[{"publisher":"Springer Nature","date_created":"2026-07-13T09:47:21Z","PlanS_conform":"1","supplementarymaterial":"yes","OA_type":"hybrid","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"status":"public","pmid":1,"scopus_import":"1","day":"17","language":[{"iso":"eng"}],"ddc":["570"],"article_type":"original","citation":{"mla":"Schwarz, Lena A., et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” <i>Nature</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41586-026-10679-1\">10.1038/s41586-026-10679-1</a>.","ama":"Schwarz LA, Dotter C, Isaev S, et al. Cortical development dynamics across autism spectrum disorder mouse models. <i>Nature</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41586-026-10679-1\">10.1038/s41586-026-10679-1</a>","apa":"Schwarz, L. A., Dotter, C., Isaev, S., Lisi, M., Malzl, D., Büschl, C., … Novarino, G. (2026). Cortical development dynamics across autism spectrum disorder mouse models. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-026-10679-1\">https://doi.org/10.1038/s41586-026-10679-1</a>","ieee":"L. A. Schwarz <i>et al.</i>, “Cortical development dynamics across autism spectrum disorder mouse models,” <i>Nature</i>. Springer Nature, 2026.","short":"L.A. Schwarz, C. Dotter, S. Isaev, M. Lisi, D. Malzl, C. Büschl, S. Ladstätter, B. Oliveira, M. Barel, B. Basilico, C. Chintaluri, S. Gorkiewicz, M. Goudarzi, T. Belinova, S. Reichl, G. Sendžikaitė, S. Arcot Jayaram, P. Koppensteiner, C.M. Sommer, T.P. Vogels, J. Menche, I. Adameyko, P.V. Kharchenko, C. Bock, G. Novarino, Nature (2026).","chicago":"Schwarz, Lena A, Christoph Dotter, Sergey Isaev, Michela Lisi, Daniel Malzl, Christoph Büschl, Sabrina Ladstätter, et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” <i>Nature</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41586-026-10679-1\">https://doi.org/10.1038/s41586-026-10679-1</a>.","ista":"Schwarz LA, Dotter C, Isaev S, Lisi M, Malzl D, Büschl C, Ladstätter S, Oliveira B, Barel M, Basilico B, Chintaluri C, Gorkiewicz S, Goudarzi M, Belinova T, Reichl S, Sendžikaitė G, Arcot Jayaram S, Koppensteiner P, Sommer CM, Vogels TP, Menche J, Adameyko I, Kharchenko PV, Bock C, Novarino G. 2026. Cortical development dynamics across autism spectrum disorder mouse models. Nature."},"project":[{"grant_number":"101044865","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"name":"Neurobiology of anxiety in autism spectrum disorders","grant_number":"FG1803 49015","_id":"ebb38b5d-77a9-11ec-83b8-a42e08120a88"}],"department":[{"_id":"AnKi"},{"_id":"GaNo"},{"_id":"TiVo"},{"_id":"ScienComp"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"PreCl"}],"OA_place":"publisher","researchdata_availability":"yes","corr_author":"1","doi":"10.1038/s41586-026-10679-1","date_updated":"2026-07-13T12:58:19Z","title":"Cortical development dynamics across autism spectrum disorder mouse models","dataavailabilitystatement":"Single-nucleus multiomics data are available from the Gene Expression Omnibus (GSE328363). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). Single-cell data can be accessed and visualized through a CELLxGENE database (https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/.2026_Nature_Schwarz). Source data are provided with this paper. Scripts and analyses that support the main findings of this study are accessible in a GitHub repository (https://git.ista.ac.at/research-sofware/mouseome).","publication":"Nature","external_id":{"pmid":["42310454"]},"quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","type":"journal_article","oa_version":"Published Version","publication_status":"epub_ahead","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22295","has_accepted_license":"1","date_published":"2026-06-17T00:00:00Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"article_processing_charge":"Yes (via OA deal)","main_file_link":[{"url":"https://doi.org/10.1038/s41586-026-10679-1","open_access":"1"}],"abstract":[{"text":"Despite the functional diversity of over 100 causal genes1,2,3, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Lena A"},{"first_name":"Christoph","last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096"},{"full_name":"Isaev, Sergey","first_name":"Sergey","last_name":"Isaev"},{"full_name":"Lisi, Michela","id":"39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c","last_name":"Lisi","first_name":"Michela"},{"first_name":"Daniel","last_name":"Malzl","full_name":"Malzl, Daniel"},{"full_name":"Büschl, Christoph","last_name":"Büschl","first_name":"Christoph","id":"2a8c054c-0913-11ee-9159-f8ef515809ed"},{"last_name":"Ladstätter","first_name":"Sabrina","full_name":"Ladstätter, Sabrina"},{"first_name":"Bárbara","last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara"},{"first_name":"Matteo","last_name":"Barel","id":"8959927b-2236-11ed-bd6e-ea83d94ade0e","full_name":"Barel, Matteo"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette"},{"first_name":"Chaitanya","last_name":"Chintaluri","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","full_name":"Chintaluri, Chaitanya","orcid":"0000-0003-4252-1608"},{"full_name":"Gorkiewicz, Sarah","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","first_name":"Sarah","last_name":"Gorkiewicz"},{"full_name":"Goudarzi, Mohammad","last_name":"Goudarzi","first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tereza","last_name":"Belinova","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","full_name":"Belinova, Tereza"},{"last_name":"Reichl","first_name":"Stephan","full_name":"Reichl, Stephan"},{"full_name":"Sendžikaitė, Gintarė","last_name":"Sendžikaitė","first_name":"Gintarė","id":"dd6d52f2-c50d-11eb-9548-bcf0ff82b344"},{"full_name":"Arcot Jayaram, Satish","orcid":"0000-0002-2479-2669","id":"b0bbee33-09f7-11eb-909c-8b358058d28a","last_name":"Arcot Jayaram","first_name":"Satish"},{"full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner"},{"last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"},{"id":"0095641e-7eb7-11f1-8665-aec51a2ab5e0","last_name":"Kharchenko","first_name":"Peter Vasili","full_name":"Kharchenko, Peter Vasili"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"oa":1,"acknowledgement":"We thank F. Freeman, V. Voronin and M. Ladron de Guevara for technical assistance; A. Stichelberger and S. Liegenfeld for the management of our animal colony; M. Schunn, C. Gold and the Preclinical Facility team for technical assistance; C. Jansen and the Scientific Computing Facility for bioinformatics support and technical assistance; the Biomedical Sequencing Facility at CeMM for assistance with next-generation sequencing; and J. Lin and T. Krausgruber in the laboratory of C. Bock for support with flow cytometry; J. Kirchner for illustrating the multi-omics approach depicted in Fig. 1; and all members of the laboratory of G.N. for their support and discussions. This study was supported by the Scientific Service Units of ISTA through resources provided by the Imaging & Optics Facility and the Laboratory Support Facility. Bulk RNA-seq was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities, member of the Vienna BioCenter. This work was supported by a European Research Council Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the Austrian Science Fund (PE1028W1232 and PR1028FG1803) to G.N. Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2026"},{"scopus_import":"1","pmid":1,"article_type":"original","article_number":"7959","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"day":"17","ddc":["570"],"publisher":"Springer Nature","volume":13,"status":"public","date_created":"2023-05-19T11:12:25Z","doi":"10.1038/s41598-023-35162-z","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","date_updated":"2025-04-23T08:56:48Z","intvolume":"        13","external_id":{"pmid":["37198326"],"isi":["000995271600104"]},"file_date_updated":"2023-05-22T07:57:37Z","publication":"Scientific Reports","department":[{"_id":"Bio"}],"citation":{"ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>.","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” <i>Scientific Reports</i>, vol. 13, no. 1. Springer Nature, 2023.","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &#38; Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>"},"file":[{"checksum":"8c1b769693ff4288df8376e59ad1176d","relation":"main_file","date_created":"2023-05-22T07:57:37Z","file_size":3055077,"file_id":"13047","file_name":"2023_ScientificReports_Zavadakova.pdf","success":1,"access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2023-05-22T07:57:37Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13033","has_accepted_license":"1","date_published":"2023-05-17T00:00:00Z","type":"journal_article","quality_controlled":"1","oa_version":"Published Version","publication_status":"published","month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"first_name":"Anna","last_name":"Zavadakova","full_name":"Zavadakova, Anna"},{"full_name":"Vistejnova, Lucie","first_name":"Lucie","last_name":"Vistejnova"},{"last_name":"Belinova","first_name":"Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","full_name":"Belinova, Tereza"},{"full_name":"Tichanek, Filip","last_name":"Tichanek","first_name":"Filip"},{"last_name":"Bilikova","first_name":"Dagmar","full_name":"Bilikova, Dagmar"},{"first_name":"Peter R.","last_name":"Mouton","full_name":"Mouton, Peter R."}],"issue":"1","abstract":[{"text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.","lang":"eng"}],"acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","keyword":["Multidisciplinary"],"year":"2023","oa":1,"isi":1,"publication_identifier":{"issn":["2045-2322"]},"article_processing_charge":"No"}]