Level in the post-therapeutic tumours and they demonstrate that the observed differences are likely to be restricted to patients treated by chemotherapy. Of note, the increase in NOTCH2 expression was related to an increase in the cytoplasmic staining intensity rather than to an increase in the number of cells expressing NOTCH2. This result argues against an enrichment of a subpopulation of NOTCH2-expressing tumour cells and more likely suggests a chemotherapy-induced increase in gene expression in the tumour cells, which may be related to the tumour biological features after neoadjuvant treatment. However, a clear distinction between these possibilities may be limited by the semiquantitative evaluation of immunohistochemical staining. As similar alterations in nuclear staining were observed in all tumour groups including the control we considered these changes as unrelated to chemotherapy. Irrespective of the mechanism and the true nature of the residual tumour cells expressing NOTCH2, our results may have therapeutic implications. Notch signalling has emerged as a potential new therapeutic target, and gamma-secretase inhibitors, which inhibit the processing of the Notch receptors, are currently being evaluated in clinical trials. Our study suggests that targeting Notch signalling may also represent a new strategy to treat GC patients. As an adverse prognostic effect was only associated with NOTCH2 and not NOTCH1, our data also indicate that a detailed characterisation of the individual Notch receptors and a thorough functional investigation are mandatory and further strongly favour the development of Notch paralog-specific inhibitory agents. A significant increase in POU5F1 expression was observed after chemotherapy in the resected specimens in our study. The POU5F1 transcription factor is essential for the maintenance of self-renewal, and its high expression in residual cancer cells after radiochemotherapy is correlated with poor prognosis in colon cancer. Interestingly we also observed an increased expression of LGR5, a promising intestinal CSC marker, after chemotherapy in tumours with TRG2. These results are compatible with the potential enrichment of drug-resistant tumour cells expressing POU5F1 or LGR5, but the underlying mechanism for these alterations and the particular properties of the cells expressing these genes remain to be determined. In our study, no association with survival were observed for the cell surface molecules CD44 or CD133, both of which have been widely used to identify putative CSCs in various tumours. This result supports recent Ibrutinib findings demonstrating that these cell surface molecules do not identify CSCs in primary gastric tumours. Taken together, our findings demonstrate that the expression signature of GSK3Bhigh, CTNNB1high and NOTCH2low in chemotherapy-resistant residual GC tumour cells is a strong predictor for favourable patient prognosis. This prognostic relevance was also demonstrated for GC patients using publically available gene expression data. The results of the differential expression analysis of the pre- and post-therapeutic tumour specimen also suggests that the impact of GSK3B and CTNNB1 to this signature is not dependent on chemotherapy but rather related to a property of the primary tumour. They further indicate a prominent role for NOTCH2 and chemotherapy resistance in GC, which is more likely related to an effect of the chemotherapeutic agents on NOTCH2 expression rather than to an enrichment of NOTCH2 expressing tumour cells. Rapid high throughput diagnostic methods can identify the causative pathogens at an early stage of the illness.