Bulk RNA-seq and 16S rRNA profiling of ileal tissues in Crohn's disease surgery
Background and Aims Endoscopic recurrence after ileocecal resection for Crohn's disease remains common, even when resection-flanking ileal tissue appears macroscopically non-inflamed at surgery. We aimed to test whether surgery-time molecular features in resection-flanking tissue are associated with later endoscopic recurrence. Methods Resection-flanking ileal formalin-fixed paraffin-embedded (FFPE) tissue collected at surgery was profiled using matched host transcriptome sequencing and bacterial 16S ribosomal RNA gene amplicon sequencing from the same tissue section. Endoscopic recurrence was assessed at follow-up colonoscopy and classified by the Rutgeerts score. Host transcriptome differences were quantified using gene-expression and pathway-enrichment analyses, supported by gene co-expression networks. Microbial differences were assessed using alpha and beta diversity metrics and genus-level comparisons. Host–microbe links were explored using Spearman rank correlation between host gene co-expression module eigengenes with relative abundances of bacterial genera.  Results Compared with patients without recurrence, patients who later developed endoscopic recurrence showed a consistent, significant, increase in immune and inflammatory gene programs at surgery, including interferon-related responses, tumor necrosis factor (TNF) and nuclear factor kappa B (NF-?B) signalling, interleukin 6 signalling, complement pathways, and other immune signatures. Microbial community structure differed between groups after adjustment for age, sex, and body mass index (BMI). Several genera showed shifts in relative abundance with nominal significance, including Acinetobacter, Christensenellaceae_R-7_group, and Desulfovibrio. Correlations between these genera and recurrence-associated host modules provided exploratory evidence of linked host and microbial changes. Conclusions Matched host and microbial profiling of resection-flanking ileal tissue at surgery indicates that subclinical inflammatory activation and alterations in gut microbiota precede postoperative endoscopic recurrence in Crohn's disease.
Background and Aims Endoscopic recurrence after ileocecal resection for Crohn's disease remains common, even when resection-flanking ileal tissue appears macroscopically non-inflamed at surgery. We aimed to test whether surgery-time molecular features in resection-flanking tissue are associated with later endoscopic recurrence. Methods Resection-flanking ileal formalin-fixed paraffin-embedded (FFPE) tissue collected at surgery was profiled using matched host transcriptome sequencing and bacterial 16S ribosomal RNA gene amplicon sequencing from the same tissue section. Endoscopic recurrence was assessed at follow-up colonoscopy and classified by the Rutgeerts score. Host transcriptome differences were quantified using gene-expression and pathway-enrichment analyses, supported by gene co-expression networks. Microbial differences were assessed using alpha and beta diversity metrics and genus-level comparisons. Host–microbe links were explored using Spearman rank correlation between host gene co-expression module eigengenes with relative abundances of bacterial genera.  Results Compared with patients without recurrence, patients who later developed endoscopic recurrence showed a consistent, significant, increase in immune and inflammatory gene programs at surgery, including interferon-related responses, tumor necrosis factor (TNF) and nuclear factor kappa B (NF-?B) signalling, interleukin 6 signalling, complement pathways, and other immune signatures. Microbial community structure differed between groups after adjustment for age, sex, and body mass index (BMI). Several genera showed shifts in relative abundance with nominal significance, including Acinetobacter, Christensenellaceae_R-7_group, and Desulfovibrio. Correlations between these genera and recurrence-associated host modules provided exploratory evidence of linked host and microbial changes. Conclusions Matched host and microbial profiling of resection-flanking ileal tissue at surgery indicates that subclinical inflammatory activation and alterations in gut microbiota precede postoperative endoscopic recurrence in Crohn's disease.
University Medical Center of Groningen