Project 3: Molecular Risk Stratification of Gastric Precancerous Lesions

ABSTRACT – PROJECT 3 Project 3 proposes a concerted effort to decrease the 10-15% rate of Helicobacter pylori (Hp) recrudescence that is currently experienced by patients. Previous work by the investigators in this Program Project Grant has shown that a small number of Hp colonies persist deep within the gastric glands after eradication therapy. These

colonies may not be detected using conventional clinical tests, as the colonies reside in recrudescence niches that are consequently resistant to antibiotic treatment. Highly sensitive molecular technology can reveal the presence of Hp in conventionally ‘negative’ gastric histology samples. The central hypothesis of Project 3 is that

use of highly sensitive, sequencing-based technology to identify persistent Hp organisms and guide eradication may both prevent Hp recrudescence and arrest neoplastic progression. The specific aims of Project 3 are: (1) Leverage gene expression profiles of gastric epithelial cells as a predictor of gastric intestinal

metaplasia (GIM) progression in Hp negative individuals. (2) Develop molecular risk-stratification strategies in Hp histology negative subjects. In Aim 1, 300 Hp negative subjects will undergo RNA sequencing, and concordance with the ‘high-risk’ patterns will be assessed through a gene expression vector. We will then translate the ‘high-risk’ expression signature

into a clinically useful multiplex IHC test. In Aim 2, samples from patients with GIM who are histology negative for Hp on biopsies will be sequenced for molecular detection of Hp. A subset of patients will participate in a randomized, placebo-controlled trial evaluating the effect of antibiotic therapy on molecular Hp titers. This trial

will demonstrate whether a sequencing-based eradication strategy can reduce Hp burden to molecularly undetectable levels in human subjects.