Progress in treating cancer is remarkable, thanks to the understanding of cell biological and genetic mechanisms. Yet, patients develop resistance to novel targeted treatments, compromising success of new, so-called smart, anti-cancer drugs. It is widely accepted that molecular characterization of tumors can help the diagnosis of patients and the proper selection of treatment (individualized medical approach). Resistance to targeted treatments is often assigned to the presence and actions of cancer stem cells (CSC). These CSCs then generate new tumors and spread disease in new locations of the patient’s body. Tumor cell invasiveness and metastasis are properties of cancer associated to CSCs that remain partially understood and demand better prognostic prospect. We focus our research on this fundamental question and study malignancies with strong invasive behavior. Our scientific contributions are based on molecular understanding of networks of proteins, RNAs and genes that regulate the generation of CSCs, their potential to differentiate and to invade. The project has multiple parts, most of them analyzing transcriptomic and epigenetic changes in cancer cells that a) respond to cytokines, such as TGFbeta, b) undergo changes in differentiation, such as EMT, c) key genes, including long non-coding RNAs have been genetically perturbed.