Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways

Abstract

Gene-expression profiling has been used to define 3 molecular subtypes of diffuse large B-cell lymphoma (DLBCL), termed germinal center B-cell-like (GCB) DLBCL, activated B-cell-like (ABC) DLBCL, and primary mediastinal B-cell lymphoma (PMBL). To investigate whether these DLBCL subtypes arise by distinct pathogenetic mechanisms, we analyzed 203 DLBCL biopsy samples by high-resolution, genome-wide copy number analysis coupled with gene-expression profiling. Of 272 recurrent chromosomal aberrations that were associated with gene-expression alterations, 30 were used differentially by the DLBCL subtypes (P < 0.006). An amplicon on chromosome 19 was detected in 26% of ABC DLBCLs but in only 3% of GCB DLBCLs and PMBLs. A highly up-regulated gene in this amplicon was SPIB, which encodes an ETS family transcription factor. Knockdown of SPIB by RNA interference was toxic to ABC DLBCL cell lines but not to GCB DLBCL, PMBL, or myeloma cell lines, strongly implicating SPIB as an oncogene involved in the pathogenesis of ABC DLBCL. Deletion of the INK4a/ARF tumor suppressor locus and trisomy 3 also occurred almost exclusively in ABC DLBCLs and was associated with inferior outcome within this subtype. FOXP1 emerged as a potential oncogene in ABC DLBCL that was up-regulated by trisomy 3 and by more focal high-level amplifications. In GCB DLBCL, amplification of the oncogenic mir-17-92 microRNA cluster and deletion of the tumor suppressor PTEN were recurrent, but these events did not occur in ABC DLBCL. Together, these data provide genetic evidence that the DLBCL subtypes are distinct diseases that use different oncogenic pathways.

Fig. 1.

Schematic of the Gene Expression and Dosage Integration algorithm (see methods).

Fig. 2.

Identification of DLCBL subtype-specific genomic aberrations by aCGH.

Fig. 3.

Candidate oncogenes and tumor suppressors in DLBCL identified by aCGH. The left panels illustrate genes within each MCR that had the greatest fold change in cases with the aberration versus wild-type cases within the DLBCL subtype linked to each MCR. The middle panels show the expression levels of the candidate gene in each case, with red bars indicating cases with the aberration. The right panels show the average expression of the candidate gene in cases grouped as indicated. (A) FOXP1 is a candidate oncogene associated with trisomy 3 in ABC DLBCL. (B) SPIB is a candidate oncogene associated with a gain/amp MCR on chromosome 19 in ABC DLBCL. (C) CDKN2A (p16) is a candidate tumor suppressor associated with single/double deletion on chromosome 9. CDKN2B (p15) and p14^ARF are other tumor suppressors encoded in this MCR. (D) MIHG1, encoding the mir-17–92 microRNA cluster, is a candidate oncogene associated with an amplification in GCB DBLCL.

Fig. 4.

SPIB is required for survival of ABC DLBCL cells. (A) Two independent SPIB shRNAs were toxic to ABC DLBCL cell lines but not to GCB DLBCL, PMBL, and myeloma cell lines. (B) Quantitative PCR analysis of SPIB mRNA 48 h after induction of SPIB shRNAs.

Fig. 5.

Genomic aberrations associated with survival in ABC DLBCL. (A) Trisomy 3 and (B) single/double deletion of the INK4a/ARF locus were associated with adverse survival in ABC DLBCL. (C) Cases with either trisomy 3 or single/double deletion of the INK4a/ARF locus had inferior overall survival within ABC DBLCL.