Whole genome sequencing of 2,023 colorectal cancers reveals mutational landscapes, new driver genes and immune interactions

Abstract

To characterise the somatic alterations in colorectal cancer (CRC), we conducted whole-genome sequencing analysis of 2,023 tumours. We provide the most detailed high-resolution map to date of somatic mutations in CRC, and demonstrate associations with clinicopathological features, in particular location in the large bowel. We refined the mutational processes and signatures acting in colorectal tumorigenesis. In analyses across the sample set or restricted to molecular subtypes, we identified 185 CRC driver genes, of which 117 were previously unreported. New drivers acted in various molecular pathways, including Wnt (CTNND1, AXIN1, TCF3), TGF-beta/BMP (TGFBR1) and MAP kinase (RASGRF1, RASA1, RAF1, and several MAP2K and MAP3K loci). Non-coding drivers included intronic neo-splice site alterations in APC and SMAD4. Whilst there was evidence of an excess of mutations in functionally active regions of the non-coding genome, no specific drivers were called with high confidence. Novel recurrent copy number changes included deletions of PIK3R1 and PWRN1, as well as amplification of CCND3 and NEDD9. Putative driver structural variants included BRD4 and SOX9 regulatory elements, and ACVR2A and ANKRD11 hotspot deletions. The frequencies of many driver mutations, including somatic Wnt and Ras pathway variants, showed a gradient along the colorectum. The Pks-pathogenic E. coli signature and TP53 mutations were primarily associated with rectal cancer. A set of unreported immune escape driver genes was found, primarily in hypermutated CRCs, most of which showed evidence of genetic evasion of the anti-cancer immune response. About 25% of cancers had a potentially actionable mutation for a known therapy. Thirty-three of the new driver genes were predicted to be essential, 17 possessed a druggable structure, and nine had a bioactive compound available. Our findings provide further insight into the genetics and biology of CRC, especially tumour subtypes defined by genomic instability or clinicopathological features.

PTENandARID1Ahaploinsufficiency equip colonic epithelium for oncogenic transformation

“…While STAG2 has a high mutational burden in normal tissue and lower in cancer, compared to the other tumour suppressor genes, SMAD4 has the opposite phenotype of lower mutational burden in normal tissue but enrichment in CRC. Recent studies reconstructing the timing of CRC events assign SMAD4 mutation to a late stage of progression as it is predominantly found to be subclonal (Gerstung et al ., 2020; Cornish et al ., 2022). Despite this, the occasional presence of truncal SMAD4 mutations might be indicative of a weak driver which relies on additional synergising events for transformation but does not employ a probabilistic strategy of increasing its tissue representation for co-occurrence.…”

Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule

“…This analysis identified likely ancestral amplifications involving two canonical oncogenes in CedBTN1: MDM2 (10-13 copies; mean CN=10.9; gene CN percentile=98.3), encoding an important inhibitor of tumour suppressor proteins, and CCND3 (8-18 copies; mean CN=10.7; gene CN percentile=98.2), encoding a cyclin that promotes G1/S cell cycle transition (Supplementary Data 14). Recurrent amplification of these genes has been observed in multiple cancer types, and is thought to prevent cell cycle arrest and apoptosis under conditions of genomic instability [47][48][49][50][51][52] . In CedBTN2, we found evidence of a likely ancestral MYC amplification (7-11 copies; mean CN=9.2; gene CN percentile=96.3; Supplementary Data 14).…”

Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer

“…mutations that reduce the immune system's ability to engage with neoantigens) has been thoroughly investigated and found to be common in CRCs 4,13 . Our previous mathematical modelling found that escape is essential for MMRd CRC development, and is a crucial step in MMRp CRC formation when immune surveillance is stringent 4,8,14 . The role of the epigenome in modulating tumour antigenicity, however, has received less attention: somatic changes in chromatin organisation are known to contribute to the cancer immunophenotype, but their impact on immune escape and editing have not been completely assessed [15][16][17] .…”

“…Colorectal cancers (CRCs) generally display a relatively active immune microenvironment with substantial tumour-infiltrating lymphocytes 2 . About 15% of CRCs are mismatch repair deficient (MMRd), which is associated with a higher neoantigen burden, enhanced immune presence 3,4 and good response to immune checkpoint blockade therapies (ICBs), however, still up to 30% of MMRd CRCs do not respond 5 . Mismatch repair proficient (MMRp) CRCs harbour a lower mutation burden than MMRd CRCs and ICB treatments are ineffective 6 , indicating that immune evasion in MMRp tumours likely occurs through mechanisms alternative to those targeted by current ICB drugs.…”

“…Immune evasion through genetic means (e.g. mutations that reduce the immune system’s ability to engage with neoantigens) has been thoroughly investigated and found to be common in CRCs 4,13 . Our previous mathematical modelling found that escape is essential for MMRd CRC development, and is a crucial step in MMRp CRC formation when immune surveillance is stringent 4,8,14 .…”