Pathophysiological mechanisms involved in liver steatosis in metabolic dysfunction-associated steatohepatitis over time: a bulk RNAseq data analysis

Background and aims: Liver steatosis results from metabolic dysregulations of lipid homeostasis. Drugs targeting lipid metabolism are being evaluated in clinical trials with inconsistent results.We suggest that steatosis pathophysiology evolves with MASLD progression resulting in a mismatch between the deregulated mechanisms and the drug used. Our aim is to analyze the evolution of gene expressions of key lipid metabolism genes during MASH progression in mice. Method: Foz/foz mice (FOZ) were fed normal diet (ND) (3.39 kcal/g, 16% of lipids) or high-fat diet (HFD) (5.24 kcal/g, 60% of lipids). Liver tissue was harvested at baseline (control group, N = 5) and after 4 (HFD = 4), 12 (HFD = 8) or 32 (HFD = 6) weeks. Liver samples were scored histologically (SAF score) using hematoxylin & eosin staining. Total RNA from liver samples was extracted using Qiagen® mini kits prior to bulk RNA sequencing. Sequencing data were normalized according to timepoint and diet (RStudio). Differentially expressed genes (DEG) and enrichment analysis reported by the Normalized Enrichment Score (NES) of FOZ HFD mice were compared at each timepoint with the control group. Results: Maximal liver weight to bodyweight ratiowas reached at 32 weeks (p < 0.001). Insulin resistance assessed by the HOMA-IR index was present at 4 weeks of HFD (p < 0.01). Liver histology showed the whole MASH spectrum with transcriptomics changes over time. At week 4, steatosis was observed with 284 DEG notably involved in fatty acid biosynthetic process (NES = 13.9, padj = 1.2e-4), lipid transport (NES = 9.7, padj = 8.0e-8), lipid storage (FES = 21.5, padj = 3.0e-6) and fatty acid oxidation (FAO) (NES = 9.4, padj = 0.02). At week 12, steatohepatitis was observed with 469 DEG involved in 504 enriched pathways including lipid transport (NES = 14.7, padj = 3.6e-15), lipid storage (NES = 24.2, padj = 1.66e-7) and FAO (NES = 22.2, padj = 2.7e-7). At week 32, fibrosing steatohepatitis was observed with 750 DEG involved in 1167 enriched pathways including lipid transport (NES = 11.3, padj = 6.3e-21), lipid storage (NES = 24, padj = 1.4e-15) and FAO (NES = 11, padj = 7.4e-7). At the gene level, the lipid metabolism key regulator Pparɣ was downregulated in a time-dependent manner: Log2FC = − 1.6, padj = 9e-5 at week 4; Log2FC = −1.8, padj = 9e-6 at week 12 and Log2FC = −2.35, padj = 6.6e-9 at week 32. Fatty acid oxidation related genes are all downregulated at week 12, such as Obp2a (Log2FC = −3.17, padj = 0.003) and Acaa1b (Log2FC = −1.64, padj = 9.9e-9). Lipid storage genes expression also greatly change over time. Both Cidec and Fitm1involved in lipid droplet homeostasis are significantly downregulated at week 12 (Log2FC = −2.13, padj = 3e-6; Log2FC = −1.37, padj = 1.68e-7 respectively) and at week 32 (Log2FC = − 2.7, padj = 2e-5; Log2FC = −1.02, padj = 2e-4 respectively). Conclusion: Gene expression of key-lipid metabolism genes significantly change over time during MASH occurence. These shifts in gene expression of potential therapeutic targets may significantly influence the response to MASLD treatments.

Affiliations

UCLouvainSSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie

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Henin, G., Lamotte, A., Nachit, M., Loriot, A., Leclercq, I., & Lanthier, N. (2025). Pathophysiological mechanisms involved in liver steatosis in metabolic dysfunction-associated steatohepatitis over time: a bulk RNAseq data analysis. Journal of Hepatology, 82(S1), 594. https://hdl.handle.net/2078.5/245021 (Original work published 2025)