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The serotonin reuptake transporter is reduced in the epithelium of active Crohn’s disease and ulcerative colitis

Crohn’s disease (CD) and ulcerative colitis (UC) are incurable inflammatory conditions also known as inflammatory bowel disease (IBD). The disease may be acute or have chronic components and mostly affects the intestines. Onset, progression and severity is affected by a number of factors such as genetic susceptibility, unknown environmental factors, the microbiota and immune dysregulation limiting our understanding of the disease. Dysbiosis of the intestinal epithelium such as barrier dysfunction and intestinal permeability have been used as markers of IBD, however, recent studies have demonstrated a role for the epithelium in other IBD-related pathophysiologies such as alterations in immune regulation, regeneration and interplay with the microbiome.

Serotonin, 5-hydroxytryptamine (5‑HT), is a ubiquitous signalling molecule that regulates many biological functions, which includes the inflammatory response. Serotonin is expressed in lung, CNS blood and liver, however it is mainly produced by the GI tract enterochromaffin cells (EC‑cells) in the intestinal epithelium. Serotonin synthesis is controlled by Tryptophan hydroxylase 1 (TPH‑1) and interstitial serotonin is removed by the serotonin reuptake transporter (SERT or 5‑HTT). SERT, encoded by the SLC6A4 gene, is the most efficient transporter of serotonin and although there is some redundancy SET KO mice still develop intestinal mobility defects and increased IBD in a TNBS model. Several studies have demonstrated a link between inflammation and SERT expression; mice that spontaneously develop UC have reduced levels of SERT, however there is very little information in humans.

In this study, the authors built on previous work where they sequenced pinch biopsies from CD, UC and healthy controls and found SLC6A4 (SERT) was one of the most downregulated genes in the IBD samples. They used microarray analysis, IHC, qPCR and laser capture microdissection to determine the levels of SERT and TPH‑1 in a biobank of IBD and healthy samples. They also derived organoids from colon tissue to analyse they effects of TNFα on the levels of SERT and TPH‑1.

Microarray analyses of endoscopic pinch biopsies demonstrated that SLC6A4 expression was downregulated in active CD ileitis, active CD colitis and active UC colitis.

qPCR also demonstrated SLC6A4 downregulation in active CD ileitis, active CD colitis and active UC colitis compared to healthy controls.

Downregulation of serotonin reuptake transporter protein was confirmed with IHC, demonstrating significant decrease in anti-SERT staining in the epithelial monolayer during inflammatory IBD conditions.

Colonic epithelial monolayer was isolated using laser capture microdissection and analysed using RNA‑seq. In the colon of patients with IBD SLC6A4 mRNA levels were significantly reduced during active inflammation of both CD and UC compared to healthy controls.

No changes in the levels of TPH1 mRNA were observed in the same samples.

Colonoids (organoids) were constructed from one patient with UC and two healthy donors. Mature differentiated colonoids were treated with TNFα and analysed by RT‑qPCR. There was a significant reduction in SLC6A4 mRNA when colonoids from UC or healthy colonoids were treated with TNFα.

In this study, the authors demonstrated for the first time that the SERT protein is downregulated in inflamed intestinal tissue. This may explain the increased serotonin levels found in IBD patients. Anti-TNFα therapies are used to treat inflammatory disorders and this study also demonstrates that TNFα can significantly reduce the levels of SERT in colonoids derived from both IBD patients and healthy controls.


Jørandli et al. The serotonin reuptake transporter is reduced in the epithelium of active Crohn’s disease and ulcerative colitis. Gastrointestinal and Liver Physiology, Volume 319, 2020.

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Epistem is a GCLP-accredited laboratory specialising in providing biomarker, target discovery and personalised medicine information. We offer microarray, qPCR and NGS services (including the 10X genomics platform for single cell sequencing) for gene expression, whole genome and epigenetic analysis in all species.

We also specialise in laser capture microdissection (LCM) for the isolation of specific highly enriched populations of cells of interest for subsequent transcriptional profiling and epigenetic analysis. We have GCLP-accredited histology and IHC labs and we have used our expertise in this area to develop “RNA-friendly” stains compatible with LCM to isolate specific cell types, making them amenable for gene expression studies. All of our histology and gene expression, LCM and hair IHC applications are GCLP-compliant and we have supported many clinical studies. We also have in-house bioinformatics support for all of our genomics studies and have extensive experience identifying biomarkers or biomarker signatures in a variety of tissues.

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