Key Points
-
For more then half a century, C. H. Waddington's metaphor of a marble rolling down a landscape that segregates into different grooves has served as a sophisticated illustration of cell specification during development. However, some shortcomings emerge when trying to apply such a model to recent reprogramming and cell fate conversion studies.
-
This Review discusses the current state of the art in direct cell fate conversion and also presents a new 'epigenetic disc' model. This model provides an alternative hierarchy-free landscape for modelling cell programming and accomodates new findings in this rapidly developing field.
-
Recent studies demonstrate that direct cell conversion is not limited to cell types from the same germ layer. With a set of just a few transcription factors and/or microRNAs, direct cell conversion can be achieved between several germ layers. Yet, parameters for validating such conversion processes are still to be defined. They include conversion efficiency and identity, stability, functionality and safety of the converted cell types.
-
The recent advances in cell fate conversion have raised exciting new questions in the field and have paved the way for new research studies, which address the induction of distinct cellular subtypes and expandable progenitor cells, how to enhance conversion efficiency and how to translate this approach to an in vivo scenario.
Abstract
For decades, Waddington's concept of the 'epigenetic landscape' has served as an educative hierarchical model to illustrate the progressive restriction of cell differentiation potential during normal development. While still being highly valuable in the context of normal development, the Waddington model falls short of accommodating recent breakthroughs in cell programming. The advent of induced pluripotent stem (iPS) cells and advances in direct cell fate conversion (also known as transdifferentiation) suggest that somatic and pluripotent cell fates can be interconverted without transiting through distinct hierarchies. We propose a non-hierarchical 'epigenetic disc' model to explain such cell fate transitions, which provides an alternative landscape for modelling cell programming and reprogramming.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Bernstein, B. E., Meissner, A. & Lander, E. S. The mammalian epigenome. Cell 128, 669–681 (2007).
Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001).
Waddington, C. H. The strategy of the genes; a discussion of some aspects of theoretical biology (Allen & Unwin, 1957). The presentation of C. H. Waddington's famous metaphor of a marble rolling down a hill as a model for progressive restriction of cell differentiation potential during development.
Briggs, R. & King, T. J. Transplantation of living nuclei from blastula cells into enucleated frogs' eggs. Proc. Natl Acad. Sci. USA 38, 455–463 (1952).
Campbell, K. H., McWhir, J., Ritchie, W. A. & Wilmut, I. Sheep cloned by nuclear transfer from a cultured cell line. Nature 380, 64–66 (1996).
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).
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).
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
Davis, R. L., Weintraub, H. & Lassar, A. B. Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell 51, 987–1000 (1987).
Vierbuchen, T. et al. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463, 1035–1041 (2010). Describes the induction of functional neurons, termed induced neuron-like cells, from mouse fibroblasts, thereby providing the first evidence for successful trans-germ layer cell fate conversion.
Pang, Z. P. et al. Induction of human neuronal cells by defined transcription factors. Nature 476, 220–223 (2011).
Taylor, S. M. & Jones, P. A. Multiple new phenotypes induced in 10T1/2 and 3T3 cells treated with 5-azacytidine. Cell 17, 771–779 (1979).
Lassar, A. B., Paterson, B. M. & Weintraub, H. Transfection of a DNA locus that mediates the conversion of 10T1/2 fibroblasts to myoblasts. Cell 47, 649–656 (1986).
Weintraub, H. et al. Activation of muscle-specific genes in pigment, nerve, fat, liver, and fibroblast cell lines by forced expression of MyoD. Proc. Natl Acad. Sci. USA 86, 5434–5438 (1989).
Choi, J. et al. MyoD converts primary dermal fibroblasts, chondroblasts, smooth muscle, and retinal pigmented epithelial cells into striated mononucleated myoblasts and multinucleated myotubes. Proc. Natl Acad. Sci. USA 87, 7988–7992 (1990).
Schafer, B. W., Blakely, B. T., Darlington, G. J. & Blau, H. M. Effect of cell history on response to helix–loop–helix family of myogenic regulators. Nature 344, 454–458 (1990).
Orkin, S. H. & Zon, L. I. Hematopoiesis: an evolving paradigm for stem cell biology. Cell 132, 631–644 (2008).
Reya, T., Morrison, S. J., Clarke, M. F. & Weissman, I. L. Stem cells, cancer, and cancer stem cells. Nature 414, 105–111 (2001).
Arinobu, Y. et al. Reciprocal activation of GATA-1 and PU.1 marks initial specification of hematopoietic stem cells into myeloerythroid and myelolymphoid lineages. Cell Stem Cell 1, 416–427 (2007).
Iwasaki, H. & Akashi, K. Myeloid lineage commitment from the hematopoietic stem cell. Immunity 26, 726–740 (2007).
Okuno, Y. et al. Potential autoregulation of transcription factor PU.1 by an upstream regulatory element. Mol. Cell. Biol. 25, 2832–2845 (2005).
Kulessa, H., Frampton, J. & Graf, T. GATA-1 reprograms avian myelomonocytic cell lines into eosinophils, thromboblasts, and erythroblasts. Genes Dev. 9, 1250–1262 (1995).
Visvader, J. E., Elefanty, A. G., Strasser, A. & Adams, J. M. GATA-1 but not SCL induces megakaryocytic differentiation in an early myeloid line. EMBO J. 11, 4557–4564 (1992).
Heyworth, C., Pearson, S., May, G. & Enver, T. Transcription factor-mediated lineage switching reveals plasticity in primary committed progenitor cells. EMBO J. 21, 3770–3781 (2002).
Nerlov, C. & Graf, T. PU.1 induces myeloid lineage commitment in multipotent hematopoietic progenitors. Genes Dev. 12, 2403–2412 (1998).
Xie, H., Ye, M., Feng, R. & Graf, T. Stepwise reprogramming of B cells into macrophages. Cell 117, 663–676 (2004).
Zhang, P. et al. Enhancement of hematopoietic stem cell repopulating capacity and self-renewal in the absence of the transcription factor C/EBPα. Immunity 21, 853–863 (2004).
Bussmann, L. H. et al. A robust and highly efficient immune cell reprogramming system. Cell Stem Cell 5, 554–566 (2009).
Iwasaki, H. et al. The order of expression of transcription factors directs hierarchical specification of hematopoietic lineages. Genes Dev. 20, 3010–3021 (2006).
Feng, R. et al. PU.1 and C/EBPα/β convert fibroblasts into macrophage-like cells. Proc. Natl Acad. Sci. USA 105, 6057–6062 (2008).
Natoli, G. Maintaining cell identity through global control of genomic organization. Immunity 33, 12–24 (2010).
Senyo, S. E. et al. Mammalian heart renewal by pre-existing cardiomyocytes. Nature 493, 433–436 (2013).
Ieda, M. et al. Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142, 375–386 (2010). Describes conversion of mouse fibroblasts into functional cardiomyocytes through the overexpression of three transcription factors.
Qian, L. et al. In vivo reprogramming of murine cardiac fibroblasts into induced cardiomyocytes. Nature 485, 593–598 (2012).
Song, K. et al. Heart repair by reprogramming non-myocytes with cardiac transcription factors. Nature 485, 599–604 (2012).
Olson, E. N. Gene regulatory networks in the evolution and development of the heart. Science 313, 1922–1927 (2006).
Srivastava, D. Making or breaking the heart: from lineage determination to morphogenesis. Cell 126, 1037–1048 (2006).
Cirillo, L. A. et al. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell 9, 279–289 (2002).
Jayawardena, T. M. et al. microRNA-mediated in vitro and in vivo direct reprogramming of cardiac fibroblasts to cardiomyocytes. Circ. Res. 110, 1465–1473 (2012).
Yoo, A. S., Staahl, B. T., Chen, L. & Crabtree, G. R. microRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature 460, 642–646 (2009).
Puri, S. & Hebrok, M. Cellular plasticity within the pancreas — lessons learned from development. Dev. Cell 18, 342–356 (2010).
Teta, M., Rankin, M. M., Long, S. Y., Stein, G. M. & Kushner, J. A. Growth and regeneration of adult β-cells does not involve specialized progenitors. Dev. Cell 12, 817–826 (2007).
Xu, X. et al. β-cells can be generated from endogenous progenitors in injured adult mouse pancreas. Cell 132, 197–207 (2008).
Zaret, K. S. Genetic programming of liver and pancreas progenitors: lessons for stem-cell differentiation. Nature Rev. Genet. 9, 329–340 (2008).
Gu, G., Dubauskaite, J. & Melton, D. A. Direct evidence for the pancreatic lineage: NGN3+ cells are islet progenitors and are distinct from duct progenitors. Development 129, 2447–2457 (2002).
Ferber, S. et al. Pancreatic and duodenal homeobox gene 1 induces expression of insulin genes in liver and ameliorates streptozotocin-induced hyperglycemia. Nature Med. 6, 568–572 (2000).
Grapin-Botton, A., Majithia, A. R. & Melton, D. A. Key events of pancreas formation are triggered in gut endoderm by ectopic expression of pancreatic regulatory genes. Genes Dev. 15, 444–454 (2001).
Horb, M. E., Shen, C. N., Tosh, D. & Slack, J. M. Experimental conversion of liver to pancreas. Curr. Biol. 13, 105–115 (2003).
Sapir, T. et al. Cell-replacement therapy for diabetes: generating functional insulin-producing tissue from adult human liver cells. Proc. Natl Acad. Sci. USA 102, 7964–7969 (2005).
Yechoor, V. et al. Neurogenin3 is sufficient for transdetermination of hepatic progenitor cells into neo-islets in vivo but not transdifferentiation of hepatocytes. Dev. Cell 16, 358–373 (2009).
Gu, C. et al. Pancreatic β-cells require NeuroD to achieve and maintain functional maturity. Cell. Metab. 11, 298–310 (2010).
Kataoka, K. et al. MafA is a glucose-regulated and pancreatic β-cell-specific transcriptional activator for the insulin gene. J. Biol. Chem. 277, 49903–49910 (2002).
Matsuoka, T. A. et al. Members of the large Maf transcription family regulate insulin gene transcription in islet β-cells. Mol. Cell. Biol. 23, 6049–6062 (2003).
Artner, I., Hang, Y., Guo, M., Gu, G. & Stein, R. MafA is a dedicated activator of the insulin gene in vivo. J. Endocrinol. 198, 271–279 (2008).
Zhang, C. et al. MafA is a key regulator of glucose-stimulated insulin secretion. Mol. Cell. Biol. 25, 4969–4976 (2005).
Zhou, Q., Brown, J., Kanarek, A., Rajagopal, J. & Melton, D. A. In vivo reprogramming of adult pancreatic exocrine cells to β-cells. Nature 455, 627–632 (2008). Describes transcription factor-based in vivo transdifferentiation of exocrine pancreatic cells into functional insulin-producing β-cells.
Guillemot, F. Cellular and molecular control of neurogenesis in the mammalian telencephalon. Curr. Opin. Cell Biol. 17, 639–647 (2005).
Jessell, T. M. Neuronal specification in the spinal cord: inductive signals and transcriptional codes. Nature Rev. Genet. 1, 20–29 (2000).
Molyneaux, B. J., Arlotta, P., Menezes, J. R. & Macklis, J. D. Neuronal subtype specification in the cerebral cortex. Nature Rev. Neurosci. 8, 427–437 (2007).
Wonders, C. P. & Anderson, S. A. The origin and specification of cortical interneurons. Nature Rev. Neurosci. 7, 687–696 (2006).
Bellefroid, E. J. et al. X-MyT1, a Xenopus C2HC-type zinc finger protein with a regulatory function in neuronal differentiation. Cell 87, 1191–1202 (1996).
Lee, J. E. et al. Conversion of Xenopus ectoderm into neurons by NeuroD, a basic helix–loop–helix protein. Science 268, 836–844 (1995).
Turner, D. L. & Weintraub, H. Expression of achaete-scute homolog 3 in Xenopus embryos converts ectodermal cells to a neural fate. Genes Dev. 8, 1434–1447 (1994).
Berninger, B. et al. Functional properties of neurons derived from in vitro reprogrammed postnatal astroglia. J. Neurosci. 27, 8654–8664 (2007).
Heins, N. et al. Glial cells generate neurons: the role of the transcription factor Pax6. Nature Neurosci. 5, 308–315 (2002).
Heinrich, C. et al. Directing astroglia from the cerebral cortex into subtype specific functional neurons. PLoS Biol. 8, e1000373 (2010).
Probst, A. V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. Nature Rev. Mol. Cell Biol. 10, 192–206 (2009).
Costa, M. R., Gotz, M. & Berninger, B. What determines neurogenic competence in glia? Brain Res. Rev. 63, 47–59 (2010).
LoTurco, J. J. & Bai, J. The multipolar stage and disruptions in neuronal migration. Trends Neurosci. 29, 407–413 (2006).
Heng, J. I. et al. Neurogenin 2 controls cortical neuron migration through regulation of Rnd2. Nature 455, 114–118 (2008).
Marro, S. et al. Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. Cell Stem Cell 9, 374–382 (2011).
Hevner, R. F., Hodge, R. D., Daza, R. A. & Englund, C. Transcription factors in glutamatergic neurogenesis: conserved programs in neocortex, cerebellum, and adult hippocampus. Neurosci. Res. 55, 223–233 (2006).
Qiang, L. et al. Directed conversion of Alzheimer's disease patient skin fibroblasts into functional neurons. Cell 146, 359–371 (2011). Demonstrates induced neuron-like cells from patients with Alzheimer's disease and thus the possibility to model neurodegenerative disorders in directly converted cells.
Yoo, A. S. et al. microRNA-mediated conversion of human fibroblasts to neurons. Nature 476, 228–231 (2011).
Ambasudhan, R. et al. Direct reprogramming of adult human fibroblasts to functional neurons under defined conditions. Cell Stem Cell 9, 113–118 (2011).
Xue, Y. et al. Direct conversion of fibroblasts to neurons by reprogramming PTB-regulated microRNA circuits. Cell 152, 82–96 (2013). Demonstrates the efficient generation of induced neuron-like cells by repression of a single RNA-binding PTB protein.
Ladewig, J. et al. Small molecules enable highly efficient neuronal conversion of human fibroblasts. Nature Methods 9, 575–578 (2012). A combination of pro-neural transcription factors and small molecule pathway inhibitors is used for highly efficient conversion of human fibroblasts and cord blood cells into neurons.
Chambers, S. M. et al. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nature Biotech. 27, 275–280 (2009).
Li, W. et al. Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors. Proc. Natl Acad. Sci. USA 108, 8299–8304 (2011).
Polo, J. M. & Hochedlinger, K. When fibroblasts MET iPSCs. Cell Stem Cell 7, 5–6 (2010).
Li, R. et al. A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 7, 51–63 (2010).
Samavarchi-Tehrani, P. et al. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7, 64–77 (2010).
Moore, K. B., Schneider, M. L. & Vetter, M. L. Posttranslational mechanisms control the timing of bHLH function and regulate retinal cell fate. Neuron 34, 183–195 (2002).
Huang, P. et al. Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors. Nature 475, 386–389 (2011).
Sekiya, S. & Suzuki, A. Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors. Nature 475, 390–393 (2011). Provides, together with reference 84, the first evidence for the induction of functional hepatocyte-like cells from fibroblasts.
Sheng, C. et al. Direct reprogramming of Sertoli cells into multipotent neural stem cells by defined factors. Cell Res. 22, 208–218 (2012). Demonstrates the generation of expandable neural stem-like cells from a mesenchymal starting population.
Lujan, E., Chanda, S., Ahlenius, H., Sudhof, T. C. & Wernig, M. Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells. Proc. Natl Acad. Sci. USA 109, 2527–2532 (2011).
Tao, W. & Lai, E. Telencephalon-restricted expression of BF-1, a new member of the HNF-3/fork head gene family, in the developing rat brain. Neuron 8, 957–966 (1992).
Han, D. W. et al. Direct reprogramming of fibroblasts into neural stem cells by defined factors. Cell Stem Cell 10, 465–472 (2012).
Ring, K. L. et al. Direct reprogramming of mouse and human fibroblasts into multipotent neural stem cells with a single factor. Cell Stem Cell 11, 100–109 (2012).
Szabo, E. et al. Direct conversion of human fibroblasts to multilineage blood progenitors. Nature 468, 521–526 (2010).
Corcoran, L. M. et al. Oct-2, although not required for early B-cell development, is critical for later B-cell maturation and for postnatal survival. Genes Dev. 7, 570–582 (1993).
Wang, V. E., Schmidt, T., Chen, J., Sharp, P. A. & Tantin, D. Embryonic lethality, decreased erythropoiesis, and defective octamer-dependent promoter activation in Oct-1-deficient mice. Mol. Cell. Biol. 24, 1022–1032 (2004).
Efe, J. A. et al. Conversion of mouse fibroblasts into cardiomyocytes using a direct reprogramming strategy. Nature Cell Biol. 13, 215–222 (2011).
Kim, J. et al. Direct reprogramming of mouse fibroblasts to neural progenitors. Proc. Natl Acad. Sci. USA 108, 7838–7843 (2011).
Koch, P., Opitz, T., Steinbeck, J. A., Ladewig, J. & Brüstle, O. A rosette-type, self-renewing human ES cell-derived neural stem cell with potential for in vitro instruction and synaptic integration. Proc. Natl Acad. Sci. USA 106, 3225–3230 (2009).
Thier, M. et al. Direct conversion of fibroblasts into stably expandable neural stem cells. Cell Stem Cell 10, 473–479 (2012).
Matsui, T. et al. Neural stem cells directly differentiated from partially reprogrammed fibroblasts rapidly acquire gliogenic competency. Stem Cells 30, 1109–1119 (2012).
Silva, J. & Smith, A. Capturing pluripotency. Cell 132, 532–536 (2008).
Kim, K. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010).
Ohi, Y. et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nature Cell Biol. 13, 541–549 (2011).
Polo, J. M. et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nature Biotechnol. 28, 848–855 (2010).
Smale, S. T. Pioneer factors in embryonic stem cells and differentiation. Curr. Opin. Genet. Dev. 20, 519–526 (2010).
Zaret, K. S. et al. Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. Cold Spring Harb. Symp. Quant. Biol. 73, 119–126 (2008).
Magnani, L., Eeckhoute, J. & Lupien, M. Pioneer factors: directing transcriptional regulators within the chromatin environment. Trends Genet. 27, 465–474 (2011).
Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008).
Stadtfeld, M., Maherali, N., Breault, D. T. & Hochedlinger, K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell 2, 230–240 (2008).
Miyoshi, N. et al. Reprogramming of mouse and human cells to pluripotency using mature microRNAs. Cell Stem Cell 8, 633–638 (2011).
Ichida, J. K. et al. A small-molecule inhibitor of Tgf-β signaling replaces Sox2 in reprogramming by inducing Nanog. Cell Stem Cell 5, 491–503 (2009).
Peleg, S. et al. Altered histone acetylation is associated with age-dependent memory impairment in mice. Science 328, 753–756 (2010).
Pfisterer, U. et al. Direct conversion of human fibroblasts to dopaminergic neurons. Proc. Natl Acad. Sci. USA 108, 10343–10348 (2011).
Caiazzo, M. et al. Direct generation of functional dopaminergic neurons from mouse and human fibroblasts. Nature 476, 224–227 (2011).
Son, E. Y. et al. Conversion of mouse and human fibroblasts into functional spinal motor neurons. Cell Stem Cell 9, 205–218 (2011).
Kim, J. et al. Functional integration of dopaminergic neurons directly converted from mouse fibroblasts. Cell Stem Cell 9, 413–419 (2011).
Acknowledgements
Work in the laboratory of O. B. is supported by the European Union (FP7-HEALTH-2007-B-22943-NeuroStemCell and FP7-HEALTH-2010-266753-SCR&Tox, COLIPA; to O.B.), the Federal Ministry of Education and Research (BMBF; grants 01GS0860, 01GN1008C, 01GN1009B, 0315799; to O.B.; ERA-Net for Research Programmes on Rare Diseases 01GM1309A; to P.K.), BIO.NRW (project StemCellFactory; to O.B. and P.K.), the Hertie Foundation (to O.B.), the Ministry of Innovation, Science and Research of the State of North Rhine-Westphalia (to J.L. and P.K.) and BONFOR (to J.L.).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Related links
Glossary
- Anlage
-
The initial clustering of embryonic cells from which a part of an organ, or the whole organ, develops.
- Exocrine cells
-
Cells that secrete hormones, factors or other material.
- Type I diabetes
-
A variant of diabetes that is caused by an autoimmune reaction against insulin-producing cells; previously also known as juvenile diabetes.
- Ground state
-
A physics and chemistry term that denotes the state of having the least energy of all the possible states. This term was recently adopted in cell biology to denote the most primordial or authentic state, or differentiation stage (such as ground state pluripotency), of a cell.
Rights and permissions
About this article
Cite this article
Ladewig, J., Koch, P. & Brüstle, O. Leveling Waddington: the emergence of direct programming and the loss of cell fate hierarchies. Nat Rev Mol Cell Biol 14, 225–236 (2013). https://doi.org/10.1038/nrm3543
Published:
Issue Date:
DOI: https://doi.org/10.1038/nrm3543
This article is cited by
-
Direct cardiac reprogramming: basics and future challenges
Molecular Biology Reports (2023)
-
Human-induced pluripotent stem cells-derived retinal pigmented epithelium, a new horizon for cells-based therapies for age-related macular degeneration
Stem Cell Research & Therapy (2022)
-
Engineered biomaterials for in situ tissue regeneration
Nature Reviews Materials (2020)
-
Determining Relative Dynamic Stability of Cell States Using Boolean Network Model
Scientific Reports (2018)
-
Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency
Scientific Reports (2018)
