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DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia

Nature Genetics volume 48, pages 253–264 (2016)Cite this article

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Abstract

Charting differences between tumors and normal tissue is a mainstay of cancer research. However, clonal tumor expansion from complex normal tissue architectures potentially obscures cancer-specific events, including divergent epigenetic patterns. Using whole-genome bisulfite sequencing of normal B cell subsets, we observed broad epigenetic programming of selective transcription factor binding sites coincident with the degree of B cell maturation. By comparing normal B cells to malignant B cells from 268 patients with chronic lymphocytic leukemia (CLL), we showed that tumors derive largely from a continuum of maturation states reflected in normal developmental stages. Epigenetic maturation in CLL was associated with an indolent gene expression pattern and increasingly favorable clinical outcomes. We further uncovered that most previously reported tumor-specific methylation events are normally present in non-malignant B cells. Instead, we identified a potential pathogenic role for transcription factor dysregulation in CLL, where excess programming by EGR and NFAT with reduced EBF and AP-1 programming imbalances the normal B cell epigenetic program.

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Figure 1: Epigenetic programming during B cell maturation.
Figure 2: Evaluation of the maturation state of CLL using DNA methylation.
Figure 3: The impact of DNA methylation programming in patients with CLL.
Figure 4: Previously identified aberrant methylation in CLL is found in comparison of normal B cell subtypes.
Figure 5: Deficiency in DNA methylation programming in LP-CLLs results from loss of expression of the EBF1 and FOS transcription factors.
Figure 6: Transcription factor binding sites enriched in CLL-specific hypomethylation.
Figure 7: Summary of global and transcription factor binding site DNA methylation programming in normal B cells and CLL.

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Acknowledgements

We would like to thank the Genomics and Proteomics Core Facility at the German Cancer Research Center, in particular R. Fisher and M. Schick for their excellent technical support and expertise. We thank Imaging Center Essen (IMCES) for support in B cell sorting. We are grateful to M. Bähr, O. Mücke, M. Helf and S. Ohl for technical support. We also thank J. Edelmann, M. Seiffert, L. Sellner, B. Wu, V. Hovestadt, A. Kundaje and J.I. Martín-Subero for providing samples, data and/or analytical tools. S.S. is supported by the Else Kröner Fresenius Stiftung (2012_A146), the Virtual Helmholtz Institute (VH-VI-404) and the Deutsche Forschungsgemeinschaft (SFB 1074 projects B1 and B2). This work was supported in part by the Helmholtz Association, from the DKFZ–Heidelberg Center for Personalized Oncology (DKFZ-HIPO), the German Cancer Consortium (DKTK), the CLL Research Consortium (CRC), the German Federal Ministry of Education and Research CancerEpiSys network (BMBF 031 6049C), the Virtual Helmholtz Institute (VH-VI-404), the Deutsche Forschungsgemeinschaft (GKR1431 and SE1885/2-1), the Leukemia and Lymphoma Society (P01 CA081534), the Four Winds Foundation, the European Union's Seventh Framework Programme through the Blueprint Consortium, the German Ministry of Education and Research (BMBF) through the ICGC MMML-Seq Project (01KU1002A-J) and the US National Institutes of Health (PO1-CA81534).

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Author notes

  1. Christopher C Oakes & Peter Lichter

    Present address: Present address: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA.,

Authors and Affiliations

  1. Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Christopher C Oakes, Yassen Assenov, David Brocks, Daniel B Lipka, Olga Bogatyrova, Dieter Weichenhan & Christoph Plass

  2. Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany

    Marc Seifert, Martina Przekopowitz & Ralf Küppers

  3. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA

    Lei Gu

  4. Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts, USA

    Lei Gu

  5. Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, USA

    Amy S Ruppert & John C Byrd

  6. Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Qi Wang, Charles D Imbusch, Sandra D Koser & Benedikt Brors

  7. Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Qi Wang, Charles D Imbusch, Sandra D Koser & Benedikt Brors

  8. Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Andrius Serva, Marc Zapatka & Peter Lichter

  9. Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California, USA

    Laura Rassenti & Thomas J Kipps

  10. Cooperation Unit Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Daniel Mertens & Stephan Stilgenbauer

  11. Department of Internal Medicine III, University of Ulm, Ulm, Germany

    Daniel Mertens & Hartmut Döhner

  12. Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany

    Thorsten Zenz

  13. Department of Medicine V, University of Heidelberg, Heidelberg, Germany

    Thorsten Zenz

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Contributions

C.C.O., M.S., M.P., A.S., D.W. and C.P. designed and performed experimental work. C.C.O., Y.A., L.G., A.S.R., Q.W., C.D.I., S.D.K., D.B., D.B.L. and O.B. performed data analysis. M.S., L.R., T.J.K., H.D., R.K., T.Z., S.S. and J.C.B. provided clinical samples or data. C.C.O., M.S. and C.P. prepared the manuscript and figures. B.B., D.M., M.Z., P.L., T.Z., S.S., J.C.B. and C.P. provided project leadership. All authors contributed to the final manuscript.

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Correspondence to Christopher C Oakes or Christoph Plass.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Note and Supplementary Tables 2–11. (PDF 17289 kb)

Supplementary Table 1

DNA methylation levels of the top 5,000 hypermethylated windows. (XLSX 1089 kb)

Supplementary Table 12

TWGBS windows overlapping a TFBS with the corresponding motif. (XLSX 2403 kb)

Supplementary Table 13

450K probes overlapping a TFBS with the corresponding motif. (XLSX 74 kb)

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Oakes, C., Seifert, M., Assenov, Y. et al. DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat Genet 48, 253–264 (2016). https://doi.org/10.1038/ng.3488

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