Objective IBD confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multiregion sequencing.
Design Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 patients with CA-CRC (n=55 exomes), and key variants were validated with orthogonal methods. Genome-wide copy number profiling was performed using single nucleotide polymorphism arrays and low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD; n=30), high-grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19). Phylogenetic trees were reconstructed, and evolutionary analysis used to reveal the temporal sequence of events leading to CA-CRC.
Results 10/12 tumours were microsatellite stable with a median mutation burden of 3.0 single nucleotide alterations (SNA) per Mb, ~20% higher than S-CRC (2.5 SNAs/Mb), and consistent with elevated ageing-associated mutational processes. Non-dysplastic mucosa had considerable mutation burden (median 47 SNAs), including mutations shared with the neighbouring CA-CRC, indicating a precancer mutational field. CA-CRCs were often near triploid (40%) or near tetraploid (20%) and phylogenetic analysis revealed that copy number alterations (CNAs) began to accrue in non-dysplastic bowel, but the LGD/HGD transition often involved a punctuated ‘catastrophic’ CNA increase.
Conclusions Evolutionary genomic analysis revealed precancer clones bearing extensive SNAs and CNAs, with progression to cancer involving a dramatic accrual of CNAs at HGD. Detection of the cancerised field is an encouraging prospect for surveillance, but punctuated evolution may limit the window for early detection.
- inflammatory bowel disease
- colorectal cancer
- IBD - genetics
This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://creativecommons.org/licenses/by/4.0/.
Statistics from Altmetric.com
A-MB, WC, KC, IAB and C-HRC are Joint first authors.
31 ALH, SJL and TAG are Joint senior authors.
Contributors AMB performed experimental work, with HLD, IAB and CHRC assisting with DNA extractions. MM, MRJ, MJ, LMW and NAW performed histological analysis. CHRC, JOL, RF, RV, SACM, IAB, MM, SJH, SB, AS, JEE and LMW performed sample identification and collection. AMB, WC, KC, IAB, CHRC, DT, PM, IPMT, MW, SJL and TAG analysed the data. Figures were compiled by AMB, WC, KC, DT and MJ. ALH, SJL and TAG supervised the project. SJL and TAG designed the study and secured funding. AMB, SJL and TAG wrote the first draft of the manuscript and all authors read and approved the final version.
Funding This work was supported by Cancer Research UK (A14895, AMB and NAW; A19771, TAG; A16581, SJL), Crohn’s and Colitis UK (Research grant M/15/5 to SJL and TAG), Barts Charity (472-2300, TAG and KC), the Medical Research Council (MR/P00122X/1 to IAB, ALH and TAG), the St Mark’s Hospital Foundation Research Grant (RES198 to IAB, ALH, TAG), the Derek Willoughby Fund for Inflammatory Research (CHRC, ALH and TAG), UKRI Innovation/Rutherford Fund (KC), the Engineering and Physical Science Research Council (EP/F500351/1, DT), the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre Programme (JEE and SJL), and the NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust and University College London (MRJ).
Disclaimer The role of the MCRC Biobank is to distribute samples and therefore cannot endorse studies performed or the interpretation of results.
Competing interests None declared.
Patient consent Not required.
Ethics approval London Stanmore committee, 11/LO/1613.
Provenance and peer review Not commissioned; externally peer reviewed.
Data sharing statement All raw sequence data and array files are available on the EGA-GPA via accession number EGAS00001003028. Processed data (eg, mutation calls) are provided as supplementary material in this manuscript. Bioinformatics scripts to repeat our analysis are available at: https://github.com/BCI-EvoCa/Evo_history_CACRC.
If you wish to reuse any or all of this article please use the link below which will take you to the Copyright Clearance Center’s RightsLink service. You will be able to get a quick price and instant permission to reuse the content in many different ways.