Clonal evolution underlying leukemia progression and Richter transformation in patients with ibrutinib-relapsed CLL

Ibrutinib has generated remarkable responses in patients with chronic lymphocytic leukemia (CLL), including those with an unfavorable cytogenetic profile. However, patients develop resistance, with poor outcomes and no established treatment options. Mutations in <i>BTK</i> and <i>PLCG2</i> have emerged as main mechanisms of drug resistance, but not all patients carry these mutations. Further understanding of mechanisms of resistance is urgently needed and will support rational development of new therapeutic strategies. To that end, we characterized the genomic profiles of serial samples from 9 patients with ibrutinib-relapsed disease, including 6 who had Richter transformation. Mutations, indels, copy-number aberrations, and loss of heterozygosity were assessed using next-generation sequencing and single-nucleotide polymorphism array. We found that 18p deletion (del(18p)), together with del(17p)/<i>TP53</i> mutations, was present in 5 of 9 patients before ibrutinib therapy. In addition to <i>BTK^C481</i> , we identified <i>BTK^T316A</i> , a structurally novel mutation located in the SH2 domain of BTK. Minor <i>BTK</i> clones with low allele frequencies were captured in addition to major <i>BTK</i> clones. Although <i>TP53</i> loss predisposes patients for relapse, clone size of <i>TP53</i> loss may diminish during disease progression while mutant <i>BTK</i> clone expands. In patients who had Richter transformation, we found that the transformed cells were clonal descendants of circulating leukemia cells but continued to undergo evolution and drifts. Surprisingly, transformed lymphoma cells in tissue may acquire a different <i>BTK</i> mutation from that in the CLL leukemia cells. Collectively, these results provide insights into clonal evolution underlying ibrutinib relapse and prompt further investigation on genomic abnormalities that have clinical application potential.