The Gene Expression Profile in CLL Better Reflects the Igvh-Mutational Status Than the Most Common Chromosome Aberrations.
Authors: Dicker Frank , Kohlmann Alexander , Schoch Claudia , Schnittger Susanne , Merk Sylvia , Dugas Martin , Hiddemann Wolfgang , Kern Wolfgang , Haferlach Torsten 
Published: October 2019

Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western world. The clinical course of patients is highly variable. The Rai and Binet staging systems have shown considerable prognostic value. However, recently introduced cytogenetic and molecular markers were able to further improve prognostication: (i) Five chromosomal aberrations, detectable by fluorescence in situ hybridization were shown as independent predictors of disease progression and survival: del(17p), del(11q), trisomy 12, normal karyotype, and del(13q). (ii) somatic mutations in the immunoglobulin variable heavy chain (IgVH) region have been correlated with a favorable prognosis. In order to correlate these prognostic parameters with differences in global gene expression profiles we analyzed mononuclear peripheral blood samples from untreated CLL patients using Affymetrix microarrays (HG-U133 set). The following questions were addressed: a) Identification of signatures correlated to cytogenetic subgroups. In a first step, a cohort of 44 patients comprising the following aberrations as sole abnormalities were analyzed: 4 del(11q), 19 del(13q), 4 del(17p), 12 no abnormality detected, 5 trisomy 12. Overall, using stringent criteria for significance of differentially expressed genes only 21/44 cases, mainly del(13q) patients were correctly predicted. Of the other 4 subgroups trisomy 12 samples tend to share also a pattern of genes significantly differing from other subgroups. b) Mining for gene dosage effects. Here we focused on group comparisons including only genes located in affected regions. In detail, for all affected regions a positive correlation of genomic aberration and gene expression was observable, e.g. higher expression of genes located on chromosome 12 when comparing trisomy 12 to all other cases. c) Identification of signatures correlated to IgVH-mutational status. Finally, a cohort of 41 patients (16 mutated, 25 non-mutated) was analyzed in a supervised approach. Genes that separated the mutated from the non-mutated samples were tested for their applicability in a classification algorithm (SVM). Overall, 78% of the samples were correctly assigned. These finding could be confirmed when 31 patients of an independent validation cohort were added. In this expanded cohort of 72 patients, similar power of gene expression profiling to predict mutational status was observed (79% accuracy). 8/22 mutated and 7/35 non-mutated samples were misclassified. In conclusion, despite their prognostic relevance, genetic aberrations do not seem to translate into gene expression signatures that are robust enough to be used for a classification algorithm. However, analysis of the affected, aberrant chromosomal regions suggests significant differences in the expression levels of genes located in the respective regions. Differential gene expression signatures based on the IgVH-mutational status tend to have better predictive information suggesting that the IgVH-mutational status has disease defining feature. In contrast to specific fusion genes resulting from balanced chromosomal rearrangements in acute myeloid leukemias, which are associated with unique expression profiles, genomic imbalances as observed in CLL seem to influence the gene expression pattern less dramatically.