Comprehensive genetic analysis by targeted sequencing identifies risk factors and predicts patient outcome in Mantle Cell Lymphoma: results from the EU-MCL network trials

Abstract

Recent studies highlighted genetic aberrations associated with prognosis in Mantle Cell lymphoma (MCL), yet comprehensive testing is not implemented in clinical routine. We conducted a comprehensive genomic characterization of 180 patients from the European MCL network trials by targeted sequencing of peripheral blood DNA using the EuroClonality(EC)-NDC assay. The IGH::CCND1 fusion was identified in 94% of patients, clonal IGH-V-(D)-J rearrangements in all, and 79% had ≥1 somatic gene mutation. The top mutated genes were ATM, TP53, KMT2D, SAMHD1, BIRC3 and NFKBIE. Copy number variations (CNVs) were detected in 83% of patients with RB1, ATM, CDKN2A/B and TP53 being the most frequently deleted and KLF2, CXCR4, CCND1, MAP2K1 and MYC the top amplified genes. CNVs and mutations were more frequently observed in older patients with adverse impact on prognosis. TP53^mut, NOTCH1^mut, FAT1^mut TRAF2^del, CDKN2A/B^del and MAP2K1^amp were linked to inferior failure-free (FFS) and overall survival (OS), while TRAF2^mut, EGR2^del and BCL2^amp related to inferior OS only. Genetic complexity (≥3 CNVs) observed in 51% of analysed patients was significantly associated with impaired FFS and OS. We demonstrate that targeted sequencing from peripheral blood and bone marrow reliably detects diagnostically and prognostically important genetic factors in MCL patients, facilitating genetic characterization in clinical routine.

Fig. 1. Patient selection.

CONSORT diagram representing the selection of analyzed patients among the whole cohort.

Fig. 2. Targeted sequencing in 180 MCL cases using the EuroClonality (EC)-NDC approach.

A Oncoplot with the mutation pattern of the top 20 recurrent mutated genes (n = 180). B Table summarizing the number of detected somatic mutations per patient. C Heatmap plot with the copy number variation patterns of the top 15 affected genes (D) Oncoplot with the aberration pattern of the top 5 genes with the highest combined number of somatic mutations and copy number alterations (n = 118).

Fig. 3. Failure-free (FFS) and Overall survival (OS) analysis of Elderly and younger MCL patients included in the present molecular analysis.

Kaplan–Meier estimates of FFS and OS of TP53mut (A, B), TP53del (C), EGR2del (D), NOTCH1mut (E, F), FAT1mut (G, H), TRAF2del (I, J), TRAF2mut (K), BCL2amp (L), CDKN2A/Bdel (M, N), MAP2K1amp (O, P). Aberrant cases were represented by a light blue line, while patients with wildtype genotypes were represented by a red line. Number of patients at risk are indicated in a separate table below the curves. Mutated: mut, Copy number gains: amp, Copy number deletions: del.

Fig. 4. Association of Immunoglobulin heavy chain usage and number of genetic events with outcomes of patients with MCL.

Kaplan–Meier estimates of FFS (left) and OS (right) according to the IGHV gene usage (A, B), the number of detected copy number variations (C, D) and number of detected mutations and copy number variations (E, F). Patients with clonal VH3-23 or VH4-34 usage were represented by a light blue line, while patients with other gene usage were represented by a red line. Patients with 0–2 events were represented by a red line, while patients with 3–5 events were represented by green line and patients with >5 events were represented by blue line. Number of patients at risk are indicated in a separate table below the curves.