Through single-cell analysis of 10,388 NAFLD cells and 35,846 IVDD cells, Scissor analysis was employed to identify disease-associated cell populations and revealed two additional common biomarkers (PHACTR1 and RIPOR2), with experimental validation demonstrating significant alterations in patients with concurrent MASLD-IVDD. This evidence concerns the gene PHACTR1 and metabolic dysfunction-associated steatotic liver disease.