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Mackowiak B, Fu Y, Maccioni L, Gao B. Alcohol-associated liver disease. J Clin Invest 2024; 134:e176345. [PMID: 38299591 PMCID: PMC10836812 DOI: 10.1172/jci176345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Alcohol-associated liver disease (ALD) is a major cause of chronic liver disease worldwide, and comprises a spectrum of several different disorders, including simple steatosis, steatohepatitis, cirrhosis, and superimposed hepatocellular carcinoma. Although tremendous progress has been made in the field of ALD over the last 20 years, the pathogenesis of ALD remains obscure, and there are currently no FDA-approved drugs for the treatment of ALD. In this Review, we discuss new insights into the pathogenesis and therapeutic targets of ALD, utilizing the study of multiomics and other cutting-edge approaches. The potential translation of these studies into clinical practice and therapy is deliberated. We also discuss preclinical models of ALD, interplay of ALD and metabolic dysfunction, alcohol-associated liver cancer, the heterogeneity of ALD, and some potential translational research prospects for ALD.
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Listopad S, Magnan C, Day LZ, Asghar A, Stolz A, Tayek JA, Liu ZX, Jacobs JM, Morgan TR, Norden-Krichmar TM. Identification of integrated proteomics and transcriptomics signature of alcohol-associated liver disease using machine learning. PLOS Digit Health 2024; 3:e0000447. [PMID: 38335183 PMCID: PMC10857706 DOI: 10.1371/journal.pdig.0000447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Distinguishing between alcohol-associated hepatitis (AH) and alcohol-associated cirrhosis (AC) remains a diagnostic challenge. In this study, we used machine learning with transcriptomics and proteomics data from liver tissue and peripheral mononuclear blood cells (PBMCs) to classify patients with alcohol-associated liver disease. The conditions in the study were AH, AC, and healthy controls. We processed 98 PBMC RNAseq samples, 55 PBMC proteomic samples, 48 liver RNAseq samples, and 53 liver proteomic samples. First, we built separate classification and feature selection pipelines for transcriptomics and proteomics data. The liver tissue models were validated in independent liver tissue datasets. Next, we built integrated gene and protein expression models that allowed us to identify combined gene-protein biomarker panels. For liver tissue, we attained 90% nested-cross validation accuracy in our dataset and 82% accuracy in the independent validation dataset using transcriptomic data. We attained 100% nested-cross validation accuracy in our dataset and 61% accuracy in the independent validation dataset using proteomic data. For PBMCs, we attained 83% and 89% accuracy with transcriptomic and proteomic data, respectively. The integration of the two data types resulted in improved classification accuracy for PBMCs, but not liver tissue. We also identified the following gene-protein matches within the gene-protein biomarker panels: CLEC4M-CLC4M, GSTA1-GSTA2 for liver tissue and SELENBP1-SBP1 for PBMCs. In this study, machine learning models had high classification accuracy for both transcriptomics and proteomics data, across liver tissue and PBMCs. The integration of transcriptomics and proteomics into a multi-omics model yielded improvement in classification accuracy for the PBMC data. The set of integrated gene-protein biomarkers for PBMCs show promise toward developing a liquid biopsy for alcohol-associated liver disease.
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Affiliation(s)
- Stanislav Listopad
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Christophe Magnan
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Le Z. Day
- Biological Sciences Division and Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Aliya Asghar
- Medical and Research Services, VA Long Beach Healthcare System, Long Beach, California, United States of America
| | - Andrew Stolz
- Division of Gastrointestinal & Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John A. Tayek
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Department of Internal Medicine, David Geffen School of Medicine, University of California Los Angeles, Torrance, California, United States of America
| | - Zhang-Xu Liu
- Division of Gastrointestinal & Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jon M. Jacobs
- Biological Sciences Division and Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Timothy R. Morgan
- Medical and Research Services, VA Long Beach Healthcare System, Long Beach, California, United States of America
| | - Trina M. Norden-Krichmar
- Department of Computer Science, University of California, Irvine, California, United States of America
- Department of Epidemiology and Biostatistics, University of California, Irvine, California, United States of America
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Ganesan R, Yoon SJ, Suk KT. Microbiome and Metabolomics in Liver Cancer: Scientific Technology. Int J Mol Sci 2022; 24. [PMID: 36613980 DOI: 10.3390/ijms24010537] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Primary liver cancer is a heterogeneous disease. Liver cancer metabolism includes both the reprogramming of intracellular metabolism to enable cancer cells to proliferate inappropriately and adapt to the tumor microenvironment and fluctuations in regular tissue metabolism. Currently, metabolomics and metabolite profiling in liver cirrhosis, liver cancer, and hepatocellular carcinoma (HCC) have been in the spotlight in terms of cancer diagnosis, monitoring, and therapy. Metabolomics is the global analysis of small molecules, chemicals, and metabolites. Metabolomics technologies can provide critical information about the liver cancer state. Here, we review how liver cirrhosis, liver cancer, and HCC therapies interact with metabolism at the cellular and systemic levels. An overview of liver metabolomics is provided, with a focus on currently available technologies and how they have been used in clinical and translational research. We also list scalable methods, including chemometrics, followed by pathway processing in liver cancer. We conclude that important drivers of metabolomics science and scientific technologies are novel therapeutic tools and liver cancer biomarker analysis.
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