Integrative transcriptomic, single-cell and ultrasound analyses identify shared lipid metabolism and immune remodeling signatures in MASLD and carotid atherosclerosis

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease, is closely associated with atherosclerotic cardiovascular risk. However, lipid metabolism-related mechanisms shared by fatty liver and carotid atherosclerosis remain incompletely defined. Bulk transcriptomic datasets were used to identify shared lipid metabolism-related differentially expressed genes between MASLD-spectrum liver samples and carotid plaques. Lipid metabolism-related genes were collected from GeneCards, GSEA and Harmonizome. LASSO and SVM-RFE were applied for candidate gene selection, followed by fixed-model assessment in additional liver cohorts. Carotid plaque scRNA-seq datasets were integrated for cell localization, subclustering and CellChat analysis. Liver-side snRNA-seq was used for hepatic cellular localization. An independent ultrasound cohort of 122 participants was analyzed separately to assess phenotype-level associations between fatty liver severity and carotid atherosclerotic burden. We identified 44 directionally consistent shared lipid metabolism-related genes, including 21 commonly upregulated and 23 commonly downregulated genes. Enrichment analysis indicated immune activation, inflammation, extracellular matrix organization and vascular remodeling. FILIP1L and TNFSF10 were selected as machine learning consensus candidate genes. Plaque signals localized to macrophages, smooth muscle, fibroblast and endothelial populations. FILIP1L was enriched in contractile smooth muscle cells and myofibroblast-like cells, whereas TNFSF10 was mainly enriched in endothelial states. Functional analyses indicated macrophage immune activation, smooth-muscle contraction and myofibroblast matrix remodeling. CellChat predicted CXCL8–ACKR1, SPP1/FN1–integrin, APP–CD74 and MIF-related interactions. Liver signals localized to hepatocytes, cholangiocytes and endothelial cells. ATI-mean and Hamaguchi grade were associated with carotid intima-media thickness and plaque total score. The original two-gene liver model had limited discrimination in GSE48452 (AUC 0.569). In the additional microarray cohort E-MEXP-3291, TNFSF10 upregulation was reproduced, but FILIP1L changed in the opposite direction. The primary combined-disease AUC was 0.579. These findings indicate cohort- and case-definition-dependent expression and performance rather than a validated liver diagnostic signature. This study reports shared lipid metabolism and immune remodeling signatures in MASLD and carotid atherosclerosis. FILIP1L and TNFSF10 emerged as exploratory cross-tissue candidate genes with distinct cellular localization patterns. The ultrasound findings provide phenotype-level support for an association between fatty liver severity and carotid atherosclerotic burden. Overall, the study is hypothesis-generating and requires confirmation in larger independent molecular and clinical cohorts.