Exploiting escape from Y-inactivation as a synthetic dependency in MYC-driven lymphoma
Jake Shortt
PhDMonash University
Project Term: July 1, 2024 - June 30, 2027
As a lymphoma develops it expresses genes that are normally silenced to convey a survival advantage. When these genes are on the X or Y (sex chromosomes) they may present a gender-specific therapeutic target. We have identified a gene (DDX3X in females or DDX3Y in males) that is reactivated in lymphomas such that the lymphomas cannot survive if this gene is removed. This project will develop new ways to inhibit DDX3X and Y as a novel treatment for poor-risk and aggressive lymphoma.
Some of most aggressive lymphomas are caused by activation of a powerful cancer causing gene called 'MYC'. Examples include Burkitt lymphoma (BL) and poor-risk subtypes of Diffuse Large B-cell lymphoma (DLBCL; the most common aggressive lymphoma). MYC-positive DLBCL is particularly problematic as it tends to develop resistance to chemotherapy and even modern immune-therapies such as CART cells.
When MYC is turned in a cell it drives growth and proliferation - properties a cancer likes to exploit. However, this comes at the cost of stressing the cell to the point that it may die and prevent lymphoma from forming. DDX3X is a gene on the X-chromosome that helps unwind RNA to allow protein production and cell growth. When MYC is first switched on, protein production by DDX3X amplifies the cell stress that MYC induces. This explains why DDX3X mutations (ie, changes that switch DDX3X off) are some of the most common mutations seen in BL and MYC-positive DLBCL. Critically, when the lymphoma cell recovers from the initial stress of MYC activation, it needs DDX3X back again to continue to grow. Lymphomas do this by turning on a 'spare' DDX3X copy on their other X-chromosome in females or activating a closely related gene called DDX3Y in males (normally DDX3Y is only 'on' in the testes).
Using a gene editing technique called 'CRISPR' we have shown that DDX3X mutant lymphomas are exquisitely dependent on their spare intact copy of DDX3X (females) or reactivated DDX3Y (males). Thus, DDX3X and DDX3Y represent promising therapeutic targets in lymphomas with a gender-determined pattern of vulnerability. In this grant we will map how and why DDX3X mutated lymphomas rely on DDX3X or Y. We have engineered lymphoma cells in which we can rapidly degrade DDX3X or Y using tool compounds that mimic drugs to show us how such drugs kill lymphoma. We have already undertaken large scale screening efforts (testing literally billions of compounds) to triage a list of around 100 promising candidate DDX3X/Y inhibitors. These will be properly validated and the best inhibitors from this pool tested as lymphoma drugs.
However, DDX3X and Y are very similar, which may make it impossible to develop a drug that only inhibits one or the other. To address this problem we will use CRISPR to find out in an unbiased way how a male lymphoma cell manages to turn DDX3Y back on when it is normally only present in the testes. This will help us devise strategies to actively turn DDX3Y back off and kill male lymphomas. Finally, we will develop a new technology called CRISPR/Cas13 which uses the precise discriminatory power of RNA to distinguish between closely related molecules (ie, DDX3X and Y). By packaging Cas13 into vaccine-like particles, we will develop a parallel treatment for DDX3Y silencing in lymphoma.
Together our research aims will leverage cutting edge gene-editing and drug discovery techniques to develop a precision therapy for DDX3X mutated poor-risk lymphoma