Translational research
IDH1
GASTROINTESTINAL CANCERS
It is intended to collect plasma and serum samples from all patients, following separate declaration of consent. Samples are to be taken at baseline, at each restaging visit and at the end of the treatment visit. After centrifugation, the serum and plasma have to be stored at -80° Celsius for further analyses. The aim is to measure concentrations of inflammatory cytokines using FACS bead technology in the serum of patients. This panel will include analysis of Osteopontin, suPAR, APRIL, TWEAK, TRAIL, CCL1, 2, 5, and CXCR1, 2, 5, 9, which all have been demonstrated being regulated in the serum of patients with gastrointestinal cancers. Moreover concentrations of circulating miRNAs and lncRNAs will be measured in these samples. The ultimate aim of these retrospective analyses is to study the predictive value with regard to response, survival periods and development of resistance.Liquid biopsies will be taken to perform translational research on cell-free DNA in blood, following separate declaration of consent. cfDNA exome sequencing will be performed using a panel of 28 mutations (e.g. IDH1, IDH2, SMAD4). These mutations will be recapitulated in patients´ serum by using cfDNA exome sequencing and correlated with clinical response, survival and development of resistance.Stool analyses will be collected at baseline, at each restaging visit and at the end of the study treatment, following separate declaration of consent. In order to analyze the gut macrobiota we will perform different molecular-genetic examinations. First stool DNA will be prepared and bacterial gene sequences coding for 16S RNA will be quantified. As a screening examination a quantitative PCR using group-specific primer against variable parts of bacterial 16S RNA will be used. Next we will use a defined panel of 15 primer-pairs against the most prominent species of the gut microbiota to analyze rifaximin dependent alterations. Moreover it is planned to apply the highly innovative high-throughput sequencing of bacterial 16S RNA for complete and unbiased analysis of the gut microbiota.