Swanton lab

Cancer Evolution and Genome Instability Laboratory

: Identification of mechanisms of chromosomal instability initiation and toleranc

Illustration of chromosomes from a cancer cell showing large-scale alterations.

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Chromosomal instability (CIN) contributes to intratumour heterogeneity in the majority of epithelial carcinomas.

We and others have demonstrated the association of CIN with poor prognosis and drug resistance (Lee et al., 2011; McGranahan et al., 2012; EMBO Rep. 13(6): 528-38; Turajlic et al Cell 2018; Jamal-Hanjani et al NEJM 2017).

Both structural and numerical CIN frequently occur together in tumours, however a mechanistic basis explaining this phenomenon in tumours is the subject of active investigation.

Our group has been deciphering a mechanistic basis for structural and numerical CIN in colorectal cancer (CRC), revealing that many chromosome segregation errors in these cells are caused by structural chromosome defects (Burrell et al., 2013). Hallmarks of DNA replication stress were elevated in CIN CRC cell lines relative to diploid controls, and segregation errors could be attenuated through exposure to exogenous nucleosides, previously shown to alleviate replication stress, suggesting that replication contributes to CIN in CRC.

In attempting to characterise a genetic basis for the generation of CIN in CRC, we used a bioinformatics analysis of CRC datasets to define a region on chromosome 18q that was consistently lost in aneuploid CRC compared to diploid chromosomally stable CRC. Chromosome 18q was lost during the adenoma-adenocarcinoma transition in tumours, and was temporally associated with the onset of aneuploidy. Furthermore, 18q is subject to copy number loss in a range of solid tumours including pancreatic and upper gastrointestinal malignancies.

18q-encoded genes were examined in an RNA interference screen for chromosome segregation error induction, revealing three genes, ZNF516, MEX3C and PIGN, the silencing of which increased the chromosome segregation error rate in diploid cells. Silencing these three candidate 'CIN Suppressors' in diploid cells resulted in an increase in the hallmarks of replication stress. Similar to CIN cells with 18q loss, exogenous nucleoside addition resulted in the attenuation of segregation errors in diploid cells following loss of the three CIN suppressors.

These data implicate replication stress in the generation of structural and numerical CIN and intratumour heterogeneity, and provide evidence that combining tumour bioinformatics approaches with intricate functional genomics analysis can reveal novel mechanisms contributing to intratumour heterogeneity.

Finally we have found evidence for somatic mutations in cancer impacting the ability of cells to tolerate chromosome segregation errors. Recently we found evidence for APC/C mutations in cancer resulting in the lengthening of mitosis, enhancing the fidelity of chromosome segregation events in CIN tumour cells (Sansregret et al Cancer Discovery 2017). We also found evidence for mutations in the tumour suppressor gene BCL9L in colorectal cancer driving a CIN permissive state in both p53 null and wild-type cells (Lopez-Garcia et al. Cancer Cell 2017).

Our group is building on the experimental frameworks established through this approach to identify novel mechanisms generating chromosomal instability initiation and tolerance utilizing high resolution genomic data deriving from the TRACERx clinical programs.