Dissecting the mechanism of N6-Methyladenosine (m6A) mediated RNA translation-decay in yeast and cancer cells

A PhD project for the 2022 doctoral clinical fellows programme with Folkert van Werven (primary supervisor, Crick), Kamil Kranc (Barts Cancer Institute/QMUL) and Paolo Gallipoli (Barts Cancer Institute/QMUL)

Project description

Kamil Kranc

Clinical Professor of Haematology, CRUK Senior Cancer Research Fellow & Deputy Centre Lead and Group Leader, Barts Cancer Institute/QMUL

Paolo Gallipoli

Clinical Senior Lecturer in Haemato-Oncology & Group Leader, Barts Cancer Institute/QMUL

How gene expression is regulated during cell differentiation remains poorly understood. The Van Werven laboratory studies the molecular mechanism of gene expression changes during cell fate programming in yeast, mammalian, and cancer cells.

A widely used strategy for cells to alter gene expression is through the biochemical modifications of RNAs. As such, the mRNA N6-methyladenosise (m6A) modification is the most abundant RNA modification that alters the fate of messenger RNAs in various ways. The m6A modified transcripts can stimulate turnover of transcripts, promote translation, RNA splicing, alter transcript localization and more. The m6A mark also has essential functions in development. More recently, m6A writer and reader machinery have been identified as potential targets for cancer treatment. Specifically, in acute myeloid leukemia (AML), an aggressive clonal disorder of hematopoietic stem cells, both the m6A writer and reader protein complexes have been promising candidates for therapeutics [1-4]. 

In budding yeast, m6A is deposited on mRNAs during early meiosis where it functions to promote progression into meiosis [5]. The long-term aim is to dissect the molecular functions of m6A in regulating gene expression using yeast as a model. Given that the proteins of the m6A writing and reading machinery are conserved, we hope gain new insight how the m6A mark contributes to development and cancer progression. 

Recently we found that only one reader protein in yeast, related to YTHDF2 in mammals, interacts with m6A marked mRNAs. YTHDF2 has been implicated as therapeutic target for AML [1, 4]. In yeast, we have evidence that the reader protein directs mRNA transcripts to ribosomes for translation coupled mRNA decay (unpublished). The mechanism is yet to be identified. The goal of the project is to identify the molecular players that mediate targeting of m6A transcripts for translation coupled mRNA decay. 

For the project we will make use of the yeast genetics to identify mutants in RNA decay and translation pathways that affect m6A methylation patterns. Additionality, we will use various molecular and genomic techniques to dissect the mechanism of m6A mediated translational coupled decay. The conserved proteins identified in yeast will be further validated in AML cells as a paradigmatic model system for cancer stem cell disease (in collaboration with the Kranc lab). Briefly, we will use CRISPR-Cas9 approach to delete or mutagenize the identified m6A regulators in mouse AML cells and examine their potential to initiate and propagate AML.

This project will combine the strengths of yeast genetics (in van Werven’s lab) to reveal novel m6A regulators and functionally interrogate their significance in AML (in the Kranc lab). Given the recent discoveries indicating that the m6A pathway is druggable with therapeutic potential in cancer, our work may reveal novel therapeutic targets which will be applicable to many malignancies [1, 4]. Thus, this work will form the basis for drug discovery against new m6A regulators which we will identify and validate as key players in AML. 

The ideal candidate must have a strong interest in basic science (required) and ideally research experience in molecular biology, biochemistry, genomics, or cancer biology (desired).

The partner institution for this project is Barts Cancer Institute/QMUL.

References

  1. Paris, J., Morgan, M., Campos, J., Spencer, G. J., Shmakova, A., Ivanova, I., . . . Kranc, K. R. (2019). Targeting the RNA m(6)A Reader YTHDF2 Selectively Compromises Cancer Stem Cells in Acute Myeloid Leukemia. Cell Stem Cell 25: 137-148 e136.
  2. Barbieri, I., Tzelepis, K., Pandolfini, L., Shi, J., Millan-Zambrano, G., Robson, S. C., . . . Kouzarides, T. (2017). Promoter-bound METTL3 maintains myeloid leukaemia by m(6)A-dependent translation control. Nature 552: 126-131.
  3. Yankova, E., Blackaby, W., Albertella, M., Rak, J., De Braekeleer, E., Tsagkogeorga, G., . . . Kouzarides, T. (2021). Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature 593: 597-601.
  4. Mapperley, C., van de Lagemaat, L. N., Lawson, H., Tavosanis, A., Paris, J., Campos, J., . . . Kranc, K. R. (2021). The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell function. J Exp Med 218. 
  5. Schwartz, S., Agarwala, S. D., Mumbach, M. R., Jovanovic, M., Mertins, P., Shishkin, A., . . . Regev, A. (2013). High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155: 1409-1421.