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CSL-Tox

This tutorial contains the necessary scripts and data to reproduce the work explained in the paper “CSL-Tox: An open-source analytical framework for the comparison of short-term and long-term toxicity end points and exploring the opportunities for decreasing in-vivo studies conducted for drug development programs.”

Naga D and Dimitrakopoulou S et al.

An overview of the steps performed and implemented in the CSL-Tox workflow.

1- Data refinement

  • Uploading necessary libraries and scripts
library(tidyverse)
library(purrr)
#importing scripts containing functions for reading the data and transform the dataset
source("ReadingData.R")
source("ChangeDataset.R")
options(knitr.kable.NA = '')
  • Assigning the file names. The main and pathology datasets are provided in the Data folder: Tables S3 and S4 respectively.
MainData_file="Data/S3.txt" 
PathologyData_file="Data/S4.txt"
  • Reading the data
Data=ReadingData(MainData_file,PathologyData_file)
  • Refining the dataset:
  1. Grouping all species into rodents & non rodents
  2. Apply controled terminology
  3. Group findings into the six high level defined categories described in the paper :
High level categories
body_weight
body_weight_gain
git_clinical_signs
other_clinical_signs
macroscopic
pathology
organ_weight
cardiovascular_effects
Data=ChangeData(Data)

2- Data exploration

  • Viewing the data
knitr::kable(head(Data$MainData))
study_id identifier therapeutic_area type route_of_administration species duration dose adj_dose pre_treatment dose_interval dose_lethality noael noael_sex adverse_findings body_weight body_weight_gain death_diagnosis neurological_clinical_signs git_clinical_signs other_clinical_signs lab_measurements macroscopic pathology organ_weight cardiovascular_effects group
Study 1 Compound 1 Cardiovascular and Metabolism sm subcutaneous non-rodent 39 0 0.00 bi weekly no no no no no no no no no no no no no long
Study 1 Compound 1 Cardiovascular and Metabolism sm subcutaneous non-rodent 39 5 0.36 bi weekly no no no no no no no no no no no no no long
Study 1 Compound 1 Cardiovascular and Metabolism sm subcutaneous non-rodent 39 25 1.79 bi weekly no no no no no no no no no no no no no long
Study 1 Compound 1 Cardiovascular and Metabolism sm subcutaneous non-rodent 39 100 7.14 bi weekly yes both no no yes no no no no no no no no no long
Study 2 Compound 1 Cardiovascular and Metabolism sm subcutaneous rodent 26 0 0.00 bi weekly no no no no no no no no no no no no no long
Study 2 Compound 1 Cardiovascular and Metabolism sm subcutaneous rodent 26 2.5 0.18 bi weekly no no yes yes no yes yes yes yes-r yes yes no no long
knitr::kable(summary(Data))
Length Class Mode
MainData 27 data.frame list
body_weight_Dataset 14 data.frame list
neurological_clinical_signs_Dataset 14 data.frame list
git_clinical_signs_Dataset 14 data.frame list
other_clinical_signs_Dataset 14 data.frame list
macroscopic_Dataset 15 data.frame list
organ_weight_Dataset 15 data.frame list
cardiovascular_effects_Dataset 14 data.frame list
pathology_Dataset 15 data.frame list
  • Plotting an overview of the data:
#importing the script containing the functions
source("DataExploratoryPlots.R")
Therapeutic_Areas.fn(Data$MainData)

Different_Species.fn(Data$MainData)

Dist.St.fn(Data$MainData)

StudiesPerFindingCat(Data$MainData)

 Dist.St.fn(Data$MainData)

3- Data analysis

This section reproduces the main results included in the paper: Overall adversity of molecules, NOAEL changes and likelihood ratios.

  • Calculation of the “Appearance” dataframe : Table containing the drug,modality,species, findings and whether those findings were observed “1” or not observed “0” in short, middle and long studies
#importing the script containing the functions
source("Appearance_Functions.R")
Appearance=map_dfr(.x =unique(Data$MainData$identifier),.f = Appear_Drug, Data)
#Viewing the head of the appearance table 
knitr::kable(head(Appearance))
drug modality species finding short middle long
Compound 1 sm rodent Weight changes 1 1 1
Compound 1 sm non-rodent Weight changes 1 0 1
Compound 1 sm rodent Neurological clinical signs 1 0 1
Compound 1 sm non-rodent Neurological clinical signs 0 0 0
Compound 1 sm rodent Gastrointestinal clinical signs 0 0 1
Compound 1 sm non-rodent Gastrointestinal clinical signs 0 0 0
  • Refining the appearance dataframe: Grouping short and middle study together
Summarised.Appearance = Cond.Appearance.fn(Appearance)
#head of summarized appearance table
knitr::kable(head(Summarised.Appearance))
drug modality species finding short.cond middle.cond long.cond short_middle.cond
Compound 1 sm non-rodent Cardiovascular System FALSE FALSE FALSE FALSE
Compound 1 sm non-rodent Cutaneous TRUE FALSE TRUE TRUE
Compound 1 sm non-rodent Endocrine System FALSE FALSE FALSE FALSE
Compound 1 sm non-rodent Exocrine System FALSE FALSE FALSE FALSE
Compound 1 sm non-rodent Eye/conjuctiva FALSE FALSE FALSE FALSE
Compound 1 sm non-rodent Gastrointestinal clinical signs FALSE FALSE FALSE FALSE

Note: The finding coloumn in the summarized appearance table contains the high level terms, for more detailed findings the following function can be used:

Summarised.Appearance.detailed = Cond.Appearance.ext.fn(Appearance)
knitr::kable(head(Summarised.Appearance.detailed))
drug modality species finding short.cond middle.cond long.cond short_middle.cond
Compound 1 sm non-rodent Cardiovascular System/ microscopic pathology FALSE FALSE FALSE FALSE
Compound 1 sm non-rodent Cardiovascular System/macroscopic pathology FALSE FALSE FALSE FALSE
Compound 1 sm non-rodent Cardiovascular System/organ weight change FALSE FALSE FALSE FALSE
Compound 1 sm non-rodent Cutaneous/ microscopic pathology TRUE FALSE TRUE TRUE
Compound 1 sm non-rodent Cutaneous/macroscopic pathology TRUE FALSE TRUE TRUE
Compound 1 sm non-rodent Endocrine System/ microscopic pathology FALSE FALSE FALSE FALSE
  • Repeating previous analysis but for adverse events only
Adverse.Data=AdverseData.fn(Data)
Adverse.Appearance=map_dfr(.x =unique(Adverse.Data$MainData$identifier),.f = Appear_Drug, Adverse.Data)
Summarised.Adverse.Appearance=Cond.Appearance.fn(Adverse.Appearance)

(i) Calculation of the overall adversity per modality

  • For SM
adversity_sm = Adversity.Summary.fn(Summarised.Adverse.Appearance, type="sm")
knitr::kable(adversity_sm, caption = "Adversity summary for small molecules")
drug short_middle long
Compound 1 FALSE FALSE
Compound 2 FALSE FALSE
Compound 3 FALSE FALSE
Compound 4 FALSE FALSE
Compound 5 FALSE FALSE
Compound 6 FALSE TRUE
Compound 7 FALSE TRUE
Compound 10 TRUE FALSE
Compound 11 TRUE FALSE
Compound 8 TRUE FALSE
Compound 9 TRUE FALSE
Compound 12 TRUE TRUE
Compound 13 TRUE TRUE
Compound 14 TRUE TRUE
Compound 15 TRUE TRUE
Compound 16 TRUE TRUE
Compound 17 TRUE TRUE
Compound 18 TRUE TRUE
Compound 19 TRUE TRUE
Compound 20 TRUE TRUE
Compound 21 TRUE TRUE
Compound 22 TRUE TRUE
Compound 23 TRUE TRUE
Compound 24 TRUE TRUE
Compound 25 TRUE TRUE

Adversity summary for small molecules

  • For LM
adversity_lm = Adversity.Summary.fn(Summarised.Adverse.Appearance, type="lm")
knitr::kable(adversity_lm, caption = "Adversity summary for large molecules")
drug short_middle long
Compound a FALSE FALSE
Compound b FALSE FALSE
Compound c FALSE FALSE
Compound d FALSE FALSE
Compound e FALSE FALSE
Compound f FALSE FALSE
Compound g FALSE FALSE
Compound h FALSE FALSE
Compound i FALSE FALSE
Compound j FALSE FALSE
Compound k FALSE FALSE
Compound l FALSE FALSE
Compound m FALSE FALSE
Compound n FALSE FALSE
Compound o FALSE TRUE
Compound p TRUE TRUE
Compound q TRUE TRUE
Compound r TRUE TRUE

Adversity summary for large molecules

(ii) Calculation of the NOAEL changes from short to long-term studies

#importing the script containing the functions
source("NOAEL_Change.R")
#table with results for sm
knitr::kable(result_sm, caption = "Noael changes for small molecules")
identifier noael species
Compound 1 Increase non-rodent
Compound 2 Same non-rodent
Compound 3 Increase non-rodent
Compound 4 Same non-rodent
Compound 5 Decrease non-rodent
Compound 6 Decrease non-rodent
Compound 8 Increase non-rodent
Compound 9 Same non-rodent
Compound 10 Same non-rodent
Compound 11 Increase non-rodent
Compound 12 Decrease non-rodent
Compound 13 Decrease non-rodent
Compound 14 Decrease non-rodent
Compound 15 Increase non-rodent
Compound 17 Same non-rodent
Compound 18 Decrease non-rodent
Compound 19 Same non-rodent
Compound 20 Decrease non-rodent
Compound 21 Increase non-rodent
Compound 22 Increase non-rodent
Compound 24 Decrease non-rodent
Compound 25 Decrease non-rodent
Compound 1 Same rodent
Compound 2 Same rodent
Compound 3 Same rodent
Compound 4 Decrease rodent
Compound 5 Decrease rodent
Compound 6 Same rodent
Compound 9 Same rodent
Compound 10 Decrease rodent
Compound 11 Increase rodent
Compound 12 Same rodent
Compound 13 Same rodent
Compound 14 Decrease rodent
Compound 15 Increase rodent
Compound 16 Same rodent
Compound 17 Same rodent
Compound 18 Decrease rodent
Compound 19 Increase rodent
Compound 20 Decrease rodent
Compound 21 Same rodent
Compound 22 Decrease rodent
Compound 23 Decrease rodent
Compound 24 Increase rodent
Compound 25 Decrease rodent

Noael changes for small molecules

#table with results for lm
knitr::kable(result_lm,caption = "Noael changes for large molecules")
identifier noael species
Compound a Same non-rodent
Compound b Same non-rodent
Compound c Increase non-rodent
Compound d Decrease non-rodent
Compound e Decrease non-rodent
Compound f Increase non-rodent
Compound g Increase non-rodent
Compound h Increase non-rodent
Compound i Increase non-rodent
Compound j Same non-rodent
Compound k Increase non-rodent
Compound l Increase non-rodent
Compound m Same non-rodent
Compound n Same non-rodent
Compound o Decrease non-rodent
Compound q Same non-rodent
Compound r Decrease non-rodent
Compound d Same rodent
Compound k Increase rodent
Compound m Same rodent
Compound n Same rodent
Compound p Decrease rodent
Compound q Decrease rodent

Noael changes for large molecules

(iii) Calculation of the Likelihood ratios

#importing the script containing the functions
source("LikelihoodRatio.R")
  • Calculate contingency tables and likelihood ratios for all findings

Specify rodent or non-rodent:

animal = "rodent"
Likelihood.Ratio=Likelihood.Ratio.fn(Summarised.Appearance %>% filter(species== animal))
  • Round values and select only significant likelihood ratios with p-values < 0.05
Likelihood.Ratio[,-1]=round(Likelihood.Ratio[,-1],2)

#Likelihood ratios with p.value<0.05
Likelihood.Ratio.imp=Likelihood.Ratio %>% filter(p_value<=0.05) %>% 
  arrange(desc(LR_pos), desc(iLR_neg)) %>% select(-c(Sensitivity,Specificity))

knitr::kable(Likelihood.Ratio.imp,caption = "Significant Likelihood ratios for rodents for all findings")
finding TP FP FN TN LR_pos iLR_neg p_value
Reproductive System 4 1 2 23 16.00 2.87 0.00
Gastrointestinal clinical signs 7 2 2 19 8.17 4.07 0.00
GI tract 5 2 4 19 5.83 2.04 0.01
Cutaneous 5 3 3 19 4.58 2.30 0.02
Endocrine System 13 4 1 12 3.71 10.50 0.00
liver 14 4 2 10 3.06 5.71 0.00
Lymphoid Tissues 9 5 4 12 2.35 2.29 0.04
Weight changes 14 4 4 8 2.33 3.00 0.02

Significant Likelihood ratios for rodents for all findings

  • Plot frequency of fp and fn across the findings in rodent and non-rodent
Appear_plot(dataf = Likelihood.Ratio.imp ,species = "rodent", legend_pos=c(0.90,0.90))

  • Calculate contingency tables and likelihood ratios for adverse findings only (using the adverse appearance table this time)
Adverse.Likelihood.Ratio=Likelihood.Ratio.fn(Summarised.Adverse.Appearance %>% filter(species== animal))
  • Round values and select only significant likelihood ratios with p-values < 0.05
Adverse.Likelihood.Ratio[,-1]=round(Adverse.Likelihood.Ratio[,-1],2)

#Likelihood ratios with p.value<0.05
Adverse.Likelihood.Ratio.imp=Adverse.Likelihood.Ratio %>% filter(p_value<=0.05) %>% 
arrange(desc(LR_pos), desc(iLR_neg)) %>%  select(-c(Sensitivity,Specificity))

knitr::kable(Adverse.Likelihood.Ratio,caption = "Significant Likelihood ratios for rodents for adverse findings in rodents")
finding TP FP FN TN Sensitivity Specificity LR_pos iLR_neg p_value
Cardiovascular System 0 1 3 26 0.00 0.96 0.00 0.96 1.00
Cutaneous 0 4 2 24 0.00 0.86 0.00 0.86 1.00
Endocrine System 2 4 1 23 0.67 0.85 4.50 2.56 0.09
Exocrine System 1 1 4 24 0.20 0.96 5.00 1.20 0.31
Eye/conjuctiva 0 0 1 29 0.00 1.00 1.00 1.00
Gastrointestinal clinical signs 0 1 0 29 0.97 1.00
GI tract 2 3 1 24 0.67 0.89 6.00 2.67 0.06
In life cardiovascular effects 0 0 0 30 1.00 1.00
liver 3 0 1 26 0.75 1.00 Inf 4.00 0.00
Lymphoid Tissues 2 2 1 25 0.67 0.93 9.00 2.78 0.04
MuscularSkeletal System 0 3 1 26 0.00 0.90 0.00 0.90 1.00
Nervous System 1 0 3 26 0.25 1.00 Inf 1.33 0.13
Neurological clinical signs 2 2 2 24 0.50 0.92 6.50 1.85 0.07
Other clinical signs 1 4 2 23 0.33 0.85 2.25 1.28 0.43
Reproductive System 0 2 2 26 0.00 0.93 0.00 0.93 1.00
Respiratory System 0 1 1 28 0.00 0.97 0.00 0.97 1.00
Urinary System 0 1 5 24 0.00 0.96 0.00 0.96 1.00
Weight changes 0 6 3 21 0.00 0.78 0.00 0.78 1.00

Significant Likelihood ratios for rodents for adverse findings in rodents

  • Plot frequency of fp and fn across the adverse findings
Appear_plot(dataf = Adverse.Likelihood.Ratio.imp ,species = "rodent", legend_pos=c(0.90,0.90))

The previous steps are repeated to generate the results for the non-rodent species.

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