Mucosal expression of PI3, ANXA1, and VDR discriminates Crohn's disease from ulcerative colitis

Causal Relationship between Branched-Chain Amino Acids and Inflammatory Bowel Disease: A Bidirectional and Multivariable Mendelian Randomization Study

Aims/Background The relationship between dysregulated branched-chain amino acid (BCAA) and inflammatory bowel disease (IBD) is not fully understood. This study applied a bidirectional, two-sample Mendelian randomization (MR) approach to explore the potential causal relationship between circulating BCAA levels and IBD. Methods Genome-wide association studies (GWAS) data on total BCAA levels, comprising leucine, valine, and isoleucine, were utilized. Data on IBD and its subtypes were sourced from the FinnGen study. The primary analytical method was the inverse-variance weighted (IVW) MR. To determine the direct causal effect of BCAA levels on IBD risk while accounting for confounders, we employed multivariable Mendelian randomization (MVMR). Results IVW analysis revealed a positive correlation between circulating total BCAA levels, including valine, leucine, and isoleucine, and an increased risk of Crohn's disease (CD). No causal link was detected between BCAA levels and overall IBD or ulcerative colitis (UC). In the MVMR analysis, adjusting for common risk factors further validated a direct causal effect of elevated BCAA levels on CD risk. Conclusion Our findings suggest that elevated circulating BCAA levels are associated with an increased risk of CD. Further research is warranted to explore the potential implications of these findings for CD risk management.

Gene expression regulation and polyadenylation in ulcerative colitis via long-chain RNA sequencing

BACKGROUND

Ulcerative colitis (UC) is an immune-mediated chronic intestinal disease, with a pathogenesis that remains incompletely understood. The purpose of this study is to analyze the difference of gene expression between UC patients and healthy controls using Oxford Nanopore Technology's long-read RNA sequencing (ONT-RNA-seq) and to explore how alternative polyadenylation (APA) site selection contributes to UC pathogenesis.

METHODS

Colon tissue samples from UC and normal controls (NC) were collected, and total RNA was extracted and sequenced using ONT-RNA-seq technology. Various bioinformatics analyses were performed, including differential expression gene (DEG) analysis, functional enrichment analysis, APA site analysis, and prediction miRNAs and RNA binding proteins (RBPs) targets, to explore the molecular mechanism underlying UC.

RESULTS

ONT-RNA-seq analysis revealed that the expression levels of ACSF2, NPY, SLC26A3, BRINP3, and PKLPP2 were significantly lower in UC patients compared to the NC group, while the expression levels of CCL20, CCL21, CD55, IDO1, LCN2, NOS2, CCL11, OLFM4, ANXA1, REG1A, S100A9, SLPI, SPINK1, and AGR2 were significantly higher. Functional enrichment analysis showed that DEGs were closely related to immune and inflammatory responses, which in turn are related to many challenges in the diagnosis and treatment of UC. Mechanistically, APA site selection was found to contribute to the regulation of gene expression in UC, and some APA genes were identified as potential regulators of miRNAs and RBPs. Vene diagram revealed significant overlap between miRNA- and RBP-targeted genes and DEGs, suggesting that APA genes may modulate genes expression in UC through miRNA and RBP targeting. Additionally, five key APA genes--CD38, NCALD, SMIM31, GPX7, and SWAP70--were identified as potentially playing crucial role in UC pathogenesis.

CONCLUSIONS

This study provides new insights into the molecular mechanisms of UC through ONT-RNA-seq technology, especially in gene expression regulation and APA site selection.

Proof of Concept Study: Comparison of Semi-Automated RNA Isolation Methods from Archived Formalin-Fixed, Paraffin-Embedded Tissues with Clinical Routine RNA Isolation Methods

High-quality RNA is crucial in clinical diagnostics and precision medicine. Formalin-fixed and paraffin-embedded (FFPE) tissues pose a challenge due to nucleic acid fragmentation and crosslinking. In this pilot study, various commercially available techniques for extracting RNA from small FFPE samples were compared. We evaluated the KingFisher Duo automated system or the manual MagMAX FFPE DNA/RNA Ultra Kit as an RNA extraction method combined with either a xylene, d-limonene, or AutoLys M tubes deparaffinization method. Additionally, the automated Maxwell RSC RNA FFPE kit and the High Pure FFPET RNA Isolation Kit were examined using FFPE samples from inflammatory bowel disease (IBD) patients, as well as samples from ovarian, kidney, and breast cancer and the skin. The KingFisher Duo system gave a higher yield and more consistent RNA quantities, especially from small volumes of IBD samples, compared to manual extraction. The deparaffinization method also impacted results, with AutoLys M tubes proving effective in combination with the KingFisher Duo system. Conversely, the High Pure kit exhibited higher yields for larger FFPE samples. While RNA integrity is a critical factor, particularly for messenger RNA (mRNA) expression studies, its role is less prominent in microRNA (miRNA) analyses. Recognizing this, our study focused on RNA yield and purity (A260/A230) to evaluate RNA extraction methods for various sample types. These findings emphasize the importance of selecting appropriate RNA extraction methods based on sample characteristics and research goals, highlighting the performance of automated methods and the impact of deparaffinization choices. The findings contribute to refining RNA extraction for molecular biology analyses, suggesting avenues for further exploration, including cost-effectiveness under specific experimental conditions.

Short noncoding RNAs as predictive biomarkers for the development from inflammatory bowel disease unclassified to Crohn's disease or ulcerative colitis

Numerous pathogenic processes are mediated by short noncoding RNAs (sncRNA). Twenty percent of inflammatory bowel disease (IBD) patients are labelled as IBD unclassified (IBDU) at disease onset. Most IBDU patients are reclassified as Crohn's disease (CD) or ulcerative colitis (UC) within few years. Since the therapeutic methods for CD and UC differ, biomarkers that can forecast the categorization of IBDU into CD or UC are highly desired. Here, we investigated whether sncRNAs can predict CD or UC among IBDU patients. 35 IBDU patients who were initially diagnosed with IBDU were included in this retrospective investigation; of them, 12, 15, and 8 were reclassified into CD (IBDU-CD), UC (IBDU-UC), or remained as IBDU (IBDU-IBDU), respectively. Eight IBD patients, were included as references. SncRNA profiling on RNA from mucosal biopsies were performed using Affymetrix miRNA 4.0 array. Selected probe sets were validated using RT-qPCR. Among all patients and only adults, 306 and 499 probe sets respectively were differentially expressed between IBDU-CD and IBDU-UC. Six of the probe sets were evaluated by RT-qPCR, of which miR-182-5p, miR-451a and ENSG00000239080 (snoU13) together with age and sex resulted in an AUC of 78.6% (95% CI: 60-97) in discriminating IBDU-CD from IBDU-UC. Based on the three sncRNAs profile it is possible to predict if IBDU patients within 3 years will be reclassified as CD or UC. We showed that the expression profile of IBDU patients differ from that of definite CD or UC, suggesting that a subgroup of IBDU patients may compose a third unique IBD subtype.