The 2024 Pilot Award Awardees

Current frontline treatments for MDS suffer from dose-limiting toxicities and a high rate of treatment failures. Targeted therapies aimed at the malignant cells are needed. We recently discovered that the malignant cells that arise in MDS abnormally express the gene TCL1A, which seems to be important for their growth. Importantly, TCL1A is not expressed in normal blood stem cells. Therefore, anti-TCL1A therapies are expected to lead to a reduction in the number of mutant MDS cells with minimal toxicity. However, there are currently no therapeutics that target TCL1A. In this proposal, we outline a novel screening approach to identify potential drugs or drug targets which can suppress TCL1A and have the potential to become therapies for MDS.

Here, we will leverage an innovative screening method to identify novel ways to target TCL1A. The principle of the screen is that a protein of interest (in this case, TCL1A) is fused to another protein (called DCK) that causes cells to die after the addition of a compound not found in nature. We will use CRISPR, a technology that allows us to inactivate any gene in the human genome, to determine which proteins are necessary for stabilizing TCL1A (Screen 1). In addition, we will screen chemical compounds to see if any lead to degradation of TCL1A (Screen 2). Hits from these screens may identify novel drugs or drug targets to treat MDS.

Upon successful completion of these two screens, we will 1) identify stabilizers of TCL1A that will teach us about how TCL1A levels are regulated, and 2) identify chemicals that degrade TCL1A. This work will provide preliminary data for future funding applications to follow up on the hits that are discovered.

Myelodysplastic neoplasms (MDS) are a group of clonal disorders of dysfunctional hematopoietic stem and progenitor cells (HSPC). Despite decades of research efforts, MDS remains life threatening, and many fundamental questions remain unanswered. For example, the differentiation-defective HSPCs (blast cells) in different MDS patients remain uncharacterized at the molecular level, how are they different from their healthy counterparts? Another long-lasting question is why some MDS patients will progress to acute myeloid leukemia (AML), but others won’t.

Unlike prior studies mainly focusing on driver gene mutations, in this pilot study, we aim to explore how the regulatory genome is perturbed in MDS patients. Genomes harbor, interpret, and propagate genetic and epigenetic information. However, only about 3% of the human genome is protein-coding, and the remaining 97% likely plays a regulatory role in controlling the expression of protein-coding genes, via the three-dimensional (3D) organization of the cis-regulatory elements (CRE) in the nucleus. Chromatin looping between gene promoter and CREs (P-E loop) is an important epigenetic mechanism of gene regulation and frequently perturbated by disease causing genetic lesions. To test our hypothesis that 3D genome disruption provides a common epigenetic mechanism for MDS development, we will use cutting-edge technologies to survey the landscapes of P-E loops in relation to gene expression at the single-cell level in MDS cells. We aim to construct the spatial atlas of CREs, build MDS-specific gene-CRE networks, and identify disease-causing cell types. Successful completion of our project will gain novel insights into the epigenetic mechanisms underlying hematopoiesis and MDS pathogenesis.

Blood cancers such as myelodysplastic syndromes (MDS) occur when blood stem cells acquire mutations that then expand to from stem cell clones that are defective in normal blood production. One of the most common mutation found in stem cells of MDS patients is in the gene called DNMT3A. It is unknown how these expanding MDS stem cell clones escape body’s natural defense mechanisms provided by immune cells. Recent human genetic studies have provided a clue that several healthy individuals are protected from developing DNMT3A mutant stem cell clones when they carry inherited genetic variants in DEC-205, a gene that presents foreign proteins to immune cells. In this project, using a mouse model that harbor DNMT3A mutation in its blood stem cells, we will study how DNMT3A mutant stem cells alter DEC-205 expression to escape from immune attack. We hypothesize that DNMT3A mutant stem cells in risk individuals, escape from immune attack by directly presenting mutant proteins using DEC-205 to a subset of immune cells called regulatory T cells that induces immune tolerance. We will test the ability of stem cells from DNMT3A mutant mice to present foreign proteins and test the capacity of regulatory T cells from these animals to suppress immune cells. We expect these functions to highly depend upon DEC-205 expression in stem cells. Knowledge gained from our research will experimentally validate the correlative findings from human genetic studies and could enable the development of new treatments that target DNMT3A clones through DEC-205 and prevent MDS development.  

Myelodysplastic syndrome (MDS) is characterized by ineffective production of blood cells and leads to an increased risk of developing leukemia. Our research project focuses on DNA methylation, a crucial epigenetic regulatory mechanism, which we believe plays a significant role in the progression of MDS. In patients with MDS, DNA methylation patterns are often disrupted due to genetic mutations, leading to abnormal blood cell development.

Our project introduces a novel approach by targeting these abnormal methylation patterns directly. We hypothesize that by altering the methylation at key positions in the DNA, we can potentially reverse the faulty blood cell development and restore normal function. This innovative strategy could significantly advance the treatment of MDS by providing a method to correct the underlying genetic disturbances.
To achieve this, we have developed a cutting-edge technology called SHARE-ME-seq. This method allows us to examine DNA methylation, alongside gene activity and accessibility, in individual cells at an unprecedented level of detail. By applying this technology to samples from MDS patients, we aim to pinpoint the exact locations where methylation goes awry and subsequently attempt to correct these errors using targeted genetic tools, specifically CRISPR/Cas9.

The expected outcomes of our research include a detailed mapping of methylation changes in MDS, an understanding of how these changes affect blood cell development, and the identification of potential new targets for therapy. If successful, our work could pave the way for novel treatments that adjust the abnormal methylation patterns in MDS cells, leading to improved patient outcomes.

Patients with myelodysplastic syndrome (MDS) are frequently treated with a class of drugs called hypomethylating agents, which include azacytidine (AZA) and decitabine (DAC). AZA and DAC are thought to exert their therapeutic effects by altering the composition of DNA, but we have found that they act through distinct mechanisms with AZA, but not DAC, altering cellular metabolism by inhibiting a critical enzyme required for the generation of pyrimidines, which are the building blocks of RNA and DNA. Based on these findings, we hypothesize that AZA’s therapeutic effect primarily depends on its ability to inhibit an enzyme called UMP synthase (UMPS) to reduce pyrimidine synthesis. We will use a combination of biochemical and structural biology approaches to determine if AZA alters UMPS’ structure and to identify where AZA binds to UMPS. We will also determine how cells adapt to overcome the inhibition of UMPS by AZA. Completion of these studies will fundamentally alter our understanding of AZA’s mechanism of action and provide the scientific rationale for testing novel therapies in combination with AZA to treat MDS. Additionally, the insights gained from these studies will spur the development of lab tests to assess the ability of AZA to inhibit UMPS in patient cells, thereby allowing better identification and selection of patients to therapies containing AZA. This would represent an important advance since there is no reliable method to predict which MDS patients will respond to AZA or DAC treatment at this time.