title: High-throughput imaging-based nephrotoxicity prediction for xenobiotics with diverse chemical structures.
abstract: The kidney is a major target for xenobiotics, which include drugs, industrial chemicals, environmental toxicants and other compounds. Accurate methods for screening large numbers of potentially nephrotoxic xenobiotics with diverse chemical structures are currently not available. Here, we describe an approach for nephrotoxicity prediction that combines high-throughput imaging of cultured human renal proximal tubular cells (PTCs), quantitative phenotypic profiling, and machine learning methods. We automatically quantified 129 image-based phenotypic features, and identified chromatin and cytoskeletal features that can predict the human in vivo PTC toxicity of 44 reference compounds with ~82 % (primary PTCs) or 89 % (immortalized PTCs) test balanced accuracies. Surprisingly, our results also revealed that a DNA damage response is commonly induced by different PTC toxicants that have diverse chemical structures and injury mechanisms. Together, our results show that human nephrotoxicity can be predicted with high efficiency and accuracy by combining cell-based and computational methods that are suitable for automation.
authors.affiliation: Bioinformatics Institute, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.
authors.forename: Ran
authors.initials: R
authors.lastname: Su
authors.affiliation: Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore.
authors.forename: Sijing
authors.initials: S
authors.lastname: Xiong
authors.affiliation: Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore, 138669, Singapore. dzink@ibn.a-star.edu.sg.
authors.forename: Daniele
authors.initials: D
authors.lastname: Zink
authors.affiliation: Bioinformatics Institute, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore. loolh@bii.a-star.edu.sg.|Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Singapore. loolh@bii.a-star.edu.sg.
authors.forename: Lit-Hsin
authors.initials: LH
authors.lastname: Loo
mesh_terms: D057205:Automation, Laboratory; D016923:Cell Death / Q000187:drug effects; D002461:Cell Line, Transformed; D002478:Cells, Cultured; D042002:Chromatin Assembly and Disassembly / Q000187:drug effects*; D019295:Computational Biology; D003599:Cytoskeleton / Q000187:drug effects*; D004249:DNA Damage; D004353:Drug Evaluation, Preclinical; D005240:Feasibility Studies; D057166:High-Throughput Screening Assays; D006801:Humans; D007687:Kidney Tubules, Proximal / Q000166:cytology / Q000187:drug effects*; D000069550:Machine Learning; D008958:Models, Molecular; D015394:Molecular Structure; D009153:Mutagens / Q000737:chemistry / Q000633:toxicity*; D009994:Osmolar Concentration; D054852:Small Molecule Libraries; D015262:Xenobiotics / Q000737:chemistry / Q000633:toxicity*
chemical_list: D009153:Mutagens; D054852:Small Molecule Libraries; D015262:Xenobiotics
keywords: DNA damage response; High-content screening; In vitro model; Nephrotoxicity; Phenotypic profiling; Toxicity prediction