{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T21:11:24Z","timestamp":1791925884276,"version":"4.3.4"},"reference-count":58,"publisher":"American Association for the Advancement of Science (AAAS)","issue":"44","content-domain":{"domain":["www.science.org"],"crossmark-restriction":true},"short-container-title":["Sci. Adv."],"published-print":{"date-parts":[[2025,10,31]]},"abstract":"<jats:p>Protocols for deriving midbrain dopaminergic (mDA) neurons for Parkinson\u2019s disease (PD) modeling and therapy remain incompletely benchmarked against in vivo references. To establish transcriptomic standards, we generated an integrated human fetal whole-brain atlas and a midbrain subatlas. Whole-brain analysis revealed strong region-specific signatures, underscoring the need for global mapping before refined midbrain annotation. We implemented this two-tier strategy, BrainSTEM (Brain Single-cell Two tiEr Mapping), to systematically reassess published single-cell datasets of human midbrain culture models. BrainSTEM confirmed the presence of bona fide midbrain cell types (\u201con-target\u201d), but also revealed substantial populations aligning with nonmidbrain regions (\u201coff-target\u201d), inflating reported mDA yields across protocols. This unbiased framework enables rigorous evaluation of differentiation outcomes, clarifies current limitations of midbrain-directed models, and provides a foundation for refining protocols toward more faithful in vitro systems for PD research and regenerative applications.<\/jats:p>","DOI":"10.1126\/sciadv.adu7944","type":"journal-article","created":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T17:58:57Z","timestamp":1761933537000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":9,"title":["BrainSTEM: A single-cell multiresolution fetal brain atlas reveals transcriptomic fidelity of human midbrain cultures"],"prefix":"10.1126","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-7817-4915","authenticated-orcid":true,"given":"Hilary S. Y.","family":"Toh","sequence":"first","affiliation":[{"name":"Duke-NUS Medical School, Signature Research Program in Neuroscience and Behavioural Disorders, Singapore, Singapore."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-4967-8904","authenticated-orcid":true,"given":"Lisheng","family":"Xu","sequence":"additional","affiliation":[{"name":"Duke-NUS Medical School, Signature Research Program in Neuroscience and Behavioural Disorders, Singapore, Singapore."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9225-7086","authenticated-orcid":true,"given":"Carissa","family":"Chen","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Unit, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1098-3138","authenticated-orcid":true,"given":"Pengyi","family":"Yang","sequence":"additional","affiliation":[{"name":"Computational Systems Biology Unit, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia."},{"name":"Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7893-2006","authenticated-orcid":true,"given":"Alfred X.","family":"Sun","sequence":"additional","affiliation":[{"name":"Duke-NUS Medical School, Signature Research Program in Neuroscience and Behavioural Disorders, Singapore, Singapore."},{"name":"Department of Research, National Neuroscience Institute, Singapore, Singapore."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1239-1577","authenticated-orcid":true,"given":"John F.","family":"Ouyang","sequence":"additional","affiliation":[{"name":"Duke-NUS Medical School, Centre for Computational Biology, Singapore, Singapore."},{"name":"Duke-NUS Medical School, Signature Research Program in Cardiovascular and Metabolic Disorders, Singapore, Singapore."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(04)16305-8"},{"key":"e_1_3_2_3_2","first-page":"503","article-title":"Evaluation of models of Parkinson\u2019s disease","volume":"9","author":"Jagmag S. A.","year":"2015","unstructured":"S. A. Jagmag, N. Tripathi, S. D. Shukla, S. Maiti, S. Khurana, Evaluation of models of Parkinson\u2019s disease. Front. Neurosci. 9, 503 (2015).","journal-title":"Front. Neurosci."},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21072464"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10648"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2012.04.009"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1002\/stem.1152"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.10.037"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1242\/dev.000141"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.3390\/cells9061489"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/oons\/kvad009"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/bs.pbr.2016.11.011"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/bs.pbr.2017.02.008"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/bs.pbr.2016.11.004"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1654-9"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.09.010"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.09.027"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1242\/dev.200504"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.stemcr.2022.12.002"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.adf1226"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2023.04.016"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.21-09-03126.2001"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1186\/1749-8104-6-23"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1242\/dev.094565"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00429-020-02171-x"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.3389\/fnana.2020.00013"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1006\/mcne.2002.1182"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2016.10.003"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1002\/dneu.20685"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1111\/jnc.15579"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2020.05.037"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16225-5"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.108263"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-00801-6"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27464-5"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-021-02973-7"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2021.12.009"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41531-022-00423-7"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI156768"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2023.02.007"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2023.100261"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-02080-x"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202400847"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2016.07.005"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aaz2978"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05487-2"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroscience.2020.06.010"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2021.03.015"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06569-5"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2014.05.033"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06812-z"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae911"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1006\/exnr.1996.0096"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1651-2227.2001.tb02792.x"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41380-024-02534-4"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.05.031"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2859"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21246-9"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0292-x"}],"container-title":["Science Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.science.org\/doi\/pdf\/10.1126\/sciadv.adu7944","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T17:59:36Z","timestamp":1761933576000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.science.org\/doi\/10.1126\/sciadv.adu7944"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,31]]},"references-count":58,"journal-issue":{"issue":"44","published-print":{"date-parts":[[2025,10,31]]}},"alternative-id":["10.1126\/sciadv.adu7944"],"URL":"https:\/\/doi.org\/10.1126\/sciadv.adu7944","relation":{},"ISSN":["2375-2548"],"issn-type":[{"value":"2375-2548","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,31]]},"assertion":[{"value":"2024-11-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-09-30","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-10-31","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"eadu7944"}}