Epigenetic evolution and lineage histories of chronic lymphocytic leukemia

Description: Summary from the GEO: "Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer. In addition to genetic mutations, chronic lymphocytic leukemia (CLL) undergoes diversification through stochastic DNA methylation changes – epimutations. To measure the epimutation rate at single-cell resolution, we applied multiplexed reduced representation bisulfite sequencing (MscRRBS) to healthy donors B cells and CLL patient samples. We observed that the common clonal CLL origin results in consistently elevated epimutation rate (i.e., 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 sample. 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. To validate the inferred tree topology, we integrated MscRRBS with single-cell transcriptomes and genotyping, which 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 CLL samples prior to and during ibrutinib-associated lymphocytosis. Lineage trees revealed divergent clades of cells preferentially expelled from the lymph node with ibrutinib therapy, marked by distinct transcriptional profiles. These data offer direct single-cell integration of genetic, epigenetic and transcriptional information in the study of leukemia evolution, providing deeper insight into its lineage topology and enabling the charting of its evolution with therapy.
We profiled the single-cell DNA methylomes of 831 normal B cells from six healthy donor samples and 1,821 cells from 12 primary IGHV mutated and unmutated CLLs. Single-cell methylome profiling was performed with multiplexed single-cell reduced representation bisulfite sequencing (MscRRBS), an adaption of a previous scRRBS protocol that allows to increase throughput through the addition of cell barcodes early in the scRRBS protocol. We also integrated single-cell DNAme and whole transcriptome sequencing with targeted sequencing of known somatic mutations in the cDNA."

Subject of Study

Homo sapiens

Subject(s)

B-Lymphocytes

Epigenetics

Leukemia, Lymphocytic, Chronic, B-Cell

OncoTree Cancer Type(s)

Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma
Lymphoid Neoplasm

Access via GEO
CSV, Plain Text, and XLSX sequencing data in 13 files.
Accession #: GSE109085

Access via SRA
Bisulfite and RNA Sequence reads for 843 samples.
Accession #: SRP128904

Access via BioProject
Additional information about overall initiative.
Accession #: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA429620
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Pastore A, Gaiti F, Lu S, et al. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nature Communications. 2019; 10:1874.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2500
High throughput sequencing system
Dataset Format(s): CSV, Plain Text, SRA, XLSX
Dataset Size: 7.9 Mb in 13 files (CSV, Plain Text, and XLSX), 1,000+ Gb (SRA).

Data Catalog Record Updated: 2023-12-07