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Comparison of three congruent patient-specific cell types for the modelling of a human genetic Schwann-cell disorder

Nature Biomedical Engineering volume 3, pages 571–582 (2019)Cite this article

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Abstract

Patient-specific human-induced pluripotent stem cells (hiPSCs) hold great promise for the modelling of genetic disorders. However, these cells display wide intra- and interindividual variations in gene expression, which makes distinguishing true-positive and false-positive phenotypes challenging. Data from hiPSC phenotypes and human embryonic stem cells (hESCs) harbouring the same disease mutation are also lacking. Here, we report a comparison of the molecular, cellular and functional characteristics of three congruent patient-specific cell types—hiPSCs, hESCs and direct-lineage-converted cells—derived from currently available differentiation and direct-reprogramming technologies for use in the modelling of Charcot−Marie−Tooth 1A, a human genetic Schwann-cell disorder featuring a 1.4 Mb chromosomal duplication. We find that the chemokines C−X−C motif ligand chemokine-1 (CXCL1) and macrophage chemoattractant protein-1 (MCP1) are commonly upregulated in all three congruent models and in clinical patient samples. The development of congruent models of a single genetic disease using somatic cells from a common patient will facilitate the search for convergent phenotypes.

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Fig. 1: Directed differentiation and prospective isolation of Schwann cells from hESCs.
Fig. 2: Modelling CMT1A with human Schwann cells from patient-derived hiPSCs.
Fig. 3: Development of congruent CMT1A disease models by employing different cell-fate manipulating methods.
Fig. 4: Validation of the converged CMT1A phenotype from congruent Schwann-cell models.
Fig. 5: Association between PMP22 gene dosage and inflammatory signatures.

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Data availability

All data supporting the results of this study are available within the Article and the Supplementary Information. RNA sequencing data from CMT1A and control hESC−SCPs, hiPSC−SCPs and hiNC−Schwann cells have been uploaded to GEO under accession code GSE85598.

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Acknowledgements

The work in the Lee lab was supported by grants from the Robertson Investigator Award from the New York Stem Cell Foundation (G.L.), the CMT Association (G.L.), the National Institutes of Health through grant no. R01NS093213 (G.L.), the Muscular Dystrophy Association (G.L.) and MSCRF/TEDCO (G.L.). We also acknowledge salary support from the Johns Hopkins MD/PhD program (B.M.-C.), the FARMS Fellowship (B.M.-C.), the Adrienne Helis Malvin Medical Research Foundation (G.L., Y.O.) and the GRDC Programme through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology (2017K1A4A3014959). The work in the Kim lab was supported by grants from Kyung Hee University in 2016 (KHU-20160535), the Korea Health Technology R&D Project through the KHIDI funded by the Ministry of Health & Welfare, the Republic of Korea (HI16C2216) and NRF grants funded by the Korean government (NRF-2017R1C1B3009321, NRF-2017M3C7A1047640 and NRF-2017M3A9E4047243). The work in the Baloh lab was supported by grant nos. RN3-06530 (California Institute for Regenerative Medicine) and NS097545 (National Institutes of Health). The work in the Studer lab was supported by the New York State Stem Cell Fund (G.L., K.E. and L.S.) and New York state stem cell science program (NYSTEM, contract C32599GG). The work in the Hoke lab was supported by MSCRF/TEDCO and the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation. The work in the Brandacher lab was supported by MSCRF/TEDCO.

Author information

Author notes

  1. Yohan Oh

    Present address: Department of Medicine, College of Medicine, Hanyang University, Seoul, South Korea

  2. Benjamin Lannon

    Present address: Boston IVF, Waltham, MA, USA

Authors and Affiliations

  1. Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Bipasha Mukherjee-Clavin, In Young Choi, Hotae Lim, Yohan Oh & Gabsang Lee

  2. Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Bipasha Mukherjee-Clavin, Ruifa Mi, Ahmet Hoke & Gabsang Lee

  3. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Ruifa Mi, Ahmet Hoke & Gabsang Lee

  4. Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Barbara Kern & Gerald Brandacher

  5. Department of Surgery, Charité−Universitätsmedizin, Berlin, Germany

    Barbara Kern

  6. Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA

    Benjamin Lannon & Kevin Eggan

  7. Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Benjamin Lannon

  8. Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA

    Kevin J. Kim, Shaughn Bell & Robert H. Baloh

  9. Department of Pathology, College of Medicine, Kyung Hee University, Seoul, South Korea

    Junho K. Hur, Omer Habib & Yong Jun Kim

  10. Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, South Korea

    Junho K. Hur, Young Hyun Che & Yong Jun Kim

  11. Data Science for Knowledge Creation Research Centre, Seoul National University, Seoul, South Korea

    Woochang Hwang

  12. Department of Neurology, Cedars−Sinai Medical Center, Los Angeles, CA, USA

    Robert H. Baloh

  13. Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA

    Lorenz Studer

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Contributions

R.H.B., G.B., A.H., L.S. and G.L. conceived the study. B.M.-C., Y.J.K., K.E., R.H.B., G.B., A.H. and L.S. designed the study. B.M.-C., Y.J.K., R.M., B. K., I.Y.C., H.L., Y.O., B.L., K.J.K., S.B., J.K.H., W.H., O.H., Y.H.C. and G.L. performed experiments. B.M.-C., Y.J.K., R.M., B. K., I.Y.C., H.L., Y.O., B.L., K.J.K., S.B., J.K.H., W.H., O.H., Y.H.C., L.S. and G.L. analysed the data. B.M.-C., Y.J.K. and G.L. contributed to the data assembly. B.M.-C., Y.J.K. and G.L. interpreted the results. B.M.-C., Y.J.K. and G.L. wrote the manuscript.

Corresponding authors

Correspondence to Yong Jun Kim or Gabsang Lee.

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Supplementary information

Supplementary Information

Supplementary figures and table captions.

Reporting Summary

Supplementary Table 1

Unfiltered microarray results for CMT1A versus control hiPSC-derived Schwann cells.

Supplementary Table 2

Detailed data characterizing the original patient and embryonic sources of the fibroblasts and hESCs used.

Supplementary Table 3

RNA-sequencing data from control hESC-derived, hiPSC-derived and hiNC-derived Schwann cells, analysed with conventional methodologies and DAVID.

Supplementary Table 4

RNA-sequencing data from control hESC-derived, hiPSC-derived and hiNC-derived Schwann cells, analyzed with ‘power kit’ methodology and DAVID.

Supplementary Table 5

RNA-sequencing data evaluated for differentially expressed genes between CMT1A versus control cells from hESC-derived, hiPSC-derived and hiNC-derived Schwann cells. Analysed with DAVID and filtered for inflammation-related categories.

Supplementary Table 6

RNA-sequencing data evaluated for differentially expressed genes between CMT1A versus control cells from hESC-derived, hiPSC-derived and hiNC-derived Schwann cells. Analysed with Ingenuity Pathway Analysis in search of candidate pathologic pathways.

Supplementary Table 7

Cytokine-array results from hESC-derived, hiPSC-derived and hiNC-derived Schwann cells.

Supplementary Table 8

List of qRT-PCR primers used.

Supplementary Table 9

List of primary antibodies used.

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Mukherjee-Clavin, B., Mi, R., Kern, B. et al. Comparison of three congruent patient-specific cell types for the modelling of a human genetic Schwann-cell disorder. Nat Biomed Eng 3, 571–582 (2019). https://doi.org/10.1038/s41551-019-0381-8

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