Dear Editor,
We are grateful for the thoughtful and constructive feedback on our review article addressing amino acid metabolism in metabolic dysfunction-associated steatotic liver disease (MASLD)/metabolic dysfunction-associated steatohepatitis (MASH) [
1]. We appreciate the opportunity to respond to the insightful points raised. The letter [
2] highlights several emerging challenges and opportunities in this field, and we are pleased to engage in scholarly dialogue on how the integration of spatial, microbial, and nutrient-sensing frameworks can deepen our understanding of this complex disease.
Spatial reorganization of amino acid metabolism: We appreciate the emphasis on hepatic zonation as a dynamic and disease-modifiable feature rather than a static anatomical principle. Indeed, the spatial distribution of amino acid-metabolizing enzymes such as GLS2 and GS must be re-evaluated in the context of inflammatory remodeling, fibrosis, and hypoxia, all of which reshape lobular organization during disease progression.
Recent spatial transcriptomics studies support the notion that classical zonation becomes blurred or is replaced by novel microenvironmental domains in MASH, including regenerative nodules and periseptal regions. While our review presented a simplified architectural view, we agree that the next phase of investigation must move beyond gene localization to address metabolic flux at the functional level. In recent years, it has become possible to map nutrient metabolic pathways in detail by combining stable isotope tracing with multiscale microscopy, machine learning– based image segmentation, and spatial analysis tools [
3]. Furthermore, high-resolution volume electron microscopy (FIB-SEM) unprecedented 3D visualization and precise quantification of ER and mitochondrial architecture, as well as their interactions within liver tissue [
4]. These advances are expected to provide new insights into the alterations in amino acid metabolism and mitochondrial dysfunction associated with the progression of MASH.
Amino acids, microbiota, and disease modulation: We welcome the discussion regarding the role of the gut microbiota in shaping host amino acid profiles, particularly the production of branched-chain amino acids (BCAAs) and their potential effects on insulin resistance and hepatic metabolism. While existing studies has often emphasized correlation, the field is now poised to establish causation using emerging microbial engineering approaches.
Although the causal relationship between elevated circulating levels of BCAAs and hepatic steatosis remains controversial, recent clinical trials have demonstrated that promoting BCAA catabolism can improve insulin resistance in patients with type 2 diabetes [
5]. Based on these findings, it is anticipated that improved hepatic insulin sensitivity may also contribute to the amelioration of fatty liver. However, other studies have reported that the improvement in insulin resistance induced by enhanced BCAA catabolism may occur in tissues other than the liver or skeletal muscle [
6]. On the other hand, it is well known that the gut microbiota profile varies significantly depending on species and sex [
7], and that the levels of certain amino acids, such as BCAAs, also change with sex and age [
8]. Therefore, analyses must be conducted with careful consideration of these factors. While a range of microbiota-targeted interventions may become available for patients with MASLD in the future [
9], comprehensive analyses of resulting alterations in portal vein amino acid profiles, particularly BCAAs, will be crucial.
Amino acid sensing and disease progression: We appreciate the letter’s attention to mTORC1 and GCN2/ATF4 as central nutrient-sensing pathways with therapeutic potential. Indeed, amino acid sensing not only controls hepatic anabolism and catabolism but also shapes immune tone, redox status, and fibrogenic signaling. As the field matures, understanding how these pathways respond to nutrient cues in disease-relevant microenvironments is critical. However, at present, sensing mechanisms have been clearly elucidated for only a subset of the 20 amino acids, thereby limiting our ability to comprehensively define their individual contributions to steatosis. One of the amino acids most closely associated with steatosis is methionine (Met). While the discovery of SAMTOR clarified the link between Met and mTORC1, recent a study have revealed that PRMT1 and SAMTOR coordinately sense methionine/SAM levels to regulate mTORC1 signaling [
10]. On the other hand, Recent a study elucidated that HDAC6 is a valine sensor for regulating DNA damage by dictating TET2-mediated DNA demethylation [
11]. Future research should focus on elucidating the relationship between amino acid fluctuations both within and outside the liver and metabolic regulation mediated by amino acid sensors. Integrating this approach with stable isotope-based amino acid tracing analyses will be crucial for clarifying the link between amino acid metabolism and lipogenesis, thereby advancing our understanding of MASLD pathogenesis.
We appreciate the opportunity to engage in this dialogue and agree that amino acid metabolism represents a dynamic and actionable axis in MASLD/MASH. Future research should integrate spatial and flux-based analyses, microbiome-derived metabolic profiling, and cell-specific nutrient sensing to develop precision therapies. We believe that such efforts will transform amino acids from passive biomarkers into active therapeutic targets.
FOOTNOTES
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Authors’ contribution
Drafting of the manuscript (EK), critical revision of the manuscript for important intellectual content (MM, TK).
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Conflicts of Interest
The authors have no conflicts to disclose.
Abbreviations
branched-chain amino acid
metabolic dysfunction-associated steatohepatitis
metabolic dysfunction-associated steatotic liver disease
REFERENCES
- 1. Kakazu E, Mino M, Kanto T. Role of amino acids in the regulation of hepatic gluconeogenesis and lipogenesis in metabolic dysfunctionassociated steatotic liver disease. Clin Mol Hepatol 2025;31:771-795.
- 2. Cai X, Zhang L, Li T. Letter to the editor on “Male preference for TERT alterations and HBV integration in young-age HBV related HCC: implications for sex disparity”. Clin Mol Hepatol 2026;32:e136-e138.
- 3. Habashy A, Acree C, Kim KY, Zahraei A, Dufresne M, Phan S, et al. Spatial patterns of hepatocyte glucose flux revealed by stable isotope tracing and multi-scale microscopy. Nat Commun 2025;16:5850.
- 4. Parlakgül G, Pang S, Artico LL, Min N, Cagampan E, Villa R, et al. Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity. Nat Commun 2024;15:3982.
- 5. Vanweert F, Neinast M, Tapia EE, van de Weijer T, Hoeks J, Schrauwen-Hinderling VB, et al. A randomized placebo-controlled clinical trial for pharmacological activation of BCAA catabolism in patients with type 2 diabetes. Nat Commun 2022;13:3508.
- 6. Blair MC, Neinast MD, Jang C, Chu Q, Jung JW, Axsom J, et al. Branched-chain amino acid catabolism in muscle affects systemic BCAA levels but not insulin resistance. Nat Metab 2023;5:589-606.
- 7. Pirola CJ, Landa MS, Schuman M, García SI, Salatino A, Sookoian S. Metabolic dysfunction-associated steatotic liver disease exhibits sex-specific microbial heterogeneity within intestinal compartments. Clin Mol Hepatol 2025;31:179-195.
- 8. Mino M, Kakazu E, Sano A, Tsuruoka M, Matsubara H, Kakisaka K, et al. Comprehensive analysis of peripheral blood free amino acids in MASLD: the impact of glycine-serine-threonine metabolism. Amino Acids 2024;57:3.
- 9. Saeed H, Díaz LA, Gil-Gómez A, Burton J, Bajaj JS, Romero-Gomez M, et al. Microbiome-centered therapies for the management of metabolic dysfunction-associated steatotic liver disease. Clin Mol Hepatol 2025;31(Suppl):S94-S111.
- 10. Jiang C, Liu J, He S, Xu W, Huang R, Pan W, et al. PRMT1 orchestrates with SAMTOR to govern mTORC1 methionine sensing via Arg-methylation of NPRL2. Cell Metab 2023;35:2183-2199.e7.
- 11. Jin J, Meng T, Yu Y, Wu S, Jiao CC, Song S, et al. Human HDAC6 senses valine abundancy to regulate DNA damage. Nature 2025;637:215-223.
Citations
Citations to this article as recorded by
- Metabolic and genetic mechanisms of metabolic dysfunction-associated steatotic liver disease: an integrative perspective from molecular pathways to clinical challenges
Jingyuan Ma, Yanna Ma, Xing Wan, Junchen Li, Yunshu Zhang, Jifeng Liu, Yunhai Gao
Frontiers in Endocrinology.2025;[Epub] CrossRef
