Ibrutinib Unmasks Critical Role of Bruton Tyrosine Kinase in Primary CNS Lymphoma

Abstract

Bruton tyrosine kinase (BTK) links the B-cell antigen receptor (BCR) and Toll-like receptors with NF-κB. The role of BTK in primary central nervous system (CNS) lymphoma (PCNSL) is unknown. We performed a phase I clinical trial with ibrutinib, the first-in-class BTK inhibitor, for patients with relapsed or refractory CNS lymphoma. Clinical responses to ibrutinib occurred in 10 of 13 (77%) patients with PCNSL, including five complete responses. The only PCNSL with complete ibrutinib resistance harbored a mutation within the coiled-coil domain of CARD11, a known ibrutinib resistance mechanism. Incomplete tumor responses were associated with mutations in the B-cell antigen receptor-associated protein CD79B. CD79B-mutant PCNSLs showed enrichment of mammalian target of rapamycin (mTOR)-related gene sets and increased staining with PI3K/mTOR activation markers. Inhibition of the PI3K isoforms p110α/p110δ or mTOR synergized with ibrutinib to induce cell death in CD79B-mutant PCNSL cells.Significance: Ibrutinib has substantial activity in patients with relapsed or refractory B-cell lymphoma of the CNS. Response rates in PCNSL were considerably higher than reported for diffuse large B-cell lymphoma outside the CNS, suggesting a divergent molecular pathogenesis. Combined inhibition of BTK and PI3K/mTOR may augment the ibrutinib response in CD79B-mutant human PCNSLs. Cancer Discov; 7(9); 1018-29. ©2017 AACR.See related commentary by Lakshmanan and Byrd, p. 940This article is highlighted in the In This Issue feature, p. 920.

Figure 1. Clinical Response to Ibrutinib in recurrent/refractory CNS Lymphoma

A, Representative tumor response to ibrutinib as determined by magnetic resonance imaging (MRI) T1+contrast sequences in a Primary CNS Lymphoma (PCNSL; patient #3). B, Best response to ibrutinib in PCNSL patients, assessed using International PCNSL Collaborative Group (IPCG) guidelines (47). Displayed is the change in target lesion diameter from baseline (%) by magnetic resonance imaging or clearance of cerebrospinal fluid; negative values indicate tumor shrinkage. Shown are subjects who underwent at least 15 days of drug treatment and one post-treatment evaluation. Dashed lines indicate 25% change. Black: progression of disease (PD); orange: stable disease (SD); blue: partial response (PR), and green: complete response (CR). C, Progression-free survival in PCNSL. ➙, patient still receiving ibrutinib; #, drug discontinued because of personal choice (#4, #7) or infection (#11); ◆, progression. CR, complete response; PR, partial response; SD, stable disease; PD, progressive disease; n/a, not assessable. Two patients withdrew from treatment despite clinical and radiographic response (#4, #7). Treatment was discontinued due to a fungal infection (grade 3) in one patient (#11) with MTX-refractory disease. The ibrutinib dose was reduced in one patient with colitis (#13) from 840 to 560mg. D, Representative tumor response to ibrutinib in a Secondary CNS Lymphoma (SCNSL; patient #15). E, Best response to ibrutinib in SCNSL. Shown are subjects who underwent at least 15 days of drug treatment and one post-treatment evaluation. Dashed lines indicate 25% change. Black: progression of disease (PD); orange: stable disease (SD); blue: partial response (PR), and green: complete response (CR). F, Progression-free survival in SCNSL. ➙, patient still receiving ibrutinib; *, hematopoietic stem cell transplantation (in CR); ◆, progression. CR, complete response; PR, partial response; SD, stable disease; PD, progressive disease; n/a, not assessable.

Figure 2. Genomic Landscape of PCNSL

A, Shown are mutation frequencies in PCNSLs (n=177), grouped into genes with recurrent somatic mutations, genes affected by aberrant somatic hypermutation, and genes meeting both criteria (see Supplementary Table S5). B, Relationship between PCNSL disease subtypes and mutations in BCR pathway members in PCNSL. The disease subtype is shown in the top row and was determined by IHC (GCB: germinal center B-cell like; non-GCB: non-germinal center B-cell like; T-cell). Missense mutations are displayed in green, in-frame mutations in grey, truncating mutations in black, amplifications in red and deletions in blue.

Figure 3. PI3K/mTOR pathway promotes survival in CD79B-mutant PCNSL

A, Cartoon of the BCR/NFκB signaling axis. Genes harboring mutations in PCNSL are highlighted in red. B, Gene-set enrichment analysis (GSEA) of PCNSL biopsies shows enrichment of mTOR related gene sets in CD79B-mutated PCNSL. C, Activation of PI3K/mTOR in CD79B-mutant PCNSL. PCNSL tissue was stained with antibodies against 4EBP1 (T37/46) and S6 Ribosomal protein (S240/244). Tumors staining with both antibodies, labeled as “double positive”, were more common in CD79B-mutated PCNSL than in CD79B-wildtype PCNSL. (see bargraph on top ****: p<0.0001). The images below the bargraph show representative IHC images for a “double-positive” (left column) and “double-negative” (right column) PCNSL. D, BKM120, a pan-class I PI3K inhibitor, induces cell death in slice cultures from two CD79B-mutant PCNSL xenograft models. Shown are Western Blots of whole cell lysates after incubation for 24 hours with the indicated concentrations of BKM120. E, Combination of the PI3Kα-specific inhibitor BYL719 and the PI3Kδ-specific inhibitor Idelalisib, but neither inhibitor alone, induces cell death in a CD79B-mutant PCNSL cell line. F, The PI3Kα/δ specific inhibitor BAY 80-6946 induces cell death in PCNSL-MSK cells. G, Synergistic cell death induction by combination of ibrutnib and BAY 80-6946. H, Combination of ibrutnib and BAY 80-6946 is not associated with further NF-κB inhibition. n. oligo, oligonucleotides with the NF-κB binding domain are added and serve as a negative control for the assay. ***: p<0.001 I, Increased inhibition of the PI3K/mTOR pathway by combination of ibrutinib and BAY 80-6946; shown are Western Blots. J, Synergism between Ibrutinib and the dual mTOR inhibitor INK128 in PCNSL-MSK cells. ****: p<0.0001.