1
|
Goel H, Printz RL, Shiota C, Estes SK, Pannala V, AbdulHameed MDM, Shiota M, Wallqvist A. Assessing Kidney Injury Induced by Mercuric Chloride in Guinea Pigs with In Vivo and In Vitro Experiments. Int J Mol Sci 2023; 24:7434. [PMID: 37108594 PMCID: PMC10138559 DOI: 10.3390/ijms24087434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Acute kidney injury, which is associated with high levels of morbidity and mortality, affects a significant number of individuals, and can be triggered by multiple factors, such as medications, exposure to toxic chemicals or other substances, disease, and trauma. Because the kidney is a critical organ, understanding and identifying early cellular or gene-level changes can provide a foundation for designing medical interventions. In our earlier work, we identified gene modules anchored to histopathology phenotypes associated with toxicant-induced liver and kidney injuries. Here, using in vivo and in vitro experiments, we assessed and validated these kidney injury-associated modules by analyzing gene expression data from the kidneys of male Hartley guinea pigs exposed to mercuric chloride. Using plasma creatinine levels and cell-viability assays as measures of the extent of renal dysfunction under in vivo and in vitro conditions, we performed an initial range-finding study to identify the appropriate doses and exposure times associated with mild and severe kidney injuries. We then monitored changes in kidney gene expression at the selected doses and time points post-toxicant exposure to characterize the mechanisms of kidney injury. Our injury module-based analysis revealed a dose-dependent activation of several phenotypic cellular processes associated with dilatation, necrosis, and fibrogenesis that were common across the experimental platforms and indicative of processes that initiate kidney damage. Furthermore, a comparison of activated injury modules between guinea pigs and rats indicated a strong correlation between the modules, highlighting their potential for cross-species translational studies.
Collapse
Affiliation(s)
- Himanshu Goel
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Richard L. Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chiyo Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Shanea K. Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Venkat Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Mohamed Diwan M. AbdulHameed
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Frederick, MD 21702, USA
| |
Collapse
|
2
|
Pannala VR, Estes SK, Rahim M, Trenary I, O’Brien TP, Shiota C, Printz RL, Reifman J, Shiota M, Young JD, Wallqvist A. Toxicant-Induced Metabolic Alterations in Lipid and Amino Acid Pathways Are Predictive of Acute Liver Toxicity in Rats. Int J Mol Sci 2020; 21:ijms21218250. [PMID: 33158035 PMCID: PMC7663358 DOI: 10.3390/ijms21218250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Liver disease and disorders associated with aberrant hepatocyte metabolism can be initiated via drug and environmental toxicant exposures. In this study, we tested the hypothesis that gene and metabolic profiling can reveal commonalities in liver response to different toxicants and provide the capability to identify early signatures of acute liver toxicity. We used Sprague Dawley rats and three classical hepatotoxicants: acetaminophen (2 g/kg), bromobenzene (0.4 g/kg), and carbon tetrachloride (0.3 g/kg), to identify early perturbations in liver metabolism after a single acute exposure dose. We measured changes in liver genes and plasma metabolites at two time points (5 and 10 h) and used genome-scale metabolic models to identify commonalities in liver responses across the three toxicants. We found strong correlations for gene and metabolic profiles between the toxicants, indicative of similarities in the liver response to toxicity. We identified several injury-specific pathways in lipid and amino acid metabolism that changed similarly across the three toxicants. Our findings suggest that several plasma metabolites in lipid and amino acid metabolism are strongly associated with the progression of liver toxicity, and as such, could be targeted and clinically assessed for their potential as early predictors of acute liver toxicity.
Collapse
Affiliation(s)
- Venkat R. Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
| | - Shanea K. Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
| | - Tracy P. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Chiyo Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Richard L. Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Jamey D. Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
| |
Collapse
|
3
|
Schyman P, Printz RL, AbdulHameed MDM, Estes SK, Shiota C, Shiota M, Wallqvist A. A toxicogenomic approach to assess kidney injury induced by mercuric chloride in rats. Toxicology 2020; 442:152530. [PMID: 32599119 DOI: 10.1016/j.tox.2020.152530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022]
Abstract
Kidney injury caused by disease, trauma, environmental exposures, or drugs may result in decreased renal function, chronic kidney disease, or acute kidney failure. Diagnosis of kidney injury using serum creatinine levels, a common clinical test, only identifies renal dysfunction after the kidneys have undergone severe damage. Other indicators sensitive to kidney injury, such as the level of urine kidney injury molecule-1 (KIM-1), lack the ability to differentiate between injury phenotypes. To address early detection as well as detailed categorization of kidney-injury phenotypes in preclinical animal or cellular studies, we previously identified eight sets (modules) of co-expressed genes uniquely associated with kidney histopathology. Here, we used mercuric chloride (HgCl2)-a model nephrotoxicant-to chemically induce kidney injuries as monitored by KIM-1 levels in Sprague Dawley rats at two doses (0.25 or 0.50 mg/kg) and two exposure lengths (10 or 34 h). We collected whole transcriptome RNA-seq data derived from five animals at each dose and time point to perform a toxicogenomics analysis. Consistent with documented injury phenotypes for HgCl2 toxicity, our kidney-injury-module approach identified the onset of necrosis and dilation as early as 10 h after a dose of 0.50 mg/kg that produced only mild injury as judged by urinary KIM-1 excretion. The results of these animal studies highlight the potential of the kidney-injury-module approach to provide a sensitive and histopathology-specific readout of renal toxicity.
Collapse
Affiliation(s)
- Patric Schyman
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA.
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mohamed Diwan M AbdulHameed
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Chiyo Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, USA
| |
Collapse
|
4
|
Schyman P, Printz RL, Estes SK, O’Brien TP, Shiota M, Wallqvist A. Concordance between Thioacetamide-Induced Liver Injury in Rat and Human In Vitro Gene Expression Data. Int J Mol Sci 2020; 21:ijms21114017. [PMID: 32512829 PMCID: PMC7312807 DOI: 10.3390/ijms21114017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
The immense resources required and the ethical concerns for animal-based toxicological studies have driven the development of in vitro and in silico approaches. Recently, we validated our approach in which the expression of a set of genes is uniquely associated with an organ-injury phenotype (injury module), by using thioacetamide, a known liver toxicant. Here, we sought to explore whether RNA-seq data obtained from human cells (in vitro) treated with thioacetamide-S-oxide (a toxic intermediate metabolite) would correlate across species with the injury responses found in rat cells (in vitro) after exposure to this metabolite as well as in rats exposed to thioacetamide (in vivo). We treated two human cell types with thioacetamide-S-oxide (primary hepatocytes with 0 (vehicle), 0.125 (low dose), or 0.25 (high dose) mM, and renal tubular epithelial cells with 0 (vehicle), 0.25 (low dose), or 1.00 (high dose) mM) and collected RNA-seq data 9 or 24 h after treatment. We found that the liver-injury modules significantly altered in human hepatocytes 24 h after high-dose treatment involved cellular infiltration and bile duct proliferation, which are linked to fibrosis. For high-dose treatments, our modular approach predicted the rat in vivo and in vitro results from human in vitro RNA-seq data with Pearson correlation coefficients of 0.60 and 0.63, respectively, which was not observed for individual genes or KEGG pathways.
Collapse
Affiliation(s)
- Patric Schyman
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc. (HJF), Bethesda, MD 20817, USA
- Correspondence: (P.S.); (M.S.)
| | - Richard L. Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (R.L.P.); (S.K.E.); (T.P.O.)
| | - Shanea K. Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (R.L.P.); (S.K.E.); (T.P.O.)
| | - Tracy P. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (R.L.P.); (S.K.E.); (T.P.O.)
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (R.L.P.); (S.K.E.); (T.P.O.)
- Correspondence: (P.S.); (M.S.)
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
| |
Collapse
|
5
|
AbdulHameed MDM, Pannala VR, Wallqvist A. Mining Public Toxicogenomic Data Reveals Insights and Challenges in Delineating Liver Steatosis Adverse Outcome Pathways. Front Genet 2019; 10:1007. [PMID: 31681434 PMCID: PMC6813744 DOI: 10.3389/fgene.2019.01007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/23/2019] [Indexed: 12/19/2022] Open
Abstract
Exposure to chemicals contributes to the development and progression of fatty liver, or steatosis, a process characterized by abnormal accumulation of lipids within liver cells. However, lack of knowledge on how chemicals cause steatosis has prevented any large-scale assessment of the 80,000+ chemicals in current use. To address this gap, we mined a large, publicly available toxicogenomic dataset associated with 18 known steatogenic chemicals to assess responses across assays (in vitro and in vivo) and species (i.e., rats and humans). We identified genes that were differentially expressed (DEGs) in rat in vivo, rat in vitro, and human in vitro studies in which rats or in vitro primary cell lines were exposed to the chemicals at different doses and durations. Using these DEGs, we performed pathway enrichment analysis, analyzed the molecular initiating events (MIEs) of the steatosis adverse outcome pathway (AOP), and predicted metabolite changes using metabolic network analysis. Genes indicative of oxidative stress were among the DEGs most frequently observed in the rat in vivo studies. Nox4, a pro-fibrotic gene, was down-regulated across these chemical exposure conditions. We identified eight genes (Cyp1a1, Egr1, Ccnb1, Gdf15, Cdk1, Pdk4, Ccna2, and Ns5atp9) and one pathway (retinol metabolism), associated with steatogenic chemicals and whose response was conserved across the three in vitro and in vivo systems. Similarly, we found the predicted metabolite changes, such as increases of saturated and unsaturated fatty acids, conserved across the three systems. Analysis of the target genes associated with the MIEs of the current steatosis AOP did not provide a clear association between these 18 chemicals and the MIEs, underlining the multi-factorial nature of this disease. Notably, our overall analysis implicated mitochondrial toxicity as an important and overlooked MIE for chemical-induced steatosis. The integrated toxicogenomics approach to identify genes, pathways, and metabolites based on known steatogenic chemicals, provide an important mean to assess development of AOPs and gauging the relevance of new testing strategies.
Collapse
Affiliation(s)
- Mohamed Diwan M AbdulHameed
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States
| |
Collapse
|
6
|
Rojas JM, Bolze F, Thorup I, Nowak J, Dalsgaard CM, Skydsgaard M, Berthelsen LO, Keane KA, Søeborg H, Sjögren I, Jensen JT, Fels JJ, Offenberg HK, Andersen LW, Dalgaard M. The Effect of Diet-induced Obesity on Toxicological Parameters in the Polygenic Sprague-Dawley Rat Model. Toxicol Pathol 2018; 46:777-798. [DOI: 10.1177/0192623318803557] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Florian Bolze
- Toxicology Development Projects, Novo Nordisk A/S, Måløv, Denmark
| | - Inger Thorup
- Toxicopathology, Novo Nordisk A/S, Måløv, Denmark
| | - Jette Nowak
- Toxicopathology, Novo Nordisk A/S, Måløv, Denmark
| | | | | | | | | | | | | | | | | | | | | | - Majken Dalgaard
- Early Regulatory Toxicology, Novo Nordisk A/S, Måløv, Denmark
| |
Collapse
|