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L.V. Abruzzo et al.
Figure 2. Results of two-way clustering according to cytogenetic subtype using the genes found to be differen- tially expressed. The samples include 40 del(13q) (blue), 32 diploid (brown), 10 del(11q) (pink), and trisomy 12 (+12) (green). Each column is one sample; each row contains the stan- dardized log expression values for one gene.
criteria in the analysis that compared +12 cases to all other samples. Starting with these 92 genes, we used the net- work building tools in IPA. First, the “connect” operation joins any pair of genes whose interaction is supported in the literature. Then the “grow” operation adds genes from the literature (not from the initial list) that are significantly connected to genes already in the network. We per- formed the “connect” and “grow” operations twice; the resulting network is shown in Figure 3. Genes not con- nected to the main network and not on chromosome 12 were omitted from the final diagram.
Discussion
Despite important differences in the clinical and patho- physiological features of +12 CLL compared to other cyto- genetic subtypes, only a few transcriptional profiling stud- ies (some on small numbers of samples) have focused on identifying dysregulated pathways that characterize +12 CLL and that may serve as therapeutic targets.7,8,18 Furthermore, these studies have classified cases using a hierarchical system, i.e. cases with more than one recur- rent abnormality are categorized according to the abnor- mality with the poorest prognosis.1 Thus, cases with both del(13q) and +12 are classified as +12, and cases with both +12 and del(11q) are classified as del(11q). To exclude the likely confounding effects of multiple cytoge-
netic abnormalities on gene expression, our +12 patient cohort had +12 as the only abnormality.
Similar to previous studies, we found that patients with +12 and with diploid cytogenetics required treatment ear- lier during their disease course than patients with del(13q), but later than patients with del(11q). Following FCR chemoimmunotherapy, our +12 cohort had a longer PFS than patients with other cytogenetic subtypes, but showed no difference in OS. Thus, +12 CLL patients may require treatment earlier, but respond better to FCR, than patients with other cytogenetic abnormalities. Higher CD20 expression by +12 CLL compared to other cytoge- netic subtypes may account, in part, for the high rate of response to rituximab-based therapy.19 However, despite the good response of +12 CLL patients to FCR, it is poorly tolerated by unfit patients or those over 65 years of age. Some patients develop myelosuppression and neutropenic fevers, and cannot receive a full course of therapy. Finally, a small percentage of patients treated with alkylating agents and fludarabine develop secondary myeloid malig- nancies.20 Thus, there is a need for less toxic, targeted ther- apies.
As expected, we identified genes whose expression pat- terns are known to be associated with cytogenetic sub- types, giving us confidence in our methods. For example, we identified statistically significant differences in gene expression between +12 cases with and without NOTCH1 mutation. Although the number of cases is rel-
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haematologica | 2018; 103(12)