Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver Disease
ABSTRACT Background Skeletal muscle is a major target for ethanol‐induced perturbations, leading to sarcopenia in alcohol‐related liver disease (ALD). The complex interactions and pathways involved in adaptive and maladaptive responses to ethanol in skeletal muscle are not well understood. Unlike hy...
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Wiley
2025-06-01
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| Series: | Journal of Cachexia, Sarcopenia and Muscle |
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| Online Access: | https://doi.org/10.1002/jcsm.13818 |
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| author | Nicole Welch Pugazhendhi Kannan Saurabh Mishra Annette Bellar Vandana Agrawal Grahame Kidd Emily Benson Ryan Musich Raya Tabbalat Ling Li J. Mark Brown Belinda Willard Karyn A. Esser Laura E. Nagy Srinivasan Dasarathy |
| author_facet | Nicole Welch Pugazhendhi Kannan Saurabh Mishra Annette Bellar Vandana Agrawal Grahame Kidd Emily Benson Ryan Musich Raya Tabbalat Ling Li J. Mark Brown Belinda Willard Karyn A. Esser Laura E. Nagy Srinivasan Dasarathy |
| author_sort | Nicole Welch |
| collection | DOAJ |
| description | ABSTRACT Background Skeletal muscle is a major target for ethanol‐induced perturbations, leading to sarcopenia in alcohol‐related liver disease (ALD). The complex interactions and pathways involved in adaptive and maladaptive responses to ethanol in skeletal muscle are not well understood. Unlike hypothesis‐driven experiments, an integrated multiomics‐experimental validation approach provides a comprehensive view of these interactions. Methods We performed multiomics analyses with experimental validation to identify novel regulatory mechanisms of sarcopenia in ALD. Studies were done in a comprehensive array of models including ethanol‐treated (ET) murine and human‐induced pluripotent stem cell–derived myotubes (hiPSCm), skeletal muscle from a mouse model of ALD (mALD) and human patients with alcohol‐related cirrhosis and controls. We generated 13 untargeted datasets, including chromatin accessibility (assay for transposase accessible chromatin), RNA sequencing, proteomics, phosphoproteomics, acetylomics and metabolomics, and conducted integrated multiomics analyses using UpSet plots and feature extraction. Key findings were validated using immunoblots, redox measurements (NAD+/NADH ratio), imaging and senescence‐associated molecular phenotype (SAMP) assays. Mechanistic studies included mitochondrial‐targeted Lactobacillus brevis NADH oxidase (MitoLbNOX) to increase redox ratio and MitoTempo as a mitochondrial free radical scavenger. Results Multiomics analyses revealed enrichment in mitochondrial oxidative function, protein synthesis and senescence pathways consistent with the known effects of hypoxia‐inducible factor 1α (HIF1α) during normoxia. Across preclinical and clinical models, HIF1α targets (n = 32 genes) and signalling genes (n > 100 genes) (n = 3 ATACseq, n = 65 phosphoproteomics, n = 10 acetylomics, n = 6 C2C12 proteomics, n = 106 C2C12 RNAseq, n = 64 hiPSC RNAseq, n = 30 hiPSC proteomics, n = 3 mouse proteomics, n = 25 mouse RNAseq, n = 8 human RNAseq, n = 3 human proteomics) were increased. Stabilization of HIF1α (C2C12, 6hEtOH 0.24 ± 0.09; p = 0.043; mALD 0.32 ± 0.074; p = 0.005; data shown as mean difference ± standard error mean) was accompanied by enrichment in the early transient and late change clusters, −log(p‐value) = 1.5–3.8, of the HIF1α signalling pathway. Redox ratio was reduced in ET myotubes (C2C12: 15512 ± 872.1, p < 0.001) and mALD muscle, with decreased expression of electron transport chain components (CI–V, p < 0.05) and Sirt3 (C2C12: 0.067 ± 0.023, p = 0.025; mALD: 0.41 ± 0.12, p = 0.013). Acetylation of mitochondrial proteins was increased in both models (C2C12: 107364 ± 4558, p = 0.03; mALD: 40036 ± 18 987, p = 0.049). Ethanol‐induced SAMP was observed across models (P16: C2C12: 0.2845 ± 0.1145, p < 0.05; hiPSCm: 0.2591, p = 0.041). MitoLbNOX treatment reversed redox imbalance, HIF1α stabilization, global acetylation and myostatin expression (p < 0.05). Conclusions An integrated multiomics approach, combined with experimental validation, identifies HIF1α stabilization and accelerated post‐mitotic senescence as novel mechanisms of sarcopenia in ALD. These findings show the complex molecular interactions leading to mitochondrial dysfunction and progressive sarcopenia in ALD. |
| format | Article |
| id | doaj-art-9c5d2297553b4e87bcce979458f623f7 |
| institution | Kabale University |
| issn | 2190-5991 2190-6009 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Cachexia, Sarcopenia and Muscle |
| spelling | doaj-art-9c5d2297553b4e87bcce979458f623f72025-08-20T03:32:26ZengWileyJournal of Cachexia, Sarcopenia and Muscle2190-59912190-60092025-06-01163n/an/a10.1002/jcsm.13818Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver DiseaseNicole Welch0Pugazhendhi Kannan1Saurabh Mishra2Annette Bellar3Vandana Agrawal4Grahame Kidd5Emily Benson6Ryan Musich7Raya Tabbalat8Ling Li9J. Mark Brown10Belinda Willard11Karyn A. Esser12Laura E. Nagy13Srinivasan Dasarathy14Departments of Gastroenterology and Hepatology Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Inflammation and Immunity Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Inflammation and Immunity Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Inflammation and Immunity Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Inflammation and Immunity Cleveland Clinic, Lerner Research Institute Cleveland Ohio USA3D EM Ultrastructural Imaging and Computation Core Cleveland Clinic, Lerner Research Institute Cleveland Ohio USA3D EM Ultrastructural Imaging and Computation Core Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Inflammation and Immunity Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Inflammation and Immunity Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Proteomics Core Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Cancer Biology Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Proteomics Core Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartment of Physiology and Aging University of Florida Gainesville Florida USADepartments of Inflammation and Immunity Cleveland Clinic, Lerner Research Institute Cleveland Ohio USADepartments of Gastroenterology and Hepatology Cleveland Clinic, Lerner Research Institute Cleveland Ohio USAABSTRACT Background Skeletal muscle is a major target for ethanol‐induced perturbations, leading to sarcopenia in alcohol‐related liver disease (ALD). The complex interactions and pathways involved in adaptive and maladaptive responses to ethanol in skeletal muscle are not well understood. Unlike hypothesis‐driven experiments, an integrated multiomics‐experimental validation approach provides a comprehensive view of these interactions. Methods We performed multiomics analyses with experimental validation to identify novel regulatory mechanisms of sarcopenia in ALD. Studies were done in a comprehensive array of models including ethanol‐treated (ET) murine and human‐induced pluripotent stem cell–derived myotubes (hiPSCm), skeletal muscle from a mouse model of ALD (mALD) and human patients with alcohol‐related cirrhosis and controls. We generated 13 untargeted datasets, including chromatin accessibility (assay for transposase accessible chromatin), RNA sequencing, proteomics, phosphoproteomics, acetylomics and metabolomics, and conducted integrated multiomics analyses using UpSet plots and feature extraction. Key findings were validated using immunoblots, redox measurements (NAD+/NADH ratio), imaging and senescence‐associated molecular phenotype (SAMP) assays. Mechanistic studies included mitochondrial‐targeted Lactobacillus brevis NADH oxidase (MitoLbNOX) to increase redox ratio and MitoTempo as a mitochondrial free radical scavenger. Results Multiomics analyses revealed enrichment in mitochondrial oxidative function, protein synthesis and senescence pathways consistent with the known effects of hypoxia‐inducible factor 1α (HIF1α) during normoxia. Across preclinical and clinical models, HIF1α targets (n = 32 genes) and signalling genes (n > 100 genes) (n = 3 ATACseq, n = 65 phosphoproteomics, n = 10 acetylomics, n = 6 C2C12 proteomics, n = 106 C2C12 RNAseq, n = 64 hiPSC RNAseq, n = 30 hiPSC proteomics, n = 3 mouse proteomics, n = 25 mouse RNAseq, n = 8 human RNAseq, n = 3 human proteomics) were increased. Stabilization of HIF1α (C2C12, 6hEtOH 0.24 ± 0.09; p = 0.043; mALD 0.32 ± 0.074; p = 0.005; data shown as mean difference ± standard error mean) was accompanied by enrichment in the early transient and late change clusters, −log(p‐value) = 1.5–3.8, of the HIF1α signalling pathway. Redox ratio was reduced in ET myotubes (C2C12: 15512 ± 872.1, p < 0.001) and mALD muscle, with decreased expression of electron transport chain components (CI–V, p < 0.05) and Sirt3 (C2C12: 0.067 ± 0.023, p = 0.025; mALD: 0.41 ± 0.12, p = 0.013). Acetylation of mitochondrial proteins was increased in both models (C2C12: 107364 ± 4558, p = 0.03; mALD: 40036 ± 18 987, p = 0.049). Ethanol‐induced SAMP was observed across models (P16: C2C12: 0.2845 ± 0.1145, p < 0.05; hiPSCm: 0.2591, p = 0.041). MitoLbNOX treatment reversed redox imbalance, HIF1α stabilization, global acetylation and myostatin expression (p < 0.05). Conclusions An integrated multiomics approach, combined with experimental validation, identifies HIF1α stabilization and accelerated post‐mitotic senescence as novel mechanisms of sarcopenia in ALD. These findings show the complex molecular interactions leading to mitochondrial dysfunction and progressive sarcopenia in ALD.https://doi.org/10.1002/jcsm.13818alcohol‐related liver diseasehypoxia‐inducible factor‐1‐alphamitochondrial oxidative dysfunctionprotein acetylationredox ratiosarcopenia |
| spellingShingle | Nicole Welch Pugazhendhi Kannan Saurabh Mishra Annette Bellar Vandana Agrawal Grahame Kidd Emily Benson Ryan Musich Raya Tabbalat Ling Li J. Mark Brown Belinda Willard Karyn A. Esser Laura E. Nagy Srinivasan Dasarathy Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver Disease Journal of Cachexia, Sarcopenia and Muscle alcohol‐related liver disease hypoxia‐inducible factor‐1‐alpha mitochondrial oxidative dysfunction protein acetylation redox ratio sarcopenia |
| title | Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver Disease |
| title_full | Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver Disease |
| title_fullStr | Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver Disease |
| title_full_unstemmed | Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver Disease |
| title_short | Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol‐Related Liver Disease |
| title_sort | integrated multiomics analyses of the molecular landscape of sarcopenia in alcohol related liver disease |
| topic | alcohol‐related liver disease hypoxia‐inducible factor‐1‐alpha mitochondrial oxidative dysfunction protein acetylation redox ratio sarcopenia |
| url | https://doi.org/10.1002/jcsm.13818 |
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