bluuebunny/crossref_metadata_2025 huggingface dataset:
Sparse species interactions reproduce abundance correlation patterns in microbial communities
Authors: Camacho-Mateu José , Lampo Aniello , Sireci Matteo , Muñoz Miguel A. , Cuesta José A.
Published: January 2024

During the last decades, macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full understanding of the dynamical processes behind them. In particular, abundance fluctuations of different species are found to be correlated, both across time and across communities in metagenomic samples. Reproducing such correlations through appropriate population models remains an open challenge. The present paper tackles this problem and points to sparse species interactions as a necessary mechanism to account for them. Specifically, we discuss several possibilities to include interactions in population models and recognize Lotka–Volterra constants as a successful ansatz. For this, we design a Bayesian inference algorithm to extract sets of interaction constants able to reproduce empirical probability distributions of pairwise correlations for diverse biomes. Importantly, the inferred models still reproduce well-known single-species macroecological patterns concerning abundance fluctuations across both species and communities. Endorsed by the agreement with the empirically observed phenomenology, our analyses provide insights into the properties of the networks of microbial interactions, revealing that sparsity is a crucial feature.
Structural phase purification of bulk HfO
2
:Y through pressure cycling
Authors: Musfeldt J. L. , Singh Sobhit , Fan Shiyu , Gu Yanhong , Xu Xianghan , Cheong S.-W. , Liu Z. , Vanderbilt David , Rabe Karin M.
Published: January 2024

We combine synchrotron-based infrared absorption and Raman scattering spectroscopies with diamond anvil cell techniques and first-principles calculations to explore the properties of hafnia under compression. We find that pressure drives HfO

2

:7%Y from the mixed monoclinic (

P

2
1

/
c

)

+

antipolar orthorhombic (

Pbca

) phase to pure antipolar orthorhombic (

Pbca

) phase at approximately 6.3 GPa. This transformation is irreversible, meaning that upon release, the material is kinetically trapped in the

Pbca

metastable state at 300 K. Compression also drives polar orthorhombic (

P
c
a

2
1

) hafnia into the tetragonal (

P

4
2

/
n
m
c

) phase, although the latter is not metastable upon release. These results are unified by an analysis of the energy landscape. The fact that pressure allows us to stabilize targeted metastable structures with less Y stabilizer is important to preserving the flat phonon band physics of pure HfO

2

.
Nation Branding in Latin America: Repositioning Brazil to Reset Its Brand Image
Authors: Ocke Marco , Braga Debora Cordeiro
Published: January 2024

By performing country brand initiatives and hosting mega sporting events as international promotional tools, Brazil, the largest economy in Latin America, has tried to leverage its brand awareness as a promising hub for investment for a great variety of sectors and add new attributes to the country’s image, such as a strong, innovative and sustainable economy. However, the country has accumulated instability and turbulence over the years, which has discredited reputation-building efforts. The lack of public financial management, economic crisis associated with widespread corruption, inappropriate responses to the COVID-19 pandemic and lack of environmental management affected the country’s image negatively. Currently, the relaunch of “Marca Brasil” represents an effort to reset its brand image based on a repositioning strategy oriented to stand the country as a protagonist on the global stage, adding value to how the country is perceived.

Information

© The Authors 2024
The first case of methotrexate-associated lymphoproliferative disorder in the sacrum: a case report
Authors: Yamaguchi Yuichi , Morimoto Tadatsugu , Toda Yu , Tsukamoto Masatsugu , Yoshihara Tomohito , Hirata Hirohito , Kobayashi Takaomi , Mawatari Masaaki
Published: January 2024

Methotrexate (MTX) is a drug used for treating rheumatoid arthritis. Recently, the reported incidence of methotrexate-associated lymphoproliferative disease (MTX-LPD) has increased, especially in Japan. Extranodal involvement is observed in half of MTX-LPD cases. However, only a few spinal lesions have been reported, with none in the sacrum. Additionally, Epstein-Barr virus (EBV) infection has also been implicated in the pathogenesis of MTX-LPD. Herein, we describe the case of a 74-year-old woman with MTX-LPD in the sacral spine who complained of severe back pain and nocturnal pain. Radiographs revealed a tumour on the right wing of the sacrum and a positive EBV immunoglobulin G antibody titre. MTX-LPD was suspected based on imaging findings and a history of MTX administration. A pathological examination was performed on the CT-guided biopsy specimen. The histopathological diagnosis was MTX-LPD, and MTX was discontinued. Three months after MTX administration ended, the tumour tended to shrink, and 1 year later, significant tumour shrinkage was observed. This experience suggests that MTX-LPD can be treated by discontinuing MTX administration. Therefore, early and accurate diagnosis is required, as is avoiding unnecessary treatment such as surgery. MTX-LPD should be considered, especially in spinal origin tumours in EBV-infected patients on MTX.
OP26 Programmable probiotic local delivery of anti-TNF-α nanobody to alleviate DSS-induced colitis
Authors: Kang G , Zhu Z , Gao M , Wang L , Cao X , Liu X , Huang H
Published: January 2024

Background

Biological agents represented by Infliximab have brought a milestone leap forward in the treatment of IBD. However, the overall response rate of anti-TNF-α antibodies in clinical practice is just 40-60% and the adverse reactions caused by the lack of gut-selective further limit its clinical application. Systemic effects of intravenous administration may be an essential cause of paradoxical response and immune adaptive succession (secondary loss of response). Rapid advances in synthetic biology allow targeted delivery of antibody drugs via engineered probiotics to improve bioavailability while reducing the risk of systemic effects.

Methods

Here, we developed an engineered probiotic (EcN-VHH2M3) that intelligently responds to the inflammatory marker thiosulfate and produces the anti-TNF-α nanobody VHH2M3. At the same time, controlled release of anti-TNF-α biologic was achieved in response to colitis marker nitrate and quorum sensing mechanism. The dextran sulfate sodium (DSS)-induced colitis model was used to explore the feasibility of EcN-VHH2M3 for the IBD treatment. The disease activity index of the subject animals was detected and evaluated. The colon length and spleen weight were measured and HE staining. Real-time polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA) are used to detect cytokine expression levels in colon tissue.

Results

In vivo results showed that EcN-VHH2M3 group significantly reduced disease activity index and restored intestinal mucosal barrier compared with control group. DSS administration resulted in hyperemia, ulceration, and thickening of the bowel wall, which were reduced in the treatment group. In addition, spleen weight and colon length were close to the control group. EcN-VHH2M3 treatments significantly decreased the expression levels of pro-inflammatory cytokines IL-1β, TNF-α, and IFN-γ, while the expression of anti-inflammatory cytokines IL-10 and TGF-β was enhanced.

Conclusion

Inflammatory microenvironment-responsive programmable probiotics effectively alleviate DSS-induced colitis in mice and restore the intestinal mucosal barrier through the targeted release of anti-TNF-α nanobody. This study preliminarily confirmed that the controlled intestinal release of anti-TNF biologics by engineered probiotics provides a promising paradigm for IBD treatment with non-gut-selective antibodies.
OP29 Haematopoietic stem cell gene therapy as a treatment for severe Crohn’s Disease associated with pathogenic NOD2 genetic variants
Authors: Enjalbert F , del Mar Masdeu M , Zabinski T , Narean J S , Elavazhagan S , Whiting C , Pennucci V , Luiz A , Du L , Recchi C , Cattoni M , Heal P , Gaspar B , Mavilio F , Sagoo P
Published: January 2024

Background

Pathogenic variants of the NOD2 (nucleotide-binding oligomerization domain containing protein 2) gene demonstrate the strongest genetic association to Crohn’s inflammatory bowel disease (CD), with mounting evidence linking NOD2 deficiency with poor clinical outcome. CD patients with NOD2 variants, particularly carriers of more than one risk allele, frequently present an aggressive, fistulizing and fibrostenotic disease, requiring multiple surgical resections. NOD2-deficiency is implicated to drive CD pathogenesis through failure of gut innate immunity to resolve bacterial infections and by loss of tissue homeostasis within the intestinal microenvironment. Here we present preclinical data on OTL-104, an autologous haematopoietic stemcell gene therapy (HSC-GT) which aims to stably restore NOD2 expression in gut resident macrophages, to correct immune dysfunction linked to NOD2-deficient CD pathogenesis.

Methods

We used in vitro and in vivo models of NOD2 deficiency to demonstrate the mechanism of action and the efficacy of OTL-104 autologous HSC-GT.

Results

NOD2KO human myeloid cells differentiated in vitro from CRISPR-generated NOD2KO CD34+ HSCs are unable to mount a proinflammatory cytokine response to MDP stimulation. Similarly, myeloid cells differentiated from CD34+ cells obtained from peripheral blood of genetically characterized NOD2-deficient CD patients, are also refractory to MDP stimulation and unable to generate a normal cytokine response profile. In both NOD2 deficient CD34+ derived monocyte models, transduction with a lentiviral vector (LVV) expressing NOD2 fully restores NOD2-dependent cytokine and chemokine responses, restoring an immune profile that is comparable to monocytes derived from CD34+ cells from NOD2 wild-type healthy donors (Figure 1).

Transplantation of lineage negative (Lin-) haematopoietic stem/progenitor cells (HSPCs) transduced with the OTL-104 LVV in NOD2KO mice was used as an in vivo model of gene therapy for CD. Compared to WT mice, NOD2KO mice fail to release systemic inflammatory mediators and recruit myeloid cells in response to MDP administration. Transplantation of transduced Lin- HSPCs restores MDP-induced systemic release of IL-6 and CXCL1 as well as innate mobilization of monocyte/macrophage cells and gut associated gene expression. Key to our therapeutic approach, histopathological analysis of intestinal lamina propria from transplanted mice shows a normal biodistribution and physiological NOD2 gene expression in tissue resident cells.

Conclusion

These results confirm the impact of NOD2 deficiency in primary immune activation and demonstrates the therapeutic potential of OTL-104 HSC-GT for long-term correction of NOD2-deficient CD.
OP30 Endothelial cell-mediated smooth muscle hyperplasia in Crohn’s disease intestinal strictures: Caveolin 1 as a potential therapeutic target
Authors: Acharjee A , Shivaji U N , Santacroce G , Jeffery L , Amamou A , Reynolds G , Majumder S , Akiror S , Zardo D , Gkoutos G V , Ghosh S , Iacucci M
Published: January 2024

Background

Intestinal stricture is a severe and common complication of Crohn’s disease (CD). Current therapies offer limited success and surgery is often needed. Smooth muscle hyperplasia and hypertrophy play a key role in CD stricture development. This study explores the transcriptomic features of fibrostenotic CD, focusing on the endothelial contribution to smooth muscle changes within intestinal strictures.

Methods

9 CD patients undergoing surgery for fibrotic strictures were prospectively enrolled. Dissected samples from the stricture and the adjacent proximal and distal non-strictured areas were obtained from fresh specimens collected directly from the operating theatre. RNA was extracted from all samples for bulk-transcriptomic analysis. Differentially expressed genes (adj. p-value <0.05) were identified and pathway enrichment analysis pinpointed relevant pathways. Subsequently, single-cell RNA sequencing (scRNAseq) analysis was performed using the 10x Chromium Controller® platform. A total of 31.195 cells were sequenced and bioinformatic analysis revealed 13 distinct clusters based on the expression of key lineage target genes. To better characterise the nature of clusters expressing stromal like markers and positioned closely in the UMAP plot, a further subclustering was performed. This resulted in 5 groups, including plasma cells, endothelial cells, fibroblasts, epithelial cells and dendritic like cells.

Results

Bulk-transcriptomic analysis identified 81 genes differentially expressed in strictures compared to both proximal and distal regions. Notably, genes associated with leukocyte and macrophage recruitment and chemotaxis, namely Platelet and Endothelial Cell Adhesion Molecule 1 (PECAM1), C-C motif Chemokine Ligand 2 (CCL2), and Endothelin Receptor Type B (EDNRB), resulted overexpressed in strictures. scRNAseq identified a distinct subset of endothelial cells (CD34+, PECAM1+). Caveolin 1 (CAV1), a gene encoding for a structural protein predominantly expressed in smooth muscle cell plasma membrane invaginations, was exclusively up-regulated in endothelial cells of ileal stricture samples. Previous research linked CAV1 to smooth muscle proliferation and fibrosis in various organs.

Conclusion

This study highlights the pivotal role of endothelial cells in CD strictures. The transcriptomic analysis shows the involvement of inflammatory targets featured genes involved in transendothelial immune cell migration. Furthermore, the up-regulation of CAV1 in endothelial cells within stricture segments suggests a mechanistic connection between endothelial cells and smooth muscle hyperplasia in intestinal strictures. CAV1 holds promise as a potential therapeutic target in fibrostenotic CD.
DOP19 High dimensional profiling of IL-23-responsive cells revealed molecular signatures that predict response to anti-IL-23 therapy in patients with Crohn’s Disease
Authors: Cao S , Colonna M , Deepak P
Published: January 2024

Background

The interleukin (IL)-23 signaling plays a crucial role in the pathogenesis of Crohn’s disease (CD). IL-23 activates T-helper (Th) 17 cells, IL-17-secreting CD8 T (Tc)17 cells, gd T cells, nature killer (NK) T cells, and group 3 innate lymphoid cells (ILC3) to secrete proinflammatory cytokines including IL-17, IFN-g, and TNF-a. Risankizumab is the first selective IL-23 antagonist approved for moderate-severe CD. However, there is currently no biomarker to predict response to anti-IL-23 antibodies in IBD. Here, we characterized the cell type- and cytokine-specific pathways in IL-23-responsive cells that predict response to risankizumab in CD patients.

Methods

Adult patients with a history of ileal, colonic, or ileocolonic CD were included. Active CD in terminal ileum and/or colon were confirmed by colonoscopy and/or MRI. Blood samples were collected within 3 months before and 4, 8, 12, and 52 weeks after the initiation of risankizumab. Peripheral blood mononuclear cells (PBMC) were isolated and cryopreserved for batch analysis using mass cytometry (CyTOF). Pre-treatment PBMCs were stimulated ex vivo with IL-23, and stained for lineage markers to identify Th17, Tc17, gd T, NKT cells, and ILC3, as well as intracellular cytokines including IL-17, IFN-g, TNF-a, IL-22, IL-6, and GM-CSF, using a pre-optimized and validated antibody panel. The CyTOF data were analyzed using the viSNE tool in Cytobank and FlowJo. Patients’ responses were evaluated 12-40 weeks after the initiation of risankizumab based on clinical symptoms and endoscopic/radiographic assessment.

Results

Among IL-23-responsive cells, increased frequency of NKT cells was identified in the peripheral blood of non-responders before initiation of risankizumab (Figure 1A). In non-responders, Tc17 cells, gd T cells, and ILC3 demonstrated significant elevations in TNF-a, a key pathogenic mediator in CD. gd T cells from non-responders also showed increased IL-17F before treatment. In contrast, NKT cells from non-responders expressed significantly lower GM-CSF, which was previously shown to alleviate intestinal inflammation in patients and mouse models (Figure 1B). Ongoing study is investigating the cytokine production in IL-23-responsive cells after the initiation of risankizumab, as well as before and after starting ustekinumab, an anti-IL-12/IL-23 antibody.

Conclusion

High dimensional profiling of pre-treatment PBMCs revealed molecular signatures, e.g., elevated TNF-a in multiple IL-23-responsive cells, which are associated with resistance to risankizumab in CD patients. Those findings may help identify response biomarkers for IL-23 antagonists and provide a rationale for using anti-IL-23/anti-TNF combination therapy in some patients with refractory CD.
DOP28 Yield of surveillance colonoscopy in patients with Primary Sclerosing Cholangitis
Authors: Van De Pol N , Mol B , de Jong M J , Weersma R K , Inderson A , Slooter F C , Gibbes L A , van der Meer A J , Derikx L A A P , Ponsioen C Y , de Vries A C
Published: January 2024

Background

Patients with primary sclerosing cholangitis (PSC) have a higher risk of developing colorectal cancer (CRC), in particular in patients with concurrent diagnosis of inflammatory bowel disease (IBD). Therefore, strict surveillance colonoscopy in patients with PSC and PSC-IBD is recommended with consideration of random biopsies. The aim of this study was to assess the method and yield of surveillance colonoscopy in patients with PSC and PSC-IBD in routine practice in the Netherlands.

Methods

An observational cohort study was performed within the EpiPSC2 cohort in The Netherlands. Patients with a confirmed PSC diagnosis were included from January 2008 onwards. Data were collected retrospectively from the date of diagnosis until inclusion, and prospectively from that date forward. Patient demographics, PSC and IBD disease characteristics were collected at study inclusion and during annual follow-up. For this study, data collection was expanded retrospectively with colonoscopy and pathology reports. Outcomes were endoscopic surveillance technique, whether random or targeted biopsies were taken, if polypectomy was performed, dysplasia detection rate and type of dysplasia.

Results

The study population included 1,203 PSC patients, of whom 82.1% had large duct PSC, and 70.6% concomitant IBD (table 1). A total of 4,099 colonoscopies were performed in 759 individual patients, with a median of 4 colonoscopies per patient (IQR 2 – 8). The median follow-up duration was 11 years (IQR 12 – 17). In total, 11.5% (n=473) of colonoscopies were performed with chromo-endoscopy. Among the conducted colonoscopies, 2,543 included biopsies, 355 involved polypectomies, and 86 comprised both biopsies and polypectomies. Dysplasia was identified in 11.4% (341 out of 2,984) of the colonoscopies, including 14.1% indefinite for dysplasia (n=48), 75.1% low grade dysplasia (n=256), 7.6% high grade dysplasia (n=26), and 5.9% adenocarcinoma (n=20). The detection of dysplasia occurred through random biopsies in 89 colonoscopies (26.1%), targeted biopsies in 114 colonoscopies (33.4%) and polypectomy in 153 colonoscopies (44.9%) (figure 1). Dysplasia was observed in 195 (26%) individual patients, of whom 80.5% had PSC-IBD.

Conclusion

Our data highlights the importance of colonoscopic surveillance in PSC and PSC-IBD patients. Dysplasia was detected in over a quarter of patients undergoing surveillance colonoscopy. Notably, 26.1% of dysplasia cases were identified through random biopsies, emphasizing the importance of incorporating random biopsies into surveillance protocols for this specific patient population.
DOP34 Deciphering immune-epithelial interactions in health and in Inflammatory Bowel Disease
Authors: Jowett G M , Read E , Pena-Cearra A , Coman D , Coales I , Kromann E , Ilangovan J , Roberts L , Gentleman E , Lord G M , Neves J F
Published: January 2024

Background

Intestinal homeostasis is dependent on appropriate interactions between various compartments including immune, mesenchymal, neural, epithelial and bacteria cells. Disrupt of these interactions has been associated with the development of Inflammatory Bowel Disease (IBD).

Using intestinal organoids as a starting point, we built complexity into this model by adding other cellular components to be able to study these interactions in health and disease.

One of the key immune players in the intestine is Innate Lymphoid Cells (ILC). ILC precursors (ILCP) migrate to mucosa where they mature, promote homeostasis, and provide a potent, antigen-non-specific sources of cytokines. Deciphering what local stimuli drive the final stages of ILCP maturation in these tissues remains a pressing question, as ILC frequencies can become dysregulated in IBD.

Methods

Here, we develop and use co-cultures gut organoids with Innate Lymphoid Cells precursors (ILCP) and with mature intestinal Innate Lymphoid Cells (ILC).

Results

Harnessing these versatile models, we demonstrate that epithelial cells provide a complex niche capable of supporting the final maturation of all subsets including ILC1, ILC2, ILC3 and Natural Killer (NK) cells, Notably, organoid identity was sufficient to robustly recapitulate tissue-specific ILC imprints and frequencies, even in the absence of microbial stimuli, other cell types, or cytokine supplementation.

In addition, we show that human gut ILC1 drive intestinal and extracellular matrix remodelling through production of TGFβ. This indicates the potential impact of ILC1 accumulation in IBD patients in driving intestinal cancer and fibrosis, two sequelae of IBD.

Finally, we identify a new module of interaction between ILCs and the intestinal epithelium: goblet cells provide Notch ligands that are essential for maintenance of NC3R+ ILC3 and for their production of IL-22. In turn, ILC3 drive intestinal epithelial cells towards a secretory phenotype.

Conclusion

Taken together, our work provides unprecedented insight into in situ ILC maturation, which we show to be driven by epithelial signals, and into ILC function through deciphering new modules of ILC-epithelial interaction in health and IBD.
DOP35 Spatial transcriptomics reveals cellular niches associated with histological inflammation in postoperative Crohn’s Disease
Authors: Battat R , Sangiorgi B , Linggi B , Gui S , Torti D , Smith M I , Mehandru S , Longman R , Lukin D J , Scherl E J , Qin L , Ma C , Teft W , Vande Casteele N
Published: January 2024

Background

Postoperative Crohn’s disease (CD) recurs in ~70% of patients ≤1 year following ileocolonic resection (ICR), as observed endoscopically. Current understanding of molecular determinants underlying histological intestinal inflammation in patients with postoperative CD recurrence is minimal. To address this issue, we used advanced spatial transcriptomic analyses on intestinal biopsy samples with matched histological and endoscopic assessments from neoterminal ileum, anastomosis, and colon of patients with CD who had undergone colonoscopy following ICR.

Methods

Formalin-fixed paraffin-embedded (FFPE) tissue biopsies from neoterminal ileum, anastomosis, and colon were prospectively collected from a 15-patient cross-sectional cohort with CD who underwent routine endoscopic assessment following ICR. Spatial transcriptomics was performed on samples using 10X Genomics Visium CytAssist Spatial Gene Expression for FFPE V2.0. Annotation of tissue regions of histologically active inflammation and classification of histologically inactive (Robarts Histopathology Index ≤3 with subscores of 0 for neutrophils in the lamina propria and epithelium) or active disease were performed by an expert gastrointestinal pathologist. R programming language was used for data analysis (Figure).

Results

Fourteen of the 43 (32.6%) FFPE biopsies had histological evidence of inflammation. Spatial transcriptomics clustering revealed a distinct transcriptional signature by the segregation of 4 clusters ("inflamed clusters") composed mostly (≥69%) of cells from samples defined by histologically active disease. Tissue regions identified as inflamed by expert pathologist annotation contributed to >46% of inflamed clusters’ composition and <15% of remaining clusters. Cell type decomposition and cellular niche analysis revealed immune (e.g., myeloid, T cells, and B cells) and epithelial cells in close proximity sharing a similar microenvironment in 3 inflamed clusters while the 4th cluster was composed of >90% epithelial cells. Differentially expressed genes from the inflamed clusters were similarly expressed across intestinal segments including inflamed anastomotic biopsies and were enriched for signalling pathways involving immune cells recruitment/activation, inflammatory signalling, extracellular matrix organisation, and oxidative stress response.

Conclusion

This is the first study to explore spatial transcriptomic signatures associated with histological inflammation in patients with postoperative CD recurrence. Our analysis revealed a spatial signature of cellular niches and signalling pathways arising upon histological inflammation, providing insight into therapeutic targets and biomarkers across anatomic locations and the anastomosis.
DOP37 Noninvasive assessment of gut function using transcriptional recording sentinel cells
Authors: Zimmermann J , Macpherson A
Published: January 2024

Background

Bacteria within the human gut continuously adapt their gene expression to environmental conditions that are associated with diet, health, and disease. Noninvasive measurements of bacterial gene expression patterns throughout the intestine are important to understand in vivo microbiota physiology and pathophysiology. Current methods do not offer sufficient information about transient or proximal events within the intestine without using indirect or invasive approaches that disturb normal physiology and are inapplicable to clinical practice.

Methods

Here we used transcriptional recording sentinel cells that through a reverse transcriptase-Cas1–Cas2 complex record their own short-lived mRNA expression into long-lived DNA-based CRISPR arrays to report on gut function. We colonized gnotobiotic mice with E. coli sentinel cells and performed Record-seq on fecal samples to reconstruct their cellular histories as they passed along the gastrointestinal tract.

Results

Upon colonization of the mouse intestine, sentinel cells reported on diet, inflammation, and microbial interactions. Through transcriptome-scale information, Record-seq elucidated E. coli’s adaptations to intraluminal conditions including pH, oxygen levels, and ion availability. Unlike RNA-seq, Record-seq performed on stool samples retained information from proximal gut sections to noninvasively report on the luminal conditions in vivo. In a mouse model of inflammatory bowel disease, Record-seq not only diagnosed the inflammation in a severity-dependent manner but also revealed pathological gut conditions such as mucus depletion and hyperoxygenation.

Conclusion

Transcriptional recording sentinel cells noninvasively report on gut function and reveal environmental cues such as diet, inflammation, and microbial interactions, even in proximal gut sections that are otherwise unamenable to unbiased diagnostic interrogation.
DOP58 Human Leukocyte Antigen drives methylation signatures in primary sclerosing cholangitis but not in IgG4-related sclerosing cholangitis
Authors: Cabras S , Adams A , Noble A , Motta R , Moron Flores B , Glapa-Nowak A , Nowak J , Geremia A , Culver E , Satsangi J
Published: January 2024

Background

Primary sclerosing cholangitis (PSC) and IgG4-related sclerosing cholangitis (IgG4-SC) are fibro-inflammatory hepatobiliary conditions, with genetic, environmental, and immunologic risk factors, in which epigenetic alterations may provide insights into pathophysiology and novel biomarkers.

Methods

Whole blood DNA methylation profiling and genotyping was performed in 70 PSC (57 with PSC and ulcerative colitis (PSC-UC)), 56 IgG4-SC, 66 UC, and 88 healthy controls (HC), with MethylationEPIC and Global Screening arrays (Illumina). UC patients were selected to match the clinical characteristics of UC in the PSC-UC cohort. Methylation data was processed with Minfi and limma, genotyping analysed with Plink, and meQTLs with linear models.

Results

There were 31, 13 and 8 Holm-significant methylation differences between PSC and controls, IgG4-SC and controls, and UC and controls respectively (8 probes shared). Inflammatory genes (including CEP97, IFNAR1, TXK, and SMAD2) and methylation loci associated with mitochondrial DNA copy number (C5orf36, PYY, and MTRNR2L1) were predominant. Sub-analyses of PSC-UC and PSC without IBD detected 25 and 4 differences with HC respectively (p<0.05). DNA methylation age acceleration was observed in IgG4-SC, but not on PSC, PSC-IBD or UC. MeQTL analyses to identify genetic determinants of methylation revealed a strong HLA signal in PSC but not IgG4-SC, with 19/40 significant findings in 5 clusters (HLA-DRB1, HLA-DPB1, BTNL2, CSNK2B, and SFTA2). There was no overlap with the 36 meQTLs found in IgG4-SC. Using multivariate adaptive shrinkage for meQTLs in PSC, IgG4-SC, and UC yielded 5505 meQTLs with local false discovery rate <0.05 in at least one condition, with 1230 unique to PSC, and 1043 to IgG4-SC.

Conclusion

We identify characteristic epigenetic alterations in PSC and IgG4-related disease, providing insights into disease pathogenesis; and highlight the potential interaction with germ-line variation.
DOP67 MB310: From Clinical FMT to a Phase 1 Study with a Defined, Orally Administered Live Bacterial Therapeutic for Mild Moderate Ulcerative Colitis
Authors: Villemin C , Schreiber F , Bakdash G , Rimington O , McCluskey S , Neville A , Robinson M , Birrell C , Wilkinson A , Carter R , Lawley T
Published: January 2024

Background

The composition of the gut microbiome is a key determinant in inflammatory bowel disease. Consequently, modifying the composition of the gut microbiota has the potential to transform the treatment of ulcerative colitis (UC). The clinical use of faecal microbiota transplantation (FMT) has become widespread, especially for the treatment of C. difficile associated diseases, as a method of changing the composition of the gut microbiome from a diseased to a healthy state. FMT is, by its nature, an undefined and variable therapy due to differences between donors. Microbiotica has taken a "patient-first" discovery approach to identify a defined consortium, which is being developed as a live bacterial therapeutic for treatment of mild-to-moderate UC patients in a Phase 1b clinical trial, the COMPOSER-1 study, in 2024.

Methods

A clinical trial in UC patients (Costello et al., 2019), in which patients were treated with FMT from healthy donors, showed a 32% clinical remission rate in the active treatment group, as compared to 9% in the placebo arm. Donor, pre-treatment recipient, and post-FMT recipient samples were analysed using shotgun metagenomic sequencing. All samples were analysed using Microbiotica’s precision microbiome analysis platform to identify bacteria associated with patient response. These bacteria were assessed in cellular assays using relevant human cell/cell lines including: Caco2, dendritic cells, M1 macrophages, and CD4+ T-cells.

Results

We defined a signature of therapeutic response based on bacteria that engrafted from the donor into UC patients and were associated with clinical benefit. A sub-species level analysis identified 8 bacteria, which have been developed into a defined live bacterial therapeutic, MB310. The consortium bacteria enhanced the barrier integrity of an epithelial cell monolayer, and protected the barrier from inflammatory challenge by LPS. In vitro, the bacteria also have an anti-inflammatory effect when incubated with different primary innate immune cells, dendritic cells and M1 macrophages. Specific MB310 bacteria, either directly or via metabolites, are able to regulate T-cell responses.

Conclusion

In summary, we have identified a consortium of bacteria using patient-first discovery in a successful FMT study that is being developed as a treatment for UC. The consortium of 8 bacteria is able to impact multiple disease-relevant mechanisms including epithelial barrier integrity and immunomodulation. MB310 is being advanced to a first-in-human study in 2024 to explore safety and initial signs of efficacy.

Costello, et al. (2019) Jama 321.2: 156-164.
DOP69 Longitudinal gut microbiome dynamics in relation to disease flares in Inflammatory Bowel Disease, pilot data from the IBD-Tracker study
Authors: Gacesa R , Klaassen M A Y , Collij V , Björk J R , Blankenstein A D , Jansen B H , Dijkstra G , Visschedijk M , Festen E A M , Ananthakrishnan A , Alm E , Weersma R K
Published: January 2024

Background

The pathogenetic mechanisms that lead to IBD flares are unknown and the absence of reliable predictive biomarkers results in a therapeutic approach focused on treating active flares rather than prevention. While IBD is known to be associated to changes in gut microbiota, the longitudinal dynamics of the microbiome in relation to disease flares and its biomarker potential remain poorly understood. We initiated the IBD -racker study which aims to include 100 patients with weekly fecal sampling along other biomaterials and clinical data. The aim is to elucidate patient-specific dynamics of the gut microbiome, including changes during IBD flares, strain replacements, and the potential for personalized prediction of flares based on microbiome. Here we present pilot microbiome data from the first 5 patients that completed the collection.

Methods

A comprehensive analysis of microbiome dynamics was conducted by collecting 52 weekly fecal samples, calprotectin measurements and clinical disease scores from five IBD patients. Metagenomic sequencing was employed on 248 samples, followed by biobakery4 tools for profiling of microbiome composition and function. Stability and dynamics of gut microbiota were evaluated through analysis of autocorrelation and stable states, while bacterial strains were profiled using markers and metagenomic assembly and binning based approaches. Finally, microbiome signatures associated with IBD flares were identified using multivariate generalized regression models correcting for patient-driven heterogeneity.

Results

The core gut microbiome of IBD patients (43 to 82 patient-specific highly prevalent species) is highly personalized and largely stable over time, regardless of flares (patient ID R2 > 0.4 in ADONIS of microbiome composition and function). The bacterial strains of these core species cluster by patients, indicating flares do not perturb them. Despite this stability of the core microbome, ~60% of identified bacterial taxa were present in <70% of weekly samples, indicating that a large part of the microbiome is dynamic. Differential abundance analysis revealed 32 bacterial species genomic bins (e.g. Clostridia pathobionts) and one pathway significantly associated with IBD flares (FDR < 0.1). Intriguingly, several species (e.g. Faecalibacterium sp. SGB15346, Clostridium inoocum) showed switches between high and low abundance stable states correlated with flares, and certain bacteria (e.g., Blautia wexlerae) underwent strain replacement during flares, which was not reversed post flare.

Conclusion

Our results indicate that IBD flares perturb a large part of the non-core gut microbiome, implying that personalized longitudinal monitoring of microbiota has potential for prediction and monitoring of IBD flares.
DOP71 Efficacy of once-daily, orally administered obefazimod in patients with moderately to severely active UC at weeks 8, 48, and 96 broken down by induction treatment dose
Authors: Vermeire S , Danese S , Peyrin-Biroulet L , Dubinsky M , Dulai P , Tilg H , Siegmund B , Sloan S , Gineste P , Rabbat C , Sands B E
Published: January 2024

Background

Obefazimod (obe) is an investigational, oral, once-daily, small molecule which enhances expression of microRNA-124 and is currently in phase 3 clinical trials for the treatment of patients with moderately to severely active ulcerative colitis (UC) [1]. Obe demonstrated efficacy in patients with UC at week-8 in a phase 2b, double-blind, placebo-controlled, dose ranging, induction trial and in the subsequent open-label maintenance (OLM) study [2].

Methods

During the induction Phase 2b trial, patients received placebo or obe 25mg, 50mg or 100mg once daily (od). Irrespective of their clinical response, patients could enter the optional 96-week OLM study with obe 50mg od. Of the 222 eligible patients, 217 continued treatment in the OLM. We examine the efficacy outcomes at weeks 8, 48, and 96, for patients enrolled in the OLM according to their induction dose group.

Results

Among the 58 patients who initially received obe 25 mg during the induction period, 28% (16/58) achieved clinical remission at week 8. After switching to 50 mg in the OLM, the rate of clinical remission increased to 60% (35/58) at weeks 48 and 96. Similar trends were observed for clinical response (66% (38/58) at week 8, 85% (49/58) at week 48, and 74% (43/58) at week 96), endoscopic improvement (36% (21/58) at week 8, 60% (35/58) at week 48, and 66% (38/58) at week 96), and endoscopic remission (7% (4/58) at week 8, 28% (16/58) at week 48, and 47% (27/58) at week 96).

In the group of patients who received obe 50 mg in the induction period (n= 51), 20% (10/51) achieved clinical remission at week 8. After switching to 50 mg in the OLM, the rate of clinical remission increased to 49% (25/51) at week 48 and 96. Similar trends were observed for clinical response and endoscopic improvement (Table 1).

Among the 53 patients who received obe 100 mg in the induction period, 28% (15/53) achieved clinical remission at week 8. After switching to 50 mg in the OLM, the rate of clinical remission increased to 55% (29/53) at week 48 and week 96. Similar trends were observed for clinical response and endoscopic improvement (Table 1).

Among the 55 patients who received placebo in the induction period, 15% (8/55) achieved clinical remission at week 8. After switching to 50 mg in the OLM, the rate of clinical remission increased to 55% (30/55) at week 48, and 45% (25/55) at week 96. Similar trends were observed for clinical response and endoscopic improvement (Table 1).

Conclusion

These findings suggest that patients with UC treated with obefazimod 50mg od after the week 8 induction period maintained efficacy and continued to improve, irrespective of their induction dose, as evidenced by higher percentages of patients reaching clinical endpoints at weeks 48 and 96 relative to week 8.
DOP78 Efficacy of ozanimod by patient response trajectory subgroups identified using group-based trajectory modelling: a post hoc analysis of the phase 3 True North study
Authors: Schreiber S W , Feagan B G , Sands B E , Rieder F , Torres J , Liu Z , Jain A , Poehler A M , Wu H , Osterman M T , Abreu M T , Dulai P S
Published: January 2024

Background

Ozanimod (OZA) is approved for the treatment of adults with moderately to severely active ulcerative colitis (UC). A previous post hoc analysis of the phase 3 True North (TN) trial identified 5 discrete groups of patient (pt)-response trajectories to OZA using group-based trajectory modelling (GBTM). The current analysis further evaluated symptomatic, clinical, and mucosal outcomes in these groups.

Methods

Five trajectory groups were previously identified by GBTM using change from baseline (BL) in partial Mayo score in pts on continuous OZA treatment until W52 (OZA/OZA; N=229): super-response (Group 1; n=38), sustained improvement (Group 2; n=85), partial improvement (Group 3; n=60), fast rebound (Group 4; n=25), and slow rebound (Group 5; n=21) (Schreiber et al. Am J Gastroenterol. 2023;118:S671–2). In each of these groups, symptomatic remission and response were evaluated through W52, and results were compared with placebo (PBO). Clinical and mucosal EPs were evaluated at W10 and/or W52 using nonresponder imputation analysis.

Results

Significantly more pts in Group 1 vs PBO achieved early symptomatic response on Day (D) 5 (34.2% vs 11.1%; P=0.0002) and remission on D6 (10.5% vs 2.8%; P=0.0264). Symptomatic EPs were sustained for 52 wk in Groups 1–3, whereas Groups 4 and 5 started losing symptomatic efficacy by W18 (Figure 1). The highest proportions of symptomatic remission at W10 were achieved by pts in Groups 1 and 2 (97.4% and 75.3%) and were sustained until W52 (73.7% and 64.7%) (Figure 1A); similarly ~100% of pts in Groups 1 and 2 achieved symptomatic response by W10 and it was sustained in >80% of pts until W52 (Figure 1B). Generally, Groups 1>2>3 had sustained or increased rates of clinical and mucosal EPs from W10 to W52, whereas Groups 4 and 5 had decreased rates of clinical and mucosal EPs at W52 (Table). Corticosteroid (CS)-free remission at W52 was greatest in Groups 1>2>3. Analysis of BL parameters showed that Group 1 had the least prior CS (60.5%), immunomodulator (26.3%), and anti–tumor necrosis factor (TNF) use (23.7%).

Conclusion

This analysis shows 3 distinctly different OZA populations within the responders, with the super-response Group 1 achieving symptomatic response as early as D5. Early response was related to long-term benefits, with Group 1 (and to a lesser extent with Groups 2 and 3) being more likely to achieve disease control at W52 with OZA. These findings demonstrate the utility of personalized medicine to direct therapeutic choice but need to be confirmed in future prospective cohorts.
DOP84 Colonic CD4+ T cell senescence is implicated in the progression of experimental colitis in aged mice
Authors: Zhang Y , Xu J , Zhang Y , Ke Z , Fang X , Lin Y , Liu Y
Published: January 2024

Background

Evidence from recent epidemiological data suggests that the burden of IBD in the elderly is increasing globally. However, the mechanisms underlying the age-related IBD susceptibility remain elusive. Aging leads to a progressive functional decline of the immune system, rendering the elderly increasingly susceptible to autoimmune disease. Herein, we sought to determine the role of immunosenescence in age-dependent colitis and to explore the underlying mechanisms.

Methods

Young (2-3 months), middle-aged (10-12 months), and aged (20-24 months) mice were established models of colitis by 2% dextran sulfate sodium salt (DSS) treatment. Weight loss, colon length, disease activity indexes (DAI) and histological scores were evaluated to assess the severity of colitis. Using a second-generation fluorogenic substrate for β-galactosidase and multi-parameter flow cytometry, we detected the senescence-associated β-galactosidase (SA-βGal) activity in lymphocytes isolated from colon, including CD4+ T cells, CD8+ T cells, B cells, natural killer cells, microphages, neutrophils and dendritic cells. Based on the immunocytes that exhibit greatest age-related increases in SA-βGal activity, inflammatory cytokines such as TNF-α、IFN-γ、IL-17 were evaluated in senescent immunocytes through flow cytometry. Single-cell and bulk RNA-seq of colonic immune cells in mice with different ages were performed to further investigate the precise molecular mechanisms.

Results

Ageing increased the severity of DSS-induced colitis wherein aged mice exhibited worsened weight loss, shortened colon length, higher DAI and histological scores compared to young mice. The greatest age-associated increases of SA-βGal activity were observed in colonic CD4+ T cell populations. Additionally, aging resulted in systemic activation of CD4+ T cells, exhibiting an expansion of CD4+ effector memory T (TEM) cells in colon, as well as in spleen. Aged colonic CD4+ T cells generate higher levels of IFN-γ and IL-17 comparing to young colonic CD4+ T cells, especially in status of colitis. Moreover, the accumulated CD4+ TEM cells in the aged colon were the main source of IL-17 production. Single-cell analysis revealed that aging increased colonic CD4+ TEM cells, which were associated with T cell-mediated cytotoxicity and cytokine-mediated signaling pathway. Splenic CD4+ TEM cells isolated from aged colitis mice were confirmed to involve in cellular senescence, Th17 differentiation and inflammatory signaling pathway through bulk RNA-seq.

Conclusion

These results provide a significant insight into the contribution of senescent CD4+ T cells to age-dependent colitis and provide an attractive possibility that targeting T cell specifically might be a potential strategy to treat elderly IBD patients.
P001 MicroRNA-155-5p contributes to the development of Ulcerative Colitis by regulating T lymphocyte proliferation and functions
Authors: Sumiyoshi N , Toyonaga T , Shumway A , Nakagawa F , Tanaka M , Saeki C , Furey T , Sheikh S , Sethupathy P , Saruta M
Published: January 2024

Background

MicroRNA (miRNA) is a small non-coding RNA which regulate a variety of cell functions by suppressing target mRNAs in a post-transcriptional manner. Recent works have identified an increased expression of miR-155-5p in the colonic mucosa of UC patients. However, the role of miR-155-5p in the pathophysiology of UC remains understudied. This study aims to clarify the role of miR-155-5p in development of colitis in UC patients.

Methods

MiRNA and mRNA expression profiles in colon were compared between 15 UC and 5 healthy controls by running small RNA-sequencing (smRNA-Seq) and RNA-Seq on the matched colon tissue. Candidate target genes of miR-155-5p were identified by analyzing sequencing data sets using a statistical simulation method (miRhub). MiR-155-5p expressing cells were identified by in situ hybridization in combination with immunohistochemistry on inflamed colon tissue of UC patients. The impact of miR-155-5p on colonic inflammation was tested in the dextran sulfate sodium (DSS) -induced colitis model using miR-155 deficient mice.

Results

MiR-155-5p expression was significantly higher in the inflamed colonic tissue of UC patients than in healthy controls with more pronounced up-regulation in the treatment refractory UC patients compared to the treatment naïve UC patients (UC vs. healthy controls, log2FC = 0.83, adjusted p-value = 0.014). MiRhub analysis identified 10 candidate target genes of miR-155-5p including SHANK2, MYO1D, ADD3, AHCYL2, NR3C2, MIER3, TRIM2, GPD1L, SEMA5A, and SATB2 most of which were involved in cell proliferation and immune response (NR3C2, MIER3, TRIM2, GPD1L, SEMA5A, and SATB2). In situ hybridization identified a group of CD3 positive T lymphocytes with increased miR-155-5p expression in the inflamed colonic mucosa. MiR-155 deficient mice showed attenuated DSS-induced inflammation in colon compared to the control wild type mice (colon weight/length ratio, miR-155 deficient mice vs. controls, 27.2 vs. 44.6, p<0.01).

Conclusion

MiR-155-5p may contribute to the development of colitis in UC by regulating T lymphocyte proliferation and functions.