Paper reading (四十九)：Prediction of drug-induced nephrotoxicity and injury mechanisms

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

scholar 引用：51

页数：15

发表时间：2015.07

发表刊物：Scientific Reports

作者：Karthikeyan Kandasamy, Jacqueline Kai Chin Chuah1,...,Daniele Zink1

摘要：

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.

Introduction：

• renal proximal tubular cells (PTC)  肾近端小管细胞
• Drug-induced nephrotoxicity 药物引起的肾毒性
• acute kidney injury (AKI) 急性肾损伤
• human embryonic stem cells (hESC) 人类胚胎干细胞
• the differentiation period comprised 20 days when the hESC-based approach was used, which made this model relatively inefficient.
• due to ethical and legal issues associated with hESC, hESC-based assays for drug safety screening are not widely applicable.
• human induced pluripotent stem cells (hiPSC) 人诱导多能干细胞
• Currently no renal in vitro model is available that would be suitable for automated cellular imaging.
• Furthermore, no in vitro model based on hiPSC-derived renal cells is available, neither for the prediction of nephrotoxicity, nor for the analysis of cellular pathways and injury mechanisms.
• we report a rapid and simple 1-step protocol for the differentiation of hiPSC into HPTC-like cells with >90% purity. 
• Using this protocol, compound screening could be immediately performed after a differentiation period of only 8 days without the requirement of cell harvesting or purification. 
• The combination of the hiPSC-based renal in vitro model with machine learning methods allowed us to predict drug-induced proximal tubular toxicity in humans with high accuracy.
• Injury mechanisms and drug-induced cellular pathways could be reliably identified by using automated cellular imaging.

正文组织架构：

1. Introduction

2. Results and Discussion

2.1 Differentiation of hiPSC into HPTC-like cells

2.2 Characterization of hiPSC-derived cells

2.3 Transporter-mediated drug uptake and drug-induced interleukin expression

2.4 Predictive performance

2.5 Drug-induced injury mechanisms

3.  Methods

3.1 Expansion and differentiation of hiPSC

3.2 HPTC

3.3 Fluorescence-activated cell sorting (FACS)

3.4 Immunofluorescence

3.5 Quantitative analysis of immunofluorescence images

3.6 Determination of marker expression levels

3.7 Transporter-mediated drug uptake and interleukin induction

3.8 Scanning electron microscopy (SEM)

3.9 GGT activity

3.10 Drug transporter activity

3.11 Compound treatment and determination of IL6 and IL8 expression levels

3.12 Automated cellular imaging

3.13 Calculations and Statistics

3.14 Computational analysis

正文部分内容摘录：

Based on these features, an automated classifier called random forest (RF) was used to classify the compounds as toxic or not toxic for PTC (in comparison to other classifiers, RF showed the best performance when tested with HPTC). 

第40篇参考文献：Supervised prediction of drug-induced nephrotoxicity based on interleukin-6 and -8 expression levels

引用次数：22

1. Biological Problem: What biological problems have been solved in this paper?

• nephrotoxicity(肾毒性) prediction performance of the cells 
• prediction of drug-induced nephrotoxicity