Neuroblastoma Patients' Outcome and Chromosomal Instability

Abstract

Chromosomal instability (CIN) induces a high rate of losses or gains of whole chromosomes or parts of chromosomes. It is a hallmark of most human cancers and one of the causes of aneuploidy and intra-tumor heterogeneity. The present study aimed to evaluate the potential prognostic role of CIN in NB patients at diagnosis. We performed array comparative genomic hybridization analyses on 451 primary NB patients at the onset of the disease. To assess global chromosomal instability with high precision, we focused on the total number of DNA breakpoints of gains or losses of chromosome arms. For each tumor, an array-CGH-based breakpoint instability index (BPI) was assigned which defined the total number of chromosomal breakpoints per genome. This approach allowed us to quantify CIN related to whole genome disruption in all NB cases analyzed. We found differences in chromosomal breakages among the NB clinical risk groups. High BPI values are negatively associated with survival of NB patients. This association remains significant when correcting for stage, age, and MYCN status in the Cox model. Stratified analysis confirms the prognostic effect of BPI index in low-risk NB patients with non-amplified MYCN and with segmental chromosome aberrations.

Keywords: aneuploidy; breakpoint instability index; chromosome instability; neuroblastoma.

Figure 1

Examples of putative breakpoints in areas of frequent chromosomal rearrangements and of points of steep copy number changes called within larger aberrations in neuroblastoma. Breakpoints on chromosomes 2p (A–C) and 17q (D) are indicated by black arrows. In particular, (B) shows two breakpoints within the amplicon containing the MYCN oncogene. Each panel shows data points for the log2 ratio of fluorescence between tumor DNA labeled with a red fluorophore (Cyanine 5) and the normal reference DNA labeled with a green fluorophore (Cyanine 3). Shaded areas detect aberrations called by the ADM-1 algorithm. The genes are indicated by blue boxes.

Figure 2

Examples of chromosomes 3 and 11 displaying the characteristic features of chromothripsis in neuroblastoma. Array-CGH ideograms showing chromosome losses (green dots) and amplifications (red dots) identified with the ADM-1 algorithm. Breakpoints are indicated by black arrows. Vertical blue lines indicate DNA losses and gains.

Figure 3

Association between BPI and survival in a cohort of 451 NB patients. Overall survival (A) and event free survival (B). Five-year survival probabilities are shown. CI: confidence intervals. p: p-value obtained via the log-rank test for trend.

Figure 4

Association between BPI and survival in a cohort of 451 NB patients stratified by MYCN status. Normal MYCN (A,B) and amplified MYCN (C,D). Five-year survival probabilities are shown. CI: confidence intervals. p: p-value obtained via the log-rank test for trend.

Figure 5

Association between BPI and survival in a cohort of 451 NB patients by stage at diagnosis: localized stage (A,B) and stage M (C,D). Five-year survival probabilities are shown. CI: confidence intervals. p: p-value obtained via the log-rank test for trend. n.e.: not evaluable due to the violation of the proportional hazard’s assumption.

Figure 6

Chromosome-breakage genomic instability in NB with a genomic profile with recurrent segmental chromosomal aberrations (SCAs) and NB tumors with a genomic profile that presents only alterations in the number of whole chromosomes (NCA). Box plot of data representing genomic instability calculated as a total number of chromosomal putative breakpoints per genome (BPI). Green box: numerical chromosomal aberrations. Red box: segmental chromosomal aberrations. p: p-value obtained with the Mann–Whitney U test.

Figure 7

Association between type of chromosomal aberrations in the primary tumors at diagnosis and survival in a cohort of 451 NB patients. Overall survival (A) and event free survival (B). Five-year survival estimates probabilities are shown. NCA: numerical chromosomal aberrations. SCA: segmental chromosomal aberrations. p: p-value obtained with the log-rank test.

Figure 8

Association between BPI and survival in a cohort of 261 NB patients with segmental chromosomal aberrations in the primary tumors at diagnosis: overall survival (A) and event free survival (B). Five-year survival probabilities are shown. p: p-value obtained by the log-rank test for trend.