bluuebunny/crossref_metadata_2025_split huggingface dataset:
P031 Microbiota-driven appendiceal B lymphocytes aggravate DSS-induced murine colitis through facilitating colonic CD4+ T cells polarization
Authors: Zhang Y , Xu J , Liu Y , Ke Z , Fang X , Zhang Y , Liu Y 
Published: January 2024

Abstract

Background
The appendix is an immunological organ sustaining a microbiome inoculum that plays a vital role in intestinal mucosal immunity and colonic microbiome stability. Previous studies have proposed the appendix exerts effects on ulcerative colitis (UC)’s pathogenesis, but the nature and basis underlying this connection remain unclear. B lymphocytes account for the largest proportion of appendiceal immunocytes and activate in the experimental colitis model, we systematically investigated how appendiceal B lymphocytes (appB) participate in UC’s pathogenesis and provided rational evidence for appendectomy and B cell immunotherapy being used in UC treatments.

Methods
The chronic colitis model was established in C57BL/6J mice by three cycles of 2% dextran sodium sulfate (DSS) treatment. Bulk RNA sequencing and 16S rRNA sequencing were used to explore appB’s characteristics and the potential causes of appB activation in DSS-induced colitis. Adoptive appB transfer and intravital imaging were used to evaluate appB’s homing and functional features in DSS-induced chronic colitis. Magnetic microbead-based cell sorting and cells experiments in vitro were used to investigate the underlying mechanisms of appB’s activation and effects on DSS-induced chronic colitis. Flow cytometry was used to assess the colonic mucosal adaptive immunity alterations in colitis mice adopted appB.

Results
Firmicutes and Bacteroidetes are the dominant phylum in the normal appendix, while Firmicutes, Verrucomicrobia, and Proteobacteria are prominent in the colitis appendix. The appendiceal IgG+ B cells expended in colitis mice compared with the normal mice; and the DSS colitis appB (DSS_appB), compared with the normal control appB (NC_appB), had much more potential to migrate to the colon and fired the gut flare, accompanied by the increment of CD19+ IgG+ cells, CD4+ IFN-γ+ cells and CD4+ IL-17+ cells in the colonic lamina propria in colitis mice. In vitro, DSS_appB secreted more inflammatory cytokines (IFN-γ, IL-6) than NC_appB under the stimulation of Toll-like receptor agonist analogs (Pam3CSK4, LPS, and ODN1826); DSS_appB facilitated colonic CD4+ T cells to secrete IFN-γ and IL-17 by up-regulating surface marker (CD80/86) and secreting IFN-γ and IL-6.

Conclusion
In DSS-induced chronic colitis mice, appB activated, driven by appendiceal microbiota,migrated to the colonic lamina propria and aggravated colitis through facilitating CD4+ Tcells polarize to Th1 and Th17 by up-regulating CD80/86 and secreting IFN-γ and IL-6 (Figure 1). Our research provides evidence for the connection between the appendix and UC, and we propose that appendectomy or B cell immunotherapy is promising to treat UC.
P034 Peripheral immune cell activity and biopsy gene expression in chronic pouchitis patients treated with tofacitinib: early induction results from the STOPit trial
Authors: Davies J , Amiss A , Khoo E , An Y K , Begun J 
Published: January 2024

Abstract

Background
The Study of TOfacitinib for the treatment of chronic PouchITis (STOPit) is an investigator-initiated, open-label induction, double-blind, placebo-controlled, maintenance withdrawal study to determine the effectiveness of tofacitinib at inducing and maintaining remission in patients with chronic pouchitis. In this interim assessment, we evaluated blood samples and biopsy gene expression collected during the open-label induction period to discover biomarkers of initial clinical response.

Methods
We collected blood (n = 10 pairs, n = 5 non-responders) and biopsies (n = 21 pairs, n = 9 non-responders) at baseline and after 8 weeks of tofacitinib induction therapy (all participants received 10 mg twice daily induction). We classified patients as responders if they achieved a decrease of ≥ 2 in their modified pouchitis disease activity index after 8 weeks. Bulk peripheral blood mononuclear cells (PBMCs) and memory CD4+ T cells (TMEMs) were isolated from whole blood samples. Cytokines induced by stimulation in the presence or absence of tofacitinib were assessed in culture supernatants by bead array (PBMCs stimulated with PMA/Io or LPS, TMEMs stimulated with CD3/CD28 tetramer). Gene expression was measured in biopsies by qPCR in the pouch and pre-pouch ileum at both time points.

Results
At baseline, non-responders produced more IL-17 from both their PBMCs stimulated with PMA/Io and TMEMs stimulated with tetramer than responders, but responders secreted more IL-12p70, MCP, IL-10 and IL-8. Tofacitinib inhibited stimulation-induced IL-10 and IL-6 secretion in PBMCs in both responders and non-responders but failed to reduce IFNγ and TNF secretion selectively in non-responders only. All cytokine responses investigated in TMEMs, including IFNγ and TNF, were inhibited by tofacitinib in both responders and non-responders, suggesting the PBMC cell type refractory to inhibition with tofacitinib in non-responders is not TMEMs. Baseline biopsy ileal gene expression of IL18, HES1 and CXCL10 was decreased in responders compared to non-responders, while MMP7 was increased. Clinical response to tofacitinib led to a reduction in pouch expression of GLIS3, G0S2 and WNT5a from baseline to week 8 whereas these genes were unchanged or increased in non-responders.

Conclusion
Baseline functional immune cell responses and biopsy gene expression may discriminate chronic pouchitis patients' response to tofacitinib therapy and point to a mechanism underlying non-responsiveness. Recruitment for this trial is ongoing, allowing us to bolster and expand our findings with increasing sample sizes.
P050 Paneth cell retinoid X receptor alpha drives metabolic gut inflammation
Authors: Meyer M , Grabherr F , Plattner C , Rieder D , Marteau V , Schwärzler J , Mayr L , Enrich B , Hilbe R , Jukic A , Grander C , Zollner A , Trajanoski Z , Tilg H , Adolph T E 
Published: January 2024

Abstract

Background
The rising incidence of inflammatory bowel diseases throughout the western world could be partially explained by changes in dietary behaviour such as an increased consumption of polyunsaturated fatty acids (PUFA). In previous projects we demonstrated that PUFA induce a Crohn’s disease (CD) like gut inflammation in mice lacking antioxidant GPX4 in their intestinal epithelial cells. Cellular stress within Paneth cells has been shown to drive enteritis in mice. In this project we investigated the role of the PUFA receptor and transcription factor RXRα as driver of PUFA induced metabolic gut inflammation.

Methods
We generated mice lacking GPX4 (GPX4ΔPC) and GPX4 as well as RXRα (GPX4/RXRαΔPC) specifically in Paneth cells and fed them and littermate controls a Western-style diet enriched with PUFA (PUFA-WD). Mice were treated with 9-cis retinoic acid, HX531 or a neutralizing CXCL1 antibody. MODE-K cells (murine IECs) were stimulated with PUFA and were analysed by biochemical methods including ELISA, qPCR, ChIP and RNA sequencing for mechanistical workup in vitro.

Results
When stimulated with PUFA, GPX4 deficient IECs showed an increased activation of RXRα as well as an increased transcription and production of neutrophil attracting chemokine CXCL1, the murine homologue of IL-8. This could be attenuated by ablation of RXRα or treatment with HX531, an RXRα antagonist. By using ChIP we can demonstrate that RXRα is directly binding to the promoter region of CXCL1 upon PUFA stimulation, thereby regulating its transcription. GPX4ΔPC mice develop a CD like enteritis with mucosal to submucosal infiltration of neutrophils, macrophages, B and T cells. GPX4/RXRαΔPC mice were protected from PUFA induced enteritis and gut inflammation could be significantly ameliorated by treatment of GPX4ΔPC mice with RXRα antagonist HX531 or a neutralizing CXCL1 antibody after a PUFA-WD challenge. Moreover 9-cis retinoic acid treatment dose dependently blunted CXCL1 response and attenuated PUFA induced intestinal inflammation in GPX4ΔPC mice, thus indicating a competitive binding of PUFA to RXRα.

Conclusion
Our findings reveal, that PUFA binding to RXRα within Paneth cells regulates the transcription of cytokines and is crucially involved in the development of diet induced metabolic gut inflammation. Future studies are now warranted to prove if RXRα could be a promising new druggable target in human CD patients.
P054 R. intestinalis improves inflammatory bowel disease by preventing gut uric acid absorption through inhibiting METTL3 mediated m6A modification of SLC2A9
Authors: Nie K 
Published: January 2024

Abstract

Background
Inflammatory bowel disease (IBD) is a chronic inflammatory disease with persistent, recurrent, unsatisfactory response, and a poor prognosis. The incidence of Chinese IBD has increased rapidly, and Westernized diets such as purine-rich foods play an important role in its rapid growth. The alteration of purine-urate metabolism by microbiota may contribute to the development of IBD.

Methods
In this study, metagenomic and metabolomic analyses were performed on fecal samples from 30 untreated IBD patients and 30 healthy controls. R. intestinalis was used to observe the effect on serum uric acid levels in mice, respectively. Body weight, colon length, disease activity score, serum uric acid levels, and electron microscopy were all assessed. The RNAseq analysis of intestinal tissue from DSS-induced colitis mice intervened with R. intestinalis and co-cultured with R. intestinalis and the normal intestinal epithelial cell line NCM460, combined with m6A antibody dot blot assay, RM2Target database, and MeRIP sequencing data analysis, provided evidence that SLC2A9 was modified by METTL3, and SRAMP database predicted the potential for SLC2A9 mRNA to be modified by m6A after R. intestinalis intervention.

Results
Multi-omics analysis revealed that the abundance of R. intestinalis was significantly decreased in untreated IBD patients, and metabolomics revealed a correlation between high uric acid levels and disease severity, while the multi-omics integrated analysis suggested a significant negative correlation between R. intestinalis and uric acid. The research team confirmed that R. intestinalis can lower blood uric acid levels in mice and found that R. intestinalis intervention can alleviate the intestinal mucosal inflammation exacerbated by uric acid treatment in a DSS-induced mouse colitis model. Butyric acid has been reported to regulate m6A, and dot blot assays showed that R. intestinalis can reduce the m6A modification level of intestinal epithelial cells, METTL3, and SLC2A9. RM2Target database identified the protein-RNA interaction of the m6A regulator (WER) for SLC2A9 mRNA, and MeRIP sequencing data further indicated that METTL3 can bind to SLC2A9 mRNA through m6A modification. Meanwhile, based on sequence prediction, the research team identified 13 potential m6A modification sites on SLC2A9 mRNA, of which 4 sites had extremely high credibility . The highest credibility site had a score of 0.694, with a modification site sequence of GGACU located on an adenosine nucleotide.

Conclusion
R. intestinalis inhibit the METTL3 mediated m6A modification of intestinal epithelial SLC2A9, reducing the expression of SLC2A9, preventing the epithelial absorption of uric acid, and relieving IBD-related colitis
P060 Increased metabolic activity of faecal Sutterella Wadsworthensis at IBD onset is associated with an increased risk of escalation to biologic therapies - Results from the Birimingham Inception Cohort Study
Authors: Rimmer P , Cheesbrough J , Horniblow R , Tull S , Sharma N , Cooney R , Beggs A , Regan-Komito D , Iqbal A , Iqbal T , Quraishi M N 
Published: January 2024

Abstract

Background
Gut microbiome disruption is an established characteristic of IBD. The lack of treatment naïve longitudinal microbiome data makes it challenging to separate the influence of potential confounders. We present detailed stool metagenomics analysis from a treatment naïve cohort of IBD patients seen in our rapid-access IBD inception clinic.

Methods
Stool collected in DNA Genotek OM-200 kits was collected pre-diagnosis, alongside a faecal calprotectin (FCP). Microbial DNA was extracted. Libraries were prepared using NEBNext Ultra II FS DNA Library Prep Kit, NEBNext Multiplex Oligos and sequenced using an Illumina NextSeq550. Data processing was undertaken using the HUMAnN 3.0 workflow. After quality control, a median of 3.6 million reads per sample were obtained. Abundance was mapped to the ChocoPhlAn database and functional pathways derived from MetaCyc. Diversity analysis was undertaken in Vegan, with MaAsLin2 for taxa differences. A False discovery Rate (FDR) &lt;0.2 was considered relevant, &lt;0.05 highly significant.

Results
A total of 45 CD and 33 UC inception patients were included. There was no significant difference in alpha diversity (Shannon; UC median 2.58[IQR 0.8], CD 2.69[1.04] p=0.36) or differential clustering for beta diversity. Shannon alpha diversity significantly associated with FCP across IBD (n=74, Spearman’s Rho [SR] -0.33 p=0.004) and endoscopic severity in both IBD subtypes (UCEIS n=30 SR -0.37 p=0.047, SESCD n=44 SR -0.35 p=0.016). Across IBD, patients going on to require biologic therapy had a significantly lower baseline Shannon (BioYes 2.26[0.98], BioNo 2.77[0.88] p=0.02, split by IBD subtype in Figure 1).
Across IBD, increased FCP associated with depletion of two strains of Faecalibacterium Prausnitzii (SGB15318, log2 fold change[L2FC] -1.2 FDR 0.09; SGB15342 L2FC -1.1 FDR 0.15) alongside Roseburia Intestinalis (SGB4951 L2FC -0.7 FDR 0.09). R.Intestinalis also negatively correlated with Harvey Bradshaw Index (L2FC -0.93 FDR 0.02), whilst F.Prausnitzii (SGB15342) did with UCEIS (L2FC -2.3 FDR 0.05).
82 metabolic pathways correlated with UCEIS (FDR &lt;0.2, 8 &lt;0.05), with 89 for SESCD (6 &lt;0.05). Increased activity of Sutterella Wadsworthensis associated positively with UCEIS (5 pathways). On initial comparison across IBD, no significant signal was seen for future biologic utilisation. However, if analyses were corrected for baseline inflammation (derived by FCP), increased activity of S.Wadsworthensis was again seen (Table 1).

Conclusion
Reduced alpha diversity at IBD onset associated with increased disease severity and future utilisation of biologic treatment. Increased activity of S.Wadsworthensis associated with an increased risk of future biologic requirement above that explained by mucosal inflammation alone.
P065 The evolution of inflammatory bowel disease can be monitored through multi-omics characterization of gut tissues
Authors: Tout I , Toufiq M , Missous G N , Chin-Smith E , Mathew R , Tomei S , Ibrahim N , Abunahia N S , Mifsud W , Charles A , Ammar A , Al Kaabi S , Van Panhuys N , Al-Mohannadi M J , Mamoun E , Maccalli C 
Published: January 2024

Abstract

Background
The aim of the study is to dissect the mechanisms associated with the evolution of Inflammatory Bowel Disease (IBD), including Crohn’s Disease (CD) and Ulcerative Colitis (UC) in both pediatric and adult patients, along with the severity of the disease and the risk to develop malignancy.

Methods
A multiomics approach, including miRNA (N=700), gene expression (N=800 genes) (nCounter platform; Nanostring) and methylation (Infinium Methylation Epic Bead Chip kit, Illumina), was utilized to characterize the gut tissue biopsies from pediatric (N=20) and adult (N=18) IBD patients. Moreover, a cohort of patients with gut malignancies with history of IBD were also enrolled in the study. Additionally, the role of Natural Killer Group 2D ligands (NKG2DLs) along with different stages of IBD (remission, mild, moderate and severe) were investigated.

Results
Differential miRNA and gene signatures were found by the comparison of tissues from pediatric and adult patients with different stages of the disease. N=83 miRs were significantly differentially detected between pediatric and adult patients (P&lt;0.05). miR-630, miR-493-3p and miR-370-3p were found over-expressed in adult vs. pediatric gut tissues. These miRs are involved in epithelial-to-mesenchymal transition (EMT) through the WNT/β-catenin pathway. These miRNAs can also regulate cell proliferation, cell adhesion and migration and cancer development. Interestingly, miR-20a and miR-34a, which are known modulators of NKG2DLs expression were upregulated in tissues from severe vs. mild disease. The gene expression analysis highlighted, among multiple differentially detected pathways in tissues with different grades of IBD, genes, such as SMAD4, EGR1, CHUCK and JAG1, associated with inflammation, stemness, immune regulation, cell proliferation and migration. Through qPCR analyses, the higher expression of the NKG2DLs MICB was detected in tissues from left or right sides, respectively for both pediatric and adult patients while similar observation occurred for MICA only in adult patients. Soluble NKG2DLs were also detected in the plasma of IBD patients, with in some cases differences (P&lt;0.05) in patients vs. healthy donors. sULBP3 correlated with the presence of active inflammation in adult IBD tissues. Confocal imaging of IBD tissues showed upregulation of stemness-associated markers (e.g., LGR5) and NKG2DLs (ULBP-1 and ULBP-3) in adult vs. pediatric patients.

Conclusion
The ongoing integration of data from multi-omics and the expression of immune-related molecules can lead to the identification of candidate molecular mechanisms associated with the evolution of IBD.
P069 Ultra-processed food intake and dietary insufficiencies are common in adults with Crohn’s Disease in remission. The INTICO 2 Study
Authors: Westoby C , Katarachia V , McDonnell M , Sartain S , Cummings F , Wootton S 
Published: January 2024

Abstract

Background
Adults with Crohn’s Disease (CD) may have dietary restrictions and micronutrient inadequacies. Consumption of ultra processed foods (UPF) has been associated with an increased need for IBD-related surgery and is a growing area of research. This study aimed to investigate the habitual diet of adults with CD during disease remission to understand the nutritional adequacy, diet diversity and diet quality.

Methods
196 adult CD outpatients in remission (Harvey Bradshaw Index &lt;5 and calprotectin &lt;250µg) were recruited from a single UK IBD centre outpatients as part of the INTICO 2 observational study. Seven-day food diaries were electronically recorded using Nutritics® (Libro) software. UPF intake was determined using NOVA Score . Data cleaning was undertaken by a dietitian prior to analysis to identify input errors. NOVA Score1 criteria was utilised to determine UPF intake. Product ingredient lists were examined using supermarket websites and ‘Open food Facts’ by two research dietitians to assign a NOVA score. Consensus on NOVA Scoring was achieved, and a data dictionary was prospectively updated to justify the assigned score.

Results
97% (189/195) of those who underwent food diary analysis had at least one micronutrient below the LNRI. The intake was below the LNRI for a mean of 6 (SD 4.2) micronutrients per subject. The number of subjects who failed to meet the LNRI from diet (with and without inclusion of usual supplements) is listed for each micronutrient in table 1. Of note, 93% (181/195) of subjects failed to meet the SACN recommended 30g of fibre per day (median intake 17.7g). 33% of dietary intake was classified as UPF (Nova 4) and 13% processed (NOVA 3).

Conclusion
Both micronutrient insufficiencies and UPF intake are common in a CD remission population and should be considered alongside one another in studies of dietary intake. UPF intake should be interpreted with caution as NOVA does not account for nutritional content. Blanket recommendations to avoid UPFs need to be carefully considered within this already nutritionally vulnerable population as avoidance of UPF products such as fortified cereals or oral nutritional supplements could lead to increased dietary inadequacies.
References:
Monteiro, C.A. et al, P. 2019. Ultra-processed foods, diet quality, and health using the NOVA classification system. Rome, FAO.
P078 Inflammatory transcriptomic signatures and cell type compositions in colonic mucosa of ulcerative colitis
Authors: Song E M , Jung S A , Joo Y H , Moon C M , Kim J 
Published: January 2024

Abstract

Background
Previous studies have explored transcriptomic profiles associated with active inflammation in patients with IBD patients, but consistent characteristics of gene expression and enriched pathways, particularly in Asian patients with UC, remain unconfirmed. Here, we aimed to assess distinctive transcriptomic changes associated with persistent active mucosal inflammation in Asian patients with UC despite of medical treatment.

Methods
We obtained colonic mucosa biopsies of inflamed and noninflamed tissue from 15 patients with UC and 15 healthy controls and performed RNA sequencing analysis. Utilizing publicly available single cell RNA sequencing (scRNAseq) data, we also identified cell types expressing differentially expressed genes from RNAseq data and performed data deconvolution using CIBERSORTx.

Results
Transcriptomics profiling revealed that the inflammatory transcriptomic signature was highly enriched in the colonic mucosa of UC-active compared to UC-inactive and controls. By incorporating scRNAseq data, the genes upregulated in UC-active were highly expressed in M cells, inflammatory monocytes, and inflammatory fibroblasts, while downregulated genes were prominent in BEST4+ enterocytes and WNT5B+ fibroblasts. Notably, a sub-cluster of enterocytes associated with SAA1, SLC6A14, and DUOXA2 genes exhibited high expression in UC-active. Deconvolution analysis using CIBERSORTx identified significant enrichment of natural killer cells, inflammatory monocytes, Tuft cells, inflammatory fibroblast, WNT2B+Fos-lo1, and pericytes in UC-active.

Conclusion
Our RNAseq analysis not only identified significant gene expression changes but also revealed shifts in cell type proportions associated with persistent inflammation. These findings offer valuable insights for developing novel treatment strategies for UC.