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Drug-Induced Liver Injury (DILI) Classification and Its Application On Human DILI Risk Prediction
Drug-Induced Liver Injury (DILI) Classification and Its Application On Human DILI Risk Prediction
Drug-Induced Liver Injury (DILI) Classification and Its Application On Human DILI Risk Prediction
Abstract
Drug-induced liver injury (DILI) is one of the primary reasons for drugs being terminated in premarket
studies or being withdrawn from the market after approval. Many new methodologies have been examined
to improve DILI prediction, including high-throughput/high- content screening assays, in silico
approaches and toxicogenomics, all of which rely on a truth set of drugs with well-defined DILI potential.
However, defining a drug’s DILI risk is on varying interpretations, leading to differing classification
schemes. Even when the same drug list is employed, variability in scheme affects predictive variables and
models which lead to disparate risk prediction. Each model imbeds truth and knowledge in a different
manner and context. An integrative approach melding models and variables should yield a system with
enhanced prediction accuracy and better characterized mechanisms of action. Toward such an integrative
predictor, we present four different classification schemes, i.e., an FDA labeling data-based approach
(DILIrank dataset), a clinical evidence-based approach (LiverTox dataset), literature-based approaches
(Greene and Xu datasets), and a registry-based approach (Suzuki dataset). Comparative analyses showed
good general agreement between these approaches, with the most substantial difference observed between
in silico models for drug-centric classification methods (i.e., drug-labeling and literature based approaches)
versus clinical evidence-based methods (i.e., case reports and registry based approaches). The results sug-
gest that substantial benefits can be obtained by consolidating various classification schemes to generate a
larger dataset imbedding more diverse knowledge, and especially the new data streams from emerging
technologies.
Key words Drug-induced liver injury, Risk assessment, DILI classification, Rule-of-two model,
DILIscore model
1 Introduction
Minjun Chen and Yvonne Will (eds.), Drug-Induced Liver Toxicity, Methods in Pharmacology and Toxicology,
https://doi.org/10.1007/978-1-4939-7677-5_3, © Springer Science+Business Media, LLC, part of Springer Nature 2018
45
46 Shraddha Thakkar et al.
Fig. 1 Development and performance of a predictive model for assessing the human DILI risk depends heavily
upon the accuracy and consistency of the DILI classification. DILI classification differentiates drugs as DILI
positive (drugs that can cause liver injury) and DILI negative (drugs that have not revealed signs of liver injury),
and used to identify mechanistic parameters using emerging methodologies for DILI prediction. Emerging
technologies used for DILI prediction included, but are not limited to, in vitro methods (e.g., High Content
Screening and High Throughput Screening assays), and in silico methodologies
injury is?) [8]. Using different data sources, (e.g., the number of
case reports [8–12] or FDA approved-drug labeling [8, 13]) and
weighing differently on each of these factors could vary the assign-
ment of DILI classification to the same drugs. In this paper, we
first summarize the four different DILI classifications within five
reported large DILI datasets (n > 200). We then conducted com-
parative analysis between these classification schemas and demon-
strated the variability in classification on the model prediction by
applying our DILIscore model (a quantitative predictive model for
DILI severity).
2 DILI Classifications
Table 1
Various DILI classification datasets
Fig. 2 DILIrank data set was generated using FDA drug labeling and DILI causality approach and contains the
drugs approved by the US FDA before 2010. It also contains number of drugs from the other type of DILI clas-
sifications that are overlapped with DILIrank such as Greene (325 drugs), Suzuki (268 drugs), LiverTox (493
drugs), and Xu (343 drugs). This analysis was done to understand the coverage of drugs from each database
and overlapping with others. However, this analysis is independent of DILI classification assigned by each
dataset. Besides DILIrank, other four datasets follow different approaches to identify DILI positive and DILI
negative drugs and there is very little overlap (15.3%) between them. Greene and Xu classifications used simi-
lar approach and thus with the largest overlap (47.5%) while Suzuki’s and LiverTox method contain unique list
of DILI drugs and non-DILI drugs (Those drugs were not identified by any other classification system)
2.1 DILIrank: A Drug The DILIrank dataset contained 1036 drugs approved by the FDA
Labeling Based before 2010 with classified DILI categories [8]. This classification
Approach was based on the FDA drug labeling documents and in addition, it
also accounted for DILI causality evidence in literature. DILI cat-
egories were classified for the drugs as vNo-, vLess-, or vMost-
DILI-Concerns while the drugs that could not be categorized in
the above classification for the DILI concern was classified as
“Ambiguous-DILI-Concern.” vMost-DILI-concern drugs are
50 Shraddha Thakkar et al.
those drugs that were (a) withdrawn due to DILI, or (b) have
“Black-Box Warning and Precautions” labeling section (192
drugs). vLess-DILI-Concern drugs are those drugs that have DILI
statements in “Warning and Precautions” labeling section that rep-
resents only mild indications or DILI indication present in “Adverse
Reactions” section (278 drugs). For drugs recorded with DILI
evidences in drug labeling (i.e., vMost- and vLess-DILI-Concern)
were further verified for their DILI causality in literature, other-
wise they were classified as having “Ambiguous-DILI-Concern” as
such drugs should be used with caution (254 drugs); whereas
v
No-DILI-Concern indicates that there is no DILI indication pres-
ent in any of three labeling sections (i.e., Boxed Warning, Warnings
and Precautions, and Adverse Reactions) and no litrature evidence
available (312 drugs).
2.3 Greene This dataset consists of DILI information from both human and
Classification: animal studies, but only human data were used in this paper (shown
A Literature Based in Table 1 column 3 and 5). The number of case reports in con-
Approach junction with literature based evidence were used for human DILI
classification of 325 drugs in Greene classification [9]. Drugs are
classified into human hepatotoxicity (189 drugs) with weak evi-
dence (50 drugs) or no evidence (86 drugs) for DILI.
2.4 Suzuki Classification from Suzuki [16] has consolidated the DILI
Classification: information from major DILI registries, including the Spanish
A Registry Based DILI registry, the Swedish adverse reaction databases and the DILI
Approach network from USA. This classification system has identified 157
DILI Classifications and the Predictive Models 51
drugs with general liver injury and 87 drugs with acute liver failure.
Additionally, 43 drugs were identified as withdrawn or suspended
due to concern for DILI.
2.5 Xu Classification: Xu et al. [15] have classified 343 drugs based on the case reports
A Literature Based and information available in the various literature. The drugs were
Approach classified as either DILI positive or negative. There were 196 drugs
identified as DILI positive and 147 drugs identified as DILI
negative.
Fig. 3 (a) Comparison of DILIrank with LiverTox database (i.e., the labeling based classification against the
clinical report based classification). (b) Comparison of DILIrank with Greene classification (i.e., the labeling
based classification against a literature based approach). (c) Comparison of DILIrank with Suzuki classification
(i.e., the labeling based classification against the clinical report based classification). (d) Comparison of
DILIrank with Xu classification (i.e., the labeling based classification against the literature based
classification)
v
Less-DILI-Concern of DILIrank compared to weak hepatotoxic-
ity of Greene (c) VNo-DILI-Concern of the DILIrank compared
to no hepatotoxicity of Greene. For example, 50 out of 63 drugs
(79%) have no evidence of causing liver injury were also found to
be in the category of no-DILI-Concern drugs in DILIrank.
Similarly, 36 out of 39 drugs (92%) with weak evidence of hepato-
toxicity based on literature evidence are also defined as vLess-DILI-
Concern by DILIrank. The Human hepatotoxicity classification of
Greene, demonstrated the overlap with vLess-DILI-Concern cate-
gory (39%) as well as vMost-DILI-Concern category (54%). Of
note, Greene classification reports that all the drugs are hepato-
toxic to humans in the human hepatotoxicity category, irrespective
of the severity of the classification. However, majority of drugs
from Human Hepatotoxicity category (86 out of 158 drugs) were
the vMost-DILI-Concern drugs. Thus, Greene classification shows
concordance in data of the general trend in comparison with the
DILIrank dataset.
A similar trend was observed for Xu dataset which is also a
literature-based approach (Fig. 3d), where 55% of the drugs belong
to the DILI positive categories by Xu are represented in the VMost-
DILI-Concern category of DILIrank.
The Suzuki dataset is derived from the DILI information based
on the case registry, which divided the dataset into three categories
based on severity and liver injury risk to humans. Suzuki dataset
contains information related to human hepatotoxicity and it does
not contain the list of drugs that does not cause liver injury. As
depicted in Fig. 3c, all the drugs that are either withdrawn or sus-
pended due to DILI on Suzuki’s are represented in the vMost-
DILI-Concern category of DILIrank. Additionally, 73% of the
drugs that cause general liver injury in Suzuki dataset belong to the
v
Less-DILI-Concern category of DILIrank.
By comparing DILIrank with other four classification schemes
for the drugs overlapped, there is an apparent trend between these
classification schemes (highlighted as red circles). However, differ-
ences were also observed between data sets, which could affect the
performance of predictive models. Therefore, a predictive model
developed using one classification scheme would not necessary
converge when using a different classification scheme.
Fig. 4 (a) Comparison of DILIscore hepatotoxicity model with the DILIrank dataset. The DILIrank dataset
classified drugs based on drug labeling. In comparison of DILIrank with the DILIscore, we could demonstrate
some degree of separation in the dataset. The vNo-DILI-Concern drugs (green) and vMost-DILI concern drugs
(pink) showed most amount of separation. Most of the vNo-DILI-Concern drugs (green) had the DILIscore of
~2.5 and most of the vMost-DILI-Concern drugs with the DILIscore of ~7. Weak Hepatotoxic drugs demonstrated
the average DILIscore of ~4. (b) Comparison of DILIscore hepatotoxicity model with the Greene dataset. The
Greene dataset classified drugs based on the literature evidence. On comparison with the DILIscore, we were
able to see some degree of separation in the dataset based on the DILIscore. However, comparing the No
Hepatotoxicity evidence drugs (green) and Human Hepatotoxicity drugs (pink) showed most amount of
separation. Most of the no DILI evidence drugs had the DILIscore of ~2.5 and most of the Human Hepatotoxicity
drugs with the DILIscore of ~7. Weak Hepatotoxic drugs demonstrated the average DILIscore of ~5.
56 Shraddha Thakkar et al.
Fig. 4 (continued) (c) Comparison of DILIscore hepatotoxicity model with the Xu dataset. The Xu dataset is
derived from the literature based evidence. On comparison with the DILIscore, we were able to see some
degree of separation in the dataset based on the Xu classification. Comparing of DILI Positive (pink) and DILI
negative (green) showed the separation. Majority of drugs with DILI negative annotation at Xu classification
demonstrated DILIscore of ~4. Majority of drugs with DILI Positive annotation from Xu classification demon-
strated DILIscore of ~7. (d) Comparison of DILIscore hepatotoxicity model with the LiverTox data set. The
LiverTox data set classified based on the likelihood of liver injury by considering the patients case reports.
DILIscore gives the quantitative value (−1.9 to 8.64) where higher number denotes, higher hepatotoxicity risk.
On comparison of the LiverTox (category A to E) with the DILIscore distribution was not able to separate drugs
classified based on clinical reports. However, few of the drugs with no hepatotoxic indications (DILIScore) and
no chances (to cause liver injury category E (LiverTox) (green) and fatal hepatotoxic indication with most likely
chances to cause liver injury (pink) were differentiable. Majority of drugs with no likelihood to cause liver injury
from LiverTox demonstrated DILIscore of ~4. Majority of drugs with most likely to cause liver injury from
LiverTox demonstrated DILIscore of ~7. (e) Comparison of DILIscore hepatotoxicity model with the Suzuki
dataset. The Suzuki dataset is derived from the DILI based on case registry based approach. On comparison
with the DILIscore, we were able to see some degree of separation in the dataset based on the Suzuki clas-
sification. A comparison of withdrawn drugs (pink) and general DILI drugs (cream) showed most amount of
separation. Suzuki classification does not classify the list of drugs that did not show
5 Conclusion
Disclaimer
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