Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma.

The incidence of esophageal adenocarcinoma (EAC) has risen significantly over recent decades. Although survival has improved, cure rates remain poor, with <20% of patients surviving 5 years. This is the first study to explore methylome, transcriptome and ENCODE data to characterize the role of methylation in EAC. We investigate the genome-wide methylation profile of 250 samples including 125 EAC, 19 Barrett's esophagus (BE), 85 squamous esophagus and 21 normal stomach. Transcriptome data of 70 samples (48 EAC, 4 BE and 18 squamous esophagus) were used to identify changes in methylation associated with gene expression. BE and EAC showed similar methylation profiles, which differed from squamous tissue. Hypermethylated sites in EAC and BE were mainly located in CpG-rich promoters. A total of 18575 CpG sites associated with 5538 genes were differentially methylated, 63% of these genes showed significant correlation between methylation and mRNA expression levels. Pathways involved in tumorigenesis including cell adhesion, TGF and WNT signaling showed enrichment for genes aberrantly methylated. Genes involved in chromosomal segregation and spindle formation were aberrantly methylated. Given the recent evidence that chromothripsis may be a driver mechanism in EAC, the role of epigenetic perturbation of these pathways should be further investigated. The methylation profiles revealed two EAC subtypes, one associated with widespread CpG island hypermethylation overlapping H3K27me3 marks and binding sites of the Polycomb proteins. These subtypes were supported by an independent set of 89 esophageal cancer samples. The most hypermethylated tumors showed worse patient survival.

Clinical issues in oesophageal adenocarcinoma: could DNA copy number hold the key?

While not being considered a common cancer, since 1975 oesophageal adenocarcinoma (OAC) has had the fastest-rising incidence of any malignancy in Caucasian Western populations. In the absence of major improvements in treatment since this rise began, the number of deaths has also increased rapidly. In contrast, there have been significant advances in basic science in this period. One such advance is the discovery of DNA copy number aberrations (CNAs), and their potential role in carcinogenesis. The study of CNAs offers the potential to answer fundamental clinical questions in OAC, which in turn may lead to improved diagnosis, staging and treatment. This review outlines current clinical dilemmas in OAC, discusses the role that CNAs have been shown to play to date and highlights potential future applications.

What's in a cancer syndrome? Genes, phenotype and pathology.

Syndromes are characterised by a group of specific signs and symptoms. This review aims to provide an overview of cancer syndromes and sheds light on possible roles for general health professionals in relation to their abilities to identify patients with cancer syndromes and therefore to refer such patients to specialists.

Colocalisation of predicted exonic splicing enhancers in BRCA2 with reported sequence variants.

Disruption of the breast cancer susceptibility gene BRCA2 is associated with increased risk of developing breast and ovarian cancer. Over 1800 sequence changes in BRCA2 have been reported, although for many the pathogenicity is unclear. Classifying these changes remains a challenge, as they may disrupt regulatory sequences as well as the primary protein coding sequence. Sequence changes located in the splice site consensus sequences often disrupt splicing, however sequence changes located within exons are also able to alter splicing patterns. Unfortunately, the presence of these exonic splicing enhancers (ESEs) and the functional effect of variants within ESEs it is currently difficult to predict. We have previously developed a method of predicting which sequence changes within exons are likely to affect splicing, using BRCA1 as an example. In this paper, we have predicted ESEs in BRCA2 using the web-based tool ESEfinder and incorporated the same series of filters (increased threshold, 125 nt limit and evolutionary conservation of the motif) in order to identify predicted ESEs that are more likely to be functional. Initially 1114 ESEs were predicted for BRCA2, however after all the filters were included, this figure was reduced to 31, 3% of the original number of predicted ESEs. Reported unclassified sequence variants in BRCA2 were found to colocalise to 55% (17/31) of these conserved ESEs, while polymorphisms colocalised to 0 of the conserved ESEs. In summary, we have identified a subset of unclassified sequence variants in BRCA2 that may adversely affect splicing and thereby contribute to BRCA2 disruption.

Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1 gene with missense sequence changes and in-frame deletions, but not polymorphisms.

INTRODUCTION: Aberrant pre-mRNA splicing can be more detrimental to the function of a gene than changes in the length or nature of the encoded amino acid sequence. Although predicting the effects of changes in consensus 5' and 3' splice sites near intron:exon boundaries is relatively straightforward, predicting the possible effects of changes in exonic splicing enhancers (ESEs) remains a challenge. METHODS: As an initial step toward determining which ESEs predicted by the web-based tool ESEfinder in the breast cancer susceptibility gene BRCA1 are likely to be functional, we have determined their evolutionary conservation and compared their location with known BRCA1 sequence variants. RESULTS: Using the default settings of ESEfinder, we initially detected 669 potential ESEs in the coding region of the BRCA1 gene. Increasing the threshold score reduced the total number to 464, while taking into consideration the proximity to splice donor and acceptor sites reduced the number to 211. Approximately 11% of these ESEs (23/211) either are identical at the nucleotide level in human, primates, mouse, cow, dog and opossum Brca1 (conserved) or are detectable by ESEfinder in the same position in the Brca1 sequence (shared). The frequency of conserved and shared predicted ESEs between human and mouse is higher in BRCA1 exons (2.8 per 100 nucleotides) than in introns (0.6 per 100 nucleotides). Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database. Applying the filters described above increased the colocalization of predicted ESEs with missense changes, in-frame deletions and unclassified variants predicted to be deleterious to protein function, whereas they decreased the colocalization with known polymorphisms or unclassified variants predicted to be neutral. CONCLUSION: In this report we show that evolutionary conservation analysis may be used to improve the specificity of an ESE prediction tool. This is the first report on the prediction of the frequency and distribution of ESEs in the BRCA1 gene, and it is the first reported attempt to predict which ESEs are most likely to be functional and therefore which sequence variants in ESEs are most likely to be pathogenic.