Contig Array CGH at 3p14.2 Points to the FHIT Gene as the Deleted Gene in Diffuse Large B Cell Lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin’s lymphoma (NHL), accounting for 30 – 40% of adult NHL. Genomic alterations in DLBCL have been investigated by various methods and many regions of amplifications and losses have been detected. Genomic deletions of the 3p arm have been reported in many solid tumors and leukemias, but no study published to date has reported genomic deletions of this region in DLBCL. Recently we demonstrated that 3p14.2 was deleted in approximately 30% of DLBCL patients and cell lines by use of a genome-wide array-comparative genomic hybridization (array-CGH) (Tagawa et al., 2004). For a more detailed examination of the genomic losses at 3p14.2, here we made use of contig BAC array for 3p14.2, and found that 12 of 27 DLBCL samples displayed losses. All of the deleted regions were located within the Fragile Histidine Triad (FHIT) gene, and the most frequently region of loss was mapped to 0.4 Mbp of the region encompassing the introns 4 and 5 and exon 5 of the FHIT gene. Genomic deletions of the FHIT gene have been observed in most common forms of cancer and it is therefore conceivable that the FHIT gene is the target one of the genomic deletion at 3p in DLBCL. To investigate the relationship between genomic deletions and transcript alterations, we performed nested reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. Aberrant transcripts or loss of expression was detected in 33% (19 of 57) of the DLBCL samples, and the lost exons of the aberrant transcripts were correlated with genomic deletions detected by array CGH. We also investigated the CpG island methylation status of the promotor of the FHIT gene by means of methylation specific PCR (MSP). One case with genomic loss of the FHIT gene, and three cases without genomic loss showed methylated allele. These findings indicate that 1) Loss of genomic material at 3q14.2 is responsible for exon losses of the FHIT gene, and 2) Genomic loss of the FHIT gene is one of the causes of the generation of aberrant transcripts. 3) Both genomic deletions and methylations are involved in the causes of inactivation of the FHIT gene.