Unique gene expression and clinical characteristics are associated with the 11q23 deletion in chronic lymphocytic leukaemia

Abstract

Summary Chromosome abnormalities influence prognosis and tumour progression in B‐cell Chronic Lymphocytic Leukaemia (CLL). This study sought to determine whether these different disease subgroups were associated with unique gene expression patterns. Thirty‐four cases of CLL were screened for the 11q23, 13q14, 17p13 deletions, and trisomy 12 by fluorescence in situ hybridization (FISH). Expression of 205 cell signalling and apoptosis genes were compared by cDNA array among cases with different chromosome abnormalities. A majority of the statistically differentially expressed genes were present in the 11q23 deletion group by hierarchical clustering. CDC2, a serine/threonine kinase, was overexpressed in the 11q23 deletion group (P = 0·0004) and confirmed by TaqmanTM real‐time polymerase chain reaction. Several other genes associated with cell signalling were overexpressed in the 11q23 deletion group. A strong overall correlation existed between the presence of different chromosome abnormalities and a number of prognostic factors including immunoglobulin heavy chain variable region mutation status (P = 0·011), time to treatment (P = 0·025) and lymphocyte doubling time (P = 0·034). This study confirmed the prognostic impact of chromosome abnormalities identified by FISH in CLL, particularly the 11q23 deletion and trisomy 12. In addition, the 11q23 deletion group was associated with a unique gene expression pattern involving cell signalling and apoptosis genes.

Molecular basis of aggressive disease in chronic lymphocytic leukemia patients with 11q deletion and trisomy 12 chromosomal abnormalities

“…The CLL RNAs were used for gene expression profiling using DNA microarray chip (MWG Biotech, Germany, Human 10K oligo set A) consisting of 50-mer oligonucleotide representing 10,000 different genes. The RNA from CLL samples and Stratagene™ reference mRNA were reverse transcribed, then labeled with Cy3 or Cy5 fluorescence dyes and hybridized with array chip as described earlier (11,12). The hybridized microarray slides were scanned and images were collected by using an Axon 4000B scanner (Axon Instruments, Union City, CA, USA).…”

“…Mononuclear cells (MNCs) were isolated from heparinized whole blood from CLL patients using Accu-Prep™ lymphocyte separation medium by Ficoll-Hypaque density centrifugation method (Accurate Chemical and Scientific Corp., Westbury, NY, USA) as described previously (11,14). The immunophenotypes of the isolated MNCs were determined by flow cytometry with flurochrome (phycoerythrin/PE or fluoroscein isothiocyanate/FITC)-labeled antibodies specific for cell surface markers (11).…”

“…Mononuclear cells (MNCs) were isolated from heparinized whole blood from CLL patients using Accu-Prep™ lymphocyte separation medium by Ficoll-Hypaque density centrifugation method (Accurate Chemical and Scientific Corp., Westbury, NY, USA) as described previously (11,14). The immunophenotypes of the isolated MNCs were determined by flow cytometry with flurochrome (phycoerythrin/PE or fluoroscein isothiocyanate/FITC)-labeled antibodies specific for cell surface markers (11). The cells were stained using the following flurochrome-conjugated antibodies: CD3-FITC, CD5-PE, CD19-PE, CD38-PE (BD Pharmingen, San Jose, CA, USA) and a combination of conjugated antibodies: CD3-FITC and CD38-PE; CD5-PE and CD19-FITC; CD19-FITC and CD38-PE (12) (12).…”

“…We (11,12) and others (10) have shown that CLL cases with 11q deletion, 17p deletion and trisomy 12 have a more aggressive disease compared to CLL with 13q deletion or normal karyotype. Krober et al (13) have shown that the frequency of occurrence of genomic aberrations was equal in the mutated and unmutated V H subgroups, but chromosomal abnormalities associated with poor prognosis, such as 11q deletion and 17p deletion, were almost exclusively found in the IgV H unmutated subgroup, whereas favorable abnormalities such as 13q deletion were associated with IgV H CLL-mutated subgroups.…”

Atypical 11q deletions identified by array CGH may be missed by FISH panels for prognostic markers in chronic lymphocytic leukemia

“…The identification of high-risk patients is essential for treatment planning and is of particular importance in earlystage, asymptomatic CLL patients, for whom rapid disease progression and a poor prognosis can be predicted by the presence of specific genomic abnormalities such as 11q and 17p deletions. [6][7][8] Recently, array comparative genomic hybridization (array CGH) has been gaining acceptance as a diagnostic tool that can also be applied to detect genomic gains and losses of prognostic importance in CLL, because of the advantages afforded by simultaneous genome-wide and locus-specific assessment of the leukemia with a single assay. [9][10][11][12][13][14] Array CGH is well suited for the identification of genomic alterations of prognostic importance in CLL, because the most common and important aberrations are comprised of genomic losses and gains, whereas chromosomal translocations are relatively rare.…”