Elucidating the contribution of AID to the clonal evolution of CLL

The activation induced cytidine deaminase (AID) is specifically expressed in germinal centre B cells where it is required for both somatic hypermutation and class switch recombination of the immunoglobulin (Ig) genes by directly deaminating cytosines to uracils. As AID causes a substantial amount of off-target mutations, its activity has been associated with lymphomagenesis and clonal evolution of B cell malignancies. In Chronic lymphocytic leukemia (CLL), the leukemic B cells share a clonal B cell receptor consisting of specifically rearranged VDJ heavy and VJ light chain genes. In our preliminary experiments, we could show a substantial subclonal diversity at VDJ as well as at IgM switch (S) regions, showing ongoing AID on-target activity in vivo during disease progression. In parallel, we could show that in a CLL mouse model, AID is required for the development of a more aggressive, transplantable CLL clone. Our preliminary data strongly support the involvement of AID in clonal evolution of CLL. In this project, we hence aim at elucidating how AID contributes to clonal evolution of CLL, which genomic targets are hit by AID and whether AID inhibition might improve treatment outcome in CLL.

The project's most significant results can be summarized as follows: First, we could identify RNA-editing as a mechanism in chronic lymphocytic leukaemia (CLL) that largely contributes to epitranscriptome diversification. RNA editing (a specific alteration of single bases in RNA transcripts) leads to many changes in the CLL transcriptome and stratifies CLL in different groups with distinct course of disease. Finally, RNA editing is an important factor determining treatment resistance and likely, novel drugs that inhibit RNA editing could be very promising in rendering CLL cells vulnerable towards a diverse battery of treatment regimens, including immune checkpoint therapies. Second, we revealed the mutational landscape of an important mouse model for CLL and determined clonal evolution of CLL and the contribution of AID in this regard. This information is very important to evaluate this mouse as a model system for CLL and interpret the outcome of research studies performed in these mice. Finally, the project led to important discoveries in the field of DNA double strand break repair. We could show that leukemic cells repair damaged DNA with less precision and fidelity than non-malignant cells. We show that an increased activity of alternative end joining pathways accounts responsible for this phenomenon, which likely contributes to increased chromosomal aberrations in leukemic cells. In parallel, we could identify the protein SAMHD1 as a novel factor in DNA end joining. Simultaneously with a report from the laboratory of the Nobel laureate Tasuku Honjo, we were the first to show that by regulating the DNA precursor pool, SAMHD1 is decisive for the aberrant insertion of distant DNA regions into repair junctions generated by non-homologous end joining. This finding draws light on an important mechanism that is causative for the diversification of genomes during cancer progression.