Distinct molecular profile of IRF4-rearranged large B-cell lymphoma

Abstract

Pediatric large B-cell lymphomas (LBCLs) share morphological and phenotypic features with adult types but have better prognosis. The higher frequency of some subtypes such as LBCL with IRF4 rearrangement (LBCL-IRF4) in children suggests that some age-related biological differences may exist. To characterize the genetic and molecular heterogeneity of these tumors, we studied 31 diffuse LBCLs (DLBCLs), not otherwise specified (NOS); 20 LBCL-IRF4 cases; and 12 cases of high-grade B-cell lymphoma (HGBCL), NOS in patients ≤25 years using an integrated approach, including targeted gene sequencing, copy-number arrays, and gene expression profiling. Each subgroup displayed different molecular profiles. LBCL-IRF4 had frequent mutations in IRF4 and NF-κB pathway genes (CARD11, CD79B, and MYD88), losses of 17p13 and gains of chromosome 7, 11q12.3-q25, whereas DLBCL, NOS was predominantly of germinal center B-cell (GCB) subtype and carried gene mutations similar to the adult counterpart (eg, SOCS1 and KMT2D), gains of 2p16/REL, and losses of 19p13/CD70. A subset of HGBCL, NOS displayed recurrent alterations of Burkitt lymphoma-related genes such as MYC, ID3, and DDX3X and homozygous deletions of 9p21/CDKN2A, whereas other cases were genetically closer to GCB DLBCL. Factors related to unfavorable outcome were age >18 years; activated B-cell (ABC) DLBCL profile, HGBCL, NOS, high genetic complexity, 1q21-q44 gains, 2p16/REL gains/amplifications, 19p13/CD70 homozygous deletions, and TP53 and MYC mutations. In conclusion, these findings further unravel the molecular heterogeneity of pediatric and young adult LBCL, improve the classification of this group of tumors, and provide new parameters for risk stratification.

Graphical abstract

Figure 1.

Morphological, immunophenotypic, and genetic features of a LBCL with IRF4 rearrangement (case D62). Architecture effacement by an atypical lymphoid proliferation with nodular growth pattern (A; hematoxylin and eosin) that corresponds to expanded follicles with highly disrupted follicular dendritic cell meshwork (B; CD21). The atypical cells were negative for CD10 (C) and positive for BCL6 (D). BCL2 was positive in the accompanying reactive T cells but negative in the tumor (E), which exhibits a high proliferation rate (F; Ki67). The immunohistochemical study for IRF4/MUM1 (G; MUM1) shows strong and diffuse positivity in the neoplastic proliferation, and FISH with IRF4 break-apart probe shows a signal constellation of 1 colocalization (yellow arrow) and 1 split signal (red and green arrows) consistent with the gene rearrangement (H). Original magnification ×100 (A), ×40 (B-G).

Figure 2.

Overview of clinical and histological findings in 63 pediatric and young adult LBCL cases. Each column of the heatmap represents 1 LBCL case and each line a specific analysis. On the right side of the figure, the frequency of the particular result of the analysis is shown. LN, lymph node; UNC, unclassified.

Figure 3.

Morphological, immunophenotypic and genetic features of an HGBCL, NOS with MYC rearrangement (Case D59). Hematoxylin and eosin stain (A) depicting mild heterogeneity with certain cellular irregularity of the neoplastic cells that are BCL6 positive (B) with partial expression of BCL2 (C). (D) FISH with MYC break-apart shows a signal constellation of 1 colocalization (yellow arrow) and 1 split signal (green and red arrows). (E) Ideogram of the CN, CNN-LOH, and mutational features of this case. Original magnification ×400 (A,C), ×100 (B).

Figure 4.

Mutational landscape of 47 pediatric and young adult LBCL cases. (A) Bar graphs show mutated genes in >5% of 47 pediatric and young adult primary LBCL cases excluding mPMBL. Each color bar indicates histological subtypes. An asterisk represents mutated genes significantly enriched in 1 of the subtypes. SNV, single-nucleotide variant. (B) A diagram of the relative positions of driver mutations is shown for IRF4, CARD11, CD79B, SOCS1, EZH2, and MYC genes. x-axes indicate amino acid position: IRF4 domains (DBD, DNA-binding domain; IAD, IRF association domain), CARD11 domains (CARD, caspase activation and recruitment domain; SH, Src homology 3 domain), CD79B domains (IG, immunoglobulin-like; ITAM, immunoreceptor tyrosine-based activation motif), SOCS1 domains (ESS, extended SH2 subdomain; KIR, kinase inhibitory region), EZH2 domains (CXC, cysteine-rich domain; SANT, SWI3-ADA2-N-CoR-TFIIIB domains; WDB, WD-40 binding domain), and MYC domains (HLH, helix-loop-helix; LZ, leucine zipper; MBI/II, Myc box I and II; TAD, transactivation domain).

Figure 5.

CN profile of pediatric and young adult LBCL cases. (A) Global CN profiles of 20 LBCL-IRF4 cases; 22 DLBCL, NOS cases; and 7 HGBCL, NOS cases. x-axis indicates chromosomes from 1 to Y and p to q. The vertical axis indicates frequency of each genomic aberration among the analyzed cases. Gains are depicted in blue and losses in red. Most frequently recurrent regions are indicated for LBCL-IRF4; DLBCL, NOS (>20%); and HGBCL, NOS (≥2 cases). Asterisks indicate significant differences between LBCL-IRF4 and DLBCL (Fisher’s test, P < .05). (B) Comparative plot of CNN-LOH among the 3 morphological groups described above. Green identifies LBCL-IRF4; blue DLBCL, NOS; and yellow HGBCL, NOS.

Figure 6.

EFS of 45 pediatric and young adult LBCL cases according to morphological and molecular subtypes, age, LDH levels, and specific molecular features. wt, wild type.