Investigating ribosomal RNA biogenesis as a driver of translational dysregulation in acute leukaemia

Primary supervisor: Diu Nguyen, Queen Mary University of London

Secondary supervisor: Ivana Bjedov, UCL

Project

As the ultimate step in gene expression, translation provides the abundance and diversity of the proteome, defining cell identity and function. Not surprisingly, translation regulation is often derailed in cancer, promoting protein synthesis of specific mRNAs supporting cancer hallmarks. While transcriptional regulation mechanisms are established at a great extent, contribution of translational control in cancer is poorly understood [1,2].

We aim to fill this fundamental knowledge gap focusing on acute myeloid leukaemia (AML). AML is a bone marrow cancer with poor survival rate (30%), highlighting the unmet clinical needs. AML is propagated by leukaemic stem cells (LSCs) – major contributors of therapy resistance and relapse. Our preliminary data show that only a small fraction of changes in the LSC proteome vs. normal cells can be explained by corresponding transcriptomic alterations, suggesting translational dysregulation in AML. Remarkably, the modulated proteins enriched for multiple biological pathways known to support LSCs survival.

Moreover, AML cells are known to have enlarged nucleoli, site of ribosomal RNA (rRNA) genesis and assembly of ribosomes – translation machineries. Our analysis shows that multiple rRNA biogenesis factors are upregulated in primary AML patient samples versus normal myeloid counterparts. Depletion of these factors is detrimental to AML cells survival while dispensable for normal blood cells, suggesting their therapeutic potentials. (Supplemental information).

We hypothesize that aberrantly expressed rRNA genesis factors lead to alterations in translation of specific pathways fuelling cancer cell behaviours. Thus, this PhD project will address our hypothesis by following aims:

Aim 1: Mapping of position and activity of rRNA biogenesis factors in AML. Although many of these factors (44/200) are upregulated in AML, it’s unclear whether their activities are increased. Here, we will map rRNA binding sites and measure binding activity of these rRNA processors in human AML using TREX approach [3]. We will then quantify pre-rRNA and mature rRNAs in AML and normal cells [4]. Together, these approaches will quantitatively assess ribosome biogenesis in AML vs normal blood cells.

Aim 2: Functional role of rRNA genesis factors in AML. Following our preliminary study, we will fully characterise the consequences of loss-of-function of Processing-Of-Precursor 4 (RPP29/POP4), as well as POP1, the most highly expressed factors in AML vs normal cells, in leukaemogenesis in vitro and patient/cell line xenograft. We will also deplete these factors in human normal blood cells to assess their therapeutic potentials in AML.

Aim 3: Defining how rRNA genesis factors influence translation dysregulation and AML development. We will first determine how ribosome biogenesis is modulated by POP4 (and 1) loss using approaches in aim 1, and how tRNA genesis might be affected, as these are also components of tRNA processing complex. Using the reporter system developed by co-supervisor Dr. Bjedov [5], combined with polysome profiling, we will investigate how translation efficiency and accuracy is modulated. Finally, our RiboSTAMP approach will simultaneously identify the transcriptome and translatome programmes regulated by these rRNA genesis factors to support AML survival.

Candidate background

The project would suit candidates with strong background in cancer biology, molecular biology or biomedical science and an interest in cutting-edge genomics/proteomics approaches. Prior experience in leukaemia biology, RNA biology, flow cytometry and strong bioinformatics skills is highly desirable.

Potential Research Placements

1. Ivana Bjedov, Cancer Institute, UCL
2. Vardhman Rakyan, Blizzard Institute, Queen Mary University of London
3. Anob Chakrabarti, Respiratory Infection, UCL

References

1. Nguyen, D.T.T., Lu, Y., Chu, K.L., Yang, X., Park, S.M., Choo, Z.N., Chin, C.R., Prieto, C., Schurer, A., Barin, E., et al. (2020). HyperTRIBE uncovers increased MUSASHI-2 RNA binding activity and differential regulation in leukemic stem cells. Nat Commun 11, 2026. 10.1038/s41467-020-15814-8.
2. Mlynarczyk, C., Teater, M., Pae, J., Chin, C.R., Wang, L., Arulraj, T., Barisic, D., Papin, A., Hoehn, K.B., Kots, E.,…Nguyen, D., et al. (2023). BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science 379, eabj7412. 10.1126/science.abj7412.
3. Dodel, M., Guiducci, G., Dermit, M., Krishnamurthy, S., Alard, E.L., Capraro, F., Rekad, Z., Stojic, L., and Mardakheh, F.K. (2024). TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 21, 423-434. 10.1038/s41592-024-02181-1.
4. Antony, C., George, S.S., Blum, J., Somers, P., Thorsheim, C.L., Wu-Corts, D.J., Ai, Y., Gao, L., Lv, K., Tremblay, M.G., et al. (2022). Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell. 10.1016/j.molcel.2022.08.027.
5. Martinez-Miguel, V.E., Lujan, C., Espie-Caullet, T., Martinez-Martinez, D., Moore, S., Backes, C., Gonzalez, S., Galimov, E.R., Brown, A.E.X., Halic, M., et al. (2021). Increased fidelity of protein synthesis extends lifespan. Cell Metab 33, 2288-2300 e2212. 10.1016/j.cmet.2021.08.017.