{"topic":"organoids","sort":"top","limit":25,"offset":0,"count":25,"papers":[{"id":"doi:10.1038/nature12517","kind":"article","title":"Cerebral organoids model human brain development and microcephaly","authors":["Madeline A. Lancaster","Magdalena Renner","Carol-Anne Martin","Daniel Wenzel","Louise S. Bicknell","Matthew E. Hurles","Tessa Homfray","Josef Martin Penninger","Andrew P. Jackson","Juergen A. Knoblich"],"author_count":10,"year":2013,"published":"2013-08-27","venue":"Nature","cited_by":5369,"doi":"10.1038/nature12517","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature12517","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature12517","updated":null,"pmid":"23995685","pmcid":null,"openalex_id":"W2018286352","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Neurogenesis and neuroplasticity mechanisms"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1159/000433566","kind":"review","title":"Organoid Models and Applications in Biomedical Research","authors":["Christodoulos Xinaris","Valerio Brizi","Giuseppe Remuzzi"],"author_count":3,"year":2015,"published":"2015-01-01","venue":"The Nephron journals/Nephron journals","cited_by":3515,"doi":"10.1159/000433566","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1159/000433566","archive_url":"https://space-kitty.com/papers/doi:10.1159/000433566","updated":null,"pmid":"26112599","pmcid":null,"openalex_id":"W1483496013","pdf_url":null,"abstract":null,"abstract_license":null,"license":"other-oa","is_open_access":true,"peer_reviewed":null,"categories":["Pluripotent Stem Cells Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1016/j.cell.2016.05.082","kind":"review","title":"Modeling Development and Disease with Organoids","authors":["Hans C. Clevers"],"author_count":1,"year":2016,"published":"2016-06-01","venue":"Cell","cited_by":3196,"doi":"10.1016/j.cell.2016.05.082","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2016.05.082","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2016.05.082","updated":null,"pmid":"27315476","pmcid":null,"openalex_id":"W2441337908","pdf_url":"http://www.cell.com/article/S0092867416307292/pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Pluripotent Stem Cells Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1084/jem.20162024","kind":"article","title":"Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer","authors":["Öhlund D","Handly-Santana A","Biffi G","Elyada E","Almeida AS","Ponz-Sarvise M","Corbo V","Oni TE","Hearn SA","Lee EJ","Chio II","Hwang CI","Tiriac H","Baker LA","Engle DD","Feig C","Kultti A","Egeblad M","Fearon DT","Crawford JM","Clevers H","Park Y","Tuveson DA"],"author_count":23,"year":2017,"published":"2017-02-23","venue":"The Journal of experimental medicine","cited_by":2274,"doi":"10.1084/jem.20162024","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1084/jem.20162024","archive_url":"https://space-kitty.com/papers/doi:10.1084/jem.20162024","updated":null,"pmid":"28232471","pmcid":"PMC5339682","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC5339682/pdf","abstract":"Pancreatic stellate cells (PSCs) differentiate into cancer-associated fibroblasts (CAFs) that produce desmoplastic stroma, thereby modulating disease progression and therapeutic response in pancreatic ductal adenocarcinoma (PDA). However, it is unknown whether CAFs uniformly carry out these tasks or if subtypes of CAFs with distinct phenotypes in PDA exist. We identified a CAF subpopulation with elevated expression of α-smooth muscle actin (αSMA) located immediately adjacent to neoplastic cells in mouse and human PDA tissue. We recapitulated this finding in co-cultures of murine PSCs and PDA organoids, and demonstrated that organoid-activated CAFs produced desmoplastic stroma. The co-cultures showed cooperative interactions and revealed another distinct subpopulation of CAFs, located more distantly from neoplastic cells, which lacked elevated αSMA expression and instead secreted IL6 and additional inflammatory mediators. These findings were corroborated in mouse and human PDA tissue, providing direct evidence for CAF heterogeneity in PDA tumor biology with implications for disease etiology and therapeutic development.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer\" by Öhlund D, Handly-Santana A, Biffi G et al., https://doi.org/10.1084/jem.20162024, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1126/science.1247125","kind":"review","title":"Organogenesis in a dish: Modeling development and disease using organoid technologies","authors":["Madeline A. Lancaster","Juergen A. Knoblich"],"author_count":2,"year":2014,"published":"2014-07-17","venue":"Science","cited_by":2930,"doi":"10.1126/science.1247125","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1126/science.1247125","archive_url":"https://space-kitty.com/papers/doi:10.1126/science.1247125","updated":null,"pmid":"25035496","pmcid":null,"openalex_id":"W2044928246","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":false,"peer_reviewed":null,"categories":["Pluripotent Stem Cells Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41580-020-0259-3","kind":"review","title":"Human organoids: model systems for human biology and medicine","authors":["Jihoon Kim","Bon‐Kyoung Koo","Juergen A. Knoblich"],"author_count":3,"year":2020,"published":"2020-07-07","venue":"Nature Reviews Molecular Cell Biology","cited_by":2186,"doi":"10.1038/s41580-020-0259-3","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41580-020-0259-3","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41580-020-0259-3","updated":null,"pmid":"32636524","pmcid":null,"openalex_id":"W3040646360","pdf_url":"https://www.nature.com/articles/s41580-020-0259-3.pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Pluripotent Stem Cells Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41586-021-03944-y","kind":"article","title":"SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion","authors":["Mlcochova P","Kemp SA","Dhar MS","Papa G","Meng B","Ferreira IATM","Datir R","Collier DA","Albecka A","Singh S","Pandey R","Brown J","Zhou J","Goonawardane N","Mishra S","Whittaker C","Mellan T","Marwal R","Datta M","Sengupta S","Ponnusamy K","Radhakrishnan VS","Abdullahi A","Charles O","Chattopadhyay P"],"author_count":52,"year":2021,"published":"2021-09-06","venue":"Nature","cited_by":1142,"doi":"10.1038/s41586-021-03944-y","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41586-021-03944-y","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41586-021-03944-y","updated":null,"pmid":"34488225","pmcid":"PMC8566220","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC8566220/pdf","abstract":"The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha) 1 . In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion\" by Mlcochova P, Kemp SA, Dhar MS et al., https://doi.org/10.1038/s41586-021-03944-y, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1016/j.cell.2014.12.021","kind":"article","title":"Organoid Models of Human and Mouse Ductal Pancreatic Cancer","authors":["Sylvia F. Boj","Chang‐Il Hwang","Lindsey A. Baker","Iok In Christine Chio","Dannielle D. Engle","Vincenzo Corbo","Myrthe Jager","Mariano Ponz‐Sarvisé","Hervé Tiriac","Mona S. Spector","Ana Gracanin","Tobiloba E. Oni","Kenneth H. Yu","Ruben van Boxtel","Meritxell Huch","Keith D. Rivera","John P. Wilson","Michael E. Feigin","Daniel Öhlund","Abram Handly‐Santana","Christine Ardito-Abraham","Michael Ludwig","Ela Elyada","Brinda Alagesan","Giulia Biffi"],"author_count":48,"year":2014,"published":"2014-12-31","venue":"Cell","cited_by":2149,"doi":"10.1016/j.cell.2014.12.021","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2014.12.021","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2014.12.021","updated":null,"pmid":"25557080","pmcid":null,"openalex_id":"W2010916968","pdf_url":"https://www.sciencedirect.com/science/article/pii/S009286741401592X/pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Pancreatic and Hepatic Oncology Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1016/j.cell.2016.04.032","kind":"article","title":"Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure","authors":["Xuyu Qian","Ha Nam Nguyen","Mingxi M. Song","Christopher Hadiono","Sarah C. Ogden","Christy Hammack","Bing Yao","Gregory R. Hamersky","Fadi Jacob","Chun Zhong","Ki‐Jun Yoon","William J. Jeang","Li Lin","Yujing Li","Jai Thakor","Daniel A. Berg","Ce Zhang","Eunchai Kang","Michael Chickering","David W. Nauen","Cheng‐Ying Ho","Zhexing Wen","Kimberly M. Christian","Pei‐Yong Shi","Brady J. Maher"],"author_count":30,"year":2016,"published":"2016-04-30","venue":"Cell","cited_by":2127,"doi":"10.1016/j.cell.2016.04.032","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2016.04.032","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2016.04.032","updated":null,"pmid":"27118425","pmcid":null,"openalex_id":"W2341041396","pdf_url":"http://www.cell.com/article/S0092867416304676/pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Neurogenesis and neuroplasticity mechanisms"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41568-018-0007-6","kind":"review","title":"Organoids in cancer research","authors":["Jarno Drost","Hans C. Clevers"],"author_count":2,"year":2018,"published":"2018-04-24","venue":"Nature reviews. Cancer","cited_by":1787,"doi":"10.1038/s41568-018-0007-6","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41568-018-0007-6","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41568-018-0007-6","updated":null,"pmid":"29692415","pmcid":null,"openalex_id":"W2799444748","pdf_url":null,"abstract":null,"abstract_license":null,"license":"other-oa","is_open_access":true,"peer_reviewed":null,"categories":["Cancer Cells and Metastasis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nprot.2014.158","kind":"article","title":"Generation of cerebral organoids from human pluripotent stem cells","authors":["Madeline A. Lancaster","Juergen A. Knoblich"],"author_count":2,"year":2014,"published":"2014-09-04","venue":"Nature Protocols","cited_by":1807,"doi":"10.1038/nprot.2014.158","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nprot.2014.158","archive_url":"https://space-kitty.com/papers/doi:10.1038/nprot.2014.158","updated":null,"pmid":"25188634","pmcid":null,"openalex_id":"W1985958520","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Pluripotent Stem Cells Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nature15695","kind":"article","title":"Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis","authors":["Minoru Takasato","Pei Xuan Er","Han Sheng Chiu","Barbara Maier","Gregory J. Baillie","Charles Ferguson","Robert G. Parton","Ernst Jurgen Wolvetang","Matthias S. Roost","Susana M. Chuva de Sousa Lopes","Melissa Helen Little"],"author_count":11,"year":2015,"published":"2015-10-07","venue":"Nature","cited_by":1627,"doi":"10.1038/nature15695","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature15695","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature15695","updated":null,"pmid":"26444236","pmcid":null,"openalex_id":"W1802574002","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":false,"peer_reviewed":null,"categories":["Renal and related cancers"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1016/j.cell.2014.11.050","kind":"article","title":"Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver","authors":["Meritxell Huch","Helmuth Gehart","Ruben van Boxtel","Karien M. Hamer","Francis Blokzijl","Monique M. A. Verstegen","Ewa C. S. Ellis","Martien van Wenum","Sabine A. Fuchs","Joep de Ligt","Marc van de Wetering","Nobuo Sasaki","Susanne J. Boers","Hans Kemperman","Jeroen de Jonge","Jan N.M. IJzermans","Edward E. S. Nieuwenhuis","Ruurdtje Hoekstra","Stephen C. Strom","Robert Vries","Luc J. W. van der Laan","Edwin P. J. G. Cuppen","Hans C. Clevers"],"author_count":23,"year":2014,"published":"2014-12-19","venue":"Cell","cited_by":1619,"doi":"10.1016/j.cell.2014.11.050","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2014.11.050","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2014.11.050","updated":null,"pmid":"25533785","pmcid":null,"openalex_id":"W2085652695","pdf_url":"http://www.cell.com/article/S0092867414015669/pdf","abstract":"Despite the enormous replication potential of the human liver, there are currently no culture systems available that sustain hepatocyte replication and/or function in vitro. We have shown previously that single mouse Lgr5+ liver stem cells can be expanded as epithelial organoids in vitro and can be differentiated into functional hepatocytes in vitro and in vivo. We now describe conditions allowing long-term expansion of adult bile duct-derived bipotent progenitor cells from human liver. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from α1-antitrypsin deficiency and Alagille syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine, and gene therapy.","abstract_license":"CC-BY (publisher license, via OpenAlex)","license":"cc-by","is_open_access":true,"peer_reviewed":null,"categories":["Liver physiology and pathology"],"details":null,"provenance":"openalex","attribution":"Abstract of \"Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver\" by Meritxell Huch, Helmuth Gehart, Ruben van Boxtel et al., https://doi.org/10.1016/j.cell.2014.11.050, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1038/s41467-019-11867-6","kind":"article","title":"Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening","authors":["Kim M","Mun H","Sung CO","Cho EJ","Jeon HJ","Chun SM","Jung DJ","Shin TH","Jeong GS","Kim DK","Choi EK","Jeong SY","Taylor AM","Jain S","Meyerson M","Jang SJ"],"author_count":16,"year":2019,"published":"2019-09-05","venue":"Nature communications","cited_by":641,"doi":"10.1038/s41467-019-11867-6","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41467-019-11867-6","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41467-019-11867-6","updated":null,"pmid":"31488816","pmcid":"PMC6728380","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC6728380/pdf","abstract":"Lung cancer shows substantial genetic and phenotypic heterogeneity across individuals, driving a need for personalised medicine. Here, we report lung cancer organoids and normal bronchial organoids established from patient tissues comprising five histological subtypes of lung cancer and non-neoplastic bronchial mucosa as in vitro models representing individual patient. The lung cancer organoids recapitulate the tissue architecture of the primary lung tumours and maintain the genomic alterations of the original tumours during long-term expansion in vitro. The normal bronchial organoids maintain cellular components of normal bronchial mucosa. Lung cancer organoids respond to drugs based on their genomic alterations: a BRCA2-mutant organoid to olaparib, an EGFR-mutant organoid to erlotinib, and an EGFR-mutant/MET-amplified organoid to crizotinib. Considering the short length of time from organoid establishment to drug testing, our newly developed model may prove useful for predicting patient-specific drug responses through in vitro patient-specific drug trials.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Patient-derived lung cancer organoids as in vitro cancer models for therapeutic screening\" by Kim M, Mun H, Sung CO et al., https://doi.org/10.1038/s41467-019-11867-6, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.7554/elife.05098","kind":"article","title":"In vitro generation of human pluripotent stem cell derived lung organoids","authors":["Briana R. Dye","David R. Hill","Michael A.H. Ferguson","Yu-Hwai Tsai","Melinda S. Nagy","Rachel Dyal","James M. Wells","Christopher N. Mayhew","Roy Nattiv","Ophir D. Klein","Eric S. White","Gail H. Deutsch","Jason R. Spence"],"author_count":13,"year":2015,"published":"2015-03-23","venue":"eLife","cited_by":824,"doi":"10.7554/elife.05098","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.7554/elife.05098","archive_url":"https://space-kitty.com/papers/doi:10.7554/elife.05098","updated":null,"pmid":"25803487","pmcid":"PMC4370217","openalex_id":"W2156862506","pdf_url":"https://europepmc.org/articles/PMC4370217/pdf","abstract":"Recent breakthroughs in 3-dimensional (3D) organoid cultures for many organ systems have led to new physiologically complex in vitro models to study human development and disease. Here, we report the step-wise differentiation of human pluripotent stem cells (hPSCs) (embryonic and induced) into lung organoids. By manipulating developmental signaling pathways hPSCs generate ventral-anterior foregut spheroids, which are then expanded into human lung organoids (HLOs). HLOs consist of epithelial and mesenchymal compartments of the lung, organized with structural features similar to the native lung. HLOs possess upper airway-like epithelium with basal cells and immature ciliated cells surrounded by smooth muscle and myofibroblasts as well as an alveolar-like domain with appropriate cell types. Using RNA-sequencing, we show that HLOs are remarkably similar to human fetal lung based on global transcriptional profiles, suggesting that HLOs are an excellent model to study human lung development, maturation and disease.","abstract_license":"CC-BY (publisher license, via OpenAlex)","license":"cc-by","is_open_access":true,"peer_reviewed":null,"categories":["Pluripotent Stem Cells Research"],"details":null,"provenance":"openalex+europepmc","attribution":"Abstract of \"In vitro generation of human pluripotent stem cell derived lung organoids\" by Briana R. Dye, David R. Hill, Michael A.H. Ferguson et al., https://doi.org/10.7554/elife.05098, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1016/j.cell.2014.08.016","kind":"article","title":"Organoid Cultures Derived from Patients with Advanced Prostate Cancer","authors":["Dong Gao","Ian Vela","Andrea Sboner","Phillip J. Iaquinta","Wouter R. Karthaus","Anuradha Gopalan","Catherine Dowling","Jackline Wanjala","Eva A. Undvall","Vivek K. Arora","John Wongvipat","Myriam Kossaï","Sinan Ramazanoglu","Luendreo P. Barboza","Wei Di","Zhen Cao","Qi Fan Zhang","Inna Sirota","Leili Ran","Theresa Y. MacDonald","Himisha Beltran","Juan‐Miguel Mosquera","Karim A. Touijer","Peter T. Scardino","Vincent Paul Laudone"],"author_count":39,"year":2014,"published":"2014-09-01","venue":"Cell","cited_by":1559,"doi":"10.1016/j.cell.2014.08.016","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2014.08.016","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2014.08.016","updated":null,"pmid":"25201530","pmcid":null,"openalex_id":"W2059586354","pdf_url":"http://www.cell.com/article/S0092867414010472/pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Prostate Cancer Treatment and Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1016/j.stem.2020.06.020","kind":"article","title":"Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration","authors":["Choi J","Park JE","Tsagkogeorga G","Yanagita M","Koo BK","Han N","Lee JH"],"author_count":7,"year":2020,"published":"2020-08-03","venue":"Cell stem cell","cited_by":598,"doi":"10.1016/j.stem.2020.06.020","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.stem.2020.06.020","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.stem.2020.06.020","updated":null,"pmid":"32750316","pmcid":"PMC7487779","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC7487779/pdf","abstract":"Tissue regeneration is a multi-step process mediated by diverse cellular hierarchies and states that are also implicated in tissue dysfunction and pathogenesis. Here we leveraged single-cell RNA sequencing in combination with in vivo lineage tracing and organoid models to finely map the trajectories of alveolar-lineage cells during injury repair and lung regeneration. We identified a distinct AT2-lineage population, damage-associated transient progenitors (DATPs), that arises during alveolar regeneration. We found that interstitial macrophage-derived IL-1β primes a subset of AT2 cells expressing Il1r1 for conversion into DATPs via a HIF1α-mediated glycolysis pathway, which is required for mature AT1 cell differentiation. Importantly, chronic inflammation mediated by IL-1β prevents AT1 differentiation, leading to aberrant accumulation of DATPs and impaired alveolar regeneration. Together, this stepwise mapping to cell fate transitions shows how an inflammatory niche controls alveolar regeneration by controlling stem cell fate and behavior.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration\" by Choi J, Park JE, Tsagkogeorga G et al., https://doi.org/10.1016/j.stem.2020.06.020, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1038/ncb3312","kind":"review","title":"Organoids as an in vitro model of human development and disease","authors":["Aliya Fatehullah","Si Hui Tan","Nick Barker"],"author_count":3,"year":2016,"published":"2016-02-25","venue":"Nature Cell Biology","cited_by":1508,"doi":"10.1038/ncb3312","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/ncb3312","archive_url":"https://space-kitty.com/papers/doi:10.1038/ncb3312","updated":null,"pmid":"26911908","pmcid":null,"openalex_id":"W2282335838","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":false,"peer_reviewed":null,"categories":["3D Printing in Biomedical Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nm.4438","kind":"article","title":"Human primary liver cancer–derived organoid cultures for disease modeling and drug screening","authors":["Laura Broutier","Gianmarco Mastrogiovanni","Monique M. A. Verstegen","Hayley E. Francies","Lena Morrill Gavarró","Charles Richard Bradshaw","George Edward Allen","Robert Arnes‐Benito","Olga Alexandra Sidorova","Marcia Patricia Gaspersz","Nikitas Georgakopoulos","Bon‐Kyoung Koo","Sabine Dietmann","Susan E. Davies","Raaj Praseedom","Ruby Lieshout","Jan N.M. IJzermans","Stephen J. Wigmore","Kourosh Saeb‐Parsy","Mathew J. Garnett","Luc J. W. van der Laan","Meritxell Huch"],"author_count":22,"year":2017,"published":"2017-11-13","venue":"Nature Medicine","cited_by":1469,"doi":"10.1038/nm.4438","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nm.4438","archive_url":"https://space-kitty.com/papers/doi:10.1038/nm.4438","updated":null,"pmid":"29131160","pmcid":null,"openalex_id":"W2771057425","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Cancer Cells and Metastasis"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41588-021-00972-2","kind":"article","title":"Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro","authors":["Garcia-Alonso L","Handfield LF","Roberts K","Nikolakopoulou K","Fernando RC","Gardner L","Woodhams B","Arutyunyan A","Polanski K","Hoo R","Sancho-Serra C","Li T","Kwakwa K","Tuck E","Lorenzi V","Massalha H","Prete M","Kleshchevnikov V","Tarkowska A","Porter T","Mazzeo CI","van Dongen S","Dabrowska M","Vaskivskyi V","Mahbubani KT"],"author_count":40,"year":2021,"published":"2021-12-02","venue":"Nature genetics","cited_by":563,"doi":"10.1038/s41588-021-00972-2","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41588-021-00972-2","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41588-021-00972-2","updated":null,"pmid":"34857954","pmcid":"PMC8648563","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC8648563/pdf","abstract":"The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps of the human uterus and three-dimensional endometrial organoid cultures. We dissect the signaling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids reveals the pathways and cell states regulating differentiation of the secretory and ciliated lineages both in vivo and in vitro. In vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. We utilize our cellular maps to deconvolute bulk data from endometrial cancers and endometriotic lesions, illuminating the cell types dominating in each of these disorders. These mechanistic insights provide a platform for future development of treatments for common conditions including endometriosis and endometrial carcinoma.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro\" by Garcia-Alonso L, Handfield LF, Roberts K et al., https://doi.org/10.1038/s41588-021-00972-2, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1016/j.cell.2020.08.013","kind":"article","title":"Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution","authors":["Cowan CS","Renner M","De Gennaro M","Gross-Scherf B","Goldblum D","Hou Y","Munz M","Rodrigues TM","Krol J","Szikra T","Cuttat R","Waldt A","Papasaikas P","Diggelmann R","Patino-Alvarez CP","Galliker P","Spirig SE","Pavlinic D","Gerber-Hollbach N","Schuierer S","Srdanovic A","Balogh M","Panero R","Kusnyerik A","Szabo A"],"author_count":34,"year":2020,"published":"2020-09-01","venue":"Cell","cited_by":574,"doi":"10.1016/j.cell.2020.08.013","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1016/j.cell.2020.08.013","archive_url":"https://space-kitty.com/papers/doi:10.1016/j.cell.2020.08.013","updated":null,"pmid":"32946783","pmcid":"PMC7505495","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC7505495/pdf","abstract":"Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable \"developed\" state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution\" by Cowan CS, Renner M, De Gennaro M et al., https://doi.org/10.1016/j.cell.2020.08.013, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."},{"id":"doi:10.1038/nature22330","kind":"article","title":"Assembly of functionally integrated human forebrain spheroids","authors":["Fikri Birey","Jimena Andersen","Christopher D. Makinson","Saiful Islam","Wei Wu","Nina Huber","H. Christina Fan","Kimberly R. Cordes Metzler","Georgia Panagiotakos","Nicholas Thom","Nancy A. O’Rourke","Lars Michael Steinmetz","Jonathan Adam Bernstein","Joachim Franz Hallmayer","John R. Huguenard","Sergiu P. Pașca"],"author_count":16,"year":2017,"published":"2017-04-25","venue":"Nature","cited_by":1364,"doi":"10.1038/nature22330","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature22330","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature22330","updated":null,"pmid":"28445465","pmcid":null,"openalex_id":"W2609473806","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Neurogenesis and neuroplasticity mechanisms"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/s41578-021-00279-y","kind":"review","title":"Engineering organoids","authors":["Moritz Hofer","Matthias P. Lütolf"],"author_count":2,"year":2021,"published":"2021-02-19","venue":"Nature Reviews Materials","cited_by":1184,"doi":"10.1038/s41578-021-00279-y","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/s41578-021-00279-y","archive_url":"https://space-kitty.com/papers/doi:10.1038/s41578-021-00279-y","updated":null,"pmid":"33623712","pmcid":null,"openalex_id":"W4211240480","pdf_url":"https://www.nature.com/articles/s41578-021-00279-y.pdf","abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["3D Printing in Biomedical Research"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.1038/nature22047","kind":"article","title":"Cell diversity and network dynamics in photosensitive human brain organoids","authors":["Giorgia Quadrato","Tuan N. Nguyen","Evan Z. Macosko","J. L. Sherwood","Sung Min Yang","Daniel Raimund Berger","Natalie Maria","Jörg Scholvin","Melissa Goldman","Justin P. Kinney","Edward S. Boyden","Jeff William Lichtman","Ziv M. Williams","Steven A. McCarroll","Paola Arlotta"],"author_count":15,"year":2017,"published":"2017-04-25","venue":"Nature","cited_by":1320,"doi":"10.1038/nature22047","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1038/nature22047","archive_url":"https://space-kitty.com/papers/doi:10.1038/nature22047","updated":null,"pmid":"28445462","pmcid":null,"openalex_id":"W2609844460","pdf_url":null,"abstract":null,"abstract_license":null,"license":null,"is_open_access":true,"peer_reviewed":null,"categories":["Neurogenesis and neuroplasticity mechanisms"],"details":null,"provenance":"openalex","attribution":"Metadata and citation counts: OpenAlex (CC0)."},{"id":"doi:10.3390/ijms160818149","kind":"review","title":"A Review of Cell Adhesion Studies for Biomedical and Biological Applications","authors":["Khalili AA","Ahmad MR"],"author_count":2,"year":2015,"published":"2015-08-05","venue":"International journal of molecular sciences","cited_by":582,"doi":"10.3390/ijms160818149","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.3390/ijms160818149","archive_url":"https://space-kitty.com/papers/doi:10.3390/ijms160818149","updated":null,"pmid":"26251901","pmcid":"PMC4581240","openalex_id":null,"pdf_url":"https://europepmc.org/articles/PMC4581240/pdf","abstract":"Cell adhesion is essential in cell communication and regulation, and is of fundamental importance in the development and maintenance of tissues. The mechanical interactions between a cell and its extracellular matrix (ECM) can influence and control cell behavior and function. The essential function of cell adhesion has created tremendous interests in developing methods for measuring and studying cell adhesion properties. The study of cell adhesion could be categorized into cell adhesion attachment and detachment events. The study of cell adhesion has been widely explored via both events for many important purposes in cellular biology, biomedical, and engineering fields. Cell adhesion attachment and detachment events could be further grouped into the cell population and single cell approach. Various techniques to measure cell adhesion have been applied to many fields of study in order to gain understanding of cell signaling pathways, biomaterial studies for implantable sensors, artificial bone and tooth replacement, the development of tissue-on-a-chip and organ-on-a-chip in tissue engineering, the effects of biochemical treatments and environmental stimuli to the cell adhesion, the potential of drug treatments, cancer metastasis study, and the determination of the adhesion properties of normal and cancerous cells. This review discussed the overview of the available methods to study cell adhesion through attachment and detachment events.","abstract_license":"CC-BY (article license as recorded by Europe PMC; abstract reproduced unmodified apart from markup removal)","license":"CC-BY","is_open_access":true,"peer_reviewed":null,"categories":[],"details":null,"provenance":"europepmc","attribution":"Abstract of \"A Review of Cell Adhesion Studies for Biomedical and Biological Applications\" by Khalili AA, Ahmad MR, https://doi.org/10.3390/ijms160818149, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified."}],"next":"https://space-kitty.com/api/v1/topics/organoids/papers?sort=top&limit=25&offset=25"}