[{"date_created":"2026-06-09T08:08:53Z","OA_type":"green","type":"preprint","author":[{"full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889","first_name":"Osvaldo","last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425"},{"full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amarbayasgalan","full_name":"Davaatseren, Amarbayasgalan","id":"70ADC922-B424-11E9-99E3-BA18E6697425","last_name":"Davaatseren"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"last_name":"Villalba Requena","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana","first_name":"Ana"},{"last_name":"Heger","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","full_name":"Heger, Anna-Magdalena","first_name":"Anna-Magdalena"},{"last_name":"Marie","first_name":"Corentine","full_name":"Marie, Corentine"},{"last_name":"Hassan","full_name":"Hassan, Bassem A.","first_name":"Bassem A."},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ieee":"O. Miranda <i>et al.</i>, “Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production,” <i>bioRxiv</i>. .","ama":"Miranda O, Contreras X, Pauler F, et al. Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.64898/2026.05.01.722191\">10.64898/2026.05.01.722191</a>","chicago":"Miranda, Osvaldo, Ximena Contreras, Florian Pauler, Amarbayasgalan Davaatseren, Nicole Amberg, Carmen Streicher, Ana Villalba Requena, et al. “Pten Orchestrates Neurogenic Radial Glia Lineage Progression and Tunes Neocortical Astrocyte Production.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.64898/2026.05.01.722191\">https://doi.org/10.64898/2026.05.01.722191</a>.","mla":"Miranda, Osvaldo, et al. “Pten Orchestrates Neurogenic Radial Glia Lineage Progression and Tunes Neocortical Astrocyte Production.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.64898/2026.05.01.722191\">10.64898/2026.05.01.722191</a>.","ista":"Miranda O, Contreras X, Pauler F, Davaatseren A, Amberg N, Streicher C, Villalba Requena A, Heger A-M, Marie C, Hassan BA, Rülicke T, Hippenmeyer S. Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production. bioRxiv, <a href=\"https://doi.org/10.64898/2026.05.01.722191\">10.64898/2026.05.01.722191</a>.","short":"O. Miranda, X. Contreras, F. Pauler, A. Davaatseren, N. Amberg, C. Streicher, A. Villalba Requena, A.-M. Heger, C. Marie, B.A. Hassan, T. Rülicke, S. Hippenmeyer, BioRxiv (n.d.).","apa":"Miranda, O., Contreras, X., Pauler, F., Davaatseren, A., Amberg, N., Streicher, C., … Hippenmeyer, S. (n.d.). Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production. <i>bioRxiv</i>. <a href=\"https://doi.org/10.64898/2026.05.01.722191\">https://doi.org/10.64898/2026.05.01.722191</a>"},"project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"},{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"publication_status":"submitted","status":"public","publication":"bioRxiv","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"ddc":["570"],"has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.64898/2026.05.01.722191"}],"OA_place":"repository","abstract":[{"text":"The cerebral cortex consists of immense numbers of neuronal and glial cell-types derived from radial glial progenitor (RGP) cells. How RGPs generate appropriate quantities of distinct cortical cell-types to safeguard a brain of correct size, is not well understood. However, genetic aberration in human, including mutations in PTEN, lead to cortical malformation such as macrocephaly, albeit with unknown etiology. Here we utilized Mosaic Analysis with Double Markers (MADM)-based clonal analysis and single cell phenotyping to decipher the role of Pten in neurogenic and gliogenic RGP lineage progression during cortical ontogeny. While neurogenic RGP lineage progression and projection neuron production was moderately altered in the absence of Pten, cortical astrocyte production was drastically increased. Through genetic epistasis experiments we show that the loss of Pten uncouples astrocyte generation from essential growth factor signaling hubs, funneling into MAPK. Collectively, our results suggest that Pten regulates RGP lineage progression with distinct sequential functions in cortical projection neurogenesis and astrocyte production to ensure the emergence of a correctly-sized cerebral cortex.","lang":"eng"}],"date_published":"2026-05-05T00:00:00Z","department":[{"_id":"SiHi"},{"_id":"PreCl"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"article_processing_charge":"No","date_updated":"2026-06-16T08:57:20Z","fulldoi":"https://doi.org/10.64898/2026.05.01.722191","oa_version":"Preprint","day":"05","year":"2026","corr_author":"1","title":"Pten orchestrates neurogenic radial glia lineage progression and tunes neocortical astrocyte production","doi":"10.64898/2026.05.01.722191","_id":"21963","acknowledgement":"We thank Kay-Uwe Wagner (Wayne State University) for generously sharing Jak1/2–flox mouse lines; A.\r\nSommer (VBCF GmbH, NGS Unit) for technical support; N. Kim, V. Mick, S. Schnabl, S. Gobeil, and L.\r\nAndersen for technical assistance; all members of the Hippenmeyer lab for discussion and B. Novitch for\r\ncomments on earlier versions of the manuscript. This research was supported by the Scientific Service Units\r\n(SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF), Lab Support-\r\n(LSF) and Preclinical Facilities (PCF). O.A.M received support from the Austrian Academy of Sciences\r\nÖAW (DOC 186584), and N.A. from FWF Elise Richter Program (Grant V1041T). This work was also\r\nsupported by IST Austria institutional funds; FWF SFB F78 (Neuro Stem Modulation) to S.H., and the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (grant agreement No 725780 LinPro) to S.H.","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05"},{"oa_version":"Published Version","fulldoi":"https://doi.org/10.1016/j.gde.2026.102487","quality_controlled":"1","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"date_updated":"2026-08-12T09:56:19Z","volume":99,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"21948","acknowledgement":"We wish to thank all members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. We apologize to colleagues whose work we could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the discussed topic is supported by ISTA institutional funds, an EMBO LTF (ALTF 994–2023) to F.P., FWF SFB F78 (10.55776/F78) to S.H., and FWF Cluster of Excellence COE16 (10.55776/COE16) to S.H.","publisher":"Elsevier","doi":"10.1016/j.gde.2026.102487","title":"Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics","corr_author":"1","PlanS_conform":"1","year":"2026","day":"29","publication_status":"epub_ahead","project":[{"name":"Role of cell lineage in generating cell-type diversity in developing neocortex’","grant_number":"ALTF 994-2023","_id":"7c084566-9f16-11ee-852c-c88a1dbbf1cf"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"citation":{"apa":"Varela Martínez, I., Pipicelli, F., &#38; Hippenmeyer, S. (2026). Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102487\">https://doi.org/10.1016/j.gde.2026.102487</a>","short":"I. Varela Martínez, F. Pipicelli, S. Hippenmeyer, Current Opinion in Genetics &#38; Development 99 (2026).","ieee":"I. Varela Martínez, F. Pipicelli, and S. Hippenmeyer, “Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99. Elsevier, 2026.","ama":"Varela Martínez I, Pipicelli F, Hippenmeyer S. Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics. <i>Current Opinion in Genetics &#38; Development</i>. 2026;99. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102487\">10.1016/j.gde.2026.102487</a>","chicago":"Varela Martínez, Irene, Fabrizia Pipicelli, and Simon Hippenmeyer. “Tracing Cell Lineages in the Developing Brain: Insights from Mosaic Analysis and Clone-Resolved Transcriptomics.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102487\">https://doi.org/10.1016/j.gde.2026.102487</a>.","mla":"Varela Martínez, Irene, et al. “Tracing Cell Lineages in the Developing Brain: Insights from Mosaic Analysis and Clone-Resolved Transcriptomics.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99, 102487, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102487\">10.1016/j.gde.2026.102487</a>.","ista":"Varela Martínez I, Pipicelli F, Hippenmeyer S. 2026. Tracing cell lineages in the developing brain: Insights from mosaic analysis and clone-resolved transcriptomics. Current Opinion in Genetics &#38; Development. 99, 102487."},"author":[{"last_name":"Varela Martínez","id":"a69b5985-8829-11f0-8fc2-d0af58f64471","full_name":"Varela Martínez, Irene","first_name":"Irene"},{"first_name":"Fabrizia","full_name":"Pipicelli, Fabrizia","id":"649134fd-d012-11ed-8f82-db1e5050f9ba","last_name":"Pipicelli"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"hybrid","type":"journal_article","date_created":"2026-06-07T22:01:35Z","article_number":"102487","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"external_id":{"pmid":["42214837"]},"oa":1,"date_published":"2026-05-29T00:00:00Z","department":[{"_id":"SiHi"}],"intvolume":"        99","abstract":[{"lang":"eng","text":"The cerebral cortex comprises diverse neuron and glial cell types generated by radial glial progenitors (RGPs) during development. Although RGPs broadly differentiate according to temporally and spatially regulated molecular logics, the lineage hierarchies linking individual progenitors to defined cell (sub)types are not well understood. Clone-resolved transcriptomics, combining molecular barcoding and single-cell RNA sequencing, allow high-resolution lineage tracing at the single-clone/cell level across different species and models. In this mini-review, we synthesize recent advances in this field, uncovering unexpected lineage relationships in the developing brain, with a particular focus on the cerebral cortex. We further highlight new insights into species-specific differences in the developmental programs generating cell-type diversity, linking changes in clonal architecture to lineage diversification during cortical evolution."}],"pmid":1,"OA_place":"publisher","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.gde.2026.102487"}],"has_accepted_license":"1","scopus_import":"1","ddc":["570"],"publication":"Current Opinion in Genetics & Development","status":"public"},{"pmid":1,"OA_place":"publisher","date_published":"2026-08-07T00:00:00Z","department":[{"_id":"SiHi"}],"intvolume":"        12","abstract":[{"lang":"eng","text":"Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. We combined Mosaic Analysis with Double Markers at embryonic stages (E)12.5 and E13.5 with early postnatal callosal tracing to dissect RGP lineage progression. We find that multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs via parallel sublineages that emerge simultaneously at neurogenesis onset. ET-PN production progresses exclusively via small, self-consuming lineages; IT-PN lineages feature RGPs generating large translaminar outputs. The early emergence of IT-PN–fated RGPs, coinciding with a switch to direct neurogenesis, contributes to the stereotyped population-level progression of the multipotent lineage. We also identify POU3F transcription factors as candidate regulators of IT-PN fate via noncanonical mitotic chromatin binding. The results support a model whereby IT- and ET-PNs arise from an early bifurcation and parallel specification within the multipotent RGP lineage."}],"article_processing_charge":"Yes","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["42555737"]},"status":"public","publication":"Science Advances","has_accepted_license":"1","scopus_import":"1","ddc":["570"],"dataavailabilitystatement":"All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials. Source data underlying all figures (including the clonal atlas) are provided in the Supplementary Materials. RnA-seq analysis code has been deposited in Zenodo (dOi: 10.5281/zenodo.14609057). this study did not generate new materials.","file":[{"checksum":"487c3703387080e8f3c4675d67763f0e","file_id":"22738","relation":"main_file","date_created":"2026-08-20T05:39:32Z","date_updated":"2026-08-20T05:39:32Z","file_name":"2026_ScienceAdv_VarelaMartinez.pdf","content_type":"application/pdf","creator":"dernst","file_size":3056744,"access_level":"open_access","success":1}],"citation":{"ama":"Varela Martínez I, Villalba Requena A, García-Marqués J, et al. Early fate diversification of radial glial progenitors during corticogenesis. <i>Science Advances</i>. 2026;12(32):eadw5487. doi:<a href=\"https://doi.org/10.1126/sciadv.adw5487\">10.1126/sciadv.adw5487</a>","mla":"Varela Martínez, Irene, et al. “Early Fate Diversification of Radial Glial Progenitors during Corticogenesis.” <i>Science Advances</i>, vol. 12, no. 32, AAAS, 2026, p. eadw5487, doi:<a href=\"https://doi.org/10.1126/sciadv.adw5487\">10.1126/sciadv.adw5487</a>.","chicago":"Varela Martínez, Irene, Ana Villalba Requena, Jorge García-Marqués, Alfonso Aguilera, Diogo S. Castro, Simon Hippenmeyer, and Marta Nieto. “Early Fate Diversification of Radial Glial Progenitors during Corticogenesis.” <i>Science Advances</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/sciadv.adw5487\">https://doi.org/10.1126/sciadv.adw5487</a>.","ieee":"I. Varela Martínez <i>et al.</i>, “Early fate diversification of radial glial progenitors during corticogenesis,” <i>Science Advances</i>, vol. 12, no. 32. AAAS, p. eadw5487, 2026.","ista":"Varela Martínez I, Villalba Requena A, García-Marqués J, Aguilera A, Castro DS, Hippenmeyer S, Nieto M. 2026. Early fate diversification of radial glial progenitors during corticogenesis. Science Advances. 12(32), eadw5487.","apa":"Varela Martínez, I., Villalba Requena, A., García-Marqués, J., Aguilera, A., Castro, D. S., Hippenmeyer, S., &#38; Nieto, M. (2026). Early fate diversification of radial glial progenitors during corticogenesis. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.adw5487\">https://doi.org/10.1126/sciadv.adw5487</a>","short":"I. Varela Martínez, A. Villalba Requena, J. García-Marqués, A. Aguilera, D.S. Castro, S. Hippenmeyer, M. Nieto, Science Advances 12 (2026) eadw5487."},"publication_status":"published","date_created":"2026-08-16T22:01:43Z","page":"eadw5487","issue":"32","author":[{"full_name":"Varela Martínez, Irene","first_name":"Irene","last_name":"Varela Martínez","id":"a69b5985-8829-11f0-8fc2-d0af58f64471"},{"orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana","first_name":"Ana","last_name":"Villalba Requena","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247"},{"first_name":"Jorge","full_name":"García-Marqués, Jorge","last_name":"García-Marqués"},{"full_name":"Aguilera, Alfonso","first_name":"Alfonso","last_name":"Aguilera"},{"last_name":"Castro","full_name":"Castro, Diogo S.","first_name":"Diogo S."},{"first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"full_name":"Nieto, Marta","first_name":"Marta","last_name":"Nieto"}],"OA_type":"gold","type":"journal_article","file_date_updated":"2026-08-20T05:39:32Z","DOAJ_listed":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","article_type":"original","year":"2026","day":"07","title":"Early fate diversification of radial glial progenitors during corticogenesis","PlanS_conform":"1","acknowledgement":"We thank M. caouyette for the plasmid construction for Pou3f1overexpression; d. Pinto-Benito for valuable assistance with shRnA validation in n2A cells andqPcR experiments; c. Varela-Martínez for help with the code for graphical analysis; allmembers from the nieto’s lab for comment on the manuscript, specially to F. Martín for theinsightful discussions; J. c. Oliveros and J. A. García from the computational service of the cnBfor help with the analysis of RnAseq dataset; c. O. Sorzano for help with statistical analysis; andA. Oña and the service of Advance Optical Microscopy of the cnB for technical advice.Funding: i.V.-M. holds a fellowship funded by MciciU (PRe-2018-083376) and 2023 eMBOscientific exchange grant 10214. the work was funded by grants to M.n. (Pid2020-112831GB- i00 and Pid2023-146322nB- i00 by Mcin/Aei/10.13039/501100011033 and by“eRdF A way of making europe”).","_id":"22714","publisher":"AAAS","doi":"10.1126/sciadv.adw5487","researchdata_availability":"yes","oa_version":"Published Version","volume":12,"das_tickbox":"1","date_updated":"2026-08-20T05:45:28Z","quality_controlled":"1","publication_identifier":{"eissn":["2375-2548"]},"supplementarymaterial":"yes","fulldoi":"https://doi.org/10.1126/sciadv.adw5487"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_type":"original","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Temporal uncoupling of radial glia lineage progression in cortical organoids","corr_author":"1","PlanS_conform":"1","year":"2026","day":"12","_id":"22753","acknowledgement":"We thank M. L. de Guevara, S. Jayaram and A. Heger for technical assistance with mESC derivation; M. Goudarzi for assistance with organoid imaging; M. Leeb and F. Freeman for advice in culturing mESCs and organoids; S. Gobeil and L. Sweeney for reagents and advice for organoid clearing; A. Heger for mouse colony management; J. Hauser for technical assistance; the Stanford Brain Organogenesis Workshop; and all members of the Hippenmeyer laboratory for discussion and/or comments on the manuscript. This study was supported by the Scientific Service Units (SSU) of the Institute of Science and Technology, Austria through resources provided by the Imaging and Optics Facility (IOF), Laboratory Support Facility (LSF) and Preclinical Facility (PCF). M.S. received funding from the European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds to S.H., FWF SFB F78 Neuro Stem Modulation to S.H., and by the European Research Council (ERC) under the European Union’s Horizon 2020 Research And Innovation Program (grant agreement 725780 LinPro) to S.H. Open access funding provided by Institute of Science and Technology (IST Austria).","publisher":"Springer Nature","doi":"10.1038/s41586-026-10916-7","researchdata_availability":"yes","oa_version":"Published Version","das_tickbox":"1","date_updated":"2026-09-09T07:11:02Z","fulldoi":"https://doi.org/10.1038/s41586-026-10916-7","quality_controlled":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"supplementarymaterial":"yes","pmid":1,"OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["42587153"]},"department":[{"_id":"SiHi"}],"date_published":"2026-08-12T00:00:00Z","abstract":[{"lang":"eng","text":"Radial glial progenitors (RGPs) produce all excitatory neurons in the developing cerebral cortex. Mosaic analysis with double markers (MADM)-based lineage tracing in vivo has revealed a quantitative framework of RGP lineage progression1. Here we established MADM technology2,3 in mouse embryonic stem cells to probe RGP lineage progression in a self-organizing cortical organoid system. We found that RGPs exhibit a high level of plasticity in proliferative potential in organoids rather than strict temporally stereotyped lineage progression as observed in vivo. RGPs in organoids showed increased lineage restriction, diminishing cell-type diversity in clones of cortical projection neurons, despite uniform single-cell transcriptional signatures of RGPs and a unitary lineage trajectory. Thus, critical non-cell-autonomous cues that are absent in self-organizing systems and/or the genuine stem cell niche are essential for faithful temporal control of RGP lineage progression and the generation of clonal cortical cell-type diversity."}],"publication":"Nature","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"status":"public","scopus_import":"1","has_accepted_license":"1","ddc":["570"],"file":[{"access_level":"open_access","success":1,"file_size":48513068,"creator":"dernst","file_name":"2026_Nature_Stouffer.pdf","content_type":"application/pdf","date_updated":"2026-09-07T13:24:10Z","relation":"main_file","date_created":"2026-09-07T13:24:10Z","file_id":"22844","checksum":"11383e28fc430b28d2666f73833e8b56"}],"citation":{"short":"M.A. Stouffer, O. Miranda, F. Pauler, F. Pipicelli, C. Streicher, G.T. Cheung, S. Hippenmeyer, Nature (2026).","apa":"Stouffer, M. A., Miranda, O., Pauler, F., Pipicelli, F., Streicher, C., Cheung, G. T., &#38; Hippenmeyer, S. (2026). Temporal uncoupling of radial glia lineage progression in cortical organoids. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-026-10916-7\">https://doi.org/10.1038/s41586-026-10916-7</a>","mla":"Stouffer, Melissa A., et al. “Temporal Uncoupling of Radial Glia Lineage Progression in Cortical Organoids.” <i>Nature</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41586-026-10916-7\">10.1038/s41586-026-10916-7</a>.","chicago":"Stouffer, Melissa A, Osvaldo Miranda, Florian Pauler, Fabrizia Pipicelli, Carmen Streicher, Giselle T Cheung, and Simon Hippenmeyer. “Temporal Uncoupling of Radial Glia Lineage Progression in Cortical Organoids.” <i>Nature</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41586-026-10916-7\">https://doi.org/10.1038/s41586-026-10916-7</a>.","ieee":"M. A. Stouffer <i>et al.</i>, “Temporal uncoupling of radial glia lineage progression in cortical organoids,” <i>Nature</i>. Springer Nature, 2026.","ama":"Stouffer MA, Miranda O, Pauler F, et al. Temporal uncoupling of radial glia lineage progression in cortical organoids. <i>Nature</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41586-026-10916-7\">10.1038/s41586-026-10916-7</a>","ista":"Stouffer MA, Miranda O, Pauler F, Pipicelli F, Streicher C, Cheung GT, Hippenmeyer S. 2026. Temporal uncoupling of radial glia lineage progression in cortical organoids. Nature."},"dataavailabilitystatement":"All data generated and analysed in this study are included in the paper, source data and/or Supplementary Tables 2 and 3. Raw sequencing data have been deposited with Gene Expression Omnibus (GEO) accession number GSE327470. Source data are provided with this paper. All scripts used to prepare data and figures for this manuscript are accessible on GitHub at https://github.com/fpauler/Temporal-Uncoupling-of-Radial-Glia-Lineage-Progression-in-Cortical-Organoid.","publication_status":"epub_ahead","project":[{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Stouffer","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","full_name":"Stouffer, Melissa A","first_name":"Melissa A"},{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Miranda","first_name":"Osvaldo","orcid":"0000-0001-6618-6889","full_name":"Miranda, Osvaldo"},{"first_name":"Florian","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"full_name":"Pipicelli, Fabrizia","first_name":"Fabrizia","last_name":"Pipicelli","id":"649134fd-d012-11ed-8f82-db1e5050f9ba"},{"full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"type":"journal_article","OA_type":"hybrid","date_created":"2026-08-23T22:01:47Z","file_date_updated":"2026-09-07T13:24:10Z"},{"publication_status":"published","file":[{"date_created":"2025-04-03T11:19:26Z","relation":"main_file","file_id":"19467","checksum":"64a6a6f86e24b21fe72c7a7fd6056fed","date_updated":"2025-04-03T11:19:26Z","content_type":"application/pdf","file_name":"2025_eLife_Bose.pdf","creator":"dernst","success":1,"access_level":"open_access","file_size":17462771}],"citation":{"short":"M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, ELife 13 (2025).","apa":"Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole, S. (2025). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.101851.3\">https://doi.org/10.7554/elife.101851.3</a>","mla":"Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” <i>ELife</i>, vol. 13, 101851, eLife Sciences Publications, 2025, doi:<a href=\"https://doi.org/10.7554/elife.101851.3\">10.7554/elife.101851.3</a>.","ieee":"M. Bose <i>et al.</i>, “Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2025.","ama":"Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. <i>eLife</i>. 2025;13. doi:<a href=\"https://doi.org/10.7554/elife.101851.3\">10.7554/elife.101851.3</a>","chicago":"Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav, Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” <i>ELife</i>. eLife Sciences Publications, 2025. <a href=\"https://doi.org/10.7554/elife.101851.3\">https://doi.org/10.7554/elife.101851.3</a>.","ista":"Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole S. 2025. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. eLife. 13, 101851."},"file_date_updated":"2025-04-03T11:19:26Z","author":[{"first_name":"Mahima","full_name":"Bose, Mahima","last_name":"Bose"},{"full_name":"Suresh, Varun","first_name":"Varun","last_name":"Suresh"},{"last_name":"Mishra","full_name":"Mishra, Urvi","first_name":"Urvi"},{"last_name":"Talwar","first_name":"Ishita","full_name":"Talwar, Ishita"},{"first_name":"Anuradha","full_name":"Yadav, Anuradha","last_name":"Yadav"},{"full_name":"Biswas, Shiona","first_name":"Shiona","last_name":"Biswas"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"first_name":"Shubha","full_name":"Tole, Shubha","last_name":"Tole"}],"OA_type":"gold","type":"journal_article","date_created":"2023-12-06T13:07:01Z","article_number":"101851","article_processing_charge":"Yes","oa":1,"external_id":{"pmid":["40085500"]},"language":[{"iso":"eng"}],"date_published":"2025-03-14T00:00:00Z","department":[{"_id":"SiHi"}],"abstract":[{"text":"In the developing vertebrate central nervous system, neurons and glia typically arise\r\nsequentially from common progenitors. Here, we report that the transcription factor Forkhead\r\nBox G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic cues in newborn neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons non-autonomously enhances gliogenesis in the progenitors via FGF signalling. These results fit well with the model that newborn neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex. ","lang":"eng"}],"intvolume":"        13","pmid":1,"OA_place":"publisher","scopus_import":"1","has_accepted_license":"1","ddc":["570"],"publication":"eLife","status":"public","oa_version":"Published Version","fulldoi":"https://doi.org/10.7554/elife.101851.3","quality_controlled":"1","publication_identifier":{"eissn":["2050-084X"]},"date_updated":"2025-05-14T11:41:52Z","volume":13,"article_type":"original","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"acknowledgement":"We thank the animal house staff of the Tata Institute of Fundamental Research, Mumbai (TIFR), for their excellent support; Gordon Fishell (Harvard Medical School, USA), and Goichi Miyoshi (Gunma University, Japan) for the Foxg1 floxed mouse line; Hiroshi Kawasaki (Kanazawa University, Japan) for the plasmids pCAG-FGF8 and pCAG-sFgfr3c; Soo Kyung Lee (University at Buffalo, The State University of New York, USA) for the Foxg1lox/lox genotyping primers and protocol. We thank Deepak Modi and Vainav Patel (National Institute for Research in Reproductive and Child Health, NIRRCH, Mumbai, India) for the use of the NIRRCH FACS Facility, and the staff of the NIRRCH and TIFR FACS facilities for their assistance. We thank Denis Jabaudon (University of Geneva, Switzerland) for his critical comments on the manuscript and members of the Jabaudon lab for helpful discussions. This work was funded by the Department of Atomic Energy (DAE), Govt. of India (Project Identification no. RTI4003,\r\nDAE OM no. 1303/2/2019/R&D-II/DAE/2079). ","_id":"14647","publisher":"eLife Sciences Publications","doi":"10.7554/elife.101851.3","title":"Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway","year":"2025","day":"14"},{"oa_version":"None","editor":[{"last_name":"Garcia-Marques","first_name":"Jorge","full_name":"Garcia-Marques, Jorge"},{"last_name":"Lee","first_name":"Tzumin","full_name":"Lee, Tzumin"}],"volume":2886,"date_updated":"2025-04-14T07:43:46Z","quality_controlled":"1","publication_identifier":{"eissn":["1940-6029"],"isbn":["9781071643099"],"issn":["1064-3745"],"eisbn":["9781071643105"]},"fulldoi":"https://doi.org/10.1007/978-1-0716-4310-5_7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","year":"2025","day":"03","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","corr_author":"1","publisher":"Springer Nature","_id":"18765","acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","doi":"10.1007/978-1-0716-4310-5_7","citation":{"ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>.","ama":"Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. <i>Lineage Tracing</i>. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>","ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in <i>Lineage Tracing</i>, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>.","apa":"Cheung, G. T., Pauler, F., &#38; Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques &#38; T. Lee (Eds.), <i>Lineage Tracing</i> (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151."},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","date_created":"2025-01-07T08:36:47Z","page":"139-151","author":[{"first_name":"Giselle T","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung"},{"first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"OA_type":"closed access","place":"New York, NY","pmid":1,"department":[{"_id":"SiHi"}],"date_published":"2025-01-03T00:00:00Z","intvolume":"      2886","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.","lang":"eng"}],"ec_funded":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"external_id":{"pmid":["39745639"]},"status":"public","publication":"Lineage Tracing","acknowledged_ssus":[{"_id":"Bio"}],"scopus_import":"1","series_title":"MIMB"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_type":"original","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","PlanS_conform":"1","title":"How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex","day":"01","year":"2025","doi":"10.1016/j.conb.2025.103046","_id":"19718","acknowledgement":"We wish to thank all members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. We apologize to colleagues whose work we could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the discussed topic is supported by ISTA institutional funds, an EMBO LTF (ALTF 994–2023) to F.P, and FWF SFB F78 to S.H.","publisher":"Elsevier","isi":1,"oa_version":"Published Version","date_updated":"2025-12-30T10:54:14Z","volume":93,"fulldoi":"https://doi.org/10.1016/j.conb.2025.103046","publication_identifier":{"issn":["0959-4388"]},"quality_controlled":"1","OA_place":"publisher","pmid":1,"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["001496227000001"],"pmid":["40383049"]},"article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"The cerebral cortex is arguably the most complex organ in humans. The cortical architecture is characterized by a remarkable diversity of neuronal and glial cell types that make up its neuronal circuits. Following a precise temporally ordered program, radial glia progenitor (RGP) cells generate all cortical excitatory projection neurons and glial cell-types. Cortical excitatory projection neurons are produced either directly or via intermediate progenitors, through indirect neurogenesis. How the extensive cortical cell-type diversity is generated during cortex development remains, however, a fundamental open question. How do RGPs quantitatively and qualitatively generate all the neocortical neurons? How does direct and indirect neurogenesis contribute to the establishment of neuronal and lineage heterogeneity? Whether RGPs represent a homogeneous and/or multipotent progenitor population, or if RGPs consist of heterogeneous groups is currently also not known. In this review, we will summarize the latest findings that contributed to a deeper insight into the above key questions.","lang":"eng"}],"intvolume":"        93","date_published":"2025-08-01T00:00:00Z","department":[{"_id":"SiHi"}],"publication":"Current Opinion in Neurobiology","status":"public","ddc":["570"],"scopus_import":"1","has_accepted_license":"1","citation":{"ista":"Pipicelli F, Villalba Requena A, Hippenmeyer S. 2025. How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex. Current Opinion in Neurobiology. 93, 103046.","mla":"Pipicelli, Fabrizia, et al. “How Radial Glia Progenitor Lineages Generate Cell-Type Diversity in the Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>, vol. 93, 103046, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.conb.2025.103046\">10.1016/j.conb.2025.103046</a>.","ama":"Pipicelli F, Villalba Requena A, Hippenmeyer S. How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. 2025;93. doi:<a href=\"https://doi.org/10.1016/j.conb.2025.103046\">10.1016/j.conb.2025.103046</a>","ieee":"F. Pipicelli, A. Villalba Requena, and S. Hippenmeyer, “How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex,” <i>Current Opinion in Neurobiology</i>, vol. 93. Elsevier, 2025.","chicago":"Pipicelli, Fabrizia, Ana Villalba Requena, and Simon Hippenmeyer. “How Radial Glia Progenitor Lineages Generate Cell-Type Diversity in the Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.conb.2025.103046\">https://doi.org/10.1016/j.conb.2025.103046</a>.","apa":"Pipicelli, F., Villalba Requena, A., &#38; Hippenmeyer, S. (2025). How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2025.103046\">https://doi.org/10.1016/j.conb.2025.103046</a>","short":"F. Pipicelli, A. Villalba Requena, S. Hippenmeyer, Current Opinion in Neurobiology 93 (2025)."},"file":[{"checksum":"05bacb4acbe6275d43e873dec9ba1d52","file_id":"20894","relation":"main_file","date_created":"2025-12-30T08:25:49Z","date_updated":"2025-12-30T08:25:49Z","content_type":"application/pdf","file_name":"2025_CurrentOpNeurobiology_Pipicelli.pdf","creator":"dernst","file_size":1592649,"success":1,"access_level":"open_access"}],"publication_status":"published","project":[{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"_id":"7c084566-9f16-11ee-852c-c88a1dbbf1cf","grant_number":"ALTF 994-2023","name":"Role of cell lineage in generating cell-type diversity in developing neocortex’"}],"type":"journal_article","OA_type":"hybrid","author":[{"id":"649134fd-d012-11ed-8f82-db1e5050f9ba","last_name":"Pipicelli","first_name":"Fabrizia","full_name":"Pipicelli, Fabrizia"},{"first_name":"Ana","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","last_name":"Villalba Requena"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"date_created":"2025-05-20T10:20:09Z","article_number":"103046","file_date_updated":"2025-12-30T08:25:49Z"},{"pmid":1,"abstract":[{"lang":"eng","text":"Research question: Is LINC01638 involved in regulation of epithelial-to-mesenchymal transition (EMT) in endometriosis?\r\nDesign: A prospective patient cohort study was combined with functional experiments in the 12Z endometriosis epithelial cell line to investigate the role of LINC01638 in endometriosis. Eutopic endometrial samples were collected by curettage, and ectopic endometrial lesion samples were collected by laparoscopic surgery from 24 control patients and 41 patients with endometriosis. The phenotype of 12Z cells was assessed following LINC01638 knockdown using siRNA, performing proliferation, adhesion, migration and invasion assays, as well as assessing apoptosis and cell cycle changes with flow cytometry assays. In order to assess the relationship between LINC01638 and histone deacetylase class 1 enzyme (HDAC1), LINC01638 knockdown was combined with HDAC inhibition with the specific HDAC inhibitor romidepsin.\r\nResults: LINC01638 was up-regulated in the epithelial layer of endometriotic lesions, and LINC01638 knockdown in 12Z cells led to reduced proliferation, adhesion, migration and invasion. The reduction in proliferation was associated with increased p21 and p27 expression, and G1 phase arrest. Further analysis of LINC01638 control and knockdown cells revealed that a number of transcription factors associated with EMT are down-regulated in knockdown cells, along with the cytoskeleton regulatory gene RHOB, while HDAC1 was up-regulated. Chromatin immunoprecipitation analysis and HDAC1 inhibitory treatment combined with LINC01638 knockdown indicated that LINC01638 regulates RHOB expression via HDAC1-mediated promoter deacetylation. RHOB is up-regulated in the epithelial layer of endometriotic lesions compared with eutopic endometrium, supporting a role in the disease.\r\nConclusions: LINC01638 is an epigenetic regulator of the pathogenesis of endometriosis, promoting proliferation and EMT of endometriotic lesions."}],"intvolume":"        51","department":[{"_id":"SiHi"}],"date_published":"2025-07-17T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["001549819000002"],"pmid":["40680553"]},"article_processing_charge":"No","publication":"Reproductive Biomedicine Online","status":"public","scopus_import":"1","citation":{"chicago":"Yotova, Iveta, Katharina Proestling, Florian Pauler, Lisa Rainer, Leonie Kaup, Jana Heine, Lejla Sandrieser, René Wenzl, and Quanah J. Hudson. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>.","ama":"Yotova I, Proestling K, Pauler F, et al. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. 2025;51(3). doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>","ieee":"I. Yotova <i>et al.</i>, “LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression,” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3. Elsevier, 2025.","mla":"Yotova, Iveta, et al. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3, 104942, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>.","ista":"Yotova I, Proestling K, Pauler F, Rainer L, Kaup L, Heine J, Sandrieser L, Wenzl R, Hudson QJ. 2025. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. Reproductive Biomedicine Online. 51(3), 104942.","short":"I. Yotova, K. Proestling, F. Pauler, L. Rainer, L. Kaup, J. Heine, L. Sandrieser, R. Wenzl, Q.J. Hudson, Reproductive Biomedicine Online 51 (2025).","apa":"Yotova, I., Proestling, K., Pauler, F., Rainer, L., Kaup, L., Heine, J., … Hudson, Q. J. (2025). LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>"},"publication_status":"published","article_number":"104942","date_created":"2025-07-27T22:01:25Z","OA_type":"closed access","type":"journal_article","author":[{"full_name":"Yotova, Iveta","first_name":"Iveta","last_name":"Yotova"},{"last_name":"Proestling","first_name":"Katharina","full_name":"Proestling, Katharina"},{"first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"last_name":"Rainer","first_name":"Lisa","full_name":"Rainer, Lisa"},{"full_name":"Kaup, Leonie","first_name":"Leonie","last_name":"Kaup"},{"last_name":"Heine","first_name":"Jana","full_name":"Heine, Jana"},{"first_name":"Lejla","full_name":"Sandrieser, Lejla","last_name":"Sandrieser"},{"last_name":"Wenzl","full_name":"Wenzl, René","first_name":"René"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"}],"issue":"3","month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","day":"17","year":"2025","title":"LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression","doi":"10.1016/j.rbmo.2025.104942","_id":"20079","acknowledgement":"The authors wish to thank all the participants and health professionals involved in this study. In addition, the authors wish to thank technical assistants Barbara Widmar, Matthias Witzmann-Stern and Isabella Haslinger for their work assisting with this study; and Simon Hippenmeyer for access to bioinformatic infrastructure and resources.\r\nOpen access funding was provided by the Medical University of Vienna.","publisher":"Elsevier","isi":1,"oa_version":"None","volume":51,"date_updated":"2025-09-30T14:10:46Z","quality_controlled":"1","publication_identifier":{"issn":["1472-6483"],"eissn":["1472-6491"]},"fulldoi":"https://doi.org/10.1016/j.rbmo.2025.104942"},{"month":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","title":"Role of NOTCH signaling in radial glial progenitor lineage progression","day":"09","year":"2025","doi":"10.15479/AT-ISTA-20737","acknowledgement":"I also want to thank ISTA and the Austrian Science Fund FWF SFB F78 (F7805) for financially\r\nsupporting my research.","_id":"20737","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","date_updated":"2026-04-14T08:16:58Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20737","publication_identifier":{"isbn":["978-3-99078-072-5"],"issn":["2663-337X"]},"OA_place":"publisher","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2025-12-09T00:00:00Z","supervisor":[{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","ddc":["570"],"has_accepted_license":"1","citation":{"ista":"Casado Polanco R. 2025. Role of NOTCH signaling in radial glial progenitor lineage progression. Institute of Science and Technology Austria.","ieee":"R. Casado Polanco, “Role of NOTCH signaling in radial glial progenitor lineage progression,” Institute of Science and Technology Austria, 2025.","ama":"Casado Polanco R. Role of NOTCH signaling in radial glial progenitor lineage progression. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20737\">10.15479/AT-ISTA-20737</a>","chicago":"Casado Polanco, Raquel. “Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20737\">https://doi.org/10.15479/AT-ISTA-20737</a>.","mla":"Casado Polanco, Raquel. <i>Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20737\">10.15479/AT-ISTA-20737</a>.","apa":"Casado Polanco, R. (2025). <i>Role of NOTCH signaling in radial glial progenitor lineage progression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20737\">https://doi.org/10.15479/AT-ISTA-20737</a>","short":"R. Casado Polanco, Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression, Institute of Science and Technology Austria, 2025."},"file":[{"date_updated":"2025-12-11T11:18:37Z","date_created":"2025-12-11T09:28:09Z","relation":"source_file","file_id":"20793","checksum":"71e0fdf4619b0d70d03657ad7348137d","access_level":"closed","file_size":78207207,"creator":"rcasadop","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_CasadoPolanco_Raquel_Thesis.docx"},{"date_updated":"2025-12-11T09:28:04Z","file_id":"20794","checksum":"58cf2f25c33567723bc754a019c3e396","date_created":"2025-12-11T09:28:04Z","relation":"main_file","embargo_to":"open_access","embargo":"2026-12-01","file_name":"2025_CasadoPolanco_Raquel_Thesis.pdf","content_type":"application/pdf","file_size":6261874,"access_level":"closed","creator":"rcasadop"}],"publication_status":"published","project":[{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"keyword":["NOTCH","radial glial progenitor","lineage progression","cortical development"],"alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","last_name":"Casado Polanco","first_name":"Raquel","full_name":"Casado Polanco, Raquel","orcid":"0000-0001-8293-4568"}],"page":"133","date_created":"2025-12-09T09:04:18Z","file_date_updated":"2025-12-11T11:18:37Z"},{"publication_status":"published","project":[{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"citation":{"short":"X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M. Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte, Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang, L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X. Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo, W. Ge, Nature Communications 16 (2025).","apa":"Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (2025). Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-60308-0\">https://doi.org/10.1038/s41467-025-60308-0</a>","ieee":"X. Gao <i>et al.</i>, “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ama":"Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-60308-0\">10.1038/s41467-025-60308-0</a>","chicago":"Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-60308-0\">https://doi.org/10.1038/s41467-025-60308-0</a>.","mla":"Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” <i>Nature Communications</i>, vol. 16, 5840, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-60308-0\">10.1038/s41467-025-60308-0</a>.","ista":"Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y, Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge W. 2025. Reduction of neuronal activity mediated by blood-vessel regression in the brain. Nature Communications. 16, 5840."},"file":[{"date_updated":"2025-07-07T09:52:46Z","checksum":"f59748cb67232cfb210035d9aef60836","file_id":"19971","date_created":"2025-07-07T09:52:46Z","relation":"main_file","file_size":17018106,"success":1,"access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_name":"2025_NatureComm_Gao.pdf"}],"file_date_updated":"2025-07-07T09:52:46Z","OA_type":"gold","type":"journal_article","author":[{"full_name":"Gao, Xiaofei","first_name":"Xiaofei","last_name":"Gao"},{"last_name":"Li","first_name":"Jun-Liszt","full_name":"Li, Jun-Liszt"},{"first_name":"Xingjun","full_name":"Chen, Xingjun","last_name":"Chen"},{"full_name":"Ci, Bo","first_name":"Bo","last_name":"Ci"},{"full_name":"Chen, Fei","first_name":"Fei","last_name":"Chen"},{"first_name":"Nannan","full_name":"Lu, Nannan","last_name":"Lu"},{"full_name":"Shen, Bo","first_name":"Bo","last_name":"Shen"},{"last_name":"Zheng","first_name":"Lijun","full_name":"Zheng, Lijun"},{"full_name":"Jia, Jie-Min","first_name":"Jie-Min","last_name":"Jia"},{"last_name":"Yi","full_name":"Yi, Yating","first_name":"Yating"},{"first_name":"Shiwen","full_name":"Zhang, Shiwen","last_name":"Zhang"},{"full_name":"Shi, Ying-Chao","first_name":"Ying-Chao","last_name":"Shi"},{"last_name":"Shi","full_name":"Shi, Kaibin","first_name":"Kaibin"},{"full_name":"Propson, Nicholas E","first_name":"Nicholas E","last_name":"Propson"},{"last_name":"Huang","first_name":"Yubin","full_name":"Huang, Yubin"},{"full_name":"Poinsatte, Katherine","first_name":"Katherine","last_name":"Poinsatte"},{"last_name":"Zhang","full_name":"Zhang, Zhaohuan","first_name":"Zhaohuan"},{"last_name":"Yue","first_name":"Yuanlei","full_name":"Yue, Yuanlei"},{"full_name":"Bosco, Dale B","first_name":"Dale B","last_name":"Bosco"},{"last_name":"Lu","full_name":"Lu, Ying-mei","first_name":"Ying-mei"},{"full_name":"Yang, Shi-bing","first_name":"Shi-bing","last_name":"Yang"},{"last_name":"Adams","first_name":"Ralf H.","full_name":"Adams, Ralf H."},{"last_name":"Lindner","first_name":"Volkhard","full_name":"Lindner, Volkhard"},{"last_name":"Huang","first_name":"Fen","full_name":"Huang, Fen"},{"last_name":"Wu","first_name":"Long-Jun","full_name":"Wu, Long-Jun"},{"full_name":"Zheng, Hui","first_name":"Hui","last_name":"Zheng"},{"last_name":"Han","full_name":"Han, Feng","first_name":"Feng"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"last_name":"Stowe","first_name":"Ann M.","full_name":"Stowe, Ann M."},{"first_name":"Bo","full_name":"Peng, Bo","last_name":"Peng"},{"full_name":"Margeta, Marta","first_name":"Marta","last_name":"Margeta"},{"full_name":"Wang, Xiaoqun","first_name":"Xiaoqun","last_name":"Wang"},{"last_name":"Liu","full_name":"Liu, Qiang","first_name":"Qiang"},{"last_name":"Körbelin","first_name":"Jakob","full_name":"Körbelin, Jakob"},{"last_name":"Trepel","full_name":"Trepel, Martin","first_name":"Martin"},{"first_name":"Hui","full_name":"Lu, Hui","last_name":"Lu"},{"last_name":"Zhou","first_name":"Bo O.","full_name":"Zhou, Bo O."},{"full_name":"Zhao, Hu","first_name":"Hu","last_name":"Zhao"},{"full_name":"Su, Wenzhi","first_name":"Wenzhi","last_name":"Su"},{"last_name":"Bachoo","full_name":"Bachoo, Robert M.","first_name":"Robert M."},{"last_name":"Ge","full_name":"Ge, Woo-ping","first_name":"Woo-ping"}],"date_created":"2020-10-06T08:58:59Z","article_number":"5840","oa":1,"external_id":{"isi":["001523450500035"]},"language":[{"iso":"eng"}],"ec_funded":1,"article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we report that a substantial proportion of blood vessels in the adult mouse brain sporadically occlude and regress. Their regression proceeds through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels are found to be widespread in mouse, monkey and human brains. We further reveal that blood vessel regression cause a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain."}],"intvolume":"        16","date_published":"2025-07-01T00:00:00Z","department":[{"_id":"SiHi"}],"OA_place":"publisher","ddc":["570"],"has_accepted_license":"1","scopus_import":"1","status":"public","publication":"Nature Communications","oa_version":"Published Version","isi":1,"fulldoi":"https://doi.org/10.1038/s41467-025-60308-0","quality_controlled":"1","publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2025-09-04T07:08:37Z","volume":16,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"DOAJ_listed":"1","doi":"10.1038/s41467-025-60308-0","_id":"8616","acknowledgement":"The project was initiated in the Jan lab at UCSF. We thank Lily Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing MADM-7 mice and Rolf A Brekken for VEGF-antibodies.  Drs. Yuanquan Song (UPenn), Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics, Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion. Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.) for critical reading. We acknowledge the assistance of the CIBR Imaging core. We also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.; National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key Research and Development Program of China (2016YFE0125400)to F.H.;National Natural Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865) to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670 and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780 to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking Outside the Box Award.","publisher":"Springer Nature","title":"Reduction of neuronal activity mediated by blood-vessel regression in the brain","day":"01","year":"2025"},{"oa_version":"Preprint","fulldoi":"https://doi.org/10.1101/2025.05.22.655488","date_updated":"2026-08-13T07:18:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"_id":"19762","acknowledgement":"We thank A. Iñigo for assistance with imaging, and members of the Borrell and Herrera labs for\r\ninsightful discussions and critical reading of the manuscript. Funding to our lab members was\r\nprovided by the Spanish Research Agency (AEI): FPI contract (BES-2016-077737) to L.dV.A., FPI SO contract (SEV-2017-0723-18-1) to A.E., JdC-Incorporación contract (IJC2020-044653-I) to V.F., and JAE-Intro fellowship (JAEICU23EX_0071) to I.C., as well as by La Caixa Foundation: La Caixa-Severo Ochoa fellowship (E-03-2016-0557140) to S.A., INPhINIT-Retaining fellowship (LCF/BQ/DR21/11880012) to E.F.O., INPhINIT-Incoming fellowship (LCF/BQ/DI22/11940006) to E.N., and Junior Leader-Retaining grant to A.C. (LCF/BQ/PR23/11980051). Work was supported by grants from FWF (SFB F78) to S.H.; AEI (PID2021-125618NB-I00) and European Research Council (101118729) to V.B., who also acknowledges financial support from AEI through the “Severo Ochoa” Programme for Centers of Excellence in R&D (CEX2021-001165-S).","doi":"10.1101/2025.05.22.655488","biorxivid":1,"title":"Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development","year":"2025","day":"23","publication_status":"submitted","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"citation":{"ama":"Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>","ieee":"A. Cárdenas <i>et al.</i>, “Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development,” <i>bioRxiv</i>. .","mla":"Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","chicago":"Cárdenas, Adrián, Irem Çelik, Alexandre Espinós, Carmen Streicher, Lara López-González, Lucia del-Valle-Anton, Virginia Fernández, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>.","ista":"Cárdenas A, Çelik I, Espinós A, Streicher C, López-González L, del-Valle-Anton L, Fernández V, Amin S, Negri E, Ortuño EF, Hippenmeyer S, Borrell V. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","short":"A. Cárdenas, I. Çelik, A. Espinós, C. Streicher, L. López-González, L. del-Valle-Anton, V. Fernández, S. Amin, E. Negri, E.F. Ortuño, S. Hippenmeyer, V. Borrell, BioRxiv (n.d.).","apa":"Cárdenas, A., Çelik, I., Espinós, A., Streicher, C., López-González, L., del-Valle-Anton, L., … Borrell, V. (n.d.). Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>"},"author":[{"full_name":"Cárdenas, Adrián","first_name":"Adrián","last_name":"Cárdenas"},{"last_name":"Çelik","first_name":"Irem","full_name":"Çelik, Irem"},{"last_name":"Espinós","first_name":"Alexandre","full_name":"Espinós, Alexandre"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen"},{"full_name":"López-González, Lara","first_name":"Lara","last_name":"López-González"},{"last_name":"del-Valle-Anton","first_name":"Lucia","full_name":"del-Valle-Anton, Lucia"},{"last_name":"Fernández","full_name":"Fernández, Virginia","first_name":"Virginia"},{"first_name":"Salma","full_name":"Amin, Salma","last_name":"Amin"},{"last_name":"Negri","first_name":"Enrico","full_name":"Negri, Enrico"},{"last_name":"Ortuño","full_name":"Ortuño, Eduardo Fernández","first_name":"Eduardo Fernández"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"last_name":"Borrell","full_name":"Borrell, Víctor","first_name":"Víctor"}],"OA_type":"green","type":"preprint","date_created":"2025-05-29T10:45:55Z","article_processing_charge":"No","oa":1,"external_id":{"biorxivid":["10.1101/2025.05.22.655488"]},"language":[{"iso":"eng"}],"date_published":"2025-05-23T00:00:00Z","department":[{"_id":"SiHi"}],"abstract":[{"lang":"eng","text":"The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process."}],"OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.22.655488"}],"publication":"bioRxiv","status":"public"},{"oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"text":"Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise.","lang":"eng"}],"date_published":"2025-05-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","department":[{"_id":"SiHi"}],"OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.07.652665","open_access":"1"}],"doi":"10.1101/2025.05.07.652665","acknowledgement":"We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression; C. Varela747 Martínez for help with the code for graphical analysis; all members from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU (PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI /10.13039/501100011033.\r\n","_id":"19717","status":"public","publication":"bioRxiv","title":"Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis","day":"07","year":"2025","publication_status":"submitted","oa_version":"Preprint","citation":{"chicago":"Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer, and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>.","ama":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>","ieee":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis,” <i>bioRxiv</i>. .","mla":"Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","ista":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","short":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (n.d.).","apa":"Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer, S., &#38; Nieto, M. (n.d.). Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>"},"fulldoi":"https://doi.org/10.1101/2025.05.07.652665","OA_type":"green","type":"preprint","date_updated":"2026-08-13T07:16:48Z","author":[{"last_name":"Varela-Martínez","full_name":"Varela-Martínez, I","first_name":"I"},{"last_name":"Villalba Requena","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","full_name":"Villalba Requena, Ana","orcid":"0000-0002-5615-5277","first_name":"Ana"},{"first_name":"J.","full_name":"Garcia-Marqués, J.","last_name":"Garcia-Marqués"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"last_name":"Nieto","first_name":"M.","full_name":"Nieto, M."}],"date_created":"2025-05-20T10:19:29Z"},{"corr_author":"1","title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM","day":"22","year":"2025","doi":"10.15479/AT-ISTA-20212","acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253).","_id":"20212","related_material":{"record":[{"status":"public","id":"17425","relation":"part_of_dissertation"}]},"publisher":"Institute of Science and Technology Austria","month":"08","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-08-26T22:30:03Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20212","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-063-3"]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"status":"public","degree_awarded":"PhD","ddc":["570"],"has_accepted_license":"1","OA_place":"publisher","oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"date_published":"2025-08-22T00:00:00Z","supervisor":[{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"keyword":["Pten","mtor","cortical development","MADM","Mapk"],"type":"dissertation","author":[{"orcid":"0000-0001-6618-6889","full_name":"Miranda, Osvaldo","first_name":"Osvaldo","last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425"}],"page":"119","date_created":"2025-08-22T14:07:00Z","file_date_updated":"2026-08-26T22:30:02Z","citation":{"mla":"Miranda, Osvaldo. <i>Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>.","ama":"Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20212\">10.15479/AT-ISTA-20212</a>","chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>.","ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025.","ista":"Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria.","short":"O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025.","apa":"Miranda, O. (2025). <i>Unraveling the role of Pten in cortical stem cell lineage progression using MADM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20212\">https://doi.org/10.15479/AT-ISTA-20212</a>"},"file":[{"embargo_to":"open_access","relation":"source_file","date_created":"2025-08-26T09:03:50Z","file_id":"20230","checksum":"3331f76bbef74ff4908e2d2c9262045c","date_updated":"2026-08-26T22:30:02Z","creator":"omiranda","access_level":"closed","file_size":32887334,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx"},{"content_type":"application/pdf","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf","creator":"omiranda","access_level":"open_access","file_size":28636240,"relation":"main_file","date_created":"2025-08-26T09:05:55Z","checksum":"02509d50cff8e35c5bcbf71e8d658176","file_id":"20231","date_updated":"2026-08-26T22:30:02Z","embargo":"2026-08-26"}],"publication_status":"published","project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","corr_author":"1","year":"2024","day":"17","_id":"12875","acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","description":"News on ISTA Website","relation":"press_release"}]},"publisher":"Elsevier","doi":"10.1016/j.neuron.2023.11.009","isi":1,"oa_version":"Published Version","date_updated":"2025-12-30T10:54:12Z","volume":112,"fulldoi":"https://doi.org/10.1016/j.neuron.2023.11.009","publication_identifier":{"issn":["0896-6273"]},"quality_controlled":"1","pmid":1,"article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["001163937900001"],"pmid":["38096816"]},"date_published":"2024-01-17T00:00:00Z","department":[{"_id":"SiHi"},{"_id":"RySh"}],"intvolume":"       112","abstract":[{"lang":"eng","text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny."}],"publication":"Neuron","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"scopus_import":"1","has_accepted_license":"1","ddc":["570"],"file":[{"file_id":"14944","checksum":"32b3788f7085cf44a84108d8faaff3ce","date_created":"2024-02-06T13:56:15Z","relation":"main_file","date_updated":"2024-02-06T13:56:15Z","file_name":"2024_Neuron_Cheung.pdf","content_type":"application/pdf","creator":"dernst","file_size":5942467,"access_level":"open_access","success":1}],"citation":{"apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>.","mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>.","ieee":"G. T. Cheung <i>et al.</i>, “Multipotent progenitors instruct ontogeny of the superior colliculus,” <i>Neuron</i>, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. 2024;112(2):230-246.e11. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11."},"publication_status":"published","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"issue":"2","author":[{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T"},{"first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","first_name":"Peter"},{"full_name":"Krausgruber, Thomas","first_name":"Thomas","last_name":"Krausgruber"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen"},{"id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","last_name":"Schrammel","first_name":"Martin","full_name":"Schrammel, Martin"},{"id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","last_name":"Özgen","first_name":"Natalie Y","full_name":"Özgen, Natalie Y"},{"full_name":"Ivec, Alexis","first_name":"Alexis","last_name":"Ivec","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"type":"journal_article","date_created":"2023-04-27T09:41:48Z","page":"230-246.e11","file_date_updated":"2024-02-06T13:56:15Z"},{"fulldoi":"https://doi.org/10.1016/j.xpro.2023.102771","quality_controlled":"1","publication_identifier":{"issn":["2666-1667"]},"date_updated":"2025-04-15T08:23:06Z","volume":5,"oa_version":"Published Version","_id":"14683","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","publisher":"Elsevier","doi":"10.1016/j.xpro.2023.102771","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","corr_author":"1","year":"2024","day":"15","article_type":"review","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2024-07-16T11:50:03Z","issue":"1","author":[{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"date_created":"2023-12-13T11:48:05Z","article_number":"102771","publication_status":"published","project":[{"call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T01031","name":"Role of Eed in neural stem cell lineage progression"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"file":[{"date_updated":"2024-07-16T11:50:03Z","file_id":"17260","checksum":"3f0ee62e04bf5a44b45b035662826e95","date_created":"2024-07-16T11:50:03Z","relation":"main_file","file_name":"2024_STARProtoc_Amberg.pdf","content_type":"application/pdf","file_size":8871807,"success":1,"access_level":"open_access","creator":"dernst"}],"citation":{"ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024)."},"scopus_import":"1","has_accepted_license":"1","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication":"STAR Protocols","status":"public","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","oa":1,"external_id":{"pmid":["38070137"]},"language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"date_published":"2024-03-15T00:00:00Z","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"intvolume":"         5","pmid":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"review","year":"2024","day":"15","title":"Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers","corr_author":"1","related_material":{"link":[{"url":"http://github.com/hippenmeyerlab","relation":"software"}]},"_id":"14794","acknowledgement":"We thank Florian Pauler for discussion and his expert technical support. This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging and Optics Facility (IOF) and Preclinical Facility (PCF). A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences.","publisher":"Elsevier","doi":"10.1016/j.xpro.2023.102795","oa_version":"Published Version","volume":5,"date_updated":"2025-04-15T07:32:40Z","publication_identifier":{"eissn":["2666-1667"]},"quality_controlled":"1","fulldoi":"https://doi.org/10.1016/j.xpro.2023.102795","pmid":1,"department":[{"_id":"SiHi"}],"date_published":"2024-03-15T00:00:00Z","intvolume":"         5","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3","lang":"eng"}],"article_processing_charge":"Yes","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["38165800"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication":"STAR Protocols","status":"public","has_accepted_license":"1","scopus_import":"1","ddc":["570"],"file":[{"date_updated":"2024-07-16T12:04:46Z","relation":"main_file","date_created":"2024-07-16T12:04:46Z","checksum":"4644d537451c5c114a9d7c7829b65bba","file_id":"17264","file_name":"2024_STARProtoc_Hansen.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":3758943,"creator":"dernst"}],"citation":{"apa":"Hansen, A. H., &#38; Hippenmeyer, S. (2024). Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>","short":"A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024).","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 5, no. 1, 102795, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>.","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">https://doi.org/10.1016/j.xpro.2023.102795</a>.","ama":"Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102795\">10.1016/j.xpro.2023.102795</a>","ieee":"A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","ista":"Hansen AH, Hippenmeyer S. 2024. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 5(1), 102795."},"project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular mechanisms of radial neuronal migration"}],"publication_status":"published","article_number":"102795","date_created":"2024-01-14T23:00:56Z","author":[{"last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H","first_name":"Andi H"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"issue":"1","type":"journal_article","file_date_updated":"2024-07-16T12:04:46Z"},{"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"month":"05","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","day":"15","year":"2024","corr_author":"1","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","doi":"10.15479/AT:ISTA:15385","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17142"}]},"publisher":"Institute of Science and Technology Austria","acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. ","_id":"15385","oa_version":"Published Version","date_updated":"2025-09-08T07:57:11Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:15385","abstract":[{"lang":"eng","text":"Relevant information about the data can be found in the 'Readme_Data.txt' file. \r\nA previous version of the publication can be found on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.11.511691v4\r\nand published in Plos Biology (2024)"}],"department":[{"_id":"MaJö"},{"_id":"PreCl"},{"_id":"SiHi"},{"_id":"RySh"},{"_id":"GaNo"}],"date_published":"2024-05-15T00:00:00Z","oa":1,"article_processing_charge":"No","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"}],"status":"public","ddc":["570"],"has_accepted_license":"1","citation":{"chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>.","ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>","mla":"Burnett, Laura, et al. <i>Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024.","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">10.15479/AT:ISTA:15385</a>.","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, (2024).","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:15385\">https://doi.org/10.15479/AT:ISTA:15385</a>"},"file":[{"date_updated":"2024-05-15T06:09:17Z","date_created":"2024-05-15T06:09:17Z","relation":"main_file","file_id":"15396","checksum":"9205eb0876f0f08552dbad80d6884b4b","access_level":"open_access","success":1,"file_size":"1149617663","creator":"mjoesch","file_name":"PatchClamp.zip","content_type":"application/zip"},{"file_id":"15397","date_created":"2024-05-15T06:09:12Z","relation":"main_file","date_updated":"2024-05-15T06:09:12Z","content_type":"application/zip","file_name":"SiliconProbe.zip","creator":"mjoesch","file_size":"564903112","access_level":"open_access","success":1},{"date_updated":"2024-05-15T06:09:14Z","relation":"main_file","date_created":"2024-05-15T06:09:14Z","file_id":"15398","checksum":"49a807bbab06b5fada38f532e2176e2e","content_type":"application/zip","file_name":"WesternBlot.zip","success":1,"access_level":"open_access","file_size":"11685703","creator":"mjoesch"},{"date_created":"2024-05-15T06:09:38Z","relation":"main_file","file_id":"15399","checksum":"beeeeaa43770090f3b291209ed6b0623","date_updated":"2024-05-15T06:09:38Z","file_name":"Behaviour.zip","content_type":"application/zip","creator":"mjoesch","access_level":"open_access","success":1,"file_size":"1335626779"},{"content_type":"text/plain","file_name":"Readme_Data.txt","file_size":18841,"access_level":"open_access","success":1,"creator":"mjoesch","date_updated":"2024-05-16T09:08:20Z","checksum":"8862ad7719388304d1d19f8e7db8bb00","file_id":"15400","date_created":"2024-05-16T09:08:20Z","relation":"main_file"}],"date_created":"2024-05-13T15:04:04Z","type":"research_data","keyword":["ASD","periaqueductal gray","perception","behavior","potassium channels"],"author":[{"last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura","first_name":"Laura"},{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","first_name":"Olga","full_name":"Symonova, Olga","orcid":"0000-0003-2012-9947"},{"first_name":"Tomas","full_name":"Masson, Tomas","orcid":"0000-0002-2634-6283","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","last_name":"Masson"},{"id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A"},{"full_name":"Contreras, Ximena","first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"file_date_updated":"2024-05-16T09:08:20Z"},{"title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","corr_author":"1","APC_amount":"804 EUR","year":"2024","day":"20","_id":"17187","acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","publisher":"Elsevier","doi":"10.1016/j.xpro.2024.103157","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_type":"original","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-30T10:54:11Z","volume":5,"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103157","publication_identifier":{"eissn":["2666-1667"]},"quality_controlled":"1","oa_version":"Published Version","status":"public","publication":"STAR Protocols","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"scopus_import":"1","has_accepted_license":"1","ddc":["570"],"pmid":1,"OA_place":"publisher","article_processing_charge":"Yes","ec_funded":1,"external_id":{"pmid":["38935508"]},"language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"SiHi"}],"date_published":"2024-09-20T00:00:00Z","intvolume":"         5","abstract":[{"lang":"eng","text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1"}],"author":[{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon"}],"issue":"3","OA_type":"gold","type":"journal_article","article_number":"103157","date_created":"2024-06-30T22:01:04Z","file_date_updated":"2025-01-09T12:12:40Z","file":[{"file_id":"18809","checksum":"d8a8cdba82a394e731aa699ace1ae433","relation":"main_file","date_created":"2025-01-09T12:12:40Z","date_updated":"2025-01-09T12:12:40Z","creator":"dernst","file_size":5186071,"access_level":"open_access","success":1,"file_name":"2024_STARProtoc_Cheung.pdf","content_type":"application/pdf"}],"citation":{"short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>","mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>."},"publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}]},{"citation":{"short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168."},"file":[{"file_name":"2024_STARProtoc_Cheung2.pdf","content_type":"application/pdf","creator":"dernst","access_level":"open_access","success":1,"file_size":6445556,"relation":"main_file","date_created":"2025-01-09T12:16:53Z","file_id":"18810","checksum":"464f52ecc6ec92f509552823bb82bf79","date_updated":"2025-01-09T12:16:53Z"}],"project":[{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"publication_status":"published","date_created":"2024-07-14T22:01:10Z","article_number":"103168","OA_type":"gold","type":"journal_article","issue":"3","author":[{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2025-01-09T12:16:53Z","OA_place":"publisher","pmid":1,"abstract":[{"lang":"eng","text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1"}],"intvolume":"         5","date_published":"2024-09-20T00:00:00Z","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"oa":1,"external_id":{"pmid":["38968076"]},"language":[{"iso":"eng"}],"article_processing_charge":"Yes","publication":"STAR Protocols","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"ddc":["570"],"scopus_import":"1","has_accepted_license":"1","oa_version":"Published Version","volume":5,"date_updated":"2025-12-30T10:54:12Z","publication_identifier":{"eissn":["2666-1667"]},"quality_controlled":"1","fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","article_type":"original","day":"20","year":"2024","corr_author":"1","APC_amount":"804 EUR","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","doi":"10.1016/j.xpro.2024.103168","_id":"17232","publisher":"Elsevier","acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation)."},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","day":"13","year":"2024","corr_author":"1","edition":"1","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","doi":"10.1007/978-1-0716-3969-6_19","_id":"17425","publisher":"Springer Nature","related_material":{"record":[{"status":"public","id":"20212","relation":"dissertation_contains"}]},"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","oa_version":"None","editor":[{"last_name":"Toyooka","first_name":"Kazuhito","full_name":"Toyooka, Kazuhito"}],"volume":2831,"date_updated":"2026-09-13T22:30:11Z","quality_controlled":"1","publication_identifier":{"issn":["1064-3745"],"eisbn":["9781071639696"],"isbn":["9781071639689"],"eissn":["1940-6029"]},"fulldoi":"https://doi.org/10.1007/978-1-0716-3969-6_19","pmid":1,"intvolume":"      2831","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology."}],"date_published":"2024-08-13T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["39134857"]},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"}],"publication":"Neuronal Morphogenesis","status":"public","series_title":"MIMB","scopus_import":"1","citation":{"ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>"},"project":[{"grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"publication_status":"published","page":"283-299","date_created":"2024-08-13T12:16:41Z","type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"author":[{"id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Miranda","first_name":"Osvaldo","full_name":"Miranda, Osvaldo","orcid":"0000-0001-6618-6889"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"place":"New York, NY"}]