New epigenetic reprogramming factors: functional testing in ES and iPS cells and development of small molecule modulators

Stem cells and regenerative medicine hold great promise for human health and healthy ageing in the future. A number of exciting technologies have recently been developed by which the derivation of embryonic stem cells from adult cell types is now possible, albeit inefficiently. This includes the transfer of reprogramming factors into adult cells, resulting in the generation of induced pluripotent stem cells (iPS cells). This technology, however, is inefficient and a particular bottleneck appears to be the reprogramming of the epigenome. Epigenetics or the epigenome refers to all the modifications to DNA and the chromatin that are important for the function of the genome in the context of development and in the adult organism in different organs and tissues. Importantly, in germ cells and early embryos, the epigenome is reprogrammed on a genome-wide scale, so that development of a new organism and of new stem cells is possible. Work in our laboratory and that of others has revealed several features of this genome-wide epigenetic reprogramming. In collaboration with the company CellCentric, we have begun to set up a number of systematic screens for the isolation of epigenetic reprogramming factors, including those that can erase DNA methylation from the genome. The current programme of work, again with CellCentric, aims to assess the function of these new reprogramming factors in germ cells and early embryos, embryonic stem cells, and in the generation of iPS cells. CellCentric will, in particular, work on the isolation of small molecules that can alter the function of our reprogramming factors, which will then be tested in embryonic stem cells and iPS cells. The combined programme of work will shed new light on the fundamental process of epigenetic reprogramming, and provide new tools for the manipulation of stem cells and the translation into approaches to regenerative medicine and healthy ageing.

In this application, in full collaboration with the company CellCentric, we propose (1) to fully annotate lists of candidate reprogramming factors that emerge from four screens that we are in the process of completing, including epigenomics, E coli genetic, in vitro compartmentalisation (IVC), and mammalian screens (2) to carry out functional testing of a select number of candidates in ES cells in a stable shRNA knockdown system that we have established, including the assessment of self-renewal, differentiation potential, and reprogramming capacity (3) to test specific candidates in an iPS system for their reprogramming ability, including in a system that is sensitised by specific Yamanaka factors or epigenetic drugs (4) to develop small molecule modulators for at least two key factor to use as a pharmacological tool in developmental biology, in ES and iPS cells, and finally (5) to test the function of specific candidates in vivo in germ cells and early embryos, by conditional knockouts and genome-scale epigenomic profiling by Next Generation Sequencing, especially in small numbers of cells. This integrated programme of work will identify novel reprogramming factors whose functions will shed new light on the biology of the reprogramming process and improve the generation of iPS cells. Overall, this project will contribute to our understanding of the healthy ageing process and provide new avenues for regenerative medicine and the pharmaceutical industry.

The major impact of this research programme will be in elucidating in an integrative fashion the biology of epigenetic reprogramming in germ cells and early embryos, pinpointing in a systematic way reprogramming factors and their role in shaping the Epigenome in ES cells and iPS cell generation. The industrial collaboration will enable systematic screens for small molecules that modulate the reprogramming progress, and further the translational development of factors, small molecules, and screens, including by licensing to key pharmaceutical companies. This will contribute to Health and Wealth generation in the UK and make distinctive contributions to the Healthy Ageing priority of BBSRC. This is a full collaboration between an academic partner with an internationally leading track record in Epigenetics research, and a company with an exciting business model and an international visibility and portfolio in developing epigenetic medicines and entering into licensing agreements with world leaders (Pfizer, Takeda). Hence there will be a joint impact on i) the academic field in the form of high quality and high impact publications, publication on websites and through high quality and high visibility links (eg NoE The Epigenome), and public engagement (public lectures, media), and ii) the industrial field by developing and characterising new factors, small molecule modulators of reprogramming, protecting IP, and licensing deals. This will contribute to further integration between academic and industry leaders in this important new area of post-genomic biology. This integration will include career development of the postdoctoral scientist, Dr Cassandra Farthing, at this exciting interface, as well as contributing to that of other members of the Reik lab and members of CellCentric, creating new opportunities for development and employment in the future.