Linear and Branching Progression of Chronic Lymphocytic Leukemia (CLL) Under PI3K Inhibition (PI3Ki)

Introduction: B-cell receptor (BCR) signaling is a critical pathway in chronic lymphocytic leukemia (CLL). BTK or PI3K antagonists can abolish BCR-derived signals. Idelalisib inhibits the delta isoform of PI3K and has been already approved for patients with CLL, whereas duvelisib inhibits both the delta and gamma isoforms of PI3K and is currently being evaluated in clinical trials. Despite their remarkable efficacy, a proportion of patients develop progressive disease after initial response to the drug, sometimes in the form of transformation to high-grade lymphoma. Several mechanisms of resistance have been described in patients taking the BTK inhibitor ibrutinib, including BTK or phospholipase C gamma-2 mutations. There is, however, little information regarding the mechanisms of resistance to PI3Ki.

In our institution, out of 12 patients who received PI3Ki as salvage therapy, 6 patients had their medication stopped due to progressive disease, 3 with transformed disease and 1 with accelerated CLL. In this study, we comprehensively evaluated the genomic aberrations of these last 4 patients with the aim of unraveling the molecular mechanisms of disease progression in this patient population.

Patients and methods: DNA (tumor and germline) was extracted from peripheral blood/lymphoid tissue samples drawn before and after progression under PI3Ki. One case showed a CLL with increased proliferation (accelerated CLL), two cases showed transformation to a diffuse large B-cell lymphoma (DLBCL), and one to a plasmablastic lymphoma (PBL). Somatic copy number alterations (CNA) were identified using genome-wide copy number arrays. Whole-exome sequencing (WES) or whole-genome sequencing (WGS) was performed as previously described (Puente et al. Nature 2015).

Results: All patients had relapsed after rituximab, fludarabine and cyclophosphamide (RFC) first-line therapy, and rituximab plus bendamustine second-line therapy with the exception of one patient, who received RFC twice. All had significant lymphadenopathy before PI3Ki initiation, initially responded to PI3Ki, and then experienced progression 103, 151, 329 and 752 days after treatment initiation. IGH rearrangement analysis revealed that the relapsed tumor was clonally related to the original CLL in all cases. Pre-PI3Ki samples from all patients harbored high-risk genomic aberrations by FISH/SNP arrays, including del(11q) in 3 patients and del(17p) in 1 patient. In 3 patients, all abnormalities identified before PI3Ki were maintained at progression, but several other alterations (1, 14, and 2 lesions, respectively) were acquired, consistent with a linear pattern of evolution. In the PBL transformation, some initial alterations were maintained (8q gain, 17p and 19p losses), some were not found (4q, and 19q gains, 2q loss), and 54 new alterations emerged at relapse, suggesting that the resistant clone arose from an early branch during CLL evolution. Together, 3 out of 4 patients (all except the patient with accelerated CLL) have alterations involving ARID1A (1 patient with a point mutation, and 2 patients with selective losses) . Other acquired aberrations in these patients were CDKN2A losses (2 patients), TP53 disruption (2 patients), MYC activating mutation (1 patient), 1 frameshift mutation in USP28 (1 patients), 2p16 gain (1 patient) and NFKBIE mutation (1 patient).

Conclusion: Overall, CLL progression after PI3Ki may follow different pathways including linear progression with increasing proliferation and transformation to DLBCL through different mechanisms (TP53, CDKN2A, NFKBIE inactivation, MYC activation or ARID1A inactivation among others) and branching transformation to PBL that may represent an alternative pathway to escape from BCR-dependent activation.