Combined copy number and mutation analysis identifies oncogenic pathways associated with transformation of follicular lymphoma

Abstract

Follicular lymphoma (FL) is typically an indolent disease, but 30-40% of FL cases transform into an aggressive lymphoma (tFL) with a poor prognosis. To identify the genetic changes that drive this transformation, we sequenced the exomes of 12 cases with paired FL and tFL biopsies and identified 45 recurrently mutated genes in the FL-tFL data set and 39 in the tFL cases. We selected 496 genes of potential importance in transformation and sequenced them in 23 additional tFL cases. Integration of the mutation data with copy-number abnormality (CNA) data provided complementary information. We found recurrent mutations of miR-142, which has not been previously been reported to be mutated in FL/tFL. The genes most frequently mutated in tFL included KMT2D (MLL2), CREBBP, EZH2, BCL2 and MEF2B. Many recurrently mutated genes are involved in epigenetic regulation, the Janus-activated kinase-signal transducer and activator of transcription (STAT) or the nuclear factor-κB pathways, immune surveillance and cell cycle regulation or are TFs involved in B-cell development. Of particular interest are mutations and CNAs affecting S1P-activated pathways through S1PR1 or S1PR2, which likely regulate lymphoma cell migration and survival outside of follicles. Our custom gene enrichment panel provides high depth of coverage for the study of clonal evolution or divergence.

Figure 1

Genes found to be recurrently mutated specifically in tFLs in 35 FL/tFL cases. Only genes with at least one Tier 1 mutation were included (Materials and Methods). The block color represents the mutation status of the individual cases by gene. Blocks with 2 colors indicate that more than one mutated codon was observed. For example, one case had a truncating mutation and a mutation affecting the initiating methionine codon that occurred on separate alleles, likely resulting in complete loss of functional SOCS1. The other cases had single missense SOCS1 mutations. Genes also affected by copy number gain or loss in the tFL case are noted. Copy number data are not available for cases 8, 22, and 31. Tier 3 mutations which were “rescued” from the stringent filtering criteria associated with Tier 1 and 2 mutations are noted as “cannot exclude being germline”.

Figure 2

Diagram of tFL-only mutated genes found in more than two cases. The data were summarized from a combined set of 42 FL/tFL paired cases. Only genes expressed in B-cells are shown. The color of each block represents the mutation type of the corresponding genes and cases.

Figure 3

Schematic of domains/regions affected by mutations for CD79B (A), CARD11 (B), miR-142 (C) and RRAGC (D). The IG-like V-type domain, transmembrane domain, immunoreceptor tyrosine-based activation motif (ITAM), caspase activation and recruitment domain (CARD), coiled-coil domain, inhibitory domain, PDZ domain, SRC homology 3 domain (SH3), guanylate kinase-like domain, and P-loop containing nucleoside triphosphate hydrolase domain are depicted. Sites of GTP binding are noted. The mutations from our case series are labeled in regular font, while those from the other two published datasets^, are labeled in italics.

Figure 4

Abnormalities of the S1PR1 and S1PR2 pathway are associated with FL transformation. Black arrows and bar-headed lines indicate activation or inhibition, respectively; dotted lines indicate an indirect effect. Different color and border lines were used to mark the types of mutations or copy changes observed in our case series (n=35), within which, 80% of the cases carry at least one of the genetic abnormalities. Of note, one case had a mutation in S1PR2 in the tFL that was subclonal in the FL. That same case had 3 separate FL-tFL shared mutations in ARHGEF1. A second case had a shared mutation in GNA13. Additionally, Pasqualucci, et al identified GNA13 mutations in 3 cases (2 tFL-unique and 1 FL-unique).