Transcriptomic Profiling Identifies Hub Transcription Factors Associated with the Protective Effects of Licochalcone A Against HFD-Induced MASLD

Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD) lacks approved specific pharmacological treatments and exhibits complex pathogenesis. Licochalcone A (LA), a flavonoid extracted from Glycyrrhiza glabra, possesses anti-inflammatory and lipid-modulating activities, yet its protective effects and transcriptional regulatory mechanisms against MASLD remain poorly defined. Methods: We established an HFD-induced MASLD mouse model to assess the in-vivo protective effect of LA. Hepatic RNA-sequencing was performed to profile transcription factor (TF) expression and identify differentially expressed transcription factors (DE-TFs). Functional enrichment and protein–protein interaction (PPI) network analysis were conducted to characterize DE-TFs and screen hub TFs. RT-qPCR was used to validate the expression patterns of identified hub TFs. Results: LA administration attenuated hepatic lipid deposition in HFD-fed MASLD mice. In total, 149 DE-TFs were identified, including 95 DE-TFs from the comparison of HFD versus control mice and 122 DE-TFs from LA-treated mice versus HFD mice, with 68 DE-TFs shared between the two comparisons. Functional enrichment indicated that these DE-TFs were associated with RNA polymerase II-dependent transcription, nuclear components, DNA binding, signal transduction, and metabolic-disease-related pathways. Nine hub TFs (Myc, Fos, Runx1, Mef2c, Spi1, Sox9, E2f1, Cebpa, and Pparg) were screened via PPI analysis. Seven hub TFs were up-regulated, while Cebpa and Pparg were down-regulated in MASLD mice; LA intervention partly reversed this dysregulated expression profile, as further verified by RT-qPCR. Conclusions: LA mitigates the development of HFD-provoked MASLD-associated hepatic lesions and is associated with partially restored transcript levels of aberrantly expressed hub TFs in mice. This work provides transcriptome-level resources for understanding LA-mediated hepatoprotection against HFD-induced MASLD development and highlights candidate TF targets relevant to MASLD research.