Dissection of subclonal evolution by temporal mutation profiling in chronic lymphocytic leukemia patients treated with ibrutinib

Abstract

The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib is inducing durable responses in chronic lymphocytic leukemia (CLL) patients with refractory/relapsed disease or with TP53 defect, with BTK and phospholipase C gamma 2 (PLCG2) mutations representing the predominant mechanisms conferring secondary ibrutinib resistance. To understand the landscape of genomic changes and the dynamics of subclonal architecture associated with ibrutinib treatment, an ultra‐deep next‐generation sequencing analysis of 30 recurrently mutated genes was performed on sequential samples of 20 patients, collected before and during single‐agent ibrutinib treatment. Mutations in the SF3B1, MGAand BIRC3 genes were enriched during ibrutinib treatment, while aberrations in the BTK, PLCG2, RIPK1, NFKBIE and XPO1 genes were exclusively detected in posttreatment samples. Besides the canonical mutations, four novel BTK mutations and three previously unreported PLCG2 variants were identified. BTK and PLCG2 mutations were backtracked in five patients using digital droplet PCR and were detectable on average 10.5 months before clinical relapse. With a median follow‐up time of 36.5 months, 7/9 patients harboring BTK mutations showed disease progression based on clinical and/or laboratory features. In conclusion, subclonal heterogeneity, dynamic clonal selection and various patterns of clonal variegation were identified with novel resistance‐associated BTK mutations in individual patients treated with ibrutinib.

Overcoming Ibrutinib Resistance in Chronic Lymphocytic Leukemia

“…Secondary resistance to BTK inhibitors is far better characterized in CLL, where it can be manifested as a Richter transformation during the first year of therapy or as progressive CLL [62,78,[84][85][86]. It was shown that CLL cells under ibrutinib pressure are prone to clonal shifts as determined by whole-exome sequencing studies [87,88]. So far, complex karyotype, 17p deletion and BCL6 abnormalities were shown to be risk factors for acquired secondary resistance [84,89].…”

“…So far, complex karyotype, 17p deletion and BCL6 abnormalities were shown to be risk factors for acquired secondary resistance [84,89]. Whole-exome sequencing analysis of patients with late relapses showed acquired mutations in BTK at the binding site of ibrutinib (C481) with a cysteine to serine mutation, and PLCγ2, the kinase immediately downstream of BTK, where multiple activating mutations were identified [87,88,90].…”

“…The serine residues in the C481 position prevents the ibrutinib covalent from binding, making the bond reversible and reducing the ability to inhibit the mutant form of BTK, and therefore reducing its clinical activity [91]. Importantly, these mutations may be found in CLL cells up to one year before the clinical relapse occurs, allowing potentially for preemptive therapy modification [88,92,93]. Additional mutations at the T474 (T474I and T474S) locus leading to diminished ibrutinib selectivity and affinity have been described [94].…”

“…It is predicted that this results in diminished BTK interactions with BLNK and other proteins that drive ibrutinib resistance [95]. Nevertheless, mutations in BTK may occur simultaneously with PLCG2, which may pose problems when selecting proper next line treatment [88,93,96].…”

“…Mutations identified in PLCG2 have all been demonstrated to potentially gain a function, allowing BCR signaling activation in the presence of inactive BTK [88,93,97]. In PLCG2, the R665W mutation causes missense alteration leading to BTK-independent activation after BCR engagement, allowing it to bypass the BTK.…”