Background: Bone marrow studies using standard cytogenetic methods have shown that clonal chromosomal aberrations are detected only in half of patients with chronic lymphocytic leukemia (CLL) at the onset of the disease and in 70% in the advanced stages. Structural chromosomal abnormalities are included as one of the criteria for the international prognostic index CLL (CLL-IPI) for the patients’ stratification into prognostic groups. Analysis of genes polymorphic variants can provide a broader idea of the genetic events initiating CLL and additional information on the prognosis of the disease course already in the its onset.
Aims: To determine gene-gene interactions in the patients’ stratification with chronic lymphocytic leukemia into groups with different cytogenetic prognostic factors at the onset of the disease.
Methods: 71 patients in the CLL onset were examined. Cytogenetic studies included standard karyotyping and FISH analysis. Genotyping of polymorphic regions of the genes IL1β, -2, -4, -6, -10, -17A, TNFα, CD14, TGFβ1, FCGR2A, TLR2, -3, -4, -6, -9 was performed by restriction fragment length polymorphism analysis (“SNP-express”, Russia) with allele-specific primers and detection of amplification products in 2% agarose gel. Statistical analysis of gene arrays in order to establish intergenic interactions was performed using the non-parametric method of multifactor dimension reduction (MDR, Multifactor Dimensionality Reduction), including its modified version GMDR (Generalized Multifactor Dimensionality Reduction) http://www.healthsystem.virginia.edu/internet/addiction-genomics/Software/]. A permutation test was performed (1000 permutations with 10 cross-validations, corresponding to pperm<0.001).
Results: According to CLL-IPI and the presence of cytogenetic aberrations, patients were divided into 3 risk groups: 1 - with favorable prognostic markers (n=44); 2 - with intermediate risk markers (n=9); 3 - with unfavorable prognostic factors (n=18). The first group consisted of patients with no chromosomal aberrations (n=34) and the presence of del13q14 as the only karyotype disorder (n=10), group 2 - patients with trisomy of chromosome 12 (n=6) and with del11q22 (n=3), group 3 - with del17p13 (n=8) and with complex karyotype (n=10). Among complex karyotype, 3 patients had del11q22 with del13q14; 3 - del17p13 with del13q14; one case each: del13q14 with partial or complete hexasomy of 11 and 17; del13q14 with trisomy 12; del17p13 with del13q14 and with del11q22; del13q14 with del11q13 or monosomy 11. The carriage of genotypes with the wild-type allele of the gene IL1β-31C>T (OR 5.23, p=0.012) was found in CLL patients with no unfavorable cytogenetic risk factors at the onset of the disease. In patients of intermediate and high cytogenetic risk groups, two models of gene-gene interactions were identified. Thus, in the group of patients with intermediate cytogenetic risk factors for CLL, the interaction of loci IL1β-31C>T, TLR4 1196C>T, IL17А-197G>A, TLR3 1234C>G, IL1β-1473G>C and TGFβ 74G>G was established. Among them, the three-locus model of the polymorphic variants combination of the genes TLR3, IL1β-1473G>C and TGFβ was significant (CVC 10/10 (100%), OR=59.00, p<0.0001). In the study of gene-gene interactions of cytogenetic markers of a CLL unfavorable prognosis, the participation of the TLR4 896A>G, IL10-1082G>A and IL6-174G>C genes was established with the formation of a two-locus model for the combination of polymorphic variants of the genes TLR4 896A>G and IL10-1082G>A (CVC 10/10 (100%), OR=33.88, p<0.0001).
Summary/Conclusion: The presence of gene polymorphisms IL1β-1473G>C, IL10-1082G>A, TLR3 1234C>G, TLR4 896A>G, and TGFβ 74G>C can serve to identify groups of patients with poor prognosis for CLL.
Keywords: Chronic lymphocytic leukemia, Cytogenetics, Gene polymorphism, Prognosis