Palin K, Pitkänen E, Turunen M, Sahu B, Pihlajamaa P, Kivioja T, Kaasinen E, Välimäki N, Hänninen UA, Cajuso T, Aavikko M, Tuupanen S, Kilpivaara O, van den Berg L, Kondelin J, Tanskanen T, Katainen R, Grau M, Rauanheimo H, Plaketti R, Taira A, Sulo P, Hartonen T, Dave K, Schmierer B, Botla S, Sokolova M, Vähärautio A, Gladysz K, Ongen H, Dermitzakis E, Bramsen JB, Ørntoft TF, Andersen CL, Ristimäki A, Lepistö A, Renkonen-Sinisalo L, Mecklin J, Taipale J, Aaltonen LA
Nat Commun 9 (1) 3664 [2018-09-10; online 2018-09-10]
Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge. Unbiased CRISPR-Cas9 knockout and activation screens identified in total 79 genes within AI peaks regulating cell growth. Genetic and functional data implicate loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.
QC bibliography QC xrefs
European Nucleotide Archive: PRJEB25645 CRISPR/Cas9 knockout and activation screening of colorectal cancer allelic imbalance target genes
European Genome-phenome Archive: EGAS00001002966 High-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole genome sequenced (WGSed)
European Genome-phenome Archive: EGAS00001003010 Somatic mutations of 256 whole-genome sequenced colorectal tumors
Zenodo: https://doi.org/10.5281/zenodo.1222172 Contribution of allelic imbalance to colorectal cancer