Plasma epigenomic profiling captures B-cell lymphoma biology

Background: B-cell lymphomas (BCLs), including diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), display widespread epigenetic dysregulation. The histone methyltransferase EZH2 catalyzes the repressive mark H3K27me3 and is an important epigenetic regulator for B-cell development. Although previous work has examined H3K27me3 in BCL tumour samples, the landscape of H3K27me3-decorated cell-free chromatin in BCL remains largely unexplored. Methods: We performed cfChIP-seq targeting H3K27me3 on n=55 DLBCL, n=19 FL, and n=21 non-cancer controls from the Princess Margaret LIBERATE study. For global analyses, reads were counted in 10kb genomic windows and background reads were subtracted using a truncated Poisson MLE and data were library size normalized. BCL scores were computed using leave-one-out NNLS against a healthy reference panel and a high-burden lymphoma archetype. For promoter analyses, reads ±2kb of the TSS were counted and library size normalized. Results: Global plasma H3K27me3 profiles in advanced-stage BCL separate from limited-stage BCL and non-lymphoma samples. Mean BCL scores were higher in advanced-stage BCL(p<0.0001) and limited-stage BCL (p<0.05) compared to non-lymphoma controls. Moreover, both DLBCL (p<0.0001) and FL (p<0.001) had higher mean BCL scores than non-lymphoma controls. BCL scores were highly correlated to PC1 (ρ=0.902, p=2.97e-35) and the orthogonal tumour fraction metrics including mean VAF from targeted sequencing (ρ=0.850, p=4.79e-18), ichorCNA tumour fraction from ~0.5X WGS (ρ=0.779, p=3.86e-12), and total lesion glycolysis from FDG-PET/CT (ρ=0.669, p=1.37e-10). Correlation analysis between H3K27me3 signal at promoters and mean VAF revealed a negative association at B-cell lineage loci such as PAX5 (r=-0.705, p=1.29e-09) and DTX1 (r=-0.622, p=3.11e-07), and a positive association at other hematopoietic lineage loci such as MCEMP1 (r=0.746, p=4.1e-11) and IL6R (r=0.635, p=1.46e-07), indicating an increased contribution of B-cell lineage contribution with increasing tumour fraction. Conclusions: These data show that plasma H3K27me3 profiles capture disease burden and reflect underlying tumour biology in BCL. Furthermore, these profiles capture lineage-specific promoter repression patterns, manifesting in negative correlations between H3K27me3 signal B-cell lineage markers and tumour fraction, contrasting positive correlations observed at markers of other hematopoietic lineages. Overall, cfChIP-seq of H3K27me3 provides a non-invasive epigenomic readout of circulating cell-free chromatin in BCL.