Genomic instability is a hallmark of cancer, providing a means by which cancer cells can adapt to selective pressures and acquire drug-resistance. In the treatment of chronic myeloid leukaemia (CML), a subset of patients develop resistance to treatment with tyrosine kinase inhibitors (TKI's). We investigate DNA transposition as a source of genomic instability in CML, identifying the RAG (recombination activation genes) as potential drivers of transformation of CML. RAG1 has recently been shown to have evolved from DNA transposons but are well known for their essential role in acquired immunity; RAG1 is physiologically expressed in developing lymphocytes where it cuts and pastes immunoglobulin genes together to enable antibody diversity. The potential for RAG1 to act as a transposon has been demonstrated in vitro, but its ability to contribute widely to genomic instability is only recently being recognised with application of high throughput sequencing strategies.
We have applied, RNAseq and whole exome sequencing (WES) on a cohort (n=186) of CML patient samples, in an effort to identify drivers of therapy-resistance. Analysis of gene expression has revealed aberrant expression of RAG1 and associated genes, specifically in patients at lymphoid blast crisis (advanced CML). Through analysis of copy number variation (CNV), we observe loss of immunoglobulin loci in CML patients matching RAG expression, indicative of RAG activity. This is supported by breakpoint analysis showing DNA breaks occurring at known RAG target sites. We also identify hundreds of putative fusion genes that occur since diagnosis, from which unbiased motif enrichment searches reveal an enrichment for the known RAG1 target motif, and in many cases include immunoglobulin genes mobilised throughout the genome.
This work provides evidence that RAG1 mediated DNA transposition may be a major driving force behind genomic instability in advanced CML, and potentially the source of drug-resistance.