Association between ustekinumab therapy and changes in specific anti-microbial response, serum biomarkers, and microbiota composition in patients with IBD: A pilot study

Abstract

Background: Ustekinumab, is a new therapy for patients with IBD, especially for patients suffering from Crohn's disease (CD) who did not respond to anti-TNF treatment. To shed light on the longitudinal effect of ustekinumab on the immune system, we investigated the effect on skin and gut microbiota composition, specific immune response to commensals, and various serum biomarkers.

Methodology/principal findings: We recruited 11 patients with IBD who were monitored over 40 weeks of ustekinumab therapy and 39 healthy controls (HC). We found differences in the concentrations of serum levels of osteoprotegerin, TGF-β1, IL-33, and serum IgM antibodies against Lactobacillus plantarum between patients with IBD and HC. The levels of these biomarkers did not change in response to ustekinumab treatment or with disease improvement during the 40 weeks of observation. Additionally, we identified differences in stool abundance of uncultured Subdoligranulum, Faecalibacterium, and Bacteroides between patients with IBD and HC.

Conclusion/significance: In this preliminary study, we provide a unique overview of the longitudinal monitoring of fecal and skin microbial profiles as well as various serum biomarkers and humoral and cellular response to gut commensals in a small cohort of patients with IBD on ustekinumab therapy.

Fig 1. PCA of biomarker concentrations in healthy controls and patients with IBD sampled during ustekinumab treatment.

Each dot represents an individual at a specific time point. A) Sample clustering along the first two PCA axes. B) Contribution of each biomarker to the sample ordination (blue arrows).

Fig 2. Abundance variation of biomarkers exhibiting differential expression between patients with IBD (blue) and healthy controls (red) during ustekinumab treatment.

Four biomarkers identified by linear mixed effect model-based differential abundance analysis. Statistical details can be found in S3 Table. A) Serum anti-Lactobacillus plantarum IgM levels. B) Serum levels of TGF-β1, osteoprotegerin, and IL-33.

Fig 3. Alpha diversity variation in the stool microbiome of healthy controls and patients with Crohn’s disease and ulcerative colitis during ustekinumab treatment.

The line charts show changes in disease activity scores, Shannon entropy, Chao1 diversity estimator, number of observed ASVs and Faith’s phylogenetic diversity over time for patients with Crohn’s disease, ulcerative colitis, and healthy controls. Each line represents one individual, the bold lines represent locally weighted regression with a confidence interval fill. (HBI) Harvey-Bradshaw Index, (pMayo) partial Mayo score, (PD) phylogenetic diversity.

Fig 4. Principal coordinate analyses for stool microbiome in patients with IBD on ustekinumab therapy.

Shown are A) bacteriome and B) mycobiome profiles based on different beta diversity dissimilarity measures. Beta diversity dissimilarities include Bray-Curtis, Jaccard, unweighted unique fraction metric and weighted unique fraction metric distances. Phylogenetic dissimilarities are shown only for the bacterial microbiome. UniFrac (unique fraction metric).

Fig 5. Temporal changes in different alpha diversity metrics of the skin microbiome of healthy controls, patients with Crohn’s disease, and patients with ulcerative colitis during 40 weeks of ustekinumab therapy.

The line charts show changes in disease activity scores, Shannon entropy, Chao1 diversity estimator, number of observed ASVs, and Faith’s phylogenetic diversity over time for patients with Crohn’s disease, patients with ulcerative colitis, and healthy controls. Each line represents one individual, the bold lines represent locally weighted regression with a confidence interval fill. (HBI) Harvey-Bradshaw Index, (pMayo) partial Mayo score, (PD) phylogenetic diversity.

Fig 6. Production of IL-17 and TNF-α by circulating microbiota-reactive T cells of patients with IBD on ustekinumab therapy at baseline (week 0) and at week 40.

IL-17 A) and TNF-α B) production by CD3+CD4+ T cells isolated from patients PBMC after stimulation with assorted bacterial lysates, as determined by a paired t-test. *p<0.05, IBD (n = 8), SEB (Staphylococcal enterotoxin B).