Gene Expression Profile of Serial Samples of Transformed B-Cell Lymphomas

Abstract

SUMMARY:Follicular lymphoma (FL) is characterized by a continuous rate of relapse and transformation to a high-grade lymphoma, usually diffuse large B-cell lymphoma (DLBCL), associated with a dismal prognosis and a poor response to conventional chemotherapy. The progression of indolent to aggressive FL is accompanied by the successive accumulation of recurrent chromosomal defects, but the resultant alterations of gene expression are largely unknown. To expand the understanding of the pathogenesis of FL transformation, we initially performed oligonucleotide microarray analyses using Affymetrix HuFL chips on five cases with matched snap-frozen lymph nodes before and after transformation. Expression data were analyzed using the Affymetrix Microarray Suite 4.0 and Genespring 4.0. Thirty-six genes with increased expression and 66 genes with decreased expression associated with transformation were identified and functionally classified. The expression of differentially expressed genes was confirmed by real-time quantitative RT-PCR (QRT-PCR) using a total of seven matched pairs and an additional five FL and five unrelated DLBCL. In addition, selected genes were further analyzed by QRT-PCR or immunohistochemistry using a large, unrelated series of FL (grades 1 to 3) as well as transformed and de novo DLBCL (total of 51 samples). The microarray results correlated with the protein expression data obtained from samples at the time of initial diagnosis and transformation. Furthermore, the expression of 25 candidate genes was evaluated by QRT-PCR with a 78% confirmation rate. Some of the identified genes, such as nucleobindin, interferon regulatory factor 4, and tissue inhibitor of metalloproteinases 1, are already known to be associated with high-grade non-Hodgkin's lymphoma. Novel candidate genes with confirmed increased and decreased expression in transformed DLBCL include ABL2 and NEK2, and PDCD1 and VDUP1, respectively. In summary, this study shows that transformation of FL to DLBCL is associated with a distinct set of differentially expressed genes of potential functional importance. (Lab Invest 2003, 83:271-285).

Molecular pathways in follicular lymphoma

“…Interestingly, of their top list of 36 upregulated and 66 downregulated genes upon transformation, seven genes were also identified by Lossos et al 129 Among others, this involved increased expression of CDA and GAPD, two genes reflecting levels of metabolism, and decreased expression of the transcription factor IRF8 and of PTPRC (CD45). De Vos et al 130 also noted downregulation of different T-cell markers upon transformation such as CD7, FYB (Fyn binding protein) and SEMA4D (CD100). Elenitoba-Johnson et al 131 studied 11 FLs that transformed into DLBCL.…”

“…132,133 Interestingly, it was shown that the CD4 þ CD25 þ FOX-P3 þ regulatory T cells also expressed high levels of CD7, which was one of the T-cell markers identified in the microarray studies. 127,130,134 In addition, the number of FOX-P3 þ regulatory T cells decreased dramatically in five FLs that underwent transformation into DLBCLs. 132 Regulatory T cells can either inhibit CD4 þ CD25 À T cells, including GC T cells, which may support FL B-cell proliferation/survival.…”

“…Dave et al 127 divided FLs in two prognostic groups, merely based on the expression of markers from the nonmalignant cells present in whole tissues. Interestingly, the good prognosis groups of Dave et al, 127 Glas et al 128 as well as in the FLs before transformation of De Vos et al 130 were characterized by high expression of T-cell-related genes CD7, CD8, CD3D, FYB and CD100 and of the FDC-and macrophage-derived BAFF (Figure 2). These good prognosis groups may coincide with FLs displaying follicles containing the immunohistochemically defined 'full' GC phenotype FDCs, which is also associated with the presence of numerous intra-follicular T cells.…”

“…According to these investigators, at least two distinct profiles can be discerned in association with FL progression: Five out of the 12 cases displayed enhanced expression of C-MYC and its target genes, whereas in four cases a decreased expression of C-MYC and its target genes was observed. De Vos et al 130 studied four FLs with documented progression. Interestingly, of their top list of 36 upregulated and 66 downregulated genes upon transformation, seven genes were also identified by Lossos et al 129 Among others, this involved increased expression of CDA and GAPD, two genes reflecting levels of metabolism, and decreased expression of the transcription factor IRF8 and of PTPRC (CD45).…”

Structure and Regulation of the Human Nek2 Centrosomal Kinase

“…Furthermore, high expression levels of Nek2 have been strongly associated with disease progression in non-Hodgkin lymphomas (38). Moreover, deregulation of Nek2 has been linked to centrosome abnormalities and aneuploidy.…”