Intratumoral Genetic Heterogeneity Provides Additional Prognostic Significance of the CLL Genomic Features

Background: Cytogenetic aberration remains the gold standard and basis for the long-standing hierarchical classification of CLL, with which 17p deletion (17p-) and 11q deletion (11q-)  have been considered as independent adverse prognostic factors. But even in these subgroups, prognosis is also heterogenetic. CLL is also characterized by the coexistence of multiple genetic clones within the tumor. Whether this intratumoral genetic heterogeneity will further classify CLL has been less investigated.

Patients and methods:  We used a panel of DNA probes to detect cytogenetic aberrations in CLL patients by FISH, including RB1/D13S25 at 13q14, ATM at 11q22, TP 53 at 17p13, CEP12 and IGH translocation at 14q32. The cut-off for positive values (mean of normal control + 3SD), determined from samples of ten cytogenetically normal persons, were7.5% for CEP 12 and deletion of MYB, 6.5% for deletion of D13S25, ATM and P53, 4.5% for IgH translocation. If there were greater than or equal to two cytogenetic aberrations and the difference of percentage of each aberration is less than 30 percentages, then we defined it as one clone aberration. On the contrast, if the difference between each aberration is greater than 30 percentages, one more clone is considered.

Results: Totally315 patients were enrolled in this study. 249 patients (79.3%) had at least one of the aberrations mentioned above, with the incidence of each cytogenetic aberration as follow: 47.6% for del 13q14, 11.7% for del 11q22, 14.4% for del 17p13 , 23.7%  for +12, and 21.8% for t(14q32). With a median follow-up of 52.5 months (2-288), the estimated median PFS was 89.0 months (95% CI 74.6-103.4), with estimated median OS 131 months (94.6-167.4). Both del 11q and del 17p were the adverse predictors for PFS and OS (p＜.018), and the patients with sole del 13q had advantageous PFS  (p=.000) and OS (p=.004). Trisomy 12 and t(14q32) had no significantly influence on both PFS and OS(p≥.142).

Sixty-five patients had no aberrations, which was defined as “no clone”. 150 patients had only one aberrations, 78 with two aberrations, 18 with three aberrations and 4 patients with four aberrations. 151 patients had only one clone within aberrations with del 13q and/or trisomy 12 and/or t(14q32), which we defined as “good clone”; fifty-two patients had only one clone with del 11q and/or del 17p aberrations, which was defined as “poor clone”.  The other forty- seven patients had two clones, 22 patients with two good clones, 12 patients with good clone as the priority and 13 patients with poor clone as the priority.  So, 77 patients contained poor clone and 173 patients contain only good clones.

Between the patients with only good clones, the median PFS and OS were similar between patients with one or two clones. 129 patients had only one aberration, 39 with two aberrations and 5 patients with three aberrations. The median PFS and OS of the 5 patients with three aberrations were 45months (95% CI 32.0-58.0) and 88 months(95% CI 21.0-155.1), which was significantly shorter than those with one or two aberrations , with a median PFS 104 months (95% CI 80.0-12.0, p=.043) and OS 162 months (95% CI 90.3-233.7 p=.008).

Within patients containing poor clones, 21 patients had only one aberration, 39 with two aberrations, 13 with three aberrations and 4 with four aberrations. The PFS and OS between these 4 subgroups were similar (p=.434 and p=.392 respectively).  The median PFS for patients with only poor clone, poor clone as the priority and good clone as the priority (poor clone as minority) was 45.0 months (95% CI  9.0-81.0), 27 months (95% CI 25.5-28.5) and 113.0 months, while the median OS was 78.0 months (95% CI 61.0-94.6), 53.0 months (95% CI 13.5-92.5) and not reached respectively. The patients with poor clone as the minority had significantly survival advantage on both PFS and OS (p=.024 for both) compared to other patients with poor clones.

Conclusions: Although the cytogenetic aberrations were the main survival predictors, the cytogenetic aberration burden and the type of predominant clone add the prognostic significance.