Multi-Omics and Machine Learning-Based Characterization of the Lactylation Microenvironment and Biomarker...

Crohn's disease (CD) is characterized by transmural inflammation and intestinal fibrosis, in which metabolic reprogramming may contribute to fibrotic remodeling through lactate-associated epigenetic and transcriptional regulation, but key cellular states and candidate biomarkers remain unclear. Therefore, we integrated single-cell RNA sequencing (scRNA-seq) with a lactylation-associated transcriptional score to estimate lactate/lactylation-related transcriptional activity in CD intestinal tissues. High-dimensional weighted gene co-expression network analysis (hdWGCNA) and an integrated machine learning framework identified core lactylation-associated biomarkers, which were validated in clinical tissue and a TNBS-induced mouse model. Additionally, we evaluated the ability of these core genes to predict anti-TNF-α treatment response in an independent clinical cohort, and analyzed cellular communication and trajectories, using CellChat, Monocle 2, and spatial transcriptomics. In this study, an enterocyte state with high lactylation-associated transcriptional scores was identified. CALD1 and CALM1 were identified as core transcriptional biomarkers associated with this high-lactylation-score epithelial state. A diagnostic nomogram exhibited robust predictive performance (AUC > 0.75, p < 0.05). Notably, increased CALM1 expression was associated with favorable anti-TNF-α response (AUC > 0.70, p < 0.05). Mechanistically, CALD1/CALM1 dysregulation was associated with enhanced GDF15- and MIF-related signaling, potentially contributing to endothelial and macrophage-associated microenvironmental remodeling. Together, CALD1 and CALM1 represent lactylation-score-associated transcriptional biomarkers that may link metabolic reprogramming, epithelial dysfunction, and fibrotic remodeling in CD, serving as candidate diagnostic and treatment-response-associated biomarkers.