Malformations of the human cortex represent a major cause of disability1. Mouse models with mutations in known causal genes only partially recapitulate the phenotypes and are therefore not unlimitedly suited for understanding the molecular and cellular mechanisms responsible for these conditions2. Here we study periventricular heterotopia (PH) by analyzing cerebral organoids derived from induced pluripotent stem cells (iPSCs) of patients with mutations in the cadherin receptor–ligand pair DCHS1 and FAT4 or from isogenic knockout (KO) lines1,3. Our results show that human cerebral organoids reproduce the cortical heterotopia associated with PH. Mutations in DCHS1 and FAT4 or knockdown of their expression causes changes in the morphology of neural progenitor cells and result in defective neuronal migration dynamics only in a subset of neurons. Single-cell RNA-sequencing (scRNA-seq) data reveal a subpopulation of mutant neurons with dysregulated genes involved in axon guidance, neuronal migration and patterning. We suggest that defective neural progenitor cell (NPC) morphology and an altered navigation system in a subset of neurons underlie this form of PH.

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Data availability

The scRNA-seq data used in this study have been deposited in the Gene Expression Omnibus under accession number GSE124031. All relevant accession codes are provided. Further details on the methods can be found in the Life Sciences Reporting Summary. Additional data that support the findings of this study are available from the corresponding author upon reasonable request.

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We thank the families participating in this study for their involvement. We thank Y. Lu for help generating the microRNAs, M. Karow and I. Buchsbaum for helping with experiments and fruitful discussions in the lab, T. Öztürk for excellent technical support, A. Weigert for organoid culture, J. Kageyama for helping with data processing, R. Snabel for helping with Smart-seq2 libraries, the Core Unit Flow Cytometry at the Zentrum für Infektionsmedizin (veterinary faculty of the University of Leipzig) and the Core Unit Qualitätsmanagement/Technologieplattform at the Sächsischer Inkubator für Klinische Translation (SIKT) in Leipzig for karyotyping. This work was supported by funding from the DFG CA1205/2-1 (S.C.), ForIPS (M.G.), by the Max Planck Society (S.C., B.T.), by the Boehringer Ingelheim Fonds (S.K.), by the Health Research Council of NZ and Curekids (S.P.R.) and by an ERC Starting Grant (B.T.).

Author information

Author notes

  1. These authors contributed equally: Johannes Klaus, Sabina Kanton, Christina Kyrousi.


  1. Max Planck Institute of Psychiatry, Munich, Germany

    • Johannes Klaus
    • , Christina Kyrousi
    • , Ane Cristina Ayo-Martin
    • , Rossella Di Giaimo
    • , Chiara Tocco
    • , Mariana Schroeder
    •  & Silvia Cappello
  2. Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

    • Sabina Kanton
    • , Stephan Riesenberg
    • , J. Gray Camp
    • , Malgorzata Santel
    •  & Barbara Treutlein
  3. International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Munich, Germany

    • Ane Cristina Ayo-Martin
  4. Department of Biology, University of Naples Federico II, Naples, Italy

    • Rossella Di Giaimo
  5. Department of Women’s and Children’s Health, University of Otago, Dunedin, New Zealand

    • Adam C. O’Neill
    •  & Stephen P. Robertson
  6. Institute of Stem Cell Research, Helmholtz Center Munich, Munich, Germany

    • Adam C. O’Neill
    •  & Magdalena Götz
  7. Institute of Stem Cell Research, iPSC Core Facility, Helmholtz Center Munich, Munich, Germany

    • Ejona Rusha
    •  & Micha Drukker
  8. Ludwig Maximilian University, Munich, Germany

    • Magdalena Götz
  9. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

    • Barbara Treutlein
  10. Technical University Munich, Department of Biosciences, Freising, Germany

    • Barbara Treutlein


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S.C. conceived and designed the research project, J.K., S.K., C.K., A.C.A.-M., R.D.G., S.R., A.C.O., C.T., M. Santel. and E.R. performed experiments and collected data, J.K., C.K., S.K., J.G.C., M. Schroeder, B.T. and S.C. analyzed data, M.D. reprogrammed patients’ samples, M.G. was involved in the start of the project, contributed to data discussion and supervision of J.K. S.P.R. was involved in patient sample collection and critical discussion, J.K., S.K., C.K., B.T. and S.C. wrote the manuscript. All authors provided ongoing critical review of results and commented on the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Barbara Treutlein or Silvia Cappello.

Extended data

  1. Extended Data Fig. 1 Expression of DCHS1 and FAT4 in cerebral organoids and temporal development of DCHS1- and FAT4-mutant organoids.

    a, Axial T1 image demonstrating laminar PH lining the occipital horns and peritrigonal region of the ventricles (arrows). b, Axial T2 demonstrating linear lesions iso-intense with cortical gray matter adjacent to the lateral walls of the bodies of the lateral ventricles2. c, Schematic representation of the main experimental approach used. d, Timeline of the organoid generation. EBs, embryoid bodies; hESC, low-bFGF human embryonic stem cell medium; NIM, neural induction medium; Y, Rock inhibitor; NDM, neural differentiation medium; +/– A: B27 supplement with or without vitamin; IHC, immunohistochemistry; RNA-seq, RNA sequencing. eh′, Detection of DCHS1 and FAT4 by in situ hybridization, b = 2, o = 5 per condition. i,j, mRNA expression of DCHS1 and FAT4 in single cells (c = 316) derived from control organoids, showing similar expression patterns between DCHS1 and FAT4 but often in different cells. i, Cells (columns) are ordered based on their PC 2 loading, corresponding to the trajectory from NPCs to neurons. Side bar shows maximal zone correlation for each single cell (ventricular zone, VZ, yellow; inner subventricular zone, iSVZ, orange; outer SVZ, oSVZ, red; cortical plate, CP, purple). j, Biplot showing transcript levels (in log2(FPKM)) of FAT4 (x axis) and DCHS1 (y axis) in 316 single cells of control organoids. k,l, Temporal development of patient-derived cerebral organoids compared with control organoids (o = 14 CTRL, 17 DCHS1, 17 FAT4); the diameters of organoids derived from DCHS1- and FAT4-mutant cells are slightly smaller compared to those of control organoids until day 12 (d12), shown in k. Significance based on two-way ANOVA, P = 0.000, Tukey HSD post hoc for multiple comparisons was performed for defining statistical differences between the three genotypes. Dotted lines highlight ventricles (V). Data in graphs are represented as mean ± s.e.m. Scale bars, 100 µm in eh,k. Source data

  2. Extended Data Fig. 2 Heterotopically located neurons in DCHS1 and FAT4-mutant and KO organoids.

    ac,ej,lo, Micrographs of sections of mutant or KO organoids immunostained as indicated in the panels. Note the mispositioning of neurons marked by arrows in mutant or in electroporated cerebral organoids. ac, b = 2, o = 6 per condition; ej, b = 2, o = 6 per condition; llʹʹʹ, b = 5, o = 15 per condition; mo, b = 5, o = 15 per condition. d, MAP2 fluorescence intensity measured only in the ventricular zones (VZ) (v = 6 CTRL, 18 DCHS1, 11 FAT4; significance based on one-way ANOVA, P = 0.0166, Tukey HSD post hoc for multiple comparisons for defining statistical differences between the three genotypes). k, Quantification measured by qPCR of the knockdown of DCHS1 and FAT4 by microRNAs (miRNA) against DCHS1 or FAT4, respectively (b = 2, independent cultures per time = 3 CTRL, 3 miRNA DCHS1, 3 miRNA FAT4, significance based on one-way ANOVA, P = 0.0377, Tukey HSD post hoc for multiple comparisons for defining statistical differences between the three genotypes) in SH-SY5Y cells 48 h after nucleofection. llʹʹʹ, Nodule of TUBB3+ neurons intermingling with NESTIN+ processes of NPCs in the germinal zone of DCHS1-mutant organoids. mo DCHS1- and FAT4-mutant organoids show changes in the morphology and thickness of their neuritis, as depicted by arrowheads. Dotted lines highlight ventricles (V). Data in graphs are represented as mean ± s.e.m. Scale bars, 100 µm in ac and ej and 30 µm in lo. Source data.

  3. Extended Data Fig. 3 Neural progenitor proliferation and signatures in mutant organoids.

    ai,km, Micrographs of sections of mutant cerebral organoids from day 20 immunostained for NESTIN (ac) and DCX (df) and from day 42 immunostained for PAX6 (gi) and PH3 (km). af, b = 1, o = 3 per condition; gi,km, b = 3, o = 9 per condition. j, Quantification of thickness of ventricular zone (VZ) and cortical plate (CP) structures in cerebral organoids (v = 6 CTRL, 11 DCHS1, 12 FAT4). n, Quantification of PH3+ cells per length of apical surface (o = 3, v = 23 CTRL, 41 DCHS1, 17 FAT4, F(2,80) = 2.41, P = 0.097, comparison between CTRL and FAT4 F(1,39) = 5.18, P = 0.029). o, Hierarchical clustering visualizing for all NPCs (338 single cells), expression of genes identified by PCA (top 50 positively and negatively correlating with PC 1) on all NPCs. p, Number of NPCs and neurons for each experiment shown in o. q, FACS plots depicting the definition of the sorting gates (secondary antibodies control) and sorting of KI67+ or DCX+ cells in control, DCHS1- and FAT4-mutant organoids (b = 2, o = 6 CTRL, 6 DCHS1, 3 FAT4). r,s, Z scores of the quantification of KI67+ cells (r) and DCX+ cells (s) from FACs analysis shown in q. Statistical analysis was performed using two-tailed Mann Whitney test. r, CTRL to DCHS1 P = 0.0022, CTRL to FAT4 P = 0.0238. s, CTRL to DCHS1 P = 0.0317, CTRL to FAT4 P = 0.0357. Results are mean ± s.e.m. (j,n) or z scores as mean ± s.e.m. (r,s). Dotted lines highlight ventricles (V). Scale bars, 30 µm for af and 50 µm for gm.Source data.

  4. Extended Data Fig. 4 Morphological changes in the NPCs upon DCHS1 and FAT4 deletion.

    ac, Micrographs of sections of KO cerebral organoids day 40 immunostained for NESTIN. Arrows indicate the disrupted morphology of NPCs (b,c). df, Micrographs of sections of control organoids electroporated with miRNA against DCHS1 or FAT4 at day 42 and analyzed at day 49. Arrows indicate the disrupted morphology upon downregulation of DCHS1 and FAT4 (e,f). ac, b = 2, o = 6 per condition; df, b = 2, o = 6 per condition. Dotted lines highlight ventricles (V). Scale bars, 30 µm.

  5. Extended Data Fig. 5 Apicobasal polarity in cerebral organoids.

    ac, Micrographs of sections of organoids (day 42) immunostained for ACETYLATED TUBULIN, b = 2, o = 6 per condition. d,e, Western blot and quantification of ACETYLATED TUBULIN (d) (independent cultures = 5 CTRL, 4 DCHS1, 4 FAT4, significance based on one sample two-tailed t test, P = 0.562 CTRL vs DCHS1, P = 0.013 CTRL vs FAT4) and TYROSINATED TUBULIN (e) (independent cultures = 3 CTRL, 3 DCHS1, 3 FAT4) levels in NPCs, significance based on one sample two-tailed t test, P = 0.967 CTRL vs DCHS1, P = 0.728 CTRL vs FAT4. fn,pr, Micrographs of sections of cerebral organoids (day 42) immunostained as indicated in the panels. fn,pr, b = 3, o = 9 per condition. o, Quantification of the distance from the apical surface (positive for β-CATENIN and PALS1) and DAPI+ nuclei of NPCs (v = 27 CTRL, 26 DCHS1, 26 FAT4; 5 different positions were measured and averaged for each ventricle; significance based on one-sample two-tailed t test, P = 0.0025 CTRL vs DCHS1, P = 0.001 CTRL vs FAT4). s, Ratio of ARL13B fluorescence intensity measured at the apical surface (cilia facing the ventricular lumen) and at basal position (all the rest of the cilia in the germinal and cortical zones) (b = 5, o = 15, v = 9 CTRL, 4 DCHS1, 14 FAT4, significance based on one-sample t test). Results are mean ± s.e.m. Dotted lines highlight ventricles (V). Scale bar, 50 µm (ac) and 20 µm (fr). Source data Source data

  6. Extended Data Fig. 6 2D time-lapse imaging experimental design and morphological changes of mutant neurons.

    a, Experimental design for 2D live imaging of migrating neurons. Neural progenitors were differentiated for 7 d and imaged for 3 d every 5 min. b, Quantification of the percentage of cells expressing DCX, MAP2 or both markers in neuronal cultures after 10 d in culture. ccʹʹ, Immunostaining for DoubleCortin (DCX), MAP2 (mature neurons) and VGLUT (glutamatergic neurons) in 2D neurons derived from control cells in monolayer culture, b = 3, independent cultures = 9 per condition. df, Immunostaining for TUBB3 in 2D neurons derived from control and mutant cells in monolayer culture, b = 3, independent cultures = 9 per condition. Results are mean ± s.e.m. Scale bar, 20 µm. Source data

  7. Extended Data Fig. 7 Characterization of mutant and KO organoid regions.

    al, Micrographs of sections of mutant and KO organoids immunostained as depicted in the panels. ac,gi, b = 3, o = 9 per condition; df,jl, b = 2, o = 6 per condition. m, Heat map showing expression of genes marking neurons in the cortex/forebrain (columns) for all neuronal cells from control and mutant organoids (rows, 467 single cells). Scale bar, 30 µm.

Supplementary information

  1. Reporting Summary

  2. Supplementary Tables 1–5

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  5. Source Data Extended Data Fig. 1

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