BIOMARKERS & MOLECULAR TOXICITY PATHWAYS

Modules, or gene groups associated with specific adverse outcomes, offer a source of potential diagnostic biomarkers. We explore unbiased systems approaches to identify toxicity modules for specific histopathologies of liver and kidney injuries. Projects include, identifying molecular toxicity pathways associated with such injuries (e.g., fibrosis and steatosis); developing and validating biomarkers in animal models; examining in vitro–in vivo correlations; and studying specific chemical exposures in detail.

Publications

Hari, A., M. D. M. AbdulHameed, M. R. Balik-Meisner, D. Mav, D. P. Phadke, E. H. Scholl, R. R. Shah, W. Casey, S. S. Auerbach, A. Wallqvist, and V. R. Pannala. Exposure to PFAS chemicals induces sex-dependent alterations in key rate-limiting steps of lipid metabolism in liver steatosis. Frontiers in Toxicology. 2024 June 5; 6:1390196. [PDF, Pubmed]

Goel, H., R. L. Printz, V. R. Pannala, M. D. M. AbdulHameed, and A. Wallqvist. Probing liver injuries induced by thioacetamide in human in vitro pooled hepatocyte experiments. International Journal of Molecular Sciences. 2024 March 13; 25:3265. [PDF, Pubmed]

Pannala, V. R., M. R. Balik-Meisner, D. Mav, D. P. Phadke, E. H. Scholl, R. R. Shah, S. S. Auerbach, and A. Wallqvist. High-throughput transcriptomics differentiates toxic versus non-toxic chemical exposures using a rat liver model. International Journal of Molecular Sciences. 2023 December 13; 24:17425. [PDF, Link]

Goel, H., R. L. Printz, C. Shiota, S. K. Estes, V. Pannala, M. D. M. AbdulHameed, M. Shiota, and A. Wallqvist. Assessing kidney injury induced by mercuric chloride in guinea pigs with in vivo and in vitro experiments. International Journal of Molecular Sciences. 2023 April 18; 24(8):7434. [PDF, Pubmed]

Schyman, P., R. L. Printz, V. R. Pannala, M. D. M. AbdulHameed, S. K. Estes, C. Shiota, K. L. Boyd, M. Shiota, and A. Wallqvist. Genomics and metabolomics of early-stage thioacetamide-induced liver injury: an interspecies study between guinea pig and rat. Toxicology and Applied Pharmacology. 2021 November 1; 430:115713. [PDF, PubMed]

Schyman, P., Z. Xu, V. Desai, and A. Wallqvist. TOXPANEL: a gene-set analysis tool to assess liver and kidney injuries. Frontiers in Pharmacology. 2021 February 9; 12:601511. [PDF, PubMed]

Rawls, K. D., B. V. Dougherty, K. C. Vinnakota, V. R. Pannala, A. Wallqvist, G. L. Kolling, and J. A. Papin. Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model. Toxicology and Applied Pharmacology. 2021 February 1; 412:115390. [PDF, PubMed]

Pannala, V. R., S. K. Estes, M. Rahim, I. Trenary, T. P. O’Brien, C. Shiota, R. L. Printz, J. Reifman, M. Shiota, J. D. Young, and A. Wallqvist. Toxicant-induced metabolic alterations in lipid and amino acid pathways are predictive of acute liver toxicity in rats. International Journal of Molecular Sciences. 2020 November 4; 21:8250. [PDF, PubMed]

Schyman, P., R. L. Printz, M. D. M. AbdulHameed, S. K. Estes, C. Shiota, M. Shiota, and A. Wallqvist. A toxicogenomic approach to assess kidney injury induced by mercuric chloride in rats. Toxicology. 2020 June 26; 442:152530. [PDF, PubMed]

Pannala, V. R., S. K. Estes, M. Rahim, I. Trenary, T. P. O'Brien, C. Shiota, R. L. Printz, J. Reifman, T. Oyama, M. Shiota, J. D. Young, and A. Wallqvist. Mechanism-based identification of plasma metabolites associated with liver toxicity. Toxicology. 2020 May 30; 441:152493. [PDF, PubMed]

Pannala, V. R., K. C. Vinnakota, S. K. Estes, I. Trenary, T. P. O'Brien, R. L. Printz, J. A. Papin, J. Reifman, T. Oyama, M. Shiota, J. D. Young, and A. Wallqvist. Genome-scale model-based identification of metabolite indicators for early detection of kidney toxicity. Toxicological Sciences. 2020 February 1; 173(2):293-312. [PDF, PubMed]

Rawls, K. D., E. M. Blais, B. V. Dougherty, K. C. Vinnakota, V. R. Pannala, A. Wallqvist, G. L. Kolling, and J. A. Papin. Genome-scale characterization of toxicity-induced metabolic alterations in primary hepatocytes. Toxicological Sciences. 2019 December 1; 172(2):279-291. [PDF, PubMed]

AbdulHameed, M. D. M., V. R. Pannala, and A. Wallqvist. Mining public toxicogenomic data reveals insights and challenges in delineating liver steatosis adverse outcome pathways. Frontiers in Genetics. 2019 October 18; 10:1007. [PDF, PubMed]

Pannala, V. R., K. C. Vinnakota, K. D. Rawls, S. K. Estes, T. P. O'Brien, R. L. Printz, J. A. Papin, J. Reifman, M. Shiota, J. D. Young, and A. Wallqvist. Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats. Toxicology and Applied Pharmacology. 2019 June 1; 372:19-32. [PDF, PubMed]

Vinnakota, K. C., V. R. Pannala, M. L. Wall, M. Rahim, S. K. Estes, I. Trenary, T. P. O'Brien, R. L. Printz, J. Reifman, M. Shiota, J. D. Young, and A. Wallqvist. Network modeling of liver metabolism to predict plasma metabolite changes during short-term fasting in the laboratory rat. Frontiers in Physiology. 2019 March 1; 10:161. [PDF, PubMed]

Schyman, P., R. L. Printz, S. K. Estes, K. L. Boyd, M. Shiota, and A. Wallqvist. Identification of the toxicity pathways associated with thioacetamide-induced injuries in rat liver and kidney. Frontiers in Pharmacology. 2018 November 6; 9(1272). [PDF, PubMed]

Pannala, V. R., M. L. Wall, S. K. Estes, I. Trenary, T. P. O’Brien, R. L. Printz, K. C. Vinnakota, J. Reifman, M. Shiota, J. D. Young, and A. Wallqvist. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Scientific Reports. 2018 August 3; 8:11678. [PDF, PubMed]

Liu, R., R. L. Printz, E. C. Jenkins, T. P. O'Brien, J. A. Te, M. Shiota, and A. Wallqvist. Genome-wide gene expression changes associated with exposure of rat liver, heart, and kidney cells to endosulfan. Toxicology in Vitro. 2018 April; 48:244-254. [PDF, PubMed]

McDyre, B. C., M. D. M. AbdulHameed, M. G. Permenter, W. E. Dennis, C. E. Baer, J. M. Koontz, M. H. Boyle, A. Wallqvist, J. A. Lewis, and D. L. Ippolito. Comparative proteomic analysis of liver steatosis and fibrosis after oral hepatotoxicant administration in Sprague-Dawley rats. Toxicologic Pathology. 2018 February; 46(2):202-223. [PDF, PubMed]

Liu, R., M. D. M. AbdulHameed, and A. Wallqvist. Molecular structure-based large-scale prediction of chemical-induced gene expression changes. Journal of Chemical Information and Modeling. 2017 September 25; 57(9):2194-2202. [PDF, PubMed]

Liu, R., X. Yu, and A. Wallqvist. Using chemical-induced gene expression in cultured human cells to predict chemical toxicity. Chemical Research in Toxicology. 2016 November 21; 29(11):1883-1893. [PDF, PubMed]

AbdulHameed, M. D., D. L. Ippolito, and A. Wallqvist. Predicting rat and human pregnane X receptor activators using Bayesian classification models. Chemical Research in Toxicology. 2016 October 17; 29(10):1729-1740. [PDF, PubMed]

AbdulHameed, M. D., D. L. Ippolito, J. D. Stallings, and A. Wallqvist. Mining kidney toxicogenomics using gene co-expression modules. BMC Genomics. 2016 October 10; 17:790. [PDF, PubMed]

Te, J. A., M. D. AbdulHameed, and A. Wallqvist. Systems toxicology of chemically induced liver and kidney injuries: histopathology-associated gene co-expression modules. Journal of Applied Toxicology. 2016 September; 36(9):1137-1149. [PDF, PubMed]

Ippolito, D. L., M. D. AbdulHameed, G. J. Tawa, C. E. Baer, M. G. Permenter, B. C. McDyre, W. E. Dennis, M. H. Boyle, C. A. Hobbs, M. A. Streicker, B. S. Snowden, J. A. Lewis, A. Wallqvist, and J. D. Stallings. Gene expression patterns associated with histopathology in toxic liver fibrosis. Toxicological Sciences. 2016 January; 149(1):67-88. [PDF, PubMed]

Stallings, J. D., D. L. Ippolito, A. Wallqvist, B. C. McDyre, and J. Reifman. Host response to environmental hazards: using literature, bioinformatics, and computation to derive candidate biomarkers of toxic industrial chemical exposure. Proceedings of the HFM-254 Symposium on Health Surveillance and Informatics in Missions: Multidisciplinary Approaches and Perspectives. Paris, France. 2015 October 12-14; 7:1-14. [PDF, DTIC]

Te, J. A., K. D. Spradling-Reeves, J. F. Dillman III, and A. Wallqvist. Neuroprotective mechanisms activated in non-seizing rats exposed to sarin. Brain Research. 2015 June 4; 1618:136-148. [PDF, PubMed]

AbdulHameed, M. D., G. J. Tawa, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Systems level analysis and identification of pathways and networks associated with liver fibrosis. PLOS ONE. 2014 November 8; 9(11):e112193. [PDF, PubMed]

Tawa, G. J., M. D. AbdulHameed, X. Yu, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Characterization of chemically induced liver injuries using gene co-expression modules. PLOS ONE. 2014 September 16; 9(9):e107230. [PDF, PubMed]