Serum Mass Spectrometry Proteomics and Protein Set Identification in Response to FOLFOX-4 in Drug-Resistant Ovarian Carcinoma

SIMPLE SUMMARY: A mass spectrometry (MS) proteomics and molecular pathway study was applied to serum samples of patients with ovarian serous carcinoma administered the FOLFOX-4 drug combination protocol, before the second cycle of therapy. This exploratory study aimed at identifying a protein panel that could be significantly modulated during two different collection time intervals and associated with patient response to therapy. The label-free differential MS proteomic analysis of 14 serum samples was conducted and identified 291 shared expressed proteins; 12 proteins resulted in being significantly associated with response to treatment and time of sample collection. The network enrichment analysis performed through STRING and other bioinformatic tools provided a metadata validation of the panel in which the identified proteins were related to resistant ovarian cancers at the molecular level. We concluded that the discovered protein panel that guided the identification of the associated molecular pathways could be further explored in a higher number of patients. Considering the lack of biomarkers that can guide the selection of further therapeutic approaches after drug resistance appearance, our study may suggest a new direction in the discovery and validation of a protein panel as biomarkers for future clinical application. ABSTRACT: Ovarian cancer is a highly lethal gynecological malignancy. Drug resistance rapidly occurs, and different therapeutic approaches are needed. So far, no biomarkers have been discovered to predict early response to therapies in the case of multi-treated ovarian cancer patients. The aim of our investigation was to identify a protein panel and the molecular pathways involved in chemotherapy response through a combination of studying proteomics and network enrichment analysis by considering a subset of samples from a clinical setting. Differential mass spectrometry studies were performed on 14 serum samples from patients with heavily pretreated platinum-resistant ovarian cancer who received the FOLFOX-4 regimen as a salvage therapy. The serum was analyzed at baseline time (T0) before FOLFOX-4 treatment, and before the second cycle of treatment (T1), with the aim of understanding if it was possible, after a first treatment cycle, to detect significant proteome changes that could be associated with patients responses to therapy. A total of 291 shared expressed proteins was identified and 12 proteins were finally selected between patients who attained partial response or no-response to chemotherapy when both response to therapy and time dependence (T0, T1) were considered in the statistical analysis. The protein panel included APOL1, GSN, GFI1, LCATL, MNA, LYVE1, ROR1, SHBG, SOD3, TEC, VPS18, and ZNF573. Using a bioinformatics network enrichment approach and metanalysis study, relationships between serum and cellular proteins were identified. An analysis of protein networks was conducted and identified at least three biological processes with functional and therapeutic significance in ovarian cancer, including lipoproteins metabolic process, structural component modulation in relation to cellular apoptosis and autophagy, and cellular oxidative stress response. Five proteins were almost independent from the network (LYVE1, ROR1, TEC, GFI1, and ZNF573). All proteins were associated with response to drug-resistant ovarian cancer resistant and were mechanistically connected to the pathways associated with cancer arrest. These results can be the basis for extending a biomarker discovery process to a clinical trial, as an early predictive tool of chemo-response to FOLFOX-4 of heavily treated ovarian cancer patients and for supporting the oncologist to continue or to interrupt the therapy.