Cell Reprogramming - What we can learn from the embryo

@Burton et al. 2020, Nature Cell Bio; Epigenetics@HMGU

Cellular potency provides cells with the capacity to differentiate into multiple tissues and cell types. This process normally occurs during development, at the time in which our organs, tissues and body forms. Since all cells in the body contain the same genetic code -the same DNA- this process is controlled by epigenetics. Epigenetics therefore mediates changes in gene expression, that is, in the way our genes are ‘read’ from our genetic makeup, most notably by regulating how accessible the DNA is, through the packing of DNA in the macromolecule called chromatin. One of the most fascinating aspects of life is that the fertilized egg (zygote) can form a full new organism. In mammals, development starts with fertilization of the oocyte by the sperm, two highly differentiated cells. The resulting cell, the zygote can form a full new organism by itself. We call this capacity ‘totipotency’ which is the highest degree of cellular plasticity. Since all cells of an organism have the same zygote as ancestor, they all contain the same genetic code – the same DNA. The cells of our tissues, such as heart or liver, do not require the same proteins and thus, they only express the genes of the proteins that they need. How do cells control this?Within a mammalian cell, the DNA molecule is packaged into a structure called chromatin to fit the long genetic material into the tiny nucleus of a cell. The degree of DNA packaging is not the same for all our genes and this also varies between cell types. Some genes have a more open chromatin structure (euchromatin) and are available for gene expression, but other genes are very densely packed into a very compact chromatin structure known as heterochromatin. Therefore, it is epigenetic (Greek: epi – over; genetikos from genesis – origin) mechanisms, which must control the on-and-off status of a gene. And they do so by remodeling the chromatin structure so that only genes required for the function of the cell type are available for expression. Thus, each cell type has a characteristic chromatin or ‘epigenetic’ landscape.Totipotency emerges only after an extensive process of chromatin remodelling in the embryo whereby the epigenetic landscape of the gametes is reprogrammed to form the totipotent zygote. In recent years, the work of the lab of Prof. Maria-Elena Torres-Padilla, Director of the Institute of Epigenetics and Stem Cells and others has indicated that the chromatin in these totipotent cells of the early embryo is dramatically different to the chromatin of differentiated somatic cells, and even of pluripotent stem cells. Therefore, the distinctive epigenetic features of the early embryonic chromatin likely constitute the basis of totipotency and are fundamental for efficient reprogramming of the gametes at fertilization. Leveraging this knowledge to improve reprogramming methods, which are generally very inefficient, is an outstanding opportunity and research priority of the years to come. In fact, learning lessons from the embryo will enable the more efficient and timely generation of high-quality, fully reprogrammed stem cells, which are vital for the full implementation of regenerative medicine approaches in the clinic.

Epigenetic reprogramming during early mammalian development is in the center of your research. What is it and how is it linked to ‘Totipotency’?

Maria-Elena: Totipotency is the highest level of cellular plasticity – imagine being able to generate cells that can produce any cell type? That would be really fantastic! When you think about using healthy cells to replace sick cells, for example in regeneration and replacement therapies, you need to think about how to generate those ‘new’ healthy cells. For that, you often need to ‘reprogram’ other cells, that means, to be able to change one cell into the cell type of interest. Cellular reprogramming occurs purely epigenetically, since the DNA content of those cells is not different, only the genes they express, which is largely imposed by the chromatin and therefore is epigenetic.

Adam: Studying this process in the egg is very unique. In fact, the process of reprogramming in embryos is extremely efficient; some people even think that it is 100% efficient. Therefore, adopting strategies for reprogramming based on our knowledge on how the embryo does it is a very promising avenue of research. These strategies can help us increase the efficiency of reprogramming for regenerative medicine, because currently reprogramming efficiencies tend to be very low.What happens if cellular reprogramming fails during embryonic development?

Maria-Elena: If the embryo does not reprogram, if reprograming fails, there is simply no embryo surviving. In fact, if I would go wild about it, that would mean, that there is no perpetuation of any species! Reprogramming at fertilization is fundamental for any species, including mouse, which we use as a model system. That does not mean that this is an easy process, as the epigenetic reprogramming at fertilization is extensive, and involves chromatin regulation at multiple levels, from histone* modifications to how the DNA is arranged in the cell nucleus. Heterochromatin is one of the hurdles, because it is thought to be difficult to reprogram this part of our genomes which is so compact and inaccessible.

You had a closer look at how early embryos deals with heterochromatin. What did you find out?

Adam: What is interesting is that when you reprogram for example, somatic cells to pluripotent stem cells, the so-called induced pluripotent stem cells (iPS), a major bottleneck is heterochromatin. Heterochromatin refers to the part of the chromatin that is tightly packed and not accessible. What we wanted to understand is how the embryo deals with heterochromatin, what is its function, and how does the embryo ‘keeps heterochromatin in check’ so that reprogramming can occur so efficiently.Indeed, we found that the histone modification H3K9me3, which is the classical marker of heterochromatin, is in fact present in the embryo from early on. However, we found that it is not transcriptionally repressive! This was very unexpected, since we know for years by work from many people that H3K9me3 correlates strongly with genes that are silenced. We also identified the enzyme that methylates H3K9me3 in embryos as the Suv39h2 histone methyltransferase.One of our major findings was to discover that the methyltransferase activity of Suv39h2 and the H3K9me3 deposition itself is regulated by a non-coding RNA derived from the centromere, which is an essential structure for cell division. Thus this early heterochromatin is tightly controlled. Globally, we concluded that heterochromatin in the early mammalian embryo is immature. This is probably due to the absence of critical downstream factors, which we are currently investigating.

Maria-Elena: We also wanted to address whether a mature heterochromatin would jeopardise reprogramming and development. Here, we studied another enzyme, Suv39h1 that is not regulated by RNA and is first active only several days later. We artificially introduced Suv39h1 in early embryos and found that it actually can establish mature heterochromatin early on. Quite remarkably, introduction of Suv39h1 at such early stages resulted in developmental failure and a block in epigenetic reprogramming. This suggests that the timely acquisition and maturation of heterochromatin is essential for embryonic development.

Adam: We next plan to investigate in a more global manner the role of heterochromatin factors in development. Through this, we hope to identify the ones that contribute to the maturation of heterochromatin and how this enables transcriptional repression and developmental progression.

How could we use this new knowledge for cell reprogramming

Adam: Essentially what our work documents is a potential way to ‘tune’ down heterochromatin. Ideally, this will provide us with the factors that we can manipulate for making e.g. iPS or direct reprogramming more efficient and achieve higher cell conversion rates. The key take-home message is that we can learn from the epigenetic remodeling that occurs during the natural process of reprogramming at fertilization, which is highly efficient and can transfer this knowledge to improve currently inefficient artificial reprogramming strategies. We know that the early Suv39h2-mediated heterochromatin is permissive to reprogramming and can be modulated, even if it is tightly regulated. Thus, this knowledge should be quickly translated into cell reprogramming protocols to recapitulate the more complex natural heterochromatin dynamics occurring in vivo.

*Histones are basic proteins that are important for the packaging of the DNA into chromatin. The DNA wraps around an histone octamer and this structure is known as nucleosome. Generally, chromatin consists of arrays of nucleosomes and under the microscope this structure lookss like beads-on-a-string.

To read the full article, go here.