Single-Cell Whole Genome Sequencing Reveals the Evolution and Migration of Lymphoma

In contrast to RNA expression, which captures the current state of a cell, DNA is the only biomolecule in a cell that is not constantly replaced but copied and passed on during cell divisions. As a result, mutations that occur in the DNA code are fixed and gradually accumulate forming an archive of the life history of cells. DNA from pediatric cancers usually do not have high mutational loads. However, this is not the case with pediatric lymphomas which tend to harbor many mutations. This makes pediatric lymphomas an ideal model disease to study mutation accumulation. Here, we have applied state-of-the-art single-cell whole genome sequencing on pediatric Burkitt, T-lymphoblastic and Hodgkin lymphoma using the Primary Template-directed Amplification technique. Using this method, we have compared the genomes of malignant and non-malignant cells from the same tumors. We have also included patients in our cohort which have multiple-site involvement to investigate clonal dynamics across tissues. Using in-depth mutational analyses, we have generated detailed phylogenetic trees of each patient, identified processes unique to tumorigenesis and timed the occurrence of driver mutations and mutagenic processes. This type of analysis has not been applied to lymphoma before. Outcome of lymphoma in children is excellent (>90% survival), whereas survival in adults is much lower (~50%), because children can be treated with higher doses of chemotherapy. Consequently, treatment is extremely toxic, and relapses are mostly lethal. We envision that our research will contribute to improved diagnostics and ultimately the development of more targeted, less toxic treatment and a strongly improved quality of life.