ArticleBMC genomics2016
A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 18 citations in OpenAlex.
- Dynamic rewiring of microRNA networks in the brainstem autonomic control circuits during hypertension development in the female spontaneously hypertensive rat.Physiological genomics · 2025Article
- Dynamic dysregulation of transcriptomic networks in brainstem autonomic nuclei during hypertension development in the female spontaneously hypertensive rat.Physiological genomics · 2024Article
- Alcohol-related liver disease (ALD): current perspectives on pathogenesis, therapeutic strategies, and animal models.Frontiers in pharmacology · 2024Review
- Cell division cycle-associated 8 is a prognostic biomarker related to immune invasion in hepatocellular carcinoma.Cancer medicine · 2023Article
- Alcohol-Associated Tissue Injury: Current Views on Pathophysiological Mechanisms.Annual review of physiology · 2022Review
- Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration.Physiological genomics · 2021Article
- Modeling alcohol-associated liver disease in a human Liver-Chip.Cell reports · 2021Article
- Retinoic Acid Fluctuation Activates an Uneven, Direction-Dependent Network-Wide Robustness Response in Early Embryogenesis.Frontiers in cell and developmental biology · 2021Article
- Hepatocyte nuclear factor 4α negatively regulates connective tissue growth factor during liver regeneration.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- Mechanisms involved in the activation of C/EBPα by small activating RNA in hepatocellular carcinoma.Oncogene · 2019Article
- Single-Cell Gene Expression Analysis Identifies Chronic Alcohol-Mediated Shift in Hepatocyte Molecular States After Partial Hepatectomy.Gene expression · 2019Article
- Regulatory signatures of liver regeneration distilled by integrative analysis of mRNA, histone methylation, and proteomics.The Journal of biological chemistry · 2017Article
- Pattern analysis uncovers a chronic ethanol-induced disruption of the switch-like dynamics of C/EBP-β and C/EBP-α genome-wide binding during liver regeneration.Physiological genomics · 2017Article
- Inhibition of miR-21 rescues liver regeneration after partial hepatectomy in ethanol-fed rats.American journal of physiology. Gastrointestinal and liver physiology · 2016Article
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Authors and funding
5 authors at 1 institution in 1 country.
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Abstract
backgroundLiver regeneration is inhibited by chronic ethanol consumption and this impaired repair response may contribute to the risk for alcoholic liver disease. We developed and applied a novel data analysis approach to assess the effect of chronic ethanol intake in the mechanisms responsible for liver regeneration. We performed a time series transcriptomic profiling study of the regeneration response after 2/3rd partial hepatectomy (PHx) in ethanol-fed and isocaloric control rats.
resultsWe developed a novel data analysis approach focusing on comparative pattern counts (COMPACT) to exhaustively identify the dominant and subtle differential expression patterns. Approximately 6500 genes were differentially regulated in Ethanol or Control groups within 24 h after PHx. Adaptation to chronic ethanol intake significantly altered the immediate early gene expression patterns and nearly completely abrogated the cell cycle induction in hepatocytes post PHx. The patterns highlighted by COMPACT analysis contained several non-parenchymal cell specific markers indicating their aberrant transcriptional response as a novel mechanism through which chronic ethanol intake deregulates the integrated liver tissue response.
conclusionsOur novel comparative pattern analysis revealed new insights into ethanol-mediated molecular changes in non-parenchymal liver cells as a possible contribution to the defective liver regeneration phenotype. The results revealed for the first time an ethanol-induced shift of hepatic stellate cells from a pro-regenerative phenotype to that of an anti-regenerative state after PHx. Our results can form the basis for novel interventions targeting the non-parenchymal cells in normalizing the dysfunctional repair response process in alcoholic liver disease. Our approach is illustrated online at http://compact.jefferson.edu .
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