Year 3

In addition to the four main letters (bases) in the DNA alphabet – A, C, G and T – there is also a ‘fifth’ base known as 5-methylcytosine (5mC) that has a disproportionately crucial role, despite the fact that it is expressed at quite low levels in cells. 5mC is important in the development of the embryo, in the expression of genes, in brain function and in cancer. It was originally thought that 5mC was a very stable and unchanging mark, but our recent discovery that a class of proteins known as TET proteins converts 5mC to derivatives known as oxidized methylcytosines – 5hmC, 5fC and 5caC, thus proving that 5mC can indeed be altered dynamically. TET proteins and oxidized methylcytosines have important roles in embryonic development, normal cellular functions, and the properties of nerve cells in the brain. They also have a major role in the reprogramming of mouse fibroblasts into induced pluripotent stem (iPS) cells, which have great potential to treat many human diseases. Mutations in TET proteins lead to developmental abnormalities, infertility, genetic diseases and cancer.

In our CIRM project, we had proposed to discover the role of TET proteins in a class of cells of the immune system known as T cells, and especially in a subclass of these known as regulatory T cells (Tregs). T cells are important because they are involved in fighting bacterial and viral infections as well as cancers; among their harmful features, however, is that they also reject transplanted organs and may cause “autoimmune” responses to the body’s own constituents and unnecessarily overactive responses to harmless components of the environment such as those that provoke food allergies and asthma. Tregs oppose the actions of normal T cells, and so are useful in preventing autoimmune disease and suppressing allergies and asthma, but are harmful since they also prevent the rejection of cancer cells by the immune system.

TET proteins have been associated with human cancers, and we have now mimicked this process in mice. By generating mice that lack two of the three TET proteins, we found that these mice develop a striking and very rapidly progressing cancer that involves the uncontrolled growth of certain immune system cells. The mice may also possess diminished numbers or functions of Tregs. Further study of these mice should allow us to understand the role of TET proteins in Treg function as well as in the development of T cell leukemias and lymphomas.

In addition, we have looked at the distribution of 5hmC during the development of normal T cells and Tregs in an organ known as the thymus. We find that the levels of 5hmC in genes correlate strongly with the degree to which those genes are expressed. We also find that during T cell and Treg development, 5hmC levels change rapidly at certain genes before the genes are most highly expressed. These are important new findings that may relate to the role of 5hmC in normal development as well as in cancer cells.

Although our research has been performed mostly in mice, we believe that it will be possible to translate it quickly into humans, and that if successful, it will address some pressing clinical needs. For patients receiving transplanted organs, and for cancer patients who have been given chemotherapy followed by a bone marrow transplant from a different person, we may be able to build on our understanding of the role of TET proteins in Treg development to generate Tregs more efficiently. Our analysis suggests that these Tregs would also be more stable and more effective in suppressing rejection of the organs or the bone marrow transplant. In contrast for patients suffering from autoimmune diseases, or whose cancers have arisen due to problems with TET protein function, we might be able to increase Treg function and/or suppress cancer cell growth by increasing the activity of TET proteins in the Tregs and cancer cells. We believe that all these approaches are feasible in principle, given recent discoveries from our own and other labs.