bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOP28 Aconitate decarboxylase 1 (ACOD1) represents a crucial regulator of monocyte recruitment, survival and proinflammatory status in intestinal inflammation
Authors: Jones G R , Hegarty L , T'Jonck W , Adams C , Drury B , Byrne A , Ho G T , Bain C 
Published: January 2023

Abstract

Background
Aconitate decarboxylase 1 (ACOD1; also known as IRG-1) is the ubiquitous source of itaconate, which dampens inflammasome activation by preventing HIF1a production of IL-1b and prevents TNF production through NRF2 activation. We reasoned that expression of ACOD1 is an inhibitory pathway within monocytes to curtail their inflammatory function, which could be manipulated in IBD therapy.

Methods
We performed single-cell RNA sequencing of monocytes from colonoscopic biopsies of treatment naïve IBD patients, as well as complementary analysis of DSS treated C57BL/6J (WT) mice, using single-cell protein-mRNA (Primeflow) technologies for validation. To determine the role of ACOD1 in colitis, Acod1–/– mice were administered 2% DSS in drinking water for 6 days (acute colitis) or 4 days followed by 14 day recovery period (inflammation resolution) and assessed the colon myeloid compartment by multi-parameter flow cytometry. This was complemented with competitive bone marrow chimeric mice to assess the intrinsic role of ACOD1 controlling monocyte survival and proinflammatory status. Transcriptional profiling (Nanostring) was used to determine the molecular pathways influenced by ACOD1.

Results
We found that ACOD1/Acod1 represented an evolutionarily conserved of feature of inflammation-associated monocytes, with expression present in mucosal but not blood monocytes. Acod1–/– mice demonstrated increased susceptibility to acute intestinal injury with DSS compared to co-housed WT controls, characterised by increased weight loss and colon shortening with significant accumulation of colonic neutrophils and CD64+Ly6C+ MHC-II+/– monocytes. Consistent with Acod1 limiting inflammasome activation, Acod1–/– monocytes demonstrated significantly greater IL-1b producing capabilities than WT controls.
To assess Acod1 deficient and sufficient haemopoietic cells in in the same environment, we generated competitive bone marrow chimeric mice. Acod1 deficiency conferred a significant advantage to monocyte recruitment to the colon, characterised by a 10fold increase in Ly6C+ MHC-II–colon monocytes in colitis.
Transcriptional profiling of WT and Acod1–/– colonic monocytes revealed significantly greater expression of molecules required for monocyte extravasation, including Sell (CD62L), Icam1, Ccr2 and Itgal (CD11a). In addition, expression of genes indicative of macrophage maturation such as Itgax (CD11c), Cd163 and Cx3cr1 were lower in the context of Acod1 deficiency, suggesting that normal maturation of these cells may be perturbed by loss of Acod1.

Conclusion
ACOD1/Acod1 represents an evolutionarily conserved, monocyte specific immuno-metabolic pathway that acts to limit monocyte recruitment, fate and pro-inflammatory function within the inflamed intestine.
DOP33 Single-cell analysis identifies pathological fibroblasts as a new therapeutic target to prevent intestinal fibrosis in Crohn’s disease.
Authors: Ke B J , Abdurahiman S , Biscu F , Verstockt S , Verstockt B , de Hertogh G , Vermeire S , Matteoli G 
Published: January 2023

Abstract

Background
Recurrent episodes of intestinal inflammation and tissue remodeling progressively result in fibro-stenosis and bowel obstruction in Crohn’s disease (CD). This irreversible end-stage complication is the main indication for surgical intervention but is often associated with postoperative recurrence of inflammation and repeated tissue resection.

Methods
To understand transmural inflammation-induced fibro-stenosis, full-thickness ileum from CD patients (n=10) undergoing ileocecal resection were profiled using single-cell RNA sequencing (scRNA seq) on 10x Genomics platform. Our tissue sampling strategy aimed at recapitulating different disease stages from the same patient including normal ileum, chronic active inflammation and stenotic ileum, allowing a better definition of cell heterogeneity, inter-cellular communication, and tissue organization in CD. Healthy ileum from CRC patients (n=5) undergoing right hemicolectomy were included as external control. Flow cytometry (FACS) was carried out to confirm scRNA seq findings. For functional validation, intestinal fibroblasts were co-cultured with NicheNet-predicted cytokines and FACS-sorted myeloid supernatants. Finally, the chronic dextran sulfate sodium (DSS)-induced colitis model was used to validate the transcription regulation in activated fibroblasts.

Results
Using scRNA seq, we identified a specific subset of activated fibroblasts during chronic inflammation and fibrosis. FACS showed increasing FAP+ fibroblasts in both inflamed and stenotic ileum, compared to control ileum and proximal ileum (p&lt;0.01). Computational methods predicting ligand-receptor signaling suggest that fibroblast activation is mostly mediated by myeloid cell-derived inflammatory signals resulting in collagen deposition and tissue fibrosis. Intestinal fibroblasts co-cultured with inflammatory monocyte supernatant and predicted ligands expressed higher protein levels of FAP, COL3A1 and showed signs of EMT transformation. Furthermore, stimulated intestinal fibroblasts secreted higher levels of ECM proteins, including COL1 (p&lt;0.001), and COL3A1 (p&lt;0.005). After inhibiting an EMT-related transcription factor identified in the activated fibroblasts, collagen expression and extracellular matrix accumulation were decreased in fibroblasts. Finally, inhibition of EMT transformation in chronic DSS colitis resulted in reduced ECM deposition, compared to vehicle mouse (p&lt;0.05).

Conclusion
Our findings suggest that inflammatory monocytes mediate local activation of fibroblasts promoting excessive collagen deposition. We furthermore show that targeting activated fibroblasts was able to reduce tissue remodeling and may therefore prevent fibrostenosis in CD.
DOP48 Key Anti-Inflammatory Faecalibacterium prausnitzii is Heterogeneous and Diverse in the East and West and in Health and Crohn’s disease. The ENIGMA study.
Authors: Teh J J , Kang S , Leonard A , Zhang J , Hu J , Hamilton A L , Wilson-O'Brien A , Trakman G L , Lin W , Ching J , Sung J J Y , Yu J , Ng S C , Kamm M A , Morrison M 
Published: January 2023

Abstract

Background
There is insufficient knowledge about the key characteristics of the pathogenic and protective bacteria in inflammatory bowel disease. The ENIGMA study aimed to identify the phylogenetic and functional characteristics of Faecalibacterium prausnitzii, considered a protective “anti-inflammatory” bacterium, in both health and Crohn’s disease in populations in the West (high Crohn’s incidence) and Hong Kong (rapidly increasing Crohn’s incidence).

Methods
Total DNA was extracted from tissue (right colon and terminal ileum) and stool collected from case-control cohorts in Hong Kong (n=51; 30 Crohn’s, 21 controls) and Australia (n=49; 29 Crohn’s, 20 controls). In parallel, the colonic mucosa-associated microbiota (MAM) for each subject was cultured from anaerobically preserved tissue. Shotgun metagenomic sequencing was used to characterise the stool and colonic MAM, augmented with 16S rRNA gene profiling and F. prausnitzii qPCR. The HUMANn3 and/or QIIME2 packages were used for the taxonomic and/or functional characterisation of the datasets. Metagenome-assembled genomes (MAG) were also produced from colonic MAM datasets using the MetaWRAP pipeline, and taxonomy deduced using the Genome Taxonomy Database-Tool kit (GTDB-tk).

Results
F. prausnitzii was detected in all case-control cohorts from Hong Kong and Australia. However, the prevalence was greater for the colonic MAM cultures of the Australian subjects, which provided 24/32 high-quality Faecalibacterium-affiliated MAG. No less than 6 different species-level lineages were predicted by GTDB-tk, and a similar phylogeny predicted using the gene encoding immunomodulatory peptides (mam). Functional features for the MAG from Crohn’s disease and control subjects were compared, and genes involved with histidine, riboflavin, purine and pyrimidine metabolism, pentose phosphate pathway, and oxidoreductases were enriched in the control subject MAG. In contrast, MAG derived from Crohn’s disease subjects possessed more functions putatively assigned to antibiotic resistance mechanisms and other protective functions. Differences were also observed in the carbohydrate-active enzyme profiles of the MAG recovered from Crohn’s disease and control subjects.

Conclusion
The populations of F. prausnitzii recovered from the colonic mucosa associated microbiota are both diverse and vary between Crohn’s disease and control subjects in both countries. The differences include metabolic and physiological characteristics. Therapeutic modification of F. prausnitzii needs to consider phylogenetic and functional characteristics.
The ENIGMA study is supported by a grant from the Leona M. and Harry B. Helmsley Charitable Trust
DOP50 Impact of Inflammatory Bowel Disease associated dysbiosis on bacterial quorum sensing mediated by Acyl-homoserine Lactone in human gut microbiota
Authors: Grellier N , Suzuki M , Brot L , Rodrigues A , Humbert L , Escoubeyrou K , Rainteau D , Grill J P , Lami R , Seksik P 
Published: January 2023

Abstract

Background
Intestinal dysbiosis is a key feature in the pathogenesis of inflammatory bowel diseases (IBD). Bacterial quorum sensing mediated by acyl-homoserine lactones (AHL) might play a role in the dialogue between the gut microbiota and the host. The main objective of our study was to investigate the presence and expression of AHL synthase and receptor genes in the human gut ecosystem during IBD.

Methods
To confirm the presence of AHL in the gut, mass spectrometric detection was performed on stool samples from IBD patients and non-IBD subjects. Then, by an in silico approach, we exploited the open access database: Inflammatory Bowel Disease Multi’omics Database, an American cohort with bacterial metagenomes and metatranscriptomes data of stool samples from non-IBD and IBD subjects. To characterise gut dysbiosis, the most discriminating bacterial species between non-IBD and IBD patients were identified by multivariate analysis and allowed us to define two groups (dysbiosis/non-dysbiosis). The search for AHL synthase (luxI) and receptor (luxR) known homolog genes, was performed using Basic Local Alignment Search Tool (BLAST) from previously assembled gene files (presence/absence) as well as raw data sequencing files (relative abundance and expression).

Results
Mass spectrometry confirmed a higher concentration of AHL molecules in healthy subjects than in relapsing IBD. Regarding in silico analysis, 103 subjects were selected including 50 with Crohn’s disease (CD), 27 with ulcerative colitis (UC), and 26 non-IBD subjects. No luxI-like synthase genes were retrieved by BLAST searches. However, several homologs of receptor genes were identified: sdiA gene from Escherichia coli (7/103 patients) and luxR-like homologs from Bacteroides fragilis and Bacteroides dorei present in all patients. According to disease, only one luxR-like gene from Bacteroides dorei was under-expressed in IBD patients (p = 0.02) compared to non-IBD, especially in CD (p = 0.02) (Figure 1). In dysbiosis situation, one luxR receptor gene from Bacteroides fragilis appeared to be over-expressed (p = 0.04) compared to non-dysbiotic patients (Figure 2).

Conclusion
Through this computational approach, AHL-synthesising bacteria have not been found. However, the expression of quorum sensing receptor genes appears to be modulated by IBD-associated gut dysbiosis. The role of LuxR receptors, especially in Bacteroides species, should be investigated to understand its impact on gut microbiota (Figure 3). Targeting LuxR receptors of bacterial quorum sensing might represent a new approach to modulate the gut microbiota in IBD.
DOP65 T-cell derived TGFβ1 remodels the rectum mesenchyme in Crohn’s Disease patients with perianal fistulizing disease
Authors: Gudiño V , Cho J W , Corraliza A M , Caballol B , Garrido-Trigo A , Masamunt M C , Ordás I , Ricart E , Hemberg M , Panés J , Salas A 
Published: January 2023

Abstract

Background
Perianal fistulizing disease (PFD) is a complication occurring in about 20% of Crohn’s Disease (CD) patients. It consists of the formation of new epithelised tracks connecting the intestine with the outer perianal region, which dramatically worsens a patient’s quality of life. The mechanisms driving fistula formation have not been elucidated and therefore, there are currently no specific treatments for PFD.

Methods
We collected rectum biopsies of CD patients with and without PFD in the absence of rectal inflammation (CD and CD+PFD), and with active rectal inflammation (CDinf and CD+PFDinf) (Fig.1). Rectal tissue samples were processed for RT-qPCR, or histologic analysis, and single-cell RNA sequencing (scRNAseq) for each patient.

Results
Differential expression gene (DEG) analysis of CD4+ and CD8+ T cells comparing CD vs CD+PFD and CDinf vs CD+PFDinf patients, respectively, revealed increased expression of TGFB1 in patients with fistulae. To investigate the main cellular subsets TGFB1 was interacting with, we performed ligand-receptor interaction analysis using CellphoneDB, which indicated that T-cell derived TGFB1 was primary interacting with the stromal compartment (Fig.2). 365 DEG were found in lamina propria (LP) fibroblasts of CD+PFD compared to CD, including TGFβ1-inducible genes such as TFPI2, SERPINE2 and MMPs 1 and 3. These changes were validated by bulk RT-qPCR, underscoring their potential use as PFD biomarkers (Fig.3). Moreover, we also identified a signature of elastin fibre assembly genes dysregulated in CD+PFD fibroblasts, suggesting molecular changes in the formation of elastin fibres in these patients. To determine whether the differentiation of fibroblasts was altered in the context of PFD, we conducted trajectory analysis using RNA velocity. Whilst fibroblasts in CD patients preferentially differentiate towards myofibroblasts, patients with PFD are biased towards LP fibroblasts, indicating an overall structural rearrangement of the mesenchyme in the rectum of patients with PFD, regardless of their inflammatory status (Fig.4). Importantly, analysis of an independent scRNAseq dataset of CD and ulcerative colitis (UC) patients showed higher expression of TGFB1 in T cells of active CD compared to active UC patients, suggesting that these alterations are already present in CD patients before the onset of a fistulizing phenotype and might potentially contribute to explain the absence of PFD in UC patients.

Conclusion
Based on these results, we suggest that the rectum of patients suffering from PFD present cellular and transcriptomic differences compared to CD patients without PFD. These changes are inflammation independent and point towards the TGFβ pathway as the main driver of this complication.
DOP69 Glycans as an actor in the microbiome-immune response crosstalk.
Authors: Rodrigues C , Gaifem J , Pereira M , Lavelle A , Colombel J F , Sokol H , Pinho S 
Published: January 2023

Abstract

Background
The perturbation of the symbiotic relationship between microbes and the intestinal immune system contributes to Inflammatory Bowel Disease (IBD) development even years before diagnosis. However, the causes underlying the loss of gut microbial equilibrium (dysbiosis) associated with inflammation still remain unknow. The host glycocalyx (repertoire of glycans/sugar-chains at the surface of gut mucosa) constitutes a major biological interface between gut mucosa and microorganisms1. In this study we aimed to evaluate whether and how an altered host glycome perturbs microbiome composition associated with dysbiosis and initiation of intestinal inflammation.

Methods
We have modulated the glycosylation profile at the level of gut mucosa using specific glycoengineered mouse models (KO) that exhibit specific alterations (deficiencies) in glycosylation composition. Colitis was induced using DSS and microbiome analysis was performed by 16S rDNA sequencing both in WT and KO mice. The mucosa glyco-immunoprofile was characterized.

Results
We first demonstrated in different glycoengineered mice that changes in the composition of glycans at gut mucosa resulted in dysbiosis characterized by a significant decrease in beneficial members of the Firmicutes phylum compared with WT mice. These mice with deficiency in mucosa glycosylation exhibited a higher susceptibility to colitis2. Then, and to determine the causal effect of mucosa glycosylation-induced microbiota modulation, we co-housed KO and WT mice. After 5 weeks of cohousing with WT mice, the KO mice exhibited a much less severe colitis and an increased proportion of bacteria from Firmicutes phylum compared to single housed KO mice. Inferred metagenomics analysis further revealed an alteration of the glycosylation biosynthetic pathway that was apparently shared and gained upon co-housing the KO mice with WT. The analysis of colonic inflammatory infiltrate from cohoused KO mice showed an increased expression of IL17 and IL22 production in gut mucosa, at baseline and before DSS. This pinpoints a potential protective effect of the enhancement of glycosylation biosynthesis (through microbiome sharing with WT) for preventing dysbiosis and dysregulation of gut immune response.

Conclusion
In this study, we demonstrate that changes in composition of glycans at the gut mucosa level is associated with dysbiosis and susceptibility to colitis. These results illustrate the relevance of the gut glycome in shaping the gut microbiota, highlighting its role in maintaining a homeostatic crosstalk between the microbiome and host immunity.
This study was funded by ECCO Pioneer Award.
1.Verhelst, Gastroenterology 2020. PMID: 31626754
2.Dias et al PNAS 2018 PMID: 29720442
DOP77 Is durable remission achievable after ileocolic resection for Crohn’s disease ? Long-term results of a prospective multicentric cohort study of the GETAID Chirurgie
Authors: Abdalla S , Benoist S , Maggiori L , Lefevre J , Denost Q , Cotte E , Germain A , Beyer-Berjot L , Desfourneaux V , Rahili A , Duffas J P , Pautrat K , Denet C , Bridoux V , Meurette G , Faucheron J L , Loriau J , Souche F R , Corte H , Zerbib P , Panis Y , Brouquet A ,   GETAID Chirurgie
Published: January 2023

Abstract

Background
Most of the patients undergoing bowel resection for Crohn’s disease (CD) develop postoperative recurrence requiring medical treatment intensification or surgery. Is there a subgroup of patients for which surgery allows durable remission?

Methods
In this retrospective follow-up study, we collected data from 592 patients undergoing ileocolic resection for CD who were included from 2013 to 2015 in a prospective nation-wide cohort of the GETAID Chirurgie group. Patients with follow-up superior to 36 months were included. Primary outcome was durable remission, defined as the absence of endoscopic recurrence (Rutgeerts ≥i2) and/or absence of medical treatment intensification. Uni- and multivariate analyses of the predictive factors for durable remission were carried out.

Results
Among 268 included patients, 158 (59%) had a B2 stricturing phenotype, 92 (34%) had a B3 penetrating phenotype and 18 (7%) had a non-stricturing non-perforating phenotype (Montreal classification). One hundred and eighty-eight patients (70%) had a primary ileocolic resection. One hundred and sixty-seven patients (66%) had postoperative medical treatment to prevent postoperative recurrence (Table 1). After a median follow-up of 85 (36-104) months, 52 patients (19%) had a durable remission, among which 24 (46%) had no medical treatment and 28 (54%) maintained the same postoperative prophylactic treatment, including anti-TNF therapy in 15 patients (54%) (Table 2). Durable remission rate was significantly increased in B1 phenotype vs B2/B3 (n=7/18 ;39% vs n=45/250; 18%, p=0.030) and in primary ileocolic resection vs redo ileocolic resection (n=43/184 ; 23% vs n=9/80 ; 11%, p=0.023). In multivariate analysis, B1 phenotype was an independent predictive factor for durable remission (OR=3.59, IC95%[1.13-11.37], p=0.030) (Table 3).

Conclusion
These long-term data obtained from a nation-wide prospective cohort are in line with those of a randomised controlled trial (LIR!C) and show that durable remission is obtained in nearly 40% of CD patients with non-stricturing non-penetrating phenotype operated for CD refractory to medical treatment. This important result should be considered when medical treatment intensification versus surgery is discussed in these patients.
P026 Cost per Response/Remission analysis of biologic therapies availables in Argentina for the treatment of Bio-exposed patients with moderate-to-severe active Ulcerative Colitis
Authors: Elgart J , Balderramo S , Calvi G , Kanevsky D , Sánchez Gonzalez Y 
Published: January 2023

Abstract

Background
Response and remission are among the most clinically relevant outcomes for patients treated for ulcerative colitis (UC). The aim of the study is comparing the cost of a sustained clinical response or remission (at 52 weeks’ follow-up) across biologics available in Argentina for the treatment of bio-exposed patients with moderate-to-severe UC.

Methods
Using a model developed in Excel, which combine efficacy event rates (clinical response/remission) and treatment costs, we estimated the cost per response or remission of the following UC treatments: adalimumab (ADA), tofacitinib (TOFA), upadacitinib (UPA), ozanimod, ustekinumab and vedolizumab (VEDO). Event rates were obtained from a published network meta-analysis (NMA) of Phase 3 randomized controlled trials (RCTs) in moderately-to-severely active UC (bio-naïve or bio-exposed patients) for the following efficacy outcomes: Clinical response and Clinical remission per Full Mayo (FM) score. Costs of treatments were estimated based on approved regimens and doses of each drug as well as drug prices obtained from a publicly available list of prices. The cost per event was calculated as treatment cost divided by efficacy rate. For sensitivity, costs per event were also calculated using the 95% credible intervals from the NMA efficacy results. Costs per response/remission are expressed in US-dollars (exchange rate: US$1=AR$152.25, Sept 2022).

Results
Considering the Clinical Response at 52 weeks, the lowest cost per responder therapies were: UPA (induction x maintenance: 45mg QD x 15mg QD) $58.216 [95% CrI $42.854 - $98.094]; UPA (45mg QD x 30mg QD) $79.270 [$62.146 - $121.400]; TOFA (10mg BID x 5mg BID) $109.708 [$65.205-$ 232.217]; and TOFA (10mg BID x 10mg BID) $154.218 [$99.169 -$296.204].

Likewise considering sustained remission the lowest costs per responder therapies were: UPA (45mg QD x 15mg QD) $64.782 [$42.658 - $136.390]; UPA (45mg QD x 30mg QD) $92.874 [$64.488 - $182.236]; VEDO (300mg x 300mg Q8W) $278.299 [$124.766 - $779.009]; and TOFA (10mg BID x 5mg BID) $305.534 [$126.845 - $904.439]. The cost per responder was consistently lower for upadacitinib compared to all biologic treatments available in Argentina across both clinical measures.

Conclusion
Among therapies for the treatment of bio-exposed patients with moderate-to-severe UC evaluated, upadacitinib have shown the lowest median cost per clinical remission and response from an Argentinian healthcare payer perspective.