--- OA_place: repository OA_type: green _id: '21212' abstract: - lang: eng text: "Malignant glioma is incurable. Using a mouse genetic mosaic system to generate sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null OPCs outcompete wildtype counterparts during their expansion. Blocking competition by mutating/strengthening wildtype OPCs impeded both pre-malignant progression and malignant expansion of glioma.\r\n\r\n“In-tissue” phosphoproteomic profiling revealed an enrichment of phosphopeptides related to RNA splicing and protein translation at the peak of cell competition, suggesting that competitiveness may stem from unique protein species. Among candidates was mTORC1, whose pharmacological inhibition or genetic disruption resulted in a loss of competitiveness in our mouse model. Finally, analysis of patient biopsies and interrogating the role of individual gliomagenic mutations in OPC competition supported its relevance in human gliomas. Together, these findings identified the driving role of competitive interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic strategies to target this process." acknowledgement: "We thank Dr. Wenjie Liu for providing critical feedback on the manuscript. We also thank Dr.\r\nPat Pramoonjago at the Biorepository and Tissue Research Facility, and Hope Davis at the\r\nvivarium for their assistance on the project. These Core Facilities are supported by UVA Cancer\r\nCenter grant #P30-CA044579. We are grateful to Dr. Jonathan A. Epstein for providing the\r\nNf1GRD/+ mouse strain (https://pubmed.ncbi.nlm.nih.gov/26460546/). This work was partly\r\nsupported by the National Institute of Neurological Diseases and Stroke R21 NS125479-01A1\r\n(H.Z.), American Cancer Society Institutional Research Grant to the University of Virginia\r\n(Y.J.), the National Natural Science Foundation of China #82072787 (M.Y.), the National\r\nCancer Institute U54 CA238114 (F.W.), U01 CA284193 (K.M.N.), and U54 CA274499 (K.A.J.,\r\nM.F-S.), the National institute of General Medical Sciences R35 GM133404 (M.F-S.), the Dr.\r\nMiriam and Sheldon G. Adelson Medical Research Foundation (H.I.K., S.A.G.), the National\r\nCenter for Advancing Translational Sciences KL2TR001882 (K.S.P.), Tower Cancer Career Development Grant (K.S.P.), McKnight Neurobiology of Brain Disorders Grant (K.S.P.). The\r\ncontent is solely the responsibility of the authors and does not necessarily represent the official\r\nviews of the National Institutes of Health. Illustrations in this manuscript were created with\r\nBioRender (BioRender.com)." article_processing_charge: No author: - first_name: Ying full_name: Jiang, Ying last_name: Jiang - first_name: Ryuhjin full_name: Ahn, Ryuhjin last_name: Ahn - first_name: Arthur full_name: Huang, Arthur last_name: Huang - first_name: Phillippe P. full_name: Gonzalez, Phillippe P. last_name: Gonzalez - first_name: Jungeun full_name: Kim, Jungeun last_name: Kim - first_name: Guoxin full_name: Zhang, Guoxin last_name: Zhang - first_name: Zihao full_name: Liu, Zihao last_name: Liu - first_name: Zhenqiang full_name: He, Zhenqiang last_name: He - first_name: Lindsey full_name: Dudley, Lindsey last_name: Dudley - first_name: Kunal S. full_name: Patel, Kunal S. last_name: Patel - first_name: Godfrey A. full_name: Dzhivhuho, Godfrey A. last_name: Dzhivhuho - first_name: Sam full_name: Crowl, Sam last_name: Crowl - first_name: Piotr full_name: Przanowski, Piotr last_name: Przanowski - first_name: Luisa Quesada full_name: Camacho, Luisa Quesada last_name: Camacho - first_name: Sijie full_name: Hao, Sijie last_name: Hao - first_name: Jianhao full_name: Zeng, Jianhao last_name: Zeng - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Mohammad full_name: Fallahi-Sichani, Mohammad last_name: Fallahi-Sichani - first_name: Kevin A. full_name: Janes, Kevin A. last_name: Janes - first_name: Kristen M. full_name: Naegle, Kristen M. last_name: Naegle - first_name: Marie-Louise full_name: Hammarskjold, Marie-Louise last_name: Hammarskjold - first_name: Steven A. full_name: Goldman, Steven A. last_name: Goldman - first_name: Harley I. full_name: Kornblum, Harley I. last_name: Kornblum - first_name: Maojin full_name: Yao, Maojin last_name: Yao - first_name: Forest full_name: White, Forest last_name: White - first_name: Hui full_name: Zong, Hui last_name: Zong citation: ama: Jiang Y, Ahn R, Huang A, et al. Critical role of cell competition in gliomagenesis. bioRxiv. 2026. doi:10.64898/2026.01.15.699808 apa: Jiang, Y., Ahn, R., Huang, A., Gonzalez, P. P., Kim, J., Zhang, G., … Zong, H. (2026). Critical role of cell competition in gliomagenesis. bioRxiv. https://doi.org/10.64898/2026.01.15.699808 chicago: Jiang, Ying, Ryuhjin Ahn, Arthur Huang, Phillippe P. Gonzalez, Jungeun Kim, Guoxin Zhang, Zihao Liu, et al. “Critical Role of Cell Competition in Gliomagenesis.” BioRxiv, 2026. https://doi.org/10.64898/2026.01.15.699808. ieee: Y. Jiang et al., “Critical role of cell competition in gliomagenesis,” bioRxiv. 2026. ista: Jiang Y, Ahn R, Huang A, Gonzalez PP, Kim J, Zhang G, Liu Z, He Z, Dudley L, Patel KS, Dzhivhuho GA, Crowl S, Przanowski P, Camacho LQ, Hao S, Zeng J, Hippenmeyer S, Fallahi-Sichani M, Janes KA, Naegle KM, Hammarskjold M-L, Goldman SA, Kornblum HI, Yao M, White F, Zong H. 2026. Critical role of cell competition in gliomagenesis. bioRxiv, 10.64898/2026.01.15.699808. mla: Jiang, Ying, et al. “Critical Role of Cell Competition in Gliomagenesis.” BioRxiv, 2026, doi:10.64898/2026.01.15.699808. short: Y. Jiang, R. Ahn, A. Huang, P.P. Gonzalez, J. Kim, G. Zhang, Z. Liu, Z. He, L. Dudley, K.S. Patel, G.A. Dzhivhuho, S. Crowl, P. Przanowski, L.Q. Camacho, S. Hao, J. Zeng, S. Hippenmeyer, M. Fallahi-Sichani, K.A. Janes, K.M. Naegle, M.-L. Hammarskjold, S.A. Goldman, H.I. Kornblum, M. Yao, F. White, H. Zong, BioRxiv (2026). date_created: 2026-02-10T12:55:55Z date_published: 2026-01-16T00:00:00Z date_updated: 2026-02-16T10:12:42Z day: '16' ddc: - '570' department: - _id: SiHi doi: 10.64898/2026.01.15.699808 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.64898/2026.01.15.699808 month: '01' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: published status: public title: Critical role of cell competition in gliomagenesis tmp: 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: repository OA_type: green _id: '21290' abstract: - lang: eng text: Gene duplication underlies evolutionary innovation, yet many paralogues remain highly similar, raising questions about their functional divergence and physiological relevance. The spliceosomal Sm core protein SNRPB and its mammalian-specific paralogue SNRPN share over 90% sequence identity, but their distinct expression patterns - SNRPB being ubiquitous and SNRPN confined to the brain - suggest specialized functions. Why mammals have two different spliceosomes has remained obscure. Here, we generated isogenic human cell lines expressing ectopically either SNRPB or SNRPN exclusively and found that SNRPN stabilizes transcripts involved in energy metabolism and mitochondrial function, leading to increased mitochondrial abundance and oxygen consumption. Despite similar spliceosomal interactomes, SNRPN more strongly associates with the PRMT5 methylosome complex and exhibits dynamic arginine methylation in its C-terminal region that is sensitive to translation inhibition and amino acid availability. The SNRPN-dependent transcriptome responds to translation inhibition by stabilizing long, intron-rich genes involved in amino acid and energy metabolism. Our findings reveal a nutrient-sensitive, methylation-dependent mechanism that differentiates the two paralogues. This suggests that SNRPN functions as a metabolic-specialized spliceosomal subunit thereby providing tissue-specific adaptation of RNA processing in mammals. acknowledgement: "We thank Oliver Mühlemann and Alex Hofer (University of Bern) for sharing SMG inhibitors\r\nand for their expertise in nonsense-mediated mRNA decay and Maria Hondele for critical\r\nreading of the manuscript draft. We also thank the IMB Genomics Core Facility for assistance\r\nwith library preparation and sequencing, Martin Möckel and the IMB Protein Production Core\r\nFacility for providing enzymes used in this work, Marton Gelleri together with the IMB\r\nMicroscopy Core Facility for support with microscopy and FRAP experiments, Jasmin Cartano\r\nfor proteomics sample processing and the IMB Flow Cytometry Core Facility for support. In\r\naddition, we thank the Imaging Core Facility (IMCF) and the FACS Core Facility at the\r\nBiozentrum, University of Basel, for technical assistance. CIKV acknowledges funding by the\r\nDeutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Individual Grant\r\nProject no. 513744403, Scientific Network Grant Project no. 531902894, GRK2526 “Genevo”\r\n- Project no. 407023052”, GRK2859 (“4R”) - Project no. 491145305, Forschungsinitiative\r\nRheinland-Pfalz (ReALity), the EMBO Young Investigator Program (5795), institutional\r\nfunding from the Institute of Molecular Biology and funds from the Kanton Basel-Stadt and\r\nBasel-Land provided to the Biozentrum of the University Basel. J.H.G.F.G. was part of the\r\n‘Science of Healthy Ageing Research Programme’ (SHARP) initiative funded by RhinelandPalatinate’s Ministry of Science, Education and Culture. PR is funded by the Biozentrum PhD\r\nFellowships Program. MFB received financial support from the intramural High Potentials\r\nGrant program of the University Medical Center Mainz, Forschungsinitiative Rheinland-Pfalz\r\n(ReALity) and Stiftungen zugunsten der Medizinischen Fakultät der LMU Klinikum (26069).\r\nInstruments in the IMB core facilities were supported by funds from the DFG: Laser Scanning\r\nConfocal (Leica Stellaris 8 Falcon, funded by the DFG - Project #497669232), Orbitrap Astral system (funded by the DFG - Project #524805621) and BD LSRFortessa SOPR is funded by\r\nthe DFG - Project #210253511.\r\n" article_processing_charge: No author: - first_name: Feyza full_name: Polat Haas, Feyza last_name: Polat Haas - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: Polina full_name: Rusina, Polina last_name: Rusina - first_name: Anusha full_name: Gopalan, Anusha last_name: Gopalan - first_name: Hector full_name: Fritz, Hector last_name: Fritz - first_name: Azamat full_name: Akhmetkaliyev, Azamat last_name: Akhmetkaliyev - first_name: Frank full_name: Ruehle, Frank last_name: Ruehle - first_name: Anna full_name: Einsiedel, Anna last_name: Einsiedel - first_name: Anna full_name: Szczepinska, Anna last_name: Szczepinska - first_name: Fridolin full_name: Kielisch, Fridolin last_name: Kielisch - first_name: Jia-Xuan full_name: Chen, Jia-Xuan last_name: Chen - first_name: Susanne full_name: Nguyen, Susanne last_name: Nguyen - first_name: Thierry full_name: Schmidlin, Thierry last_name: Schmidlin - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: M. Felicia full_name: Bailicata, M. Felicia last_name: Bailicata - first_name: Claudia Isabelle full_name: Keller Valsecchi, Claudia Isabelle last_name: Keller Valsecchi citation: ama: Polat Haas F, Villalba Requena A, Rusina P, et al. The splicing paralogues SNRPB and SNRPN control differential metabolic states. bioRxiv. doi:10.64898/2026.02.11.705284 apa: Polat Haas, F., Villalba Requena, A., Rusina, P., Gopalan, A., Fritz, H., Akhmetkaliyev, A., … Keller Valsecchi, C. I. (n.d.). The splicing paralogues SNRPB and SNRPN control differential metabolic states. bioRxiv. https://doi.org/10.64898/2026.02.11.705284 chicago: Polat Haas, Feyza, Ana Villalba Requena, Polina Rusina, Anusha Gopalan, Hector Fritz, Azamat Akhmetkaliyev, Frank Ruehle, et al. “The Splicing Paralogues SNRPB and SNRPN Control Differential Metabolic States.” BioRxiv, n.d. https://doi.org/10.64898/2026.02.11.705284. ieee: F. Polat Haas et al., “The splicing paralogues SNRPB and SNRPN control differential metabolic states.,” bioRxiv. . ista: Polat Haas F, Villalba Requena A, Rusina P, Gopalan A, Fritz H, Akhmetkaliyev A, Ruehle F, Einsiedel A, Szczepinska A, Kielisch F, Chen J-X, Nguyen S, Schmidlin T, Hippenmeyer S, Bailicata MF, Keller Valsecchi CI. The splicing paralogues SNRPB and SNRPN control differential metabolic states. bioRxiv, 10.64898/2026.02.11.705284. mla: Polat Haas, Feyza, et al. “The Splicing Paralogues SNRPB and SNRPN Control Differential Metabolic States.” BioRxiv, doi:10.64898/2026.02.11.705284. short: F. Polat Haas, A. Villalba Requena, P. Rusina, A. Gopalan, H. Fritz, A. Akhmetkaliyev, F. Ruehle, A. Einsiedel, A. Szczepinska, F. Kielisch, J.-X. Chen, S. Nguyen, T. Schmidlin, S. Hippenmeyer, M.F. Bailicata, C.I. Keller Valsecchi, BioRxiv (n.d.). date_created: 2026-02-17T11:35:59Z date_published: 2026-02-11T00:00:00Z date_updated: 2026-02-23T11:03:33Z day: '11' department: - _id: SiHi doi: 10.64898/2026.02.11.705284 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.64898/2026.02.11.705284 month: '02' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: submitted status: public title: The splicing paralogues SNRPB and SNRPN control differential metabolic states. type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: repository OA_type: green _id: '21291' abstract: - lang: eng text: The complexity and specificity of movement in vertebrates is driven by a rich diversity of spinal motor and interneuron cell types. During development, eleven spinal cord progenitor domains generate an equivalent number of cardinal neuron types. How progenitor domains, individual progenitors, and post-mitotic diversity relate is still unknown. We performed high-resolution, single-progenitor cell lineage tracing in the embryonic mouse spinal cord using mosaic analysis with double markers (MADM). Our quantitative study of lineage progression revealed that spinal cord progenitors undergo highly variable numbers of proliferative, neurogenic, and gliogenic cell divisions. The nascent clonally-related neurons migrate radially over large distances, span the dorsoventral axis, and even cross the midline, demonstrating striking bilaterality. Molecular and morphometric analysis indicate high levels of progenitor multipotency, with an individual progenitor capable of producing several molecularly and morphologically distinct neuron types, as well as astrocytes. These findings redefine spinal cord development as a process in which lineage variability — rather than rigid progenitor identity — drives the generation of cellular diversity. acknowledged_ssus: - _id: PreCl - _id: Bio acknowledgement: "We would like to thank Elizabeth Marin, Anna Kicheva, Igor Adameyko, and James Briscoe as\r\nwell as members of the Sweeney and Hippemeyer labs and SFB consortium for comments on\r\nthe manuscript. We are also grateful for the technical support of the Preclinical and Imaging and\r\nOptics Facilities support teams (ISTA). In addition, we thank our funding sources for providing\r\nthe resources to do these experiments: Horizon Europe ERC Starting Grant Number 101041551\r\n(M.S.; L.B.S.); Special Research Program (SFB) of the Austrian Science Fund (FWF)\r\nNeuroStem Modulation Project numbers F7814-B (S.A.G.; M.S.; G.S.; and L.B.S.) and F7805\r\n(G.C. and S.H.). S.A.G is supported by a Boehringer Ingelheim Fonds PhD Fellowship, F.D.S.N.\r\nby an Institute of Science and Technology Austria (ISTA) GROW fellowship, and G.C. by an\r\nISTA Plus postdoctoral fellowship from the European Commission. S.H./L.B.S. and G.C. were\r\nadditionally supported by institutional funds from the ISTA and the University of Exeter,\r\nrespectively. " article_processing_charge: No author: - first_name: Sophie A full_name: Gobeil, Sophie A id: 2f3e9efb-eb24-11ec-86b2-88efb11d59fa last_name: Gobeil - first_name: Francisco full_name: Da Silveira Neto, Francisco id: 8cfb7412-10a7-11f1-add1-82b44e6418f2 last_name: Da Silveira Neto - first_name: Giulia full_name: Silvestrelli, Giulia id: 12632ae8-799e-11ef-94a2-e5a3b5ef49e9 last_name: Silvestrelli - first_name: Matthijs Geert full_name: Smits, Matthijs Geert id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0 last_name: Smits - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Gobeil SA, Da Silveira Neto F, Silvestrelli G, et al. Lineage origin of spinal cord cell type diversity. bioRxiv. doi:10.64898/2026.02.12.705305 apa: Gobeil, S. A., Da Silveira Neto, F., Silvestrelli, G., Smits, M. G., Streicher, C., Cheung, G. T., … Sweeney, L. B. (n.d.). Lineage origin of spinal cord cell type diversity. bioRxiv. https://doi.org/10.64898/2026.02.12.705305 chicago: Gobeil, Sophie A, Francisco Da Silveira Neto, Giulia Silvestrelli, Matthijs Geert Smits, Carmen Streicher, Giselle T Cheung, Simon Hippenmeyer, and Lora B. Sweeney. “Lineage Origin of Spinal Cord Cell Type Diversity.” BioRxiv, n.d. https://doi.org/10.64898/2026.02.12.705305. ieee: S. A. Gobeil et al., “Lineage origin of spinal cord cell type diversity,” bioRxiv. . ista: Gobeil SA, Da Silveira Neto F, Silvestrelli G, Smits MG, Streicher C, Cheung GT, Hippenmeyer S, Sweeney LB. Lineage origin of spinal cord cell type diversity. bioRxiv, 10.64898/2026.02.12.705305. mla: Gobeil, Sophie A., et al. “Lineage Origin of Spinal Cord Cell Type Diversity.” BioRxiv, doi:10.64898/2026.02.12.705305. short: S.A. Gobeil, F. Da Silveira Neto, G. Silvestrelli, M.G. Smits, C. Streicher, G.T. Cheung, S. Hippenmeyer, L.B. Sweeney, BioRxiv (n.d.). corr_author: '1' date_created: 2026-02-17T11:36:20Z date_published: 2026-02-16T00:00:00Z date_updated: 2026-04-14T08:16:55Z day: '16' ddc: - '570' department: - _id: SiHi - _id: LoSw doi: 10.64898/2026.02.12.705305 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.64898/2026.02.12.705305 month: '02' oa: 1 oa_version: Preprint project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e grant_number: F7814 name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity' - _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 publication: bioRxiv publication_status: submitted status: public title: Lineage origin of spinal cord cell type diversity tmp: 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: gold _id: '14647' abstract: - lang: eng 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. " 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). " article_number: '101851' article_processing_charge: Yes article_type: original author: - first_name: Mahima full_name: Bose, Mahima last_name: Bose - first_name: Varun full_name: Suresh, Varun last_name: Suresh - first_name: Urvi full_name: Mishra, Urvi last_name: Mishra - first_name: Ishita full_name: Talwar, Ishita last_name: Talwar - first_name: Anuradha full_name: Yadav, Anuradha last_name: Yadav - first_name: Shiona full_name: Biswas, Shiona last_name: Biswas - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Shubha full_name: Tole, Shubha last_name: Tole citation: 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. eLife. 2025;13. doi:10.7554/elife.101851.3 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. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.101851.3 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.” ELife. eLife Sciences Publications, 2025. https://doi.org/10.7554/elife.101851.3. ieee: M. Bose et al., “Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway,” eLife, vol. 13. eLife Sciences Publications, 2025. 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. mla: Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” ELife, vol. 13, 101851, eLife Sciences Publications, 2025, doi:10.7554/elife.101851.3. short: M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, ELife 13 (2025). date_created: 2023-12-06T13:07:01Z date_published: 2025-03-14T00:00:00Z date_updated: 2025-05-14T11:41:52Z day: '14' ddc: - '570' department: - _id: SiHi doi: 10.7554/elife.101851.3 external_id: pmid: - '40085500' file: - access_level: open_access checksum: 64a6a6f86e24b21fe72c7a7fd6056fed content_type: application/pdf creator: dernst date_created: 2025-04-03T11:19:26Z date_updated: 2025-04-03T11:19:26Z file_id: '19467' file_name: 2025_eLife_Bose.pdf file_size: 17462771 relation: main_file success: 1 file_date_updated: 2025-04-03T11:19:26Z has_accepted_license: '1' intvolume: ' 13' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2025' ... --- OA_type: closed access _id: '18765' abstract: - lang: eng 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. acknowledged_ssus: - _id: Bio 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.' alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: 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. Lineage Tracing. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:10.1007/978-1-0716-4310-5_7' apa: 'Cheung, G. T., Pauler, F., & Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques & T. Lee (Eds.), Lineage Tracing (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-4310-5_7' 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 Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. https://doi.org/10.1007/978-1-0716-4310-5_7.' 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 Lineage Tracing, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.' 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).” Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:10.1007/978-1-0716-4310-5_7. 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. corr_author: '1' date_created: 2025-01-07T08:36:47Z date_published: 2025-01-03T00:00:00Z date_updated: 2025-04-14T07:43:46Z day: '03' department: - _id: SiHi doi: 10.1007/978-1-0716-4310-5_7 ec_funded: 1 editor: - first_name: Jorge full_name: Garcia-Marques, Jorge last_name: Garcia-Marques - first_name: Tzumin full_name: Lee, Tzumin last_name: Lee external_id: pmid: - '39745639' intvolume: ' 2886' language: - iso: eng month: '01' oa_version: None page: 139-151 place: New York, NY pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Lineage Tracing publication_identifier: eisbn: - '9781071643105' eissn: - 1940-6029 isbn: - '9781071643099' issn: - 1064-3745 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM) type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2886 year: '2025' ... --- OA_place: repository OA_type: green _id: '19717' abstract: - lang: eng 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. 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" article_processing_charge: No author: - first_name: I full_name: Varela-Martínez, I last_name: Varela-Martínez - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: J. full_name: Garcia-Marqués, J. last_name: Garcia-Marqués - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: M. full_name: Nieto, M. last_name: Nieto citation: 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. bioRxiv. 2025. doi:10.1101/2025.05.07.652665 apa: Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer, S., & Nieto, M. (2025). Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv. https://doi.org/10.1101/2025.05.07.652665 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.” BioRxiv, 2025. https://doi.org/10.1101/2025.05.07.652665. 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,” bioRxiv. 2025. ista: Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. 2025. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv, 10.1101/2025.05.07.652665. mla: Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” BioRxiv, 2025, doi:10.1101/2025.05.07.652665. short: I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (2025). date_created: 2025-05-20T10:19:29Z date_published: 2025-05-07T00:00:00Z date_updated: 2025-05-28T06:37:46Z day: '07' department: - _id: SiHi doi: 10.1101/2025.05.07.652665 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.07.652665 month: '05' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: published status: public title: Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '8616' 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. 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.' article_number: '5840' article_processing_charge: Yes article_type: original author: - first_name: Xiaofei full_name: Gao, Xiaofei last_name: Gao - first_name: Jun-Liszt full_name: Li, Jun-Liszt last_name: Li - first_name: Xingjun full_name: Chen, Xingjun last_name: Chen - first_name: Bo full_name: Ci, Bo last_name: Ci - first_name: Fei full_name: Chen, Fei last_name: Chen - first_name: Nannan full_name: Lu, Nannan last_name: Lu - first_name: Bo full_name: Shen, Bo last_name: Shen - first_name: Lijun full_name: Zheng, Lijun last_name: Zheng - first_name: Jie-Min full_name: Jia, Jie-Min last_name: Jia - first_name: Yating full_name: Yi, Yating last_name: Yi - first_name: Shiwen full_name: Zhang, Shiwen last_name: Zhang - first_name: Ying-Chao full_name: Shi, Ying-Chao last_name: Shi - first_name: Kaibin full_name: Shi, Kaibin last_name: Shi - first_name: Nicholas E full_name: Propson, Nicholas E last_name: Propson - first_name: Yubin full_name: Huang, Yubin last_name: Huang - first_name: Katherine full_name: Poinsatte, Katherine last_name: Poinsatte - first_name: Zhaohuan full_name: Zhang, Zhaohuan last_name: Zhang - first_name: Yuanlei full_name: Yue, Yuanlei last_name: Yue - first_name: Dale B full_name: Bosco, Dale B last_name: Bosco - first_name: Ying-mei full_name: Lu, Ying-mei last_name: Lu - first_name: Shi-bing full_name: Yang, Shi-bing last_name: Yang - first_name: Ralf H. full_name: Adams, Ralf H. last_name: Adams - first_name: Volkhard full_name: Lindner, Volkhard last_name: Lindner - first_name: Fen full_name: Huang, Fen last_name: Huang - first_name: Long-Jun full_name: Wu, Long-Jun last_name: Wu - first_name: Hui full_name: Zheng, Hui last_name: Zheng - first_name: Feng full_name: Han, Feng last_name: Han - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Ann M. full_name: Stowe, Ann M. last_name: Stowe - first_name: Bo full_name: Peng, Bo last_name: Peng - first_name: Marta full_name: Margeta, Marta last_name: Margeta - first_name: Xiaoqun full_name: Wang, Xiaoqun last_name: Wang - first_name: Qiang full_name: Liu, Qiang last_name: Liu - first_name: Jakob full_name: Körbelin, Jakob last_name: Körbelin - first_name: Martin full_name: Trepel, Martin last_name: Trepel - first_name: Hui full_name: Lu, Hui last_name: Lu - first_name: Bo O. full_name: Zhou, Bo O. last_name: Zhou - first_name: Hu full_name: Zhao, Hu last_name: Zhao - first_name: Wenzhi full_name: Su, Wenzhi last_name: Su - first_name: Robert M. full_name: Bachoo, Robert M. last_name: Bachoo - first_name: Woo-ping full_name: Ge, Woo-ping last_name: Ge citation: ama: Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. Nature Communications. 2025;16. doi:10.1038/s41467-025-60308-0 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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-60308-0 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.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-60308-0. ieee: X. Gao et al., “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” Nature Communications, vol. 16. Springer Nature, 2025. 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. mla: Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” Nature Communications, vol. 16, 5840, Springer Nature, 2025, doi:10.1038/s41467-025-60308-0. 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). date_created: 2020-10-06T08:58:59Z date_published: 2025-07-01T00:00:00Z date_updated: 2025-09-04T07:08:37Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1038/s41467-025-60308-0 ec_funded: 1 external_id: isi: - '001523450500035' file: - access_level: open_access checksum: f59748cb67232cfb210035d9aef60836 content_type: application/pdf creator: dernst date_created: 2025-07-07T09:52:46Z date_updated: 2025-07-07T09:52:46Z file_id: '19971' file_name: 2025_NatureComm_Gao.pdf file_size: 17018106 relation: main_file success: 1 file_date_updated: 2025-07-07T09:52:46Z has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Reduction of neuronal activity mediated by blood-vessel regression in the brain tmp: 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) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '19718' abstract: - lang: eng 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. 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. article_number: '103046' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Fabrizia full_name: Pipicelli, Fabrizia id: 649134fd-d012-11ed-8f82-db1e5050f9ba last_name: Pipicelli - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Pipicelli F, Villalba Requena A, Hippenmeyer S. How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex. Current Opinion in Neurobiology. 2025;93. doi:10.1016/j.conb.2025.103046 apa: 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. Elsevier. https://doi.org/10.1016/j.conb.2025.103046 chicago: Pipicelli, Fabrizia, Ana Villalba Requena, and Simon Hippenmeyer. “How Radial Glia Progenitor Lineages Generate Cell-Type Diversity in the Developing Cerebral Cortex.” Current Opinion in Neurobiology. Elsevier, 2025. https://doi.org/10.1016/j.conb.2025.103046. ieee: F. Pipicelli, A. Villalba Requena, and S. Hippenmeyer, “How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex,” Current Opinion in Neurobiology, vol. 93. Elsevier, 2025. 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.” Current Opinion in Neurobiology, vol. 93, 103046, Elsevier, 2025, doi:10.1016/j.conb.2025.103046. short: F. Pipicelli, A. Villalba Requena, S. Hippenmeyer, Current Opinion in Neurobiology 93 (2025). corr_author: '1' date_created: 2025-05-20T10:20:09Z date_published: 2025-08-01T00:00:00Z date_updated: 2025-12-30T10:54:14Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.conb.2025.103046 external_id: isi: - '001496227000001' pmid: - '40383049' file: - access_level: open_access checksum: 05bacb4acbe6275d43e873dec9ba1d52 content_type: application/pdf creator: dernst date_created: 2025-12-30T08:25:49Z date_updated: 2025-12-30T08:25:49Z file_id: '20894' file_name: 2025_CurrentOpNeurobiology_Pipicelli.pdf file_size: 1592649 relation: main_file success: 1 file_date_updated: 2025-12-30T08:25:49Z has_accepted_license: '1' intvolume: ' 93' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _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 - _id: 7c084566-9f16-11ee-852c-c88a1dbbf1cf grant_number: ALTF 994-2023 name: Role of cell lineage in generating cell-type diversity in developing neocortex’ publication: Current Opinion in Neurobiology publication_identifier: issn: - 0959-4388 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2025' ... --- OA_place: repository OA_type: green _id: '19762' 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. 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)." article_processing_charge: No author: - first_name: Adrián full_name: Cárdenas, Adrián last_name: Cárdenas - first_name: Irem full_name: Çelik, Irem last_name: Çelik - first_name: Alexandre full_name: Espinós, Alexandre last_name: Espinós - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Lara full_name: López-González, Lara last_name: López-González - first_name: Lucia full_name: del-Valle-Anton, Lucia last_name: del-Valle-Anton - first_name: Virginia full_name: Fernández, Virginia last_name: Fernández - first_name: Salma full_name: Amin, Salma last_name: Amin - first_name: Enrico full_name: Negri, Enrico last_name: Negri - first_name: Eduardo Fernández full_name: Ortuño, Eduardo Fernández last_name: Ortuño - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Víctor full_name: Borrell, Víctor last_name: Borrell citation: ama: Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv. doi:10.1101/2025.05.22.655488 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. bioRxiv. https://doi.org/10.1101/2025.05.22.655488 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.” BioRxiv, n.d. https://doi.org/10.1101/2025.05.22.655488. ieee: A. Cárdenas et al., “Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development,” bioRxiv. . 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, 10.1101/2025.05.22.655488. mla: Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” BioRxiv, doi:10.1101/2025.05.22.655488. 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.). date_created: 2025-05-29T10:45:55Z date_published: 2025-05-23T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '23' department: - _id: SiHi doi: 10.1101/2025.05.22.655488 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.05.22.655488 month: '05' oa: 1 oa_version: Preprint project: - _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 publication: bioRxiv publication_status: submitted status: public title: Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development tmp: 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) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- _id: '14794' abstract: - lang: eng 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" acknowledged_ssus: - _id: Bio - _id: PreCl 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. article_number: '102795' article_processing_charge: Yes article_type: review author: - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. 2024;5(1). doi:10.1016/j.xpro.2023.102795 apa: Hansen, A. H., & Hippenmeyer, S. (2024). Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102795 chicago: Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102795. ieee: A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers,” STAR Protocols, 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. mla: Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 5, no. 1, 102795, Elsevier, 2024, doi:10.1016/j.xpro.2023.102795. short: A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-01-14T23:00:56Z date_published: 2024-03-15T00:00:00Z date_updated: 2025-04-15T07:32:40Z day: '15' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2023.102795 external_id: pmid: - '38165800' file: - access_level: open_access checksum: 4644d537451c5c114a9d7c7829b65bba content_type: application/pdf creator: dernst date_created: 2024-07-16T12:04:46Z date_updated: 2024-07-16T12:04:46Z file_id: '17264' file_name: 2024_STARProtoc_Hansen.pdf file_size: 3758943 relation: main_file success: 1 file_date_updated: 2024-07-16T12:04:46Z has_accepted_license: '1' intvolume: ' 5' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular mechanisms of radial neuronal migration publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - relation: software url: http://github.com/hippenmeyerlab scopus_import: '1' status: public title: Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- _id: '12875' 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. acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: LifeSc - _id: PreCl 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. " article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Thomas full_name: Krausgruber, Thomas last_name: Krausgruber - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Martin full_name: Schrammel, Martin id: f13e7cae-e8bd-11ed-841a-96dedf69f46d last_name: Schrammel - first_name: Natalie Y full_name: Özgen, Natalie Y id: e68ece33-f6e0-11ea-865d-ae1031dcc090 last_name: Özgen - first_name: Alexis full_name: Ivec, Alexis id: 1d144691-e8be-11ed-9b33-bdd3077fad4c last_name: Ivec - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009 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. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009 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.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009. ieee: G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024. 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. mla: Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009. 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. corr_author: '1' date_created: 2023-04-27T09:41:48Z date_published: 2024-01-17T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '17' ddc: - '570' department: - _id: SiHi - _id: RySh doi: 10.1016/j.neuron.2023.11.009 external_id: isi: - '001163937900001' pmid: - '38096816' file: - access_level: open_access checksum: 32b3788f7085cf44a84108d8faaff3ce content_type: application/pdf creator: dernst date_created: 2024-02-06T13:56:15Z date_updated: 2024-02-06T13:56:15Z file_id: '14944' file_name: 2024_Neuron_Cheung.pdf file_size: 5942467 relation: main_file success: 1 file_date_updated: 2024-02-06T13:56:15Z has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 230-246.e11 pmid: 1 project: - _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 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/the-pedigree-of-brain-cells/ scopus_import: '1' status: public title: Multipotent progenitors instruct ontogeny of the superior colliculus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2024' ... --- _id: '14683' 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" acknowledged_ssus: - _id: Bio - _id: PreCl 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. article_number: '102771' article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 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. STAR Protocols. 2024;5(1). doi:10.1016/j.xpro.2023.102771 apa: Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771 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.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102771. 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,” STAR Protocols, 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. mla: Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols, vol. 5, no. 1, 102771, Elsevier, 2024, doi:10.1016/j.xpro.2023.102771. short: N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2023-12-13T11:48:05Z date_published: 2024-03-15T00:00:00Z date_updated: 2025-04-15T08:23:06Z day: '15' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2023.102771 ec_funded: 1 external_id: pmid: - '38070137' file: - access_level: open_access checksum: 3f0ee62e04bf5a44b45b035662826e95 content_type: application/pdf creator: dernst date_created: 2024-07-16T11:50:03Z date_updated: 2024-07-16T11:50:03Z file_id: '17260' file_name: 2024_STARProtoc_Amberg.pdf file_size: 8871807 relation: main_file success: 1 file_date_updated: 2024-07-16T11:50:03Z has_accepted_license: '1' intvolume: ' 5' issue: '1' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Neuroscience language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T01031 name: Role of Eed in neural stem cell lineage progression - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 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 - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: STAR Protocols publication_identifier: issn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- APC_amount: 804 EUR OA_place: publisher OA_type: gold _id: '17187' 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" acknowledged_ssus: - _id: Bio - _id: PreCl 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). article_number: '103157' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103157 apa: Cheung, G. T., Streicher, C., & Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103157 chicago: Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103157. ieee: G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024. 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. mla: Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols, vol. 5, no. 3, 103157, Elsevier, 2024, doi:10.1016/j.xpro.2024.103157. short: G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-06-30T22:01:04Z date_published: 2024-09-20T00:00:00Z date_updated: 2025-12-30T10:54:11Z day: '20' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2024.103157 ec_funded: 1 external_id: pmid: - '38935508' file: - access_level: open_access checksum: d8a8cdba82a394e731aa699ace1ae433 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:12:40Z date_updated: 2025-01-09T12:12:40Z file_id: '18809' file_name: 2024_STARProtoc_Cheung.pdf file_size: 5186071 relation: main_file success: 1 file_date_updated: 2025-01-09T12:12:40Z has_accepted_license: '1' intvolume: ' 5' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 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 publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice tmp: 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) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- APC_amount: 804 EUR OA_place: publisher OA_type: gold _id: '17232' 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" acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: PreCl 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). article_number: '103168' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: 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. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168 apa: Cheung, G. T., 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. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168 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.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168. 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,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024. 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. mla: Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols, vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168. short: G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-07-14T22:01:10Z date_published: 2024-09-20T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '20' ddc: - '570' department: - _id: SiHi - _id: PreCl doi: 10.1016/j.xpro.2024.103168 external_id: pmid: - '38968076' file: - access_level: open_access checksum: 464f52ecc6ec92f509552823bb82bf79 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:16:53Z date_updated: 2025-01-09T12:16:53Z file_id: '18810' file_name: 2024_STARProtoc_Cheung2.pdf file_size: 6445556 relation: main_file success: 1 file_date_updated: 2025-01-09T12:16:53Z has_accepted_license: '1' intvolume: ' 5' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _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 publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq tmp: 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) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- _id: '17425' 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. acknowledged_ssus: - _id: Bio 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. alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Osvaldo full_name: Miranda, Osvaldo id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425 last_name: Miranda orcid: 0000-0001-6618-6889 - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: 'Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. Neuronal Morphogenesis. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:10.1007/978-1-0716-3969-6_19' apa: 'Miranda, O., Cheung, G. T., & Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), Neuronal Morphogenesis (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-3969-6_19' chicago: 'Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3969-6_19.' ieee: 'O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in Neuronal Morphogenesis, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.' 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.' mla: Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:10.1007/978-1-0716-3969-6_19. 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. corr_author: '1' date_created: 2024-08-13T12:16:41Z date_published: 2024-08-13T00:00:00Z date_updated: 2026-04-07T12:32:35Z day: '13' department: - _id: GradSch - _id: SiHi doi: 10.1007/978-1-0716-3969-6_19 edition: '1' editor: - first_name: Kazuhito full_name: Toyooka, Kazuhito last_name: Toyooka external_id: pmid: - '39134857' intvolume: ' 2831' language: - iso: eng month: '08' oa_version: None page: 283-299 place: New York, NY pmid: 1 project: - _id: 34c9fbcb-11ca-11ed-8bc3-98fa5658610d grant_number: '26253' name: Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development - _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 publication: Neuronal Morphogenesis publication_identifier: eisbn: - '9781071639696' eissn: - 1940-6029 isbn: - '9781071639689' issn: - 1064-3745 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20212' relation: dissertation_contains status: public scopus_import: '1' series_title: MIMB status: public title: Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2831 year: '2024' ... --- OA_place: publisher OA_type: free access _id: '12542' abstract: - lang: eng text: In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo. article_processing_charge: No article_type: letter_note author: - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006 apa: Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006 chicago: Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006. ieee: A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023. ista: Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293. mla: Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006. short: A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293. corr_author: '1' date_created: 2023-02-12T23:00:58Z date_published: 2023-02-01T00:00:00Z date_updated: 2025-06-25T06:24:25Z day: '01' department: - _id: SiHi doi: 10.1016/j.neuron.2023.01.006 external_id: isi: - '000994473300001' pmid: - '36731425' intvolume: ' 111' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2023.01.006 month: '02' oa: 1 oa_version: Published Version page: 291-293 pmid: 1 publication: Neuron publication_identifier: eissn: - 1097-4199 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Going back in time with TEMPO type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2023' ... --- _id: '12562' abstract: - lang: eng text: Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons. acknowledgement: The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University. article_processing_charge: No article_type: original author: - first_name: David R. full_name: Ladle, David R. last_name: Ladle - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 2023;129(3):501-512. doi:10.1152/jn.00172.2022 apa: Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022 chicago: Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022. ieee: D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023. ista: Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512. mla: Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:10.1152/jn.00172.2022. short: D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512. date_created: 2023-02-15T14:46:14Z date_published: 2023-03-01T00:00:00Z date_updated: 2024-10-21T06:01:28Z day: '01' department: - _id: SiHi doi: 10.1152/jn.00172.2022 external_id: isi: - '000957721600001' pmid: - '36695533' intvolume: ' 129' isi: 1 issue: '3' keyword: - Physiology - General Neuroscience language: - iso: eng month: '03' oa_version: None page: 501-512 pmid: 1 publication: Journal of Neurophysiology publication_identifier: eissn: - 1522-1598 issn: - 0022-3077 publication_status: published publisher: American Physiological Society quality_controlled: '1' scopus_import: '1' status: public title: Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 129 year: '2023' ... --- _id: '14757' abstract: - lang: eng text: The cerebral cortex is comprised of a vast cell-type diversity sequentially generated by cortical progenitor cells. Faithful progenitor lineage progression requires the tight orchestration of distinct molecular and cellular mechanisms regulating proper progenitor proliferation behavior and differentiation. Correct execution of developmental programs involves a complex interplay of cell intrinsic and tissue-wide mechanisms. Many studies over the past decades have been able to determine a plethora of genes critically involved in cortical development. However, only a few made use of genetic paradigms with sparse and global gene deletion to probe cell-autonomous vs. tissue-wide contribution. In this chapter, we will elaborate on the importance of dissecting the cell-autonomous and tissue-wide mechanisms to gain a precise understanding of gene function during radial glial progenitor lineage progression. article_processing_charge: No author: - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: 'Villalba Requena A, Amberg N, Hippenmeyer S. Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Huttner W, ed. Neocortical Neurogenesis in Development and Evolution. Wiley; 2023:169-191. doi:10.1002/9781119860914.ch10' apa: Villalba Requena, A., Amberg, N., & Hippenmeyer, S. (2023). Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution (pp. 169–191). Wiley. https://doi.org/10.1002/9781119860914.ch10 chicago: Villalba Requena, Ana, Nicole Amberg, and Simon Hippenmeyer. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” In Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, 169–91. Wiley, 2023. https://doi.org/10.1002/9781119860914.ch10. ieee: A. Villalba Requena, N. Amberg, and S. Hippenmeyer, “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression,” in Neocortical Neurogenesis in Development and Evolution, W. Huttner, Ed. Wiley, 2023, pp. 169–191. ista: 'Villalba Requena A, Amberg N, Hippenmeyer S. 2023.Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Neocortical Neurogenesis in Development and Evolution. , 169–191.' mla: Villalba Requena, Ana, et al. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, Wiley, 2023, pp. 169–91, doi:10.1002/9781119860914.ch10. short: A. Villalba Requena, N. Amberg, S. Hippenmeyer, in:, W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution, Wiley, 2023, pp. 169–191. corr_author: '1' date_created: 2024-01-08T13:16:36Z date_published: 2023-08-08T00:00:00Z date_updated: 2024-10-09T21:07:46Z day: '08' department: - _id: SiHi doi: 10.1002/9781119860914.ch10 editor: - first_name: Wieland full_name: Huttner, Wieland last_name: Huttner language: - iso: eng month: '08' oa_version: None page: 169-191 publication: Neocortical Neurogenesis in Development and Evolution publication_identifier: eisbn: - '9781119860914' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12679' abstract: - lang: eng text: How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression. acknowledgement: "I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA 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 agree-ment no. 725780 LinPro) to SH." article_number: '102695' article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: 'Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4). doi:10.1016/j.conb.2023.102695' apa: 'Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2023.102695' chicago: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology. Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695.' ieee: 'S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” Current Opinion in Neurobiology, vol. 79, no. 4. Elsevier, 2023.' ista: 'Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.' mla: 'Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol. 79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.' short: S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023). corr_author: '1' date_created: 2023-02-26T12:24:21Z date_published: 2023-04-01T00:00:00Z date_updated: 2025-04-15T08:23:06Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.conb.2023.102695 ec_funded: 1 external_id: isi: - '000953497700001' pmid: - '36842274' file: - access_level: open_access checksum: 4d11c4ca87e6cbc4d2ac46d3225ea615 content_type: application/pdf creator: dernst date_created: 2023-08-16T12:29:06Z date_updated: 2023-08-16T12:29:06Z file_id: '14071' file_name: 2023_CurrentOpinionNeurobio_Hippenmeyer.pdf file_size: 1787894 relation: main_file success: 1 file_date_updated: 2023-08-16T12:29:06Z has_accepted_license: '1' intvolume: ' 79' isi: 1 issue: '4' keyword: - General Neuroscience language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _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 - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Current Opinion in Neurobiology publication_identifier: issn: - 0959-4388 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Principles of neural stem cell lineage progression: Insights from developing cerebral cortex' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 79 year: '2023' ... --- _id: '12802' abstract: - lang: eng text: Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction. acknowledged_ssus: - _id: PreCl - _id: EM-Fac - _id: Bio - _id: LifeSc acknowledgement: We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Daniel full_name: Malzl, Daniel last_name: Malzl - first_name: Maria full_name: Gerykova Bujalkova, Maria last_name: Gerykova Bujalkova - first_name: Mateja full_name: Smogavec, Mateja last_name: Smogavec - first_name: Lena A. full_name: Schwarz, Lena A. last_name: Schwarz - first_name: Sarah full_name: Gorkiewicz, Sarah id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f last_name: Gorkiewicz - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Christian full_name: Knittl-Frank, Christian last_name: Knittl-Frank - first_name: Marianna full_name: Tassinari, Marianna id: 7af593f1-d44a-11ed-bf94-a3646a6bb35e last_name: Tassinari - first_name: Nuno full_name: Maulide, Nuno last_name: Maulide - first_name: Thomas full_name: Rülicke, Thomas last_name: Rülicke - first_name: Jörg full_name: Menche, Jörg last_name: Menche - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037 apa: Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037 chicago: Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier, 2023. https://doi.org/10.1016/j.cell.2023.02.037. ieee: L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023. ista: Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25. mla: Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:10.1016/j.cell.2023.02.037. short: L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25. corr_author: '1' date_created: 2023-04-05T08:15:40Z date_published: 2023-04-27T00:00:00Z date_updated: 2026-04-14T08:34:36Z day: '27' ddc: - '570' department: - _id: SiHi - _id: GaNo doi: 10.1016/j.cell.2023.02.037 ec_funded: 1 external_id: isi: - '000991468700001' pmid: - '36996814' file: - access_level: open_access checksum: 47e94fbe19e86505b429cb7a5b503ce6 content_type: application/pdf creator: dernst date_created: 2023-05-02T09:26:21Z date_updated: 2023-05-02T09:26:21Z file_id: '12889' file_name: 2023_Cell_Knaus.pdf file_size: 15712841 relation: main_file success: 1 file_date_updated: 2023-05-02T09:26:21Z has_accepted_license: '1' intvolume: ' 186' isi: 1 issue: '9' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1950-1967.e25 pmid: 1 project: - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/feed-them-or-lose-them/ record: - id: '19557' relation: dissertation_contains status: public - id: '13107' relation: dissertation_contains status: public scopus_import: '1' status: public title: Large neutral amino acid levels tune perinatal neuronal excitability and survival tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 186 year: '2023' ...