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Background  Our previous study showed that fatty acids extract obtained from CLA-enriched egg yolks (EFA-CLA) suppressed the viability of MCF-7 cancer cell line more effectively than extract from non-enriched egg yolks (EFA). In this study, we analysed the effect of EFA-CLA and EFA on transcriptome profile of MCF-7 cells by applying the whole Human Genome Microarray technology.    Results  We found that EFA-CLA and EFA treated cells differentially regulated genes involved in cancer development and progression. EFA-CLA, compared to EFA, positively increased the mRNA expression of  TSC2  and  PTEN  tumor suppressors as well as decreased the expression of  NOTCH1 ,  AGPS ,  GNA12 ,  STAT3 ,  UCP2 ,  HIGD2A ,  HIF1A ,  PPKAR1A  oncogenes.    Conclusions  We show for the first time that EFA-CLA can regulate genes engaged in AKT/mTOR pathway and inhibiting cell cycle progression. The observed results are most likely achieved by the combined effect of both: incorporated CLA isomers and other fatty acids in eggs organically modified through hens’ diet. Our results suggest that CLA-enriched eggs could be easily available food products with a potential of a cancer chemopreventive agent.    Electronic supplementary material  The online version of this article (doi:10.1186/s12263-016-0537-z) contains supplementary material, which is available to authorized users.

Fatty acid extract from CLA-enriched egg yolks can mediate transcriptome reprogramming of MCF-7 cancer cells to prevent their growth and proliferation