Serum Metabolites Relate to Mucosal and Transmural Inflammation in Paediatric Crohn Disease

Abstract

Background and aims: We aimed to identify serum metabolites associated with mucosal and transmural inflammation in paediatric Crohn disease [pCD].

Methods: In all, 56 pCD patients were included through a pre-planned sub-study of the multicentre, prospective, ImageKids cohort, designed to develop the Paediatric Inflammatory Crohn magnetic resonance enterography [MRE] Index [PICMI]. Children were included throughout their disease course when undergoing ileocolonoscopy and MRE and were followed for 18 months, when MRE was repeated. Serum metabolites were identified using liquid chromatography/mass spectroscopy. Outcomes included: PICMI, the simple endoscopic score [SES], faecal calprotectin [FCP], and C-reactive protein [CRP], to assess transmural, mucosal, and systemic inflammation, respectively. Random forest models were built by outcome. Maximum relevance minimum redundancy [mRMR] feature selection with a j-fold cross-validation scheme identified the best subset of features and hyperparameter settings.

Results: Tryptophan and glutarylcarnitine were the top common mRMR metabolites linked to pCD inflammation. Random forest models established that amino acids and amines were among the most influential metabolites for predicting transmural and mucosal inflammation. Predictive models performed well, each with an area under the curve [AUC] > 70%. In addition, serum metabolites linked with pCD inflammation mainly related to perturbations in the citrate cycle [TCA cycle], aminoacyl-tRNA biosynthesis, tryptophan metabolism, butanoate metabolism, and tyrosine metabolism.

Conclusions: We extend on recent studies, observing differences in serum metabolites between healthy controls and Crohn disease patients, and suggest various associations of serum metabolites with transmural and mucosal inflammation. These metabolites could improve the understanding of pCD pathogenesis and assessment of disease severity.

Keywords: Serum metabolites; machine learning; paediatric Crohn disease.

Graphical Abstract

Figure 1

Study flowchart.

Figure 2

Set of action for model learning and evaluation. Maximum relevance minimum redundancy [mRMR] feature selection and a cross-validation scheme were used to optimise the model [and find the best subset of features and hyperparameter settings]. We then assess its performance, as measured by the area under its Receiver Operating Characteristic [ROC] curve.

Figure 3

Logical relationship of the 30 top mRMR metabolites. Each sphere contains the 30 top mRMR metabolites by outcome. The overlaps between the spheres represents the intersection of common top mRMR metabolites. The metabolites appearing in red have been previously reported to be associated with IBD at the Human Metabolome Database [HMD]. mRMR, maximum relevance minimum redundancy; IBD, inflammatory bowel disease. The Venny (Venny 2.1.0 [csic.es ]) online tool was used to generate the Venn Diagram.

Figure 4

Importance of metabolites determined by the different prediction models. Top ranking metabolites are expressed with their relative importance for [A] Pediatric Inflammatory Crohn Magnetic Resonance Enterography Index [PICMI], [B] simple endoscopic score [SES-CD], [C] C-reactive protein [CRP], and [D] faecal calprotectin [FCP]. The differences between the classes were tested using Mann–Whitney U test; *p < 0.05; **p < 0.01.

Figure 5

Metabolic pathway analysis [MetPA] as generated by MetaboAnalyst based on the important metabolites. Matched pathways are displayed as circles. The colour and size of each circle are based on p-value and pathway impact value, respectively. A] MetPA by Pediatric Inflammatory Crohn Magnetic Resonance Enterography Index [PICMI] metabolites. B] MetPA by simple endoscopic score [SES-CD] metabolites. C] MetPA by C-reactive protein [CRP] metabolites. D] MetPA by faecal calprotectin [FCP] metabolites. Pathway analysis as generated by MetaboAnalyst web-based platform (MetaboAnalyst).

Figure 6

Embedded projections demonstrate a zone of improvement between baseline and follow-up visit. Metabolomic profiles given by [A] Pediatric Inflammatory Crohn Magnetic Resonance Enterography Index [PICMI], [B] C-reactive protein [CRP], and [C] faecal calprotectin [FCP] classes.

Figure 7

Variable of Importance [VIP] scatter score plots depicting the most significant metabolites [VIP > 1.0] that explain the metabolite composition in the improvement group. Metabolomic composition given by [A] Pediatric Inflammatory Crohn Magnetic Resonance Enterography Index [PICMI], [B] C-reactive protein [CRP], and [C] faecal calprotectin [FCP] classes. The relative abundance of metabolites is indicated by a coloured scale from blue to red representing the low and high, respectively. VIP score calculated using MetaboAnalyst web-based platform (MetaboAnalyst).