-Author name in bold denotes the presenting author
-Asterisk * with author name denotes a Non-ASH member
Clinically Relevant Abstract denotes an abstract that is clinically relevant.

PhD Trainee denotes that this is a recommended PHD Trainee Session.

Ticketed Session denotes that this is a ticketed session.

384 Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-Cell Acute Lymphoblastic Leukemia

Program: Oral and Poster Abstracts
Type: Oral
Session: 503. Clonal Hematopoiesis: Aging and Inflammation
Hematology Disease Topics & Pathways:
Leukemia, ALL, Diseases, Biological Processes, epigenetics, Lymphoid Malignancies
Sunday, December 6, 2020: 12:30 PM

Juliette Roels1,2,3*, Morgan Thénoz1,3*, Bronisława Szarzyńska4*, Mattias Landfors5*, Stien De Coninck1,6*, Lisa Demoen1,3*, Lien Provez1,3*, Anna Kuchmiy6*, Steven Strubbe6*, Lindy Reunes1,2,3*, Tim Pieters, PhD1,2,3*, Filip Matthijssens, PhD1,3*, Wouter Van Loocke1,3*, Tim Lammens, PhD7,8,9*, Barbara De Moerloose, MD, PhD2,9,10*, Marc R. Mansour, MD, PhD11*, Utpal Dave, MD12,13, Steven Goossens, PhD6, David J. Curtis, MBBS, PhD14, Tom Taghon, PhD6*, Małgorzata Dawidowska, PhD4*, Sofie Degerman, PhD5* and Pieter Van Vlierberghe, PhD1,2,3

1Center for Medical Genetics, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
3Department for Biomolecular Medicine, Ghent University, Ghent, Belgium
4Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
5Department of Medical Biosciences, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
6Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
7Department of Pediatric Hemato-oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
8Cancer Research Institute Ghent (CRIG), Ghent, Belgium
9Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
10Belgium Society of Paediatric Hematology Oncology, Ghent, Belgium
11Cancer Institute, Department of Haematology, University College London, London, United Kingdom
12Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN
13IU Melvin and Bren Simon Cancer Center; Division of Hematology/Oncology, Vanderbilt University Medical Center, Indianapolis, IN
14Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia

During the last decade, aberrant DNA methylation has been identified as a hallmark of human cancer and several studies have highlighted the potential of DNA methylation as a clinically or diagnostically relevant biomarker. In comparison to their normal healthy counterparts, cancer cells generally display DNA hypermethylation at specific CpG islands, but the actual mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood.

To profile the DNA methylation landscape of human T-cell acute lymphoblastic leukemia (T-ALL), we analyzed 109 T-ALLs together with 10 stages of normal T cell development, which are considered the normal human counterparts of this disease, by 850 EPIC arrays. Here, we show that CpG islands are hypermethylated in all human T- ALLs compared to their normal counterparts. We designed a DNA methylation signature that can distinguish two types of T-ALL, with low or high levels of CpG island hypermethylation. This profile is dominated by CpGs in promoters of PRC2 target genes. T-ALLs with high levels of CpG island hypermethylation show low levels of H3K27me3 and vice versa, resulting in gene repression in both subtypes of T-ALL by different mechanisms.

Furthermore, we found that aberrant CpG island hypermethylation shows a strong correlation with the epigenetic age of the leukemic T cells. By investigating the DNA methylation profile of two distinct mouse T-ALL models, the Lck-Cre Ptenfl/fl and the CD2-Lmo2 transgenic mouse model, by Reduced Representation Bisulfite Sequencing, we could indeed recapitulate the DNA methylation features of the two human T-ALL subtypes in mice (Fig.1). The aggressive, fast-transforming Ptenfl/fl mouse model displays low levels of CpG island hypermethylation, which correlated with human T-ALLs that have a shorter proliferative history and a worse prognosis. In contrast, murine CD2-Lmo2 T-ALLs have a longer disease latency and display a CpG island hypermethylation phenotype that is similar to human T-ALLs with a longer proliferative history. In CD2-Lmo2 mice, a pre-leukemic phase is present with self-renewing thymocytes. We elucidate that the CpG island methylation signature is gradually established in aging pre-leukemic thymocytes of 8, 16 and 24 weeks old CD2-Lmo2 mice (Fig.1). Of note, this hypermethylation phenotype is completely absent in age matched Lck-Cre Ptenfl/fl mice that did not yet develop leukemia, suggesting that the proliferative history is responsible for aberrant CpG island DNA methylation observed in human T-ALL. Notably, this provides the first evidence that a pre-leukemic phase might be present in a large subset of human T-ALLs, and that epigenetic aberrations, either in the DNA methylation or histone methylation machinery are one of the first detectable alterations during T-ALL development.

Finally, using patient derived xenografts (PDX), we show that DNA hypomethylation by the FDA-approved hypomethylating agent Decitabine is very effective in treating T-ALL. Gene expression profiling revealed that the anti-leukemic effect is exerted by down-regulation of the oncogenic MYC pathway. However, by profiling these PDX T-ALLs by EPIC arrays, we unexpectedly uncover that the age-related CpG island hypermethylation signature is completely resistant to Decitabine treatment.

Altogether, our work demonstrates that DNA methylation reflects the epigenetic history of leukemic T cells and suggests that methylation-based subtypes of human T-ALL have followed a different trajectory towards T-cell transformation, possibly mediated by differences in the self-renewing capacity of the putative T-ALL cell-of-origin. Given that the concept of preleukemic thymocytes has only been reported in T-ALL mouse models so far, we here provide, for the first time, conceptual evidence that a pre-leukemic phase might also be involved in the pathogenesis of the human disease.

Disclosures: No relevant conflicts of interest to declare.

*signifies non-member of ASH