstrasse, Germany) 20, no. 16 (2024): e2304879.

[279] Y. Kim, Y. Nam, Y. A. Rim, and J. H. Ju, “Anti-fibrotic effect of a selective estrogen receptor modulator in systemic sclerosis,” Stem Cell Research & Therapy 13, no. 1 (2022): 303.

[280] V. V. T. Nguyen, S. Ye, V. Gkouzioti, et al., “A human kidney and liver organoid-based multi-organ-on-a-chip model to study the therapeutic effects and biodistribution of mesenchymal stromal cell-derived extracellular vesicles,” Journal of Extracellular Vesicles 11, no. 11 (2022): e12280.

[281] S. Mo, P. Tang, W. Luo, et al., “Patient-Derived Organoids From Colorectal Cancer With Paired Liver Metastasis Reveal Tumor Heterogeneity and Predict Response to Chemotherapy,” Advanced Science (Weinh) 9, no. 31 (2022): e2204097.

[282] M. Fujii, M. Shimokawa, S. Date, et al., “A Colorectal Tumor Organoid Library Demonstrates Progressive Loss of Niche Factor Requirements During Tumorigenesis,” Cell Stem Cell 18, no. 6 (2016): 827-838.

[283] T.-L. Wong, J.-J. Loh, S. Lu, et al., “ADAR1-mediated RNA editing of SCD1 drives drug resistance and self-renewal in gastric cancer,” Nature Communications 14, no. 1 (2023): 2861.

[284] J. O. Múnera, D. O. Kechele, C. Bouffi, et al., “Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon,” Cell Stem Cell 30, no. 11 (2023): 1434-1451.e9.

[285] M. G. Andrews and A. R. Kriegstein, “Challenges of Organoid Research,” Annual Review of Neuroscience 45 (2022): 23-39.

[286] M. Hofer and M. P. Lutolf, “Engineering organoids,” Nature Reviews Materials 6, no. 5 (2021): 402-420.

[287] J. Yu, “Vascularized Organoids: A More Complete Model,” International Journal of Stem Cells 14, no. 2 (2021): 127-137.

[288] B. Zhu, D. Wang, H. Pan, et al., “Three-in-one customized bioink for islet organoid: GelMA/ECM/PRP orchestrate pro-angiogenic and immunoregulatory function,” Colloids and Surfaces. B, Biointerfaces 221 (2023): 113017.

[289] S. P. Harrison, R. Siller, Y. Tanaka, et al., “Scalable production of tissue-Like vascularized liver organoids From human PSCs,” Experimental & Molecular Medicine 55, no. 9 (2023): 2005-2024.

[290] Y. Shi, L. Sun, M. Wang, et al., “Vascularized human cortical organoids (vOrganoids) model cortical development in vivo,” PLoS Biology 18, no. 5 (2020): e3000705.

[291] R. Rimal, S. Muduli, P. Desai, et al., “Vascularized 3D Human Skin Models in the Forefront of Dermatological Research,” Advanced Healthcare Materials 13, no. 9 (2024): e2303351.

RIGHTS & PERMISSIONS

2025 The Author(s). MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.