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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. PLoS Comput Biol 2023; 19:e1011472. [PMID: 37721939 PMCID: PMC10538798 DOI: 10.1371/journal.pcbi.1011472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such dependencies. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights into the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics/Center for Cancer Research/National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Teresa M. Przytycka
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Siphepho PY, Liu YT, Shabangu CS, Huang JF, Huang CF, Yeh ML, Yu ML, Wang SC. The Impact of Steatosis on Chronic Hepatitis C Progression and Response to Antiviral Treatments. Biomedicines 2021; 9:1491. [PMID: 34680608 PMCID: PMC8533513 DOI: 10.3390/biomedicines9101491] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolic derangement is characteristic in patients with hepatitis C virus (HCV) infection. Aside from established liver injury, various extrahepatic metabolic disorders impact the natural history of the disease, clinical outcomes, and the efficacy of antiviral therapy. The presence of steatosis, recently redefined as metabolic-associated fatty liver disease (MAFLD), is a common feature in HCV-infected patients, induced by host and/or viral factors. Most chronic HCV-infected (CHC) patients have mild steatosis within the periportal region of the liver with an estimated prevalence of 40% to 86%. Indeed, this is higher than the 19% to 50% prevalence observed in patients with other chronic liver diseases such as chronic hepatitis B (CHB). The histological manifestations of HCV infection are frequently observed in genotype 3 (G-3), where relative to other genotypes, the prevalence and severity of steatosis is also increased. Steatosis may independently influence the treatment efficacy of either interferon-based or interferon-free antiviral regimens. This review aimed to provide updated evidence of the prevalence and risk factors behind HCV-associated steatosis, as well as explore the impact of steatosis on HCV-related outcomes.
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Affiliation(s)
- Phumelele Yvonne Siphepho
- Program in Tropical Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (P.Y.S.); (M.-L.Y.)
- Center for Cancer Research, Center for Liquid Biopsy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.S.S.); (J.-F.H.)
| | - Yi-Ting Liu
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Ciniso Sylvester Shabangu
- Center for Cancer Research, Center for Liquid Biopsy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.S.S.); (J.-F.H.)
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Jee-Fu Huang
- Center for Cancer Research, Center for Liquid Biopsy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.S.S.); (J.-F.H.)
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-F.H.); (M.-L.Y.)
- Faculty of Internal Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Hepatitis Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chung-Feng Huang
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-F.H.); (M.-L.Y.)
- Faculty of Internal Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Hepatitis Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ming-Lun Yeh
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-F.H.); (M.-L.Y.)
- Faculty of Internal Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Hepatitis Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ming-Lung Yu
- Program in Tropical Medicine, Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (P.Y.S.); (M.-L.Y.)
- Hepatobiliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-F.H.); (M.-L.Y.)
- Faculty of Internal Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Hepatitis Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shu-Chi Wang
- Center for Cancer Research, Center for Liquid Biopsy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.S.S.); (J.-F.H.)
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
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Melanoma Differentiation-Associated Gene 5 Positively Modulates TNF-α-Induced CXCL10 Expression in Cultured HuH-7 and HLE Cells. Inflammation 2020; 42:2095-2104. [PMID: 31440940 DOI: 10.1007/s10753-019-01073-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The molecular mechanisms of innate immunity are closely associated with the development of non-alcoholic fatty liver disease (NAFLD). TNF-α is a key cytokine involved in the pathogenesis of metabolic inflammation like NAFLD. Melanoma differentiation-associated gene 5 (MDA5) is a member of the intracellular RNA helicase family proteins that play a pivotal role in an antiviral immune response. Previous studies have demonstrated that TNF-α induces the expression of MDA5 in some types of cells. However, the correlation between TNF-α and the expression of MDA5 in hepatocytes remains unknown. In the present study, we used two human hepatocellular carcinoma cell lines, HuH-7 and HLE, and examined the expression of MDA5 in these cells upon stimulation with TNF-α. The expression of MDA5 induced by TNF-α was analyzed by quantitative real-time RT-PCR and western blotting. Next, RNA interference against MDA5 was performed and the expressions of CXCL10 and STAT1 were examined. We found that the expression of MDA5 had increased upon stimulation with TNF-α in a concentration-dependent manner. Gene silencing against MDA5 suppressed the expression of TNF-α-induced CXCL10 in both cells. In HLE cells, gene silencing of MDA5 impaired STAT1 phosphorylation 24 h after stimulation with TNF-α. On the other hand, TNF-α-induced STAT1 phosphorylation was not detected in HuH-7 cells. These results indicated that MDA5 positively modulated the TNF-α-induced expression of CXCL10 in both STAT1-dependent and -independent manner and may be associated with metabolic inflammation in the liver.
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Jetten MJA, Ruiz-Aracama A, Coonen MLJ, Claessen SM, van Herwijnen MHM, Lommen A, van Delft JHM, Peijnenburg AACM, Kleinjans JCS. Interindividual variation in gene expression responses and metabolite formation in acetaminophen-exposed primary human hepatocytes. Arch Toxicol 2015; 90:1103-15. [PMID: 26104854 PMCID: PMC4830893 DOI: 10.1007/s00204-015-1545-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 06/03/2015] [Indexed: 12/14/2022]
Abstract
Acetaminophen (APAP) is a readily available over-the-counter drug and is one of the most commonly used analgesics/antipyretics worldwide. Large interindividual variation in susceptibility toward APAP-induced liver failure has been reported. However, the exact underlying factors causing this variability in susceptibility are still largely unknown. The aim of this study was to better understand this variability in response to APAP by evaluating interindividual differences in gene expression changes and APAP metabolite formation in primary human hepatocytes (PHH) from several donors (n = 5) exposed in vitro to a non-toxic to toxic APAP dose range. To evaluate interindividual variation, gene expression data/levels of metabolites were plotted against APAP dose/donor. The correlation in APAP dose response between donors was calculated by comparing data points from one donor to the data points of all other donors using a Pearson-based correlation analysis. From that, a correlation score/donor for each gene/metabolite was defined, representing the similarity of the omics response to APAP in PHH of a particular donor to all other donors. The top 1 % highest variable genes were selected for further evaluation using gene set overrepresentation analysis. The biological processes in which the genes with high interindividual variation in expression were involved include liver regeneration, inflammatory responses, mitochondrial stress responses, hepatocarcinogenesis, cell cycle, and drug efficacy. Additionally, the interindividual variation in the expression of these genes could be associated with the variability in expression levels of hydroxyl/methoxy-APAP and C8H13O5N-APAP-glucuronide. The before-mentioned metabolites or their derivatives have also been reported in blood of humans exposed to therapeutic APAP doses. Possibly these findings can contribute to elucidating the causative factors of interindividual susceptibility toward APAP.
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Affiliation(s)
- Marlon J A Jetten
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER, Maastricht, The Netherlands.
| | - Ainhoa Ruiz-Aracama
- RIKILT, Institute of Food Safety, Wageningen UR, PO Box 230, 6700 AE, Wageningen, The Netherlands
| | - Maarten L J Coonen
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER, Maastricht, The Netherlands
| | - Sandra M Claessen
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER, Maastricht, The Netherlands
| | - Marcel H M van Herwijnen
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER, Maastricht, The Netherlands
| | - Arjen Lommen
- RIKILT, Institute of Food Safety, Wageningen UR, PO Box 230, 6700 AE, Wageningen, The Netherlands
| | - Joost H M van Delft
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER, Maastricht, The Netherlands
| | - Ad A C M Peijnenburg
- RIKILT, Institute of Food Safety, Wageningen UR, PO Box 230, 6700 AE, Wageningen, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, Room 4.112 UNS 50, 6229 ER, Maastricht, The Netherlands
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