Several mechanisms lead to the inactivation of the CDKN2A (P16), P14ARF, or CDKN2B (P15) genes in the GCB and ABC molecular DLBCL subtypes

Abstract

Diffuse large B-cell lymphoma (DLBCL) represents the most frequent type of aggressive lymphoma. Deletions of the CDKN2A locus, encoding the proteins CDKN2A (P16), P14ARF, and of the CDKN2B locus, encoding the protein CDKN2B (P15), affect one-third of DLBCL patients. Although other mechanisms that decrease gene expression have been reported, such as promoter methylation, the prognostic value of these mechanisms is still unclear. We studied the deletion and methylation status of these genes in 171 patients and correlated the genomic results with their mRNA expression level and clinical outcome. CDKN2A, P14ARF, and CDKN2B deletions were significantly correlated with decreased mRNA expression (P<0.0001, P<0.0001, and P=0.0148, respectively). P14ARF was methylated in only two patients (1.3%), whereas CDKN2A and CDKN2B were methylated in 36.7 and 31.4% of patients, respectively. Methylation levels greater than 25% were associated with decreased expression of CDKN2A (P=0.0169). CDKN2A and CDKN2B inactivation by deletion or methylation was observed in 42.7 and 37.4% of cases, respectively. Including P14ARF deletions, we identified an inactivating mechanism for at least one of these genes in 47% of patients. Although gene inactivation was not correlated with the international prognostic index, P14ARF and CDKN2B inactivation was significantly associated with shorter survival (P=0.0048 and P=0.0413, respectively), whereas CDKN2A was not (P=0.085). Low mRNA expression levels of these genes were correlated with the ABC phenotype. Furthermore, our results show that an inactivating methylation was more frequent in the GCB phenotype.

How we treat Richter syndrome

“…The genomic complexity of RS was intermediate to that of CLL and DLBCL 38 ; RS patients with inactivation of TP53 and/or CDKN2A experienced shorter survival than RS patients without these defects, a finding consistent with the poor prognosis associated with CDKN2A loss in de novo DLBCL. [39][40][41] In another recent article, Fabbri and colleagues reported similar observations using whole-exome sequencing to compare the CLL and RS phases of 9 patients with RS. 42 Potential epigenetic events contributing to the pathogenesis of RS in CLL patients have also been explored.…”

Two main genetic pathways lead to the transformation of chronic lymphocytic leukemia to Richter syndrome

“…Importantly, in DLBCL, CDKN2A losses have been associated with a poor outcome and with a non2GCB-phenotype. 16,31,32 In addition, there are previous suggestions of the importance of cell-cycle deregulation in RS. 30,[33][34][35] In our RS series, CDKN2A losses also were associated with poor outcome and occurred mostly concomitantly with TP53 inactivation.…”

Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes

“…[32][33][34] In addition to histone modifiers and small noncoding RNAs, chemical modifications of DNA such as cytosine methylation emerged recently as paramount in regulating genome stability and gene expression. Targeted studies identified several loci with altered DNA methylation in DLBCL, including INK4A, 35,36 MGMT, 37,38 and BCL6. 39 Following these observations, we asked whether such changes are widespread in the genome of DLBCL .…”

“…This appears to be a progressive oncogenic event that is more common in more aggressive DLBCLs (clusters E and F). Prior reports highlighted frequent deletion of the INK4B-ARF-INK4A locus in patients with DLBCLs 35,36,50,51 and suggested that an alternative mechanism of gene inactivation through aberrant hypermethylation also exists and cumulatively with deletions may affect between one-third and one-half of patients with DLBCLs. In addition, we demonstrated aberrant hypermethylation of CDKN1A and CDKN1B, which is a novel finding.…”