Intestinal Microbiome, Oral Microbiome, and Whole Blood Transcriptome Analyses in Gastrointestinal Malignancies

The primary objective of this prospective observational study is to characterize the gut and oral microbiome as well as the whole blood transcriptome in gastrointestinal cancer patients and correlate these findings with cancer type, treatment efficacy and toxicity. This study will provide biospecimens from a diverse range of gastrointestinal cancer patients to allow preliminary characterization of the diversity and composition of the GIM microbiome and pilot analysis of changes in the microbiome as a function of both treatment and disease progression. This is a prospective cohort study will characterize and evaluate the microbiome of GIM patients, with various histologies. The investigators plan to enroll 200 patients with a diagnosis of gastrointestinal cancer including pancreatic, esophageal, gastric, colon, rectal, liver and biliary cancers with (i) newly diagnosed recurrent or metastatic disease initiating therapy or (ii) with progressive disease on second or later line therapies, or (iii) with locally advanced, inoperable disease receiving palliative therapy. Stool, blood and saliva samples will be collected at baseline, early in treatment (3-6 weeks), and then at 3 month intervals until progression or intolerable toxicity or up to 36 months. The results of this study are expected to provide the basis for larger, more focused studies of the microbiome in distinct GIMs and relationship to specific treatment efficacy and toxicity. Ultimately, this classification of the gastrointestinal cancer microbiome may lead to novel risk stratification paradigms, novel treatments and maintenance strategies. Furthermore, this study may lead to improved diagnostics, companion diagnostics, and nutritional interventions for cancer prevention and therapy.