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Production of human spinal-cord organoids recapitulating neural-tube morphogenesis

Nature Biomedical Engineering volume 6, pages 435–448 (2022)Cite this article

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Abstract

Human spinal-cord-like tissues induced from human pluripotent stem cells are typically insufficiently mature and do not mimic the morphological features of neurulation. Here, we report a three-dimensional culture system and protocol for the production of human spinal-cord-like organoids (hSCOs) recapitulating the neurulation-like tube-forming morphogenesis of the early spinal cord. The hSCOs exhibited neurulation-like tube-forming morphogenesis, cellular differentiation into the major types of spinal-cord neurons as well as glial cells, and mature synaptic functional activities, among other features of the development of the spinal cord. We used the hSCOs to screen for antiepileptic drugs that can cause neural-tube defects. hSCOs may also facilitate the study of the development of the human spinal cord and the modelling of diseases associated with neural-tube defects.

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Fig. 1: Generation of hSCOs recapitulating neural tube morphogenesis.
Fig. 2: Transcriptome profiling of hSCOs.
Fig. 3: Acquisition of spinal-cord-like cell fate after long-term culture of hSCOs.
Fig. 4: Electrophysiological analysis and pharmacological response in hSCOs.
Fig. 5: Size and bFGF duration-dependent tube morphogenesis in hSCOs.
Fig. 6: Modelling of antiepileptic drug-induced neural tube defects in hSCOs using deep learning-based classification.

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Data availability

The main data supporting the results in this study are available within the paper and its Supplementary Information. Gene expression data are available in the Gene Expression Omnibus (GEO) under accession numbers GSE196573 (for single-cell RNA-sequencing data) and GSE157696 (for microarray data). Source data are provided with this paper.

Code availability

The code for training the deep learning models in this study is available at https://github.com/im-namwon/stemcell-classification.

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Acknowledgements

We would like to thank the Korea Basic Science Institute, Korea Brain Research Institute, K.-S. Yang and J. Na for their technical support. We especially thank SCREEN Holdings (Kyoto, Japan) and Kim & Friends (Seoul, Republic of Korea) for technical support utilizing the OCT instrument, Cell3iMager Estier. We also thank J. Hosung (Yonsei University) for his critical comments. This research was supported by the Brain Research Program through the National Research Foundation (NRF), which is funded by the Korean Ministry of Science, ICT and Future Planning (NRF-2015M3C7A1028790, NRF-2017M3C7A1047654, NRF-2017M3A9B3061308 and NRF-2021M3E5D9021368).

Author information

Authors and Affiliations

  1. Department of Anatomy, Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul, Republic of Korea

    Ju-Hyun Lee, Mohammed R. Shaker, Hyun Jung Kim, Si-Hyung Park, June Hoan Kim, Im Joo Rhyu, Hyun Kim & Woong Sun

  2. Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea

    Hyogeun Shin & Il-Joo Cho

  3. School of Electrical and Electronics Engineering, Yonsei University, Seoul, Republic of Korea

    Il-Joo Cho

  4. InterMinds Inc., Seongnam, Republic of Korea

    Namwon Lee

  5. Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea

    Minjin Kang & Dongho Geum

  6. Department of Bio-Information Science, Ewha Womans University, Seoul, Republic of Korea

    Subin Cho & Sanghyuk Lee

  7. Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Republic of Korea

    Tae Hwan Kwak & Dong Wook Han

  8. Department of Obstetrics and Gynecology, Chonnam National University Medical School, Gwangju, Republic of Korea

    Jong Woon Kim

  9. School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea

    Mi-Ryoung Song

  10. Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea

    Seung-Hae Kwon

  11. Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea

    Sanghyuk Lee

  12. Department of Physiology, Dental Research Institute, Seoul National University School of Dentistry, Seoul, Republic of Korea

    Se-Young Choi

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Contributions

J.-H.L. and W.S. conceived the project and designed the experiments. J.-H.L. performed most of the experiments, and analysed the data. H.S. performed electrophysiological experiments and analysed the data. M.R.S., H.J.K., S.-H.P., J.H.K., M.K. and T.H.K. performed the experiments. N.L. performed machine learning experiments. S.C. performed and interpreted bioinformatics analysis. J.W.K., M.-R.S., S.-H.K., D.W.H., S.L., S.-Y.C., I.J.R., H.K., D.G. and I.-J.C. provided the resource. S.L., S.-Y.C., D.G., I.-J.C. and W.S. designed the study. W.S. and J.H.L. wrote the manuscript. W.S. supervised and administered this project. All authors discussed the results and contributed to the revision of the manuscript.

Corresponding author

Correspondence to Woong Sun.

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Competing interests

N.L. is employed by InterMinds. The authors declare no other competing interests.

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Nature Biomedical Engineering thanks Agnete Kirkeby, Matthias Lutolf and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Generation of caudal NSCs from hiPSCs in 2D.

a. Caudal induction (SB + CHIR) of hiPSCs on 2D culture showed the induction of the NMP markers SOX2/BraT and CDX2, and then subsequent leading to the conversion of hiPSCs into N-cad positive neural stem cells. b. High-magnification images of NMPs on induction day 2. These cells showed co-expression of the representative NMP markers (SOX2, BraT and CDX2). c. Real-time PCR profiles of gene expression for neuromesoderm (BraT, NKX1.2, CDX2 and SOX2), pluripotency marker (OCT4 and NANOG), mesendoderm (MIXL1), mesoderm (TBX6), neuroectoderm (SOX1 and PAX6), and rostral neuroectoderm (OTX2). d. The E- to N-cadherin switch was present during 2D induction. Immunofluorescence analysis of E-cadherin (red), N-cadherin (green), and NANOG (white). Nuclei were counterstained with Hoechst (blue). e. Relative expression of the E- and N- cadherin mRNAs, depending on the days of differentiation. f. The maintenance of apical polarity from 2D to 3D culture. During the 3D conversion process, surface neuroepithelia cells re-established their polarity within 24 hours. Apical polarity was visualised with ZO1 immunolabeling (red). Nuclei were counterstained with Hoechst (blue). g. The pseudostratified morphology of NE cells on day 4 (bFGF, day 1). Note that the internal neural stem cells (SOX2 + ) exhibit distinct cell morphology. Cell morphologies were visualised with a small fraction of GFP-labelled cells initially mixed with non-labelled hPSCs. h. Absence of mesodermal cells in 3D spheres. The neuroepithelia cells were visualised with SOX2 (green) and the mesodermal cells were visualised with BraT or TBX6 (red) staining. Nuclei were counterstained with Hoechst (blue). Although BraT expression was observed in small number of organoids at early stages of culture (day 4), they were eventually disappeared (day 7). In addition, we failed to detect any TBX6-expressing mesodermal cells. These data suggested that our induction condition exclusively drove cells toward neural fates. Data were collected and analysed from three independent experiment samples. Data are expressed as mean ± SEM. Standard one-way ANOVA with Tukey’s multiple comparison test was used for multiple comparisons (c and e). All scale bars, 50 μm.

Source data

Extended Data Fig. 2 hSCOs mimicking neurulation morphogenesis in vivo.

a. Morphology of neural folds at different stages in epidermal fibroblast-derived hiPSCs (left) and H9 hESCs (right). b. Immunofluorescence staining showed the absence of floor plate cells (FOXA2), roof plate cells (LMX1A), and neural crest cells (SLUG, p75, SOX10 and FOXD3). c. Absence of non-neural tissue components in the hSCOs. The non-neural epithelium was visualised with E-cadherin (green) and the mesodermal tissue was visualised with BraT (red) staining. Developing mouse neural tube (bottom) is shown as a control. d. High-magnification image of the planar cell polarity (PCP) region. The right-bottom image shows traces of pMLC and ZO1 expression. e. Quantification of PCP with angular analysis of pMLC linearity (left) and ZO1 linearity (right). To measure the angles of pMLC and ZO1 cables, we selected a line linking two or more cells. Compared to ZO1 cables, the pMLC cables tended to align laterally. Data are represented as mean ± SD. f. The ratio of the medio-lateral (M-L) like axis (from 45 to 135 degrees) to the anterior-posterior (A-P) like axis (from 0 to 45 and from 135 to 180 degrees). Data are represented as mean ± SD. Unpaired student’s t-test was used for comparing two groups. g. Scanning electron microscopy (SEM) images of hSCOs at different stages of development. Note that the surfaces of the first spheroids were relatively smooth with strong tight junctions, while neural tube stage hSCOs had rough surfaces. All scale bars, 50 μm.

Source data

Extended Data Fig. 3 Characterization of the neural tube in hSCOs.

a. Interkinetic nuclear migration (IKNM) in hSCO on day 15. In neural tube, S-phase cells probed by EdU (green) incorporation were localised at the basal side, while M-phase cells labelled by phospho-histone H3 (p-H3, red) were located on the apical side of tube. The neural tube structure was visualised with SOX2 (blue). Scale bar, 100 µm. b. Representative images of IKNM in the neural tube. EdU pulse (15-min)-labelled cells moved toward the apical side over time, and then back to basal side. c. Quantification of p-H3+EdU+ cells per total p-H3+ cells in the neural tube. Data are expressed as mean ± SD. The number of analysed organoids (n) were summarised in Supplementary Table 5. d. Mitotic radial glia labelled with phospho-vimentin (red) were located on the apical side of the neural tube. The nuclei were counterstained with Hoechst (blue). e. The presence of primary cilia at apical side of the neural tube-like structure. Immunofluorescence for ARL13B (red) and γ-tubulin (green) detected the primary cilia and basal bodies, respectively. The nuclei were counterstained with Hoechst (blue). f. Double immunostaining for the neural stem cell marker SOX2 (red) and the neuroblast marker DCX (green). The outside of the neural tube was surrounded by early differentiated neuronal cells. All scale bars, 20 μm; except panels (a).

Source data

Extended Data Fig. 4 Effects of perturbation of apico-basal polarity on neural tube morphogenesis.

a. Treatment scheme of Y-27632 (Rock inhibitor; 10 μM) for panels (b). b. The effects of Y-27632 on the establishment of the neural plate. Note that the Y-27632 treatments disrupted apical localisation of ZO1. c. Treatment scheme of Y-27632 for panels (d). d. The effects of Y-27632 at the neural folding-stage. Note that the neural folding was not induced by the Y-27632 treatments, and the organoids exhibited round morphology. e. Treatment scheme for Matrigel-embedding experiments on panels (f). f. Matrigel embedding at the early neural plate-stage rapidly reversed the apical polarity, and promoted cavitation (by 72 hr). g. Treatment scheme for Matrigel-embedding experiments on panels (h-j). h. Matrigel embedding at the neural folding-stage also resulted in ventricle-like morphogenesis, as previously reported with forebrain organoids. i. 3D structure of the cavities in the Matrigel embedded-hSCO. The cavities were labelled with ZO1 staining. Note that the control hSCO exhibited highly connected central canal-like structure, and Matrigel embedded-hSCO exhibited short and isolated follicle-like structure12,13. j. Quantification of total cavities in individual organoids. Data are expressed as mean ± SD. Unpaired student’s t-test was used for comparing two groups. The number of analysed organoids (n) were summarised in Supplementary Table 5. The apical polarity at the neural plate or neural folding-stage was visualised with ZO1 (red) and the nuclei were counterstained with Hoechst (blue) in all panels. All scale bars, 50 μm.

Source data

Extended Data Fig. 5 Changes in the patterns of neural activities in hSCOs.

a-d. Representative heatmaps showing neural activities at Day 24 (a), Day 46 (b), Day 72 (c), and Day 140 (d). e-h. Representative cross-correlation matrices showing synchronisation between signal-recorded electrodes at Day 24 (e), Day 46 (f), Day 72 (g), and Day 140 (h). i-l. Changes in the patterns of burst activity as the hSCOs mature. Bar graphs represent mean ± SD in total spike number in burst activities (i), burst duration (j), inter burst interval (IBI) (k), and inter spike interval (ISI) in burst activities (l). Unpaired student’s t-test was used for comparing two groups. The number of analysed organoids (n) and the number of experiments (N) were summarised in Supplementary Table 5. m. Representative transient plot showing electrically evoked activities in matured hSCOs and expanded plots of the first and fifth stimulus.

Source data

Supplementary information

Supplementary Information

Supplementary figs., tables and video captions.

Reporting Summary

Peer Review Information

Supplementary Table 5

Number of analysed organoids (n) and number of experiments (N).

Supplementary Datasets

Source data for Supplementary Figs. 11, 12 and 14.

Supplementary Video 1

Live imaging of 3D conversion. Video related to Fig. 1a.

Supplementary Video 2

Live imaging of the hSCOs exhibiting neural tube closure. Video related to Fig. 1b.

Supplementary Video 3

Time-course images of neurulation-like morphogenesis in hSCOs. Video related to Fig. 1c.

Supplementary Video 4

Morphology of hinge cells. Video related to Fig. 1g.

Supplementary Video 5

Zippering-like morphogenesis in hSCO. Video related to Fig. 1l.

Supplementary Video 6

3D architecture of neural tube-stage hSCO. Video related to Fig. 1m.

Supplementary Video 7

Core-to-shell organization of hSCOs. Video related to Fig. 3a.

Supplementary Video 8

Comparison between dispase- and accutase-based protocols for 3D conversion. Video related to Supplementary Fig. 11.

Supplementary Video 9

3D neural tube morphology in 6 AEDs-treated hSCOs. Video related to Fig. 6e.

Source data

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Source Data Fig. 5

Source data for Fig. 5.

Source Data Fig. 6

Source data and statistics for Fig. 6.

Source Data Extended Data Fig. 1

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Source data for Extended Data Fig. 3.

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Source data for Extended Data Fig. 5.

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Lee, JH., Shin, H., Shaker, M.R. et al. Production of human spinal-cord organoids recapitulating neural-tube morphogenesis. Nat. Biomed. Eng 6, 435–448 (2022). https://doi.org/10.1038/s41551-022-00868-4

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  • DOI: https://doi.org/10.1038/s41551-022-00868-4

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