Continuous DNA methylation deconvolution-based surrogate for B-cell differentiation state in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is clinically divided categorically into IGHV mutated (M-CLL) and IGHV unmutated (U-CLL) subtypes. We aimed to generate a continuous metric of CLL epigenetic state to correspond to the many steps of B-cell differentiation from which CLL neoplasms may arise. We measured genome-scale DNA methylation in purified CLL samples (n = 89) and utilized reference-based cell deconvolution techniques to develop a continuous metric of epigenetic similarity across a B-naive-like to B-memory-like scale (B-Index). We used B-Index to find epigenome-wide changes across CLL differentiation states. We also analyzed the epigenetic similarity of U-CLL to normal B-cell types, and epigenetic correlates of tumor burden. We find that B-Index accurately classifies CLL into clinical subtypes (98.8%), has a stronger epigenetic signal than IGHV gene percent identity, and demonstrates additional epigenetic signal within clinical subgroups. We demonstrate that U-CLL is epigenetically more similar to B-memory than B-naive cells and reconcile previous reports of a B-naive-like epigenetic signal. The B-memory-like program of U-CLL is enriched for binding sites of transcription factors related to the germinal center activation pathway. We also identified an epigenetic signal associated with tumor burden, which was enriched for binding sites of Epstein-Barr-Virus transcription factors. Our analyses show that more epigenetic states are present among CLL neoplasms than are captured by the clinical classification system. Our approach can be used to generate continuous metrics of epigenetic states for other neoplasms. Chronic lymphocytic leukemia (CLL) is a type of cancer that arises from a kind of cell known as B-cells. However, which types of B-cells CLL arises from has been a matter of debate. We analyzed the DNA of both cancer cells and healthy B-cells to assign continuous scores (0-1) representing how differentiated the cancer cells are. We found that the continuous approach provides more information than the usual classification approach. Our findings provide insight on the variety of possible types of CLL that can arise, and our approach to generating a continuous score may be applied to other cancers. Hage et al. utilize methylation of malignant B-cells and normal B-cell references to assign a continuous metric of differentiation to cancer cases. They find that Chronic Lymphocytic Leukemias have additional epigenetic differences within clinical subtypes, and that both subtypes are more alike to B-memory cells.