Chromatin activation profiling of stereotyped chronic lymphocytic leukemias reveals a subset 8–specific signature

• Stereotyped subset 8, an aggressive entity associated with Richter transformation, is characterized by a unique chromatin activation profile.

• A set of 209 de novo active regions in subset 8 are associated with 113 overexpressed genes, potentially related to Richter transformation.

The chromatin activation landscape of chronic lymphocytic leukemia (CLL) with stereotyped B-cell receptor immunoglobulin is currently unknown. In this study, we report the results of a whole-genome chromatin profiling of histone 3 lysine 27 acetylation of 22 CLLs from major subsets, which were compared against nonstereotyped CLLs and normal B-cell subpopulations. Although subsets 1, 2, and 4 did not differ much from their nonstereotyped CLL counterparts, subset 8 displayed a remarkably distinct chromatin activation profile. In particular, we identified 209 de novo active regulatory elements in this subset, which showed similar patterns with U-CLLs undergoing Richter transformation. These regions were enriched for binding sites of 9 overexpressed transcription factors. In 78 of 209 regions, we identified 113 candidate overexpressed target genes, 11 regions being associated with more than 2 adjacent genes. These included blocks of up to 7 genes, suggesting local coupregulation within the same genome compartment. Our findings further underscore the uniqueness of subset 8 CLL, notable for the highest risk of Richter’s transformation among all CLLs and provide additional clues to decipher the molecular basis of its clinical behavior.