Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment.

BACKGROUND: Biopsies taken from individual tumours exhibit extensive differences in their cellular composition due to the inherent heterogeneity of cancers and vagaries of sample collection. As a result genes expressed in specific cell types, or associated with certain biological processes are detected at widely variable levels across samples in transcriptomic analyses. This heterogeneity also means that the level of expression of genes expressed specifically in a given cell type or process, will vary in line with the number of those cells within samples or activity of the pathway, and will therefore be correlated in their expression. RESULTS: Using a novel 3D network-based approach we have analysed six large human cancer microarray datasets derived from more than 1,000 individuals. Based upon this analysis, and without needing to isolate the individual cells, we have defined a broad spectrum of cell-type and pathway-specific gene signatures present in cancer expression data which were also found to be largely conserved in a number of independent datasets. CONCLUSIONS: The conserved signature of the tumour-associated macrophage is shown to be largely-independent of tumour cell type. All stromal cell signatures have some degree of correlation with each other, since they must all be inversely correlated with the tumour component. However, viewed in the context of established tumours, the interactions between stromal components appear to be multifactorial given the level of one component e.g. vasculature, does not correlate tightly with another, such as the macrophage.

Fascin expression is increased in metastatic lesions but does not correlate with progression nor outcome in melanoma.

Levels of the actin bundling protein fascin correlate with invasion and metastasis and reveal prognostic value in many epithelial carcinomas. However, we know very little about the potential role of fascin in melanoma. The purpose of this study is to compare fascin expression in primary melanomas and melanoma metastasis. Fascin expression was examined through the immunohistochemistry of paraffin embedded tissue microarrays including 560 cores of primary tumour and metastasis. Fascin expression was significantly elevated in 48 metastases compared with 254 primary tumours (P=0.034). In 187 patients with primary melanomas, fascin was not correlated with survival (P=0.067), whereas low fascin was significantly correlated with the presence of ulceration (P=0.005). Our results indicate that fascin status does not correlate with progression in melanoma. Upregulated fascin expression was detected in melanoma metastases, but was not correlated to patient outcome.

Acute myeloid leukemia presenting in a mother and daughter pair with the identical acquired karyotypic abnormality consisting of inversion 3q21q26 and monosomy 7: a review of possible mechanisms.

The 3q21q26 inversion is associated with both myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), often in association with monosomy 7. In this report, we present a young woman and her mother, both diagnosed with AML, exhibiting similar morphological and identical cytogenetic features. AML with abnormalities of chromosome 3q is often characterized by abnormal megakaryopoeisis and diabetes insipidus, and both were seen in these cases. To our knowledge, this is the first report of familial aggregation of AML displaying an inversion of chromosome 3q and monosomy 7. We discuss possible mechanisms for the development of familial AML with identical karyotypic abnormalities and the link between 3q aberrations and monosomy 7.