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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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.
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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.
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Supplementary information
Supplementary Information
Supplementary figures and table captions.
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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DOI: https://doi.org/10.1038/s41551-019-0381-8
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