bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOP07 Monitoring disease activity by intestinal ultrasound predicts biologic treatment persistence in patients with Inflammatory Bowel Disease
Authors: Fremberg Ilvemark J , Christensen K R , Steenholdt C , Brynskov J , Attauabi M , Dahl E , Bjerrum J W , Seidelin J B 
Published: January 2024

Abstract

Background
Current biomarker-based monitoring strategies have limited efficacy in predicting risk of biologic treatment failure in inflammatory bowel disease (IBD). Endoscopic assessment identifies patients at risk of disease progression but is expensive and poorly accepted by patients. Therefore, we examined how intestinal ultrasound (IUS) performed as part of a monitoring program to predict treatment persistence to biologics in IBD patients.

Methods
Data were generated as part of a 1-year prospective, observational, cohort study of patients on biologics comparing tight monitoring to a historic cohort (‘Time It´ study). Data used in the present analysis included Harvey Bradshaw index (HBI), simple clinical colitis activity score (SCCAI), CRP, f-calprotectin (FC), IUS, and ileocolonoscopy all done at inclusion. The following definitions were used: Treatment persistence: no need for dose escalation or switching to another biologic or small molecule; IUS transmural remission (TR): bowel wall thickness ≤3mm in all bowel segments and zero color Doppler activity; endoscopic remission (ER): simple endoscopic score (SES)-CD≤2 or Mayo endoscopic score 0; clinical remission (CR): HBI≤4 or SCCAI≤2; FC remission (FCR): FC≤250; CRP remission (CRPR): CRP≤10 mg/L. Chi-square tests and Kaplan-Meier statistics were used to compare baseline measures in treatment persistent and non-persistent patients.

Results
Of the 91 patients included in 'Time It’, 77 had IUS performed and 69 ileocolonoscopy. Of the 77 patients, 61% were on maintenance treatment at inclusion and 39% were included during induction (Table 1). COVID-19 restrictions were the main reason for missing IUS or endoscopy. As expected, more patients with ER had 1-year treatment persistence (87% vs. 41%; p&lt;0.001). However, patients with IUS TR also had better treatment persistence (78% vs. 38%; p&lt;0.001). CR or FCR were associated with treatment persistence (p&lt;0.05 and p&lt;0.01, respectively), but not CRPR. Combining TR and FCR performed numerically as well as ER (treatment persistence 85% vs. 41%, p=0.002). Survival analysis of TR showed a mean treatment persistence of 318 days vs. 221 days without TR (p&lt;0.001); corresponding treatment persistence data were 327 days vs. 230 days for combined TR and FCR; and 338 days vs. 226 days for ER (both p&lt;0.001; Figure 1). There was no difference in mean treatment persistence between TR and ER (318 vs. 338 days; p=0.36).

Conclusion
IUS alone or combined with FCR was comparable to endoscopy to identify patients with high biologic treatment persistence. Being a non-invasive, patient friendly, cost-effective modality, IUS monitoring may improve current disease monitoring programs aiming to increase treatment persistence.
DOP24 Multi-omic sequencing reveals distinctive gene expression and DNA methylation alterations as potential predictors of primary sclerosing cholangitis development in treatment-naïve paediatric Ulcerative Colitis
Authors: Rodriguez Sosa A , Lawal O , McDonnell C , Grant L , Stephens I , Genua F , O'Brien J , Kirwan G , Kel A , Dominik A , Stack R , Yochum G , Doherty G , Hussey S , Das S 
Published: January 2024

Abstract

Background
Primary sclerosing cholangitis (PSC) is a progressive choleostatic disease and up to 80% of patients also have ulcerative colitis (PSC-UC). This presents a clinical challenge owing to difficulty in diagnosis and increased risk for developing cancer. While several multifactorial processes including inflammation and microbial dysbiosis have been associated with PSC-UC pathogenesis, the precise molecular factors that regulate the phenotype of this disease subtype remain unknown.

Methods
We applied methyl-capture sequencing and mRNA sequencing to colonic mucosal biopsies derived from the DOCHAS study (GEN-193/11), to identify transcriptomic and epigenetic differences between treatment naïve paediatric UC (n=10), PSC-UC (n=10) and healthy controls (n=10) samples.

Results
Differential gene expression between UC and PSC-UC identified 9 up-regulated genes - ADMTS14, PNCK, NLRP3, SLC6A19, DLL1, FCGR2C, KLHL17, APOB, EHBP1L1 and 5 downregulated - SLC37A2, SLC14A2, RPL27, RPS25, SLC38A4 in PSC-UC relative to UC. Importantly, we show that expression of these genes was intricately regulated by master transcriptional regulators (pro-caspases, IL7RA) and transcription factors (TFs) :AR, p53, JUND, CEBPA. Similarly, differential methylation analysis between PSC-UC and UC identified 22 differentially methylated regions (DMRs) relative to controls, where 5 were hypermethylated and 8 hypomethylated. Intriguingly, in general we show that these DMRs are largely localised in gene promoter regions as opposed to enhancers. Importantly, we show that these DMR’s identified between PSC-UC vs UC is enriched for binding sites for the TF: ASCL1, suggesting its activity likely is effected due to the altered methylation of its binding site in PSC-UC patients. Collectively, these results highlight the importance of TF’s in driving molecular differences between PSC-UC and UC paediatric patients in a treatment naïve setting.

Conclusion
In summary, for the first time this study provides a critical insight into the transcriptional differences between treatment naïve children with PSC-UC vs UC as well as highlights the intricate regulatory processes involving master transcriptional regulators, transcription factors and DNA methylation. These processes thus warrant further examination in larger cohorts to rationalise their role as diagnostic/therapeutic targets.
DOP25 Antibodies against Neutrophil Extracellular Traps (ANETAs) are associated with more severe disease course in Ulcerative Colitis
Authors: Mendieta Escalante E A , Parada-Venegas D , Roozendaal C , Hermoso M , Bourgonje A R , Faber K N , Gerard D 
Published: January 2024

Abstract

Background
Antibodies against Neutrophil Extracellular Traps (ANETAs) have emerged as markers in multiple autoimmune disorders (i.e. rheumatoid arthritis and systemic lupus) associated with disease activity. We investigated the presence of ANETAs and their influence on disease course in Inflammatory Bowel Disease (IBD).

Methods
Serum samples from UC (n=33), Crohn's Disease (CD; n=28), and healthy controls (HC; n=8) underwent incubation with non-lytic Neutrophil Extracellular Traps (NETs) for immunofluorescence microscopy. For clinical relevance, these patients were followed over ten years to track treatment resistance, extraintestinal manifestations, surgeries, and disease recurrence (Table 1). For functional relevance, in vitro generated NETs were exposed to ANETAs, followed by quantifying macrophage-mediated clearance of these ANETA pre-treated NETs by real-time microscopy via pHrodo for 24 hours, as well as assessing pro-inflammatory cytokine (IL-6, TNF-α, IL-8, and IL-23) genetic expression levels in these macrophages.

Results
Among UC patients, ANETA positivity correlated with high rates of treatment resistance, extraintestinal manifestations, colorectal surgeries, and recurrence of disease like pouchitis (93.3% vs. 6.7%, 61.5% vs. 38.5%; 71.4% vs. 28.6%; 87.5% vs. 12.5%, for ANETA+ and ANETA- UC patients, respectively). CD patients with ANETAs exhibited high rates of resistance to treatment (75% vs 25%) and lower rates of extraintestinal manifestations, colectomy, and disease recurrence (38.1% vs 61.9%, 40% vs 60%, 33.3% vs 66.7%) (Fig 1A). Macrophages displayed robust engulfment of untreated NETs and those treated with healthy control sera, while ANETA-coated NETs exhibited reduced susceptibility to macrophage phagocytosis (Fig 1B). Gene expression analysis revealed a significant upregulation of pro-inflammatory cytokines (IL-6, TNF-α, IL-8, and IL-23) when NETs were incubated with serum from ANETA-positive individuals compared to sera from healthy controls (p&lt;0.05).

Conclusion
ANETAs may serve as markers for a distinct subgroup of UC patients characterized by aggressive disease and poorer prognosis. The potential mechanism might involve impaired NETs clearance by, and inducing a proinflammatory response in macrophages. Discrepancies observed between UC and CD suggest diverse pathophysiological mechanisms in both diseases. Further research is imperative to comprehensively understand the underlying pathophysiology, function, and potential clinical applications of ANETAs in IBD.
DOP30 Cross-ethnic microbiome analyses identify shared and specific signals for Northern Indian IBD patients
Authors: Singh A , Gacesa R , Juyal G , Joshi M , Midah V , Thelma B K , Weersma R K , Sood A 
Published: January 2024

Abstract

Background
Clinical manifestation of the inflammatory bowel disease (IBD) shows considerable variation across the world. We hypothesized these differences may be influenced by geographical differences in gut microbiome. To test this, we investigated the correlation between gut microbiota and the disease phenotypes of IBD in a cohort form the Northern part of India.

Methods
Stool samples and clinical metadata were collected from 226 IBD patients (198 ulcerative colitis and 28 Crohn’s disease) and 66 controls from a population cohort from the Northern India. We used metagenomic shotgun sequencing to determine diversity, composition and function of the gut microbiota of the participants. Microbiome was then associated to IBD and its subtypes and clinical metadata (e.g. medication use, drug response, and disease activity). We replicated our results in 436 IBD patients and 903 population controls from the Netherlands analyzed using an identical workflow and used machine learning to assess how well do the Indian IBD signals generalize to Dutch IBD.

Results
We identified reduction in microbiome diversity and changes in beta diversity in Indian IBD patients (FDR &lt; 0.05, replicated in Dutch population) and identified that 319 taxa and 71 biochemical pathways are altered in Indian patients (FDR &lt; 0.05). Of note, 39% of these signals were replicated in the Dutch cohort (at FDR &lt; 0.05 level). We identified strong dysbiosis shared across Indian and Dutch IBD patients, characterized by expansion of opportunistic pathogens (e.g. Genera Clostridium, Streptococcus and Lactobacilli) and oral bacteria (e.g. Streptococcus oralis and Bifidobacterium dentium) as well as reduction in butyrate producers such as Faecalibacterium prausnitzii, Roseburia hominis and Blautia massiliensis. In addition, we found novel pathobionts specific to the Indian cohort (including oral bacteria from Genus Scardovia and Oribacterium; Actinomyces dentalis and Klebsiella pneumoniae). Machine-learning models trained on the Indian cohort were highly predictive in the Indian test set (Sensitivity 0.84, Specificity 0.95) and generalized to Dutch cohort (Sensitivity 0.77, Specificity 0.69).
In addition to IBD-associated dysbiosis, we identified links between medication use and gut microbiota independent of the disease activity: use of Tofacitinib (used by 26 UC patients) was linked to decrease in Lactobacilliales and increase in Clostridia, while Prednisolone and Azathioprine associated to reduction in Roseburia and increase in Streptococcus and Granulicatella.

Conclusion
The IBD patients from Northern India show gut dysbiosis similar to European patients, but also show enrichment in India-specific pathobionts. The microbiome-based diagnostic models generalize across these populations.
DOP31 Gene correlation network analyses reveal transcript modules and pathogenic mechanisms associated with resistance and response to ustekinumab therapy in Ulcerative Colitis
Authors: Saifuddin A , Cozzetto D , Olbei M , Hart A , Korcsmaros T , Powell N 
Published: January 2024

Abstract

Background
Precision medicine in ulcerative colitis (UC) remain elusive. The heterogeneity in patients’ mucosal transcriptomic profiles suggests that stratification based on molecular mechanisms might be possible, which may link to treatment response. We interrogated a dataset of ustekinumab-treated patients treated to determine transcript modules (TMs) in active UC, investigate pathogenic pathways and consider which cells might be driving ustekinumab resistance.

Methods
Pre-treatment mucosal transcriptomes and outcome data were available for 358 ustekinumab-treated patients enrolled in the UNIFI programme. Modules of co-expressed genes were defined with weighted gene correlation network analysis (WGCNA) and their functional roles and regulatory interactions inferred with Fisher tests. Multivariate regression was used to test the ability of clinical and transcriptomic data to predict treatment resistance. Further insights into the cellular and molecular features of ustekinumab resistance were gauged from the analysis of single cell data (Single Cell Portal accession SCP259). Analyses were performed in R 4.2.3 (Vienna, Austria).

Results
WGCNA generated 23 transcript modules (TMs) whose correlation with mucosal healing ranged from -0.26 to 0.25. The three TMs most negatively correlated with response comprised genes enriched in neutrophil degranulation, extracellular matrix activity and endoplasmic reticulum function. The modules correlating highest with response were enriched in genes involved in mitochondrial function. The constituents of the ustekinumab resistance-related modules are regulated by a hierarchy of transcription factors downstream of NFKB1, AHR, JUN and RELA. They are also densely connected by regulatory protein-protein interactions (Figure 1). A multivariate model including TM1 enrichment score and clinical variables predicts resistance with area under the curve 0.76 (95% confidence interval: 0.69–0.82). Notably, TM1 included TREM1 and OSM, which were previously associated with anti-TNF resistance. Surmising that cell populations co-expressing these genes might be key to ustekinumab resistance too, we identified TREM1+ OSM+ inflammatory monocytes (IMs). These showed higher expression of genes such as IL1B, IL8 and CXCL2 compared to other IMs, and increased activity in pathogenic processes including interleukin (IL)10, IL4 and IL13 signalling and G-protein-coupled receptor signalling.

Conclusion
Gene co-expression analysis identified transcripts and molecular mechanisms associated with response and predictive of resistance to ustekinumab. TREM1+ OSM+ IMs may be key to driving resistance, suggesting an important role for innate immunity. These findings are important for developing precision medicine approaches in UC.
DOP41 Mucosal single-cell profiling of Crohn's-like disease of the pouch reveal unique pathogenesis and therapeutic targets
Authors: Cao S , Deepak P , Colonna M 
Published: January 2024

Abstract

Background
After restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC), a subset of patients develop Crohn’s-like disease of the pouch (CDP), a chronic inflammatory condition that affects both the pouch body and extra-pouch organs including the pre-pouch ileum. The cellular and molecular identities of CDP are unknown, and its diagnosis and treatment remain challenging. To define the pathophysiology of CDP, we examined mucosal cells from patients after IPAA with and without CDP using single cell analyses.

Methods
Endoscopic samples from the pouch body and pre-pouch ileum of 50 patients with an IPAA were collected for single-cell RNA sequencing (scRNA-seq) or mass cytometry (or CyTOF). We analyzed immune and non-immune cells from both pouch body and pre-pouch ileum of patients with normal pouch/ileum and CDP using scRNA-seq. CyTOF was performed on mucosal immune cells from independent cohorts of patients with normal pouch/ileum, CDP, and pouchitis. Mucosal samples from patients with familial adenomatous polyposis (FAP) after colectomy and pouch formation were also analyzed by CyTOF. ScRNA-seq and CyTOF findings were independently validated using immunohistochemistry.

Results
We revealed distinct cell clusters in normal pouch body versus normal pre-pouch ileum in UC patients. Colitogenic immune cells expanded in normal UC pouch body compared to normal FAP pouch body. Compared to normal pouch/ileum, CDP pouch/ileum exhibited expanded TCR clonotypes, elevated Th17 signaling, and diminished T cell exhaustion markers. Elevated plasma cells, inflammatory fibroblasts and monocytes were noted in CDP pouch/ileum (Figure 1). CDP also harbored elevated Th17-inducing cytokines such as IL23, IL1B, and IL6 produced by myeloid cells. ScRNA-seq and CyTOF identified increased CD14+TREM1+ pathogenic monocytes in both pouch body and pre-pouch ileum of CDP. Ligand-receptor analysis further revealed a stromal – myeloid – lymphocyte circuit in CDP. Integrated analysis showed that upregulated immune mediators in CDP tissues were similar to those in CD and pouchitis, but not UC. In addition, the pouch body and pre-pouch ileum of CDP exhibited prominent activation of the unfolded protein response (UPR) across all major immune and non-immune cell compartments (Figure 2), which was not present in UC, CD or pouchitis based on reanalysis of published databases.

Conclusion
CDP demonstrates altered immune and non-immune cell populations/states in the pouch body and pre-pouch ileum. CDP represents a distinct entity of inflammatory bowel disease with extensive UPR activation, a unique feature that may serve as novel diagnostic markers and therapeutic targets using ER stress-alleviating agents including chemical chaperones.
DOP45 Blood-derived neutrophils give rise to differentially activated populations in the mucosa of active Inflammatory Bowel Disease patients
Authors: Veny M , Sanzo-Machuca A , Corraliza A M , Strobbe F , Garrido-Trigo A , Gudiño V , Melón-Ardanaz E , Esteller M , Teubel I , Masamunt M C , Ordás I , Prieto C , Giner À , Martin-Cardona A , Esteve M , Ricart E , Salas A 
Published: January 2024

Abstract

Background
Infiltration of neutrophils is the main histological feature in active inflammatory bowel disease (IBD). Recent data suggests that tissue- and tumour-infiltrating neutrophils can adopt remarkably different phenotypes with potentially different functions. However, the heterogeneity of this population in IBD remains unknown.

Methods
Single-cell RNA sequencing (scRNA-seq) data was generated from colonic biopsies of 92 individuals including 6 healthy controls (HC), 36 inactive IBD, 19 active Crohn’s disease (CD) and 31 active ulcerative colitis (UC) patients. Neutrophils (6038 cells) found in the inflamed colon of CD and UC patients were analysed using a curated pipeline in Seurat (v4.0.2)1. Posterior analysis included the FindAllMarkers function (differentially expressed genes), Jaccard index similarity and the AddModuleScore function (comparisons with literature-described neutrophils), Monocle3 algorithm (developmental trajectory) and clusterProfiler (v3.0.4; enrichment and pathway analysis). For in vitro stimulation, neutrophils were isolated from the blood of HC donors (n=4) using a double Ficoll gradient 1. Cells and supernatants were analysed for qPCR and ELISA determinations.

Results
We identified 6 different clusters/states of colonic neutrophils (Figure 1A). In agreement with our previous results1 we found a population of S100A12/S100A8/S100A9 neutrophils (N0), IFN-response neutrophils (N3) and CCL3/CCL4 neutrophils (N2), in addition to N1.1 and N1.2 neutrophils. N3 neutrophils were enriched in the inflamed colon of CD patients compared to UC (17.2% vs 5.8%, p-value= 0.0021; Figure 1C). Comparative analysis with published datasets revealed that N0, N1.2 and N3 resemble populations of neutrophils found in blood2,3. In contrast, N1.1 and N2-like clusters showed some similarity to umbilical cord blood3 and tumour-infiltrating neutrophils4. Trajectory analysis, originating from N0 (peripheral-like) neutrophils, showed two potential branches of differentiation, with N1.2 leading towards N3 (IFN-response) and N1.1 differentiating into N2 (CCL3) neutrophils (Figure 1B). Finally, pathway analysis showed that N2 neutrophils presented enriched gene expression of the TNF signalling pathway, and together with the N1.1 state, an enrichment of the IL1β signalling pathway as well. In vitro experiments revealed that TNF, IL1β and LPS can all induce expression of CCL3 and CCL4, top differentially expressed genes of N2 neutrophils.

Conclusion
We show that active IBD is associated with a highly heterogeneous population of infiltrating neutrophils. Some of them resemble neutrophils in peripheral blood, while others most likely differentiate in response to inflammatory cues present in the colon of active IBD patients.
DOP72 Pregnancy for IBD-patients with an enterostomy is feasible but is associated with complications
Authors: Bouwknegt D G , van der Weide A H C , Dijkstra G , van Dop W , Prins J R , Hoogenboom F J , van der Woude C J , Visschedijk M C 
Published: January 2024

Abstract

Background
As inflammatory bowel disease (IBD) is frequently diagnosed in young adults, the disease often coincides with pregnancy. There are several indications for enterostomies in the treatment of IBD. Literature on enterostomy complications during pregnancy and pregnancy-outcomes remains scarce. Gaining insight in the incidence of complications and the course of these pregnancies serves as a first step in developing guidelines for the difficult question of how, when and by whom complications during pregnancy should be monitored and treated. The aim of this study was to assess enterostomy related complications and pregnancy-outcomes in female IBD patient with an enterostomy during pregnancy.

Methods
For this multicenter cohort and survey study, all patients who have been pregnant while having an enterostomy and who gave birth between 2016 and 2023 in three Dutch university medical centers were included. Complications of the enterostomy and pregnancy-outcomes were collected retrospectively from electronic patient files. In collaboration with gastroenterologists, surgeons, gynaecologists and IBD-patients, a survey was designed. Through this digital questionnaire, all participants were asked about their experience during pregnancy and any long-term enterostomy related complaints.

Results
Data was collected on 37 patients (mean age at conception 32.6 years; 64.9% Crohn’s disease (CD), 32.4% ulcerative colitis (UC), 2.7% IBD undetermined (IBD-U)), comprising 48 pregnancies of which four ended in a miscarriage. Enterostomy related complications occurred in thirty of the full-term pregnancies (68.2%), with decreased stoma-output (43.2%), small-bowel obstruction (29.6%) and leakage (25%) being the most prevalent. In a quarter of the pregnancies, surgical revision of the stoma was needed due to obstruction (27.3%), prolapse (27.3) and peristomal herniation (45.6%). A full overview of documented complications can be found in table 1. Of the fourteen women who completed the questionnaire, six reported non-resolved complications at least six months after delivery (42.9%). Eighteen pregnancies ended in a caesarean section (40.9%). There were 45 infants (one gemelli pregnancy), of whom eight (17.8 %) were born prematurely,eight (17.8 %) had low birth weight (17.8%) and eight (17.8 %) were small for their gestational age.

Conclusion
Being pregnant and giving birth with an enterostomy is feasible, but is in two third of pregnancies associated with complications. A reduced stoma output and leakage can be prevented by early counseling. Proper guidance before, during pregnancy and postpartum is therefore crucial for IBD-patients with an enterostomy.