TP53 Abnormalities Are Underlying the Poor Outcome Associated with Chromothripsis in Chronic Lymphocytic Leukemia Patients with Complex Karyotype

Abstract

Chromothripsis (cth) has been associated with a dismal outcome and poor prognosis factors in patients with chronic lymphocytic leukemia (CLL). Despite being correlated with high genome instability, previous studies have not assessed the role of cth in the context of genomic complexity. Herein, we analyzed a cohort of 33 CLL patients with cth and compared them against a cohort of 129 non-cth cases with complex karyotypes. Nine cth cases were analyzed using optical genome mapping (OGM). Patterns detected by genomic microarrays were compared and the prognostic value of cth was analyzed. Cth was distributed throughout the genome, with chromosomes 3, 6 and 13 being those most frequently affected. OGM detected 88.1% of the previously known copy number alterations and several additional cth-related rearrangements (median: 9, range: 3-26). Two patterns were identified: one with rearrangements clustered in the region with cth (3/9) and the other involving both chromothriptic and non-chromothriptic chromosomes (6/9). Cases with cth showed a shorter time to first treatment (TTFT) than non-cth patients (median TTFT: 2 m vs. 15 m; p = 0.013). However, when stratifying patients based on TP53 status, cth did not affect TTFT. Only TP53 maintained its significance in the multivariate analysis for TTFT, including cth and genome complexity defined by genomic microarrays (HR: 1.60; p = 0.029). Our findings suggest that TP53 abnormalities, rather than cth itself, underlie the poor prognosis observed in this subset.

Keywords: TP53; chromothripsis; chronic lymphocytic leukemia; genomic complexity; genomic microarrays; optical genome mapping.

Figure 1

Two examples of cases analyzed by optical genome mapping showing only intra-chromosomal chromothripsis-related rearrangements. (A) A patient with chromothripsis in chromosome 6 in which OGM showed the presence of three intra-chromosomal translocations (case #9). When whole chromosome FISH painting (WCP) was performed, two green signals corresponding to chromosome 6 were observed, confirming the presence of material from this chromosome in the one initially reported as “der(6)add(6)(p25)del(6)(q21)” and in its normal counterpart. To ensure that this metaphase was abnormal, chromosome 2 was also stained, since both GM and OGM detected a duplication of 2p. WCP confirmed that the duplicated 2p was the marker chromosome found by CBA. (B) Patient with chromothripsis in chromosome 6 in which CBA identified a monosomy 6 and an unbalanced t(6;19)(q12;p13) (case #8). OGM revealed some rearrangements clustered in chromosome 6, but it did not detect this translocation. It was probably not called by OGM due to the involvement of the telomeric region of chromosome 19, a highly repetitive region in which the OGM detection of structural variants is known to be limited. The hybridization pattern obtained by WCP confirmed the presence of this translocation, since two different signals (orange and green), corresponding to both chromosomes, could be observed together but without showing a mixing of these signals, which suggests that they rearranged after the process underlying chromothripsis. The abnormalities detected by CBA in chromosomes with chromothripsis are highlighted in red in the karyotype. Chromosome views show the comparison of the CNA profiles identified by GM and OGM in the chromothriptic chromosomes. The Circos plot represents the abnormalities identified by OGM for the whole genome (on the left) and the chromothriptic chromosome involved in this process (on the right). Different layers show, from outer to inner, cytobands of different chromosomes, structural variants (including deletions, duplications, inversions and insertions), copy number alterations and rearrangements, which are represented by lines joining the chromosomes involved.

Figure 2

Two examples of cases with chromothripsis analyzed by optical genome mapping showing rearrangements between chromothriptic and non-chromothriptic chromosomes. (A) Patient with chromothripsis in chromosomes 3 and 13 (case #31). OGM detected 10 rearrangements between chromosomes 3 and 13 and four rearrangements between chromosomes 13 and 15. Whole chromosome FISH painting (WCP) revealed the presence of material from both chromosomes 3 and 13 inserted in chromosome 15. (B) Patient with chromothripsis in chromosome 11 (case #17). OGM revealed the presence of intra-chromosomal translocations and several additional rearrangements involving chromosomes 2, 13 and 14. Notably, t(2;11) and t(11;13) were validated by WCP. Conversely, despite showing only one line in the Circos plot, three parallel t(11;14) were identified by OGM and could not be validated by WCP. However, they could not be ruled out with certainty as true translocations since the rearranged fragment located between the breakpoints was very small and could be missed due to the low resolution of the technique. The abnormalities found by CBA in chromosomes with chromothripsis are highlighted in red in the karyotype. Additional chromosomes associated with chromothriptic events are highlighted in bold. Chromosome views show the comparison of the CNA profiles identified by GM and OGM in the chromothriptic chromosomes. The Circos plot represents the abnormalities identified by OGM for the whole genome (on the left) and for chromothriptic and non-chromothriptic chromosomes involved in this process (on the right). Different layers show, from outer to inner, cytobands of different chromosomes, structural variants (including deletions, duplications, inversions and insertions), copy number alterations and rearrangements, which are represented by lines joining the chromosomes involved.

Figure 3

Example of a case with chromothripsis that shows multiple rearrangements with other chromosomes when analyzed by optical genome mapping. Overall, the karyotype of this patient presented a high complexity, with several bits of additional material found in different chromosomes and a few chromosome markers (case #16). Chromosome 12 displayed monosomy by CBA (highlighted in red in the karyotype) but when analyzed by GM and OGM, this chromosome showed an identical pattern of chromothripsis, with >10 switches between 2–3 copy number states. In addition, OGM identified several rearrangements among different chromosomes, as shown in the Circos plot depicted at the bottom of the figure. This highly complex profile could be associated with another catastrophic phenomenon known as chromoplexy, characterized by the presence of multiple chained translocations. Those additional chromosomes associated with chromothriptic events are highlighted in bold in the karyotype.

Figure 3

Example of a case with chromothripsis that shows multiple rearrangements with other chromosomes when analyzed by optical genome mapping. Overall, the karyotype of this patient presented a high complexity, with several bits of additional material found in different chromosomes and a few chromosome markers (case #16). Chromosome 12 displayed monosomy by CBA (highlighted in red in the karyotype) but when analyzed by GM and OGM, this chromosome showed an identical pattern of chromothripsis, with >10 switches between 2–3 copy number states. In addition, OGM identified several rearrangements among different chromosomes, as shown in the Circos plot depicted at the bottom of the figure. This highly complex profile could be associated with another catastrophic phenomenon known as chromoplexy, characterized by the presence of multiple chained translocations. Those additional chromosomes associated with chromothriptic events are highlighted in bold in the karyotype.

Figure 4

Kaplan–Meier plots for time to first treatment (TTFT) based on the presence of chromothripsis and the number of oscillating switches found in chromothripsis patterns. Kaplan–Meier estimation for TTFT in patients with 7–9 switches between 2–3 copy number states and ≥10 switches between 2–3 copy number states compared to a cohort of CLL cases carrying a complex karyotype (CK) without chromothripsis (cth). Of note, patients were classified into the “Cth ≥ 10 switches” group if they showed at least one chromothripsis event with these characteristics.

Figure 5

Kaplan–Meier plots for time to first treatment (TTFT) and overall survival (OS) based on the presence of chromothripsis. Kaplan–Meier estimation for TTFT (A) and OS (B) in patients with chromothripsis (Cth; including cases with 7–9 and ≥10 switches) compared to a cohort of CLL cases carrying complex karyotype (CK) without chromothripsis (No cth).

Figure 6

Kaplan–Meier plots for time to first treatment (TTFT) based on the presence of chromothripsis and abnormalities in TP53 (deletions and/or mutations). Patients were classified according to the presence of chromothripsis (cth) and within each group (No cth vs. Cth), TTFT was assessed based on the presence of aberrations in TP53 (deletions and/or mutations).