Introduction

Women with IBD have an increased risk of preterm and cesarian delivery and low birth weight infants. Although IBD pathogenesis has been associated with different factors including genetics and dysbiosis in gut microbiome, very little is known about the relationship between IBD, microbiota, and pregnancy. Mutations in the ATG16L1 gene have been associated with Crohn’s disease susceptibility, impaired autophagy, and Paneth cell defect. Here, we explored the gut microbiome composition and functional potential of Atg16l1 knockout (KO, Atg16l1^∆IEC) restricted to intestinal epithelial cells (IEC) and their floxed littermates (WT, Atg16l1^fl/fl) mice during pregnancy.

Aims & Methods

Fecal samples of pregnant mice were collected during trimester three (just before delivery) and after weaning and the isolated DNAs were subjected to 16S rRNA amplicon sequencing and shotgun metagenomics sequencing. 16S data were pre-processed, quality filtered, trimmed, and denoised on established pipelines inside QIIME2. Shotgun reads were processed using an in-house established workflow from our institute that relies on BBtools and bowtie2 for mapping and host decontamination, and bioBakery tools for taxonomic and functional assignments. Taxonomic profiles were assigned by classifying all ASVs on the SILVA 138 rRNA reference database and clade-specific marker genes from MetaPhlAn4. Functional potential profiling (stratified pathways, gene families, and enzyme categories) in the metagenomics samples were captured using HUMAnN 3.6. Longitudinal and pair-wise differences were evaluated using the R package MaAslin2.

Results

Pregnancy resulted in a temporal shift in microbial composition between WT and KO pregnant mice at trimester 3 with partial recovery of microbial composition after the weaning period (b-diversity). Likewise, we observed longitudinal alterations in relative abundances of some IBD-specific microbiota biomarkers genera such as Lachnospiraceae, Roseburia, Ruminococcus, Colidextribacter and Turicibacter. In addition, we found that the gut microbiota of Atg16l1^∆IEC mice has increased potential to synthesize fatty acids, glutamine, and branched-chain amino acids.

Conclusion

Late stages of pregnancy induce changes in gut microbiota composition and metabolic potential in mice lacking Atg16l1 specifically in the intestinal epithelium (Atg16l1^∆IEC) compared to WT (Atg16l1^fl/fl) mice. Understanding these pregnancy-dependent microbiome changes may constitute the first steps in the identification of bacteria-specific biomarkers that could help maintaining a healthy and successful pregnancy in IBD patients.

Introduction

The gut microbiota plays a crucial role in the pathogenesis and progression of Crohn’s Disease (CD) by maintaining intestinal homeostasis, supporting metabolic and immune functions, and influencing overall health. An imbalance in the gut microbiota is associated with CD, as disruptions in microbial composition can be further impacted by dietary factors, highlighting the connection between nutrition and gut health.

Aims & Methods

This study aimed to evaluate the gut microbiota composition and its interactions with dietary factors to identify potential opportunities for targeted probiotic interventions in CD management. The study included 53 participants, of whom 20 had CD in remission, 18 had active disease, and 15 were healthy controls. CD activity was evaluated by colonoscopy assessment or by nuclear magnetic resonance scan enterography. All participants aged between 18 and 60 years were assessed using 24-hour dietary recall and gut microbiome profiling through 16S rRNA gene sequencing. Patients had confirmed diagnoses of CD with ileal and/or colonic involvement. The local ethics committee approved this study.

Results

Microbial composition analyses (beta diversity) revealed significant differences between groups. At the Operational Taxonomic Unit (OTU) level, healthy microbiome differed significantly from both remission and active CD patients, with healthy controls showing a more similar microbial composition compared to remission (p = 0.001) and active disease (p = 0.001). In addition, Shannon diversity analyses demonstrated that healthy individuals exhibited significantly higher OTU diversity compared to CD patients, further highlighting the microbial imbalance associated with the disease. Among specific taxa, Eubacterium hallii, a key butyrate producer, was significantly reduced in patients with active CD. This microorganism is integral to intestinal metabolic balance, playing essential roles in energy homeostasis, colonic motility, immunomodulation, and inflammation suppression. Furthermore, E. hallii plays a critical role in bile acid and cholesterol metabolism, highlighting its importance in gut health. Disease severity was associated with changes in microbial abundance, with specific taxa colonizing the gut at higher levels as disease activity increased, including Escherichia coli, Escherichia-Shigella, and taxa from the Enterobacteriaceae, Lachnospirales, and Bacteroides. This growth may be linked to inflammatory processes and intestinal dysbiosis, suggesting a potentially pathogenic role. Furthermore, dietary components such as saccharin, an artificial sweetener, were significantly associated with alterations in microbial composition.

Conclusion

These findings underline the potential for probiotics targeting specific taxa, such as E. hallii, to restore microbial balance and improve clinical outcomes in CD. The study also highlights the impact of dietary components, such as saccharin, in disrupting the gut microbiome, suggesting that certain dietary factors may contribute to microbial imbalance and inflammation in CD. Future research should focus on integrating dietary patterns with probiotic development to optimize gut health and mitigate inflammation in CD patients.

References

1. BOLTE, L. A. et al. Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome. Gut, p. gutjnl-2020-322670, 2 abr. 2021.
2. FAN, Y.; PEDERSEN, O. Gut microbiota in human metabolic health and disease. Nature Reviews Microbiology, v. 19, n. 1, p. 55–71, 4 jan. 2021.
3. GILL, P. A. et al. The Role of Diet and Gut Microbiota in Regulating Gastrointestinal and Inflammatory Disease. Frontiers in Immunology, v. 13, n. April, p. 1–22, 5 abr. 2022.

Clinical Case Summary

The management of Crohn’s Disease (CD) during pregnancy presents significant challenges. Active CD can be treated with corticosteroids (CS) or tumour necrosis factor-alpha (TNF-α) inhibitors (1). While these treatments are generally considered safe during pregnancy, they are not without potential side effects, leading to patient hesitancy in initiating therapy despite guidance from Inflammatory Bowel Disease (IBD) specialists (2).
We present the case of a 34-year-old woman, recently diagnosed with CD who opted not to use medication during her pregnancy. For the initial 26 to 28 weeks, she received conservative treatment. Following a deterioration in her symptoms and an increase in calprotectin levels, she commenced the Crohn’s Disease Exclusion Diet (CDED) combined with partial enteral nutrition (PEN). This resulted in significant symptomatic improvement and a decrease in faecal calprotectin levels. At 40 weeks of gestation, she delivered a healthy baby.
This case underscores the potential efficacy of CDED and PEN as dietary management strategies for CD during pregnancy, although further research is warranted to compare these approaches with conventional treatments. Additionally, it emphasises the critical role of preconception counselling regarding medication safety and effective disease management during pregnancy.

References

No references of illustrative material (endoscopic, radiological and pathological images, innovative physiological or other research data)

Introduction

Ozanimod is an oral sphingosine 1-phosphate (S1P) receptor 1 and 5 modulator approved in multiple countries for the treatment of adults with moderately to severely active ulcerative colitis (UC) and relapsing multiple sclerosis (RMS). Ozanimod is also being studied in the treatment of Crohn’s disease (CD). S1P receptors are involved in vascular formation during embryogenesis, and prescribing information for S1P receptor modulators, such as ozanimod, contain recommendations for effective contraception use as well as general statements about potential fetal risk based on data from preclinical studies.

Aims & Methods

The objective of this analysis was to review pregnancy outcomes during ozanimod use in the clinical development program in all studies in which patients with UC, CD, or RMS or healthy volunteers received ozanimod. Within studies in the ozanimod clinical development program, female patients of childbearing potential were required to use effective contraception while receiving ozanimod and for up to 3 months after discontinuing the drug; treatment discontinuation was required when pregnancy was confirmed. Pregnancy outcomes in the ozanimod clinical development program were assessed through November 19, 2022.

Results

In ozanimod clinical trials, 78 patient pregnancies occurred: 14 in those with UC, 6 in those with CD, 57 in those with RMS (there were 58 outcomes due to twins), and 1 in a healthy volunteer (Table). All patient pregnancy exposures to ozanimod occurred during the first trimester. Patients discontinued study medication promptly after pregnancy was confirmed, except for those who elected pregnancy termination and remained on study medication. The incidence of spontaneous abortion in clinical trial patients was 15%. The preterm birth rate was 10% of all live births. Outcomes in patients with UC included 7 live births (no congenital abnormalities or premature births), 3 spontaneous early losses, and 4 elective terminations (Table). No teratogenicity was observed in patients with ozanimod exposure during early pregnancy.

Pregnancy outcomes during the ozanimod clinical development program by patient population

Conclusion

Pregnancy should be avoided in patients receiving ozanimod and for 3 months after discontinuing ozanimod. Clinical experience with ozanimod during pregnancy is limited. In this small cohort of patients, there has been no increased incidence of fetal abnormalities or adverse pregnancy outcomes seen with ozanimod exposure in early pregnancy.

Disclosure

MCD: consultant for Arena, AbbVie, Bristol Myers Squibb, Celgene, Genentech, Janssen, Pfizer, Prometheus Labs, and Takeda.
LC and AK: employees and/or shareholders of Bristol Myers Squibb.
KWS: consultant for Biogen, Celgene, Genzyme, Merck, Novartis, Ono Pharma, Roche, Synthon, and Teva.
GC: received compensation for consulting and/or speaking activities from Almirall, Biogen, Celgene, EXCEMED, Forward Pharma, Genzyme, Merck, Novartis, Roche, Sanofi, and Teva.
CJVDW: received grants and or fees for advisory boards and presentations from AbbVie, Celltrion, Dr. Falk Pharma Benelux, Ferring, Janssen, Pfizer, and Takeda.
UM: consultant for AbbVie, Boehringer Ingelheim, Bristol Myers Squibb, Eli Lilly, Gilead, Janssen, Pfizer, Prometheus Biosciences, Protagonist Therapeutics, and Takeda.
This study was sponsored and funded by Bristol Myers Squibb.

Introduction

Inflammatory Bowel Disease (IBD), including Crohn’s Disease (CD), is characterized by chronic intestinal inflammation and complex host-microbiome interactions. In advanced cases of inflammation in CD patients, the terminal ileum is commonly affected, often becoming obstructed and requiring surgical removal. Approximately 70% of CD patients undergo surgical intervention, and inflammation frequently recurs even after ileocecal resection. Unfortunately, it is still unclear why recurrence happens in some patients and not in others. Increasing evidence suggests that the gut microbiome may play a crucial role in modulating inflammation and influencing disease course, yet spatial insights into host-microbe interactions in CD-affected ileum remain limited.

Aims & Methods

This project aims to spatially characterize the host and microbial transcriptomes in the terminal ileum of CD patients in remission versus recurrence following ileocecal resection, and to explore how human cell responses to host-microbiome interactions may relate to therapeutic outcomes. We collected 24 FFPE ileum samples from CD patients post-resection, including 8 remission and 16 recurrence cases. Spatial transcriptomics was performed using the 10x Genomics Xenium platform with the human colon pre-designed panel (322 genes) and a custom add-on of 100 genes. The custom panel included markers for ileum-specific cell types (32 genes), barrier function (8 genes), redox response (19 genes), and inflammation (30 genes). Additionally, we designed 11 custom bacterial probes in collaboration with 10x Genomics to enable the detection of microbial transcripts.

Results

We successfully performed spatial transcriptomic preprocessing on all 24 samples, with each yielding approximately 200,000–300,000 cells. Samples were annotated using the cell2location pipeline, and we were able to successfully identify the major cell type categories (Epithelial, Mesenchymal, Myeloid, Neuronal, Plasma Cells, Red blood cells, and T cells). The custom bacterial probes enabled detection of microbial transcripts, which were predominantly localized around the lumen and were clearly distinguishable from human tissue regions. Furthermore, we observed differences in bacterial transcript abundance across samples, which could help explain the diversified clinical outcome.

Conclusion

This preliminary analysis demonstrates the feasibility of spatially profiling host and microbial transcripts in FFPE ileum samples from CD patients. Our findings support future investigations into how host-microbiome interactions may be associated with CD progression and recurrence.