Rearrangments of the genome in breast and oesophageal cancer.
Cancers are caused by the alteration of genes, but we don’t yet know many of the genes involved, because we do not yet have detailed knowledge of how genes are altered in more than a handful of cases.
One of the most important ways in which genes are altered in cancer is by rearrangements of large segments of DNA, i.e. chromosome translocations, duplications, deletions and inversions. Until recently, very little accurate information about these rearrangements was available for common epithelial cancers such as breast cancer, indeed, textbooks and reviews generally gave the impression that breast cancers, for example, didn’t have important chromosome translocations.
In the last few years it has become clear that breast, prostate and other cancers have many chromosome rearrangements and in particular fusion genes—genes formed by fusion of two genes, like the BCR-ABL fusion of chronic myeloid leukaemia. These are powerful mutations and can be important diagnostic markers and targets for therapy. We recently estimated from recent transcriptome data that an average breast cancer expresses 10 fusion genes (Edwards & Howarth. Breast Cancer Research 2012;14, 303). Our ignorance of these events was due to the technical difficulties of analysing chromosomes in solid cancers (reviewed in Edwards, 2010).
In the last three or four years we and others have developed technology that allows us to comprehensively analyse DNA rearrangements in breast and other cancers. A good starting point is the multicolour fluorescent ‘SKY’ images like the one shown here, which outline the major chromosome translocations in a tumour (see our catalogue at http://www.path.cam.ac.uk/~pawefish). We have used two approaches to map the boundaries of the chromosome segments seen in these images. We first used ‘array painting’, in which individual chromosomes are separated in a cell sorter and then analyzed by hybridization to DNA microarrays (Howarth et al, 2008). Recently we have moved to ‘paired end read’ methods, which exploit the new massively-parallel DNA sequencing methods (Edwards, 2010). This strategy identifies rearrangements essentially by finding the junctions between rearranged bits of DNA.
We and others have analysed several breast cancers and over the next few years we can expect whole genomes of breast cancers and a range of other cancers to be sequenced. Already many new fusion genes have been found, and work is just beginning to determine their significance - some will merely be accidental consequences of genome rearrangement, others, like those in prostate cancer, may be central to cancer development and provide targets for therapy.
While characterizing fusion genes we found that reciprocal translocations often have tens of kilobases of common sequence duplicated onto both product chromosomes, leading us to propose that chromosome translocations are formed at replication bubbles (Howarth et al, 2011).
We are also studying the gene NRG1, which we have proposed to be major tumour suppressor gene on the short arm of chromosome 8, which could account for the loss of this region in many human cancers (Chua et al, 2009). NRG1 encodes ligands for the ErbB/EGFreceptor/ HER–2 family of receptors, and can drive both division and death of cells, depending on conditions.
In addition to work on breast, we are now involved in the International Genome Consortium (ICGC) project to sequence 500 oesophageal adenocarcinomas, based in Cambridge, funded by Cancer Research UK and lead by Prof. Rebecca Fitzgerald (Dept Oncology and MRC Cancer Unit). We are analysing genome rearrangements in these cancers.
It has recently been discovered that retrotransposable mobile elements of the LINE-1 family are active in human cancers and generate new insertions. We find that L1s are particularly active in oesophageal adenocarcinoma, often generating tens or hundreds of new inserts which have the potential to interrupt or activate genes.
- Group Members:
Karen Howarth, Tashfina Mirza
- Weaver JM, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong CA, Lao-Sirieix P, Dunning MJ, Smith L, Smith ML, Anderson CL, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PA, Rosenfeld N, Tavaré S, Fitzgerald RC, the OCCAMS Consortium
Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis Nat Genet. 2014; 46, 837-843
- Newman S , Howarth KD, Greenman CD, Bignell GR, Tavaré S, Edwards PAW. (2013) The relative timing of mutations in a breast cancer genome. PLoS ONE. 2013;8:e64991.
- Pole JCM, McCaughan F, Newman S, Howarth KD, Dear PH, Edwards PAW. Single-molecule mapping of genome rearrangements in cancer. Nucleic Acids Res. 2011; doi: 10.1093/nar/gkr227
- Howarth KD, Pole JCM, Beavis JC, Batty EM, Newman S, Bignell GR, Edwards PAW. Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles. Genome Research 2011; 21 525-534
- Edwards, PA. Fusion genes and chromosome translocations in the common epithelial cancers. J Pathol 2010;220:244-54.
- Chua, YL, Ito, Y, Pole, JC, Newman, S, Chin, SF, Stein, RC, Ellis, IO, Caldas, C, O'Hare, MJ, Murrell, A, Edwards, PA. The NRG1 gene is frequently silenced by methylation in breast cancers and is a strong candidate for the 8p tumour suppressor gene. Oncogene 2009;28:4041-52.