Chromosome 11q23 aberrations activating FOXR1 in B-cell lymphoma

Recurrent chromosome 11q23 abnormalities, including focal gains and losses have been described in mantle cell lymphoma, diffuse large B-cell lymphoma (DLBCL) and in a subset of high-grade B-cell lymphomas lacking MYC rearrangements. We describe a novel fusion of FOXR1 forkhead box gene, located at 11q23, with a neighboring gene in B-cell lymphoma. RNAseq and sequencing of cloned PCR products revealed fusion transcripts of 5′ Ribosomal Protein S25 (RPS25) with FOXR1 in the DLBCL cell line U-2932, both genes located at the amplified chromosomal region 11q23 (Figure 1a, Supplementary Figure S1A). Genomic cloning localized the breakpoint to intron 2/3 of RPS25 and to the promoter region of FOXR1 (bp − 3532). Cell line U-2932 comprises two distinct clones traceable to subclones present in the patient ́s tumor. These differences also affected 11q32, FOXR1 and RPS25 being tetraploid in subclone R1, and triploid in subclone R2 (3n) (Supplementary Figure S1A). In accordance with the genomic data, the RPS25/FOXR1 fusion was detected in subclone R1 but not in R2 (Figure 1b). RPS25/FOXR1 was also verified in the patient ́s DNA, which collectively suggested that the fusion had occurred at some later stages of tumor development (Figure 1b). Physiological FOXR1 (formerly FOXN5) expression is restricted to the early stages of embryogenesis. Ectopic expression as result of 11q23 intrachromosomal deletion-fusion has hitherto been described in neuroblastoma only. In-frame fusions with the 5′ MLL or PAFAH1B2 genes led to overexpression of FOXR1. In accordance with the notion that a constitutively expressed 5′ gene (RPS25) might be responsible for the ectopic expression of FOXR1 in B-cell lymphoma also, FOXR1 levels were 1000 × higher in the fusion-positive than in the fusion-negative U-2932 subclone. Expression array analyses showed that the RPS25/FOXR1-positive U-2932 subclone had the highest FOXR1 expression level of 55 B lymphoma cell lines tested, three log-scales higher than average (Figure 2a). Quantitative PCR analysis conducted to verify the expression arrays included 17 additional B lymphoma cell lines, revealing that the primary effusion lymphoma cell line CRO-AP3