Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

Abstract

Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer 1 . Chronic lymphocytic leukemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution with therapy 2 , 3 . The CLL epigenome is also an important disease-defining feature 4 , 5 , and growing CLL populations diversify through stochastic DNA methylation (DNAme) changes – epimutations 6 . However, previous studies based on bulk DNAme sequencing could not answer whether epimutations affect CLL populations homogenously. To measure epimutation rate at single-cell resolution, we applied multiplexed single-cell reduced representation bisulfite sequencing (MscRRBS) to healthy donors B cell and CLL patient samples. We observed that the common clonal CLL origin results in consistently elevated epimutation rate, with low cell-to-cell epimutation rate variability. In contrast, variable epimutation rates across normal B cells reflect diverse evolutionary ages across the B cell differentiation trajectory, consistent with epimutations serving as a molecular clock. Heritable epimutation information allowed high-resolution lineage reconstruction with single-cell data, applicable directly to patient samples. CLL lineage tree shape revealed earlier branching and longer branch lengths than normal B cells, reflecting rapid drift after the initial malignant transformation and a greater proliferative history. MscRRBS integrated with single-cell transcriptomes and genotyping confirmed that genetic subclones map to distinct clades inferred solely based on epimutation information. Lastly, to examine potential lineage biases during therapy, we profiled serial samples during ibrutinib-associated lymphocytosis, and identified clades of cells preferentially expelled from the lymph node with therapy, marked by distinct transcriptional profiles. The single-cell integration of genetic, epigenetic and transcriptional information thus charts CLL’s lineage history and its evolution with therapy.

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

“…This reversibility of the higher-order chromatin structure is very much in line with the previously observed similarity of histone modifications, chromatin accessibility and gene expression profiles in NBC and MBC. In sharp contrast to this congruent behavior of chromatin-based traits, DNA methylation is rather different between NBC and MBC, as this mark follows an accumulative pattern during cell differentiation 30, 78 and can be used to faithfully track the lineage trajectory of the cells 79 .…”

Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics

“…It is noteworthy that this is still an underestimation of the true extent of clonal diversity. Future studies with even more cells, broader coverage of the genome, and integration with single-cell transcriptomic and epigenomic states, that is becoming a reality with the recent technological advancement 35 36 , will further elucidate the clonal diversity and evolutionary trajectories of AML, which may contribute to the development of predictive biomarkers or therapies targeting clonal diversity.…”

Tumor Suppressors in Chronic Lymphocytic Leukemia: From Lost Partners to Active Targets

“…Genome and epigenome are intimately connected in cancer development, and the interplay of genomic and epigenomic factors plays a major role in CLL pathogenesis as well. In a recent analysis of the epigenomic landscape, various aberrations of the epigenome have emerged as markers in CLL pathogenesis [72,73]. However, it is also worth noting that methylation is a process that may occur both in normal and pathological hemopoiesis.…”