Genomic evolution of ibrutinib-resistant clones in Waldenström macroglobulinaemia

Abstract

Ibrutinib is highly active in Waldenström macroglobulinaemia (WM) patients, but disease progression can occur due to acquired mutations in BTK, the target of ibrutinib, or PLCG2, the protein downstream of BTK. However, not all resistant patients harbour these alterations. We have performed a whole-exome sequencing study to identify alternative molecular mechanisms that can drive ibrutinib resistance. Our findings include deletions on chromosomes 6q, including homozygous deletions, and 8p, which encompass key regulators of BTK, MYD88/NF-κB, and apoptotic signalling. Moreover, we have identified recurring mutations in ubiquitin ligases, innate immune signalling, and TLR/MYD88 pathway regulators in ibrutinib-resistant WM patients.

Keywords: Waldenström macroglobulinemia; genomic alterations; ibrutinib; resistance; whole-exome sequencing.

Fig 1.. Copy number and genomic alterations identified by whole exome sequencing in Waldenström Macroglobulinemia patients progressing on ibrutinib.

(A) Depicts copy number alterations in WM patients progressing on ibrutinib. Each square represents a chromosome. Losses are coloured in blue, gains in red, and green corresponds to normal copy number. Deletion of chromosome 6q was present in 100% patients at baseline and progression, including homozygous loss in 33% cases at baseline and in 60% at the time of ibrutinib progression. In IBR3 the homozygous deletion was inferred to be subclonal, affecting to a third of the tumour population at baseline and increasing at progression. Del8p was observed in 2/3 cases (66%) at baseline and in 4/5 cases (80%) at progression, and includes BLK, and DOK2. The patient without del8p (IBR1) harboured a truncating mutation in DOK2. Finally, 3q amplification was absent at baseline, but present in 40% patients at the time of progression. (B) Depicts genomic alterations in WM patients progressing on ibrutinib. Patients (represented with lines) are displayed by time to progression (TTP). For IBR1, IBR2 and IBR3, the proportion of persistent mutations (horizontal bars) is shown with respect to the mutations present at only one of the time points (vertical bars). On the right, the most remarkable alterations are shown for each patient: first, recurrent copy number variations and then, somatic mutations. Patients with mutated BTK^Cys481 also harboured other mutations which affect the B-cell receptor pathway. Other recurrently mutated genes were also identified (i.e. ITCH, RNF19B and TOLLIP), as well as copy number alterations, such as 3q amplification with loss of heterozygosity, with an embedded uniparental disomy that included TBL1XR1 in the two patients lacking BTK mutations.