Table 1.
Genes expressed preferentially by B cells.
Fig 1.
Analysis of the expression of 290 genes in normal PB, pure B cell and CLL samples.
(A) Venn diagram of genes expressed preferentially in the different sample groups (normal PB, n = 5; pure B cells, n = 4; and CLL samples, n = 30). Genes were considered preferentially expressed by one sample group, if they showed an expression level ≥50 counts and a ≥2-fold difference in expression levels between the 2 groups, with a p-value ≤0.05. (B) Samples from PB (n = 5), B cell samples (n = 4), and samples from CLL patients (n = 30) were analyzed by PCA, based on the results of the differential expression of 290 genes. (C) PCA analysis on the same samples as in (b), but using a restricted set of 44 genes relevant for this purpose according to their differential expression in CLL, B cells and normal blood. (D) Heat map of normal PB, pure B cells, and CLL samples, analyzed with thirteen genes overexpressed homogenously (CV<5%) in all CLL samples compared to normal PB and pure B cells. Unsupervised analysis shows a perfect clustering of the CLL samples compared to the normal samples.
Table 2.
List of genes over- or under-expressed specifically by CLL B cells.
Table 3.
Quantification of mRNA transcripts for surface proteins.
Fig 2.
Correlation between mRNA and protein expression.
(A) Correlation between CD38 protein expression, as measured by flow cytometry (% positive CLL B cells) and CD38 mRNA counts, as measured by the nCounter (arbitrary units). (B) Quantification of CD38 and ZAP70 mRNA counts in normal peripheral blood (PB), pure B cells, and in CLL B cells. CLL B cells were analyzed for ZAP70 and for CD38 expression by flow cytometry and then grouped for the mRNA determination, according to presence or absence of these two antigens. (C) Immunoglobulin light chain ratios in 30 CLL patient samples (rhombi) and in normal B cells (triangles: normal PB samples; circles: pure B cell samples). The mean +/- 2SD interval for ratios from polyclonal normal B cells and normal PB is shown (mean 0.89; SD = 0.22; small dots).
Table 4.
List of genes distinguishing mutated from unmutated CLL samples.
Fig 3.
Characterization of different types of CLL samples using PCA analysis.
Samples from PB (n = 5), B cell samples (n = 4), and samples from CLL patients (n = 30) were analyzed by PCA, based on the results of the differential expression of 44 genes. Mutated CLL cases are shown in blue (n = 11), unmutated in green (n = 17), and borderline cases in red (n = 2).
Fig 4.
(A) LDOC1 mRNA expression was measured in 30 CLL samples and samples ordered according to absent/low (No 1–17) or high expression (No 18–30); black columns. ADAM29 mRNA expression shows an inverse pattern (No 1–12); hashed columns. Mutation status is noted below (BL = borderline; M = mutated; UM = unmutated IgVH) (B) Analysis of LDOC1/ADAM29 and LPL/ADAM29 ratios.
Table 5.
LDOC1 expression in CLL samples.
Fig 5.
Comparison of CLL to other B-CLPD using PCA.
Samples from CLL patients (n = 30) and of other B-CLPD (n = 51) were analyzed by PCA, based on the results of the differential expression of the selected 44 genes.