A Novel and Disease Specific Gene in Chronic Lymphocytic Leukemia.

One of the best predictors of poor outcome in CLL is the absence of somatic hypermutations in the Ig-genes of the leukemic cells. This prognostic dichotomy, between cases of mutated and unmutated CLL, enabled us to screen for a gene associated with poor outcome CLL using differential display RT-PCR. We identified a novel transcript from chromosome 12q22, which by RT-PCR and Northern blotting seemed to be selectively over-expressed in CLL patients with poor prognosis. No matching genes or ESTs were annotated in the region, but screening of a cDNA library from unmutated CLL patients resulted in cloning of 7 cDNAs, which probably derived from alternative splicing of a common transcript. The majority of the transcripts had no significant reading frames, but one splice variant may encode a protein of 121 amino acids. Despite very low primary sequence similarity, structure modelling revealed that the peptide potentially can fold into a structure remarkably similar to human IL-4. By RT-PCR the various transcripts were undetectable in a panel of normal tissues and cell lines. Using quantitative RT-PCR (QRT-PCR), we could however detect minute amounts of the mRNAs in normal B-cells; the level was similar or slightly higher in good prognosis patients and much higher in poor prognosis patients. The expression level of the two major mRNAs was 24–50 fold higher in patients with unmutated Ig-genes compared to patients with somatic hypermutation (p<0.0001), and 20–30 fold higher in ZAP-70 positive patients compared to ZAP-70 negative patients (p<0.0001). The median time to treatment for patients with overexpression of the mRNAs (n=26) was 11 months compared to 104 months for patients with normal expression (n=31) (p=0.0005). The median overall survival for patients with overexpression was 97 months while patients with low expression had not reached a median overall survival at their last follow up (p=0.03). This prognostic power was comparable to that provided by mutational status, and stronger than that provided by ZAP-70 or CD38 expression. Finally, in 56 patients the gene dosage as defined in QRT-PCR was inversely proportional with time to treatment (p= 0.006). This novel gene therefore has several features that make it a candidate to be the first disease specific gene identified in CLL.