aUPD in the Clonal Evolution of Follicular Lymphoma

The use of Single Nucleotide Polymorphism (SNP) array profiling has uncovered extensive regions of acquired uniparental disomy (aUPD) in the cancer genome that go undetected using cytogenetics or array-CGH platforms. These regions usually arise by mitotic recombination and can render a cell homozygous for a pre-existing abnormality. SNP array analysis was performed using the Affymetrix 10K Gene-chip mapping array on DNA extracted from a series of Follicular Lymphoma (FL) lymph nodes biopsies from 42 patients, taken at time of diagnosis (n=20), progression (n=16) and transformation (t-FL) (n=32), and the t(14;18) positive lymphoma cell lines DoHH2 and RL 2261. Analysis was performed using the genome oriented laboratory file system, a software package designed to interpret SNP data. The criteria of > 96% homozygosity in at least 50 contiguous SNPs was found to detect no abnormalities in 24 normal remission bone marrows and was therefore adopted for the detection of abnormal runs of homozygosity. Abnormalities were detected in 53/68 primary specimens; these were non-random with recurring sites of aUPD on several chromosomes including 6p, 9p, 12q and 17p. This panel included 26 paired FL and t-FL samples; in 9 FL cases regions of homozygosity were identified which were not present in the subsequent t-FL sample, suggesting that t-FL may arise in a proportion of patients by a mechanism other than a process of direct clonal evolution. Homozygosity of 9p and 17p was seen primarily in the transformation samples and in three cases rendered the cell homozygous for a pre-existing mutation of either CDKN2A or TP53. Thus mutation precedes mitotic recombination which leads to the removal of the remaining wild-type allele. Nine out of 42 patients studied (21%) have aUPD of chromosome 6p. This appears to be an early event in lymphomagenesis as it was present in both FL and t-FL samples obtained from the same patient. The sites of mitotic recombination cluster in a region immediately proximal to the MHC complex at 6p21-12 in 8/9 cases. Mutations in CCND3, CDKN1A, and two translocation partners of BCL6: SRP20 and HIST1H4I, which are all located within or just distal of this cluster, were excluded by direct sequence analysis. Loss of MHC class II expression has been frequently observed in Diffuse Large B-cell lymphoma and a selective advantage gained by the lymphoma cell here would have implications in tumour surveillance. This study highlights the frequency of aUPD in follicular lymphoma and ongoing studies will elucidate the selective basis of a UPD at this location in the pathogenesis of lymphoma.