Abstract P15: Cross-species DNA methylation profiling of T and B cell populations in T-PLL and B-CLL compared to TCL1 transgenic mouse models

Abstract

Abstract The T cell leukemia/lymphoma 1 (TCL1, alias TCL1A) oncogene is aberrantly expressed in a variety of T and B cell malignancies, but its deregulation has been most closely associated with T cell prolymphocytic leukemia (T-PLL) and B cell chronic lymphocytic leukemia (B-CLL). Both diseases are known to be associated with substantial DNA methylation loss, for which the exact mechanism and the relation with TCL1 is largely unknown. We here aimed at a comparative DNA methylation profiling study of TCL1 transgenic (tg) mice developing either B-CLL, acute lymphoblastic leukeima (ALL) or T cell leukemia to elucidate the role of TCL1 on the DNA methylome. The Infinium™ Mouse Methylation BeadChip, which includes approximately 285k methylation sites, was used to investigate DNA methylomes from different cell populations of Eµ-TCL1 and Lck-TCL1A tg mice. In total, 61 samples were collected including benign, pre tumor (10-12 weeks) and tumor samples (Eµ-TCL1: ~40-60 weeks, Lck-TCL1A: ~75 weeks). In addition, we analyzed DNA methylomes of 27 Eµ-TCL1 tg mice with further gene knockouts (p53: n=5, Terc: n=10, Pten: n=6, Btk: n=2, Ig-beta: n=3, Syk: n=1). Samples from Eµ-TCL1 tg mice were either sorted for CD19+ cells or for CD19+ and CD5+ cells and samples from Lck-TCL1A tg mice were either sorted for CD3+ or CD8+ cells. For cross-species epigenetic analysis we mined DNA methylation data from human B-CLL (n=59) and T-PLL (n=60) samples as well as several benign subpopulations (memory and naïve B cells, CD4+ and CD8+ subpopulations) obtained by Infinium™ HumanMethylation450 or MethylationEPIC BeadChip analysis. We observed a global loss of DNA methylation in both tg mouse models, although to a greater extent in Eµ-TCL1 mice developing B-CLL. Differential DNA methylation analysis (t test, FDR < 0.01, |Δβ| > 0.3) revealed 89 hyper- and 21,820 hypomethylated CpGs in B-CLL and 318 hyper- and 10,375 hypomethylated CpGs in T-PLL mice. While the hypermethylated CpGs show a slight enrichment within poised promoters, hypomethylated CpGs were enriched within enhancer regions for both mouse models. Surprisingly, only minor overlaps of both models for the hypermethylated (9%) and hypomethylated (18%) CpGs could be detected. Furthermore, unsupervised and supervised analysis demonstrated no or only minor effects of the additional gene knockouts in the Eµ-TCL1 mice on the DNA methylome. In human B-CLL and T-PLL samples we also detected an enrichment of hypomethylated CpGs within enhancer regions. Remarkably, cross-species analyses identified only a minor overlap of hypomethylated CpGs in both diseases. In summary, we detected a global loss of DNA methylation in both T and B cell malignancies in human and corresponding mouse models, which was independent of other gene knockouts in the mice. However, the minor overlap of hypomethylated CpGs in B-CLL and T-PLL within and across both species suggests the involvement of different cell type specific regulatory processes in the T and B cell compartments. Citation Format: Selina Glaser, Billy Michael Chelliah Jebaraj, Annika Müller, Vera Schmid, Elias Hobeika, Dennis Jungherz, Anja Fischer, Marco Herling, Stephan Stilgenbauer, Reiner Siebert. Cross-species DNA methylation profiling of T and B cell populations in T-PLL and B-CLL compared to TCL1 transgenic mouse models [abstract]. In: Proceedings of the Blood Cancer Discovery Symposium; 2024 Mar 4-6; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(2_Suppl):Abstract nr P15.