Genetic Landscapes of Relapsed and Refractory Diffuse Large B-Cell Lymphomas

Abstract

Purpose: Relapsed or refractory diffuse large B-cell lymphoma (rrDLBCL) is fatal in 90% of patients, and yet little is known about its biology.Experimental Design: Using exome sequencing, we characterized the mutation profiles of 38 rrDLBCL biopsies obtained at the time of progression after immunochemotherapy. To identify genes that may be associated with relapse, we compared the mutation frequency in samples obtained at relapse to an unrelated cohort of 138 diagnostic DLBCLs and separately amplified specific mutations in their matched diagnostic samples to identify clonal expansions.Results: On the basis of a higher frequency at relapse and evidence for clonal selection, TP53, FOXO1, MLL3 (KMT2C), CCND3, NFKBIZ, and STAT6 emerged as top candidate genes implicated in therapeutic resistance. We observed individual examples of clonal expansions affecting genes whose mutations had not been previously associated with DLBCL including two regulators of NF-kB: NFKBIE and NFKBIZ. We detected mutations that may be affect sensitivity to novel therapeutics, such as MYD88 and CD79B mutations, in 31% and 23% of patients with activated B-cell-type of rrDLBCL, respectively. We also identified recurrent STAT6 mutations affecting D419 in 36% of patients with the germinal center B (GCB) cell rrDLBCL. These were associated with activated JAK/STAT signaling, increased phospho-STAT6 protein expression and increased expression of STAT6 target genes.Conclusions: This work improves our understanding of therapeutic resistance in rrDLBCL and has identified novel therapeutic opportunities especially for the high-risk patients with GCB-type rrDLBCL.

Diffuse large B-cell lymphoma: R-CHOP failure—what to do?

“…13 Several studies have investigated the genetic landscape of relapsing DLBCL patients and identified TP53, FOXO1, MLL3, CCND3, NFKBIZ, and STAT6 as top candidate genes for therapeutic resistance. 14 …”

Multiplex Droplet Digital PCR Quantification of Recurrent Somatic Mutations in Diffuse Large B-Cell and Follicular Lymphoma

“…FFPE samples were processed with the QiAamp DNA FFPE tissue kit (Qiagen). DNA samples were stored at Ϫ20°C in Tris-EDTA buffer for several months (13,34 ). Liquid biopsies were also collected within a clinical trial (n ϭ 17) testing the efficacy of the drug Panobinostat (a histone deacetylase inhibitor) (34 ) plus 4 additional plasma samples, 2 from 2 additional DLBCL patients and 2 samples collected from patients with lymphoplasmacytic lymphoma (see online Supplemental Table 1).…”

“…As a result, research efforts have been aimed at the design of small pharmacological inhibitors of the EZH2 catalytic subunit in these cancer types (10,11 ) and potential therapeutic inhibitors developed for treating EZH2-driven cancers have entered clinical trials. Likewise, mutations affecting the residue D419 of the transcription factor signal transducer and activator of transcription 6 (STAT6) have been detected in more than 10% of follicular lymphoma cases (12 ) and have recently been associated with therapeutic resistance and relapse in DLBCLs (13 ). Here, recurrent D419 mutations were observed in 36% of relapsed/refractory germinal center B-cell-DLBCL cases and linked to increased expression of STAT6 targets.…”

“…Each of these genes bears a mutation "hotspot" at the affected codon with 4 commonly observed alleles. Additional recurrently mutated genes are also characterized by mutation hotspots in B-cell lymphomas, including myeloid differentiation primary response 88 (MYD88; L265P), CD79b molecule (CD79B; Y196C), or cyclin D3 (CCND3; I290R) (13)(14)(15). MYD88 mutations are found in most cases of lymphoplasmacytic lymphoma (16 ), and both MYD88 and CD79B mutations are common in the more aggressive activated B-cell molecular subtype of DLBCL.…”

“…Regardless of whether the genetic profiling of patients is accomplished via invasive tumor biopsies (13,19 ) or through more attractive noninvasive methods (1,(3)(4), there is an unmet need for accurate and cost-effective assays to screen for the presence of cancerrelated genetic aberrations. Monitoring ctDNA in plasma has major clinical advantages over needle core biopsies, including reduced morbidity, faster turnaround times, and the possibility to detect subclonal mutations that may be overlooked in traditional biopsies because of tumor heterogeneity (20 ).…”