Spatial Convergent Clonal Evolution Leading to Ibrutinib Resistance and Disease Progression in Chronic Lymphocytic Leukemia

Introduction: Bruton tyrosine kinase inhibitor ibrutinib has altered the therapeutic landscape of chronic lymphocytic leukemia (CLL) with remarkable responses in relapsed or refractory CLL. Despite mostly durable responses, approximately 20% of patients experience disease progression with, in many cases, BTK or phospholipase Cg2 (PLCG2) resistance mutations predating the clinical progression by up to 15 months. Longitudinal studies have shed some light on the temporal aspects of clonal evolution processes leading to ibrutinib resistance, however, the spatial heterogeneity within the various environmental niches has not been described in detail yet.

Here, we report the case of a CLL patient in which we are able to document, for the first time, an example of ibrutinib driven spatial convergent evolution leading to disease progression. The patient developed ibrutinib resistance after 21 months of treatment with simultaneous lymphadenomegaly and lymphocytosis. Sanger sequencing revealed a canonical BTK p.C481S mutation in peripherial blood and a PLCG2 p.D993H mutation in the lymph node with the absence of the BTK p.C481S mutation present in the peripherial blood suggesting convergent evolution in terms of the BTK and PLCG2 variants with both commonly associated with ibrutinib resistance. The patient was subsequently treated with venetoclax but due to further progression despite of high-dose salvage chemotherapy and autologous stem cell transplantation the patient died.

Methods: Serial samples at ten different timepoints during the disease course were analysed. Genomic DNA was isolated from peripheral blood mononuclear cells and native lymph node tissue. Circulating cell-free DNA (ccfDNA) was isolated from peripheral blood samples. The fraction of tumor cells was determined by flow cytometry. During the Sanger sequencing BTK exons 11, 15, 16, and PLCG2 exon 12, 19, 20, 24, 27 and 30 were examined. Targeted ultra-deep next-generation sequencing (NGS) analysis of the BTK and PLCG2 genes was performed on a MiSeq platform (Illumina). Abundances of the PLCG2 p.P993H and BTK p.C481S variants were quantified using custom assays on a QX200 droplet digital PCR system (ddPCR, BioRad).

Results: To dissect this spatial heterogeneity, BTK and PLCG2 mutations were screened by NGS which confirmed the Sanger finding and in addition to the dominant PLCG2 p.D993H variant, identified the BTK p.C481S mutation as a minor clone in the lymph node, with the BTK p.C481S mutation remaining the exclusive for the peripheral blood. Next, we tested the presence of these mutations in the circulating ccfDNA with ddPCR. Notably, both mutations were identified in the ccfDNA with a VAF of 1%. The ddPCR analysis revealed that both variants were absent in the pre-ibrutinib peripheral blood sample, however their emergence predated the clinical progression by 15 months. We observed a gradual expansion of these variants in the sequential samples, demonstrating clonal selection under the selective pressure of ibrutinib. Of note, the ddPCR assay identified the PLCG2 p.D993H mutation as a minor clone (VAF: 0.2%), previously unseen in the peripheral blood by NGS at the time of ibrutinib relapse. Intriguingly, the two subclones displayed differential sensitivity to the venetoclax therapy. In the peripheral blood, we observed a reduction of the BTK p.C481S positive subclone accompanied by expansion of the subclone harbouring PLCG2 p.D993H which was previously dominant in the lymph node. With these dynamic changes in the subclonal architecture, the disease progressed and ultimately led to death of the patient.

Conclusions: Clonal evolution is a major driving force of disease progression in CLL. Several studies have traced the effect of treatment on temporal evolutionary trajectories in the context of standard and targeted therapies and identified subclonal heterogeneity and active clonal selection. However, the spatial aspect of subclonal dynamics has not been appreciated until recently. Here, we presented a unique case of CLL, developing ibrutinib resistance via multiple routes simultaneously, with the observed spatial heterogeneity leading to progression and aggressive transformation of the disease. This case highlights the importance of genetic profiling of multiple affected sites as investigations restricted to peripheral blood may underestimate the repertoire of clinically relevant genetic alterations.