Human TREX1 Knockout Cell Line-HeLa

Chromothripsis and kataegis are common in cancer and may be caused by telomere crisis, a period of genomic instability during tumorigenesis in which depletion of telomere reserves generates unstable dicentric chromosomes. Here, researchers investigated the mechanisms underlying chromothripsis and kataegis using an in vitro telomere crisis model. They found that TREX1, a cytoplasmic exonuclease that promotes the disassembly of dicentric chromosomes, plays an important role in chromosome fragmentation. In the absence of TREX1, genomic alterations caused by telomere crisis mainly involved break-fusion-bridging cycles and simple genomic rearrangements rather than chromosome fragmentation. Furthermore, the study showed that kataegis observed at chromothriptic breakpoints is the consequence of cytosine deamination by APOBEC3B. These data suggest that chromothripsis and kataegis are caused by a combination of nucleolytic processing by TREX1 and cytosine editing by APOBEC3B.

Of the 14 selected T2p1 postcrisis clones with ≥4 copy number (CN) changes in 1× coverage analysis (Figure 1e), 12 (86%) had either chromothripsis or a chromothripsis-like pattern on 30×WGS (Figure 1b,c). In contrast, among the 14 TREX1 knockout clones with complex events analyzed by 30×WGS, only 3 (21%) showed chromothripsis or chromothripsis-like patterns (Figure 1b,c). Taken together with the low-coverage data, these data suggest that chromothripsis is more common when cells undergo telomere crisis in the presence of TREX1. The patterns of structural variation in the postcrisis TREX1 knockout clones showed that other abnormalities emerge instead of chromothripsis (Figure 1c). Whereas the majority (57%) of CN changes in the T2p1 clones were classified as chromothripsis or chromothripsis-like, TREX1 knockout clones predominantly showed BFB and local jump signatures (Figure 1c,d). Consistently, the number of CN changes per event was lower in TREX1 knockout clones than in T2p1 clones (Figure 1d). These data imply that TREX1 knockout cells resolve DNA bridges formed in telomere crisis through simple structural events rather than chromothripsis.

Figure 1. TREX1 promotes chromothripsis. a, Examples of chromothripsis, chromothripsis-like, BFB and local jump patterns in postcrisis clones derived from T2p1 and TREX1 knockout cells. b, Summary of the number of clones that displayed the types of rearrangements shown in a as determined by 30× WGS of 14 T2p1 and TREX1 knockout postcrisis clones with complex events observed in 1×WGS. c, Summary of the number of chromosomes in postcrisis T2p1 and TREX1 knockout clones examined in b that display the indicated rearrangements. d, Plot of the number of CN changes associated with the complex events indicated in postcrisis T2p1 and TREX1 knockout clones described in b. (Maciejowski, John, et al. 2020)