Non-IG Aberrations of FOXP1 in B-Cell Malignancies Lead to an Aberrant Expression of N-Truncated Isoforms of FOXP1

Abstract

The transcription factor FOXP1 is implicated in the pathogenesis of B-cell lymphomas through chromosomal translocations involving either immunoglobulin heavy chain (IGH) locus or non-IG sequences. The former translocation, t(3;14)(p13;q32), results in dysregulated expression of FOXP1 juxtaposed with strong regulatory elements of IGH. Thus far, molecular consequences of rare non-IG aberrations of FOXP1 remain undetermined. Here, using molecular cytogenetics and molecular biology studies, we comprehensively analyzed four lymphoma cases with non-IG rearrangements of FOXP1 and compared these with cases harboring t(3;14)(p13;q32)/IGH-FOXP1 and FOXP1-expressing lymphomas with no apparent structural aberrations of the gene. Our study revealed that non-IG rearrangements of FOXP1 are usually acquired during clinical course of various lymphoma subtypes, including diffuse large B cell lymphoma, marginal zone lymphoma and chronic lymphocytic leukemia, and correlate with a poor prognosis. Importantly, these aberrations constantly target the coding region of FOXP1, promiscuously fusing with coding and non-coding gene sequences at various reciprocal breakpoints (2q36, 10q24 and 3q11). The non-IG rearrangements of FOXP1, however, do not generate functional chimeric genes but commonly disrupt the full-length FOXP1 transcript leading to an aberrant expression of N-truncated FOXP1 isoforms (FOXP1NT), as shown by QRT-PCR and Western blot analysis. In contrast, t(3;14)(p13;q32)/IGH-FOXP1 affects the 5′ untranslated region of FOXP1 and results in overexpress the full-length FOXP1 protein (FOXP1FL). RNA-sequencing of a few lymphoma cases expressing FOXP1NT and FOXP1FL detected neither FOXP1-related fusions nor FOXP1 mutations. Further bioinformatic analysis of RNA-sequencing data retrieved a set of genes, which may comprise direct or non-direct targets of FOXP1NT, potentially implicated in disease progression. In summary, our findings point to a dual mechanism through which FOXP1 is implicated in B-cell lymphomagenesis. We hypothesize that the primary t(3;14)(p13;q32)/IGH-FOXP1 activates expression of the FOXP1FL protein with potent oncogenic activity, whereas the secondary non-IG rearrangements of FOXP1 promote expression of the FOXP1NT proteins, likely driving progression of disease.

EBV-Positive and EBV-Negative Posttransplant Diffuse Large B Cell Lymphomas Have Distinct Genomic and Transcriptomic Features

“…This aberration, absent in EBV þ PT-DLBCL, correlated with a differential expression of 13 genes, including FOXP1 (3p13), which emerged as the most significantly upregulated gene. FOXP1 encodes a transcriptional regulator implicated in a wide range of biological processes and cancer (25), including B cell lymphomas (10,(26)(27)(28). While FOXP1 is overexpressed in EBV À DLBCL, its low expression in EBV þ PT-DLBCL confirmed by QRT-PCR and IHC suggests that the gene does not play a critical role in the pathogenesis of EBV þ PT-DLBCL.…”

N-terminally truncated FOXP1 protein expression and alternate internal FOXP1 promoter usage in normal and malignant B cells

“…Based on our data, P.J. Brown et al 864 haematologica | 2016; 101(7) RNA-sequencing data from primary DLBCL biopsies, 24 we assembled a list of FOXP1 transcripts with the potential to encode FOXP1 L and FOXP1 S proteins in ABC-DLBCL ( Figure 3A). There appear to be two transcriptional start sites within Ex6b, with the 5ʹ longer Ex6b transcript (Ex6b(L)) predicted to encode a long FOXP1 protein with an alternate N-terminus (FOXP1 AL…”

“…[19][20][21][22] FOXP1 amplification and trisomy have been described in ABC-DLBCL, 23 and translocations involving the immunoglobulin heavy chain (IGH) locus 24 drive expression of a long ~75kDa FOXP1 protein (FOXP1 L ) that may contribute to GC-DLBCL tumor growth by potentiating Wnt/β-catenin signaling. 25 Also, we have described abundant expression of short 65kDa activation-induced FOXP1 proteins (FOXP1 S ) in ABC-DLBCL.…”

“…26 Oncogenic activity of N-terminally truncated FOXP1 has been proposed following its truncation by an oncogenic virus 27 and non-IGH translocations targeting the FOXP1 coding region in lymphoma. 24,28,29 Studies manipulating Foxp1 expression have established biological roles in early B-cell development 30,31 and in mature B cells. 32 Direct FOXP1 target genes, including PAX5, PRDM1, and POU2F1, support a functional role in the GC reaction.…”

The hematopoietic oncoprotein FOXP1 promotes tumor cell survival in diffuse large B-cell lymphoma by repressing S1PR2 signaling

“…1-3 Primary FOXP1 translocations predominantly involve the immunoglobulin heavy chain locus, leading to overexpression of the full-length protein 3 ; in contrast, the rare nonimmunoglobulin rearrangements of FOXP1 generate N-truncated isoforms that are believed to drive disease progression rather than initiation. 4 Most FOXP1-expressing lymphomas exhibit no apparent structural aberrations of the gene 5 ; the short, putatively oncogenic isoforms in particular are highly expressed from the wild-type locus in ABC DLBCL as a consequence of "normal" B-cell activation. 6 We have shown earlier that aberrant FOXP1 expression in ABC DLBCL may alternatively also result from dysregulated posttranscriptional regulation.…”