UNIQUE GENE EXPRESSION IN GUT-DERIVED PHAGOCYTIC IMMUNE CELLS FROM IBD PATIENTS
Authors: Jacobsen Gillian , Fernandez Irina , Cusguen Maria Alejandra Quintero , Santander Ana , Pignac-Kobinger Judith , Damas Oriana , Deshpande Amar , Kerman David , Ban Yuguang , Gao Zhen , Silva Tiago , Wang Lily , Burgueno Juan , Abreu Maria 
Published: January 2021

Abstract

Introduction/Aim
Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), have a complex immunopathogenesis involving chronic, dysregulated inflammation of the gut in response to commensal microbes. Current therapies, such as Anti-TNF drugs, target this immune dysregulation, but many patients exhibit recurrent inflammation despite treatment (refractoriness). Research shows that IBD patient phagocytic immune cells have altered cytokine production and bacterial clearing defects. We thus set out to analyze the transcriptome of phagocytic cells (CD11b+) isolated from patient gut biopsies. To shed light on potential causes of refractoriness, we examined cells from both not inflamed (successfully treated) and inflamed (refractory) patients on Anti-TNF therapy.

Methods
We used magnetic sorting to isolate CD11b+ cells from the lamina propria of a diverse set of IBD patient biopsies and performed RNA sequencing (n = 61). We used differential expression analysis to compare combinations of four patient biopsy variables: location (ileum or colon), condition (inflamed or uninflamed), IBD type (CD or UC), and patient treatment (Anti-TNF therapy or other). We also performed pathway analysis on genes significantly upregulated or downregulated (p &lt; 0.05) between these variables.

Results
The highest number of differentially expressed genes was found in the colon (5578 genes upregulated) vs ileum (5582). Genes upregulated in colon mapped to innate immune pathways, while ileum pathways were mainly metabolic. Only 29 genes were differentially expressed in UC vs CD, regardless of inflammation status or location. 26 genes were differentially expressed between inflamed and uninflamed biopsies on Anti-TNF therapy (n = 16). Genes upregulated in inflamed biopsies were associated with neutrophils, while genes in uninflamed biopsies were associated with adaptive immunity, short chain fatty acid synthesis, transcription and translation, and protein secretion.

Conclusion
CD11b+ cells of the colon are more immunologically active, likely due to their interaction with the dense microbiome of the colon. In contrast, the metabolic pathways upregulated in ileum may point to a role for phagocytes in digestion and metabolism. These results suggest that intestinal CD11b+ gene expression is highly influenced by regional microenvironment. Fewer differences were seen comparing CD11b+ cells from CD vs UC, suggesting that this cell population is not solely responsible for the clinical differences between these diseases. The small number of differentially expressed genes in Anti-TNF refractoriness shows a clear difference between innate and adaptive immune pathways, as well as increased general cell activity in Anti-TNF responders. These genes should be further investigated to determine their precise role in refractoriness.