Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

Abstract

Next-generation sequencing approaches have been used to investigate the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer from a patient — rather than from a cell line or xenograft — over a 9-year period between the diagnosis of the primary tumour and the appearance of metastasis. Comparison of the somatic non-synonymous coding mutations in the metastasis and the primary tumour of the same patient and the combined analysis of genome and transcriptome data provided insights into the mutational evolution that can occur with disease progression. The cover shows sequence elements of the HAUS3 locus, one of the genes found to be mutated in the tissue (shown in the background) from the primary lobular cancer used for this work. Advances in next generation sequencing have made it possible to precisely characterize the coding mutations that occur during the development and progression of individual cancers. Here, this technique is used to sequence the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer; significant evolution is found to occur with disease progression. Recent advances in next generation sequencing1,2,3,4 have made it possible to precisely characterize all somatic coding mutations that occur during the development and progression of individual cancers. Here we used these approaches to sequence the genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient, which arose 9 years earlier. Five of the 32 mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and PALB2) were prevalent in the DNA of the primary tumour removed at diagnosis 9 years earlier, six (in KIF1C, USP28, MYH8, MORC1, KIAA1468 and RNASEH2A) were present at lower frequencies (1–13%), 19 were not detected in the primary tumour, and two were undetermined. The combined analysis of genome and transcriptome data revealed two new RNA-editing events that recode the amino acid sequence of SRP9 and COG3. Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.