Jonathan D. Licht, M.D.
2021 Funding recipient
DNMT3 loss facilitates KMT2C-induced enhancer switching in myeloid malignancies
Discovery Research Grant 2021
Normal blood production starts with the hematopoietic stem cells – specialized cells in the bone marrow that make mature cells of the blood in the process called differentiation. At the same time, these stem cells need to replenish themselves to maintain life-long blood production, in the process called self-renewal. Imbalance between differentiation, or production of mature blood cells, and self-renewal, or production of more stem cells, is the root cause of blood diseases such as myelodysplastic syndromes (MDS). MDS are characterized by inefficient blood production with progressive anemia and cytopenias (low numbers of red blood cells, white blood cells, and platelets in the circulation) and often progress to a more ominous acute myeloid leukemia (AML). Clearly, novel therapeutic approaches are needed.
The tight balance between differentiation, or production of mature blood cells, and self-renewal, or production of more stem cells, is maintained by many specialized genes being switched on and off in a timely and coordinated manner. Since this is such an important process, there are multiple checks and balances thanks to several layers of so-called epigenetic regulation. This means that in order to be activated, each “differentiation” or “self-renewal” gene is vetted through a process akin to two-factor authentication. Among others, permission for activation is given by an enzyme KMT2C, which leaves a mark in the gene’s specialized “enhancer” region, unless it was already “red-flagged” and inhibited by another enzyme DNMT3A, which adds a methyl chemical group to the DNA to signal inactivation of the region. When KMT2C or DNMT3A are broken or missing, it can lead to some genes being incorrectly marked for activation or not red-flagged, disturbing the balance between self-renewal and differentiation, and corrupting blood production. One of the two copies of the gene that makes the KMT2C enzyme is lost in a subtype of MDS where the whole or a part of chromosome 7 is missing. The other copy of KMT2C present on the remaining copy of chromosome 7 must struggle to meet the demands of the cell for regulated cell differentiation control. Moreover, in MDS this is often accompanied by defective DNMT3A, which fails to flag many “self-renewal” genes and allows them to slip through and become incorrectly licensed for activation by KMT2C.
We previously found that each of these two defects individually (loss of KMT2C and loss of DNMT3A) can lead to detrimental changes in blood production, reminiscent of MDS. In this project, we will investigate 1) how these two lesions collaborate in inducing MDS, and 2) whether any of the inappropriately activated genes as the result of compound loss of KMT2C and DNMT3A can be harnessed for the development of novel MDS therapies. To achieve this, we will look at gene enhancers, or special regions of DNA that control the ability of genes to be turned on, especially enhancers of genes critical for self-renewal and differentiation during blood production, catalogue their marks and flags, and determine their ability to control gene activity. This will be done in cells with both KMT2C and DNMT3A deleted by a recently developed genome editing tool called CRISPR-Cas9. Knowing which genes are incorrectly activated will give us important clues about potential ways to slow down or even reverse MDS, either by inhibiting these rogue genes using existing drugs or by developing new ones. At the same time, we will use mice in which both Kmt2c and Dnmt3a were inactivated to understand the process of disease development and gain better knowledge of the specific defects in blood stem cell function and blood production. In the longer term we would use these mice to test our proposed treatment approaches.
MDS is a common and pernicious disease in the aging population; research into the root causes and novel therapies is critically needed. By sharing our findings with other EvansMDS awardees, we hope to enable fundamental discoveries and speed up the development of cures.