Organoids: From Bench to Bedside Applications

Abstract

Organoids are three-dimensiona(3D) models derived from stem cells that closely replicate the structure and cellular complexity of human tissues, providing physiologically relevant platforms for biomedical research. This technology addresses the limitations of two-dimensional (2D) cultures, reduces species-specific discrepancies, and is particularly valuable for investigating virus–host interactions and pathogenic mechanisms under near-physiological conditions. This review systematically outlines key advancements in organoid-based virology, including the propagation of hard-to-culture pathogens such as human rhinovirus C (HRV-C) and norovirus (NoV), as well as novel insights into viral pathogenesis, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Zika virus (ZIKV) infection, and the translational utility of organoids for antiviral drug screening and preclinical assessment. It further examines the use of organoids in modeling cancer and neurological diseases, compares the strengths and limitations of different cellular sources, and discusses their potential integration with emerging technologies such as CRISPR gene editing and 3D bioprinting. In addition, it maps a translational pathway from molecular mechanisms to clinical practice to facilitate the study of disease mechanisms and accelerate drug and vaccine development. Finally, holistic strategies are proposed to address existing challenges, such as the lack of immune components and inadequate vascularization. Together, these efforts aim to promote the broader adoption of organoid technology across the life sciences and translational medicine.

Keywords

organoids / pathogenesis / stem cells

References

[1] M. A. Lancaster and J. A. Knoblich, “Organogenesis in a Dish: Modeling Development and Disease Using Organoid Technologies,” Science 345 (2014): 1247125.

[2] A. Fatehullah, S. H. Tan, and N. Barker, “Organoids as an in vitro Model of Human Development and Disease,” Nature Cell Biology 18 (2016): 246–254.

[3] T. Sato, R. G. Vries, H. J. Snippert, et al., “Single Lgr5 Stem Cells Build Crypt-villus Structures in vitro without a Mesenchymal Niche,” Nature 459 (2009): 262–265.

[4] M. A. Lancaster, M. Renner, C. A. Martin, et al., “Cerebral Organoids Model Human Brain Development and Microcephaly,” Nature 501 (2013): 373–379.

[5] S. Yang, H. Hu, H. Kung, et al., “Organoids: The Current Status and Biomedical Applications,” MedComm 4 (2023): e274.

[6] M. J. Evans and M. H. Kaufman, “Establishment in Culture of Pluripotential Cells From Mouse Embryos,” Nature 292 (1981): 154–156.

[7] J. A. Thomson, J. Itskovitz-Eldor, S. S. Shapiro, et al., “Embryonic Stem Cell Lines Derived From Human Blastocysts,” Science 282 (1998): 1145–1147.

[8] A. Marsee, F. Roos, M. Verstegen, et al., “Building Consensus on Definition and Nomenclature of Hepatic, Pancreatic, and Biliary Organoids,” Cell Stem Cell 28 (2021): 816–832.

[9] J. R. Spence, C. N. Mayhew, S. A. Rankin, et al., “Directed Differentiation of Human Pluripotent Stem Cells into Intestinal Tissue in vitro,” Nature 470 (2011): 105–109.

[10] T. Nakano, S. Ando, N. Takata, et al., “Self-formation of Optic Cups and Storable Stratified Neural Retina From Human Escs,” Cell Stem Cell 10 (2012): 771–785.

[11] C. W. Chua, M. Shibata, M. Lei, et al., “Single Luminal Epithelial Progenitors Can Generate Prostate Organoids in Culture,” Nature Cell Biology 16 (2014): 951–961.

[12] W. R. Karthaus, P. J. Iaquinta, J. Drost, et al., “Identification of Multipotent Luminal Progenitor Cells in Human Prostate Organoid Cultures,” Cell 159 (2014): 163–175.

[13] J. H. Lee, D. H. Bhang, A. Beede, et al., “Lung Stem Cell Differentiation in Mice Directed by Endothelial Cells via a Bmp4-nfatc1-thrombospondin-1 Axis,” Cell 156 (2014): 440–455.

[14] M. Kessler, K. Hoffmann, V. Brinkmann, et al., “The Notch and Wnt Pathways Regulate Stemness and Differentiation in Human Fallopian Tube Organoids,” Nature Communications 6 (2015): 8989.

[15] H. Sakaguchi, T. Kadoshima, M. Soen, et al., “Generation of Functional Hippocampal Neurons From Self-organizing Human Embryonic Stem Cell-derived Dorsomedial Telencephalic Tissue,” Nature Communications 6 (2015): 8896.

[16] J. Zhou, C. Li, X. Liu, et al., “Infection of Bat and Human Intestinal Organoids by SARS-CoV-2,” Nature Medicine 26 (2020): 1077–1083.

[17] Y. Post, J. Puschhof, J. Beumer, et al., “Snake Venom Gland Organoids,” Cell 180 (2020): 233–247.e21.

[18] M. C. Chiu, C. Li, X. Liu, et al., “A Bipotential Organoid Model of Respiratory Epithelium Recapitulates High Infectivity of SARS-CoV-2 Omicron Variant,” Cell Discovery 8 (2022): 57.

[19] K. Lõhmussaar, R. Oka, J. Espejo Valle-Inclan, et al., “Patient-derived Organoids Model Cervical Tissue Dynamics and Viral Oncogenesis in Cervical Cancer,” Cell Stem Cell 28 (2021): 1380–1396.e6.

[20] L. Drakhlis, S. Biswanath, C. M. Farr, et al., “Human Heart-forming Organoids Recapitulate Early Heart and Foregut Development,” Nature Biotechnology 39 (2021): 737–746.

[21] J. W. Rumsey, C. Lorance, M. Jackson, et al., “Classical Complement Pathway Inhibition in a ”Human-on-a-chip“ Model of Autoimmune Demyelinating Neuropathies,” Advanced Therapeutics 5 (2022): 2200030.

[22] S. T. Moore, T. Nakamura, J. Nie, et al., “Generating High-fidelity Cochlear Organoids From Human Pluripotent Stem Cells,” Cell Stem Cell 30 (2023): 950–961.e7.

[23] A. Andersson-Rolf, K. Groot, J. Korving, et al., “Long-term in vitro Expansion of a Human Fetal Pancreas Stem Cell That Generates all Three Pancreatic Cell Lineages,” 187 (2024): 7394–7413.e22.

[24] M. Mostina, J. Sun, S. L. Sim, et al., “Coordinated Development of Immune Cell Populations in Vascularized Skin Organoids From Human Induced Pluripotent Stem Cells,” Advanced Healthcare Materials 14 (2025): e02108.

[25] K. Sharma, R. Habibey, M. M. Ribeiro, et al., “Retinal Ganglion Cell Survival and Functional Maturation in Transiently Vascularized Human Retinal Organoids,” Cell Stem Cell 33 (2026): 253–271.e13.

[26] Y. Han, L. Yang, L. A. Lacko, et al., “Human Organoid Models to Study SARS-CoV-2 Infection,” Nature Methods 19 (2022): 418–428.

[27] M. A. Lancaster, “Pluripotent Stem Cell-derived Organoids: A Brief History of Curiosity-led Discoveries,” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 46 (2024): e2400105.

[28] T. Danjo, M. Eiraku, K. Muguruma, et al., “Subregional Specification of Embryonic Stem Cell-derived Ventral Telencephalic Tissues by Timed and Combinatory Treatment With Extrinsic Signals,” The Journal of Neuroscience 31 (2011): 1919–1933.

[29] H. L. Su, K. Muguruma, M. Matsuo-Takasaki, et al., “Generation of Cerebellar Neuron Precursors From Embryonic Stem Cells,” Developmental Biology 290 (2006): 287–296.

[30] T. Takebe, K. Sekine, M. Enomura, et al., “Vascularized and Functional Human Liver From an Ipsc-derived Organ Bud Transplant,” Nature 499 (2013): 481–484.

[31] M. Huch, C. Dorrell, S. F. Boj, et al., “in vitro Expansion of Single Lgr5⁺ Liver Stem Cells Induced by Wnt-driven Regeneration,” Nature 494 (2013): 247–250.

[32] D. Zhao, W. Lei, and S. Hu, “Cardiac Organoid—a Promising Perspective of Preclinical Model,” Stem Cell Research & Therapy 12 (2021): 272.

[33] M. Takasato, P. X. Er, M. Becroft, et al., “Directing Human Embryonic Stem Cell Differentiation towards a Renal Lineage Generates a Self-organizing Kidney,” Nature Cell Biology 16 (2014): 118–126.

[34] A. Taguchi, Y. Kaku, T. Ohmori, et al., “Redefining the in Vivo Origin of Metanephric Nephron Progenitors Enables Generation of Complex Kidney Structures From Pluripotent Stem Cells,” Cell Stem Cell 14 (2014): 53–67.

[35] Y. Xia, E. Nivet, I. Sancho-Martinez, et al., “Directed Differentiation of Human Pluripotent Cells to Ureteric Bud Kidney Progenitor-Like Cells,” Nature Cell Biology 15 (2013): 1507–1515.

[36] X. Y. Tang, S. Wu, D. Wang, et al., “Human Organoids in Basic Research and Clinical Applications,” Signal Transduction and Targeted Therapy 7 (2022): 168.

[37] A. E. Omole and A. Fakoya, “Ten Years of Progress and Promise of Induced Pluripotent Stem Cells: Historical Origins, Characteristics, Mechanisms, Limitations, and Potential Applications,” Peer Journal 6 (2018): e4370.

[38] L. Zhang, K. Pu, X. Liu, et al., “The Application of Induced Pluripotent Stem Cells against Liver Diseases: An Update and a Review,” Frontiers in Medicine 8 (2021): 644594.

[39] Y. Avior, I. Sagi, and N. Benvenisty, “Pluripotent Stem Cells in Disease Modelling and Drug Discovery,” Nature Reviews Molecular Cell Biology 17 (2016): 170–182.

[40] I. Ahmed, R. J. Johnston, and M. S. Singh, “Pluripotent Stem Cell Therapy for Retinal Diseases,” Annals of Translational Medicine 9 (2021): 1279.

[41] J. Kim, B. K. Koo, and J. A. Knoblich, “Human Organoids: Model Systems for Human Biology and Medicine,” Nature Reviews Molecular Cell Biology 21 (2020): 571–584.

[42] P. Karagiannis, K. Takahashi, M. Saito, et al., “Induced Pluripotent Stem Cells and Their Use in Human Models of Disease and Development,” Physiological Reviews 99 (2019): 79–114.

[43] T. Stoddard-Bennett and R. Reijo Pera, “Treatment of Parkinson's Disease through Personalized Medicine and Induced Pluripotent Stem Cells,” Cells 8 (2019): 26.

[44] F. Sampaziotis, D. Muraro, O. C. Tysoe, et al., “Cholangiocyte Organoids Can Repair Bile Ducts after Transplantation in the Human Liver,” Science 371 (2021): 839–846.

[45] H. Rezanejad, J. H. Lock, B. A. Sullivan, et al., “Generation of Pancreatic Ductal Organoids and Whole-mount Immunostaining of Intact Organoids,” Current Protocols in Cell Biology 83 (2019): e82.

[46] S. Dumont, Z. Jan, R. Heremans, et al., “Organoids of Epithelial Ovarian Cancer as an Emerging Preclinical in vitro Tool: A Review,” Journal of Ovarian Research 12 (2019): 105.

[47] H. Clevers, “Modeling Development and Disease With Organoids,” Cell 165 (2016): 1586–1597.

[48] K. W. McCracken, J. C. Howell, J. M. Wells, et al., “Generating Human Intestinal Tissue From Pluripotent Stem Cells in vitro,” Nature Protocols 6 (2011): 1920–1928.

[49] M. Huch, P. Bonfanti, S. F. Boj, et al., “Unlimited in vitro Expansion of Adult Bi-potent Pancreas Progenitors through the Lgr5/R-spondin Axis,” The EMBO Journal 32 (2013): 2708–2721.

[50] T. Sato, D. E. Stange, M. Ferrante, et al., “Long-term Expansion of Epithelial Organoids From Human Colon, Adenoma, Adenocarcinoma, and Barrett's Epithelium,” Gastroenterology 141 (2011): 1762–1772.

[51] D. Yu, H. Cao, and X. Wang, “Advances and Applications of Organoids: A Review],” Chinese Journal of Biotechnology 37 (2021): 3961–3974.

[52] S. C. Lin, K. Haga, X. L. Zeng, et al., “Generation of Crispr-cas9-mediated Genetic Knockout Human Intestinal Tissue-derived Enteroid Lines by Lentivirus Transduction and Single-cell Cloning,” Nature Protocols 17 (2022): 1004–1027.

[53] M. Beaumont, F. Blanc, C. Cherbuy, et al., “Intestinal Organoids in Farm Animals,” Veterinary Research 52 (2021): 33.

[54] R. Yang, S. Yang, J. Zhao, et al., “Progress in Studies of Epidermal Stem Cells and Their Application in Skin Tissue Engineering,” Stem Cell Research & Therapy 11 (2020): 303.

[55] L. Kang, Z. Kou, Y. Zhang, et al., “Induced Pluripotent Stem Cells (iPSCs)—a New Era of Reprogramming,” Journal of Genetics and Genomics 37 (2010): 415–421.

[56] A. C. White and W. E. Lowry, “Refining the Role for Adult Stem Cells as Cancer Cells of Origin,” Trends in Cell Biology 25 (2015): 11–20.

[57] L. Broutier, A. Andersson-Rolf, C. J. Hindley, et al., “Culture and Establishment of Self-renewing Human and Mouse Adult Liver and Pancreas 3D Organoids and Their Genetic Manipulation,” Nature Protocols 11 (2016): 1724–1743.

[58] M. Huch, H. Gehart, R. van Boxtel, et al., “Long-term Culture of Genome-stable Bipotent Stem Cells From Adult Human Liver,” Cell 160 (2015): 299–312.

[59] K. Ettayebi, S. E. Crawford, K. Murakami, et al., “Replication of Human Noroviruses in Stem Cell-derived Human Enteroids,” Science 353 (2016): 1387–1393.

[60] C. Li, Y. Yu, Z. Wan, et al., “Human Respiratory Organoids Sustained Reproducible Propagation of Human Rhinovirus C and Elucidation of Virus-host Interaction,” Nature Communications 15 (2024): 10772.

[61] C. Li, J. Huang, Y. Yu, et al., “Human Airway and Nasal Organoids Reveal Escalating Replicative Fitness of SARS-CoV-2 Emerging Variants,” Proceedings of the National Academy of Sciences of the United States of America 120 (2023): e2300376120.

[62] E. Delorme-Axford and C. B. Coyne, “The Actin Cytoskeleton as a Barrier to Virus Infection of Polarized Epithelial Cells,” Viruses 3 (2011): 2462–2477.

[63] C. T. Wu, P. V. Lidsky, Y. Xiao, et al., “SARS-CoV-2 Replication in Airway Epithelia Requires Motile Cilia and Microvillar Reprogramming,” Cell 186 (2023): 112–130.e20.

[64] C. Aguilar, M. Alves da Silva, M. Saraiva, et al., “Organoids as Host Models for Infection Biology—a Review of Methods,” Experimental & Molecular Medicine 53 (2021): 1471–1482.

[65] K. Sutton, T. Leach, V. Surendran, et al., “Organoid Technologies for SARS-CoV-2 Research,” Current Stem Cell Reports 8 (2022): 151–163.

[66] A. Carfì, R. Bernabei, and F. Landi, “Persistent Symptoms in Patients after Acute COVID-19,” The Journal of the American Medical Association 324 (2020): 603–605.

[67] C. Huang, Y. Wang, X. Li, et al., “Clinical Features of Patients Infected With 2019 Novel Coronavirus in Wuhan, China,” The Lancet 395 (2020): 496.

[68] F. Zhou, T. Yu, R. Du, et al., “Clinical Course and Risk Factors for Mortality of Adult Inpatients With COVID-19 in Wuhan, China: A Retrospective Cohort Study,” The Lancet 395 (2020): 1038.

[69] H. Latifi-Pupovci, “Molecular Mechanisms Involved in Pathogenicity of SARS-CoV-2: Immune Evasion and Implications for Therapeutic Strategies,” Biomedicine & Pharmacotherapy 153 (2022): 113368.

[70] V. Monteil, H. Kwon, P. Prado, et al., “Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-grade Soluble Human ACE2,” Cell 181 (2020): 905–913.e7.

[71] M. Takla and K. Jeevaratnam, “Chloroquine, Hydroxychloroquine, and COVID-19: Systematic Review and Narrative Synthesis of Efficacy and Safety,” Saudi Pharmaceutical Journal 28 (2020): 1760–1776.

[72] C. Muus, M. D. Luecken, G. Eraslan, et al., “Single-cell Meta-analysis of SARS-CoV-2 Entry Genes across Tissues and Demographics,” Nature Medicine 27 (2021): 546–559.

[73] C. T. Ekanger, F. Zhou, D. Bohan, et al., “Human Organotypic Airway and Lung Organoid Cells of Bronchiolar and Alveolar Differentiation Are Permissive to Infection by Influenza and SARS-CoV-2 Respiratory Virus,” Frontiers in Cellular and Infection Microbiology 12 (2022): 841447.

[74] M. C. Chiu, S. Zhang, C. Li, et al., “Apical-out Human Airway Organoids Modeling SARS-CoV-2 Infection,” Viruses 15 (2023): 1166.

[75] A. Z. Mykytyn, T. I. Breugem, M. H. Geurts, et al., “SARS-CoV-2 Omicron Entry Is Type II Transmembrane Serine Protease-mediated in Human Airway and Intestinal Organoid Models,” Journal of Virology 97 (2023): e0085123.

[76] S. Li, H. Yang, F. Tian, et al., “Unveiling the Dynamic Mechanism of SARS-CoV-2 Entry Host Cells at the Single-particle Level,” ACS Nano 18 (2024): 27891–27904.

[77] N. Sansone, M. N. Boschiero, and F. Marson, “Efficacy of Ivermectin, Chloroquine/Hydroxychloroquine, and Azithromycin in Managing COVID-19: A Systematic Review of Phase III Clinical Trials,” Biomedicines 12 (2024): 2206.

[78] S. Steiner, A. Kratzel, G. T. Barut, et al., “SARS-CoV-2 Biology and Host Interactions,” Nature Reviews Microbiology 22 (2024): 206–225.

[79] X. Nie, L. Qian, R. Sun, et al., “Multi-organ Proteomic Landscape of COVID-19 Autopsies,” Cell 184 (2021): 775–791.e14.

[80] C. R. Simoneau, P. Y. Chen, G. K. Xing, et al., “Nf-κB Inhibitor Alpha Has a Cross-variant Role During SARS-CoV-2 Infection in ACE2-overexpressing Human Airway Organoids,” Scientific Reports 14 (2022): 10 15351.

[81] I. M. Leko, R. T. Schneider, T. A. Thimraj, et al., “A Distal Lung Organoid Model to Study Interstitial Lung Disease, Viral Infection and Human Lung Development,” Nature Protocols 18 (2023): 2283–2312.

[82] J. Zhou, C. Li, N. Sachs, et al., “Differentiated Human Airway Organoids to Assess Infectivity of Emerging Influenza Virus,” Proceedings of the National Academy of Sciences of the United States of America 115 (2018): 6822–6827.

[83] N. Sachs, A. Papaspyropoulos, D. D. Zomer-van Ommen, et al., “Long-term Expanding Human Airway Organoids for Disease Modeling,” The EMBO Journal 38 (2019): e100300.

[84] S. Mallapaty, “The Mini Lungs and Other Organoids Helping to Beat COVID,” Nature 593 (2021): 492–494.

[85] C. Li, M. C. Chiu, Y. Yu, et al., “Establishing Human Lung Organoids and Proximal Differentiation to Generate Mature Airway Organoids,” Journal of Visualized Experiments 181 (2022): e63684.

[86] R. Robinot, M. Hubert, G. D. de Melo, et al., “SARS-CoV-2 Infection Induces the Dedifferentiation of Multiciliated Cells and Impairs Mucociliary Clearance,” Nature Communications 12 (2021): 4354.

[87] J. Krüger, R. Groß, C. Conzelmann, et al., “Drug Inhibition of SARS-CoV-2 Replication in Human Pluripotent Stem Cell-derived Intestinal Organoids,” Cellular and Molecular Gastroenterology and Hepatology 11 (2021): 935–948.

[88] F. Duan, L. Guo, L. Yang, et al., “Modeling COVID-19 With Human Pluripotent Stem Cell-derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages With ACE2 Inhibition against SARS-CoV-2,” Research Square (2020), 10.21203/rs.3.rs-62758/v2.

[89] R. Jeger-Madiot, D. Planas, I. Staropoli, et al., “Modeling Memory B Cell Responses in a Lymphoid Organ-chip to Evaluate MRNA Vaccine Boosting,” The Journal of Experimental Medicine 221 (2024): e20240289.

[90] C. G. Drummond, A. M. Bolock, C. Ma, et al., “Enteroviruses Infect Human Enteroids and Induce Antiviral Signaling in a Cell Lineage-specific Manner,” Proceedings of the National Academy of Sciences of the United States of America 114 (2017): 1672–1677.

[91] T. Solomon, P. Lewthwaite, D. Perera, et al., “Virology, Epidemiology, Pathogenesis, and Control of Enterovirus 71,” The Lancet Infectious Diseases 10 (2010): 778–790.

[92] S. E. Crawford, S. Ramani, S. E. Blutt, et al., “Organoids to Dissect Gastrointestinal Virus-host Interactions: What Have We Learned,” Viruses 13 (2021): 999.

[93] X. Zhao, C. Li, X. Liu, et al., “Human Intestinal Organoids Recapitulate Enteric Infections of Enterovirus and Coronavirus,” Stem Cell Reports 16 (2021): 493–504.

[94] X. Zhao, C. Li, M. C. Chiu, et al., “Rock1 is a Novel Host Dependency Factor of Human Enterovirus A71: Implication as a Drug Target,” Journal of Medical Virology 94 (2022): 5415–5424.

[95] J. Li, J. Ma, R. Cao, et al., “A Skin Organoid-based Infection Platform Identifies an Inhibitor Specific for HFMD,” Nature Communications 16 (2025): 2513.

[96] World Health Organization, “Hepatitis B,” 2025, https://www.who.int/.

[97] V. Krenn, C. Bosone, T. R. Burkard, et al., “Organoid Modeling of Zika and Herpes Simplex Virus 1 Infections Reveals Virus-specific Responses Leading to Microcephaly,” Cell Stem Cell 28 (2021): 1362–1379.e7.

[98] S. Rao, T. Hossain, and T. Mahmoudi, “3D Human Liver Organoids: An in vitro Platform to Investigate HBV Infection, Replication and Liver Tumorigenesis,” Cancer Letters 506 (2021): 35–44.

[99] Y. Z. Nie, Y. W. Zheng, K. Miyakawa, et al., “Recapitulation of Hepatitis B Virus-host Interactions in Liver Organoids From Human Induced Pluripotent Stem Cells,” EBioMedicine 35 (2018): 114–123.

[100] E. De Crignis, T. Hossain, S. Romal, et al., “Application of Human Liver Organoids as a Patient-derived Primary Model for HBV Infection and Related Hepatocellular Carcinoma,” Elife 10 (2021): e60747.

[101] R. McKenzie, M. W. Fried, R. Sallie, et al., “Hepatic Failure and Lactic Acidosis due to Fialuridine (fiau), an Investigational Nucleoside Analogue for Chronic Hepatitis B,” The New England Journal of Medicine 333 (1995): 1099–1105.

[102] E. Duizer, K. J. Schwab, F. H. Neill, et al., “Laboratory Efforts to Cultivate Noroviruses,” The Journal of General Virology 85 (2004): 79–87.

[103] M. K. Lay, R. L. Atmar, S. Guix, et al., “Norwalk Virus Does Not Replicate in Human Macrophages or Dendritic Cells Derived From the Peripheral Blood of Susceptible Humans,” Virology 406 (2010): 1–11.

[104] M. D. Moore, R. M. Goulter, and L. A. Jaykus, “Human Norovirus as a Foodborne Pathogen: Challenges and Developments,” Annual Review of Food Science and Technology 6 (2015): 411–433.

[105] B. V. Ayyar, K. Ettayebi, W. Salmen, et al., “CLIC and Membrane Wound Repair Pathways Enable Pandemic Norovirus Entry and Infection,” Nature Communications 14 (2023): 1148.

[106] K. Murakami, V. R. Tenge, U. C. Karandikar, et al., “Bile Acids and Ceramide Overcome the Entry Restriction for Gii.3 Human Norovirus Replication in Human Intestinal Enteroids,” Proceedings of the National Academy of Sciences of the United States of America 117 (2020): 1700–1710.

[107] C. D. Zorrilla, I. García García, L. García Fragoso, et al., “Zika Virus Infection in Pregnancy: Maternal, Fetal, and Neonatal Considerations,” The Journal of Infectious Diseases 216 (2017): S891–S896.

[108] F. M. Szaba, M. Tighe, L. W. Kummer, et al., “Zika Virus Infection in Immunocompetent Pregnant Mice Causes Fetal Damage and Placental Pathology in the Absence of Fetal Infection,” PLoS Pathogens 14 (2018): e1006994.

[109] G. C. Nascimento-Carvalho, E. C. Nascimento-Carvalho, M. M. VanDuijn, et al., “Cerebrospinal Fluid Immunoglobulins Are Increased in Neonates Exposed to Zika Virus During Foetal Life,” The Journal of Infection 80 (2020): 419–425.

[110] A. Depoux, A. Philibert, S. Rabier, et al., “A Multi-faceted Pandemic: A Review of the State of Knowledge on the Zika Virus,” Public Health Reviews 39 (2018): 10.

[111] H. Wu, X. Y. Huang, M. X. Sun, et al., “Zika Virus Targets Human Trophoblast Stem Cells and Prevents Syncytialization in Placental Trophoblast Organoids,” Nature Communications 14 (2023): 5541.

[112] Z. Li, J. Xu, Y. Lang, et al., “Jmx0207, a Niclosamide Derivative With Improved Pharmacokinetics, Suppresses Zika Virus Infection both in vitro and in Vivo,” ACS Infectious Diseases Journal 6 (2020): 2616–2628.

[113] M. Xu, E. M. Lee, Z. Wen, et al., “Identification of Small-molecule Inhibitors of Zika Virus Infection and Induced Neural Cell Death via a Drug Repurposing Screen,” Nature Medicine 22 (2016): 1101–1107.

[114] B. Cavalcante, L. S. Aragão-França, G. Sampaio, et al., “Betulinic Acid Exerts Cytoprotective Activity on Zika Virus-infected Neural Progenitor Cells,” Frontiers in Cellular and Infection Microbiology 10 (2020): 558324.

[115] A. Pettke, M. Tampere, R. Pronk, et al., “Broadly Active Antiviral Compounds Disturb Zika Virus Progeny Release Rescuing Virus-induced Toxicity in Brain Organoids,” Viruses 13 (2020): 37.

[116] L. Zhang, H. Wang, C. Han, et al., “AMFR-mediated Flavivirus NS2A Ubiquitination Subverts ER-phagy to Augment Viral Pathogenicity,” Nature Communications 15 (2024): 9578.

[117] J. M. Vanslambrouck, J. A. Neil, R. Rudraraju, et al., “Kidney Organoids Reveal Redundancy in Viral Entry Pathways During ACE2-dependent SARS-CoV-2 Infection,” Journal of Virology 98 (2024): e0180223.

[118] R. M. Samuel, H. Majd, M. N. Richter, et al., “Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated With Severe COVID-19 Symptoms in Men,” Cell Stem Cell 27 (2020): 876–889.e12.

[119] C. Vazquez, S. G. Negatu, C. D. Bannerman, et al., “Antiviral Immunity within Neural Stem Cells Distinguishes Enterovirus-d68 Strain Differences in Forebrain Organoids,” Journal of Neuroinflammation 21 (2024): 288.

[120] G. Moreni, H. van Eijk, G. Koen, et al., “Non-polio Enterovirus C Replicate in both Airway and Intestine Organotypic Cultures,” Viruses 15 (2023): 1823.

[121] A. Schöbel, V. Pinho Dos Reis, R. Burkhard, et al., “Inhibition of Sterol O-acyltransferase 1 Blocks Zika Virus Infection in Cell Lines and Cerebral Organoids,” Communications Biology 7 (2024): 1089.

[122] J. Dang, S. K. Tiwari, G. Lichinchi, et al., “Zika Virus Depletes Neural Progenitors in Human Cerebral Organoids through Activation of the Innate Immune Receptor TLR3,” Cell Stem Cell 19 (2016): 258–265.

[123] H. Qiao, Y. Chiu, X. Liang, et al., “Microglia Innate Immune Response Contributes to the Antiviral Defense and Blood-CSF Barrier Function in Human Choroid Plexus Organoids During HSV-1 Infection,” Journal of Medical Virology 95 (2023): e28472.

[124] L. D'Aiuto, J. K. Caldwell, C. T. Wallace, et al., “The Impaired Neurodevelopment of Human Neural Rosettes in HSV-1-infected Early Brain Organoids,” Cells 11 (2022): 3539.

[125] J. Hatterschide, L. Yang, and C. B. Coyne, “DUX4-stimulated Genes Define the Antiviral Response to Herpesviruses in Human Trophoblasts,” Journal of Experimental Medicine 222 (2025): e20250448.

[126] B. Hu, R. Wang, D. Wu, et al., “A Promising New Model: Establishment of Patient-derived Organoid Models Covering HPV-related Cervical Pre-cancerous Lesions and Their Cancers,” Advanced Science 11 (2024): e2302340.

[127] S. Koster, R. K. Gurumurthy, N. Kumar, et al., “Modelling Chlamydia and HPV Co-infection in Patient-derived Ectocervix Organoids Reveals Distinct Cellular Reprogramming,” Nature Communications 13 (2022): 1030.

[128] Y. Guo, R. A. Candelero-Rueda, L. J. Saif, et al., “Infection of Porcine Small Intestinal Enteroids With Human and Pig Rotavirus A Strains Reveals Contrasting Roles for Histo-blood Group Antigens and Terminal Sialic Acids,” PLoS Pathogens 17 (2021): e1009237.

[129] J. Lee, D. Gil, H. Park, et al., “A Multicellular Liver Organoid Model for Investigating Hepatitis C Virus Infection and Nonalcoholic Fatty Liver Disease Progression,” Hepatology 80 (2024): 186–201.

[130] V. Natarajan, C. R. Simoneau, A. L. Erickson, et al., “Modelling T-cell Immunity Against Hepatitis C Virus With Liver Organoids in a Microfluidic Coculture System,” Open Biology 12 (2022): 210320.

[131] P. Li, S. T. Pachis, G. Xu, et al., “Mpox Virus Infection and Drug Treatment Modelled in Human Skin Organoids,” Nature Microbiology 8 (2023): 2067–2079.

[132] Y. Watanabe, I. Kimura, R. Hashimoto, et al., “Virological Characterization of the 2022 Outbreak-causing Monkeypox Virus Using Human Keratinocytes and Colon Organoids,” Journal of Medical Virology 95 (2023): e28827.

[133] I. Schultz-Pernice, A. Fahmi, F. Brito, et al., “Monkeypox Virus Spreads From Cell-to-cell and Leads to Neuronal Death in Human Neural Organoids,” Nature Communications 16 (2025): 5376.

[134] G. M. Aloisio, D. Nagaraj, A. M. Murray, et al., “Infant-derived Human Nasal Organoids Exhibit Relatively Increased Susceptibility, Epithelial Responses, and Cytotoxicity During RSV Infection,” The Journal of Infection 89 (2024): 106305.

[135] T. J. Harford, F. Rezaee, B. R. Dye, et al., “RSV-induced Changes in a 3-dimensional Organoid Model of Human Fetal Lungs,” PLoS ONE 17 (2022): e0265094.

[136] M. Donadoni, S. Cakir, A. Bellizzi, et al., “Modeling HIV-1 Infection and NeuroHIV in Hipscs-derived Cerebral Organoid Cultures,” Journal of Neurovirology 30 (2024): 362–379.

[137] A. G. Rader, A. Cloherty, K. S. Patel, et al., “HIV-1 Exploits Lbpa-dependent Intraepithelial Trafficking for Productive Infection of Human Intestinal Mucosa,” PLoS Pathogens 20 (2024): e1012714.

[138] R. J. Whitley and J. W. Gnann, “Viral Encephalitis: Familiar Infections and Emerging Pathogens,” The Lancet 359 (2002): 507–513.

[139] Z. A. Brown, A. Wald, R. A. Morrow, et al., “Effect of Serologic Status and Cesarean Delivery on Transmission Rates of Herpes Simplex Virus From Mother to Infant,” The Journal of the American Medical Association 289 (2003): 203–209.

[140] S. R. Dominguez, T. Briese, G. Palacios, et al., “Multiplex Masstag-PCR for Respiratory Pathogens in Pediatric Nasopharyngeal Washes Negative by Conventional Diagnostic Testing Shows a High Prevalence of Viruses Belonging to a Newly Recognized Rhinovirus Clade,” Journal of Clinical Virology 43 (2008): 219–222.

[141] C. Esneau, A. C. Duff, and N. W. Bartlett, “Understanding Rhinovirus Circulation and Impact on Illness,” Viruses 14 (2022): 141.

[142] L. Hu, S. E. Crawford, R. Czako, et al., “Cell Attachment Protein VP8* of a Human Rotavirus Specifically Interacts With A-type Histo-blood Group Antigen,” Nature 485 (2012): 256–259.

[143] X. Jiang, Y. Liu, and M. Tan, “Histo-blood Group Antigens as Receptors for Rotavirus, New Understanding on Rotavirus Epidemiology and Vaccine Strategy,” Emerging Microbes & Infections 6 (2017): e22.

[144] L. Hu, B. Sankaran, D. R. Laucirica, et al., “Glycan Recognition in Globally Dominant Human Rotaviruses,” Nature Communications 9 (2018): 2631.

[145] E. Méndez, C. F. Arias, and S. López, “Interactions between the Two Surface Proteins of Rotavirus May Alter the Receptor-binding Specificity of the Virus,” Journal of Virology 70 (1996): 1218–1222.

[146] A. Munro, F. Martinón-Torres, S. B. Drysdale, et al., “The Disease Burden of Respiratory Syncytial Virus in Infants,” Current Opinion in Infectious Diseases 36 (2023): 379–384.

[147] R. Hashimoto, Y. Watanabe, A. Keshta, et al., “Human IPS Cell-derived Respiratory Organoids as a Model for Respiratory Syncytial Virus Infection,” Life Science Alliance 8 (2025): e202402837.

[148] T. Corsello, N. Dillman, Y. Zhao, et al., “Analysis of Proteins and Piwi-interacting RNA Cargo of Extracellular Vesicles (EVs) Isolated From Human Nose Organoids and Nasopharyngeal Secretions of Children With RSV Infections,” Viruses 17 (2025): 764.

[149] M. Q. Li, Y. P. Xu, K. Li, et al., “Recapitulating Dengue Virus Infection With Human Pluripotent Stem Cell-derived Liver Organoids for Antiviral Screening,” Nature Communications 16 (2025): 8069.

[150] M. Kakizaki, R. Hashimoto, N. Nagata, et al., “The Respective Roles of TMPRSS2 and Cathepsins for SARS-CoV-2 Infection in Human Respiratory Organoids,” Journal of Virology 99 (2025): e0185324.

[151] S. K. Tiwari, S. Wang, D. Smith, et al., “Revealing Tissue-specific SARS-CoV-2 Infection and Host Responses Using Human Stem Cell-derived Lung and Cerebral Organoids,” Stem Cell Reports 16 (2021): 437–445.

[152] M. Haschke, M. Schuster, M. Poglitsch, et al., “Pharmacokinetics and Pharmacodynamics of Recombinant Human Angiotensin-converting Enzyme 2 in Healthy Human Subjects,” Clinical Pharmacokinetics 52 (2013): 783–792.

[153] A. Khan, C. Benthin, B. Zeno, et al., “A Pilot Clinical Trial of Recombinant Human Angiotensin-converting Enzyme 2 in Acute Respiratory Distress Syndrome,” Critical Care 21 (2017): 234.

[154] R. Volle, L. Murer, A. Petkidis, et al., “Methylene Blue, Mycophenolic Acid, Posaconazole, and Niclosamide Inhibit SARS-CoV-2 Omicron Variant BA.1 Infection of Human Airway Epithelial Organoids,” Current Research in Microbial Sciences 3 (2022): 100158.

[155] Y. Han, X. Duan, L. Yang, et al., “Identification of SARS-CoV-2 Inhibitors Using Lung and Colonic Organoids,” Nature 589 (2021): 270–275.

[156] R. Strobelt, J. Adler, N. Paran, et al., “Imatinib Inhibits SARS-CoV-2 Infection by an off-target-mechanism,” Scientific Reports 12 (2022): 5758.

[157] X. Zhang, H. Lin, L. Dong, et al., “Recapitulating Influenza Virus Infection and Facilitating Antiviral and Neuroprotective Screening in Tractable Brain Organoids,” Theranostics 12 (2022): 5317–5329.

[158] E. Ravlo, A. Ianevski, J. O. Schjølberg, et al., “Synergistic Combination of Orally Available Safe-in-man Pleconaril, Ag7404, and Mindeudesivir Inhibits Enterovirus Infections in Human Cell and Organoid Cultures,” Cellular and Molecular Life Sciences: CMLS 82 (2025): 57.

[159] “Human Skin Organoids Are Valid Models of Mpox Virus Infection,” Nature Microbiology 8 (2023): 1950–1951.

[160] R. Vernuccio, A. Martínez León, C. S. Poojari, et al., “Structural Insights into Tecovirimat Antiviral Activity and Poxvirus Resistance,” Nature Microbiology 10 (2025): 734–748.

[161] Y. H. Lo, K. S. Kolahi, Y. Du, et al., “A CRISPR/Cas9-engineered ARID1A-deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation,” Cancer Discovery 11 (2021): 1562–1581.

[162] Y. Tian, X. Wang, Z. Cramer, et al., “APC and P53 Mutations Synergise to Create a Therapeutic Vulnerability to NOTUM Inhibition in Advanced Colorectal Cancer,” Gut 72 (2023): 2294–2306.

[163] T. Mair, P. König, M. Mijović, et al., “The Atypical KRAS^Q22K Mutation Directs Tgf-β Response towards Partial Epithelial-to-mesenchymal Transition in Patient-derived Colorectal Cancer Tumoroids,” Molecular Oncology 19 (2025): 2212–2232.

[164] P. Zhang, B. He, Q. Cai, et al., “Decreased Il-6 and NK Cells in Early-stage Lung Adenocarcinoma Presenting as Ground-glass Opacity,” Frontiers in Oncology 11 (2021): 705888.

[165] X. Zhu, L. Chen, L. Liu, et al., “Emt-mediated Acquired EGFR-TKI Resistance in Nsclc: Mechanisms and Strategies,” Frontiers in Oncology 9 (2019): 1044.

[166] J. L. Monster, L. Kemp, M. Gloerich, et al., “Diffuse Gastric Cancer: Emerging Mechanisms of Tumor Initiation and Progression,” Biochimica et Biophysica Acta: Reviews on Cancer 1877 (2022): 188719.

[167] H. Zhu, S. Qu, Y. Deng, et al., “Application of Organoids in Otolaryngology: Head and Neck Surgery,” European Archives of Oto-rhino-laryngology 281 (2024): 1643–1649.

[168] T. H. Koo, Y. L. Lee, X. B. Leong, et al., “Multi-omics Perspectives for Gastrointestinal Malignancy: A Systematic Review,” World Journal of Gastrointestinal Surgery 17 (2025): 107110.

[169] T. Fu, X. Jin, M. He, et al., “Interferon-induced Senescent Cd8⁺ T Cells Reduce Anti-PD1 Immunotherapy Efficacy in Early Triple-negative Breast Cancer,” Science Translational Medicine 17 (2025): eadj7808.

[170] A. S. Shankar, Z. Du, H. T. Mora, et al., “Kidney Organoids Are Capable of Forming Tumors, but Not Teratomas,” Stem Cells 40 (2022): 577–591.

[171] N. Del Piccolo, V. S. Shirure, Y. Bi, et al., “Tumor-on-chip Modeling of Organ-specific Cancer and Metastasis,” Advanced Drug Delivery Reviews 175 (2021): 113798.

[172] B. Subtil, K. K. Iyer, D. Poel, et al., “Dendritic Cell Phenotype and Function in a 3D Co-culture Model of Patient-derived Metastatic Colorectal Cancer Organoids,” Frontiers in Immunology 14 (2023): 1105244.

[173] K. Sugiura, Y. Masuike, K. Suzuki, et al., “LIN28B Promotes Cell Invasion and Colorectal Cancer Metastasis via CLDN1 and NOTCH3,” JCI Insight 8 (2023): e167310.

[174] A. E. Shin, K. Sugiura, S. W. Kariuki, et al., “LIN28b-mediated PI3k/AKT Pathway Activation Promotes Metastasis in Colorectal Cancer Models,” The Journal of Clinical Investigation 135 (2025): e186035.

[175] H. Zhang, L. Zhang, Y. He, et al., “PI3K PROTAC Overcomes the Lapatinib Resistance in PIK3ca-mutant HER2 Positive Breast Cancer,” Cancer Letters 598 (2024): 217112.

[176] Q. Li, Y. Xiao, L. Han, et al., “Microbiome Dysbiosis, Neutrophil Recruitment and Mesenchymal Transition of Mesothelial Cells Promotes Peritoneal Metastasis of Colorectal Cancer,” Nature Cancer 6 (2025): 493–510.

[177] H. H. Loong, A. M. Wong, D. T. Chan, et al., “Patient-derived Tumor Organoid Predicts Drugs Response in Glioblastoma: A Step Forward in Personalized Cancer Therapy,” Journal of Clinical Neuroscience 78 (2020): 400–402.

[178] T. Peng, X. Ma, W. Hua, et al., “Individualized Patient Tumor Organoids Faithfully Preserve Human Brain Tumor Ecosystems and Predict Patient Response to Therapy,” Cell Stem Cell 32 (2025): 652–669.e11.

[179] M. Chen, H. Shan, Q. Tao, et al., “Mimicking Tumor Metastasis Using a Transwell-integrated Organoids-on-a-chip Platform,” Small 20 (2024): e2308525.

[180] M. Ponz-Sarvise, V. Corbo, H. Tiriac, et al., “Identification of Resistance Pathways Specific to Malignancy Using Organoid Models of Pancreatic Cancer,” Clinical Cancer Research 25 (2019): 6742–6755.

[181] E. Madan, A. M. Palma, V. Vudatha, et al., “Ovarian Tumor Cells Gain Competitive Advantage by Actively Reducing the Cellular Fitness of Microenvironment Cells,” Nature Biotechnology 43 (2025): 1833–1847.

[182] D. K. Chen, S. Izadyar, R. L. Collins, et al., “Induction of Psychogenic Nonepileptic Events: Success Rate Influenced by Prior Induction Exposure, Ictal Semiology, and Psychological Profiles,” Epilepsia 52 (2011): 1063–1070.

[183] C. M. Frodella, S. B. Pruett, and B. Kaplan, “Mild Disease Course of Experimental Autoimmune Encephalomyelitis without Pertussis Toxin: Brain Transcriptome Analysis Reveals Similar Signaling to Active Lesions in Multiple Sclerosis,” Biomedicines 12 (2024): 1215.

[184] M. Simões-Abade, M. Patterer, A. M. Nicaise, et al., “Brain Organoid Methodologies to Explore Mechanisms of Disease in Progressive Multiple Sclerosis,” Frontiers in Cellular Neuroscience 18 (2024): 1488691.

[185] S. Lange, M. Ebeling, A. Loye, et al., “Human Myelinated Brain Organoids With Integrated Microglia as a Model for Myelin Repair and Remyelinating Therapies,” Science Translational Medicine 17 (2025): eadp7047.

[186] B. Acar, N. A. Pepe, A. Zivkovic, et al., “Neuroinflammatory Human Brain Organoids Enable Comprehensive Drug Screening Studies: Fingolimod and Its Analogues in Focus,” Current Medicinal Chemistry (2025), https://doi.org/10.2174/0109298673435364251002112630.

[187] N. Daviaud, E. Chen, T. Edwards, et al., “Cerebral Organoids in Primary Progressive Multiple Sclerosis Reveal Stem Cell and Oligodendrocyte Differentiation Defect,” Biology Open 12 (2023): bio05984.

[188] S. Sharma, S. Risen, V. S. Gilberto, et al., “Targeted-neuroinflammation Mitigation Using Inflammasome-inhibiting Nanoligomers Is Therapeutic in an Experimental Autoimmune Encephalomyelitis Mouse Model,” ACS Chemical Neuroscience 15 (2024): 1596–1608.

[189] Q. Wang, S. Yao, Z. X. Yang, et al., “Pharmacological Characterization of the Small Molecule 03a10 as an Inhibitor of α-synuclein Aggregation for Parkinson's Disease Treatment,” Acta Pharmacologica Sinica 44 (2023): 1122–1134.

[190] J. C. Schwamborn, “Is Parkinson's Disease a Neurodevelopmental Disorder and Will Brain Organoids Help Us to Understand It,” Stem Cells and Development 27 (2018): 968–975.

[191] E. Tolosa, M. Vila, C. Klein, et al., “LRRK2 in Parkinson Disease: Challenges of Clinical Trials,” Nature Reviews Neurology 16 (2020): 97–107.

[192] Z. Wang, S. W. Chan, H. Zhao, et al., “Outlook of Pink1/Parkin Signaling in Molecular Etiology of Parkinson's Disease, With Insights into PINK1 Knockout Models,” Zoological Research 44 (2023): 559–576.

[193] B. Galet, H. Cheval, and P. Ravassard, “Patient-derived Midbrain Organoids to Explore the Molecular Basis of Parkinson's Disease,” Frontiers in Neurology 11 (2020): 1005.

[194] L. K. Wareham, S. A. Liddelow, S. Temple, et al., “Solving Neurodegeneration: Common Mechanisms and Strategies for New Treatments,” Molecular Neurodegeneration 17 (2022): 23.

[195] A. J. Bindas, S. Kulkarni, R. A. Koppes, et al., “Parkinson's Disease and the Gut: Models of an Emerging Relationship,” Acta Biomaterialia 132 (2021): 325–344.

[196] J. Walter, S. Bolognin, S. K. Poovathingal, et al., “The Parkinson's-disease-associated Mutation LRRK2-g2019S Alters Dopaminergic Differentiation Dynamics via NR2F1,” Cell Reports 37 (2021): 109864.

[197] A. Vuidel, L. Cousin, B. Weykopf, et al., “High-content Phenotyping of Parkinson's Disease Patient Stem Cell-derived Midbrain Dopaminergic Neurons Using Machine Learning Classification,” Stem Cell Reports 17 (2022): 2349–2364.

[198] X. Zheng, D. Han, W. Liu, et al., “Human IPSC-derived Midbrain Organoids Functionally Integrate into Striatum Circuits and Restore Motor Function in a Mouse Model of Parkinson's Disease,” Theranostics 13 (2023): 2673–2692.

[199] A. Al Mamun, C. Shao, P. Geng, et al., “The Mechanism of Pyroptosis and Its Application Prospect in Diabetic Wound Healing,” Journal of Inflammation Research 17 (2024): 1481–1501.

[200] Global Burden of Disease Study 2021 Autism Spectrum Collaborators, “The Global Epidemiology and Health Burden of the Autism Spectrum: Findings From the Global Burden of Disease Study 2021,” Lancet Psychiatry 12 (2025): 111–121.

[201] J. Urresti, P. Zhang, P. Moran-Losada, et al., “Cortical Organoids Model Early Brain Development Disrupted by 16p11.2 Copy Number Variants in Autism,” Molecular Psychiatry 26 (2021): 7560–7580.

[202] F. Liu, C. Liang, Z. Li, et al., “Haplotype-specific MAPK3 Expression in 16p11.2 Deletion Contributes to Variable Neurodevelopment,” Brain 146 (2023): 3347–3363.

[203] N. Khatri and H. Y. Man, “The Autism and Angelman Syndrome Protein Ube3A/E6AP: The Gene, E3 Ligase Ubiquitination Targets and Neurobiological Functions,” Frontiers in Molecular Neuroscience 12 (2019): 109.

[204] X. Li, “Unravelling the Role of SHANK3 Mutations in Targeted Therapies for Autism Spectrum Disorders,” Discover Psychology 4 (2024): 110.

[205] C. M. Durand, C. Betancur, T. M. Boeckers, et al., “Mutations in the Gene Encoding the Synaptic Scaffolding Protein SHANK3 Are Associated With Autism Spectrum Disorders,” Nature Genetics 39 (2007): 25–27.

[206] C. Niu, X. Yue, J. J. An, et al., “Genetic Dissection of BDNF and TrkB Expression in Glial Cells,” Biomolecules 14 (2024): 91.

[207] R. Connacher, M. Williams, S. Prem, et al., “Autism NPCs From both Idiopathic and CNV 16p11.2 Deletion Patients Exhibit Dysregulation of Proliferation and Mitogenic Responses,” Stem Cell Reports 17 (2022): 1380–1394.

[208] P. M. Quinn, L. P. Pellissier, and J. Wijnholds, “The CRB1 Complex: Following the Trail of Crumbs to a Feasible Gene Therapy Strategy,” Frontiers in Neuroscience 11 (2017): 175.

[209] A. Tso, B. L. da Costa, A. Fehnel, et al., “Generation of Human Ipsc-derived Retinal Organoids for Assessment of Aav-mediated Gene Delivery,” Methods in Molecular Biology 2560 (2023): 287–302.

[210] M. E. McClements, H. Steward, W. Atkin, et al., “Tropism of AAV Vectors in Photoreceptor-Like Cells of Human IPSC-derived Retinal Organoids,” Translational Vision Science & Technology 11 (2022): 3.

[211] M. Völkner, M. Pavlou, H. Büning, et al., “Optimized Adeno-associated Virus Vectors for Efficient Transduction of Human Retinal Organoids,” Human Gene Therapy 32 (2021): 694–706.

[212] V. Marx, “Closing in on Cancer Heterogeneity With Organoids,” Nature Methods 21 (2024): 551–554.

[213] J. Yuan, X. Li, and S. Yu, “Cancer Organoid Co-culture Model System: Novel Approach to Guide Precision Medicine,” Frontiers in Immunology 13 (2022): 1061388.

[214] L. Magré, M. Verstegen, S. Buschow, et al., “Emerging Organoid-immune Co-culture Models for Cancer Research: From Oncoimmunology to Personalized Immunotherapies,” Journal for Immunotherapy of Cancer 11 (2023): e006290.

[215] Y. Yuan, K. Cotton, D. Samarasekera, et al., “Engineered Platforms for Maturing Pluripotent Stem Cell-derived Liver Cells for Disease Modeling,” Cellular and Molecular Gastroenterology and Hepatology 15 (2023): 1147–1160.

[216] L. Fülöp, A. Rajki, E. Maka, et al., “Mitochondrial Ca²⁺ Uptake Correlates With the Severity of the Symptoms in Autosomal Dominant Optic Atrophy,” Cell Calcium 57 (2015): 49–55.

[217] H. Kashfi, N. Jinks, and A. S. Nateri, “Generating and Utilizing Murine Cas9-expressing Intestinal Organoids for Large-scale Knockout Genetic Screening,” Methods in Molecular Biology 2171 (2020): 257–269.

[218] J. Beumer, M. H. Geurts, M. M. Lamers, et al., “A CRISPR/Cas9 Genetically Engineered Organoid Biobank Reveals Essential Host Factors for Coronaviruses,” Nature Communications 12 (2021): 5498.

[219] C. Mirabelli, E. J. Sherman, J. B. Cunha, et al., “ARF6 is a Host Factor for SARS-CoV-2 Infection in vitro,” Journal of General Virology 104 (2022): 001868.

[220] X. Tang, D. Xue, T. Zhang, et al., “A Multi-organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection,” Nature Cell Biology 25 (2023): 381–389.

[221] R. C. Anafi, Y. Lee, T. K. Sato, et al., “Machine Learning Helps Identify CHRONO as a Circadian Clock Component,” PLoS Biology 12 (2014): e1001840.

[222] Y. Annayev, S. Adar, Y. Y. Chiou, et al., “Gene Model 129 (GM129) Encodes a Novel Transcriptional Repressor That Modulates Circadian Gene Expression,” The Journal of Biological Chemistry 289 (2014): 5013–5024.

[223] X. Duan, T. Zhang, L. Feng, et al., “A Pancreatic Cancer Organoid Platform Identifies an Inhibitor Specific to Mutant KRAS,” Cell Stem Cell 31 (2024): 71–88.

[224] L. Cong, F. A. Ran, D. Cox, et al., “Multiplex Genome Engineering Using CRISPR/Cas Systems,” Science 339 (2013): 819–823.

[225] V. Tiroille, A. Krug, E. Bokobza, et al., “Nanoblades Allow High-level Genome Editing in Murine and Human Organoids,” Molecular Therapy Nucleic Acids 33 (2023): 57–74.

[226] D. Singh and A. Thakur, “Advancements in Organoid-based Drug Discovery: Revolutionizing Precision Medicine and Pharmacology,” Drug Development Research 86 (2025): e70121, Rakesh.

[227] H. Cheng, F. Zhang, and Y. Ding, “CRISPR/Cas9 Delivery System Engineering for Genome Editing in Therapeutic Applications,” Pharmaceutics 13 (2021): 1649.

[228] K. Pandya and D. Kumar, “CRISPR/Cas Genome Editing for Neurodegenerative Diseases: Mechanisms, Therapeutic Advances, and Clinical Prospects,” Ageing Research Reviews 113 (2026): 102922.

[229] D. Matsumoto, E. Matsugi, K. Kishi, et al., “SpCas9-HF1 Enhances Accuracy of Cell Cycle-dependent Genome Editing by Increasing HDR Efficiency, and by Reducing off-target Effects and Indel Rates,” Molecular Therapy Nucleic Acids 35 (2024): 102124.

[230] S. Q. Tsai, N. T. Nguyen, J. Malagon-Lopez, et al., “CIRCLE-seq: A Highly Sensitive in vitro Screen for Genome-wide CRISPR-Cas9 Nuclease Off-targets,” Nature Methods 14 (2017): 607–614.

[231] G. Wang, X. Liu, A. Wang, et al., “CRISPoffT: Comprehensive Database of CRISPR/Cas Off-targets,” Nucleic Acids Research 53 (2025): D914–D924.

[232] E. P. Neale, V. Guan, L. C. Tapsell, et al., “Effect of Walnut Consumption on Markers of Blood Glucose Control: A Systematic Review and Meta-analysis,” The British Journal of Nutrition 124 (2020): 641–653.

[233] Y. Song, C. Guan, Y. Zhang, et al., “A Novel CRISPR-Cas9 Nickase-mediated Rolling Circle Amplification (CRIRCA) Technique for Gene Identification and Quantitative Analysis of Extrachromosomal DNA,” Journal of Advanced Research 80 (2026): 239–248.

[234] J. Chakraborty, I. Banerjee, R. Vaishya, et al., “Bioengineered in vitro Tissue Models to Study SARS-CoV-2 Pathogenesis and Therapeutic Validation,” ACS Biomaterials Science & Engineering 6 (2020): 6540–6555.

[235] J. Berg, T. Hiller, M. S. Kissner, et al., “Optimization of Cell-laden Bioinks for 3D Bioprinting and Efficient Infection With Influenza A Virus,” Scientific Reports 8 (2018): 13877.

[236] A. Schwab, R. Levato, M. D'Este, et al., “Printability and Shape Fidelity of Bioinks in 3D Bioprinting,” Chemical Reviews 120 (2020): 11028–11055.

[237] C. McGuckin, N. Forraz, C. Milet, et al., “World's First Long-term Colorectal Cancer Model by 3D Bioprinting as a Mechanism for Screening Oncolytic Viruses,” Cancers 15 (2023): 4724.

[238] M. J. Song, R. Quinn, E. Nguyen, et al., “Bioprinted 3D Outer Retina Barrier Uncovers Rpe-dependent Choroidal Phenotype in Advanced Macular Degeneration,” Nature Methods 20 (2023): 149–161.

[239] A. Seyfoori, M. Amereh, S. Dabiri, et al., “The Role of Biomaterials and Three Dimensional (3D) in vitro Tissue Models in Fighting Against COVID-19,” Biomaterials Science 9 (2021): 1217–1226.

[240] T. Hiller, J. Berg, L. Elomaa, et al., “Generation of a 3D Liver Model Comprising Human Extracellular Matrix in an Alginate/Gelatin-based Bioink by Extrusion Bioprinting for Infection and Transduction Studies,” International Journal of Molecular Sciences 19 (2018): 3129.

[241] B. He, J. Wang, M. Xie, et al., “3D Printed Biomimetic Epithelium/Stroma Bilayer Hydrogel Implant for Corneal Regeneration,” Bioactive Materials 17 (2022): 234–247.

[242] E. Mazari-Arrighi, M. Lépine, D. Ayollo, et al., “Self-organization of Long-lasting Human Endothelial Capillary-Like Networks Guided by DLP Bioprinting,” Advanced Healthcare Materials 13 (2024): e2302830.

[243] S. Mirzababaei, L. Towery, and M. Kozminsky, “3D and 4D Assembly of Functional Structures Using Shape-morphing Materials for Biological Applications,” Frontiers in Bioengineering and Biotechnology 12 (2024): 1347666.

[244] Y. Zhu, X. Yu, H. Liu, et al., “Strategies of Functionalized Gelma-based Bioinks for Bone Regeneration: Recent Advances and Future Perspectives,” Bioactive Materials 38 (2024): 346–373.

[245] T. Agarwal, V. Onesto, D. Banerjee, et al., “3D Bioprinting in Tissue Engineering: Current State-of-the-art and Challenges towards System Standardization and Clinical Translation,” Biofabrication 17 (2025), https://doi.org/10.1088/1758-5090/ade47a.

[246] F. A. Yousef Yengej, J. Jansen, C. Ammerlaan, et al., “Tubuloid Culture Enables Long-term Expansion of Functional Human Kidney Tubule Epithelium From Ipsc-derived Organoids,” Proceedings of the National Academy of Sciences of the United States of America 120 (2023): e2216836120.

[247] B. Correa, J. Hu, L. Penalva, et al., “Patient-derived Conditionally Reprogrammed Cells Maintain Intra-tumor Genetic Heterogeneity,” Scientific Reports 8 (2018): 4097.

[248] S. E. Blutt and M. K. Estes, “Organoid Models for Infectious Disease,” Annual Review of Medicine 73 (2022): 167–182.

[249] A. M. Luoma, S. Suo, H. L. Williams, et al., “Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy,” Cell 182 (2020): 655–671.e22.

[250] Y. Wu, X. Li, H. Liu, et al., “Organoids in the Oral and Maxillofacial Region: Present and Future,” International Journal of Oral Science 16 (2024): 61.

[251] J. Qu, F. S. Kalyani, L. Liu, et al., “Tumor Organoids: Synergistic Applications, Current Challenges, and Future Prospects in Cancer Therapy,” Cancer Communications 41 (2021): 1331–1353.

[252] J. Ko, S. Hyung, S. Cheong, et al., “Revealing the Clinical Potential of High-resolution Organoids,” Advanced Drug Delivery Reviews 207 (2024): 115202.

[253] R. Tan, Z. Zhang, P. Ding, et al., “A Growth Factor-reduced Culture System for Colorectal Cancer Organoids,” Cancer Letters 588 (2024): 216737.

[254] Y. Zhou, H. Song, and G. L. Ming, “Genetics of Human Brain Development,” Nature Reviews Genetics 25 (2024): 26–45.

[255] Q. Gao, J. Wang, H. Zhang, et al., “Organoid Vascularization: Strategies and Applications,” Advanced Healthcare Materials 14 (2025): e2500301.

[256] X. Tong, A. S. Patel, E. Kim, et al., “Adeno-to-squamous Transition Drives Resistance to KRAS Inhibition in LKB1 Mutant Lung Cancer,” Cancer Cell 42 (2024): 413–428.e7.

[257] X. Mao, S. Wu, D. Huang, et al., “Complications and Comorbidities Associated With Antineoplastic Chemotherapy: Rethinking Drug Design and Delivery for Anticancer Therapy,” Acta Pharmaceutica Sinica B 14 (2024): 2901–2926.

[258] X. Wang, Z. Dai, X. Lin, et al., “Antigen/HLA-agnostic Strategies for Characterizing Tumor-responsive T Cell Receptors in PDAC Patients via Single-cell Sequencing and Autologous Organoid Application,” Cancer Letters 588 (2024): 216741.

[259] S. Maharjan, C. Ma, B. Singh, et al., “Advanced 3D Imaging and Organoid Bioprinting for Biomedical Research and Therapeutic Applications,” Advanced Drug Delivery Reviews 208 (2024): 115237.

[260] R. Yang, Y. Qi, X. Zhang, et al., “Living Biobank: Standardization of Organoid Construction and Challenges,” Chinese Medical Journal 137 (2024): 3050–3060.

[261] N. Mamidi, F. Franco De Silva, and A. Orash Mahmoudsalehi, “Advanced Disease Therapeutics Using Engineered Living Drug Delivery Systems,” Nanoscale 17 (2025): 7673–7696.

[262] J. Yao, J. Peretz, I. Bebenek, et al., “FDA/CDER/OND Experience with New Approach Methodologies (nams),” International Journal of Toxicology 45 (2025): 136–156.

[263] D. Wang, R. Villenave, N. Stokar-Regenscheit, et al., “Human Organoids as 3D in vitro Platforms for Drug Discovery: Opportunities and Challenges,” Nature Reviews Drug Discovery 25 (2025): 204–226.

RIGHTS & PERMISSIONS

2026 The Author(s). MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.