Effect of ibrutinib with R-CHOP chemotherapy in genetic subtypes of DLBCL

Abstract

In diffuse large B cell lymphoma (DLBCL), tumors belonging to the ABC but not GCB gene expression subgroup rely upon chronic active B cell receptor signaling for viability, a dependency that is targetable by ibrutinib. A phase III trial ("Phoenix;" ClinicalTrials.gov: NCT01855750) showed a survival benefit of ibrutinib addition to R-CHOP chemotherapy in younger patients with non-GCB DLBCL, but the molecular basis for this benefit was unclear. Analysis of biopsies from Phoenix trial patients revealed three previously characterized genetic subtypes of DLBCL: MCD, BN2, and N1. The 3-year event-free survival of younger patients (age ≤60 years) treated with ibrutinib plus R-CHOP was 100% in the MCD and N1 subtypes while the survival of patients with these subtypes treated with R-CHOP alone was significantly inferior (42.9% and 50%, respectively). This work provides a mechanistic understanding of the benefit of ibrutinib addition to chemotherapy, supporting its use in younger patients with non-GCB DLBCL.

Keywords: ABC DLBCL; BTK inhibitor; CD79B; MYD88; NOTCH1; cancer genomics; memory B cell; precision medicine.

Figure 1.

Identification of DLBCL genetic subtypes within the Phoenix clinical trial cohort. A. Distribution of gene expression subgroup assignments among tumors from younger (age≤60) Phoenix trial patients. The immunohistochemical method used to enrich for non-GCB DLBCL cases allowed Phoenix trial enrollment of patients with CD10⁻ GCB DLBCL. B. Kaplan-Meier plots of event-free and overall survival in younger (age ≤ 60) patients with ABC or non-ABC DLBCL assigned to the ibrutinib or placebo Phoenix trial arms, as indicated. Shown are log-rank p values for the difference in survival between patients on the ibrutinib and placebo arms. C. Distribution of the genetic subtypes among younger (age ≤ 60), older (age > 60) and all patients in the Phoenix and NCI cohorts. D. Distribution and prevalence of genetic aberrations in DLBCL genetic subtypes in the Phoenix non-China cohort. Missense or inframe deletion/insertion mutations (Mut), protein-truncating mutations (Trunc), and gene rearrangement (Fusion) are shown as indicated. Also shown is the cell-of-origin (COO) gene expression subgroup (NA: Not available), the age category (Younger: age≤60, Older: age>60), and the Phoenix study arm. E. Prevalence and significance of association between genetic aberrations and the DLBCL genetic subtypes. P values compare each subtype to all other cases in the Phoenix cohort. The prevalence of each genetic aberration in non-GCB biopsies from the NCI cohort is shown for comparison.

Figure 2.

Phenotypic and clinical characteristics of Phoenix genetic subtypes. A. Distribution of DLBCL gene expression subgroups among cases assigned to the MCD, BN2 and N1 genetic subtypes. B. Comparison of gene expression signature averages between genetic subtypes and all other DLBCL samples. Shown are Z scores (see Methods) representing the relative expression of each signature in a given subtype versus all other DLBCLs. Z scores calculated for the Phoenix and NCI cohorts are plotted on the y-axis and x-axis, respectively. The brown dashed lines indicate the Z scores corresponding to a significant difference between the two sample subsets (p=0.01). The yellow shaded areas include those signatures that are more highly expressed in the indicated subtype than in other samples and the blue shaded areas are signatures that are expressed at lower levels in the indicated subtype relative to other samples. The indicated p value is for the correlation of the Z scores from the two cohorts. C. Extranodal involvement in the genetic subtypes, subdivided by anatomic site as indicated. P values are from a 2-way Fisher’s Exact test. ns: non-significant.

Figure 3.

Survival of Phoenix trial patients subdivided by genetic subtype and treatment arm. Shown are Kaplan-Meier plots of event-free and overall survival in younger (age ≤ 60) patients assigned to the MCD, BN2 and N1 genetic subtypes. Also shown are log-rank p values for the difference in survival in the indicated genetic subtype treated with R-CHOP plus ibrutinib or placebo. The interaction p values indicate the significance of the difference in ibrutinib benefit within the indicated genetic subtype compared with all other DLBCLs. “No. at risk” indicates the number of patients remaining without events (for event-free survival) or remaining alive (for overall survival.

Figure 4.

Genetic, phenotypic, and clinical attributes of N1 DLBCL. A. Distribution of DLBCL gene expression subgroups among NOTCH1-mutant DLBCLs. B. Recurrently mutated genes in NOTCH1-mutant DLBCL. Shown are the type and prevalence of mutations in the indicated genes among NOTCH1-mutant and NOTCH1-wild type DLBCLs. Genes are assigned to functional categories, as indicated. P values are from a Fisher’s Exact Test comparing the prevalence in NOTCH1-mutant and NOTCH1-WT cases. Mut: Non-synonymous mutation; Trunc: Truncating mutation; WT: wild type; ns: non-significant. C. Prevalence of mutations targeting biologic pathways characteristic of N1 DLBCL. Prevalence is based on 1,431 DLBCL NOTCH1-WT and NOTCH1-mutant DLBCL cases for which sequencing data was available for all genes in the indicated pathways. P values are from a Fisher’s Exact Test comparing the prevalence in NOTCH1-mutant and NOTCH1-WT cases. D. Left panel: Average expression of the indicated gene expression signatures in the indicated genetic subtypes in the NCI cohort(Schmitz et al., 2018). Bmem-6: Genes upregulated in memory B and memory B precursors relative to germinal center dark zone and light zone B cell cells (Venturutti et al., 2020); TBL1XR1MutUp-1: Genes up regulated by a TBL1XR1 mutant isoform (Venturutti et al., 2020); BACH2Up-1: Genes upregulated in BACH2+ germinal center light zone cells (Venturutti et al., 2020). Right panel: Average expression of the indicated memory B cell marker genes. ****p<0.0001, ***p<0.001, **p<0.01, *p<0.05. Error bars: SEM. E. Schematic of the BCR-dependent NF-κB pathway showing the prevalence of mutations targeting each pathway component in the N1 (NOTCH1-mutant) and MCD subtypes of DLBCL according to the color scale shown. DAG: diacylglycerol; IP3: inositol triphosphate; Ca⁺⁺: calcium ion; CBM complex: CARD11-BCL10-MALT1 complex; My-T-BCR: MYD88-TLR9-B cell receptor complex. F. Kaplan-Meier plots of event-free and overall survival in younger (age ≤ 60) and older (age > 60) patients with NOTCH1-mutant DLBCL treated with R-CHOP-like chemotherapy, curated from the published literature.