Molecular Features Research Articles

Mfgnn: Multi-Scale Feature-Attentive Graph Neural Networks for Molecular Property Prediction.

In the realm of artificial intelligence-driven drug discovery (AIDD), accurately predicting the influence of molecular structures on their properties is a critical research focus. While deep learning models based on graph neural networks (GNNs) have made significant advancements in this area, prior studies have primarily concentrated on molecule-level representations, often neglecting the impact of functional group structures and the potential relationships between fragments on molecular property predictions. To address this gap, we introduce the multi-scale feature attention graph neural network (MfGNN), which enhances traditional atom-based molecular graph representations by incorporating fragment-level representations derived from chemically synthesizable BRICS fragments. MfGNN not only effectively captures both the structural information of molecules and the features of functional groups but also pays special attention to the potential relationships between fragments, exploring how they collectively influence molecular properties. This model integrates two core mechanisms: a graph attention mechanism that captures embeddings of molecules and functional groups, and a feature extraction module that systematically processes BRICS fragment-level features to uncover relationships among the fragments. Our comprehensive experiments demonstrate that MfGNN outperforms leading machine learning and deep learning models, achieving state-of-the-art performance in 8 out of 11 learning tasks across various domains, including physical chemistry, biophysics, physiology, and toxicology. Furthermore, ablation studies reveal that the integration of multi-scale feature information and the feature extraction module enhances the richness of molecular features, thereby improving the model's predictive capabilities.

Modeling Sporadic Progressive Supranuclear Palsy in 3D Midbrain Organoids: Recapitulating Disease Features for In Vitro Diagnosis and Drug Discovery.

Progressive Supranuclear Palsy (PSP) is a severe neurodegenerative disease characterized by tangles of hyperphosphorylated tau protein and tufted astrocytes. Developing treatments for PSP is challenging due to the lack of disease models reproducing its key pathological features. This study aimed to model sporadic PSP-Richardson's syndrome (PSP-RS) using multi-donor midbrain organoids (MOs). The MOs were generated by pooling induced pluripotent stem cells (iPSCs) from 4 patients with sporadic probable PSP-RS and compared them with MOs from 3 healthy control (HC) subjects. We performed comprehensive analyses of MOs over 120 days to assess neuronal death, reactive gliosis, and the accumulation of 4R-tau and hyperphosphorylated tau forms (pThr231, pSer396, pThr181, and pSer202/pThr205 [AT8]) using immunofluorescence microscopy and Western blot. On day 90, immunohistochemical analysis using pSer396 and AT8 antibodies was conducted to assess disease pathology. PSP-derived MOs showed progressive size reduction compared with HC-derived MOs, linked to upregulated apoptosis-related mRNA markers. Dopaminergic neuron degeneration was marked by decreased tyrosine hydroxylase (TH) and increased neurofilament light chain (NfL). Immunofluorescence and Western blot revealed accumulation of all investigated tau forms with a peak at 90 days, along with a significant rise in GFAP-positive cells in PSP-derived MOs. Immunochemistry confirmed typical PSP histological alterations, such as neurofibrillary tangles and tufted-shaped astrocytes, absent in HC-derived organoids. We developed a robust in vitro PSP model reproducing the key molecular and histologic features of the disease. This result holds promise for advancing basic and clinical research in PSP, paving the way for in vitro molecular diagnosis and identification of novel therapeutic targets. ANN NEUROL 2025.

Pathology of the spleen : Differential diagnosis of splenomegaly

After describing the anatomy of the spleen and the most important immunohistochemical stains for identifying cellular constituents of the normal splenic compartments, etiologies of splenomegaly and the diagnostic approach for spleen biopsies are discussed using the example of aNorth African patient with arecent migration background and sudden fever. The focus is on infectious diseases and the morphology and molecular features of hematolymphoid neoplasms, particularly the primary "splenic B‑cell lymphomas" according to the World Health Organization (WHO) classification. The importance of clinicopathological correlations and interdisciplinary cooperation in splenic pathology is emphasized.

The multi-omics signatures of telomere length in childhood

BackgroundTelomere length is an important indicator of biological age and a complex multi-factor trait. To date, the telomere interactome for comprehending the high-dimensional biological aspects linked to telomere regulation during childhood remains unexplored. Here we describe the multi-omics signatures associated with childhood telomere length.MethodsThis study included 1001 children aged 6 to 11 years from the Human Early-life Exposome (HELIX) project. Telomere length was quantified via qPCR in peripheral blood of the children. Blood DNA methylation, gene expression, miRNA expression, plasma proteins and serum and urinary metabolites were measured through microarrays or (semi-) targeted assays. The association between each individual omics feature and telomere length was assessed in omics-wide association analyses. In addition, a literature-guided, sparse supervised integration method was applied to multiple omics, and latent components were extracted as predictors of child telomere length. The association of these latent components with early-life aging risk factors (child lifestyle, body mass index (BMI), exposure to smoking, etc.), were interrogated.ResultsAfter multiple-testing correction, only two CpGs (cg23686403 and cg16238918 at PARD6G gene) out of all the omics features were significantly associated with child telomere length. The supervised multi-omics integration approach revealed robust associations between latent components and child BMI, with metabolites and proteins emerging as the primary contributing features. In these latent components, the contributing molecular features were known as involved in metabolism and immune regulation-related pathways.ConclusionsFindings of this multi-omics study suggested an intricate interplay between telomere length, metabolism and immune responses, providing valuable insights into the molecular underpinnings of the early-life biological aging.

A novel X-linked variant c.1772delG (p.G591fs*20) in IRS4 in two related patients with central hypothyroidism

Introduction: Central hypothyroidism (CeH) is characterized by thyroid hormone deficiency due to impairment of pituitary thyroid stimulating hormone (TSH) or hypothalamic TRH biosynthesis. It is extremely rare and affects approximately 1:16,000-100,000 individuals. Diagnosis, especially of isolated CeH, may be challenging. CeH is often seen as a part of multiple pituitary hormone deficiencies, but it can also be seen as isolated CeH. To date, some variants that can cause CeH have been identified; although in a number of patients the cause has not been clarified. Recently, variants of the insulin receptor substrate 4 (IRS4) gene have been reported to be the cause of isolated CeH. Herein, we report two related patients and their family with carriers with a novel X-linked frameshift variant in the IRS4 gene. It has also been shown that thyroid function may be slightly affected in the heterozygous female carriers in our study. Case Presentation: Herein, we reported two Turkish male patients with CeH due to a hemizygous variant in IRS4. The index case was a 15-year-and-2-month male who presented with a low serum free thyroxin level, which was incidentally detected. Conclusion: Isolated CeH should kept in mind in insistent low fT4 levels without an increase in TSH levels. Genetic testing can aid in identifying the underlying cause of CeH in such cases. This report demonstrates the significance of providing comprehensive laboratory and molecular features of the patients and carriers with the IRS4 variants.

Terahertz Multicolor Imaging of Opaque Objects Using Self-Mixing Interferometry with Quantum-Cascade Lasers

Self-mixing interference in a terahertz quantum-cascade laser has been demonstrated to be suitable for the detection of weak signals scattered or reflected by the target. This technology has achieved the high-sensitivity detection of complex refractive indices, surface/interface morphologies and molecular feature spectra. Here, a set of terahertz quantum-cascade lasers with different lasing frequencies is used to inspect a tiny amount of powder concealed inside a polytetrafluoroethylene tablet by using self-mixing interferometry combined with the penetration properties of terahertz waves. Multicolor spectral images were acquired, which were synthesized by absorption contrast images obtained at different lasing frequencies. They enable the detection of the spatial distribution of hidden objects which are totally opaque in visual light and allow for them to be identified with spectral absorption characteristics. Self-mixing interference technology can also obtain phase information when a terahertz wave interacts with a tablet, showing the difference between the hidden object and surroundings from another dimension. Our research may provide a strategy for the development of terahertz multispectral imaging technology for the inspection of hidden trace residues.

Multispectral laser-scanning pulse-sampling fluorescence lifetime system for large-scale tissue imaging

We report a multispectral laser-scanning pulse-sampling fluorescence lifetime imaging (LSPS-FLIm) system designed for rapid, high-resolution imaging of large tissue specimens. This system provides a substantial imaging field of view (FoV) of 6 × 15 cm2 with a high spatial resolution of ∼17.5 µm. The LSPS-FLIm system has been tested on a range of fluorescent dyes, endogenous tissue fluorophores, and tissue specimens with varied sizes and properties. These tests demonstrate the system’s versatility in resolving morphological and molecular features, enabling centimeter-scale FoV imaging, and distinguishing complex microstructures in tissue specimens. With the capability to maintain high imaging quality and acquisition speed while minimizing tissue damage, LSPS-FLIm represents a promising advancement in the field of fluorescence lifetime imaging for biological and clinical applications.

Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers.

Many transcription factors (TFs) have been shown to bind to super-enhancers, forming transcriptional condensates to activate transcription in various cellular systems. However, the genomic and epigenomic determinants of phase-separated transcriptional condensate formation remain poorly understood. Questions regardingwhich TFs tend to associate with transcriptional condensates and what factors influence their association are largely unanswered. Here we systematically analyzed 571 DNA sequence motifs across the human genome and 6650 TF binding profiles across different cell types to identify the molecular features contributing to the formation of transcriptional condensates. We found that the genomic distributions of sequence motifs for different TFs exhibit distinct clustering tendencies. Notably, TF motifs with a high genomic clustering tendency are significantly associated with super-enhancers. TF binding profiles showing a high genomic clustering tendency are further enriched at cell-type-specific super-enhancers. TFs with a high binding clustering tendency also possess high liquid-liquid phase separation abilities. Compared to nonclustered TF binding, densely clustered TF binding sites are more enriched at cell-type-specific super-enhancers with higher chromatin accessibility, elevated chromatin interactionand stronger association with cancer outcomes. Our results indicate that the clustered genomic binding patterns and the phase separation properties of TFs collectively contribute to the formation of transcriptional condensates.

Analysis of Structures of SARS-CoV-2 Papain-like Protease Bound with Ligands Unveils Structural Features for Inhibiting the Enzyme

The COVID-19 pandemic, driven by the novel coronavirus SARS-CoV-2, has drastically reshaped global health and socioeconomic landscapes. The papain-like protease (PLpro) plays a critical role in viral polyprotein cleavage and immune evasion, making it a prime target for therapeutic intervention. Numerous compounds have been identified as inhibitors of SARS-CoV-2 PLpro, with many characterized through crystallographic studies. To date, over 70 three-dimensional (3D) structures of PLpro complexed ligands have been deposited in the Protein Data Bank, offering valuable insight into ligand-binding features that could aid the discovery and development of effective COVID-19 treatments targeting PLpro. In this study, we reviewed and analyzed these 3D structures, focusing on the key residues involved in ligand interactions. Our analysis revealed that most inhibitors bind to PLpro’s substrate recognition sites S3/S4 and SUb2. While these sites are highly attractive and have been extensively explored, other potential binding regions, such as SUb1 and the Zn(II) domain, are less explored and may hold untapped potential for future COVID-19 drug discovery and development. Our structural analysis provides insights into the molecular features of PLpro that could accelerate the development of novel therapeutics targeting this essential viral enzyme.

Assessing spatial sequencing and imaging approaches to capture the molecular and pathological heterogeneity of archived cancer tissues.

Spatial transcriptomics (ST) offers enormous potential to decipher the biological and pathological heterogeneity in precious archival cancer tissues. Traditionally, these tissues have rarely been used and only examined at a low throughput, most commonly by histopathological staining. ST adds thousands of times as many molecular features to histopathological images, but critical technical issues and limitations require more assessment of how ST performs on fixed archival tissues. In this work, we addressed this in a cancer-heterogeneity pipeline, starting with an exploration of the whole transcriptome by two sequencing-based ST protocols capable of measuring coding and non-coding RNAs. We optimised the two protocols to work with challenging formalin-fixed paraffin-embedded (FFPE) tissues, derived from skin. We then assessed alternative imaging methods, including multiplex RNAScope single-molecule imaging and multiplex protein imaging (CODEX). We evaluated the methods' performance for tissues stored from 4 to 14 years ago, covering a range of RNA qualities, allowing us to assess variation. In addition to technical performance metrics, we determined the ability of these methods to quantify tumour heterogeneity. We integrated gene expression profiles with pathological information, charting a new molecular landscape on the pathologically defined tissue regions. Together, this work provides important and comprehensive experimental technical perspectives to consider the applications of ST in deciphering the cancer heterogeneity in archived tissues. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Characterizing Three Heat Shock Protein 70 Genes of Aphis gossypii and Their Expression in Response to Temperature and Insecticide Stress.

Aphis gossypii is a highly polyphagous pest that causes substantial agricultural damage. Temperature and insecticides are two major abiotic stresses affecting their population abundance. Heat shock proteins play an essential role in cell protection when insects are exposed to environmental stresses. Three ApHsp70 genes were cloned from A. gossypii, and characterized their molecular features and expression profiles in response to temperature and insecticide stress. The deduced amino acid sequences of these proteins exhibited characteristic Hsp70 family signatures, and their tissue-specific expression patterns revealed their highest activity to be in the salivary glands under 35 °C. The temperature inductive assay further indicated that the expression of the three ApHsp70 genes was markedly upregulated under heat stress but not under cold shock. Furthermore, exposure to LC25 and LC50 concentrations of three insecticides triggered the upregulation of these ApHsp70 genes. The RNA interference (RNAi)-mediated suppression of ApHsp68 expression heightened cotton aphid's susceptibility to insecticides (acetamiprid and sulfoxaflor). Moreover, our study found that the sulfoxaflor-resistant strain of A. gossypii (Sul-R) displayed a higher survival rate compared with the sulfoxaflor-sensitive strain (Sul-S) under heat shock conditions. These results suggest that these three ApHsp70 genes play an essential role in response to both heat and insecticide stress.

The clinical and molecular landscape of diffuse hemispheric glioma, H3 G34-mutant.

Diffuse hemispheric glioma, histone 3 (H3) G34-mutant, has been newly defined in the 2021 WHO classification of central nervous system tumors. Here we sought to define the prognostic roles of clinical, neuroimaging, pathological, and molecular features of these tumors. We retrospectively assembled a cohort of 114 patients (median age 22 years) with diffuse hemispheric glioma, H3 G34-mutant, CNS WHO grade 4 and profiled the imaging, histological and molecular landscape of their tumors. Compared with glioblastoma, H3 G34-mutant diffuse hemispheric gliomas exhibited less avid contrast enhancement, necrosis and edema on MRI. Comprehensive analyses of mutational and DNA copy number profiles revealed recurrent mutations in TP53 and ATRX, homozygous deletions of CDKN2A/B, and amplifications of PDGFRA, EGFR, CCND2, and MYCN. MGMT promoter methylation was detected in 79 tumors (75%); 11 tumors (13%) showed DNA copy number profiles suggestive of circumscribed deletions on 10q26.3 involving the MGMT locus. Median survival was 21.5 months. Female sex, gross total resection, and MGMT promoter methylation were positive prognostic factors on univariate analysis. Among radiological, pathological and molecular features, absence of pial invasion, and presence of microvascular proliferation and CDK6 amplification were positive prognostic factors on univariate analyses. This study refines the clinical and molecular landscape of H3 G34-mutant diffuse hemispheric gliomas. Dedicated trials for this novel tumor type are urgently needed.

P0082 Proteomic profiling of colonic mucosa in patients with ulcerative colitis: detection of molecular patterns of inflammation.

Abstract Background The mechanisms of recurrence and progression of ulcerative colitis (UC) require detailed study. Modern advances in proteomic analysis methods are ideal for studying the molecular characteristics of inflammation in the colonic mucosa (CM) of UC patients. Methods The study was comparative cohort with parallel design and included 88 patients (range from 22 to 35 years, 37 men and 51 women): 53 (60.2%) pancolitis and 35 (39.8%) left-sided UC, mild and moderate activity. The duration of UC was 5.3 years. The control group included 30 healthy individuals. Biosamples of CM in patients with UC in the active stage and in healthy persons were received by ileocolonoscopy with CM biopsy. The separation of individual proteins of CM was based on technologies of IEF, SDS-PAGE, 2DPAGE, by standard sets (MB-HIC C8 Kit, MB-IMAC Cu, MB-Wax Kit, «Bruker», USA). Automated mass spectrometry imaging was performed by MALDI-TOF-MS/MS, Ultraflex II, «Bruker», USA). The partially identified sequences were then submitted to “BLAST protein-protein” and screened against the Homo sapiens Swissprot database to check if this identification matched the MASCOT-identification (Matrix Science, UK). The data of the molecular interactions and functional features of proteins were received with STRING 10 database. Results Based on the data of standard methods of identification of UC and molecular phenotyping of colon mucosa we conducted new prognostic markers, molecular pathways of UC and diagnostic tests in patients with UC. We identified functional groups of peptides and proteins in molecular patterns of CM (fig. 1). SMAD family member 2 (SMAD2) activates the transcription of TFG1β, that leads the development of fibrosis in colon submucosa in UC patients; the stimulation of the expression of apoС-III in affected CM in UC is associated with the activation of the FOXO1 signaling pathway that supports inflammatory processes; caspase 8 protects colonocytes from TNFα-induced cell death through a necroptosis mechanism via the blockade of the RIP3 expression. Significant decrease of the expression of PPARγ promotes the activation of STAT and AP-1 signaling pathways, that promotes the increase of the synthesis of IL-2, 6, 8, 12,TNFα, matrix metalloproteinases, the activity of immune and inflammation processes in colon mucosa. The reduction of expression of β-defensin-1 in cells of colon mucosa are accompanied with increased expression of CCR6, that promotes the formation of inflammatory infiltrates in colonic submucosa in UC.The molecular interactions of β-defensin-1 are presented on figure 2. Conclusion Bioinformatics analysis revealed the presence of the new potentially markers of the progression UC, that’s may provide for the development of novel diagnostic tests for UC.

DOP128 Spatial transcriptomic analysis reveals evolutionary dynamics in colitis-associated colorectal cancer

Abstract Background Colitis-associated colorectal cancer (CAC) is a severe complication of inflammatory bowel disease, particularly ulcerative colitis. Despite its clinical significance, the spatiotemporal dynamics of neoplastic progression in CAC remain poorly understood. This study aimed to elucidate the evolutionary trajectory of CAC using spatial transcriptomics. Methods We employed spatial transcriptomics to analyze four tissue samples from three patients with ulcerative colitis at various stages of neoplastic progression. Whole-slide spatial transcriptomics RNA sequencing was performed, enabling simultaneous analysis of gene expression and tissue architecture. Integrated spatial transcriptomic data revealed recurring epithelial programs along the progression of copy number alteration. Results Our analysis using copy number variation (CNV) score and Hematoxylin and Eosin (H&E) staining image revealed progressive changes in gene expression patterns as tissue transitioned from non-tumor to pre-tumor and finally to tumor states. This progression was quantified using beta coefficient values, allowing us to track gradual alterations in gene expression across the disease continuum. We identified a core set of 48 genes that exhibited consistent changes across all four analyzed samples. Among these, 40 genes showed a progressive decrease in expression, while eight genes, including CLDN1, E2F1, and RECQL4, demonstrated a gradual increase in expression as the tissue advanced towards a tumorous state. These upregulated genes pointed to potential oncogenic drivers or compensatory mechanisms activated during tumor development. Pathway analysis of the 48 genes revealed enrichment in key cellular processes, including p53 signaling, transcriptional regulation by E2F factors, and role of PKR in interferon induction and antiviral response. Upstream Regulator analysis revealed YAP1 and TGFB1 as the most significant regulators, highlighting the importance of transcriptional control and growth factor signaling in CAC development. Conclusion This study provides unprecedented insights into the spatiotemporal dynamics of CAC progression. By leveraging spatial transcriptomics, we have mapped the evolutionary trajectory of CAC at high resolution, revealing key molecular events and spatial features associated with disease progression. These findings not only enhance our understanding of CAC pathogenesis but also highlight potential targets for early intervention and personalized treatment strategies.

P0189 Microbial and Molecular Profiling of the appendix of pediatric patients with inflammatory bowel diseases

Abstract Background Inflammatory bowel diseases (IBD), including Crohn disease (CD) and ulcerative colitis (UC), are chronic inflammatory conditions influenced by genetic, environmental, and microbial factors.1,2 Emerging evidence suggests a role for the appendix in IBD with immune and microbe impacts on the colon. Peri-appendicular patch (PAP) inflammation is observed in some UC patients; appendectomy has shown protective effects, reducing relapse and colectomy rates in UC.3,4 However, the mechanisms underlying these associations remain unclear. This study aims to explore these mechanisms by characterizing microbial species, molecular pathways, and host-microbiota interactions in the appendix of IBD patients. Methods Mucus from the appendix and non-inflamed colon of 10 pediatric IBD and 5 non-IBD patients undergoing elective surgical resection was collected for DNA and whole-genome sequencing. RNA and DNA from appendix tissues were used for RNA-seq and 16S rRNA sequencing, respectively. Metagenomic analysis was performed across all platforms. Fluorescence in-situ hybridization (FISH) and immunofluorescence defined localization. Results Proteobacteria were significantly enriched in IBD (mean = 27.23%±32%) compared to non-IBD mucus samples (mean = 1.6%±0.23%, p = 0.0052), with reduced bacterial diversity in the appendix of IBD patients. Differential abundance analysis revealed site-specific changes in MetaCyc pathways, notably in the IBD-appendix; for example, ABH and Lewis epitopes biosynthesis pathways were highly enriched in this organ. 38 of 50 MetaCyc pathways were linked to specific species, with E. coli contributing to 32 pathways. Immune and inflammatory pathways were significantly upregulated in the IBD-appendix. Strong correlations were observed between host tissue and microbial pathways in IBD mucus; for instance, Chondroitin Sulfate and Dermatan Sulfate Biosynthesis bacterial pathways were positively correlated with the upregulated host pathway Chemokine Receptors Bind Chemokines (Rho = 0.8851 and 0.88549, respectively), reflecting host-bacteria interaction in the appendix. Bacteria were observed in the mucus layer of IBD-appendix. Conclusion The appendix in IBD exhibits unique molecular and microbial features, offering key insights into its role in IBD pathogenesis and potential therapeutic avenues, reinforcing the efficacy of interventions such as appendectomy in UC.

P0146 Phosphoglycerate dehydrogenase plays a vital role in ER-stress-related intestinal inflammation

Abstract Background Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation and metabolic dysregulation in the intestinal epithelium. Serine, a non-essential amino acid synthesized via the rate-limiting enzyme phosphoglycerate dehydrogenase (PHGDH) maintains cellular redox balance. Serine metabolism is upregulated in cancer and immune cells, supporting survival and growth. Our previous story shows ER stress-mediated rewiring of serine metabolism is a key molecular feature in IBD. However, the mechanism of how it influences ER stress in IBD remains unclear. Methods To explore the molecular regulation of de novo serine synthesis via PHGDH, we used murine intestinal epithelial cells (Mode-K cells) and murine intestinal organoids. WB and IHC were performed in vivo to analyze ER stress and PHGDH on DSS colitis model. Mode-K cells were subjected to serine starvation and co-treated with LPS. Proinflammatory cytokines (Cxcl1, Tnfα, Il6) were evaluated by qPCR and ELISA. Metabolic supplement formate and hypoxanthine were tested to mitigate hyperinflammation. Total starvation was assessed by using serine deprivation medium and PHGDH inhibitor BI-4916. Tunicamycin, NAC, Y27632, and rapamycin were used to study the biofunction under ER stress effect by using qPCR, WB, and IF. Cell viability was performed by CellTiter-Glo® 2.0 Cell Viability Assay. RNA sequencing and proteomic analyses were performed to investigate molecular mechanisms. Clinical analysis of PHGDH was assessed in two cross-sectional IBD cohorts correlating PHGDH expression with endoscopic or clinical disease activity. Results We show elevated ER stress and de novo serine synthesis in DSS colitis model. Using total starvation to completely block serine pathway, we observed increased ER stress which subsequently leads to dramatically enhanced inflammation signature under LPS treatment. ER stress induced by total starvation also leads to mitochondria dysfunction as assessed by Seahorse and JC-1 assay. By using cell viability assay and IF, we show ER stress induces AIF-mediated anoikis. Autophagy induced by ROS under ER stress conditions can protect cells from anoikis and inflammation. Combining RNAseq and proteomic analysis, we identified CEBPB as the critical regulator in mediating cellular anoikis and inflammation during ER stress which were further confirmed by IF and qPCR. Finally, we observed unregulated PHGDH in IBD patients showing a strong association between serine metabolism and IBD severity. Conclusion In this study, we demonstrate the critical roles of PHGDH and Serine metabolism in regulating cellular inflammatory responses under ER stress. Notably, we reveal a protective role of ROS in ER stress and inflammation, providing new insights into ER stress and IBD severity.

P0121 Molecular features of extracellular matrix activity persist in patients who achieve mucosal healing with ustekinumab induction

Abstract Background Phase 3 trials demonstrate rates of secondary loss of response of up to 40% for many advanced therapies in ulcerative colitis (UC). At a molecular level, this may be explained by persistence of inflammatory mediators in the mucosa despite successful treatment induction, and transcripts involved in leukocyte infiltration persist in patients responding to infliximab and vedolizumab compared to non-IBD controls [1]. We considered if any disease-relevant transcripts persisted in ustekinumab induction responders and if these differed depending on symptom resolution. Methods We interrogated data from the UNIFI trial, where baseline mucosal biopsies from patients treated with ustekinumab for moderate-to-severe UC underwent RNA profiling (Gene Expression Omnibus, GSE206285). Patients who achieved combined histo-endoscopic (mucosal) healing either with (disease clearance, “DC”) or without (mucosal healing, “MH only”) clinical remission at week 8 were included in subsequent analyses, along with non-IBD controls from this cohort (n=18). We compared gene expression and the enrichment of functional pathways using limma and GSEA (gene set enrichment analysis), respectively, between the two groups of responders and controls in R (v 4.2.3, Vienna). The Reactome database of pathway annotations was used. Gene signature enrichment was calculated by gene set variation analysis. Results Of the 54 patients who responded to ustekinumab, 15 experienced MH only and 39 had DC. Principal component analysis showed that these responders were distinct from controls but overlapped with each other (figure 1). For MH only compared to controls, there were 8375 differentially expressed genes (DEGs), of which 4936 were upregulated. There were 8778 DEGs between DC and controls, with 5331 upregulated. GSEA revealed that the DEGs in each comparison mainly represented pathways relating to the extracellular matrix (ECM), such as ECM degradation and collagen formation. There were no DEGs between MH only and DC but GSEA suggested that interleukin signalling and ECM organisation were upregulated in MH only. Interestingly, there was large heterogeneity in enrichment of the DEGs amongst all the responders. Similarly, there was wide variation in the enrichment of genes relating to the ECM. Conclusion Despite resolution of histo-endoscopic disease activity at week 8 in ustekinumab-treated UC patients, there was persistence of molecular inflammation, particularly ECM-related genes. However, the extent of this varied between patients; future work will examine if this explains why some eventually lose response whilst others maintain long-term remission. Ongoing inflammatory mechanisms may explain symptom persistence despite mucosal healing.

P1193 Cross-Disease Analysis Unveils CXCL6 as a Shared Immune Mediator in Ulcerative Colitis and Periodontitis: Novel Insights from Bioinformatics

Abstract Background Emerging evidence underscores a pathological bidirectional relationship between ulcerative colitis (UC) and periodontitis (PD) through the oral-gut axis, highlighting a complex interplay with significant implications for patient health. However, the shared molecular features underlying this interaction have yet to be explored. Methods In this study, we initially established a potential link between periodontitis and ulcerative colitis based on Mendelian randomization. Following this, we analyzed gene expression profiles from the Gene Expression Omnibus (GEO) for both UC and PD, identifying overlapping genes between UC-differentially expressed genes (DEGs) and PD-DEGs. Results Functional enrichment analysis revealed associations with various immune pathways, underscoring the immunological relevance of these genes. Intersection with immune-related genes (IRGs) yielded 25 candidate genes, among which CXCL6 emerged as a central hub gene identified through three machine learning methods: LASSO, RF, and SVM-RFE. Subgroup analysis based on CXCL6 expression demonstrated that the CXCL6-high group exhibited increased immune cell infiltration and enhanced immune function. Moreover, our investigation of CXCL6 in relation to biological therapies in UC patients indicated a reduction in CXCL6 levels following treatment, suggesting potential benefits of biological therapies. Finally, we validated the expression of CXCL6 in a rat model of dual diseases. Conclusion In summary, CXCL6 is identified as a diagnostic biomarker and potential therapeutic target for UC combined with PD, warranting further investigation into its clinical significance and associated mechanisms.

P0252 Mild Crohn’s disease is associated with altered sphingolipid metabolism and reduced neutrophilic inflammation

Abstract Background Around 20-30% of patients with Crohn's disease (CD) experience a mild disease course. However, identifying patients likely to maintain a mild course is challenging. This study aimed to identify molecular features of mild CD by exploring biological datasets from two large patient cohorts. Methods Patients with mild CD were analysed from two longitudinal cohorts: the Mount Sinai Crohn's and Colitis Registry (MSSCR) observational cohort and the Ocean State Crohn’s and Colitis Registry (OSCCAR) inception cohort. Baseline assessments in both cohorts included biological/immunomodulator use, history of IBD-related surgeries, and complications (stricturing, penetrating, and perianal CD). Mild CD was defined by the absence of these variables at baseline and after five years of follow-up (Fig. 1A). The remaining patients were mild at baseline but progressed during follow-up. Patients with mild CD and those who progressed after being mild at baseline were evaluated for potential molecular biomarkers including circulating metabolites (metabolomics), immune cell profiles (multiparametric flow cytometry), serum proteomics, and intestinal transcriptomics. Results In total, 100 (MSSCR) and 152 (OSCCAR) patients were characterized, with 55 (55.0%) and 74 (48.7%) classified as mild CD, respectively. Intestinal transcriptomic analysis revealed downregulation of genes associated with neutrophilic inflammation and innate immunity, including SAA, DUOXA2, FCGR3B, LCN2, S100A8, and AQP9 (Fig. 1B). Flow cytometry showed lower frequencies of neutrophils (CD16+), lower neutrophil-to-lymphocyte ratios (NLR), and higher counts of NK and total B cells in mild CD (Fig. 1C). Metabolomic analysis identified ceramide- and sphingomyelin compounds (particularly acyl-CoA chain lengths C14-16 and C22-26) as positively associated with mild CD (odds ratios [OR] >2.0), whereas primary and secondary bile acids and amino acid derivatives from lysine, tyrosine, and proline metabolism were inversely associated (Fig. 1D). Proteomic analysis in OSCCAR demonstrated associations between C-X-C motif chemokine ligand 9 (CXCL9), macrophage colony stimulating factor (CSF-1), and TGF-β1 latency-associated peptide (LAP-TGF-β), and an inverse association for Delta and Notch-like epidermal growth factor-related receptor (DNER) with mild CD (adjusted P<0.05) (Fig. 1E). Conclusion This study provides multi-omics-based biomarker signatures of mild CD, which primarily relate to altered ceramide- and sphingomyelin metabolites and lower systemic neutrophilic inflammation. Future studies focusing on the biological significance and potential clinical impact on disease monitoring and therapeutic strategies are warranted.

High CDC20 levels increase sensitivity of cancer cells to MPS1 inhibitors.

Spindle assembly checkpoint (SAC) inhibitors are a recently developed class of drugs, which perturb chromosome segregation during cell division, induce chromosomal instability (CIN), and eventually lead to cell death. The molecular features that determine cellular sensitivity to these drugs are not fully understood. We recently reported that aneuploid cancer cells are preferentially sensitive to SAC inhibition. Here we report that sensitivity to SAC inhibition by MPS1 inhibitors is largely driven by the expression of CDC20, a main mitotic activator of the anaphase-promoting complex (APC/C),and that the effect of CDC20 is larger than that of the APC/C itself. Mechanistically, we discovered that CDC20 depletion prolongs metaphase duration, diminishes mitotic errors, and reduces sensitivity to SAC inhibition. We found that aneuploid cells express higher basal levels of CDC20, which shortens the duration of metaphase and leads to multiple mitotic errors, resulting in increased long-term sensitivity to the additional CIN induced by SAC inhibition. Our findings propose high CDC20 expression as a molecular feature associated with the sensitivity to SAC inhibition therapy and as a potential aneuploidy-induced cellular vulnerability.