APOBEC1-Dependent RNA Eiting of TNF Signaling Orchestrates Ileal Villus Morphogenesis in Pigs: Integrative Transcriptomic and Editomic Insights

The ileum serves as the primary site for nutrient digestion and absorption in the intestine, with villus height representing a critical indicator of intestinal absorptive capacity. To investigate the regulatory mechanisms underlying ileal villus development, we conducted a feeding trial using crossbred pigs (Duroc × Landrace × Yorkshire) with an initial body weight of 27.74 ± 0.28 kg, stratifying them into high-villus and low-villus groups based on ileal villus height (n = 4). The results revealed 849 differentially RNA-edited genes (REGs) between the two groups, including 472 hyper-edited genes in the low-villus group and 377 in the high-villus group. Functional enrichment analysis showed that these REGs were significantly enriched in inflammation-related pathways, particularly the TNF signaling pathway and IL-17 signaling pathway, with TNF pathway genes exhibiting notably higher editing levels in the high-villus group. Additionally, 46 differentially expressed genes (DEGs) were identified, comprising 22 upregulated in the low-villus group and 24 in the high-villus group, which were similarly enriched in TNF and IL-17 signaling pathways. Integrated quadrant analysis of the RNA editing and transcriptomic profiles demonstrated that pro-inflammatory genes CXCL10 (C-X-C motif chemokine 10), CCL2 (C-C motif chemokine ligand 2), CREB3L2 (CAMP-responsive element-binding protein 3-like 2), and PIK3R1 (Phosphoinositide-3-kinase regulatory subunit 1) were highly expressed in the low-villus group but exhibited significantly lower RNA editing levels compared to the high-villus group. Furthermore, the expression of the inflammation-suppressive RNA editing enzyme APOBEC1 (apolipoprotein B mRNA editing enzyme catalytic subunit 1) showed correlation with villus height (R = 0.81, <i>p</i> < 0.05). Collectively, our findings indicate that RNA editing dynamics influence the variation in ileal villus height within inflammation-associated pathways, particularly the TNF signaling pathway. Enhanced RNA editing of this pathway may mitigate intestinal inflammation and promote healthy ileal villus developments.