Study Identifies 2 Distinct Epigenetic Subtypes Within Aggressive CLL

Researchers have identified 2 previously unrecognized biological subtypes within IGHV-unmutated chronic lymphocytic leukemia (U-CLL), a form of the disease long associated with poor prognosis. The findings, published in HemaSphere, suggest that even among patients classified as high-risk, leukemia cells may follow distinct epigenetic and genetic paths that help explain differences in disease biology.¹

Among CLL, one of the most important prognostic factors is whether tumor cells carry somatic hypermutation in the immunoglobulin heavy-chain variable (IGHV) region.² Patients with unmutated IGHV typically experience more aggressive disease, earlier need for treatment, and inferior outcomes compared with those with mutated IGHV. But U-CLL itself is not uniform, and the new study adds nuance to that category.

The research team analyzed genome-wide DNA methylation profiles from 52 patients with U-CLL using high-resolution EPIC arrays. DNA methylation patterns capture both a cell’s developmental origin and its proliferative history, offering insight beyond standard genetic testing.

The study was initially designed to explore whether complex karyotype, a known adverse prognostic feature, was linked to specific epigenetic signatures. That association turned out to be weak. Instead, the analysis revealed an unexpected result where U-CLL cases consistently separated into 2 epigenetically distinct groups the researchers labeled U-CLL C1 and U-CLL C2. These groups differed markedly in both epigenetic programming and genetic alterations, despite sharing the same IGHV-unmutated classification.

The 2 “epitypes” showed strikingly different genetic profiles. U-CLL C1 was enriched for ATM deletions (P = .015) and mutations (P = .017), as well as deletion of chromosome 13q (P = .007). In contrast, U-CLL C2 contained all cases with TP53 deletions or mutations (P = .004) and was also associated with trisomy 12 (P = .004).

Importantly, these differences were not driven by complex karyotypes, which were evenly distributed between the 2 groups. This, the researchers explained, suggests that epigenetic profiling is capturing biological variation that is not explained by traditional cytogenetic risk factors alone.

Further analysis of more than 4000 differentially methylated sites showed that the 2 epitypes reflect different levels of B-cell maturation–related epigenetic programming.

“Remarkably, when we analyzed B-cell-related differential CpGs, we noticed that the higher methylation levels in U‐CLL C1 resembled pre‐germinal center (GC) B cells, while methylation loss in U‐CLL C2 was shared with GC‐experienced B cells,” wrote the researchers. “Congruent with this observation, Component 1 of a PCA using these differential CpGs clustered U‐CLL C1 cases together with naïve B cells and U‐CLL C2 cases together with GC B, memory B, and plasma cell samples.”

These findings support a growing model in which CLL arises along a continuum of B-cell maturation stages rather than from a single defined cell of origin, the authors explained.

To confirm that the 2 epitypes were not unique to the initial dataset, the researchers validated their findings in 2 independent population-based cohorts totaling more than 240 additional U-CLL cases. The same epitypes emerged, with consistent methylation patterns and similar enrichment of genetic alterations.

Across cohorts, U-CLL C1 showed lower scores on an epigenetic “proliferative history” clock, suggesting fewer past cell divisions, while U-CLL C2 exhibited evidence of greater proliferative and epigenetic activity. Despite these biological differences, the 2 epitypes did not show significant differences in overall survival or time to first treatment. However, within U-CLL C2, higher epigenetic proliferation scores were associated with earlier treatment initiation, hinting that epigenetic features may still influence clinical behavior in subtler ways.

References

1. Charalampopoulou S, Ramos-Campoy S, Duran-Ferrer M, et al. Identification of two epitypes of IGHV unmutated chronic lymphocytic leukemia with distinct B-cell-related epigenetic imprinting and genetic alterations. HemaSphere. Published online January 8, 2026. doi:10.1002/hem3.70211

2. Choi DS, Sarkar UA, Ren Y, et al. Characterization of IGHV subgroups and their prognostic relevance in CLL. Blood. 2025;146(S1):3899. doi:10.1182/blood-2025-3899