{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T18:54:16Z","timestamp":1791917656951,"version":"4.3.4"},"reference-count":36,"publisher":"Ovid Technologies (Wolters Kluwer Health)","issue":"4","funder":[{"DOI":"10.13039\/100009268","name":"Alport Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014989","name":"Chan Zuckerberg Initiative","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015629","name":"Chinook Therapeutics","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100015629","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100005205","name":"Janssen Research and Development","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005205","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007519","name":"NephCure Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007519","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["CJASN"],"published-print":{"date-parts":[[2020,4]]},"abstract":"<jats:p>Methods to differentiate human pluripotent stem cells into kidney organoids were first introduced about 5 years ago, and since that time, the field has grown substantially. Protocols are producing increasingly complex three-dimensional structures, have been used to model human kidney disease, and have been adapted for high-throughput screening. Over this same time frame, technologies for massively parallel, single-cell RNA sequencing (scRNA-seq) have matured. Now, both of these powerful approaches are being combined to better understand how kidney organoids can be applied to the understanding of kidney development and disease. There are several reasons why this is a synergistic combination. Kidney organoids are complicated and contain many different cell types of variable maturity. scRNA-seq is an unbiased technology that can comprehensively categorize cell types, making it ideally suited to catalog all cell types present in organoids. These same characteristics also make scRNA-seq a powerful approach for quantitative comparisons between protocols, batches, and pluripotent cell lines as it becomes clear that reproducibility and quality can vary across all three variables. Lineage trajectories can be reconstructed using scRNA-seq data, enabling the rational adjustment of differentiation strategies to promote maturation of desired kidney cell types or inhibit differentiation of undesired off-target cell types. Here, we review the ways that scRNA-seq has been successfully applied in the organoid field and predict future applications for this powerful technique. We also review other developing single-cell technologies and discuss how they may be combined, using \u201cmultiomic\u201d approaches, to improve our understanding of kidney organoid differentiation and usefulness in modeling development, disease, and toxicity testing.<\/jats:p>","DOI":"10.2215\/cjn.07470619","type":"journal-article","created":{"date-parts":[[2020,1,28]],"date-time":"2020-01-28T19:25:45Z","timestamp":1580239545000},"page":"550-556","source":"Crossref","is-referenced-by-count":30,"title":["Single Cell Sequencing and Kidney Organoids Generated from Pluripotent Stem Cells"],"prefix":"10.2215","volume":"15","author":[{"given":"Haojia","family":"Wu","sequence":"first","affiliation":[{"name":"Division of Nephrology, Department of Medicine; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6420-8703","authenticated-orcid":false,"given":"Benjamin D.","family":"Humphreys","sequence":"additional","affiliation":[{"name":"Division of Nephrology, Department of Medicine; and"},{"name":"Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"276","published-online":{"date-parts":[[2020,1,28]]},"reference":[{"key":"B1-20230813","doi-asserted-by":"crossref","first-page":"2905","DOI":"10.1681\/ASN.2015070832","article-title":"Bridging translation by improving preclinical study design in AKI","volume":"26","author":"de Caestecker","year":"2015","journal-title":"J Am Soc Nephrol"},{"key":"B2-20230813","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1126\/science.1186176","article-title":"Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding","volume":"328","author":"Schmidt","year":"2010","journal-title":"Science"},{"key":"B3-20230813","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/ng2047","article-title":"Tissue-specific transcriptional regulation has diverged significantly between human and mouse","volume":"39","author":"Odom","year":"2007","journal-title":"Nat Genet"},{"key":"B4-20230813","doi-asserted-by":"crossref","first-page":"17224","DOI":"10.1073\/pnas.1413624111","article-title":"Comparison of the transcriptional landscapes between human and mouse tissues","volume":"111","author":"Lin","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"B5-20230813","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1681\/ASN.2017080890","article-title":"Conserved and divergent features of mesenchymal progenitor cell types within the cortical nephrogenic niche of the human and mouse kidney","volume":"29","author":"Lindstr\u00f6m","year":"2018","journal-title":"J Am Soc Nephrol"},{"key":"B6-20230813","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1681\/ASN.2017091036","article-title":"Conserved and divergent molecular and anatomic features of human and mouse nephron patterning","volume":"29","author":"Lindstr\u00f6m","year":"2018","journal-title":"J Am Soc Nephrol"},{"key":"B7-20230813","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1681\/ASN.2017080887","article-title":"Conserved and divergent features of human and mouse kidney organogenesis","volume":"29","author":"Lindstr\u00f6m","year":"2018","journal-title":"J Am Soc Nephrol"},{"key":"B8-20230813","doi-asserted-by":"crossref","first-page":"738","DOI":"10.5301\/jn.5000053","article-title":"C57BL\/6 and 129\/Sv mice: Genetic difference to renal ischemia-reperfusion","volume":"25","author":"Lu","year":"2012","journal-title":"J Nephrol"},{"key":"B9-20230813","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1097\/00007890-200003150-00065","article-title":"Genetic susceptibility to renal ischemia reperfusion injury revealed in a murine model","volume":"69","author":"Burne","year":"2000","journal-title":"Transplantation"},{"key":"B10-20230813","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.kint.2015.10.019","article-title":"Adriamycin susceptibility among C57BL\/6 substrains","volume":"89","author":"Arif","year":"2016","journal-title":"Kidney Int"},{"key":"B11-20230813","doi-asserted-by":"crossref","first-page":"2628","DOI":"10.2337\/diabetes.54.9.2628","article-title":"Characterization of susceptibility of inbred mouse strains to diabetic nephropathy","volume":"54","author":"Qi","year":"2005","journal-title":"Diabetes"},{"key":"B12-20230813","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1038\/nature15695","article-title":"Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis","volume":"526","author":"Takasato","year":"2015","journal-title":"Nature"},{"key":"B13-20230813","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1038\/nbt.3392","article-title":"Nephron organoids derived from human pluripotent stem cells model kidney development and injury","volume":"33","author":"Morizane","year":"2015","journal-title":"Nat Biotechnol"},{"key":"B15-20230813","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/492056a","article-title":"NOBEL 2012 Physiology or medicine: Mature cells can be rejuvenated","volume":"492","author":"Rossant","year":"2012","journal-title":"Nature"},{"key":"B16-20230813","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/jb\/mvz021","article-title":"How to rebuild the kidney: Recent advances in kidney organoids","volume":"166","author":"Islam","year":"2019","journal-title":"J Biochem"},{"key":"B17-20230813","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1038\/nmat4994","article-title":"Organoid cystogenesis reveals a critical role of microenvironment in human polycystic kidney disease","volume":"16","author":"Cruz","year":"2017","journal-title":"Nat Mater"},{"key":"B19-20230813","doi-asserted-by":"crossref","first-page":"5167","DOI":"10.1038\/s41467-018-07594-z","article-title":"3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening","volume":"9","author":"Hale","year":"2018","journal-title":"Nat Commun"},{"key":"B20-20230813","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1038\/s41592-018-0253-2","article-title":"Evaluation of variability in human kidney organoids","volume":"16","author":"Phipson","year":"2019","journal-title":"Nat Methods"},{"key":"B21-20230813","doi-asserted-by":"crossref","first-page":"1334","DOI":"10.1016\/j.kint.2017.06.033","article-title":"The promise of single-cell RNA sequencing for kidney disease investigation","volume":"92","author":"Wu","year":"2017","journal-title":"Kidney Int"},{"key":"B23-20230813","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13073-019-0615-0","article-title":"Single-cell analysis reveals congruence between kidney organoids and human fetal kidney","volume":"11","author":"Combes","year":"2019","journal-title":"Genome Med"},{"key":"B24-20230813","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/bs.ctdb.2015.10.010","article-title":"Development of the mammalian kidney","volume":"117","author":"McMahon","year":"2016","journal-title":"Curr Top Dev Biol"},{"key":"B25-20230813","article-title":"Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics","author":"Subramanian","year":"2019","journal-title":"bioRxiv"},{"key":"B26-20230813","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41587-019-0071-9","article-title":"A comparison of single-cell trajectory inference methods","volume":"37","author":"Saelens","year":"2019","journal-title":"Nat Biotechnol"},{"key":"B27-20230813","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1146\/annurev.neuro.24.1.677","article-title":"Neurotrophins: Roles in neuronal development and function","volume":"24","author":"Huang","year":"2001","journal-title":"Annu Rev Neurosci"},{"key":"B28-20230813","doi-asserted-by":"crossref","first-page":"8715","DOI":"10.1038\/ncomms9715","article-title":"Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids","volume":"6","author":"Freedman","year":"2015","journal-title":"Nat Commun"},{"key":"B30-20230813","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1016\/j.ajhg.2018.03.014","article-title":"Patient-iPSC-derived kidney organoids show functional validation of a ciliopathic renal phenotype and reveal underlying pathogenetic mechanisms","volume":"102","author":"Forbes","year":"2018","journal-title":"Am J Hum Genet"},{"key":"B31-20230813","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.stemcr.2018.08.003","article-title":"Organoids from nephrotic disease-derived iPSCs identify impaired NEPHRIN localization and slit diaphragm formation in kidney podocytes","volume":"11","author":"Tanigawa","year":"2018","journal-title":"Stem Cell Reports"},{"key":"B32-20230813","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/s41587-019-0048-8","article-title":"Tubuloids derived from human adult kidney and urine for personalized disease modeling","volume":"37","author":"Schutgens","year":"2019","journal-title":"Nat Biotechnol"},{"key":"B33-20230813","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/ki.2013.368","article-title":"Lineage-tracing methods and the kidney","volume":"86","author":"Humphreys","year":"2014","journal-title":"Kidney Int"},{"key":"B34-20230813","doi-asserted-by":"crossref","first-page":"e47483","DOI":"10.15252\/embr.201847483","article-title":"Reporter-based fate mapping in human kidney organoids confirms nephron lineage relationships and reveals synchronous nephron formation","volume":"20","author":"Howden","year":"2019","journal-title":"EMBO Rep"},{"key":"B35-20230813","doi-asserted-by":"crossref","first-page":"a008300","DOI":"10.1101\/cshperspect.a008300","article-title":"Mammalian kidney development: Principles, progress, and projections","volume":"4","author":"Little","year":"2012","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"B36-20230813","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/s41586-018-0744-4","article-title":"Single-cell mapping of lineage and identity in direct reprogramming","volume":"564","author":"Biddy","year":"2018","journal-title":"Nature"},{"key":"B39-20230813","doi-asserted-by":"crossref","first-page":"e27041","DOI":"10.7554\/eLife.27041","article-title":"The human cell atlas","volume":"6","author":"Regev","year":"2017","journal-title":"eLife"},{"key":"B42-20230813","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1056\/NEJMoa1811744","article-title":"Canagliflozin and renal outcomes in type 2 diabetes and nephropathy","volume":"380","author":"Perkovic","year":"2019","journal-title":"N Engl J Med"},{"key":"B43-20230813","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1016\/S0140-6736(19)30772-X","article-title":"Atrasentan and renal events in patients with type 2 diabetes and chronic kidney disease (SONAR): A double-blind, randomised, placebo-controlled trial","volume":"393","author":"Heerspink","year":"2019","journal-title":"Lancet"},{"key":"B44-20230813","doi-asserted-by":"crossref","first-page":"e3000152","DOI":"10.1371\/journal.pbio.3000152","article-title":"Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development","volume":"17","author":"Hochane","year":"2019","journal-title":"PLoS Biol"}],"container-title":["Clinical Journal of the American Society of Nephrology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.ovid.com\/10.2215\/CJN.07470619","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T13:39:29Z","timestamp":1786369169000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.ovid.com\/10.2215\/CJN.07470619"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,28]]},"references-count":36,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2020]]}},"URL":"https:\/\/doi.org\/10.2215\/cjn.07470619","relation":{},"ISSN":["1555-9041","1555-905X"],"issn-type":[{"value":"1555-9041","type":"print"},{"value":"1555-905X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,1,28]]}}}