Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications.


Journal

Signal transduction and targeted therapy
ISSN: 2059-3635
Titre abrégé: Signal Transduct Target Ther
Pays: England
ID NLM: 101676423

Informations de publication

Date de publication:
26 Apr 2024
Historique:
received: 28 07 2023
accepted: 17 03 2024
revised: 09 03 2024
medline: 27 4 2024
pubmed: 27 4 2024
entrez: 26 4 2024
Statut: epublish

Résumé

The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.

Identifiants

pubmed: 38670977
doi: 10.1038/s41392-024-01809-0
pii: 10.1038/s41392-024-01809-0
doi:

Types de publication

Journal Article Review Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

112

Subventions

Organisme : NINDS NIH HHS
ID : U01 NS122101
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG072291
Pays : United States
Organisme : NIA NIH HHS
ID : RF1 AG079307
Pays : United States

Informations de copyright

© 2024. The Author(s).

Références

Rowe, R. G. & Daley, G. Q. Induced pluripotent stem cells in disease modelling and drug discovery. Nat. Rev. Genet. 20, 377–388 (2019).
doi: 10.1038/s41576-019-0100-z pubmed: 30737492 pmcid: 6584039
Shi, Y., Inoue, H., Wu, J. C. & Yamanaka, S. Induced pluripotent stem cell technology: a decade of progress. Nat. Rev. Drug Discov. 16, 115–130 (2017).
doi: 10.1038/nrd.2016.245 pubmed: 27980341
Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007).
doi: 10.1016/j.cell.2007.11.019 pubmed: 18035408
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
doi: 10.1016/j.cell.2006.07.024 pubmed: 16904174
Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917–1920 (2007).
doi: 10.1126/science.1151526 pubmed: 18029452
Takahashi, K. & Yamanaka, S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat. Rev. Mol. Cell Biol. 17, 183–193 (2016).
doi: 10.1038/nrm.2016.8 pubmed: 26883003
Breschi, A., Gingeras, T. R. & Guigo, R. Comparative transcriptomics in human and mouse. Nat. Rev. Genet. 18, 425–440 (2017).
doi: 10.1038/nrg.2017.19 pubmed: 28479595 pmcid: 6413734
Gharib, W. H. & Robinson-Rechavi, M. When orthologs diverge between human and mouse. Brief. Bioinform. 12, 436–441 (2011).
doi: 10.1093/bib/bbr031 pubmed: 21677033 pmcid: 3178054
Lynch, V. J. Use with caution: developmental systems divergence and potential pitfalls of animal models. Yale J. Biol. Med. 82, 53–66 (2009).
pubmed: 19562005 pmcid: 2701150
Takebe, T. & Wells, J. M. Organoids by design. Science 364, 956–959 (2019).
doi: 10.1126/science.aaw7567 pubmed: 31171692 pmcid: 8212787
Yamanaka, S. Pluripotent Stem Cell-based Cell Therapy- Promise And Challenges. Cell Stem Cell 27, 523–531 (2020).
doi: 10.1016/j.stem.2020.09.014 pubmed: 33007237
Gurdon, J. B. The generation of diversity and pattern in animal development. Cell 68, 185–199 (1992).
doi: 10.1016/0092-8674(92)90465-O pubmed: 1733498
Kiefer, J. C. Epigenetics in development. Dev. Dyn. 236, 1144–1156 (2007).
doi: 10.1002/dvdy.21094 pubmed: 17304537
Tompkins, J. D. Discovering DNA methylation, the history and future of the writing on DNA. J. Hist. Biol. 55, 865–887 (2022).
pubmed: 36239862 pmcid: 9941238
Roe, S. A. Matter, life, and generation: eighteen-century embryology and the Haller-Wolff Debate, (Cambridge University Press, 1981).
Kilgour, F. G. William Harvey and his contributions. Circulation 23, 286–296 (1961).
doi: 10.1161/01.CIR.23.2.286 pubmed: 13755936
Aulie, R. P. Caspar Friedrich Wolff and his ‘Theoria generationis’, 1759. J. Hist. Med. Allied Sci. 16, 124–144 (1961).
doi: 10.1093/jhmas/XVI.2.124 pubmed: 13685148
Weismann, A. Das Keimplasma; eine Theorie der Vererbung, (Jena, Fischer, 1892).
Waddington, C. H. The Strategy of the Genes; A Discussion of Some Aspects of Theoretical Biology, (Cambridge: Cambridge University Press, 1957).
Nanney, D. L. Epigenetic control systems. Proc. Natl. Acad. Sci. USA 44, 712–717 (1958).
doi: 10.1073/pnas.44.7.712 pubmed: 16590265 pmcid: 528649
Gurdon, J. B. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. J. Embryol. Exp. Morphol. 10, 622–640 (1962).
pubmed: 13951335
Gurdon, J. B. The transplantation of nuclei between two species of Xenopus. Dev. Biol. 5, 68–83 (1962).
doi: 10.1016/0012-1606(62)90004-0 pubmed: 13903028
Gurdon, J. B. Adult frogs derived from the nuclei of single somatic cells. Dev. Biol. 4, 256–273 (1962).
doi: 10.1016/0012-1606(62)90043-X pubmed: 13903027
Gurdon, J. B. Multiple genetically identical frogs. J. Hered. 53, 5–9 (1962).
doi: 10.1093/oxfordjournals.jhered.a107117 pubmed: 13951336
Gurdon, J. B., Elsdale, T. R. & Fischberg, M. Sexually mature individuals of Xenopus laevis from the transplantation of single somatic nuclei. Nature 182, 64–65 (1958).
doi: 10.1038/182064a0 pubmed: 13566187
Jeltsch, A. & Jurkowska, R. Z. New concepts in DNA methylation. Trends Biochem. Sci. 39, 310–318 (2014).
doi: 10.1016/j.tibs.2014.05.002 pubmed: 24947342
Riggs, A. D. X inactivation, differentiation, and DNA methylation. Cytogenet. Cell Genet. 14, 9–25 (1975).
doi: 10.1159/000130315 pubmed: 1093816
Robertson, K. D. & Wolffe, A. P. DNA methylation in health and disease. Nat. Rev. Genet. 1, 11–19 (2000).
doi: 10.1038/35049533 pubmed: 11262868
Schubeler, D. Function and information content of DNA methylation. Nature 517, 321–326 (2015).
doi: 10.1038/nature14192 pubmed: 25592537
Evans, M. J. & Kaufman, M. H. Establishment in culture of pluripotential cells from mouse embryos. Nature 292, 154–156 (1981).
doi: 10.1038/292154a0 pubmed: 7242681
Martin, G. R. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. USA 78, 7634–7638 (1981).
doi: 10.1073/pnas.78.12.7634 pubmed: 6950406 pmcid: 349323
Thomson, J. A. et al. Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147 (1998).
doi: 10.1126/science.282.5391.1145 pubmed: 9804556
Tada, M., Takahama, Y., Abe, K., Nakatsuji, N. & Tada, T. Nuclear reprogramming of somatic cells by in vitro hybridization with ES cells. Curr. Biol. 11, 1553–1558 (2001).
doi: 10.1016/S0960-9822(01)00459-6 pubmed: 11591326
Cowan, C. A., Atienza, J., Melton, D. A. & Eggan, K. Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science 309, 1369–1373 (2005).
doi: 10.1126/science.1116447 pubmed: 16123299
Davis, R. L., Weintraub, H. & Lassar, A. B. Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell 51, 987–1000 (1987).
doi: 10.1016/0092-8674(87)90585-X pubmed: 3690668
Halder, G., Callaerts, P. & Gehring, W. J. Induction of ectopic eyes by targeted expression of the eyeless gene in drosophila. Science 267, 1788–1792 (1995).
doi: 10.1126/science.7892602 pubmed: 7892602
Kulessa, H., Frampton, J. & Graf, T. Gata-1 reprograms Avian Myelomonocytic cell-lines into Eosinophils, Thromboblasts, and Erythroblasts. Gene Dev. 9, 1250–1262 (1995).
doi: 10.1101/gad.9.10.1250 pubmed: 7758949
Xie, H., Ye, M., Feng, R. & Graf, T. Stepwise reprogramming of B cells into macrophages. Cell 117, 663–676 (2004).
doi: 10.1016/S0092-8674(04)00419-2 pubmed: 15163413
Wernig, M. et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448, 318–324 (2007).
doi: 10.1038/nature05944 pubmed: 17554336
Huangfu, D. W. et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol. 26, 795–797 (2008).
doi: 10.1038/nbt1418 pubmed: 18568017 pmcid: 6334647
Huangfu, D. et al. Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nat. Biotechnol. 26, 1269–1275 (2008).
doi: 10.1038/nbt.1502 pubmed: 18849973
Hou, P. et al. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science 341, 651–654 (2013).
doi: 10.1126/science.1239278 pubmed: 23868920
Zhu, J. et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642–654 (2013).
doi: 10.1016/j.cell.2012.12.033 pubmed: 23333102 pmcid: 3563935
Apostolou, E. & Hochedlinger, K. Chromatin dynamics during cellular reprogramming. Nature 502, 462–471 (2013).
doi: 10.1038/nature12749 pubmed: 24153299 pmcid: 4216318
Apostolou, E. & Stadtfeld, M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr. Opin. Genet. Dev. 52, 77–85 (2018).
doi: 10.1016/j.gde.2018.06.002 pubmed: 29925040 pmcid: 6252123
Cacchiarelli, D. et al. Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency. Cell 162, 412–424 (2015).
doi: 10.1016/j.cell.2015.06.016 pubmed: 26186193 pmcid: 4511597
Nefzger, C. M. et al. Cell type of origin dictates the route to pluripotency. Cell Rep. 21, 2649–2660 (2017).
doi: 10.1016/j.celrep.2017.11.029 pubmed: 29212013
Borkent, M. et al. A serial shRNA screen for roadblocks to reprogramming identifies the protein modifier SUMO2. Stem Cell Rep. 6, 704–716 (2016).
doi: 10.1016/j.stemcr.2016.02.004
Buckley, S. M. et al. Regulation of Pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell 11, 783–798 (2012).
doi: 10.1016/j.stem.2012.09.011 pubmed: 23103054 pmcid: 3549668
Qin, H. et al. Systematic identification of barriers to human iPSC generation. Cell 158, 449–461 (2014).
doi: 10.1016/j.cell.2014.05.040 pubmed: 25036638 pmcid: 4130998
Simic, M. S. et al. Transient activation of the UPR(ER) is an essential step in the acquisition of pluripotency during reprogramming. Sci. Adv. 5, eaaw0025 (2019).
doi: 10.1126/sciadv.aaw0025 pubmed: 30989118 pmcid: 6457941
Wu, Y. et al. Phospholipid remodeling is critical for stem cell pluripotency by facilitating mesenchymal-to-epithelial transition. Sci. Adv. 5, eaax7525 (2019).
doi: 10.1126/sciadv.aax7525 pubmed: 31807705 pmcid: 6881163
Pei, D. Q., Shu, X. D., Gassama-Diagne, A. & Thiery, J. P. Mesenchymal-epithelial transition in development and reprogramming. Nat. Cell Biol. 21, 44–53 (2019).
doi: 10.1038/s41556-018-0195-z pubmed: 30602762
Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151, 994–1004 (2012).
doi: 10.1016/j.cell.2012.09.045 pubmed: 23159369 pmcid: 3508134
Soufi, A. et al. Pioneer transcription factors target partial DNA Motifs on nucleosomes to initiate reprogramming. Cell 161, 555–568 (2015).
doi: 10.1016/j.cell.2015.03.017 pubmed: 25892221 pmcid: 4409934
Chen, J. et al. Hierarchical Oct4 binding in concert with primed epigenetic rearrangements during somatic cell reprogramming. Cell Rep. 14, 1540–1554 (2016).
doi: 10.1016/j.celrep.2016.01.013 pubmed: 26832419
Chronis, C. et al. Cooperative binding of transcription factors orchestrates reprogramming. Cell 168, 442–459.e420 (2017).
doi: 10.1016/j.cell.2016.12.016 pubmed: 28111071 pmcid: 5302508
Zaret, K. S. & Carroll, J. S. Pioneer transcription factors: establishing competence for gene expression. Gene Dev. 25, 2227–2241 (2011).
doi: 10.1101/gad.176826.111 pubmed: 22056668 pmcid: 3219227
Vanzan, L. et al. High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. Nat. Commun. 12, 3337 (2021).
doi: 10.1038/s41467-021-23630-x pubmed: 34099689 pmcid: 8184831
Roberts, G. A. et al. Dissecting OCT4 defines the role of nucleosome binding in pluripotency. Nat. Cell Biol. 23, 834–845 (2021).
doi: 10.1038/s41556-021-00727-5 pubmed: 34354236 pmcid: 7611526
Di Giammartino, D. C. et al. KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks. Nat. Cell Biol. 21, 1179–1190 (2019).
doi: 10.1038/s41556-019-0390-6 pubmed: 31548608 pmcid: 7339746
Rahl, P. B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432–445 (2010).
doi: 10.1016/j.cell.2010.03.030 pubmed: 20434984 pmcid: 2864022
Garcia-Gutierrez, L., Delgado, M. D. & Leon, J. MYC oncogene contributions to release of cell cycle brakes. Genes 10, 244 (2019).
doi: 10.3390/genes10030244 pubmed: 30909496 pmcid: 6470592
Smith, Z. D., Sindhu, C. & Meissner, A. Molecular features of cellular reprogramming and development. Nat. Rev. Mol. Cell Biol. 17, 139–154 (2016).
doi: 10.1038/nrm.2016.6 pubmed: 26883001
Deng, W., Jacobson, E. C., Collier, A. J. & Plath, K. The transcription factor code in iPSC reprogramming. Curr. Opin. Genet. Dev. 70, 89–96 (2021).
doi: 10.1016/j.gde.2021.06.003 pubmed: 34246082 pmcid: 9469655
Hernandez, C. et al. Dppa2/4 facilitate epigenetic remodeling during reprogramming to pluripotency. Cell Stem Cell 23, 396–411.e398 (2018).
doi: 10.1016/j.stem.2018.08.001 pubmed: 30146411 pmcid: 6128737
Liu, J. et al. The oncogene c-Jun impedes somatic cell reprogramming. Nat. Cell Biol. 17, 856–867 (2015).
doi: 10.1038/ncb3193 pubmed: 26098572
Markov, G. J. et al. AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency. Proc. Natl. Acad. Sci. USA 118, e2104841118 (2021).
doi: 10.1073/pnas.2104841118 pubmed: 34088849 pmcid: 8201948
Silva, J. et al. Nanog is the gateway to the pluripotent ground state. Cell 138, 722–737 (2009).
doi: 10.1016/j.cell.2009.07.039 pubmed: 19703398 pmcid: 3437554
Nakagawa, M. et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat. Biotechnol. 26, 101–106 (2008).
doi: 10.1038/nbt1374 pubmed: 18059259
Mai, T. et al. NKX3-1 is required for induced pluripotent stem cell reprogramming and can replace OCT4 in mouse and human iPSC induction. Nat. Cell Biol. 20, 900–908 (2018).
doi: 10.1038/s41556-018-0136-x pubmed: 30013107 pmcid: 6101038
Kim, J. B. et al. Direct reprogramming of human neural stem cells by OCT4. Nature 461, 649–653 (2009).
doi: 10.1038/nature08436 pubmed: 19718018
Kim, J. B. et al. Oct4-induced pluripotency in adult neural stem cells. Cell 136, 411–419 (2009).
doi: 10.1016/j.cell.2009.01.023 pubmed: 19203577
Radzisheuskaya, A. & Silva, J. C. Do all roads lead to Oct4? the emerging concepts of induced pluripotency. Trends Cell Biol. 24, 275–284 (2014).
doi: 10.1016/j.tcb.2013.11.010 pubmed: 24370212 pmcid: 3976965
Li, D. et al. Chromatin accessibility dynamics during iPSC reprogramming. Cell Stem Cell 21, 819–833.e816 (2017).
doi: 10.1016/j.stem.2017.10.012 pubmed: 29220666
Xing, Q. R. et al. Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing. Sci. Adv. 6, eaba1190 (2020).
doi: 10.1126/sciadv.aba1190 pubmed: 32917699 pmcid: 7486102
Stadhouders, R. et al. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat. Genet. 50, 238–249 (2018).
doi: 10.1038/s41588-017-0030-7 pubmed: 29335546 pmcid: 5810905
Knaupp, A. S. et al. Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming. Cell Stem Cell 21, 834–845.e836 (2017).
doi: 10.1016/j.stem.2017.11.007 pubmed: 29220667
Cheloufi, S. et al. The histone chaperone CAF-1 safeguards somatic cell identity. Nature 528, 218–224 (2015).
doi: 10.1038/nature15749 pubmed: 26659182 pmcid: 4866648
dos Santos, R. L. et al. MBD3/NuRD facilitates induction of pluripotency in a context-dependent manner. Cell Stem Cell 15, 102–110 (2014).
doi: 10.1016/j.stem.2014.04.019 pubmed: 24835571 pmcid: 4082719
Onder, T. T. et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 483, 598–602 (2012).
doi: 10.1038/nature10953 pubmed: 22388813 pmcid: 3501145
Chen, J. et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat. Genet. 45, 34–42 (2013).
doi: 10.1038/ng.2491 pubmed: 23202127
Sridharan, R. et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1gamma in reprogramming to pluripotency. Nat. Cell Biol. 15, 872–882 (2013).
doi: 10.1038/ncb2768 pubmed: 23748610 pmcid: 3733997
Li, L. P. et al. Glis1 facilitates induction of pluripotency via an epigenome-metabolome-epigenome signalling cascade (vol 2, pg 882, 2020). Nat. Metab. 2, 1179–1179 (2020).
doi: 10.1038/s42255-020-00308-0 pubmed: 33033400
Tran, K. A. et al. Defining reprogramming checkpoints from single-cell analyses of induced pluripotency. Cell Rep. 27, 1726–1741.e1725 (2019).
doi: 10.1016/j.celrep.2019.04.056 pubmed: 31067459 pmcid: 6555151
Sun, G., Fu, C., Shen, C. & Shi, Y. Histone deacetylases in neural stem cells and induced pluripotent stem cells. J. Biomed. Biotechnol. 2011, 835968 (2011).
doi: 10.1155/2011/835968 pubmed: 21845024 pmcid: 3154389
Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356, eaaj2239 (2017).
doi: 10.1126/science.aaj2239 pubmed: 28473536 pmcid: 8009048
Lyko, F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat. Rev. Genet. 19, 81–92 (2018).
doi: 10.1038/nrg.2017.80 pubmed: 29033456
Pastor, W. A., Aravind, L. & Rao, A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 14, 341–356 (2013).
doi: 10.1038/nrm3589 pubmed: 23698584 pmcid: 3804139
Piccolo, F. M. & Fisher, A. G. Getting rid of DNA methylation. Trends Cell Biol. 24, 136–143 (2014).
doi: 10.1016/j.tcb.2013.09.001 pubmed: 24119665
Rasmussen, K. D. & Helin, K. Role of TET enzymes in DNA methylation, development, and cancer. Genes Dev. 30, 733–750 (2016).
doi: 10.1101/gad.276568.115 pubmed: 27036965 pmcid: 4826392
Caldwell, B. A. et al. Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency. Mol. Cell 81, 859–869.e858 (2021).
doi: 10.1016/j.molcel.2020.11.045 pubmed: 33352108
Doege, C. A. et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature 488, 652–655 (2012).
doi: 10.1038/nature11333 pubmed: 22902501 pmcid: 5176099
Sardina, J. L. et al. Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate. Cell Stem Cell 23, 727–741.e729 (2018).
doi: 10.1016/j.stem.2018.08.016 pubmed: 30220521
Zviran, A. et al. Deterministic somatic cell reprogramming involves continuous transcriptional changes governed by Myc and epigenetic-driven modules. Cell Stem Cell 24, 328–341.e329 (2019).
doi: 10.1016/j.stem.2018.11.014 pubmed: 30554962
Hu, X. et al. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 14, 512–522 (2014).
doi: 10.1016/j.stem.2014.01.001 pubmed: 24529596
Costa, Y. et al. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 495, 370–374 (2013).
doi: 10.1038/nature11925 pubmed: 23395962 pmcid: 3606645
Gao, Y. W. et al. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA Methylation and Hydroxymethylation in reprogramming. Cell Stem Cell 12, 453–469 (2013).
doi: 10.1016/j.stem.2013.02.005 pubmed: 23499384
Chen, J. et al. Vitamin C modulates TET1 function during somatic cell reprogramming. Nat. Genet. 45, 1504–1509 (2013).
doi: 10.1038/ng.2807 pubmed: 24162740
Guo, L. et al. Resolving cell fate decisions during somatic cell reprogramming by single-cell RNA-Seq. Mol. Cell 73, 815–829.e817 (2019).
doi: 10.1016/j.molcel.2019.01.042 pubmed: 30772174
Shakiba, N. et al. Cell competition during reprogramming gives rise to dominant clones. Science 364, eaan0925 (2019).
doi: 10.1126/science.aan0925 pubmed: 30898844
Francesconi, M. et al. Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming. Elife 8, e41627 (2019).
doi: 10.7554/eLife.41627 pubmed: 30860479 pmcid: 6435319
Schwarz, B. A. et al. Prospective Isolation of Poised iPSC intermediates reveals principles of cellular reprogramming. Cell Stem Cell 23, 289–305.e285 (2018).
doi: 10.1016/j.stem.2018.06.013 pubmed: 30017590 pmcid: 6086589
Bar-Nur, O., Russ, H. A., Efrat, S. & Benvenisty, N. Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell 9, 17–23 (2011).
doi: 10.1016/j.stem.2011.06.007 pubmed: 21726830
Kim, K. et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat. Biotechnol. 29, 1117–1119 (2011).
doi: 10.1038/nbt.2052 pubmed: 22119740 pmcid: 3357310
Marchetto, M. C. et al. Transcriptional signature and memory retention of human-induced pluripotent stem cells. PLoS One 4, e7076 (2009).
doi: 10.1371/journal.pone.0007076 pubmed: 19763270 pmcid: 2741600
Ohi, Y. et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat. Cell Biol. 13, 541–549 (2011).
doi: 10.1038/ncb2239 pubmed: 21499256 pmcid: 3987913
Kim, K. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010).
doi: 10.1038/nature09342 pubmed: 20644535 pmcid: 3150836
Rouhani, F. J. et al. Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells. Nat. Genet. 54, 1406–1416 (2022).
doi: 10.1038/s41588-022-01147-3 pubmed: 35953586 pmcid: 9470532
Wei, W., Gaffney, D. J. & Chinnery, P. F. Cell reprogramming shapes the mitochondrial DNA landscape. Nat. Commun. 12, 5241 (2021).
doi: 10.1038/s41467-021-25482-x pubmed: 34475388 pmcid: 8413449
Deuse, T. et al. De novo mutations in mitochondrial DNA of iPSCs produce immunogenic neoepitopes in mice and humans. Nat. Biotechnol. 37, 1137–1144 (2019).
doi: 10.1038/s41587-019-0227-7 pubmed: 31427818
Narsinh, K. H. et al. Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. J. Clin. Investig. 121, 1217–1221 (2011).
doi: 10.1172/JCI44635 pubmed: 21317531 pmcid: 3049389
Malik, N. & Rao, M. S. A review of the methods for human iPSC derivation. Methods Mol. Biol. 997, 23–33 (2013).
doi: 10.1007/978-1-62703-348-0_3 pubmed: 23546745 pmcid: 4176696
Manzini, S., Viiri, L. E., Marttila, S. & Aalto-Setala, K. A comparative view on easy to deploy non-integrating methods for patient-specific iPSC production. Stem Cell Rev. Rep. 11, 900–908 (2015).
doi: 10.1007/s12015-015-9619-3 pubmed: 26341105
Scesa, G., Adami, R. & Bottai, D. iPSC preparation and epigenetic memory: does the tissue origin matter? Cells 10, 1470 (2021).
doi: 10.3390/cells10061470 pubmed: 34208270 pmcid: 8230744
Macarthur, C. C. et al. Generation of human-induced pluripotent stem cells by a nonintegrating RNA Sendai virus vector in feeder-free or xeno-free conditions. Stem Cells Int. 2012, 564612 (2012).
doi: 10.1155/2012/564612 pubmed: 22550511 pmcid: 3328201
Seki, T. et al. Generation of induced pluripotent stem cells from human terminally differentiated circulating T cells. Cell Stem Cell 7, 11–14 (2010).
doi: 10.1016/j.stem.2010.06.003 pubmed: 20621043
Zhou, W. B. & Freed, C. R. Adenoviral gene delivery can reprogram human fibroblasts to induced pluripotent stem cells. Stem Cells 27, 2667–2674 (2009).
doi: 10.1002/stem.201 pubmed: 19697349
Haridhasapavalan, K. K. et al. An insight into non-integrative gene delivery approaches to generate transgene-free induced pluripotent stem cells. Gene 686, 146–159 (2019).
doi: 10.1016/j.gene.2018.11.069 pubmed: 30472380
Kaji, K. et al. Virus-free induction of pluripotency and subsequent excision of reprogramming factors. Nature 458, 771–775 (2009).
doi: 10.1038/nature07864 pubmed: 19252477 pmcid: 2667910
Woltjen, K. et al. piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature 458, 766–770 (2009).
doi: 10.1038/nature07863 pubmed: 19252478 pmcid: 3758996
Chao, J. et al. Therapeutic development for Canavan disease using patient iPSCs introduced with the wild-type ASPA gene. iScience 25, 104391 (2022).
doi: 10.1016/j.isci.2022.104391 pubmed: 35637731 pmcid: 9142666
Feng, L. et al. Cell-based therapy for canavan disease using human iPSC-Derived NPCs and OPCs. Adv. Sci. 7, 2002155 (2020).
doi: 10.1002/advs.202002155
Warren, L. et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 7, 618–630 (2010).
doi: 10.1016/j.stem.2010.08.012 pubmed: 20888316 pmcid: 3656821
Wen, W. et al. Enhanced generation of integration-free iPSCs from human adult peripheral blood mononuclear cells with an optimal combination of episomal vectors. Stem Cell Rep. 6, 873–884 (2016).
doi: 10.1016/j.stemcr.2016.04.005
Anokye-Danso, F. et al. Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell 8, 376–388 (2011).
doi: 10.1016/j.stem.2011.03.001 pubmed: 21474102 pmcid: 3090650
Miyoshi, N. et al. Reprogramming of mouse and human cells to pluripotency using mature MicroRNAs. Cell Stem Cell 8, 633–638 (2011).
doi: 10.1016/j.stem.2011.05.001 pubmed: 21620789
Kim, Y., Jeong, J. & Choi, D. Small-molecule-mediated reprogramming: a silver lining for regenerative medicine. Exp. Mol. Med. 52, 213–226 (2020).
doi: 10.1038/s12276-020-0383-3 pubmed: 32080339 pmcid: 7062739
Liuyang, S. et al. Highly efficient and rapid generation of human pluripotent stem cells by chemical reprogramming. Cell Stem Cell 30, 450–459.e459 (2023).
doi: 10.1016/j.stem.2023.02.008 pubmed: 36944335
Guan, J. et al. Chemical reprogramming of human somatic cells to pluripotent stem cells. Nature 605, 325–331 (2022).
doi: 10.1038/s41586-022-04593-5 pubmed: 35418683
Li, W. et al. Identification of Oct4-activating compounds that enhance reprogramming efficiency. Proc. Natl. Acad. Sci. USA 109, 20853–20858 (2012).
doi: 10.1073/pnas.1219181110 pubmed: 23213213 pmcid: 3529047
Zhu, S. et al. Reprogramming of human primary somatic cells by OCT4 and chemical compounds. Cell Stem Cell 7, 651–655 (2010).
doi: 10.1016/j.stem.2010.11.015 pubmed: 21112560
Lin, T. et al. A chemical platform for improved induction of human iPSCs. Nat. Methods 6, 805–808 (2009).
doi: 10.1038/nmeth.1393 pubmed: 19838168 pmcid: 3724527
Cao, S. et al. Chromatin accessibility dynamics during chemical induction of pluripotency. Cell Stem Cell 22, 529–542.e525 (2018).
doi: 10.1016/j.stem.2018.03.005 pubmed: 29625068
Zhao, Y. et al. A XEN-like state bridges somatic cells to pluripotency during chemical reprogramming. Cell 163, 1678–1691 (2015).
doi: 10.1016/j.cell.2015.11.017 pubmed: 26686652
Velychko, S. et al. Excluding Oct4 from Yamanaka cocktail unleashes the developmental potential of iPSCs. Cell Stem Cell 25, 737–753.e734 (2019).
doi: 10.1016/j.stem.2019.10.002 pubmed: 31708402 pmcid: 6900749
Shi, Y. Induced pluripotent stem cells, new tools for drug discovery and new hope for stem cell therapies. Curr. Mol. Pharm. 2, 15–18 (2009).
doi: 10.2174/1874467210902010015
Lo, B. & Parham, L. Ethical issues in stem cell research. Endocr. Rev. 30, 204–213 (2009).
doi: 10.1210/er.2008-0031 pubmed: 19366754 pmcid: 2726839
Robertson, J. A. Human embryonic stem cell research: ethical and legal issues. Nat. Rev. Genet. 2, 74–78 (2001).
doi: 10.1038/35047594 pubmed: 11253076
Fernandopulle, M. S. et al. Transcription factor–mediated differentiation of human iPSCs into neurons. Curr. Protoc. Cell Biol. 79, e51 (2018).
doi: 10.1002/cpcb.51 pubmed: 29924488 pmcid: 6993937
Lin, Y. & Zou, J. Differentiation of cardiomyocytes from human pluripotent stem cells in fully chemically defined conditions. STAR Protoc. 1, 100015 (2020).
doi: 10.1016/j.xpro.2020.100015 pubmed: 32734277 pmcid: 7392178
Iriguchi, S. et al. A clinically applicable and scalable method to regenerate T-cells from iPSCs for off-the-shelf T-cell immunotherapy. Nat. Commun. 12, 430 (2021).
doi: 10.1038/s41467-020-20658-3 pubmed: 33462228 pmcid: 7814014
Douvaras, P. & Fossati, V. Generation and isolation of oligodendrocyte progenitor cells from human pluripotent stem cells. Nat. Protoc. 10, 1143–1154 (2015).
doi: 10.1038/nprot.2015.075 pubmed: 26134954
Li, L. et al. GFAP mutations in astrocytes impair oligodendrocyte progenitor proliferation and Myelination in an hiPSC model of alexander disease. Cell Stem Cell 23, 239–251.e236 (2018).
doi: 10.1016/j.stem.2018.07.009 pubmed: 30075130 pmcid: 6230521
Wang, S. et al. Human iPSC-derived oligodendrocyte progenitor cells can Myelinate and rescue a mouse model of congenital hypomyelination. Cell Stem Cell 12, 252–264 (2013).
doi: 10.1016/j.stem.2012.12.002 pubmed: 23395447 pmcid: 3700553
Hurley, K. et al. Reconstructed single-cell fate trajectories define lineage plasticity windows during differentiation of human PSC-derived distal lung progenitors. Cell Stem Cell 26, 593–608.e598 (2020).
doi: 10.1016/j.stem.2019.12.009 pubmed: 32004478 pmcid: 7469703
Joung, J. et al. A transcription factor atlas of directed differentiation. Cell 186, 209–229.e226 (2023).
doi: 10.1016/j.cell.2022.11.026 pubmed: 36608654 pmcid: 10344468
Li, Q. V. et al. Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Nat. Genet. 51, 999–1010 (2019).
doi: 10.1038/s41588-019-0408-9 pubmed: 31110351 pmcid: 6545159
Washer, S. J. et al. Single-cell transcriptomics defines an improved, validated monoculture protocol for differentiation of human iPSC to microglia. Sci. Rep. 12, 19454 (2022).
doi: 10.1038/s41598-022-23477-2 pubmed: 36376339 pmcid: 9663826
Zheng, H. et al. Generating hematopoietic cells from human pluripotent stem cells: approaches, progress and challenges. Cell Regen. 12, 31 (2023).
doi: 10.1186/s13619-023-00175-6 pubmed: 37656237 pmcid: 10474004
Pratumkaew, P., Issaragrisil, S. & Luanpitpong, S. Induced pluripotent stem cells as a tool for modeling hematologic disorders and as a potential source for cell-based therapies. Cells 10, 3250 (2021).
doi: 10.3390/cells10113250 pubmed: 34831472 pmcid: 8623953
Chambers, S. M. et al. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat. Biotechnol. 27, 275–280 (2009).
doi: 10.1038/nbt.1529 pubmed: 19252484 pmcid: 2756723
Qi, Y. et al. Combined small-molecule inhibition accelerates the derivation of functional cortical neurons from human pluripotent stem cells. Nat. Biotechnol. 35, 154–163 (2017).
doi: 10.1038/nbt.3777 pubmed: 28112759 pmcid: 5516899
Drager, N. M. et al. A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states. Nat. Neurosci. 25, 1149–1162 (2022).
doi: 10.1038/s41593-022-01131-4 pubmed: 35953545 pmcid: 9448678
Leng, K. et al. CRISPRi screens in human iPSC-derived astrocytes elucidate regulators of distinct inflammatory reactive states. Nat. Neurosci. 25, 1528–1542 (2022).
doi: 10.1038/s41593-022-01180-9 pubmed: 36303069 pmcid: 9633461
Tian, R. et al. Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis. Nat. Neurosci. 24, 1020–1034 (2021).
doi: 10.1038/s41593-021-00862-0 pubmed: 34031600 pmcid: 8254803
Tian, R. et al. CRISPR interference-based platform for multimodal genetic screens in human iPSC-derived neurons. Neuron 104, 239–255.e212 (2019).
doi: 10.1016/j.neuron.2019.07.014 pubmed: 31422865 pmcid: 6813890
Guttikonda, S. R. et al. Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease. Nat. Neurosci. 24, 343–354 (2021).
doi: 10.1038/s41593-020-00796-z pubmed: 33558694 pmcid: 8382543
Park, J. et al. A 3D human triculture system modeling neurodegeneration and neuroinflammation in Alzheimer’s disease. Nat. Neurosci. 21, 941–951 (2018).
doi: 10.1038/s41593-018-0175-4 pubmed: 29950669 pmcid: 6800152
Kim, J., Koo, B. K. & Knoblich, J. A. Human organoids: model systems for human biology and medicine. Nat. Rev. Mol. Cell Biol. 21, 571–584 (2020).
doi: 10.1038/s41580-020-0259-3 pubmed: 32636524 pmcid: 7339799
Schutgens, F. & Clevers, H. Human organoids: tools for understanding biology and treating diseases. Annu Rev. Pathol. 15, 211–234 (2020).
doi: 10.1146/annurev-pathmechdis-012419-032611 pubmed: 31550983
Hofer, M. & Lutolf, M. P. Engineering organoids. Nat. Rev. Mater. 6, 402–420 (2021).
doi: 10.1038/s41578-021-00279-y pubmed: 33623712 pmcid: 7893133
Corsini, N. S. & Knoblich, J. A. Human organoids: new strategies and methods for analyzing human development and disease. Cell 185, 2756–2769 (2022).
doi: 10.1016/j.cell.2022.06.051 pubmed: 35868278
Rossi, G., Manfrin, A. & Lutolf, M. P. Progress and potential in organoid research. Nat. Rev. Genet. 19, 671–687 (2018).
doi: 10.1038/s41576-018-0051-9 pubmed: 30228295
Cederquist, G. Y. et al. Specification of positional identity in forebrain organoids. Nat. Biotechnol. 37, 436–444 (2019).
doi: 10.1038/s41587-019-0085-3 pubmed: 30936566 pmcid: 6447454
Morizane, R. et al. Nephron organoids derived from human pluripotent stem cells model kidney development and injury. Nat. Biotechnol. 33, 1193–1200 (2015).
doi: 10.1038/nbt.3392 pubmed: 26458176 pmcid: 4747858
Bershteyn, M. et al. Human iPSC-derived cerebral organoids model cellular features of lissencephaly and reveal prolonged mitosis of outer radial Glia. Cell Stem Cell 20, 435–449.e434 (2017).
doi: 10.1016/j.stem.2016.12.007 pubmed: 28111201 pmcid: 5667944
Qian, X. et al. Sliced human cortical organoids for modeling distinct cortical layer formation. Cell Stem Cell 26, 766–781.e769 (2020).
doi: 10.1016/j.stem.2020.02.002 pubmed: 32142682 pmcid: 7366517
Abbott, J. et al. Generation and characterization of NGLY1 patient-derived midbrain organoids. Front Cell Dev. Biol. 11, 1039182 (2023).
doi: 10.3389/fcell.2023.1039182 pubmed: 36875753 pmcid: 9978932
Sabate-Soler, S. et al. Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality. Glia 70, 1267–1288 (2022).
doi: 10.1002/glia.24167 pubmed: 35262217 pmcid: 9314680
Jacob, F. et al. Human pluripotent stem cell-derived neural cells and brain organoids reveal SARS-CoV-2 neurotropism predominates in choroid plexus epithelium. Cell Stem Cell 27, 937–950.e939 (2020).
doi: 10.1016/j.stem.2020.09.016 pubmed: 33010822 pmcid: 7505550
Ballabio, C. et al. Modeling medulloblastoma in vivo and with human cerebellar organoids. Nat. Commun. 11, 583 (2020).
doi: 10.1038/s41467-019-13989-3 pubmed: 31996670 pmcid: 6989674
van Essen, M. J. et al. PTCH1-mutant human cerebellar organoids exhibit altered neural development and recapitulate early medulloblastoma tumorigenesis. Dis. Model Mech. 17, dmm050323 (2024).
Gabriel, E. et al. Human brain organoids assemble functionally integrated bilateral optic vesicles. Cell Stem Cell 28, 1740–1757.e1748 (2021).
doi: 10.1016/j.stem.2021.07.010 pubmed: 34407456
Gagliardi, G. et al. Characterization and transplantation of CD73-positive photoreceptors isolated from human iPSC-derived retinal organoids. Stem Cell Rep. 11, 665–680 (2018).
doi: 10.1016/j.stemcr.2018.07.005
Lane, A. et al. Modeling and rescue of RP2 Retinitis Pigmentosa using iPSC-derived retinal organoids. Stem Cell Rep. 15, 67–79 (2020).
doi: 10.1016/j.stemcr.2020.05.007
Del Dosso, A., Urenda, J. P., Nguyen, T. & Quadrato, G. Upgrading the physiological relevance of human brain organoids. Neuron 107, 1014–1028 (2020).
doi: 10.1016/j.neuron.2020.08.029 pubmed: 32970996 pmcid: 10042151
Di Lullo, E. & Kriegstein, A. R. The use of brain organoids to investigate neural development and disease. Nat. Rev. Neurosci. 18, 573–584 (2017).
doi: 10.1038/nrn.2017.107 pubmed: 28878372 pmcid: 5667942
Cerneckis, J. & Shi, Y. Myelin organoids for the study of Alzheimer’s disease. Front. Neurosci. 17, 1283742 (2023).
doi: 10.3389/fnins.2023.1283742 pubmed: 37942133 pmcid: 10628225
Feng, L. et al. Developing a human iPSC-derived three-dimensional myelin spheroid platform for modeling myelin diseases. iScience 26, 108037 (2023).
doi: 10.1016/j.isci.2023.108037 pubmed: 37867939 pmcid: 10589867
Broda, T. R., McCracken, K. W. & Wells, J. M. Generation of human antral and fundic gastric organoids from pluripotent stem cells. Nat. Protoc. 14, 28–50 (2019).
doi: 10.1038/s41596-018-0080-z pubmed: 30470820 pmcid: 7951181
McCracken, K. W. et al. Wnt/beta-catenin promotes gastric fundus specification in mice and humans. Nature 541, 182–187 (2017).
doi: 10.1038/nature21021 pubmed: 28052057 pmcid: 5526592
Kanton, S. & Pasca, S. P. Human assembloids. Development 149, dev201120 (2022).
doi: 10.1242/dev.201120 pubmed: 36317797
Pasca, S. P. Assembling human brain organoids. Science 363, 126–127 (2019).
doi: 10.1126/science.aau5729 pubmed: 30630918
Pasca, S. P. et al. A nomenclature consensus for nervous system organoids and assembloids. Nature 609, 907–910 (2022).
doi: 10.1038/s41586-022-05219-6 pubmed: 36171373 pmcid: 10571504
Martins, J. M. F. et al. Self-organizing 3D human trunk neuromuscular organoids. Cell Stem Cell 26, 172–186.e176 (2020).
doi: 10.1016/j.stem.2019.12.007
Andersen, J. et al. Generation of functional Human 3D Cortico-Motor Assembloids. Cell 183, 1913–1929.e1926 (2020).
doi: 10.1016/j.cell.2020.11.017 pubmed: 33333020 pmcid: 8711252
Leung, C. M. et al. A guide to the organ-on-a-chip. Nat. Rev. Methods Prim. 2, 33 (2022).
doi: 10.1038/s43586-022-00118-6
Ma, C., Peng, Y., Li, H. & Chen, W. Organ-on-a-Chip: a new paradigm for drug development. Trends Pharm. Sci. 42, 119–133 (2021).
doi: 10.1016/j.tips.2020.11.009 pubmed: 33341248
Wu, Q. et al. Organ-on-a-chip: recent breakthroughs and future prospects. Biomed. Eng. Online 19, 1–9 (2020).
doi: 10.1186/s12938-020-0752-0
Zhang, B. Y., Korolj, A., Lai, B. F. L. & Radisic, M. Advances in organ-on-a-chip engineering. Nat. Rev. Mater. 3, 257–278 (2018).
doi: 10.1038/s41578-018-0034-7
Low, L. A., Mummery, C., Berridge, B. R., Austin, C. P. & Tagle, D. A. Organs-on-chips: into the next decade. Nat. Rev. Drug Discov. 20, 345–361 (2021).
doi: 10.1038/s41573-020-0079-3 pubmed: 32913334
Tavakol, D. N., Fleischer, S. & Vunjak-Novakovic, G. Harnessing organs-on-a-chip to model tissue regeneration. Cell Stem Cell 28, 993–1015 (2021).
doi: 10.1016/j.stem.2021.05.008 pubmed: 34087161 pmcid: 8186820
Vunjak-Novakovic, G., Ronaldson-Bouchard, K. & Radisic, M. Organs-on-a-chip models for biological research. Cell 184, 4597–4611 (2021).
doi: 10.1016/j.cell.2021.08.005 pubmed: 34478657 pmcid: 8417425
van der Helm, M. W., van der Meer, A. D., Eijkel, J. C., van den Berg, A. & Segerink, L. I. Microfluidic organ-on-chip technology for blood-brain barrier research. Tissue Barriers 4, e1142493 (2016).
doi: 10.1080/21688370.2016.1142493 pubmed: 27141422 pmcid: 4836466
Zakharova, M. et al. Multiplexed blood-brain barrier organ-on-chip. Lab Chip 20, 3132–3143 (2020).
doi: 10.1039/D0LC00399A pubmed: 32756644
Sone, N. et al. Multicellular modeling of ciliopathy by combining iPS cells and microfluidic airway-on-a-chip technology. Sci. Transl. Med 13, eabb1298 (2021).
doi: 10.1126/scitranslmed.abb1298 pubmed: 34233948
Vatine, G. D. et al. Human iPSC-derived blood-brain barrier chips enable disease modeling and personalized medicine applications. Cell Stem Cell 24, 995–1005.e1006 (2019).
doi: 10.1016/j.stem.2019.05.011 pubmed: 31173718
Michas, C. et al. Engineering a living cardiac pump on a chip using high-precision fabrication. Sci. Adv. 8, eabm3791 (2022).
doi: 10.1126/sciadv.abm3791 pubmed: 35452278 pmcid: 9032966
Zhao, Y. et al. A platform for generation of chamber-specific cardiac tissues and disease modeling. Cell 176, 913–927.e918 (2019).
doi: 10.1016/j.cell.2018.11.042 pubmed: 30686581 pmcid: 6456036
Shultz, L. D. et al. Humanized mouse models of immunological diseases and precision medicine. Mamm. Genome 30, 123–142 (2019).
doi: 10.1007/s00335-019-09796-2 pubmed: 30847553 pmcid: 6610695
Flahou, C., Morishima, T., Takizawa, H. & Sugimoto, N. Fit-for-all iPSC-derived cell therapies and their evaluation in humanized mice with NK cell immunity. Front. Immunol. 12, 662360 (2021).
doi: 10.3389/fimmu.2021.662360 pubmed: 33897711 pmcid: 8059435
Moquin-Beaudry, G. et al. Autologous humanized mouse models of iPSC-derived tumors enable characterization and modulation of cancer-immune cell interactions. Cell Rep. Methods 2, 100153 (2022).
doi: 10.1016/j.crmeth.2021.100153 pubmed: 35474871 pmcid: 9017190
Zeleniak, A. et al. De novo construction of T cell compartment in humanized mice engrafted with iPSC-derived thymus organoids. Nat. Methods 19, 1306–1319 (2022).
doi: 10.1038/s41592-022-01583-3 pubmed: 36064772
Sharma, A., Sances, S., Workman, M. J. & Svendsen, C. N. Multi-lineage human iPSC-derived platforms for disease modeling and drug discovery. Cell Stem Cell 26, 309–329 (2020).
doi: 10.1016/j.stem.2020.02.011 pubmed: 32142662 pmcid: 7159985
Abud, E. M. et al. iPSC-derived human microglia-like cells to study neurological diseases. Neuron 94, 278–293.e279 (2017).
doi: 10.1016/j.neuron.2017.03.042 pubmed: 28426964 pmcid: 5482419
Fattorelli, N. et al. Stem-cell-derived human microglia transplanted into mouse brain to study human disease. Nat. Protoc. 16, 1013–1033 (2021).
doi: 10.1038/s41596-020-00447-4 pubmed: 33424025
Hasselmann, J. et al. Development of a chimeric model to study and manipulate human microglia in vivo. Neuron 103, 1016–1033.e1010 (2019).
doi: 10.1016/j.neuron.2019.07.002 pubmed: 31375314 pmcid: 7138101
Svoboda, D. S. et al. Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain. Proc. Natl. Acad. Sci. USA 116, 25293–25303 (2019).
doi: 10.1073/pnas.1913541116 pubmed: 31772018 pmcid: 6911218
Xu, R. et al. Human iPSC-derived mature microglia retain their identity and functionally integrate in the chimeric mouse brain. Nat. Commun. 11, 1577 (2020).
doi: 10.1038/s41467-020-15411-9 pubmed: 32221280 pmcid: 7101330
Wimmer, R. A. et al. Human blood vessel organoids as a model of diabetic vasculopathy. Nature 565, 505–510 (2019).
doi: 10.1038/s41586-018-0858-8 pubmed: 30651639 pmcid: 7116578
Ho, R. et al. ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks. Nat. Neurosci. 19, 1256–1267 (2016).
doi: 10.1038/nn.4345 pubmed: 27428653 pmcid: 5003654
Alvarez, Z. et al. Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons. Cell Stem Cell 30, 219–238.e214 (2023).
doi: 10.1016/j.stem.2022.12.010 pubmed: 36638801
Yoshida, S. et al. Maturation of human induced pluripotent stem cell-derived cardiomyocytes by soluble factors from human mesenchymal stem cells. Mol. Ther. 26, 2681–2695 (2018).
doi: 10.1016/j.ymthe.2018.08.012 pubmed: 30217728 pmcid: 6224789
Giacomelli, E. et al. Human-iPSC-derived cardiac stromal cells enhance maturation in 3D cardiac microtissues and reveal non-cardiomyocyte contributions to heart disease. Cell Stem Cell 26, 862–879.e811 (2020).
doi: 10.1016/j.stem.2020.05.004 pubmed: 32459996 pmcid: 7284308
Maoz, B. M. et al. A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells. Nat. Biotechnol. 36, 865–874 (2018).
doi: 10.1038/nbt.4226 pubmed: 30125269 pmcid: 9254231
Hayashi, R. et al. Generation of 3D lacrimal gland organoids from human pluripotent stem cells. Nature 605, 126–131 (2022).
doi: 10.1038/s41586-022-04613-4 pubmed: 35444274
Mansour, A. A. et al. An in vivo model of functional and vascularized human brain organoids. Nat. Biotechnol. 36, 432–441 (2018).
doi: 10.1038/nbt.4127 pubmed: 29658944 pmcid: 6331203
Munera, J. O. et al. Differentiation of human pluripotent stem cells into colonic organoids via transient activation of BMP signaling. Cell Stem Cell 21, 51–64.e56 (2017).
doi: 10.1016/j.stem.2017.05.020 pubmed: 28648364 pmcid: 5531599
Revah, O. et al. Maturation and circuit integration of transplanted human cortical organoids. Nature 610, 319–326 (2022).
doi: 10.1038/s41586-022-05277-w pubmed: 36224417 pmcid: 9556304
Tanaka, J. et al. Human induced pluripotent stem cell-derived salivary gland organoids model SARS-CoV-2 infection and replication. Nat. Cell Biol. 24, 1595–1605 (2022).
doi: 10.1038/s41556-022-01007-6 pubmed: 36253535
Schafer, S. T. et al. An in vivo neuroimmune organoid model to study human microglia phenotypes. Cell 186, 2111–2126.e2120 (2023).
doi: 10.1016/j.cell.2023.04.022 pubmed: 37172564
Cerneckis, J. & Shi, Y. Context matters: hPSC-derived microglia thrive in a humanized brain environment in vivo. Cell Stem Cell 30, 909–910 (2023).
doi: 10.1016/j.stem.2023.05.013 pubmed: 37419102 pmcid: 10505011
Ronaldson-Bouchard, K. et al. Advanced maturation of human cardiac tissue grown from pluripotent stem cells. Nature 556, 239–243 (2018).
doi: 10.1038/s41586-018-0016-3 pubmed: 29618819 pmcid: 5895513
Tu, C. Y., Chao, B. S. & Wu, J. C. Strategies for improving the maturity of human induced pluripotent stem cell-derived cardiomyocytes. Circ. Res. 123, 512–514 (2018).
doi: 10.1161/CIRCRESAHA.118.313472 pubmed: 30355143 pmcid: 6392006
Luo, J. et al. Tissue-engineered vascular grafts with advanced mechanical strength from human iPSCs. Cell Stem Cell 26, 251–261.e258 (2020).
doi: 10.1016/j.stem.2019.12.012 pubmed: 31956039 pmcid: 7021512
Ronaldson-Bouchard, K. et al. Engineering of human cardiac muscle electromechanically matured to an adult-like phenotype. Nat. Protoc. 14, 2781–2817 (2019).
doi: 10.1038/s41596-019-0189-8 pubmed: 31492957 pmcid: 7195192
Shin, D. et al. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell 31, 421–432.e428 (2024).
doi: 10.1016/j.stem.2024.01.010 pubmed: 38382530
Regev, A. et al. The Human Cell Atlas. Elife 6, e27041 (2017).
Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A. & Teichmann, S. A. The human cell atlas: from vision to reality. Nature 550, 451–453 (2017).
doi: 10.1038/550451a pubmed: 29072289
Zheng, Y. et al. Controlled modelling of human epiblast and amnion development using stem cells. Nature 573, 421–425 (2019).
doi: 10.1038/s41586-019-1535-2 pubmed: 31511693 pmcid: 8106232
Sasaki, K. et al. Robust In vitro induction of human germ cell fate from pluripotent stem cells. Cell Stem Cell 17, 178–194 (2015).
doi: 10.1016/j.stem.2015.06.014 pubmed: 26189426
Hayashi, M., Kawaguchi, T., Durcova-Hills, G. & Imai, H. Generation of germ cells from pluripotent stem cells in mammals. Reprod. Med. Biol. 17, 107–114 (2018).
doi: 10.1002/rmb2.12077 pubmed: 29692667
Esfahani, S. N. et al. Derivation of human primordial germ cell-like cells in an embryonic-like culture. Nat. Commun. 15, 167 (2024).
doi: 10.1038/s41467-023-43871-2 pubmed: 38167821 pmcid: 10762101
Matsuda, M. et al. Recapitulating the human segmentation clock with pluripotent stem cells. Nature 580, 124–129 (2020).
doi: 10.1038/s41586-020-2144-9 pubmed: 32238941
Weatherbee, B. A. T. et al. Pluripotent stem cell-derived model of the post-implantation human embryo. Nature 622, 584–593 (2023).
doi: 10.1038/s41586-023-06368-y pubmed: 37369347 pmcid: 10584688
Zernicka-Goetz, M. The evolution of embryo models. Nat. Methods 20, 1844–1848 (2023).
doi: 10.1038/s41592-023-02077-6 pubmed: 38057512
Manor, Y. S., Massarwa, R. & Hanna, J. H. Establishing the human naive pluripotent state. Curr. Opin. Genet. Dev. 34, 35–45 (2015).
doi: 10.1016/j.gde.2015.07.005 pubmed: 26291026
Weinberger, L., Ayyash, M., Novershtern, N. & Hanna, J. H. Dynamic stem cell states: naive to primed pluripotency in rodents and humans. Nat. Rev. Mol. Cell Biol. 17, 155–169 (2016).
doi: 10.1038/nrm.2015.28 pubmed: 26860365
Zhou, J., Hu, J., Wang, Y. & Gao, S. Induction and application of human naive pluripotency. Cell Rep. 42, 112379 (2023).
doi: 10.1016/j.celrep.2023.112379 pubmed: 37043354
Giulitti, S. et al. Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics. Nat. Cell Biol. 21, 275–286 (2019).
doi: 10.1038/s41556-018-0254-5 pubmed: 30598530
Li, W. et al. Generation of rat and human induced pluripotent stem cells by combining genetic reprogramming and chemical inhibitors. Cell Stem Cell 4, 16–19 (2009).
doi: 10.1016/j.stem.2008.11.014 pubmed: 19097958
Sahakyan, A. et al. Human naive pluripotent stem cells Model X chromosome dampening and X inactivation. Cell Stem Cell 20, 87–101 (2017).
doi: 10.1016/j.stem.2016.10.006 pubmed: 27989770
Theunissen, T. W. et al. Molecular criteria for defining the naive human pluripotent state. Cell Stem Cell 19, 502–515 (2016).
doi: 10.1016/j.stem.2016.06.011 pubmed: 27424783 pmcid: 5065525
Kagawa, H. et al. Human blastoids model blastocyst development and implantation. Nature 601, 600–605 (2022).
doi: 10.1038/s41586-021-04267-8 pubmed: 34856602
Wei, Y. et al. Efficient derivation of human trophoblast stem cells from primed pluripotent stem cells. Sci. Adv. 7, eabf4416 (2021).
doi: 10.1126/sciadv.abf4416 pubmed: 34380613 pmcid: 8357231
Castel, G. et al. Induction of human trophoblast stem cells from somatic cells and pluripotent stem cells. Cell Rep. 33, 108419 (2020).
doi: 10.1016/j.celrep.2020.108419 pubmed: 33238118
Jang, Y. J., Kim, M., Lee, B. K. & Kim, J. Induction of human trophoblast stem-like cells from primed pluripotent stem cells. Proc. Natl. Acad. Sci. USA 119, e2115709119 (2022).
doi: 10.1073/pnas.2115709119 pubmed: 35537047 pmcid: 9171790
Earley, A. M., Burbulla, L. F., Krainc, D. & Awatramani, R. Identification of ASCL1 as a determinant for human iPSC-derived dopaminergic neurons. Sci. Rep. 11, 22257 (2021).
doi: 10.1038/s41598-021-01366-4 pubmed: 34782629 pmcid: 8593045
Jerber, J. et al. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nat. Genet. 53, 304–312 (2021).
doi: 10.1038/s41588-021-00801-6 pubmed: 33664506 pmcid: 7610897
Camp, J. G. et al. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc. Natl. Acad. Sci. USA 112, 15672–15677 (2015).
doi: 10.1073/pnas.1520760112 pubmed: 26644564 pmcid: 4697386
Fleck, J. S. et al. Inferring and perturbing cell fate regulomes in human brain organoids. Nature 621, 365–372 (2023).
doi: 10.1038/s41586-022-05279-8 pubmed: 36198796
Lee, J. H. et al. Production of human spinal-cord organoids recapitulating neural-tube morphogenesis. Nat. Biomed. Eng. 6, 435–448 (2022).
doi: 10.1038/s41551-022-00868-4 pubmed: 35347276
Hofbauer, P. et al. Cardioids reveal self-organizing principles of human cardiogenesis. Cell 184, 3299–3317.e3222 (2021).
doi: 10.1016/j.cell.2021.04.034 pubmed: 34019794
Marton, R. M. & Pasca, S. P. Organoid and assembloid technologies for investigating cellular crosstalk in human brain development and disease. Trends Cell Biol. 30, 133–143 (2020).
doi: 10.1016/j.tcb.2019.11.004 pubmed: 31879153
Koike, H. et al. Modelling human hepato-biliary-pancreatic organogenesis from the foregut-midgut boundary. Nature 574, 112–116 (2019).
doi: 10.1038/s41586-019-1598-0 pubmed: 31554966 pmcid: 7643931
Miura, Y. et al. Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells. Nat. Biotechnol. 38, 1421–1430 (2020).
doi: 10.1038/s41587-020-00763-w pubmed: 33273741 pmcid: 9042317
Xiang, Y. et al. Fusion of regionally specified hPSC-derived organoids models human brain development and interneuron migration. Cell Stem Cell 21, 383–398.e387 (2017).
doi: 10.1016/j.stem.2017.07.007 pubmed: 28757360 pmcid: 5720381
Soldner, F. & Jaenisch, R. iPSC disease modeling. Science 338, 1155–1156 (2012).
doi: 10.1126/science.1227682 pubmed: 23197518
Li, L., Chao, J. & Shi, Y. Modeling neurological diseases using iPSC-derived neural cells : iPSC modeling of neurological diseases. Cell Tissue Res. 371, 143–151 (2018).
doi: 10.1007/s00441-017-2713-x pubmed: 29079884
Israel, M. A. et al. Probing sporadic and familial Alzheimer’s disease using induced pluripotent stem cells. Nature 482, 216–220 (2012).
doi: 10.1038/nature10821 pubmed: 22278060 pmcid: 3338985
Kwart, D. et al. A large panel of isogenic APP and PSEN1 mutant human iPSC neurons reveals shared endosomal abnormalities mediated by APP beta-CTFs, Not Abeta. Neuron 104, 256–270.e255 (2019).
doi: 10.1016/j.neuron.2019.07.010 pubmed: 31416668
Liu, Q. et al. Effect of potent gamma-secretase modulator in human neurons derived from multiple presenilin 1-induced pluripotent stem cell mutant carriers. JAMA Neurol. 71, 1481–1489 (2014).
doi: 10.1001/jamaneurol.2014.2482 pubmed: 25285942 pmcid: 4374637
Hendriks, D., Clevers, H. & Artegiani, B. CRISPR-Cas tools and their application in genetic engineering of human stem cells and organoids. Cell Stem Cell 27, 705–731 (2020).
doi: 10.1016/j.stem.2020.10.014 pubmed: 33157047
Firth, A. L. et al. Functional gene correction for cystic fibrosis in lung epithelial cells generated from patient iPSCs. Cell Rep. 12, 1385–1390 (2015).
doi: 10.1016/j.celrep.2015.07.062 pubmed: 26299960 pmcid: 4559351
Lin, Y. T. et al. APOE4 causes widespread molecular and cellular alterations associated with Alzheimer’s disease phenotypes in human iPSC-derived brain cell types. Neuron 98, 1294–1294 (2018).
doi: 10.1016/j.neuron.2018.06.011 pubmed: 29953873 pmcid: 6048952
Liu, Z. et al. Astrocytic response mediated by the CLU risk allele inhibits OPC proliferation and myelination in a human iPSC model. Cell Rep. 42, 112841 (2023).
doi: 10.1016/j.celrep.2023.112841 pubmed: 37494190 pmcid: 10510531
Brunner, J. W. et al. Power and optimal study design in iPSC-based brain disease modelling. Mol. Psychiatry 28, 1545–1556 (2023).
doi: 10.1038/s41380-022-01866-3 pubmed: 36385170
Kondo, T. et al. Dissection of the polygenic architecture of neuronal Aβ production using a large sample of individual iPSC lines derived from Alzheimer’s disease patients. Nat. Aging 2, 125–139 (2022).
doi: 10.1038/s43587-021-00158-9 pubmed: 37117761
Kimura, M. et al. En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. Cell 185, 4216–4232.e4216 (2022).
doi: 10.1016/j.cell.2022.09.031 pubmed: 36240780 pmcid: 9617783
Park, J. C. et al. A logical network-based drug-screening platform for Alzheimer’s disease representing pathological features of human brain organoids. Nat. Commun. 12, 280 (2021).
doi: 10.1038/s41467-020-20440-5 pubmed: 33436582 pmcid: 7804132
Parenti, I., Rabaneda, L. G., Schoen, H. & Novarino, G. Neurodevelopmental disorders: from genetics to functional pathways. Trends Neurosci. 43, 608–621 (2020).
doi: 10.1016/j.tins.2020.05.004 pubmed: 32507511
Thapar, A., Cooper, M. & Rutter, M. Neurodevelopmental disorders. Lancet Psychiatry 4, 339–346 (2017).
doi: 10.1016/S2215-0366(16)30376-5 pubmed: 27979720
Fang, R. et al. Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science 377, 56–62 (2022).
doi: 10.1126/science.abm1741 pubmed: 35771910 pmcid: 9262715
Hodge, R. D. et al. Conserved cell types with divergent features in human versus mouse cortex. Nature 573, 61–68 (2019).
doi: 10.1038/s41586-019-1506-7 pubmed: 31435019 pmcid: 6919571
Pembroke, W. G., Hartl, C. L. & Geschwind, D. H. Evolutionary conservation and divergence of the human brain transcriptome. Genome Biol. 22, 1–33 (2021).
doi: 10.1186/s13059-020-02257-z
Zhu, Y. et al. Spatiotemporal transcriptomic divergence across human and macaque brain development. Science 362, eaat8077 (2018).
doi: 10.1126/science.aat8077 pubmed: 30545855 pmcid: 6900982
Li, L. & Shi, Y. When glia meet induced pluripotent stem cells (iPSCs). Mol. Cell Neurosci. 109, 103565 (2020).
doi: 10.1016/j.mcn.2020.103565 pubmed: 33068719 pmcid: 10506562
Shao, Z. et al. Dysregulated protocadherin-pathway activity as an intrinsic defect in induced pluripotent stem cell-derived cortical interneurons from subjects with schizophrenia. Nat. Neurosci. 22, 229–242 (2019).
doi: 10.1038/s41593-018-0313-z pubmed: 30664768 pmcid: 6373728
Szabo, A. et al. A human iPSC-astroglia neurodevelopmental model reveals divergent transcriptomic patterns in schizophrenia. Transl. Psychiatry 11, 554 (2021).
doi: 10.1038/s41398-021-01681-4 pubmed: 34716291 pmcid: 8556332
Topol, A. et al. Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells. Cell Rep. 15, 1024–1036 (2016).
doi: 10.1016/j.celrep.2016.03.090 pubmed: 27117414 pmcid: 4856588
Yoon, K. J. et al. Modeling a genetic risk for schizophrenia in iPSCs and mice reveals neural stem cell deficits associated with adherens junctions and polarity. Cell Stem Cell 15, 79–91 (2014).
doi: 10.1016/j.stem.2014.05.003 pubmed: 24996170 pmcid: 4237009
Murai, K. et al. The TLX-miR-219 cascade regulates neural stem cell proliferation in neurodevelopment and schizophrenia iPSC model. Nat. Commun. 7, 10965 (2016).
doi: 10.1038/ncomms10965 pubmed: 26965827 pmcid: 4793043
Schafer, S. T. et al. Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons. Nat. Neurosci. 22, 243–255 (2019).
doi: 10.1038/s41593-018-0295-x pubmed: 30617258 pmcid: 6402576
Wang, M. et al. Increased neural progenitor proliferation in a hiPSC model of autism induces replication stress-associated genome instability. Cell Stem Cell 26, 221–233.e226 (2020).
doi: 10.1016/j.stem.2019.12.013 pubmed: 32004479 pmcid: 7175642
Kathuria, A. et al. Synaptic deficits in iPSC-derived cortical interneurons in schizophrenia are mediated by NLGN2 and rescued by N-acetylcysteine. Transl. Psychiatry 9, 321 (2019).
doi: 10.1038/s41398-019-0660-x pubmed: 31780643 pmcid: 6882825
Kizner, V., Fischer, S. & Naujock, M. Multielectrode Array (MEA)-based detection of spontaneous network activity in human iPSC-derived cortical neurons. Methods Mol. Biol. 1994, 209–216 (2019).
doi: 10.1007/978-1-4939-9477-9_19 pubmed: 31124118
Sun, G. et al. Modeling human cytomegalovirus-induced microcephaly in human iPSC-derived brain organoids. Cell Rep. Med. 1, 100002 (2020).
doi: 10.1016/j.xcrm.2020.100002 pubmed: 33205055 pmcid: 7659592
Brennand, K. J. et al. Modelling schizophrenia using human induced pluripotent stem cells. Nature 473, 221–225 (2011).
doi: 10.1038/nature09915 pubmed: 21490598 pmcid: 3392969
Wen, Z. et al. Synaptic dysregulation in a human iPS cell model of mental disorders. Nature 515, 414–418 (2014).
doi: 10.1038/nature13716 pubmed: 25132547 pmcid: 4501856
Zaslavsky, K. et al. SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons. Nat. Neurosci. 22, 556–564 (2019).
doi: 10.1038/s41593-019-0365-8 pubmed: 30911184 pmcid: 6475597
Cai, H. W. et al. Brain organoid reservoir computing for artificial intelligence. Nat. Electron 6, 1032–1039 (2023).
doi: 10.1038/s41928-023-01069-w
Kagan, B. J. et al. In vitro neurons learn and exhibit sentience when embodied in a simulated game-world. Neuron 110, 3952–3969.e3958 (2022).
doi: 10.1016/j.neuron.2022.09.001 pubmed: 36228614 pmcid: 9747182
Chiaradia, I. & Lancaster, M. A. Brain organoids for the study of human neurobiology at the interface of in vitro and in vivo. Nat. Neurosci. 23, 1496–1508 (2020).
doi: 10.1038/s41593-020-00730-3 pubmed: 33139941
Wang, H. Modeling neurological diseases with human brain organoids. Front. Synaptic Neurosci. 10, 15 (2018).
doi: 10.3389/fnsyn.2018.00015 pubmed: 29937727 pmcid: 6002496
Velasco, S., Paulsen, B. & Arlotta, P. 3D brain organoids: studying brain development and disease outside the embryo. Annu Rev. Neurosci. 43, 375–389 (2020).
doi: 10.1146/annurev-neuro-070918-050154 pubmed: 32640930
Cerneckis, J. & Shi, Y. Modeling brain macrophage biology and neurodegenerative diseases using human iPSC-derived neuroimmune organoids. Front. Cell Neurosci. 17, 1198715 (2023).
doi: 10.3389/fncel.2023.1198715 pubmed: 37342768 pmcid: 10277621
Mariani, J. et al. FOXG1-dependent dysregulation of GABA/Glutamate neuron differentiation in autism spectrum disorders. Cell 162, 375–390 (2015).
doi: 10.1016/j.cell.2015.06.034 pubmed: 26186191 pmcid: 4519016
Xu, R. et al. OLIG2 drives abnormal neurodevelopmental phenotypes in human iPSC-based organoid and chimeric mouse models of down syndrome. Cell Stem Cell 24, 908–926.e908 (2019).
doi: 10.1016/j.stem.2019.04.014 pubmed: 31130512 pmcid: 6944064
Trujillo, C. A. et al. Complex oscillatory waves emerging from cortical organoids model early human brain network development. Cell Stem Cell 25, 558–569.e557 (2019).
doi: 10.1016/j.stem.2019.08.002 pubmed: 31474560 pmcid: 6778040
Passaro, A. P. & Stice, S. L. Electrophysiological analysis of brain organoids: current approaches and advancements. Front. Neurosci. 14, 622137 (2020).
doi: 10.3389/fnins.2020.622137 pubmed: 33510616
Samarasinghe, R. A. et al. Identification of neural oscillations and epileptiform changes in human brain organoids. Nat. Neurosci. 24, 1488–1500 (2021).
doi: 10.1038/s41593-021-00906-5 pubmed: 34426698 pmcid: 9070733
Windrem, M. S. et al. Human iPSC glial mouse chimeras reveal glial contributions to schizophrenia. Cell Stem Cell 21, 195–208.e196 (2017).
doi: 10.1016/j.stem.2017.06.012 pubmed: 28736215 pmcid: 5576346
Dong, X. et al. Human cerebral organoids establish subcortical projections in the mouse brain after transplantation. Mol. Psychiatry 26, 2964–2976 (2021).
doi: 10.1038/s41380-020-00910-4 pubmed: 33051604
Wilson, M. N. et al. Multimodal monitoring of human cortical organoids implanted in mice reveal functional connection with visual cortex. Nat. Commun. 13, 7945 (2022).
doi: 10.1038/s41467-022-35536-3 pubmed: 36572698 pmcid: 9792589
Cerneckis, J., Bu, G. & Shi, Y. Pushing the boundaries of brain organoids to study Alzheimer’s disease. Trends Mol. Med. 29, 659-672 (2023).
Dugger, B. N. & Dickson, D. W. Pathology of neurodegenerative diseases. Cold Spring Harb. Perspect. Biol. 9, a028035 (2017).
doi: 10.1101/cshperspect.a028035 pubmed: 28062563 pmcid: 5495060
Hardiman, O. et al. Amyotrophic lateral sclerosis. Nat. Rev. Dis. Prim. 3, 1–19 (2017).
Kalia, L. V. & Lang, A. E. Parkinson’s disease. Lancet 386, 896–912 (2015).
doi: 10.1016/S0140-6736(14)61393-3 pubmed: 25904081
Knopman, D. S. et al. Alzheimer disease. Nat. Rev. Dis. Prim. 7, 33 (2021).
doi: 10.1038/s41572-021-00269-y pubmed: 33986301
Gonzales, M. M. et al. Biological aging processes underlying cognitive decline and neurodegenerative disease. J. Clin. Investig. 132, e158453 (2022).
doi: 10.1172/JCI158453 pubmed: 35575089 pmcid: 9106343
Camandola, S. & Mattson, M. P. Brain metabolism in health, aging, and neurodegeneration. Embo J. 36, 1474–1492 (2017).
doi: 10.15252/embj.201695810 pubmed: 28438892 pmcid: 5452017
Lopez-Otin, C., Blasco, M. A., Partridge, L., Serrano, M. & Kroemer, G. Hallmarks of aging: an expanding universe. Cell 186, 243–278 (2023).
doi: 10.1016/j.cell.2022.11.001 pubmed: 36599349
Cornacchia, D. & Studer, L. Back and forth in time: directing age in iPSC-derived lineages. Brain Res. 1656, 14–26 (2017).
doi: 10.1016/j.brainres.2015.11.013 pubmed: 26592774
Studer, L., Vera, E. & Cornacchia, D. Programming and reprogramming cellular age in the era of induced pluripotency. Cell Stem Cell 16, 591–600 (2015).
doi: 10.1016/j.stem.2015.05.004 pubmed: 26046759 pmcid: 4508309
Mertens, J. et al. Age-dependent instability of mature neuronal fate in induced neurons from Alzheimer’s patients. Cell Stem Cell 28, 1533–1548.e1536 (2021).
doi: 10.1016/j.stem.2021.04.004 pubmed: 33910058 pmcid: 8423435
Miller, J. D. et al. Human iPSC-based modeling of late-onset disease via progerin-induced aging. Cell Stem Cell 13, 691–705 (2013).
doi: 10.1016/j.stem.2013.11.006 pubmed: 24315443 pmcid: 4153390
Giacomelli, E. et al. Human stem cell models of neurodegeneration: from basic science of amyotrophic lateral sclerosis to clinical translation. Cell Stem Cell 29, 11–35 (2022).
doi: 10.1016/j.stem.2021.12.008 pubmed: 34995492 pmcid: 8785905
Okano, H. & Morimoto, S. iPSC-based disease modeling and drug discovery in cardinal neurodegenerative disorders. Cell Stem Cell 29, 189–208 (2022).
doi: 10.1016/j.stem.2022.01.007 pubmed: 35120619
Virdi, G. S. et al. Protein aggregation and calcium dysregulation are hallmarks of familial Parkinson’s disease in midbrain dopaminergic neurons. Npj Parkinsons Dis. 8, 162 (2022).
doi: 10.1038/s41531-022-00423-7 pubmed: 36424392 pmcid: 9691718
Egawa, N. et al. Drug screening for ALS using patient-specific induced pluripotent stem cells. Sci. Transl. Med. 4, 145ra104 (2012).
doi: 10.1126/scitranslmed.3004052 pubmed: 22855461
Young, J. E. et al. Elucidating molecular phenotypes caused by the SORL1 Alzheimer’s disease genetic risk factor using human induced pluripotent stem cells. Cell Stem Cell 16, 373–385 (2015).
doi: 10.1016/j.stem.2015.02.004 pubmed: 25772071 pmcid: 4388804
Wightman, D. P. et al. A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease. Nat. Genet. 53, 1276–1282 (2021).
doi: 10.1038/s41588-021-00921-z pubmed: 34493870 pmcid: 10243600
Yamazaki, Y., Zhao, N., Caulfield, T. R., Liu, C. C. & Bu, G. J. Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies. Nat. Rev. Neurol. 15, 501–518 (2019).
doi: 10.1038/s41582-019-0228-7 pubmed: 31367008 pmcid: 7055192
Belloy, M. E., Napolioni, V. & Greicius, M. D. A quarter century of APOE and Alzheimer’s disease: progress to date and the path forward. Neuron 101, 820–838 (2019).
doi: 10.1016/j.neuron.2019.01.056 pubmed: 30844401 pmcid: 6407643
Serrano-Pozo, A., Das, S. & Hyman, B. T. APOE and Alzheimer’s disease: advances in genetics, pathophysiology, and therapeutic approaches. Lancet Neurol. 20, 68–80 (2021).
doi: 10.1016/S1474-4422(20)30412-9 pubmed: 33340485 pmcid: 8096522
Sienski, G. et al. APOE4 disrupts intracellular lipid homeostasis in human iPSC-derived glia. Sci. Transl. Med. 13, eaaz4564 (2021).
doi: 10.1126/scitranslmed.aaz4564 pubmed: 33658354 pmcid: 8218593
Tcw, J. et al. Cholesterol and matrisome pathways dysregulated in astrocytes and microglia. Cell 185, 2213–2233.e2225 (2022).
doi: 10.1016/j.cell.2022.05.017 pubmed: 35750033 pmcid: 9340815
Blanchard, J. W. et al. APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes. Nature 611, 769–779 (2022).
doi: 10.1038/s41586-022-05439-w pubmed: 36385529 pmcid: 9870060
Murdock, M. H. & Tsai, L. H. Insights into Alzheimer’s disease from single-cell genomic approaches. Nat. Neurosci. 26, 181–195 (2023).
doi: 10.1038/s41593-022-01222-2 pubmed: 36593328 pmcid: 10155598
Victor, M. B. et al. Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity. Cell Stem Cell 29, 1197–1212.e1198 (2022).
doi: 10.1016/j.stem.2022.07.005 pubmed: 35931030 pmcid: 9623845
Chen, X. et al. Microglia-mediated T cell infiltration drives neurodegeneration in tauopathy. Nature 615, 668–677 (2023).
doi: 10.1038/s41586-023-05788-0 pubmed: 36890231 pmcid: 10258627
Gate, D. et al. Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease. Nature 577, 399–404 (2020).
doi: 10.1038/s41586-019-1895-7 pubmed: 31915375 pmcid: 7445078
Krauskopf, J. et al. Transcriptomics analysis of human iPSC-derived dopaminergic neurons reveals a novel model for sporadic Parkinson’s disease. Mol. Psychiatry 27, 4355–4367 (2022).
doi: 10.1038/s41380-022-01663-y pubmed: 35725899
Ryan, S. D. et al. Isogenic human iPSC parkinson’s model shows nitrosative stress-induced dysfunction in MEF2-PGC1 alpha transcription. Cell 155, 1351–1364 (2013).
doi: 10.1016/j.cell.2013.11.009 pubmed: 24290359 pmcid: 4028128
Sommer, A. et al. Th17 lymphocytes induce neuronal cell death in a human iPSC-based model of Parkinson’s disease. Cell Stem Cell 23, 123–131.e126 (2018).
doi: 10.1016/j.stem.2018.06.015 pubmed: 29979986
Baxi, E. G. et al. Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines. Nat. Neurosci. 25, 226–237 (2022).
doi: 10.1038/s41593-021-01006-0 pubmed: 35115730 pmcid: 8825283
Workman, M. J. et al. Large-scale differentiation of iPSC-derived motor neurons from ALS and control subjects. Neuron 111, 1191–1204.e1195 (2023).
doi: 10.1016/j.neuron.2023.01.010 pubmed: 36764301 pmcid: 10557526
Fujimori, K. et al. Modeling sporadic ALS in iPSC-derived motor neurons identifies a potential therapeutic agent. Nat. Med. 24, 1579–1589 (2018).
doi: 10.1038/s41591-018-0140-5 pubmed: 30127392
Chakrabarti, S. & Mohanakumar, K. P. Aging and neurodegeneration: a tangle of models and mechanisms. Aging Dis. 7, 111–113 (2016).
doi: 10.14336/AD.2016.0312 pubmed: 27114843 pmcid: 4809602
Franceschi, C., Garagnani, P., Parini, P., Giuliani, C. & Santoro, A. Inflammaging: a new immune-metabolic viewpoint for age-related diseases. Nat. Rev. Endocrinol. 14, 576–590 (2018).
doi: 10.1038/s41574-018-0059-4 pubmed: 30046148
Franceschi, C., Garagnani, P., Vitale, G., Capri, M. & Salvioli, S. Inflammaging and ‘Garb-aging’. Trends Endocrinol. Metab. 28, 199–212 (2017).
doi: 10.1016/j.tem.2016.09.005 pubmed: 27789101
Grimm, A. & Eckert, A. Brain aging and neurodegeneration: from a mitochondrial point of view. J. Neurochem. 143, 418–431 (2017).
doi: 10.1111/jnc.14037 pubmed: 28397282 pmcid: 5724505
Bertucci, E. M. & Parrott, B. B. Is CpG density the link between epigenetic aging and lifespan? Trends Genet. 36, 725–727 (2020).
doi: 10.1016/j.tig.2020.06.003 pubmed: 32624337
Kosan, C., Heidel, F. H., Godmann, M. & Bierhoff, H. Epigenetic erosion in adult stem cells: drivers and passengers of aging. Cells 7, 237 (2018).
doi: 10.3390/cells7120237 pubmed: 30501028 pmcid: 6316114
Little, D. et al. A single cell high content assay detects mitochondrial dysfunction in iPSC-derived neurons with mutations in SNCA. Sci. Rep. 8, 9033 (2018).
doi: 10.1038/s41598-018-27058-0 pubmed: 29899557 pmcid: 5998042
Du, F., Yu, Q., Chen, A., Chen, D. & Yan, S. S. Astrocytes attenuate mitochondrial dysfunctions in human dopaminergic neurons derived from iPSC. Stem Cell Rep. 10, 366–374 (2018).
doi: 10.1016/j.stemcr.2017.12.021
Cheng, X. Y. et al. Human iPSCs derived astrocytes rescue rotenone-induced mitochondrial dysfunction and dopaminergic neurodegeneration in vitro by donating functional mitochondria. Transl. Neurodegener. 9, 1–14 (2020).
doi: 10.1186/s40035-020-00190-6
Zagoura, D., Canovas-Jorda, D., Pistollato, F., Bremer-Hoffmann, S. & Bal-Price, A. Evaluation of the rotenone-induced activation of the Nrf2 pathway in a neuronal model derived from human induced pluripotent stem cells. Neurochem. Int. 106, 62–73 (2017).
doi: 10.1016/j.neuint.2016.09.004 pubmed: 27615060
Benson, E. K., Lee, S. W. & Aaronson, S. A. Role of progerin-induced telomere dysfunction in HGPS premature cellular senescence. J. Cell Sci. 123, 2605–2612 (2010).
doi: 10.1242/jcs.067306 pubmed: 20605919 pmcid: 2908049
Ambasudhan, R. et al. Direct reprogramming of adult human fibroblasts to functional neurons under defined conditions. Cell Stem Cell 9, 113–118 (2011).
doi: 10.1016/j.stem.2011.07.002 pubmed: 21802386 pmcid: 4567246
Carter, J. L., Halmai, J. & Fink, K. D. The iNs and outs of direct reprogramming to induced neurons. Front. Genome Ed. 2, 7 (2020).
doi: 10.3389/fgeed.2020.00007 pubmed: 34713216 pmcid: 8525349
Drouin-Ouellet, J., Pircs, K., Barker, R. A., Jakobsson, J. & Parmar, M. Direct neuronal reprogramming for disease modeling studies using patient-derived neurons: what have we learned? Front. Neurosci. 11, 530 (2017).
doi: 10.3389/fnins.2017.00530 pubmed: 29033781 pmcid: 5625013
Mertens, J., Marchetto, M. C., Bardy, C. & Gage, F. H. Evaluating cell reprogramming, differentiation and conversion technologies in neuroscience. Nat. Rev. Neurosci. 17, 424–437 (2016).
doi: 10.1038/nrn.2016.46 pubmed: 27194476 pmcid: 6276815
Wang, H., Yang, Y., Liu, J. & Qian, L. Direct cell reprogramming: approaches, mechanisms and progress. Nat. Rev. Mol. Cell Biol. 22, 410–424 (2021).
doi: 10.1038/s41580-021-00335-z pubmed: 33619373 pmcid: 8161510
Wapinski, O. L. et al. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell 155, 621–635 (2013).
doi: 10.1016/j.cell.2013.09.028 pubmed: 24243019
Herdy, J. R. et al. Increased post-mitotic senescence in aged human neurons is a pathological feature of Alzheimer’s disease. Cell Stem Cell 29, 1637–1652.e1636 (2022).
doi: 10.1016/j.stem.2022.11.010 pubmed: 36459967 pmcid: 10093780
Traxler, L. et al. Warburg-like metabolic transformation underlies neuronal degeneration in sporadic Alzheimer’s disease. Cell Metab. 34, 1248–1263.e1246 (2022).
doi: 10.1016/j.cmet.2022.07.014 pubmed: 35987203 pmcid: 9458870
Barisano, G. et al. Blood–brain barrier link to human cognitive impairment and Alzheimer’s disease. Nat. Cardiovasc. Res. 1, 108–115 (2022).
doi: 10.1038/s44161-021-00014-4 pubmed: 35450117 pmcid: 9017393
Knox, E. G., Aburto, M. R., Clarke, G., Cryan, J. F. & O’Driscoll, C. M. The blood-brain barrier in aging and neurodegeneration. Mol. Psychiatr. 27, 2659–2673 (2022).
doi: 10.1038/s41380-022-01511-z
Montagne, A. et al. Blood-brain barrier breakdown in the aging human hippocampus. Neuron 85, 296–302 (2015).
doi: 10.1016/j.neuron.2014.12.032 pubmed: 25611508 pmcid: 4350773
Sweeney, M. D., Sagare, A. P. & Zlokovic, B. V. Blood-brain barrier breakdown in Alzheimer disease and other neurodegenerative disorders. Nat. Rev. Neurol. 14, 133–150 (2018).
doi: 10.1038/nrneurol.2017.188 pubmed: 29377008 pmcid: 5829048
Zlokovic, B. V. Neurovascular pathways to neurodegeneration in Alzheimer’s disease and other disorders. Nat. Rev. Neurosci. 12, 723–738 (2011).
doi: 10.1038/nrn3114 pubmed: 22048062 pmcid: 4036520
Chen, X. et al. Modeling sporadic Alzheimer’s disease in human brain organoids under serum exposure. Adv. Sci. 8, e2101462 (2021).
doi: 10.1002/advs.202101462
Mirabelli, P., Coppola, L. & Salvatore, M. Cancer cell lines are useful model systems for medical research. Cancers 11, 1098 (2019).
doi: 10.3390/cancers11081098 pubmed: 31374935 pmcid: 6721418
Gillet, J. P., Varma, S. & Gottesman, M. M. The clinical relevance of cancer cell lines. J. Natl. Cancer Inst. 105, 452–458 (2013).
doi: 10.1093/jnci/djt007 pubmed: 23434901 pmcid: 3691946
Wilding, J. L. & Bodmer, W. F. Cancer cell lines for drug discovery and development. Cancer Res. 74, 2377–2384 (2014).
doi: 10.1158/0008-5472.CAN-13-2971 pubmed: 24717177
Wijewardhane, N., Dressler, L. & Ciccarelli, F. D. Normal somatic mutations in cancer transformation. Cancer Cell 39, 125–129 (2021).
doi: 10.1016/j.ccell.2020.11.002 pubmed: 33220180
Smith, R. C. & Tabar, V. Constructing and deconstructing cancers using human pluripotent stem cells and organoids. Cell Stem Cell 24, 12–24 (2019).
doi: 10.1016/j.stem.2018.11.012 pubmed: 30581078
Haag, D. et al. H3.3-K27M drives neural stem cell-specific gliomagenesis in a human iPSC-derived model. Cancer Cell 39, 407–422.e413 (2021).
doi: 10.1016/j.ccell.2021.01.005 pubmed: 33545065
Crespo, M. et al. Colonic organoids derived from human induced pluripotent stem cells for modeling colorectal cancer and drug testing. Nat. Med. 23, 878–884 (2017).
doi: 10.1038/nm.4355 pubmed: 28628110 pmcid: 6055224
Ford, A. C., Yuan, Y. & Moayyedi, P. Long-term impact of helicobacter pylori eradication therapy on gastric cancer incidence and mortality in healthy infected individuals: a meta-analysis beyond 10 years of follow-up. Gastroenterology 163, 754–756.e751 (2022).
doi: 10.1053/j.gastro.2022.05.027 pubmed: 35598628
Polk, D. B. & Peek, R. M. Jr. Helicobacter pylori: gastric cancer and beyond. Nat. Rev. Cancer 10, 403–414 (2010).
doi: 10.1038/nrc2857 pubmed: 20495574 pmcid: 2957472
McCracken, K. W. et al. Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature 516, 400–404 (2014).
doi: 10.1038/nature13863 pubmed: 25363776 pmcid: 4270898
Wang, T. et al. Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of myeloid leukemia and identifies early disease targets. Cell Stem Cell 28, 1074–1089.e1077 (2021).
doi: 10.1016/j.stem.2021.01.011 pubmed: 33571445 pmcid: 8178190
Garcez, P. P. et al. Zika virus impairs growth in human neurospheres and brain organoids. Science 352, 816–818 (2016).
doi: 10.1126/science.aaf6116 pubmed: 27064148
Scoon, W. A. et al. Ebola virus infection induces a delayed type I IFN response in bystander cells and the shutdown of key liver genes in human iPSC-derived hepatocytes. Stem Cell Rep. 17, 2286–2302 (2022).
doi: 10.1016/j.stemcr.2022.08.003
Luo, Y., Zhang, M., Chen, Y., Chen, Y. & Zhu, D. Application of human induced pluripotent stem cell-derived cellular and organoid models for COVID-19 research. Front. Cell Dev. Biol. 9, 720099 (2021).
doi: 10.3389/fcell.2021.720099 pubmed: 34552930 pmcid: 8450444
Harschnitz, O. & Studer, L. Human stem cell models to study host-virus interactions in the central nervous system. Nat. Rev. Immunol. 21, 441–453 (2021).
doi: 10.1038/s41577-020-00474-y pubmed: 33398129 pmcid: 9653304
Lamers, M. M. & Haagmans, B. L. SARS-CoV-2 pathogenesis. Nat. Rev. Microbiol 20, 270–284 (2022).
doi: 10.1038/s41579-022-00713-0 pubmed: 35354968
Cevik, M., Kuppalli, K., Kindrachuk, J. & Peiris, M. Virology, transmission, and pathogenesis of SARS-CoV-2. BMJ 371, m3862 (2020).
doi: 10.1136/bmj.m3862 pubmed: 33097561
Harrison, A. G., Lin, T. & Wang, P. Mechanisms of SARS-CoV-2 transmission and pathogenesis. Trends Immunol. 41, 1100–1115 (2020).
doi: 10.1016/j.it.2020.10.004 pubmed: 33132005 pmcid: 7556779
Bestion, E., Halfon, P., Mezouar, S. & Mege, J. L. Cell and animal models for SARS-CoV-2 research. Viruses 14, 1507 (2022).
doi: 10.3390/v14071507 pubmed: 35891487 pmcid: 9319816
Chu, H., Chan, J. F. & Yuen, K. Y. Animal models in SARS-CoV-2 research. Nat. Methods 19, 392–394 (2022).
doi: 10.1038/s41592-022-01447-w pubmed: 35396468
Cleary, S. J. et al. Animal models of mechanisms of SARS-CoV-2 infection and COVID-19 pathology. Br. J. Pharm. 177, 4851–4865 (2020).
doi: 10.1111/bph.15143
Lee, C. Y. & Lowen, A. C. Animal models for SARS-CoV-2. Curr. Opin. Virol. 48, 73–81 (2021).
doi: 10.1016/j.coviro.2021.03.009 pubmed: 33906125 pmcid: 8023231
Takayama, K. In vitro and animal models for SARS-CoV-2 research. Trends Pharm. Sci. 41, 513–517 (2020).
doi: 10.1016/j.tips.2020.05.005 pubmed: 32553545
Simoneau, C. R. & Ott, M. Modeling multi-organ infection by SARS-CoV-2 using stem cell technology. Cell Stem Cell 27, 859–868 (2020).
doi: 10.1016/j.stem.2020.11.012 pubmed: 33275899 pmcid: 7713543
Huang, J. et al. SARS-CoV-2 infection of pluripotent stem cell-derived human lung alveolar Type 2 cells elicits a rapid epithelial-intrinsic inflammatory response. Cell Stem Cell 27, 962–973.e967 (2020).
doi: 10.1016/j.stem.2020.09.013 pubmed: 32979316 pmcid: 7500949
Lian, Q. et al. Differential effects of macrophage subtypes on SARS-CoV-2 infection in a human pluripotent stem cell-derived model. Nat. Commun. 13, 2028 (2022).
doi: 10.1038/s41467-022-29731-5 pubmed: 35440562 pmcid: 9018716
Elrobaa, I. H. & New, K. J. COVID-19: pulmonary and extra pulmonary manifestations. Front. Public Health 9, 711616 (2021).
doi: 10.3389/fpubh.2021.711616 pubmed: 34650947 pmcid: 8505777
Gupta, A. et al. Extrapulmonary manifestations of COVID-19. Nat. Med. 26, 1017–1032 (2020).
doi: 10.1038/s41591-020-0968-3 pubmed: 32651579
Ning, Q. et al. The mechanism underlying extrapulmonary complications of the coronavirus disease 2019 and its therapeutic implication. Signal. Transduct. Target Ther. 7, 57 (2022).
doi: 10.1038/s41392-022-00907-1 pubmed: 35197452 pmcid: 8863906
Chen, K. G., Park, K. & Spence, J. R. Studying SARS-CoV-2 infectivity and therapeutic responses with complex organoids. Nat. Cell Biol. 23, 822–833 (2021).
doi: 10.1038/s41556-021-00721-x pubmed: 34341531 pmcid: 8355201
Monteil, V. et al. Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2. Cell 181, 905–913.e907 (2020).
doi: 10.1016/j.cell.2020.04.004 pubmed: 32333836 pmcid: 7181998
Wang, W. L. et al. Detection of SARS-CoV-2 in different types of clinical specimens. Jama 323, 1843–1844 (2020).
pubmed: 32159775 pmcid: 7066521
Bojkova, D. et al. SARS-CoV-2 infects and induces cytotoxic effects in human cardiomyocytes. Cardiovasc. Res. 116, 2207–2215 (2020).
doi: 10.1093/cvr/cvaa267 pubmed: 32966582
Perez-Bermejo, J. A. et al. SARS-CoV-2 infection of human iPSC-derived cardiac cells reflects cytopathic features in hearts of patients with COVID-19. Sci. Transl. Med. 13, eabf7872 (2021).
doi: 10.1126/scitranslmed.abf7872 pubmed: 33723017
Sharma, A. et al. Human iPSC-derived cardiomyocytes are susceptible to SARS-CoV-2 infection. Cell Rep. Med. 1, 100052 (2020).
doi: 10.1016/j.xcrm.2020.100052 pubmed: 32835305 pmcid: 7323681
Ahmad, I. & Rathore, F. A. Neurological manifestations and complications of COVID-19: a literature review. J. Clin. Neurosci. 77, 8–12 (2020).
doi: 10.1016/j.jocn.2020.05.017 pubmed: 32409215 pmcid: 7200361
Niazkar, H. R., Zibaee, B., Nasimi, A. & Bahri, N. The neurological manifestations of COVID-19: a review article. Neurol. Sci. 41, 1667–1671 (2020).
doi: 10.1007/s10072-020-04486-3 pubmed: 32483687 pmcid: 7262683
Yassin, A. et al. Neurological manifestations and complications of coronavirus disease 2019 (COVID-19): a systematic review and meta-analysis. BMC Neurol. 21, 1–17 (2021).
doi: 10.1186/s12883-021-02161-4
Ramani, A. et al. SARS-CoV-2 targets neurons of 3D human brain organoids. Embo J. 39, e106230 (2020).
doi: 10.15252/embj.2020106230 pubmed: 32876341 pmcid: 7560208
Zhang, B. Z. et al. SARS-CoV-2 infects human neural progenitor cells and brain organoids. Cell Res. 30, 928–931 (2020).
doi: 10.1038/s41422-020-0390-x pubmed: 32753756
Cui, Q. et al. Compound screen identifies the small molecule Q34 as an inhibitor of SARS-CoV-2 infection. iScience 25, 103684 (2022).
doi: 10.1016/j.isci.2021.103684 pubmed: 34977495
Wang, C. et al. ApoE-isoform-dependent SARS-CoV-2 neurotropism and cellular response. Cell Stem Cell 28, 331–342.e335 (2021).
doi: 10.1016/j.stem.2020.12.018 pubmed: 33450186 pmcid: 7832490
Shen, W. B. et al. SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer’s-like neuropathology. Preprint at BioRxiv (2022).
Kleiman, R. J. & Engle, S. J. Human inducible pluripotent stem cells: Realization of initial promise in drug discovery. Cell Stem Cell 28, 1507–1515 (2021).
doi: 10.1016/j.stem.2021.08.002 pubmed: 34478628
Gu, M. et al. iPSC-endothelial cell phenotypic drug screening and in silico analyses identify tyrphostin-AG1296 for pulmonary arterial hypertension. Sci. Transl. Med. 13, eaba6480 (2021).
doi: 10.1126/scitranslmed.aba6480 pubmed: 33952674 pmcid: 8762958
Bray, M. A. et al. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat. Protoc. 11, 1757–1774 (2016).
doi: 10.1038/nprot.2016.105 pubmed: 27560178 pmcid: 5223290
Chin, M. Y., Espinosa, J. A., Pohan, G., Markossian, S. & Arkin, M. R. Reimagining dots and dashes: visualizing structure and function of organelles for high-content imaging analysis. Cell Chem. Biol. 28, 320–337 (2021).
doi: 10.1016/j.chembiol.2021.01.016 pubmed: 33600764 pmcid: 7995685
Vamathevan, J. et al. Applications of machine learning in drug discovery and development. Nat. Rev. Drug Discov. 18, 463–477 (2019).
doi: 10.1038/s41573-019-0024-5 pubmed: 30976107 pmcid: 6552674
Taubes, A. et al. Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer’s disease. Nat. Aging 1, 932–947 (2021).
doi: 10.1038/s43587-021-00122-7 pubmed: 36172600 pmcid: 9514594
Theodoris, C. V. et al. Network-based screen in iPSC-derived cells reveals therapeutic candidate for heart valve disease. Science 371, eabd0724 (2021).
doi: 10.1126/science.abd0724 pubmed: 33303684
Pangalos, M. N., Schechter, L. E. & Hurko, O. Drug development for CNS disorders: strategies for balancing risk and reducing attrition. Nat. Rev. Drug Discov. 6, 521–532 (2007).
doi: 10.1038/nrd2094 pubmed: 17599084
Waring, M. J. et al. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nat. Rev. Drug Discov. 14, 475–486 (2015).
doi: 10.1038/nrd4609 pubmed: 26091267
Inoue, H. & Yamanaka, S. The use of induced pluripotent stem cells in drug development. Clin. Pharm. Ther. 89, 655–661 (2011).
doi: 10.1038/clpt.2011.38
Liu, W., Deng, Y., Liu, Y., Gong, W. & Deng, W. Stem cell models for drug discovery and toxicology studies. J. Biochem. Mol. Toxicol. 27, 17–27 (2013).
doi: 10.1002/jbt.21470 pubmed: 23293059
Pasteuning-Vuhman, S., de Jongh, R., Timmers, A. & Pasterkamp, R. J. Towards advanced iPSC-based drug development for neurodegenerative disease. Trends Mol. Med. 27, 263–279 (2021).
doi: 10.1016/j.molmed.2020.09.013 pubmed: 33121873
Reiser, J. & Sever, S. Podocyte biology and pathogenesis of kidney disease. Annu Rev. Med. 64, 357–366 (2013).
doi: 10.1146/annurev-med-050311-163340 pubmed: 23190150
Musah, S. et al. Mature induced-pluripotent-stem-cell-derived human podocytes reconstitute kidney glomerular-capillary-wall function on a chip. Nat. Biomed. Eng. 1, 0069 (2017).
doi: 10.1038/s41551-017-0069 pubmed: 29038743 pmcid: 5639718
Richards, D. J. et al. Human cardiac organoids for the modelling of myocardial infarction and drug cardiotoxicity. Nat. Biomed. Eng. 4, 446–462 (2020).
doi: 10.1038/s41551-020-0539-4 pubmed: 32284552 pmcid: 7422941
Matsa, E. et al. Transcriptome profiling of patient-specific human iPSC-cardiomyocytes predicts individual drug safety and efficacy responses in vitro. Cell Stem Cell 19, 311–325 (2016).
doi: 10.1016/j.stem.2016.07.006 pubmed: 27545504 pmcid: 5087997
Sharma, A. et al. High-throughput screening of tyrosine kinase inhibitor cardiotoxicity with human induced pluripotent stem cells. Sci. Transl. Med. 9, eaaf2584 (2017).
doi: 10.1126/scitranslmed.aaf2584 pubmed: 28202772 pmcid: 5409837
Pellegrini, L. et al. Human CNS barrier-forming organoids with cerebrospinal fluid production. Science 369, eaaz5626 (2020).
doi: 10.1126/science.aaz5626 pubmed: 32527923 pmcid: 7116154
Kwon, O. et al. The development of a functional human small intestinal epithelium model for drug absorption. Sci. Adv. 7, eabh1586 (2021).
doi: 10.1126/sciadv.abh1586 pubmed: 34078609
Westerling-Bui, A. D. et al. Transplanted organoids empower human preclinical assessment of drug candidate for the clinic. Sci. Adv. 8, eabj5633 (2022).
doi: 10.1126/sciadv.abj5633 pubmed: 35857479 pmcid: 9258952
Brown, C. et al. Mesenchymal stem cells: cell therapy and regeneration potential. J. Tissue Eng. Regen. Med. 13, 1738–1755 (2019).
doi: 10.1002/term.2914 pubmed: 31216380
Chien, K. R. et al. Regenerating the field of cardiovascular cell therapy. Nat. Biotechnol. 37, 232–237 (2019).
doi: 10.1038/s41587-019-0042-1 pubmed: 30778231
Huang, K., Hu, S. & Cheng, K. A new era of cardiac cell therapy: opportunities and challenges. Adv. Health. Mater. 8, e1801011 (2019).
doi: 10.1002/adhm.201801011
Sterner, R. C. & Sterner, R. M. CAR-T cell therapy: current limitations and potential strategies. Blood Cancer J. 11, 69 (2021).
doi: 10.1038/s41408-021-00459-7 pubmed: 33824268 pmcid: 8024391
Brown, C. E. & Mackall, C. L. CAR T cell therapy: inroads to response and resistance. Nat. Rev. Immunol. 19, 73–74 (2019).
doi: 10.1038/s41577-018-0119-y pubmed: 30631206
Finck, A. V., Blanchard, T., Roselle, C. P., Golinelli, G. & June, C. H. Engineered cellular immunotherapies in cancer and beyond. Nat. Med. 28, 678–689 (2022).
doi: 10.1038/s41591-022-01765-8 pubmed: 35440724 pmcid: 9305718
Bashor, C. J., Hilton, I. B., Bandukwala, H., Smith, D. M. & Veiseh, O. Engineering the next generation of cell-based therapeutics. Nat. Rev. Drug Discov. 21, 655–675 (2022).
doi: 10.1038/s41573-022-00476-6 pubmed: 35637318 pmcid: 9149674
Desgres, M. & Menasche, P. Clinical translation of pluripotent stem cell therapies: challenges and considerations. Cell Stem Cell 25, 594–606 (2019).
doi: 10.1016/j.stem.2019.10.001 pubmed: 31703770
Stevens, K. R. & Murry, C. E. Human pluripotent stem cell-derived engineered tissues: clinical considerations. Cell Stem Cell 22, 294–297 (2018).
doi: 10.1016/j.stem.2018.01.015 pubmed: 29499147 pmcid: 6344123
Doss, M. X. & Sachinidis, A. Current challenges of iPSC-based disease modeling and therapeutic implications. Cells 8, 403 (2019).
doi: 10.3390/cells8050403 pubmed: 31052294 pmcid: 6562607
Lovell-Badge, R. et al. ISSCR guidelines for stem cell research and clinical translation: the 2021 update. Stem Cell Rep. 16, 1398–1408 (2021).
doi: 10.1016/j.stemcr.2021.05.012
Balboa, D. et al. Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells. Nat. Biotechnol. 40, 1042–1055 (2022).
doi: 10.1038/s41587-022-01219-z pubmed: 35241836 pmcid: 9287162
Du, Y. et al. Human pluripotent stem-cell-derived islets ameliorate diabetes in non-human primates. Nat. Med. 28, 272–282 (2022).
doi: 10.1038/s41591-021-01645-7 pubmed: 35115708
Feng, L. et al. Developing hypoimmunogenic human iPSC-derived oligodendrocyte progenitor cells as an off-the-shelf cell therapy for myelin disorders. Adv. Sci. 10, e2206910 (2023).
Madrid, M., Sumen, C., Aivio, S. & Saklayen, N. Autologous induced pluripotent stem cell-based cell therapies: promise, progress, and challenges. Curr. Protoc. 1, e88 (2021).
doi: 10.1002/cpz1.88 pubmed: 33725407
Schweitzer, J. S. et al. Personalized iPSC-derived dopamine progenitor cells for Parkinson’s disease. N. Engl. J. Med. 382, 1926–1932 (2020).
doi: 10.1056/NEJMoa1915872 pubmed: 32402162 pmcid: 7288982
Schweitzer, J. S., Song, B. & Kim, K. S. A step closer to autologous cell therapy for Parkinson’s disease. Cell Stem Cell 28, 595–597 (2021).
doi: 10.1016/j.stem.2021.03.010 pubmed: 33798419
Tang, L. V. et al. Gene editing of human iPSCs rescues thrombophilia in hereditary antithrombin deficiency in mice. Sci. Transl. Med. 14, eabq3202 (2022).
doi: 10.1126/scitranslmed.abq3202 pubmed: 36449603
Maxwell, K. G. et al. Gene-edited human stem cell-derived beta cells from a patient with monogenic diabetes reverse preexisting diabetes in mice. Sci. Transl. Med. 12, eaax9106 (2020).
doi: 10.1126/scitranslmed.aax9106 pubmed: 32321868 pmcid: 7233417
Depil, S., Duchateau, P., Grupp, S. A., Mufti, G. & Poirot, L. Off-the-shelf’ allogeneic CAR T cells: development and challenges. Nat. Rev. Drug Discov. 19, 185–199 (2020).
doi: 10.1038/s41573-019-0051-2 pubmed: 31900462
Crow, D. Could iPSCs enable “off-the-shelf” cell therapy? Cell 177, 1667–1669 (2019).
doi: 10.1016/j.cell.2019.05.043 pubmed: 31199910
Lanza, R., Russell, D. W. & Nagy, A. Engineering universal cells that evade immune detection. Nat. Rev. Immunol. 19, 723–733 (2019).
doi: 10.1038/s41577-019-0200-1 pubmed: 31417198
Wang, B. et al. Generation of hypoimmunogenic T cells from genetically engineered allogeneic human induced pluripotent stem cells. Nat. Biomed. Eng. 5, 429–440 (2021).
doi: 10.1038/s41551-021-00730-z pubmed: 34002062
Hu, X. et al. Hypoimmune induced pluripotent stem cells survive long term in fully immunocompetent, allogeneic rhesus macaques. Nat. Biotechnol. 42, 413–423 (2023).
Alvarez-Palomo, B. et al. Evaluation of the Spanish population coverage of a prospective HLA haplobank of induced pluripotent stem cells. Stem Cell Res Ther. 12, 233 (2021).
doi: 10.1186/s13287-021-02301-0 pubmed: 33849662 pmcid: 8042859
Lee, S. et al. Repurposing the cord blood bank for haplobanking of HLA-Homozygous iPSCs and their usefulness to multiple populations. Stem Cells 36, 1552–1566 (2018).
doi: 10.1002/stem.2865 pubmed: 30004605
Sullivan, S. et al. Haplobanking induced pluripotent stem cells for clinical use. Stem Cell Res. 49, 102035 (2020).
doi: 10.1016/j.scr.2020.102035 pubmed: 33221677
Yoshida, S. et al. A clinical-grade HLA haplobank of human induced pluripotent stem cells matching approximately 40% of the Japanese population. Med 4, 51–66.e10 (2023).
doi: 10.1016/j.medj.2022.10.003 pubmed: 36395757
Nguyen, P. K., Neofytou, E., Rhee, J.-W. & Wu, J. C. Potential strategies to address the major clinical barriers facing stem cell regenerative therapy for cardiovascular disease: a review. JAMA Cardiol. 1, 953–962 (2016).
doi: 10.1001/jamacardio.2016.2750 pubmed: 27579998 pmcid: 5378463
Aijaz, A. et al. Biomanufacturing for clinically advanced cell therapies. Nat. Biomed. Eng. 2, 362–376 (2018).
doi: 10.1038/s41551-018-0246-6 pubmed: 31011198 pmcid: 6594100
Lee, A. S., Tang, C., Rao, M. S., Weissman, I. L. & Wu, J. C. Tumorigenicity as a clinical hurdle for pluripotent stem cell therapies. Nat. Med. 19, 998–1004 (2013).
doi: 10.1038/nm.3267 pubmed: 23921754 pmcid: 3967018
Chour, T. et al. Method for selective ablation of undifferentiated human pluripotent stem cell populations for cell-based therapies. JCI Insight 6, e142000 (2021).
doi: 10.1172/jci.insight.142000 pubmed: 33830086 pmcid: 8119193
Kuang, Y. et al. Efficient, selective removal of human pluripotent stem cells via ecto-alkaline phosphatase-mediated aggregation of synthetic peptides. Cell Chem. Biol. 24, 685–694.e684 (2017).
doi: 10.1016/j.chembiol.2017.04.010 pubmed: 28529132
Jones, B. S., Lamb, L. S., Goldman, F. & Di Stasi, A. Improving the safety of cell therapy products by suicide gene transfer. Front. Pharm. 5, 254 (2014).
doi: 10.3389/fphar.2014.00254
Lund, R. J., Narva, E. & Lahesmaa, R. Genetic and epigenetic stability of human pluripotent stem cells. Nat. Rev. Genet. 13, 732–744 (2012).
doi: 10.1038/nrg3271 pubmed: 22965355
Ma, H. et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177–183 (2014).
doi: 10.1038/nature13551 pubmed: 25008523 pmcid: 4898064
Guo, R. et al. Generation and clinical potential of functional T lymphocytes from gene-edited pluripotent stem cells. Exp. Hematol. Oncol. 11, 1–17 (2022).
doi: 10.1186/s40164-022-00285-y
Motazedian, A. et al. Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids. Nat. Cell Biol. 22, 60–73 (2020).
doi: 10.1038/s41556-019-0445-8 pubmed: 31907413
Seet, C. S. et al. Generation of mature T cells from human hematopoietic stem and progenitor cells in artificial thymic organoids. Nat. Methods 14, 521–530 (2017).
doi: 10.1038/nmeth.4237 pubmed: 28369043 pmcid: 5426913
Wang, Z. et al. 3D-organoid culture supports differentiation of human CAR(+) iPSCs into highly functional CAR T cells. Cell Stem Cell 29, 651–653 (2022).
doi: 10.1016/j.stem.2022.03.007 pubmed: 35395190
Nagamoto, Y. et al. Transplantation of a human iPSC-derived hepatocyte sheet increases survival in mice with acute liver failure. J. Hepatol. 64, 1068–1075 (2016).
doi: 10.1016/j.jhep.2016.01.004 pubmed: 26778754
Sharma, R. et al. Clinical-grade stem cell-derived retinal pigment epithelium patch rescues retinal degeneration in rodents and pigs. Sci. Transl. Med. 11, eaat5580 (2019).
doi: 10.1126/scitranslmed.aat5580 pubmed: 30651323 pmcid: 8784963
Glaeser, J. D. et al. iPSC-neural crest derived cells embedded in 3D printable bio-ink promote cranial bone defect repair. Sci. Rep. 12, 18701 (2022).
doi: 10.1038/s41598-022-22502-8 pubmed: 36333414 pmcid: 9636385
Cichocki, F. et al. iPSC-derived NK cells maintain high cytotoxicity and enhance in vivo tumor control in concert with T cells and anti-PD-1 therapy. Sci. Transl. Med. 12, eaaz5618 (2020).
doi: 10.1126/scitranslmed.aaz5618 pubmed: 33148626 pmcid: 8861807
Moriarty, N. et al. A combined cell and gene therapy approach for homotopic reconstruction of midbrain dopamine pathways using human pluripotent stem cells. Cell Stem Cell 29, 434–448.e435 (2022).
doi: 10.1016/j.stem.2022.01.013 pubmed: 35180398
Iancu, E. M. & Kandalaft, L. E. Challenges and advantages of cell therapy manufacturing under good manufacturing practices within the hospital setting. Curr. Opin. Biotechnol. 65, 233–241 (2020).
doi: 10.1016/j.copbio.2020.05.005 pubmed: 32663771
Ackermann, M. et al. Continuous human iPSC-macrophage mass production by suspension culture in stirred tank bioreactors. Nat. Protoc. 17, 513–539 (2022).
doi: 10.1038/s41596-021-00654-7 pubmed: 35039668 pmcid: 7612500
Ackermann, M. et al. Bioreactor-based mass production of human iPSC-derived macrophages enables immunotherapies against bacterial airway infections. Nat. Commun. 9, 5088 (2018).
doi: 10.1038/s41467-018-07570-7 pubmed: 30504915 pmcid: 6269475
Yasuda, S. Y. et al. Chemically defined and growth-factor-free culture system for the expansion and derivation of human pluripotent stem cells. Nat. Biomed. Eng. 2, 173–182 (2018).
doi: 10.1038/s41551-018-0200-7 pubmed: 31015717
Zhao, Z. et al. Organoids. Nat. Rev. Methods Prim. 2, 94 (2022).
doi: 10.1038/s43586-022-00174-y
Basu, S. et al. Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD. Nat. Struct. Mol. Biol. 30, 1628–1639 (2023).
Dodonova, S. O., Zhu, F., Dienemann, C., Taipale, J. & Cramer, P. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature 580, 669–672 (2020).
doi: 10.1038/s41586-020-2195-y pubmed: 32350470
Wang, J. et al. Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions. Cell Stem Cell 28, 1868–1883.e1811 (2021).
doi: 10.1016/j.stem.2021.04.023 pubmed: 34038708
He, W. et al. De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat. Commun. 10, 4541 (2019).
doi: 10.1038/s41467-019-12489-8 pubmed: 31586052 pmcid: 6778102
Hsu, J. Y. et al. CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nat. Methods 15, 992–993 (2018).
doi: 10.1038/s41592-018-0225-6 pubmed: 30504875 pmcid: 6620603
Yang, L. et al. High-resolution characterization of gene function using single-cell CRISPR tiling screen. Nat. Commun. 12, 4063 (2021).
doi: 10.1038/s41467-021-24324-0 pubmed: 34210975 pmcid: 8249386
Liu, P., Chen, M., Liu, Y., Qi, L. S. & Ding, S. CRISPR-based chromatin remodeling of the endogenous Oct4 or Sox2 Locus enables reprogramming to pluripotency. Cell Stem Cell 22, 252–261.e254 (2018).
doi: 10.1016/j.stem.2017.12.001 pubmed: 29358044
Baumann, V. et al. Targeted removal of epigenetic barriers during transcriptional reprogramming. Nat. Commun. 10, 2119 (2019).
doi: 10.1038/s41467-019-10146-8 pubmed: 31073172 pmcid: 6509258
Takahashi, Y. et al. Transgenerational inheritance of acquired epigenetic signatures at CpG islands in mice. Cell 186, 715–731.e719 (2023).
doi: 10.1016/j.cell.2022.12.047 pubmed: 36754048
Tompkins, J. et al. Engineering CpG island DNA methylation in pluripotent cells through synthetic CpG-free ssDNA insertion. Cell Rep. Methods 3, 100465 (2023).
doi: 10.1016/j.crmeth.2023.100465 pubmed: 37323577 pmcid: 10261899
Cerneckis, J., Ming, G. L., Song, H., He, C. & Shi, Y. The rise of epitranscriptomics: recent developments and future directions. Trends Pharm. Sci. 45, 24–38 (2024).
doi: 10.1016/j.tips.2023.11.002 pubmed: 38103979
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
doi: 10.1038/s41586-021-03819-2 pubmed: 34265844 pmcid: 8371605
Stahl, K., Graziadei, A., Dau, T., Brock, O. & Rappsilber, J. Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Nat. Biotechnol. 1−10 (2023).
Greener, J. G., Kandathil, S. M., Moffat, L. & Jones, D. T. A guide to machine learning for biologists. Nat. Rev. Mol. Cell Biol. 23, 40–55 (2022).
doi: 10.1038/s41580-021-00407-0 pubmed: 34518686
Coronnello, C. & Francipane, M. G. Moving towards induced pluripotent stem cell-based therapies with artificial intelligence and machine learning. Stem Cell Rev. Rep. 18, 559–569 (2022).
doi: 10.1007/s12015-021-10302-y pubmed: 34843066
Pantazis, C. B. et al. A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell Stem Cell 29, 1685–1702.e1622 (2022).
doi: 10.1016/j.stem.2022.11.004 pubmed: 36459969 pmcid: 9782786
Bisogno, L. S. et al. Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes. Sci. Adv. 6, eabc3851 (2020).
doi: 10.1126/sciadv.abc3851 pubmed: 33219026 pmcid: 7679169
Czerniecki, S. M. et al. High-throughput screening enhances kidney organoid differentiation from human pluripotent stem cells and enables automated multidimensional phenotyping. Cell Stem Cell 22, 929–940.e924 (2018).
doi: 10.1016/j.stem.2018.04.022 pubmed: 29779890 pmcid: 5984728
Lu, Y., Zhou, Y., Ju, R. & Chen, J. Human-animal chimeras for autologous organ transplantation: technological advances and future perspectives. Ann. Transl. Med. 7, 576 (2019).
doi: 10.21037/atm.2019.10.13 pubmed: 31807557 pmcid: 6861770
Takebe, T. et al. Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature 499, 481–484 (2013).
doi: 10.1038/nature12271 pubmed: 23823721
Suchy, F., Yamaguchi, T. & Nakauchi, H. iPSC-derived organs in vivo: challenges and promise. Cell Stem Cell 22, 21–24 (2018).
doi: 10.1016/j.stem.2017.12.003 pubmed: 29304339

Auteurs

Jonas Cerneckis (J)

Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.

Hongxia Cai (H)

Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.

Yanhong Shi (Y)

Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA. yshi@coh.org.
Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA. yshi@coh.org.

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