bluuebunny/crossref_metadata_2025_split huggingface dataset:
P067 Fractal analysis of extracellular matrix as a new histological method for observer-independent quantification of intestinal fibrosis in Crohn’s Disease
Authors: Weber M C , Schmidt K , Buck A , Kasajima A , Becker S , Wilhelm D , Friess H , Neumann P A 
Published: January 2023

Abstract

Background
The prevention of intestinal fibrosis formation is still an unsolved problem in the management of Crohn’s Disease (CD) as no specific antifibrotic therapies are available yet. Appropriate analysis of fibrosis severity is essential to assess the therapeutic efficacy of potential anti-fibrotic drugs. However, up to now, no standardized method exists, that allows for automated observer-independent histological evaluation of intestinal fibrosis severity. The aim of this study was thus to develop an objective and observer-independent histological method for the quantification of intestinal fibrosis in surgical specimens of Crohn’s patients using structural analysis of the extracellular matrix (ECM).

Methods
To quantify the structural complexity of the total ECM, fractal dimension analysis was performed using the FracLac plugin in FIJI/ImageJ in fibrotic and control sections of surgical specimens from patients with CD (n = 28) stained with Masson's trichrome. To selectively assess the structure of the collagen matrix, polarized light microscopy was used on Picrosirius red-stained sections. A score to quantify collagen fiber alignment and the color of the polarized light was established. As a reference, sections were scored by a pathologist using an established histological fibrosis score (0 - 4), the proportionate collagen fraction was measured and COL1A1 and COL3A1 mRNA expression was assessed.

Results
Fractal dimension as a measure for the structural complexity correlated significantly with the histological fibrosis score (r = .68, p &lt; .0001), and differences in fractal dimension differed significantly between sections with different fibrosis scores, indicating that during fibrosis progression, there is not only an accumulation of ECM but also structural changes within the ECM network. Using Picrosirius polarized light microscopy, we found that sections with low fibrosis scores showed a meshwork-like alignment of the collagen fibers while sections with high fibrosis scores showed a parallelization of long collagen fibers. Fiber alignment (r =.71, p &lt; .0001) positively correlated with the histological fibrosis score. All measurements were significantly higher in sections from the fibrotic focus compared to the resection margin.

Conclusion
Fractal dimension analysis was suitable for fibrosis quantification in histological samples from surgical specimen of CD patients. Picrosirius polarized light microscopy underlined our findings on structural changes of the ECM network during fibrosis progression in CD. Automated structural analysis of the ECM network using fractal analysis has the potential to serve as an observer-independent histological tool for fibrosis quantification in surgical specimens of patients with CD.
P070 Global cytokine—cytokine interaction framework to uncover communication channels between elements of the immune system
Authors: Olbei M , Modos D , Cozzetto D , Powell N , Korcsmaros T 
Published: January 2023

Abstract

Background
Cytokines are small peptides that signal between a variety of cell types and are one of the fundamental communication elements of the immune system. A variety of cytokine—cytokine interactions have previously been investigated in the literature, describing cytokines activating or inhibiting other cytokines in target cell types, and thus progressing the immune response to infection and illness. Disruption of cytokine communication is often an important goal in drug development as these compounds allow quelling and managing an overactive immune response in chronic diseases, such as Inflammatory Bowel Disease (IBD). In our previous work, we have introduced CytokineLink, a novel computational framework developed to establish cytokine—cytokine interactions from transcriptomics data (Olbei et al., Cells, 2021).

Methods
In this project, we generated a global network of cytokine—cytokine interactions based on cytokine response transcriptomics data from over 2000 datasets deposited in the CytoSig database. Using CytoSig’s significance analysis protocol, we established statistically significant cytokine—cytokine interactions, and determined the likely intracellular pathways connecting upstream and target cytokines using the OmniPath interaction resource.

Results
The resulting network is a signed, directed network of cytokine communication, containing 488 cytokine—cytokine interactions of 91 cytokines. The interactions in the network are annotated with the intracellular pathways that the included cytokines are anticipated to utilise, as well as the stimulatory and inhibitory effects that the cytokines have on one another. The resource captures the cytokine—cytokine networks of cytokines crucial in the pathophysiology of IBD, such as TNF, IL2, IL21, and OSM, which may grant novel insights into the cytokine pathways important in the molecular mechanisms underlying chronic diseases like IBD. The resource can be used by the community as a knowledge base for hypothesis generation, and is freely available through the NDEx platform.

Conclusion
In our work, we generated a novel computational framework collating how cytokines differentially regulate the expression of one another based on cytokine response transcriptomics data. The resulting interactions are signed, highlighting the inhibitory or stimulatory nature of the associations, and the change in expression associated with each link. The resource could be used to identify previously unknown network pharmacology targets, and to better understand the cytokine dysregulation in chronic diseases such as IBD by illustrating the interplay of the most influential IBD associated cytokines with other cytokines.
P075 Characterisation and structural analysis of a new murine model to study postoperative fibrotic recurrence in Crohn’s disease combining ileocecal resection with chronic colitis
Authors: Schmidt K , Li C , Buck A , Wilhelm D , Friess H , Weber M C , Neumann P A 
Published: January 2023

Abstract

Background
The prevention of postoperative fibrotic recurrence in Crohn’s disease is still an unsolved problem in the management of patients undergoing bowel resection due to fibrotic intestinal strictures. Appropriate murine models are needed to examine the effect of surgery associated factors as well as mechanical and microbial alterations after ileocecal resection on the development of postoperative fibrotic recurrence in Crohn’s disease.

Methods
We developed a murine model combining chronic dextrane sodium sulfate(DSS)-colitis with ileocecal resection. 9 to 11-week-old C57BL/6 wild-type mice were exposed to 1% DSS via the drinking water for one week followed by ileocecal resection using a microsurgical technique. After surgery, mice recovered for one week after which two more cycles of DSS-administration were performed, now using 1.5% DSS. Between the two postoperative DSS-cycles one week of recovery was implemented. Histology was performed on the distal ileum, the anastomotic area, the proximal colon, and the distal colon.

Results
The inflammation (proximal colon: median score 5 vs. 0; p &lt; 0.001, distal colon: median score 3 vs. 0; p = 0.003) and fibrosis scores (proximal colon: median score 2 vs. 0; p &lt; 0.001, distal colon: median score 2 vs. 0; p = 0.008) were higher in the colon of mice with chronic DSS-colitis compared to mice without colitis. Furthermore, histomorphometric parameters such as the proportionate collagen area (proximal colon: mean area 6.6% vs. 2.6%; p &lt; 0.001, distal colon: mean area 5.4% vs. 3.7%; p = 0.17) and the submucosal thickness (proximal colon: mean 127.4µm vs. 39.7µm; p &lt; 0.001, distal colon: mean 71.5µm vs. 37.2µm; p = 0.049) were significantly higher in mice with chronic colitis. Interestingly, the most profound inflammatory and fibrotic changes were found in the proximal colon compared to the distal colon. No fibrotic changes were found in the small intestine.

Conclusion
The combination of ileocecal resection and chronic DSS colitis led to inflammatory and fibrotic changes within the colon. Histopathological features of fibrosis were more prominent in the proximal colon as opposed to the known results from the DSS-colitis model, where inflammatory and fibrotic changes of the intestinal wall worsen towards the distal colon. We thus hypothesize that mechanical and microbial changes due to the altered physiology of the lower gastrointestinal tract after ileocecal resection are responsible for these findings. Continuing research on this model might enable the examination of mechanisms of recurring fibrosis after ileocecal resection in Crohn’s disease.
P080 Mucosal clock and inflammation regulatory genes are disrupted in treatment naïve pediatric patients with ulcerative colitis
Authors: Labes S , Tabach Y , Matar M , Shamir R , Shouval D S , Froy O , Weintraub Y 
Published: January 2023

Abstract

Background
The human circadian clock is present in cells throughout the body. It consists of CLOCK and BMAL1 that heterodimerize and bind to E-box sequences to mediate transcription of a large number of genes, including Periods (PERs) and Cryptochromes (CRYs). PERs and CRYs constitute part of the negative feedback loop and inhibit CLOCK:BMAL1-mediated transcription. Recently, we have shown that patients with active ulcerative colitis (UC) display tissue-specific misalignment of the molecular clock that reverts to normal following effective treatment. Several circadian clock genes also function as anti-inflammatory regulators. RORa, PPARa and PPARg are positive regulators of the clock mechanism and induce the expression of IkB, a suppressor of NFkB. In the same manner, PCG1a induces transcription of IL10. Our aim was to characterize the expression of these regulators compared to that of core clock genes and determine their correlation in UC patients.

Methods
Clock gene expression patterns using whole transcriptome RNA sequencing were retrieved from the IBD Transcriptome and Metatranscriptome Meta-Analysis platform (TaMMA IBD). We compared rectal biopsy gene expression of 12 clock genes and their isoforms (AMPK, BMAL1, CLOCK, CRY1, CRY2, PER1, PER2, PCG1a, PPARa, PPARg, REV-ERB, RORa, RORg and SIRT1) in 206 treatment naïve pediatric patients with UC (age 12.9±3.2; 54% male) and 20 healthy controls (age 13.9±3.3; 45% male). Spearman correlations were calculated between all 12 clock genes within each of the UC and control cohorts.

Results
Core clock genes: BMAL (p&lt;0.0001), CLOCK (p&lt;0.01) and CRY1 (p&lt;0.0001), and the anti-inflammatory regulator gene RORa (p&lt;0.0001) were upregulated in UC patients compared to controls. In contrast, expression of other anti-inflammatory regulatory genes: PCG1a (p&lt;0.0001), PPARa (p&lt;0.01), PPARg (p&lt;0.0001) and RORg (p&lt;0.0001) was decreased. Clock gene expression levels of healthy controls show discordant correlations compared to UC patients. For example, correlations between BMAL/REV-ERBa as well as PPARg/REV-ERBa were inverted between controls and UC patients (r=-0.44 vs. r=0.13 and r =-0.4 vs. r=0.3, respectively).
Figure 1. Expression of clock and inflammation regulatory genes in UC patients vs. healthy controls.

Conclusion
Core clock gene expression was disrupted, and anti-inflammatory regulator gene expression was decreased in patients with active UC vs. controls. The demonstration of discordant correlations of some positive vs. negative feedback loop genes in UC highlights the clock disruption in active inflammation. Since these clock regulators also ameliorate inflammation, their reduced expression may explain not only clock dysregulation but also increased tissue inflammation.
P081 The application of multiomics to investigate the evolution of inflammatory bowel disease in pediatric and adult patients
Authors: Maccalli C , Gupta I , Toufiq M , Habib T , Mathew R , Shobha Manjunath H , Missous G N , Mifsud W , Charles A , Ammar A A , Tomei S , van Panhuys N , Al-Kaabi S , Akobeng A , Al-Mohannadi M J , Elawad M 
Published: January 2023

Abstract

Background
The aim of this study is to monitor the evolution of Inflammatory Bowel Disease (IBD), including Crohn’s Disease (CD) and Ulcerative Colitis through the integration of genomic and immunological investigations to assess the mechanisms of IBD severity and the risk to develop malignancy

Methods
The study included pediatric (N=20) and adult (N=18) IBD patients at different stages of the disease (remission, mild, moderate and severe) and CRC patients with IBD history (N=13). Retrospectively collected tissues of IBD, inflamed non-IBD and normal gut tissues (N=10) were also utilized. Gut tissue biopsies (from both left and right side) and peripheral blood were collected from patients. DNA and RNA were extracted from fresh small size (2 mm in diameter) of gut tissues using the BioMasher II (Kimble) and All Prep DNA/RNA kits (Qiagen). Multiomics approach including MicroRNA (miRNA; N=700) and gene expression (N=800 genes) profiling were performed (cCounter platform; Nanostring) as well as the methylation profiling microarray (Infinium Methylation Epic Bead Chip kit, Illumina) to interrogate up to 850,000 methylation sites across the genome. These analyses were coped with immunological investigations. See Figure 1.

Results
Differential miRNA (such as miRNA92a-3p, 135-5p, 152-3p, 612; p&lt;0.05) and gene signatures were found by the comparison of tissues from pediatric and adult patients with different stages of the disease. The differentially expressed genes belong to molecular pathways of inflammation, stemness, fibrosis, cell proliferation and migration (representative genes are: STAT3, CXCL2, MPM1, BIRC3, ISG15, ISG20, PECAM1). Pathways associated with the development of malignancy, such as PI3K/Akt/STAT and Wnt/GSK-3b were also detected as significantly differentially expressed. Differential profiles were also detected when comparing biopsies collected from right and left sides of gut in both pediatric and adult patients. Methylation sites at single nucleotide resolution have been also analyzed and correlated with miRNA and gene expression profiles

Conclusion
Although the results are currently under further investigation, the ongoing integration of data from multiple platforms provide insights of the overall molecular determinants in IBD patients along with the evolution of the disease and the clinical outcome
P082 The CCR9/CCL25 axis is specific to the ileum and is correlated with stricturing disease
Authors: Gehrmann U , Csomor E , Monkley S , Georgi B , Tian S , Cairns J , Angermann B , Khan E , Nys J , Marks D 
Published: January 2023

Abstract

Background
Crohn’s Disease (CD) is a chronic disease in which inflammation is sustained by continuous influx of inflammatory leukocytes into gut mucosa and may affect all segments of the gastrointestinal tract. Immune cell trafficking is regulated via chemokine gradients and adhesion molecules such as integrins. Here we explored the expression profile of gut-specific integrin and chemokine axes in different regions of the gut to identify possible targets for treating CD patients with different disease location or phenotype.

Methods
This study used transcriptomic data from gut tissue biopsies of the large and small intestine of 611 CD and 315 UC patients enrolled in a multicentred longitudinal Study of a Prospective Adult Research Cohort with IBD (SPARC IBD) obtained from the IBD Plexus program of the Crohn’s and Colitis Foundation. We mapped the expression of selected chemokine receptors and their ligands as well as gut-specific integrins onto the different segments of the intestine. Expression data were then linked to available clinical disease phenotypes, as well as genotype information.

Results
In both CD and UC patients, ITGA4 and ITGB7, the targets for Vedolizumab, and their endothelial ligand MADCAM1 were ubiquitously present in all regions of the gut. GPR15 and its ligand C10orf99 were predominantly expressed in colonic biopsies. On the contrary, expression of CCR9 and its ligand CCL25 were specific to the terminal ileum with only minimal transcriptional activity in the colon. Expression of CCL25 was significantly increased in patients with penetrating and/or stricturing CD, a disease feature associated with ileal CD that has high impact for patients and is currently an unmet for IBD patients. Further, we identified an expression quantitative trait loci (eQTL) upstream of the CCL25 promoter linked to small bowel expression of CCL25.

Conclusion
Our data highlight the potential for targeting the CCR9/CCL25 axis as a treatment for small bowel Crohn’s Disease which may have been incompletely targeted to date by small molecule inhibitors. Further investigations are warranted to identify a mechanistic link between this pathway and penetrating and stricturing disease.
P083 JAK/STAT pathway and IL-6 activity in moderate to severe Ulcerative Colitis
Authors: Calviño Suárez C , Martinez-Rodriguez A L , Baston-Rey I , Moreira-Alvarez D , Ferreiro-Iglesias R , Ardao-Palacios I , de la Iglesia-Garcia D , Porto-Silva S , Nieto-Garcia L , Varela-Liste M J , Brea-Floriani J M , Dominguez-Munoz J E , Loza-Garcia M , Barreiro-de Acosta M 
Published: January 2023

Abstract

Background
Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a high social and health care system burden. Despite recent advances in UC treatment with available drugs acting in different signalling pathways related to the disease, there is still a significant proportion of non-responders who end up being overtreated and exposed to treatment's secondary effects. Therefore, it would be helpful to know the activity of each inflammatory pathway involved in UC pathogenesis in order to tailor the best treatment for each patient. The aim of our study was to measure the activation of JAK/STAT pathway and IL-6 levels in colonic biopsies from patients with UC.

Methods
A prospective, observational single-centre study was designed and it is currently on going. Adult UC patients with any endoscopic activity (Mayo Endoscopic Score (MES) &gt; 0) in a routine colonoscopy were included. Biopsies from inflamed (endoscopically active) and non-inflamed (endoscopically inactive) colon of each patient were homogenised and processed by using RIPA buffer and ultrasounds to obtain cell lysates. Determination of the activation of JAK/STAT pathway was performed by detecting phosphorylated forms of JAK1, JAK2, JAK3, TYK2, STAT1, STAT3 and STAT4 by Western blot. Human Luminex discovery assay was used for IL-6 quantification. Data are shown as percentage, median, interquartile range (IQR) and mean ± standard deviation as appropriate.

Results
So far, 19 patients were consecutively included (median age 60.9 years (IQR 40.8-66.6), 58% female). About 47% had left-sided UC, 32% extensive UC and 21% had proctitis. Regarding endoscopic activity, 52.6% of patients showed MES-3, 42.1% MES-2 and 5.2% MES-1. IL-6 was increased in biopsies from inflamed colon, while no IL-6 was found in biopsies from non-inflamed colon (p=0.00). Median IL-6 in inflamed colonic biopsies from patients with MES-2 was 41.5pg/ml (IQR 7.4-106.7) and 51.9pg/ml (IQR 17.5-220.5) in patients with MES-3 (p=0.4) (Figure 1). Every patient showed, at least, one phosphorylated JAK protein and one phosphorylated STAT protein from JAK/STAT pathway in inflamed colonic biopsies. Nevertheless, the pattern of activation of JAK/STAT pathway was different in all patients as shown in Figure 2.

Conclusion
Different activated forms of JAK and STAT kinases are detected in inflamed colonic biopsies from UC patients, even though the activation pattern of JAK/STAT pathway differs among them. IL-6 levels are increased in inflamed colonic biopsies from UC patients while it is not detected in non-inflamed mucosa.
P085 Gut microbiota profile changes in patients with Ulcerative Colitis
Authors: Inčiūraitė R , Gedgaudas R , Lukosevicius R , Plingyte K , Muskieta T , Juzenas S , Kupcinskas J , Skieceviciene J 
Published: January 2023

Abstract

Background
Ulcerative Colitis (UC) is a chronic, relapsing inflammatory disease of the lower gastrointestinal tract. The frequency of UC is increasing worldwide, however, existing methods for both diagnostics and treatment of this disease are not efficient enough. It is known that besides comprised immune response, environmental and genetic factors, gut microbiota play a major role in the onset and course of UC. Therefore, efforts are currently being made to find and develop new gut microbiome-based tools to improve the management of UC. The aim of this study was to identify changes in the gut microbiome during active and quiescent UC.

Methods
Study included 72 subjects, who were divided into three age- and sex-matched groups: control (n=25), active UC (n=27) and quiescent UC (n=20). Total DNA was extracted from faeces, which was further subjected to the next generation sequencing of 16S rRNA-coding gene V1-V2 hypervariable region on MiSeq (Illumina) platform. Further, bioinformatics and statistical analysis were performed.

Results
Bacterial α-diversity, as assessed by Richness, Shannon and Simpson diversity indexes, revealed that control patients had highest α-diversity compared to patients with active UC or quiescent UC (p&lt;0.05), but there were no differences between UC disease states (p&gt;0.05). Significant microbial community clusters (β-diversity), as assessed by the Bray-Curtis dissimilarity index, were identified between control subjects and patients with active or quiescent UC (p=0.02, p&lt;0.01, respectively). However, no significant clusters were found between different disease states (p=0.22). In-between samples dissimilarity assessed by Bray-Curtis dissimilarity index showed that samples from control subjects had higher in-between sample similarity (mean 0.542 ± 0.117) than patients with active (mean 0.638 ± 0.161) and quiescent (0.6 ± 0.145) UC. In addition, 16, 13 and 27 core taxa were identified in active, quiescent UC and control group, respectively. Differential abundance of Cuneatibacter, Faecalibacterium and Prevotellamassilia genera was detected when comparing control vs UC (both active and quiescent), Paraprevotella and Cuneatibacter genera – control vs active UC, Faecalibacterium, Prevotellamassilia, Mediterraneibacter and Cuneatibacter genera – control vs quiescent UC.

Conclusion
In conclusion, this study revealed both qualitative and quantitative gut microbiota changes in active and quiescent UC.
Study was funded by the Research Council of Lithuania (Grant No. S-MIP-20-56).