Eosinophilic esophagitis (EoE) is a recently described disease in which exposure to specific foods and allergens leads to type 2 inflammation. EoE has risen rapidly over the last 15 years in western countries. The pathogenesis of EoE results from the complex interaction between genetics and environment.
The first goal of the study will be to compare the transcriptome at a single cell resolution of the esophageal tissue taken from two pediatric patients with EoE and one age-matched healthy control, by using the single cell RNA sequencing (scRNA seq) technology, in order to delineate into specific cell subpopulations expressing unique sets of genes. Interestingly, biopsy samples will be taken from both the proximal and distal district of the esophagus of patients and control to highlight possible differences in their involvement in the disease pathogenesis. Results will allow to extend the knowledge on the pathogenesis of EoE by characterizing cell subsets and heterogeneity, identifying rare cell populations with a specific role in the disease development and discovering new markers able to discriminate between health and diseased tissues.
Furthermore, in a previous study, we showed for the first time that the different tendencies to relapse in children with EoE responding to topical steroids was related to an altered transcriptome profile. In particular, the gene SERPINB12 was differentially expressed among patients with early or late relapse.
Thus, a second goal of the project will be to confirm in a cohort of 40 EoE pediatric patients the ability of SERPINB12 to discriminate between patients having a relapse within 6 months after the end of therapy and those with a longer steroid-free remission, by using RT-PCR. Results will allow to better define the steroid-dependency and provide clinicians with a valid tool to predict relapse.
Eosinophilic esophagitis (EoE) is a recently described disease in which exposure to specific foods and allergens leads to type 2 inflammation. EoE provides an opportunity to scrutinize tissue-residing cells, which co-migrate into the esophageal mucosa with eosinophil.Although it is still considered a rare disease, it is nevertheless dramatically increasing in western countries and its pathogenesis is still poorly understood.
Advances in next-generation sequencing (NGS) have allowed profiling of the collection of mRNA species (the transcriptome) expressed in specific organs, tissues, and cells, but these advances have relied on analysis of bulk populations of cells, typically a mixture of millions of cells from isolated tissue or cell culture. With advances in single-cell capture and the automated cDNA library generation pipeline, it is now possible to examine the transcriptomes of single cells, a process referred to as single-cell RNA sequencing (scRNA-seq). This breakthrough technology allows unprecedented resolution of cellular differences and better comprehension of the function of individual cells in the context of their specific microenvironment, treatment, and/or disease contexts. Conceivably, the scRNA-seq platform can achieve many unique objectives beyond conventional methodology, including identification of rare cell populations, definition of disease subtypes, discovery of novel cellular markers, characterization of cellular heterogeneity and subsets, elucidation of disease mechanisms, and opportunities for precision and personalized medicine. Really, scRNA-seq analysis is part of the dawn of a new era of fine-resolution technologies that are revolutionizing translational research.
To date, scRNA-seq has begun to be used in exploring circulating and tissue-residing cells in patients with select diseases, with a focus on cancer. Its usefulness has only recently been applied to studying allergic disease. Currently, there is a sole study that used the scRNA-seq technology to explore the tissue heterogeneity of only T cells in EoE.
Thus, in the present study, we aim to use the scRNA-seq to analyze for the first time the whole cell heterogeneity in pediatric patients with EoE and in a healthy age-matched control in order to typify all the individual cell populations involved at various levels in inflammation during the active phase of the disease, with a particular focus on the presence of rare cell populations which could have a determining role in the pathogenesis of the disease. Interestingly, biopsy samples will be taken on both the proximal and the distal esophageal districts of patients and control in order to comprehend if they are featured by different transcriptome profiles in different cell subsets.
This study is very innovative and useful. Indeed, it is the first time that the transcriptome of all cell populations will be analyzed in patients with EoE comparing different areas of the esophagus (proximal and distal,) allowing a better understanding of molecular causes of EoE, the characterization of rare cell subpopulations that may have a role in the disease development, the discover of novel biomarkers able to make a more precise diagnosis and the identification of novel pharmaceutical targets.
A second point of the study will be to confirm in a large cohort of EoE pediatric patients, responding to steroids, the role of the protein SERPINB12 as a reliable marker to distinguish between EoE patients with earlier or later relapses after the end of the steroid-based therapy. Results from this study will allow to better define the steroid-dependency and provide clinicians with a valid working tool to predict relapse and personalize the therapeutic treatment. Indeed, one of the current vital elements in the long-term management of EoE is determining whether an indefinite treatment with topical steroids is necessary for all patients. Interestingly, a clear definition of steroid-dependency on molecular factor might help physicians in avoiding treatment interruption and subsequently unnecessary endoscopies.