Crypt-top and crypt-bottom colonic epithelial cell microRNA profiling reveals cell type-specific response in active and quiescent ulcerative colitis
Inciuraite, R.; Ramonaite, R.; Kupcinskas, J.; Dalgediene, I.; Kulokiene, U.; Kiudelis, V.; Varkalaite, G.; Zvirbliene, A.; Jonaitis, L. V.; Kiudelis, G.; Franke, A.; Juzenas, S.; Skieceviciene, J.
Show abstract
Background and AimsColonic epithelial barrier loss and dysfunction are one of the early events in ulcerative colitis (UC) and microRNAs (miRNAs) participate in its regulation. However, cell type-specific profile of miRNAs during inflammation in UC is still unknown. Thus, we aimed to perform miRNA profiling on colon tissue and epithelial cell levels in active and quiescent UC. MethodsSmall RNA-sequencing in colon tissue, crypt-bottom (CD44+), and crypt-top (CD66a+) colonic epithelial cell populations from two independent cohorts of UC patients (active and quiescent, n=74), and healthy individuals (n=50) was performed. Data analysis encompassed differential expression, weighted gene co-expression network (WGCNA), correlation, gene-set enrichment analyses (GSEA). ResultsIn colon tissue of active and quiescent UC, differentially expressed miRNAs were shown to be potentially involved in intestinal barrier integrity regulation. Consecutive analysis of crypt-bottom and crypt-top colonic epithelial cells revealed distinct miRNA expression patterns in response to UC-caused inflammation. GSEA indicated that differentially expressed epithelial miRNAs are commonly involved in inflammation- and intestinal barrier integrity-related processes (such as signalling of interleukin-4 and interleukin-13), while miRNA differences between cell populations might reflect their function, i.e., crypt-bottom cell miRNA target genes involved in regulation of cell differentiation. Finally, pro-inflammatory miRNA co-expression module correlating with endoscopic UC activity was defined not only in both epithelial cell populations, but also in the colon tissue. ConclusionsmiRNA expression patterns are colon epithelial cell population- and UC state-specific and correlate with endoscopic UC activity. Irrespective of the UC stage deregulated epithelial miRNAs are potentially involved in regulation of intestinal barrier integrity.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Intestinal receptor of SARS-CoV-2 in inflamed IBD tissue is downregulated by HNF4A in ileum and upregulated by interferon regulating factors in colon 97%
- An extremes of phenotype approach confirms significant genetic heterogeneity in patients with ulcerative colitis. 96%
- Antigen-driven expansion of public clonal T cell populations in inflammatory bowel diseases 92%
Similar papers in this journal
- Multi-centre derivation and validation of a colitis-associated colorectal cancer risk prediction web-tool 94%
- E prostanoid receptor 4 expressing macrophages promote the regeneration of the intestinal epithelial barrier upon inflammation 92%
- Two microbiota subtypes identified in Irritable Bowel Syndrome with distinct responses to the low FODMAP diet 92%
Similar papers in this journal
- Linking Gene Expression to Clinical Outcomes in Pediatric Crohn's Disease Using Machine Learning 95%
- Reference-guided Genome Assembly of Long Non-coding RNA Transcripts reveals Target Genes Associated With Crohn's Disease 93%
- Molecular Drivers of Tumor Progression in Microsatellite Stable APC Mutation-Negative Colorectal Cancers 93%
Similar papers in this journal
- Assessing Cellular and Transcriptional diversity of IIeal Mucosa amongst Treatment Naïve and Treated Crohn’s disease 96%
- Molecular network analyses implicate death-associated protein kinase 3 (DAPK3) as a key factor in colitis-associated dysplasia progression 96%
- Anti-integrin αvβ6 antibodies predict pouchitis in patients with ulcerative colitis after restorative proctocolectomy with ileal pouch-anal anastomosis 94%
Similar papers in this journal
- Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria 94%
- An IBD-associated pathobiont synergises with NSAID to promote colitis which is blocked by NLRP3 inflammasome and Caspase-8 inhibitors 94%
- Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.