Genomic Complexity in Diffuse Large B-Cell Lymphoma Is Associated with p53 Expression and Inferior Survival
Authors: Ma Charles , Siddiqi Imran N , Xie Yi , Tulpule Anil , Houldsworth Jane 
Published: November 2019

Abstract
Genomic complexity in diffuse large-B-cell lymphoma has recently been reported to have strong prognostic value in patients with diffuse large B-cell lymphoma (DLBCL) treated with rituximab-based immunochemotherapy (PMID:22975378). In that study, the presence of the respective gain/loss of at least one of nine genomic markers along the CDKN2A-TP53-RB-E2F axis was used to define cases with “complex” genomes. Genomic imbalance at these specific loci were suggested to functionally contribute toward cell cycle deregulation resulting in increased overall genomic instability. Other clinicopathologic studies have clearly demonstrated that inferior survival is also associated with elevated expression of p53, which serves as a surrogate for TP53 mutation. To date, there have been very few studies, if any, that have examined the relationship between genomic imbalance and complexity, and clinicopathologic features in DLBCL, in particular with relevance to TP53.
To this end, DNA was extracted from either sections of formalin-fixed paraffin-embedded biopsies with greater than 70% tumor burden or tumor-enriched cores of 85 DLBCL specimens from patients treated at a single institution (with IRB approval). DNAs from 39 specimens have been blindly submitted to array-CGH to date, using a targeted array (Agilent Technologies). The design permitted assessment at 50 loci commonly gained/lost in DLBCL (arising within 36 minimal common regions [MCRs]) using well defined scoring criteria. Specimens were classified as “complex” if any one of the following aberrations were detected: gain of 1q23, 6p21, 7q22, 12q15, or 19p13, or loss of 9p21, 13q14, 16q12, or 17p13. For all cases, expression of p53, MYC, BCL2, Ki-67, and Epstein-Barr virus (EBV) had previously been examined and reported (PMID:24619762) as was the COO subtype. Correlative analyses with overall survival (OS) were tested using the Kaplan Meier method and log rank statistic. Significance of pathogenomic correlations were examined using the Fisher’s exact t-test (P<0.05 was considered significant). Of the 39 cases evaluated to date, IPI was available for 34.
For the preliminary analysis comprising 39 cases, genomic complexity (observed for 22 cases) did not significantly correlate with IPI, consistent with the prior report where genomic complexity associated with inferior survival independent of IPI (PMID:22975378). However, genomic complexity did portend shortened survival within the preliminary 39 patients studied to date (P<0.01) and a trend was observed for the 29 who received RCHOP or RCHOP-like therapy (P=0.05) (for the remaining 10 cases, treatment status was unknown for 7 and 3 received palliative care). Genomic complexity based on absolute number of aberrations for the entire 50 assessed (>1), did not exhibit significant association with outcome. Fourteen of 18 cases with p53 expression (>30%) had complex genomes, which was significantly enriched compared with cases with low or no p53 expression (P <0.03). No significant correlation was found between genomic complexity and BCL2 (>70%) and MYC (45%) expression, nor with COO subtype.
Specifically for TP53, loss of 17p13 was detected in 7/39 cases, and positively correlated with adverse outcome both for the entire dataset (P=0.05) and for RCHOP-treated patients (P=0.02). Interestingly, of those with loss, 3 were not positive for p53 expression and overall, p53 expression did not correlate with 17p loss. Previous analyses in this dataset had also revealed that co-expression of p53 and MYC, but not BCL2 had an enhanced negative effect on outcome. Only one of 5 cases with co-expression of p53 and MYC also displayed 17p loss.
Overall then, p53 expression was associated with underlying genomic complexity but specific loss of the TP53 locus appeared to mark another smaller subset of DLBCL patients with inferior survival, independent of p53 expression. Expansion of the study to include the additional 46 cases is currently ongoing to confirm these emerging correlative patterns, as is determination of the TP53 mutation status of each specimen. Additional correlative pathogenomic studies will also be afforded with the larger dataset, examining the role of the 8 other loci of genomic gain/loss suggested to underlie genomic complexity in DLBCL.

Disclosures
Ma: Cancer Genetics, Inc.: Employment, Stock option holder Other. Houldsworth:Cancer Genetics, Inc: Employment, Stock and stock option holder Other.