Project ID CM-HD2023_46

ThemeCM-HD

Co Supervisor 1A Comprehensive Cancer CentreWebsite

Co Supervisor 1B Comprehensive Cancer CentreWebsite

A multi-omics approach to investigate the mechanism of action of DNA hypomethylating agentinmyeloidmalignancies

Myelodysplastic syndromes (MDS) are myeloid neoplasms characterized by inefficient haematopoiesis, morphologic dysplasia and peripheral cytopenia(s). Several drugs have been tested and approved to treat MDS, including hypomethylating agent 5-azacytidine (AZA). However, the mechanism of action of AZA in MDS is largely unknown.

The recent rapid development of single multiomic approaches has provided an unprecedented opportunity to identify transcriptional changes and potential therapeutic targets that are key to establish and/or maintain leukaemia stem cells (LSCs). To further improve current MDS treatments and increase the knowledge of these heterogeneous diseases, we will employ a multi-omics approach including bulk RNA-seq, BD Rhapsody and Mission Bio Tapestry single-cell sequencing for combined cancer genome, RNA and protein expression, ATAC-seq for chromatin accessibility, ChIP-seq for key histone modification marks and whole-genome bisulfite sequencing to study samples from MDS patients treated with AZA, obtaining information on the mutation, transcriptome, comprehensive epigenome, and the simultaneous measurement of DNA mutation, mRNA and key surface marker protein expression at the single-cell level (Year 1-2). To complement and functionally validate our human data findings, we will also generate the same multi-omics data type for AML transformed DNMT3A and EZH2 mutant mice at pre and post-AZA time points to determine the effectiveness and mechanisms underlying the treatment responses (Year 2-3). This project will be supported by integrative analysis of transcriptomic and epigenomic data to identify genomic regions with a perturbed epigenetic status that are aberrantly transcribed in AZA-treated samples (Year 2-4).

One representative publication from each co-supervisor:

• 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 Medicine13(582):eabc4822. doi: 10.1126/scitranslmed.abc4822.2021

• Karimi MM, Guo Y, Cui X, Pallikonda HA, Harkova V, Wang YF, Gil SR et al. The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus. Nature communications. 2021Jan; 12(99).