Kathy Niakan: Projects

Lineage specification in human preimplantation development and derivation of novel stem cell lines

Early mammalian embryogenesis is controlled by mechanisms governing the balance between pluripotency and differentiation. We have found that the expression of early lineage-specific genes can vary significantly between species (Chen et al., 2009; Niakan and Eggan, 2013) with implications for developmental control and stem cell derivation. However, the mechanisms involved in patterning the human embryo are still unclear.

We seek to further elucidate key molecular and cellular properties of human pre-implantation embryos and compare these with early mouse development. Towards this aim, we are characterising the gene expression patterns throughout human preimplantation development. We will use this information to modulate conditions for in vitro establishment of alternative stem cells from human embryos, with the aim of expanding the repertoire of clinically relevant cells.

A major aim of this work is derivation of human extra-embryonic stem cells, which will have importance for modeling placental related failures of pregnancy and the earliest stages of embryogenesis. These early cell fate decisions are fundamental for human life and have clinical importance for the derivation and use of stem cells.

Figure 1

Molecular analysis of human preimplantation development. (Click to view larger image)

Are embryonic differentiation mechanisms conserved between mice and humans? In mice, the caudal-related homeodomain transcription factor, Cdx2 is expressed prior to blastocyst formation. By contrast, here we see that human embryos initiate CDX2 expression later, once the blastocyst is formed, and have persistent co-localisation of CDX2 and the octamer-binding transcription factor OCT4 in the trophectoderm, suggesting significant differences in the initiation and restriction of lineage defining transcription factors.

Selected publications

Niakan, KK and Eggan, K (2013) Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse Developmental Biology, 375, 54-64

Niakan, KK; Han, J; Pedersen, RA; Simon, C and Pera, RAR (2012) Human pre-implantation embryo development Development 139, 829-841

Chen, AE; Egli, D; Niakan, K; Deng, J; Akutsu, H; Yamaki, M; Cowan, C; Fitz-Gerald, C; Zhang, K; Melton, DA and Eggan, K (2009) Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines Cell Stem Cell 4, 103-106

Dimos, JT; Rodolfa, KT; Niakan, KK; Weisenthal, LM; Mitsumoto, H; Chung, W; Croft, GF; Saphier, G; Leibel, R; Goland, R; Wichterle, H; Henderson, CE and Eggan, K (2008) Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons Science 321, 11218-1221

Inducible switch of stem cells from a pluripotency to differentiation program

Although we have discovered significant differences between human and mouse preimplantation development, many of the key mechanisms are conserved, including the expression of pluripotency transcription factors Nanog and Oct4. Therefore, to complement our human research and to mechanistically understand how stem cells differentiate, we are using mouse embryonic stem cells (mESCs), which are highly amenable to genetic manipulation.

For example, we have generated mESCs that overexpress transcription factors in a controlled (doxycycline inducible) manner, allowing for inducible differentiation (Niakan et al., 2010). We hypothesise that the unique ability of specific transcription factors to induce ESC differentiation results from a dual function in activation of endoderm genes and simultaneous direct repression of pluripotency genes.

To further understand the network of gene regulatory changes during ESC differentiation, we are determining the hierarchy of gene and protein changes during early differentiation. Our preliminary analysis has revealed known as well as novel candidate regulators of stem cell self-renewal and endoderm differentiation. In the future we will analyse the function of these candidates by performing gain- and loss-of-function analyses in the context of inducible differentiation. Combination of these data with gene expression analysis will generate hypotheses concerning the genetic hierarchy of pluripotency disengagement. These experiments will directly inform derivation of human extra-embryonic stem cells, as the core network involved in embryonic stem cell self-renewal is conserved in humans and mice.

Figure 2

Inducible repression of stem cell pluripotency and promotion of differentation. (Click to view larger image)

How do transcription factors control pluripotent stem cell differentiation? We observed that Nanog and the SRY-related HMG-box transcription factor Sox17 were bound reciprocally to shared Nanog/Sox17 genomic sites, represented here by the region upstream of the Lama1 start site (arrow).

This suggests a mechanism for initiation of differentiation in which Sox17 displaces repressive Nanog complexes from shared binding sites and, in turn, activates gene expression.

Selected publications

Niakan, KK; Ji, H; Maehr, R; Vokes, SA; Rodolfa, KT; Sherwood, RI; Yamaki, M; Dimos, JT; Chen, AE; Melton, DA; McMahon, AP and Eggan, K (2010) Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal Genes & Development 24, 312-326 

Yu, C; Niakan, KK; Matsushita, M; Stamatoyannopoulos, G; Orkin, SH and Raskind, WH (2002) X-linked thrombocytopenia with thalassemia from a mutation in the amino finger of GATA-1 affecting DNA binding rather than FOG-1 interaction Blood 100, 2040-2045

Extracellular signalling and exit from stem cell self-renewal

Our laboratory has recently developed approaches using growth factors that allow for the generation of self-renewing extra-embryonic endoderm cells without the requirement for gene manipulation (Cho et al., 2012; Niakan et al., 2013). A notable advantage of this approach is potential application to mutant mESCs, allowing genetic study of extra-embryonic endoderm development.

While we have discovered that paracrine FGF-signalling compensates for the loss of endogenous Fgf4, which is necessary to exit mESC self-renewal, but not for extra-embryonic endoderm cell maintenance, several questions remain: Are downstream MAP kinases the main effectors of FGF signalling? How rapidly is FGF/MAP kinase signalling transmitted? What is the specific effect of MAP kinase activation on the pluripotency gene regulatory network?

Moreover, our method has revealed that distinct pluripotent stem cells respond uniquely to differentiation promoting signals. Extra-embryonic endoderm cells can be derived from mESCs cultured with LIF and either serum or Erk- and Gsk3-inhibitors (2i). However, we find that epiblast stem cells (EpiSCs) derived from the post-implantation embryo are refractory to extra-embryonic endoderm cell establishment in this assay, further demonstrating that EpiSCs represent a pluripotent state distinct from mESCs. Using this approach we seek to further dissect the genetic network and signalling environments that influence stem cell differentiation and to determine whether extra-embryonic stem cells can be derived from human embryonic stem cells. These experiments will provide novel insight into the impact of signal transduction on the pluripotency gene regulatory network.

Figure 3

Extracellular signaling and exit from stem cell self-renewal. (Click to view larger image)

How does stem cell state and signalling influence lineage decisions? We have established a novel directed differentiation approach, which redefines the differentiation potential of mouse embryonic stem (mES) cells to include the capacity to give rise to both embryonic and extra-embryonic lineages. We hypothesise that FGF signalling is required to exit mES cell self-renewal but not for extra-embryonic endoderm stem cell (XEN) maintenance.

Selected publications

Cho, LTY; Wamaitha, SE; Tsai, IJ; Artus, J; Sherwood, RI; Pedersen, RA; Hadjantonakis, A-K and Niakan, KK (2012) Conversion from mouse embryonic to extra-embryonic endoderm stem cells reveals distinct differentiation capacities of pluripotent stem cell states Development 139, 2866-2877

Niakan, KK; Schrode, N; Cho, LT; Hadjantonakis, AK (2013) Derivation of extraembryonic endoderm stem (XEN) cells from mouse embryos and embryonic stem cells Nature Protocols 8, 1028-1041

Kathy Niakan

+44 (0)20 379 61539

  • Qualifications and History
  • 2005 PhD, University of California, Los Angeles, USA
  • 2005 Postdoctoral Fellow, Harvard University, Cambridge, USA
  • 2009 Centre for Trophoblast Research Next Generation Fellow, University of Cambridge, UK
  • 2013 Group Leader, Medical Research Council National Institute for Medical Research, London, UK
  • 2015 Group Leader, the Francis Crick Institute, London, UK