Chromothripsis: an emerging crossroad from aberrant mitosis to therapeutic opportunities

Abstract

Chromothripsis, a type of complex chromosomal rearrangement originally known as chromoanagenesis, has been a subject of extensive investigation due to its potential role in various diseases, particularly cancer. Chromothripsis involves the rapid acquisition of tens to hundreds of structural rearrangements within a short period, leading to complex alterations in one or a few chromosomes. This phenomenon is triggered by chromosome mis-segregation during mitosis. Errors in accurate chromosome segregation lead to formation of aberrant structural entities such as micronuclei or chromatin bridges. The association between chromothripsis and cancer has attracted significant interest, with potential implications for tumorigenesis and disease prognosis. This review aims to explore the intricate mechanisms and consequences of chromothripsis, with a specific focus on its association with mitotic perturbations. Herein, we discuss a comprehensive analysis of crucial molecular entities and pathways, exploring the intricate roles of the CIP2A-TOPBP1 complex, micronuclei formation, chromatin bridge processing, DNA damage repair, and mitotic checkpoints. Moreover, the review will highlight recent advancements in identifying potential therapeutic targets and the underlying molecular mechanisms associated with chromothripsis, paving the way for future therapeutic interventions in various diseases.

Keywords: DNA damage repair; cell division; chromothripsis; genomic stability; synthetic lethality.

Figure 1

Chromosome dynamics in mitosis and aberrant chromosome structure in diseases. (A) Schematic illustration of dynamic reorganization of chromosome dynamics in various stages of mitosis. The mitotic structures including the mitotic spindle, chromosomes, centromere, central spindles, and midbody are illustrated. The structure and morphological changes are suitable for an image-based phenotypic screen of chromosome dynamics and abnormality in two-dimensional culture system (see illustration in Figure 5A). (B) Chromothripsis involves chromosome shattering and rearrangements of chromosome segments. Resulting rearranged chromosomes exhibit sequence alterations, amplified regions and fragment deletions. These alterations can contribute to oncogenesis or, as demonstrated in a case study, offer a potential cure for WHIM syndrome.

Figure 2

Exploring mechanisms of action underlying chromothripsis through diverse genetic approaches. This diagram illustrates an array of investigative methodologies employed in the examination of chromothripsis. Various techniques, including whole exome sequencing (WES), single nucleotide polymorphism (SNP) analysis, next-generation sequencing (NGS), fluorescent in situ hybridization (FISH), and comparative genome hybridization (CGH), have played instrumental roles in deciphering the intricate aspects of chromothripsis. Detection of chromothripsis ideally necessitates the integration of complementary techniques. A benchmark approach involves the combination of paired-end whole genome sequencing (WGS) with SNP microarrays, spectral karyotyping, and multi-color FISH. The precision of sequence resolution and spatial resolution varies among complementary techniques applied for chromothripsis detection. A comprehensive exploration of these methodologies, including their limitations and advancements, is available in a recent review by Krupina et al. (2023), providing valuable insights.

Figure 3

Chromosome trapping in micronuclei due to mitotic errors and impact of CIP2A–TOPBP1 complex on chromosome fragment inheritance. During mitotic cell division, incomplete congression and kinetochore–microtubule attachment of chromosomes lead to their entrapment within micronuclei post-anaphase. Mis-segregated chromosomes are enveloped by a nuclear membrane, forming micronuclei. Chromothripsis occurs in micronuclei. In the next cycle, in the presence of CIP2A and TOPBP1 proteins, aberrant chromosome fragments are cohesively linked, promoting their inheritance and subsequent rearrangement. Conversely, absence of the CIP2A–TOPBP1 complex results in random dispersion and segregation of chromosome fragments, causing genetic loss and impacting cell viability. The outstanding interests focus on how mitotic chromosome segregation errors elicit the initiation of chromothripsis and what happens on the fate of the daughter cell harboring chromothripetic fragments.

Figure 4

The SAC machinery for quality control of cell division. Various kinetochore–microtubule binding configurations occur in mitosis, including monotelic attachment where one kinetochore is unattached while the other attaches to a single spindle pole microtubule, syntelic attachment where both kinetochores attach to microtubules from the same spindle pole, and amphitelic attachment where proper microtubule numbers attach to each sister kinetochore from both spindle poles. Defects can activate SAC, halting APC activity through MCC formation, whereas accurate amphitelic attachment triggers APC activity for chromosome segregation. It is postulated that an inactivation of spindle checkpoint promotes chromothripsis and outstanding interests focus on the mechanisms of action underlying initiation and the spatiotemporal dynamics of chromothripsis.

Figure 5

Emerging technologies for delineating and interrogating chromothripsis dynamics. (A) Example of spectral imaging of six organelles in an interphase COS-7 cell, which provides a proof-of-principle for imaging organelle dynamics and chromothripsis during cell division. The six organelles are visualized, respectively (mOrange for peroxisome; EGFP for endoplasmic reticulum–Golgi intermediate compartments, ERGIC; YFP for endoplasmic reticulum; mPlum for mitochondria; mPlum for Golgi; mIFP for DNA). Magified montage of mIFP-H2B illustrates fragmented nuclei, in particular micronuclei (arrow), during cell division. The spectral image protocol has been optimized for imaging ruptured nuclear and provides an efficient platform to visualize chromothripsis in real-time cell division. Scale bar, 10 μm. (B) Schematic drawing of modeling and interrogating chromothripsis using 3D gastric organoid model. Light-sheet micrography of gastric epithelial and stem cells from gastric organoids can be used to study real-time dynamics of chromosome movements and chromothriptic responses to various therapeutic agents for synthetical lethality of cancer therapeutics. For example, organoids derived from patient gastric cancer cells, particularly the mitotic metaphase cell with two lagging chromosomes (arrow), might be used. Thus, a combination of light-sheet microscopy with 3D organoids allows high-resolution imaging of single chromosome dynamics in a 3D context and screen for targeted chemical probes. Scale bar, 10 μm. (C) A list of DDR and chromothripsis signaling components as emerging targets for interrogation and efficient therapeutics using synthetic lethality strategy.