Poster Presentation Australian Epigenetics Alliance Conference 2022

Deciphering epigenetic alterations during T-cell acute lymphoblastic leukemia development (#152)

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

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 thus 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 ATAC-seq, we showed that changes in chromatin accessibility occurred early in pre-LSCs and remained relatively stable during evolution to LSCs and overt T-ALL. A combination of ChIP-seq, transcription factor footprinting and RNA expression analyses identified increased gene expression associated with Lmo2 and Gata2 binding in more accessible regions in pre-LSC. In contrast to chromatin accessibility, most DNA methylation changes occurred later. In LSCs, hypermethylation at bivalent promoters with both H3K27me3 and H3K4me3 in normal thymocytes led to gene repression. In overt T-ALL, new hypomethylation in repetitive elements was observed. Interestingly, promoters destined for hypermethylation in LSCs were predisposed in pre-LSCs by (1) closed chromatin (2) increased heterogeneity of DNA methylation measured by epialleles, and (3) CTCF binding sites. Furthermore, the overall methylation profiles resemble two subtypes of human T-ALL, pre-LSCs were like CpG-island methylator phenotype negative (CIMP-) T-ALL and LSCs were like CIMP+ T-ALL.

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.