Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK-driven lymphomagenesis.

Elisa Redl,Patricia Hamminger,Kristina Draganić,Crhistian De Jesus Cardona,Thomas Dillinger,Maša Zrimšek,Gabriele Schweikert,Sabine Lagger,Lorena Hofbauer,Christian Seiser,Lukas Kenner,Wilfried Ellmeier,Raheleh Sheibani-Tezerji,Michael Kothmayer,Gerald Timelthaler,Gerda Egger,Andreas Tiefenbacher,Christoph Bock,C Dietz ,Melanie R Hassler ,Bernard Ramsahoye

doi:10.26508/lsa.202000794

Abstract

Malignant transformation depends on genetic and epigenetic events that result in a burst of deregulated gene expression and chromatin changes. To dissect the sequence of events in this process, we used a T-cell-specific lymphoma model based on the human oncogenic nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) translocation. We find that transformation of T cells shifts thymic cell populations to an undifferentiated immunophenotype, which occurs only after a period of latency, accompanied by induction of the MYC-NOTCH1 axis and deregulation of key epigenetic enzymes. We discover aberrant DNA methylation patterns, overlapping with regulatory regions, plus a high degree of epigenetic heterogeneity between individual tumors. In addition, ALK-positive tumors show a loss of associated methylation patterns of neighboring CpG sites. Notably, deletion of the maintenance DNA methyltransferase DNMT1 completely abrogates lymphomagenesis in this model, despite oncogenic signaling through NPM-ALK, suggesting that faithful maintenance of tumor-specific methylation through DNMT1 is essential for sustained proliferation and tumorigenesis.

Highlights

Individual tumors and tumor types show a high level of heterogeneity regarding their genetic and epigenetic constitution and in the affected signaling pathways
We found cAMP signaling, which has a role for cell proliferation, differentiation and migration as well as the homeodomain-containing transcription factor HOXA9, which is implicated in hematopoietic stem cell expansion and acute myeloid leukemia, to be up-regulated in ALK transgenic mice (ALK) tumors compared with Ctrl thymocytes [36, 37]
Cell cycle–related proteins, including CDK4/CDK6 and cyclin D1 were up-regulated upon tumor onset in thymi harboring small tumors, which was maintained in end-stage tumors for most of the samples tested. These results suggest that ALK signaling is already active in pre-tumor stages and leads to an early activation of pSTAT3 and elevated expression of DNMT1 culminating in ALK-dependent transformation in nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) transgenic mice, which is accompanied by up-regulation of cell cycle genes and c-MYC induction

Summary

Introduction

Individual tumors and tumor types show a high level of heterogeneity regarding their genetic and epigenetic constitution and in the affected signaling pathways. CGIs are often found in gene promoter regions and hypermethylated CGIs have been associated with the silencing of tumor suppressor genes in diverse cancers. Linking specific DNA methylation differences with extensive expression changes during tumorigenesis in a cause-and-effect relationship remains challenging because of the crosstalk of diverse epigenetic regulators. STAT3 acts by directly and indirectly regulating the expression of the maintenance methyltransferase DNMT1 and by directing all three major methyltransferases (DNMT1, DNMT3A, and DNMT3B) to STAT3 binding sites within promoters of genes such as SHP1 or IL2RG. The role of STAT3 as a mediator of DNA methylation of target promoters was supported by recent data, demonstrating a function of acetylated STAT3 for inducing the methylation of tumor suppressor genes in melanoma and breast cancer [5]

Methods

Results

Conclusion