Identification of Surrogate Prognostic Markers and Genes Implicated in Immunoglobulin Gene (IgV_H) Somatic Hypermutation in Small B-Cell Lymphomas.

Immunoglobulin (Ig) gene somatic hypermutation (SHM) is a prognostic factor in small B-cell lymphomas, as demonstrated by studies reporting that hypermutated chronic lymphocytic leukemia (CLL) and splenic marginal zone lymphoma (SMZL) cases show a better prognosis, while hypermutated mantle cell lymphoma (MCL) cases display specific clinicopathological features (leukemic course, increased survival).

However both the mechanisms and markers of SHM are poorly characterized, with the partial exception of the role of the genes ZAP70 and AID. With the purpose of identifying SHM surrogate markers in small B-cell lymphomas, we analyzed IgV_H mutational status and expression profiles of 93 small B-cell lymphoma patient samples including SMZL (24 cases), MCL (33 cases) and CLL (36 cases). Patients were classified into two groups: high SHM (>5% mutations) and low SHM (<5% mutations). T-test analysis with 100,000 permutations was performed and 39 genes were identified whose expression is significantly different (p<0.005, FDR<0.05) between cases with high and low SHM burdens.

To dissect the molecular mechanisms of Ig somatic hypermutation and validate the observed findings, SHM was induced in a model system and compared to results in patient samples. The BL2 cell line was used, and SHM was induced by treating the cells with IL4 and CD40. After 24 hours, active SHM was confirmed by western blot using an anti-AID monoclonal antibody on treated and untreated cells. These same cells were analyzed using microarrays, to identify the genes that were induced or downregulated during the SHM activation. A total of 29 genes (18 upregulated and 11 downregulated) were identified which are significantly differentially expressed in the cell line model during induction of SHM (expression change >0.4 Log2 scale) and are also differentially expressed between cases with high and low SHM (p<0.001, FDR<0.1). In both analyses, the upregulated genes are implicated in transcription, DNA repair and replication and chromosome maintenance, correlating well with previous hypotheses indicating that active transcription is necessary for SHM. Based on these observations, a group of 10 key genes, implicated in DNA repair, replication and transcription, were selected and protein expression was analyzed in a set of tissue microrrays containing 150 paraffin embedded small B-cell lymphoma cases, for which clinical data is available and SHM status is known. These proteins may provide a surrogate marker for prognosis and/or analysis of IgV_H SHM in patient samples using paraffin-embedded tissue samples.