Suppression of AML Stem Cells by immune reprogramming via the β-Catenin–CCR2 Axis and RNA Processing

Primary supervisor: Eric So, King’s College London

Secondary supervisor: Diu Nguyen, Queen Mary University of London

Project

Acute myeloid leukemia (AML) in particular those with MLL rearrangements (MLL-r) represents a particularly aggressive subtype of leukemia, frequently diagnosed in infants and young children. These leukemias are characterized by poor clinical outcomes, high relapse rates, and resistance to standard therapies. At the heart of disease maintenance is a rare population of leukemia stem cells (LSCs), which evade immune surveillance and sustain malignant self-renewal.

Our previous work has identified β-catenin as a central regulator of LSC function in MLL-r AML. While largely dispensable in normal hematopoiesis, β-catenin is crucial for AML maintenance and progression. Emerging evidence now reveals that β-catenin promotes immune evasion through regulation of CCR2 and downstream NF-κB signaling, while also coordinating RNA processing programs that reinforce stemness. These findings offer new opportunities for immuno-epigenetic reprogramming in a high-risk pediatric malignancy.

Project Description:

This PhD project will dissect the dual role of β-catenin in (1) immune suppression and (2) RNA processing in AML, aiming to expose therapeutic vulnerabilities that could be exploited to treat this aggressive childhood leukemia.

Aim 1: Immune Modulation via β-Catenin–CCR2–NF-κB Axis. We will define how β-catenin transcriptionally activates CCR2, a chemokine receptor that suppresses differentiation and immune clearance. Using CRISPR gene editing, small molecule inhibition, and transcriptomics, we will determine how this axis blocks macrophage-mediated phagocytosis and promotes immune evasion. Functional assays—including apoptotic body uptake, CD86 surface expression, and clodronate liposome sensitivity—will assess whether targeting β- catenin or CCR2 can reprogram AML cells toward an M1-like, immune-activated phenotype. Importantly, we have previously shown that while MLLr-AML stem cells derived from early myeloid progenitors such as granulocyte and macrophage progenitors (GMPs) are sensitive to β-catenin inhibitors; MLLr-AML stem cells derived from hematopoietic stem cells (HSCs) are refractory to β-catenin inhibition. This study will also examine the roles of immune modulation and dissect the underlying mechanisms responsible for the contrasting differences exhibited by these MLLr LSCs derived from different cells of origins.

Aim 2: In Vivo Immune Reprogramming in MLL-r AML Models. Using murine and patient-derived xenograft (PDX) models of MLL-r AML, we will validate immune reprogramming outcomes following β-catenin or CCR2 inhibition. Particular attention will be given to NF-κB activation, enrichment of phagosome/lysosome gene signatures, and macrophage infiltration as indicators of therapeutic immune activation.

Aim 3: β-Catenin’s Role in RNA Processing and AML Stemness. We will investigate how β-catenin modulates RNA processing by binding to RNA binding factors/splicing factors such as Srsf1, Sf3b1, and Rbm25. RNA-seq and CUT&RUN will identify splicing-dependent regulatory programs regulated by β-catenin that support LSC survival. HyperTRIBE developed by proposed co-supervisor, Dr Nguyen in QMUL, will be employed to identify their RNA targets. We will test whether inhibition of this key RNA processing machinery will pheno-copy the loss of β-catenin in AML using the model system indicated in aim 2 above. Finally we may also test whether combined targeting of identified phagosome and RNA processing pathways may potentiate differentiation and loss of leukemic potential.

Candidate background

This project would suit candidates with a background in cancer biology, immunology, molecular biology, or biomedical sciences, and a strong interest in tumor–immune interactions and RNA biology. Prior experience in molecular cloning, flow cytometry, transcriptomics, mouse models, imaging or hematologic malignancies is highly desirable. We particularly welcome candidates driven to explore the interface of immune escape and gene regulation in aggressive pediatric leukemia, with a view to advancing novel treatment strategies.

Potential Research Placements

1. Diu Nguyen, Barts Cancer Institute, Queen Mary University of London
2. James Arnold, Comprehensive Cancer Centre, King’s College London
3. Maddy Parson, Nikon Imaging Centre, King’s College London

References

1. Zeisig B, Tsai CT, Virely C, Fung TKK, Akin AT, Troadec E, Jiao B, Thompson R, Lau PNI, Li N, Charalambous A, Bomfim L, Lynch J, Georgiou A, Hoogeboom R, Lynn C, Zhang SY, Patten PE, Fisher C, Schuh A, Ogawa S, Mufti GJ Professor, Karimi MM, *So CW. Transposable elements as novel therapeutic targets for PARPi-induced synthetic lethality in PcG-mutated blood cancer. Blood. doi: 10.1182/blood.2025028560. 2025 (In press)
2. Lynch J, Troadec E, Fung TK, Gladysz K, Virely C, Lau PNI, Cheung N, Zeisig B, Wong JWH, Lopes M, Huang S, *So CW. Hematopoietic stem cell quiescence and DNA replication dynamics maintained by the resilient β-catenin/Hoxa9/Prmt1 axis. Blood 143 (16): 1586-98. 2024 (journal cover accompanied with a commentary)
3. Zeisig BB, Fung TK, Zarowiecki M, Chiou TT, Stanojevic B, Lynn C, Leung AY, Zuna J, Zaliova M, Bornhauser M, vo Bonin M, Lenhard B, Mufti G, *So CW. Functional reconstruction of human AML reveals stem cell origin of treatment resistant CD34-/lo MLL-rearranged leukemia. Science Translational Medicine 13(582):eabc4822. doi: 10.1126/scitranslmed.abc4822. 2021
4. Cheung N, Fung,TK, Zeisig BB, Holmes K, Rane JK, Mowen KA, Finn MG, Lenhard B, Chan LC, *So CW. Targeting aberrant epigenetic networks mediated by PRMT1 and KDM4C in acute myeloid leukemia. Cancer Cell. 29 (1): 32-48, 2016 (the top most read paper, Highlighted by Cancer Discovery AACR).
5. Esposito MT, Zhao L, Fung TK, Rane JK, Wilson A, Martin N, Gil J, Leung AY, Ashworth A, *So CW. Synthetic lethal targeting of oncogenic transcription factors in acute leukemia by PARP inhibitors. Nature Medicine. 21(12): 1481-90, 2015 (Featured article accompanied with News and Views, highlighted by Nature Reviews Cancer, Cancer Discovery AACR