Identify: Identification of the aberrant methylation program in Chronic Lymphocytic

Leukemia (CLL) compared to normal B-Cell counterparts.

Rational:
Dynamic epigenetic modifications occur during lineage development in the hematopoietic system
(1). A broad epigenetic programming has recently been described to occur during B-Cell
maturation and there is a prominent loss of methylation (hypomethylation) with increasing
maturity (2) (3). Besides, there are groups of CpGs where methylation pattern is stable during B-
Cell maturation or, gain methylation at mature B-Cells (2). The methylation program involved in
normal B-Cell maturation often have aberrations in different B-Cell neoplasms e.g., acute
lymphoblastic leukemia, chronic lymphocytic leukemia, diffuse large B-Cell lymphoma and
multiple myeloma (2). Recently, genome-wide DNA methylation studies revealed distinct
methylation subtypes in CLL bearing the signatures of B-Cell maturation (4) (3). Previous analyses
suggested that CLL patients are hypomethylated compared to the B-Cell progenitors and
methylation profiles resemble to the high maturity B-Cells (3) (2) (5). Therefore, we hypothesize
that the CpGs that are stable or, differentially methylated in CLL have aberrant methylation
programming in the context of normal B-Cell differentiation.

Protocol:
To study the aberrant methylation in CLL, we will use publicly available DNA methylation data
(array or, sequencing) of CLL patients and B-Cells subtypes from GEO database. We will collect
and process the datasets using state-of-the-art bioinformatics methods. At first, we will perform
hierarchical clustering, PCA and phylogenetic analysis of methylation data to infer the expected
separation of different cell types based on DNA methylation. Then we will find the differential
CpGs in CLL vs B-Cell lineages to identify the modules of CpGs that shows stable and dynamic
changes during B-Cell maturation.
REFERENCE:

1. N. Cabezas-Wallscheid et al., Identification of Regulatory Networks in HSCs and Their

Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome
Analysis. Cell Stem Cell. 15, 507–522 (2014).
2. M. Kulis et al., Whole-genome fingerprint of the DNA methylome during human B cell
differentiation. Nat. Genet. 47, 746–756 (2015).
3. C. C. Oakes 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).
4. A. C. Queirós et al., A B-cell epigenetic signature defines three biologic subgroups of
chronic lymphocytic leukemia with clinical impact. Leukemia. 29, 598–605 (2015).
5. M. Kulis et al., Epigenomic analysis detects widespread gene-body DNA
hypomethylation in chronic lymphocytic leukemia. Nat. Genet. 44, 1236–1242 (2012).