Chemotherapy-Based Regimes Increase Karyotype Complexity of Del(11q) CLL Cells and Impact the Response to Subsequent Ibrutinib Treatment

The introduction of targeted agents in the treatment strategy of chronic lymphocytic leukemia (CLL) has changed the prognostic implications of some traditional high-risk markers such as del(11q). Recent data has suggested that this alteration might associate with superior progression-free survival (PFS) in patients (pts) treated with the BTK inhibitor ibrutinib (Ibr), especially in treatment-naïve (TN) cases (Kipps et al. 2019). This seems to be in marked contrast to data from chemotherapy (CHT) relapsed/refractory (CHT-R/R) pts treated with Ibr, where del(11q) cases showed inferior PFS than CLLs harboring other cytogenetic abnormalities (CAs) (excluding del(17p)) (Byrd et al. 2020). In this study we aimed to elucidate the mechanism underlying this differential response between TN and CHT-R/R del(11q) CLL pts treated with Ibr.

We conducted a retrospective analysis of 211 CLL pts treated with Ibr-based regimes (n=88 TN; n=123 CHT-R/R). Median follow-up was 37 months (mo) [IQR 17-54] and CHT-R/R patients had a median of 3 therapies [1-7] (at least one line of CHT) prior to Ibr start. Thirty pts discontinued treatment due to adverse events. Restricting the analysis to the rest of the pts (n=181), the median PFS was significantly longer in del(11q) TN than del(11q) CHT-R/R cases (not reached (NR) vs 45 mo; P=0.001). TN del(11q) pts showed a 5-year PFS rate of 100% vs 75% of non-del(11q) TN pts (P=0.1). In contrast, the median PFS of del(11q) CHT-R/R pts was 45 vs 54 mo for non-del(11q) CHT-R/R cases (P=0.45). We next investigated whether differences at the genomic level would play a role in the diminished response of del(11q) CHT-R/R pts to Ibr. Targeted next-generation sequencing and miRNA profiling of del(11q) TN and CHT-R/R pts did not reveal substantial changes in the mutational and miRNA profile between both groups. In contrast, the presence of complex karyotype (≥3 CAs; CK) was able to stratify the outcome of del(11q) CHT-R/R pts (median 31 mo vs NR (CK vs non-CK); P=0.014).

To validate these findings in an ex vivo setting, we co-cultured primary CLL cells from del(11q) TN and CHT-R/R pts (n=18) with HS5 stromal cells (+CpG and IL2) in the presence of Ibr. Consistent with the clinical findings, cells from del(11q) TN pts were more sensitive to Ibr than those cells from del(11q) CHT-R/R pts (P=0.012). Moreover, del(11q) CK CHT-R/R primary cells were more resistant to Ibr ex vivo than del(11q) non-CK CHT-R/R cells (n=8; P=0.05).

To evaluate how CHT could impact the karyotype stability of del(11q) pts, we quantified the number of CAs in 263 CLL samples before (n=85) or after (n=178) treatment with CHT-based regimes and we found that the mean number of CAs was higher in del(11q) cases after treatment (mean 1.7 vs 3.7; P=0.01). Importantly, non-del(11q)/non-del(17p) pts did not show an increased number of CAs after CHT (mean 1.1 vs 1.0; P=0.36). In parallel, in a cohort of 314 CLLs treated with non-CHT agents (n=175 pre- and n=139 post-therapy), the mean number of CAs in del(11q) cases remained stable after treatment (mean 2.4 vs 1.9; P=0.1), suggesting that non-CHT regimes are less prone to induce karyotype instability in del(11q) CLL cells.

We further analyzed longitudinal karyotype samples from del(11q) CLL pts before and after treatment with CHT (n=9) or non-CHT (n=19) agents. Notably, CHT induced karyotype changes in 6/9 del(11q) pts (P=0.03), whereas the vast majority (18/19) of del(11q) pts treated with non-CHT agents did not acquire additional CAs after treatment. Karyotype clonal evolution analyses revealed linear (3/6) and branched (3/6) patterns of evolution from the founder del(11q) clone in post-CHT samples, all resulting in del(11q) clones with a higher karyotype complexity, with a particular enrichment of chromosome 8 CAs. Conversely, karyotype clonal evolution was far less frequent (1/19) in del(11q) pts treated with non-CHT agents, even in the presence of multiple lines of therapy.

Collectively, this work uncovers previously unknown differential Ibr sensitivity between del(11q) TN and del(11q) CHT-R/R CLLs and shows that such differential sensitivity could be mediated through CHT-induced karyotype complexity in the del(11q) clone of CHT-R/R del(11q) pts. Moreover, treatment with non-CHT agents maintains clonal stability of del(11q) cells, consistent with the prolonged PFS rates of del(11q) TN pts treated with Ibr. Thus, our data support the use of ibrutinib as a first-line therapy in del(11q) CLL.

Hernández-Rivas:Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; GSK: Consultancy, Honoraria; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Support, Speakers Bureau; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research support, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Research Support; Janssen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Roche: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Abbvie: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AstraZeneca: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Beigene: Membership on an entity's Board of Directors or advisory committees; Lilly: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Takeda: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Rovi: Membership on an entity's Board of Directors or advisory committees; Incyte: Membership on an entity's Board of Directors or advisory committees. Kipps:Gilead: Consultancy; Celgene: Consultancy; Oncternal: Research Funding; Pharmacyclics, LLC an AbbVie Company: Consultancy, Research Funding; Genentech-Roch: Consultancy, Research Funding; AbbVie: Consultancy, Research Funding.