STOOL-BASED EXFOLIOME RNA PROFILING ENABLES NON-INVASIVE GUT DISEASE DIAGNOSIS AND MONITORING

Abstract

Abstract The development of real-time and non-invasive methods for monitoring gut health, signaling, and inflammatory status has the potential to transform the diagnosis, treatment, management, and drug development of numerous pathologies of the gut. Inflammatory bowel disease (IBD) represents one such area of large unmet clinical and pharmaceutical needs as it affects a large proportion of the population, has continued to increase in prevalence over time, and can have devastating consequences when not appropriately diagnosed and managed. Furthermore, there are a plethora of therapeutic options to which patients can show variable responses which means patients can undergo several cycles of costly therapy before finding an effective treatment regime for their disease. Conventional methods in disease management and clinical trial measurements involve endoscopies, which are invasive, expensive, and constitute only single or limited set of timepoints that are not readily amenable to longitudinal studies. While stool or blood tests are also commonly used, they only measure a small number of biomarkers and do not provide the necessary sensitivity nor data-rich insight into disease pathology that is required to inform clinical decision making and ongoing drug development efforts. Here, we have developed Exfoliome sequencing (Exfo-seq), an innovative non-invasive method to measure the gastrointestinal transcriptome directly from stool. Our approach makes use of the trace amounts of human RNA molecules (i.e., the exfoliome) that are present within stool due to natural turnover of intestinal cells. However, due to the massive amount of microbial and diet-derived contamination in the stool, the effort to capture human intestinal transcriptomic signals has remained limited to only a handful of genes. With a highly optimized signal capturing and amplifying method coupled with deep sequencing, we can simultaneously probe the mRNA levels of hundreds to upwards of several thousand genes from stool in a highly sensitive and quantitative manner. Exfo-seq can be performed to profile gut health, inflammatory state, disease pathway activity, and therapeutic response over time, and changes in gut cell populations, such as proliferation of immune cells during inflammation, can be inferred. Exfo-seq holds great potential as a non-invasive method to guide IBD diagnosis, treatment, long-term management and future drug development.