Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma

Abstract

Diffuse large B-cell lymphoma (DLBCL) patients are typically treated with immunochemotherapy containing rituximab (rituximab, cyclophosphamide, hydroxydaunorubicin-vincristine (Oncovin), and prednisone [R-CHOP]); however, prognosis is extremely poor if R-CHOP fails. To identify genetic mechanisms contributing to primary or acquired R-CHOP resistance, we performed target-panel sequencing of 135 relapsed/refractory DLBCLs (rrDLBCLs), primarily comprising circulating tumor DNA from patients on clinical trials. Comparison with a metacohort of 1670 diagnostic DLBCLs identified 6 genes significantly enriched for mutations upon relapse. TP53 and KMT2D were mutated in the majority of rrDLBCLs, and these mutations remained clonally persistent throughout treatment in paired diagnostic-relapse samples, suggesting a role in primary treatment resistance. Nonsense and missense mutations affecting MS4A1, which encodes CD20, are exceedingly rare in diagnostic samples but show recurrent patterns of clonal expansion following rituximab-based therapy. MS4A1 missense mutations within the transmembrane domains lead to loss of CD20 in vitro, and patient tumors harboring these mutations lacked CD20 protein expression. In a time series from a patient treated with multiple rounds of therapy, tumor heterogeneity and minor MS4A1-harboring subclones contributed to rapid disease recurrence, with MS4A1 mutations as founding events for these subclones. TP53 and KMT2D mutation status, in combination with other prognostic factors, may be used to identify high-risk patients prior to R-CHOP for posttreatment monitoring. Using liquid biopsies, we show the potential to identify tumors with loss of CD20 surface expression stemming from MS4A1 mutations. Implementation of noninvasive assays to detect such features of acquired treatment resistance may allow timely transition to more effective treatment regimens.

Baseline SUV_max is related to tumor cell proliferation and patient outcome in follicular lymphoma

“…The frequency of alterations in the oncogenic pathway did not vary with the SUVmax level, but we identified a FOXO1 mutation in a subset of patients with SUVmax >14.5. The prognostic value of FOXO1 mutations has already been shown in DLBCL 36 and FL. 12,37 For instance, FOXO1 mutations were more frequently observed in high-risk FL patients with POD24 when compared with the non-POD24 subgroup (25% vs 10%, p=0.04) 12,37 and were associated with shorter failure-free survival (HR 2.74, 1.23-6.09; p=0.013) in the m7 FLIPI cohort.…”

Genetic Events Inhibiting Apoptosis in Diffuse Large B-cell Lymphoma

“…Another major gap in the understanding of the role of inhibition of apoptosis in DLBCL is the limited knowledge of the genetic determinants of rrDLBCL, notably because of the lack of repeat biopsy in most cases [24]. This problem can however be circumvented by sequencing of ctDNA isolated from plasma [7]. Current evidence suggests that BCL2, TP53, and genes from the NF-kB pathway are among the main contributors to inhibition of apoptosis and the development of rrDLBCL [7,24,127,194,195].…”

“…This problem can however be circumvented by sequencing of ctDNA isolated from plasma [7]. Current evidence suggests that BCL2, TP53, and genes from the NF-kB pathway are among the main contributors to inhibition of apoptosis and the development of rrDLBCL [7,24,127,194,195]. Increased rates of BCL2 mutations are seen in refractory cases, relapses, and in primary samples that will ultimately fail initial therapy [127].…”

“…TP53 is the most commonly mutated gene in rrDLBCL, with mutations observed in up to half of cases [7,24]. Clonal evolution studies have shown that most of these mutations are present in primary DLBCL subclones that are selected for during chemotherapy [7,127,128]. For this reason, mutation tracking of TP53 mutations in the plasma ctDNA in patients undergoing chemotherapy has the potential to detect and monitor early resistant clones [129,130].…”

“…Some of these have the potential to activate the intrinsic apoptotic pathway, independently of DNA-damage response pathway or TP53, or engage the extrinsic apoptotic pathway through cell-mediated cytotoxicity. Furthermore, the genomic characterization of DLBCL at diagnosis and relapse allows for non-invasive monitoring of disease progression and clonal evolution over time using circulating tumor DNA (ctDNA) in the plasma [7,8]. This review focuses on the genomic alterations that affect critical survival and apoptotic pathways in DLBCL.…”