Oral Presentation 44th Lorne Genome Conference 2023

Deciphering epigenetic alterations in pre-leukemic stem cells during T-cell acute lymphoblastic leukemia development (#21)

Feng Yan 1 2 , Francine E Garrett-Bakelman 3 , Jesslyn Saw 1 , Matthew P McCormack 1 , Shokoufeh Abdollahi 1 , David R Powell 4 , Pieter Van Vlierberghe 5 , Nicholas C Wong 4 , David J Curtis 1
  1. Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
  2. Bioinformatics Division, WEHI, Parkville, VIC, Australia
  3. School of Medicine, University of Virginia, New York, NY, USA
  4. Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia
  5. Department of Biomolecular Medicine, Ghent University, Ghent, Belgium

Acute lymphoblastic leukemia (ALL) is a multi-step process, beginning with chromosomal translocations in lymphoid progenitors giving rise to pre-leukemic stem cells (pre-LSCs). Acquisition of additional gene mutations leads to leukemic stem cells (LSCs), which expand to generate clinical disease. Both pre-LSCs and LSCs are sources of relapse following chemotherapy and understanding their regulation will identify new therapeutic avenues.

Whilst the genetic landscapes of ALL subtypes have been well-defined, the epigenetic landscape of pre-LSCs and their progression to LSCs have not been described. We used a multi-omics approach to study the epigenetic changes in pre-LSCs and LSCs in a Lmo2 transgenic mouse model mimicking early T-cell precursor ALL (ETP-ALL) using FACS-purified double negative 3 thymocytes.

Overall, principal component analyses demonstrated distinct trajectories for chromatin, DNA methylation and gene expression changes during leukemogenesis. Using ATAC-seq, we showed that changes in chromatin accessibility occurred early in pre-LSCs and remained relatively stable during evolution to LSCs. A combination of ChIP-seq, transcription factor footprinting and RNA expression analyses identified increased gene expression and chromatin accessibility associated with Lmo2 and heptad transcription factor (TF) binding in pre-LSC. In contrast, most DNA methylation changes occurred later. In LSCs, hypermethylation at bivalent promoters led to gene repression. These promoters were also predisposed in pre-LSCs by (1) closed chromatin (2) increased heterogeneity of DNA methylation, and (3) CTCF binding sites. In T-ALL, most of the preceding chromatin changes were lost, while DNA hypermethylation was maintained but with new hypomethylation in CpG open sea regions that were unaffected in previous stages of leukemogenesis. 

In conclusion, we have used a mouse model of T-ALL to describe the multi-step temporal DNA methylation, chromatin and transcription factor binding changes, and associated gene expression changes in leukemic stem cells during leukemogenesis. This will provide new insights into the epigenetic mechanisms of cancer development.