Abstract 3584: Genomic analysis reveals a role for BCL9L in aneuploidy tolerance in colorectal cancer
Authors: Lopez-Garcia Carlos , McGranahan Nicholas , Hobor Sebastjian , Birkbak Nicolai , Domingo Enric , Rowan Andrew , Tomlinson Ian , Swanton Charles 
Published: July 2016

Abstract
Cancer genomes are frequently characterized by changes in the number and structure of the normal diploid karyotype, normally denominated as chromosomal instability (CIN), that result in tumour cell populations with high karyotipic diversity. CIN plays a key role in tumour evolution by contributing to intratumour heterogeneity and is often associated with key clinical landmarks such as bad prognosis and drug resistance.
CIN originates from deficient segregation of chromosomes during anaphase, which generates sister cells with abnormal karyotypes. Additionally, mechanisms of tolerance need to be acquired by cancer cells to survive segregation errors.
In colorectal cancer (CRC), 20% of tumours present high levels of microsatellite instability (MSI) together with low levels of CIN. The remaining 80% present low or no MSI, together with a wide range of CIN.
In this project, we explored the mutational landscape of 25 MSI-negative CRC samples in order to extract somatic mutational patterns of aneuploid CRC associated with CIN tolerance or chromosomal missgregation. Notably, we found frequent truncating mutations in BCL9L and loss-of-heterozigosity in 5 aneuploid samples.
Further inspection of somatic alterations in the TCGA cohort showed BCL9L alterations in 14% of CIN CRC (mutations and deletions) and more importantly, bioinformatic analysis demonstrated that these tumours have significantly higher wGII scores (the fraction of the genome with alterations). We also compared wGII scores of samples with co-occurring BCL9L and TP53 mutations and found that tumours with alterations in both genes show higher levels of CIN than those with only one alteration.
Functional characterization of BCL9L showed that depletion in various diploid cell lines induces tolerance of drug-induced and naturally occurring segregation errors. Long-term BCL9L-depleted cells increased the fraction of aneuploid cells in a diploid cell line and also, and enhancement of engraftment efficiency when injected into immune deficient mice. Additionally, CRISPR mediated inactivation of BCL9L showed enrichment in monoallelic BCL9L mutant colonies when treated with a drug that induces segregation errora, which supports a role for BCL9L haploinsufficiency in CIN tolerance.
Finally, we observed that BCL9L regulates the expression of Caspase-2, a proteolytic enzyme that is activated in a p53-independent manner by segregation errors and cleaves several proteins important for cell survival such as the p53 regulator MDM2 and the mitochondrial apoptotic regulator protein BID.
Citation Format: Carlos Lopez-Garcia, Nicholas McGranahan, Sebastjian Hobor, Nicolai Birkbak, Enric Domingo, Andrew Rowan, Ian Tomlinson, Charles Swanton. Genomic analysis reveals a role for BCL9L in aneuploidy tolerance in colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3584.