We have identified 1206 probe sets and more than 10 pathways whose expression is significantly different between control and E2 treated MCF-7 cells 3-4 hrs after treatment, and 4193 probe sets and more than 20 pathways 24 hrs after treatment.
Although very little overlap exists on the gene level between the nine expression profiling studies, the meta analysis finds common functional processes and pathways. Table 3 shows that most of the genes identified in individual studies were also identified in the meta-analysis. The rank product algorithm returns a robust ranking for all the top genes, leading to higher reproducibility and increased specificity.
It should be noted that all the datasets we used were based on the Affymetrix platform. A recently available dataset , using Illumina Beadchip, provides very similar results to our analysis. Another very recent dataset , using GRO-seq, although produced with a different focus on transient early response to E2, also provides consistent results. Thus it does not seem that our results are platform-dependent.
We have used pathway analysis tools to understand the relationship between the regulated genes. Known targets of ERα, such as MYC, ERBB2, and ESRα, are central genes at early and late time points. This shows that the statistically significant genes are biologically relevant, and that our analysis captures key aspects of the underlying physiology.
Aryl hydrocarbon receptor (AhR) is a ligand activated transcription factor involved in xenobiotic metabolism and in mediating the toxic effects of dioxin-like compounds. Crosstalk has been observed between AhR and ER, specifically with respect to ER signaling . ERα has been reported to have a positive role in AhR signaling. We find this pathway highly regulated at both time points.
The top canonical pathways regulated early are involved in cellular growth, development and proliferation, whereas those regulated late are involved in DNA replication, recombination and repair, cell cycle and cell death. These canonical pathways were not evident from any of the individual studies. Another difference between early and late response to E2 is early regulation of transcription regulators, vs. late regulation of kinases and transporters.
At the late time point we also see several genes common with the SV40T/t-antigen cancer signature identified by Deeb et al. for human breast, prostate and lung carcinomas. These include genes encoding 10 centromere proteins, 8 cyclins, 15 cell division cyle proteins, 7 kinesin-like family proteins, 7 multiple minichromosome maintenance-deficient proteins, and other proliferation-related proteins and signal transduction proteins.