Prediction of drug-induced nephrotoxicity and injury mechanisms with human induced pluripotent stem cell-derived cells and machine learning methods

Abstract

The renal proximal tubule is a main target for drug-induced toxicity. The prediction of proximal tubular toxicity during drug development remains difficult. Any in vitro methods based on induced pluripotent stem cell-derived renal cells had not been developed, so far. Here, we developed a rapid 1-step protocol for the differentiation of human induced pluripotent stem cells (hiPSC) into proximal tubular-like cells. These proximal tubular-like cells had a purity of >90% after 8 days of differentiation and could be directly applied for compound screening. The nephrotoxicity prediction performance of the cells was determined by evaluating their responses to 30 compounds. The results were automatically determined using a machine learning algorithm called random forest. In this way, proximal tubular toxicity in humans could be predicted with 99.8% training accuracy and 87.0% test accuracy. Further, we studied the underlying mechanisms of injury and drug-induced cellular pathways in these hiPSC-derived renal cells, and the results were in agreement with human and animal data. Our methods will enable the development of personalized or disease-specific hiPSC-based renal in vitro models for compound screening and nephrotoxicity prediction.

Advances in predictive in vitro models of drug-induced nephrotoxicity

“…The cisplatin response was ameliorated by administration of the OCT antagonist cimetidine, suggesting functional OCT2 involvement in cisplatin tubulotoxicity, although expression of OCT2 or of other proximal tubule cell transporters was not confirmed. KIM1 expression was also significantly increased in response to gentamicin; however, KIM1 was also expressed at low levels in untreated iRECs, consistent with earlier observations that KIM1 is expressed by untreated, hiPSC-derived proximal tubule-like cells cultured in 2D 126 and suggesting that KIM1 is a nonspecific marker of tubule cell injury in in vitro models. In addition to the above caveats, the protocol for direct reprogramming produced a mixed population of iRECs that expressed markers of different nephron segments, with some individual cells expressing markers of multiple segments, suggesting that this approach generates pan-epithelial cells, which might represent an endogenous progenitor or tubular intermediate but might also represent nonspecific epithelial cell types that are not analogous to any cell type found in vivo.…”

“…126 ). However, similar to 2D cultures of renal proximal tubule cells, these hiPSC-derived cells exhibited high baseline expression of the injury marker KIM1 and the dedifferentiation marker vimentin.…”

Generation of kidney tubular organoids from human pluripotent stem cells

“…and Kandasamy et al . showed the induction of proximal tubule-like cells with the high purity, by differentiation of hPSCs with REGM supplemented with bone morphogenetic protein (BMP) 2 and 7 and formed tubule-like structures in a two-dimensional culture1553. In contrast to their studies, here we were able to purify KSP+ cells that exhibited characteristics of proximal tubular, loops of Henle, distal tubular and collecting duct cells, which is consistent with previous studies showing KSP expression in all segment of tubules from proximal tubule to collecting ducts26.…”

Translational Prospects and Challenges in Human Induced Pluripotent Stem Cell Research in Drug Discovery

“…Podocytes in the renal corpuscle and renal proximal tubular cells are usually most affected [119]. Perturbation of normal kidney function can lead to an accumulation of waste products resulting in acute kidney injury (AKI), long-term chronic kidney disease (CKD) or progression to the end-stage renal injury (ESRI).…”

“…In 2015, Kandasamy et al proposed a simplified eight-day protocol for differentiation of induced pluripotent stem cells to renal proximal tubule cells (HPTC) by culturing iPSC in renal epithelial cell growth medium (REGM) supplemented with two bone morphogenetic proteins, namely BMP2 and BMP7. Although certain stemness markers certainly require further downregulation, the response of emerging hiPSC-derived HPTC-like cells to acarbose, ethylene glycol, and potential nephrotoxins aristolochic acid, and cisplatin in the IL6/IL8 assay was highly coordinated with that of the primary HPTCs [119]. Most of the iPSC differentiation protocols, however, aim at three-dimensional derivation of mini kidney organs that would more closely recapitulate an intricate nephron structure [126,127].…”