#### QSP in R

By admin 02-Mar-2024

###### Author: Anuraag Saini

##### What do we do?

At Vantage Research, we assist decision-making throughout the drug discovery and development process. We do it via answering questions related to exposure, efficacy, toxicity in preclinical, translational and clinical settings using mechanistic models often represented by ordinary differential equations [1]. These models are quantitatively backed by extensive literature surveys on physiology of a disease, mechanism of action of a drug and are carefully calibrated to clinically relevant readouts.

##### Why do we do it?

Model informed drug discovery process aims to integrate information from diverse data sources to help decrease both uncertainty and failure rates, and to develop information that cannot or would not be generated experimentally. Mechanistic models, especially QSP, go a level deeper in providing explanations about why or why not some drugs or drug combinations will work better than others.

##### How do we do it?

Quantitative systems pharmacology (QSP) modeling is a process where physiology of a disease and mechanism of action of a drug are like individual puzzle pieces. QSP solves this puzzle by mathematically connecting molecular to cellular mechanisms, cellular mechanisms to organs, organs to patients level and from patients to populations levels.

We will understand the QSP workflow using a published insulin-regulation model. Although there are a plethora of insulin-glucose regulation models, we chose one published by Contreas et al since it captures important aspects of insulin-glucose regulation and it is structurally simple to implement[2,3].

To make things simple, let’s assume I am drinking pineapple juice. Glucose ingestion takes place in the stomach, it travels through the small intestine getting absorbed along the way from Jejunum (middle part of small intestine) to Ileum (end of small intestine).

Absorbed glucose increases my blood glucose levels. I can use this glucose to provide energy to my brain, to carry out basal metabolic functions and to store some of it as glucose reserves for later use.

Insulin plays an important role in regulating blood glucose in the body. The pancreas senses the rising glucose levels in the body and starts producing insulin which then helps glucose to be taken up by muscle for utilization and by liver for storage as glucose reserve, thereby regulating the blood glucose. Insulin’s lack of effectiveness (could be due to insulin secretion deficiency or due to insulin resistance or some combination of both) leads to elevated blood glucose levels which people most commonly known as Diabetes.

##### Let’s do it together using R!

Required libraries: mrgsolve, ggplot2, lhs, parallel, future, mrgsim.parallel, dplyr

Other required dependencies: Rtools, rstudioapi, rstan

Now that we understand the basics. Let’s do the fun stuff!

We will represent Insulin-Glucose regulation mathematically and use the MRGsolve package [4] in R for simulating a system of equations.

Consider the system of equations in Figure 2 which represents the insulin-glucose regulation (taken from Contreras et al [2]). Let us see how we can represent this system in R and simulate different scenarios using R. In the following exercises, we will see how to (a) Set up the equations in R, (b) Work with delayed ODEs, (c) Add meals as an input to the model, (d) Visualize plasma glucose using 3 meals for 2 days, (e) Input rate constants from excel into R, (f) Perform sensitivity analysis, (g) Top down data that the model will reproduce, (h) Perform a global optimization to reproduce the top down data with minimal error and finally (i) Generate a virtual population

### Exercise 1: Make the model

Let us construct a “Glucose-Insulin Regulation Model” using the MRGsolve framework in C++. This model is based on a published model from Contreras et at 2020 [2].

As a best practice, it is ideal to keep the model file separate from the execution code. Following model is saved under filename “GlucoseInsulinRegulation.cpp”. Details about the structure of the model file are discussed in detail in subsequent exercises.

##### Code

Rcpp

// To use c++ standard function library

[PARAM]

// The parameter list is declared using PARAM block

tou = 80//

kLambda = 0.04// Production rate of glucose from liver

incretin = 3.46// incretin action on glucose

eta = 0.02//bioavailability of absorbed glucose

kSI1 = 0.19// absorption in jejunum from stomach

kI1I2 = 0.043// absorption in Ileum from jejunum

kI1G = 0.13// absorption in PlasmaGlucose from jejunum

kI2G = 0.21// absorption in PlasmaGlucose from Ileum

kGB = 0.016// basal glucose utilization rate from PlasmaGlucose

kGI = 1.37e-7// Insulin dependent glucose utilization rate from PlasmaGlucose

kI = 0.017// insulin degradation rate

beta = 109// Scale for insulin production saturation

gamma = 1.4//Scale for insulin production acceleration

food_amt = 0 // Food intake

Gprod_0 = 4.0; // Basleine prdocution of glucose

PlasmaGlucose_0 = 4.0;

Pls_Ins_0 = 25.8;

[INIT]

// INIT - name and initial value of all the compartments

// Initial conditions

// compartment 1

Stomach = 0 //392.7

// compartment 2

Jejunum= 0.0

// compartment 3

Ileum = 0.0

// compartment 4

PlasmaGlucose = 4.0

// compartment 5

Pls_Ins = 25.8

// compartment 6

Gluc_24hr = 90

[GLOBAL]

// GLOBAL block is used to define Global variables, vectors, etc. that can be used anywhere in other blocks

std::list delayed_Glucose(8);

[MAIN]

// Main block is used to define repeating algebraic calculations.

double PlasmaGlucose_mgdl = PlasmaGlucose*18;

double currMinutes24hr = (TIME-std::floor(TIME/1440)*1440);

double currMinutes10min = (TIME-std::floor(TIME/10)*10);

[TABLE]

// TABLE is used to define repeating algebraic calculations.

if(currMinutes10min==0){ delayed_Glucose.push_back(Jejunum); }

[ODE]

// ODE block is used to define system of ODEs (state nodes) and other repeating algebraic calculations

double Delayed_Ileum = delayed_Glucose.back();

double Gprod = kLambda / (kLambda/Gprod_0 + PlasmaGlucose - PlasmaGlucose_0);

double G_hat = PlasmaGlucose + incretin*(kI1G * Jejunum + kI2G * Ileum);

double Gluc_24hr_Avg_Calculation = (1/1440.0)*(PlasmaGlucose_mgdl-Gluc_24hr);

//// ODEs:

// compartment 1

// Stomach

dxdt_Stomach = - kSI1 * Stomach;

// compartment 2

dxdt_Jejunum = kSI1*Stomach - kI1I2*Jejunum - kI1G*Jejunum;

// compartment 3

dxdt_Ileum = kI1I2*Delayed_Ileum - kI2G*Ileum;

// compartment 4

dxdt_PlasmaGlucose = Gprod + eta * (kI1G * Jejunum + kI2G * Ileum) - kGB*PlasmaGlucose - kGI*Pls_Ins*PlasmaGlucose;

// compartment 5

// Plasma compartment of insulin

dxdt_Pls_Ins = kI*Pls_Ins_0 *((pow(beta,gamma) + 1.0)/((pow(beta,gamma))*pow((PlasmaGlucose/G_hat),gamma) + 1.0) - Pls_Ins/Pls_Ins_0);

// compartment 6

// Proxy for 24-hour average plasma glucose

dxdt_Gluc_24hr = (1/1440.0)*(PlasmaGlucose_mgdl-Gluc_24hr);

[CAPTURE]

// CAPTURE block is used to record the values of the species/nodes other than ODE (state nodes)

Delayed_Ileum Gprod G_hat PlasmaGlucose_mgdl currMinutes10min currMinutes24hr Gluc_24hr_Avg_Calculation

### Exercise 2: How to work with delayed ODEs in mrgSolve

Here we want Ileum to follow Jejunum but with a delay of 80 mins. There isn't a standard way of doing this using standard solvers for ordinary differential equations. Hence, we are using a coding trick to solve this issue.

We have created an array of fixed size of 8 elements that will keep storing values every 10 min such that the difference in time between first element and last element is 80 mins. This is initialized under the [GLOBAL] block.

We then create a counter that resets every 10 mins under the [MAIN] block.

Every 10 mins, values of Jejunum are stored in the defined array under the [TABLE] block.

First value of the array is then used for further calculations under the [ODE] block.

##### Code

[GLOBAL]

std::list delayed_Glucose(8);

[MAIN]

double currMinutes10min = (TIME-std::floor(TIME/10)*10);

[TABLE]

if(currMinutes10min==0){

delayed_Glucose.push_back(Jejunum);

}

[ODE]

double Delayed_Ileum = delayed_Glucose.back();

// compartment 3

dxdt_Ileum = kI1I2*Delayed_Ileum - kI2G*Ileum;

### Exercise 3: Set up the model with 3 meals a day

We need to set up an event to add calorie intake in the Stomach. Let's create 3 recurring events for breakfast, lunch and dinner.

These events will require the following

Amount of food : amt

Rate of input (eating) : rate

Time of food intake : time

Repeat interval - this is constant (1440 mins); every 24 hrs : ii

Number of times food intake will be invoked : addl

##### Code

Code

n_days = 2 #(days)

bf_amt = 450

bf_time = 60

bf_time_interval = 15

lunch_amt = 600

lunch_time = 300

lunch_time_interval = 20

dinner_amt = 800

dinner_time = 660

dinner_time_interval= 30

additional_dose_food = n_days-1

breakfast <- ev(cmt ="Stomach", amt = bf_amt, rate = bf_amt/bf_time_interval, time = bf_time, ii=1440, addl = additional_dose_food)

lunch <- ev(cmt ="Stomach", amt = lunch_amt, rate = lunch_amt/lunch_time_interval, time = lunch_time, ii=1440, addl = additional_dose_food)

dinner <- ev(cmt ="Stomach", amt = dinner_amt, rate = dinner_amt/dinner_time_interval, time = dinner_time, ii=1440, addl = additional_dose_food)

# combine all the events together

Meals <- c(breakfast,lunch,dinner)

### Exercise 4: Visualise plasma glucose for 3 meals for 2 days

We need to compile the c++ model, add food intake information and run the simulation using mrgsim. For more information on the syntax visit mrgsolve user guide and ggplot documentation.

##### Code

file.model <- "GlucoseInsulinRegulation.cpp"

mod <- mread(file.model)

model_output <- mrgsim(mod,Meals,end=(n_days*1440),delta=10)

# Plot PlasmaGlucose_mgdl

sims = as.data.frame(model_output)

node_sims = "PlasmaGlucose_mgdl"

ylabel = "PlasmaGlucose_mgdl"

ggplot() +

geom_line(aes(y=sims[,node_sims],x=(sims[,"time"])/60), colour="red") + # first layer

geom_point(aes(y=sims[,node_sims],x=(sims[,"time"])/60), colour="red") +

theme(text = element_text(size=15,face='bold')) +

xlab('Time (hours)') +

ylab(ylabel) +

ggtitle(paste("Plasma glucose for 3 meals a day"))

### Exercise 5: Reading and visualising the data/excel files

Now, we have the model set up. Let's read an excel file with values of parameters (or input rate constants) defined in [PARAM] block and plot the values of each parameter. Parameter values and units are directly taken from Contreras et at 2020 [2].

##### Code

file.params = "ModelParams.csv"

# Load params as data frame

param_df = as.data.frame(read.csv(file.params))

# Converting data frame to list

param_data = setNames(data.frame(t(param_df[,2])),param_df[,1])

# Plot the params

plot(t(param_data),xlab= "Params", ylab = "Values", pch =19, cex = 2.5,log="y",xaxt = "n")

# pch : for marker shape

# cex : for marker size

# log = “y” : for converting y axis to log

# xaxt = “n”: remove the x-labels

# Add custom x-labels

xticks <- colnames(param_data)

axis(side=1, at=1:17, labels = xticks, las = 2)

# las = 2: for rotating labels by 90 degrees

### Exercise 6: Perform a sensitivity analysis of parameters and visualise using tornado plot

Sensitivity analysis can differentiate the model parameters that change the output significantly vs those which have minimal impact on the model output. Here we will evaluate the sensitivity of the parameters on 24hr avg glucose by changing the parameter values 50% up and down from their baseline values. It is important to run the model to steady state before performing this evaluation. Hence we will run the model to 150 days before performing sensitivity analysis.

##### Code

## Run the model for 150 days

# Specify the meals for 150 days

n_days <- 150

additional_dose_food = n_days-1

breakfast <- ev(cmt ="Stomach", amt = bf_amt, rate = bf_amt/bf_time_interval, time = bf_time, ii=1440, addl = additional_dose_food)

lunch <- ev(cmt ="Stomach", amt = lunch_amt, rate = lunch_amt/lunch_time_interval, time = lunch_time, ii=1440, addl = additional_dose_food)

dinner <- ev(cmt ="Stomach", amt = dinner_amt, rate = dinner_amt/dinner_time_interval, time = dinner_time, ii=1440, addl = additional_dose_food)

# combine all the events together

Meals <- c(breakfast,lunch,dinner)

## Get parameters to perform sensitivity on

num_params = length(param_data)-4

param_names_to_vary <- colnames(param_data)[1:num_params]

model_output <- mrgsim(mod,Meals,end=(n_days*1440),delta=10)

## Get mean value of Plasma Glucose from 24 hrs data points for baseline

rTotal = length(model_output$Gluc_24hr)

avgVal = mean(model_output$Gluc_24hr[rTotal-1440:rTotal])

## Specify how much the parameters should vary

foldChange = 0.5

perChange = matrix(nrow=num_params,ncol=2)

LB_avgVal = matrix(nrow=num_params,ncol=6)

UB_avgVal = matrix(nrow=num_params,ncol=6)

## Run the model for each parameters

ii=1

for(ii in 1:num_params){

print(cbind(param_data[ii]*(1-foldChange), param_data[ii]*(1+foldChange)))

## For lower value

mod % param(param_data[ii]*(1-foldChange))

output_LB <- mrgsim(mod,Meals,end=(n_days*1440),delta=10)

LB_avgVal[ii,] = mean(output_LB$Gluc_24hr[rTotal-1440:rTotal])

## For higher value

mod % param(param_data[ii]*(1+foldChange))

output_UB <- mrgsim(mod,end=(n_days*1440),Meals,delta=10)

UB_avgVal[ii,] = mean(output_UB$Gluc_24hr[rTotal-1440:rTotal])

lb <- (LB_avgVal[ii,] - avgVal)/avgVal

ub <- (UB_avgVal[ii,] - avgVal)/avgVal

perChange[ii,] = c(lb[which.max(abs(lb))], ub[which.max(abs(ub))])

## Plot both lower and higher output

par(mfrow=c(2,1))

plot(output_LB$time, output_LB$Gluc_24hr)

plot(output_UB$time, output_UB$Gluc_24hr)

mtext(param_names_to_vary[ii],side = 3,line = - 2,outer = TRUE)

mod % param(param_data)

}

## Setting up the dataframe for plots

per_change_LB2 <- data.frame(param_names_to_vary,rep(1,num_params),perChange[,1])

per_change_LB2 <- per_change_LB2[order(abs(per_change_LB2[,3]),decreasing=TRUE),]

colnames(per_change_LB2)[3] <- "per_change"

colnames(per_change_LB2)[2] <- "ID"

per_change_UB2 <- data.frame(param_names_to_vary,rep(2,num_params),perChange[,2])

per_change_UB2 <- per_change_UB2[order(abs(per_change_UB2[,3]),decreasing=TRUE),]

colnames(per_change_UB2)[3] <- "per_change"

colnames(per_change_UB2)[2] <- "ID"

## Plot tornado plot for sensitivity analysis

data <- data.frame(rbind(per_change_LB2,per_change_UB2))

ggplot(data)+ #,aes(x=hr,y=Pls_GCG_Conc,col=ID))+

geom_bar(aes(x=reorder(param_names_to_vary,abs(-per_change)),y=per_change),stat='identity',position='identity', col=as.factor(data$ID),fill=c(rep("tomato",num_params),rep("steelblue2",num_params)),lty="blank")+

ylab(paste0("Percentage change in 24hrs Avg Glucose"))+

xlab(NULL) +

ylim(c(-0.25,0.5))+

ggtitle(paste0("Tornado plot for 24hr Avg Glucose"))+

theme(plot.title = element_text(color = "red", size = 20, hjust = 0.5),legend.title = element_blank())+

theme(text = element_text(size=20)) +

theme(text=element_text(face="bold"))+

theme(legend.position="bottom")+

coord_flip()

### Exercise 7: Create and visualise a virtual cohort

Creating a virtual cohort means creating multiple patients that have different parameterizations such that their steady state values differ from each other. This is useful if you want to re-create a clinical trial and try to match baseline characteristics with mean and std dv from observed data. In this example, we will try to create 10 VPs with different 24hr Avg Glucose values. To achieve this, we will vary the parameters randomly between their lower and upper bounds to create 10 parameterizations or virtual patients for the model to run.

Visualize the parameter combinations to generate a virtual cohort

##### Code

cohort_size = 10

num_params = length(param_data)-4

param_names_to_vary <- colnames(param_data)[1:num_params]

param_cohort <- param_data[rep(seq_len(nrow(param_data)),cohort_size),]

chosen_inds<-match(param_names_to_vary,param_table$Name)

LB_params = rep(0.3,num_params)

UB_params = rep(0.3,num_params)

rand_sample <- randomLHS(cohort_size,num_params)

# parameters set for all VPs - each row representing one VP

param_cohort[,chosen_inds] <- t((param_table[chosen_inds,2]) +

((param_table[chosen_inds,2])*(1+UB_params) - (param_table[chosen_inds,2])*(1-LB_params))*t(rand_sample))

#View parameter combinations that represent a cohort

View(param_cohort)

Formatting the parameter combinations to run them in parallel and plot 24hr average glucose for 10 VPs at steady state. For more information on syntax for parallelization refer to the documentation.

##### Code

param_cohort <- cbind(param_cohort,ID=1:nrow(param_cohort))

# Slice the dataset (parameter combinations) to run them in parallel

idata <- split(param_cohort, param_cohort$ID)

future::plan(future::multisession, workers = 2L)

out <- fu_mrgsim_ei(mod, Meals, idata,end=(n_days*1440),delta=10,.seed = 123, nchunk = 6)

# Annotate simulation output for plotting

results = as.data.frame(out)

# remove invalid VPs from results, if any

invalid_ID <- (unique(results$ID[is.nan(results$Gluc_24hr)]))

results = results[!(results$ID %in% invalid_ID),]

# keep unique time points for each ID

results % distinct(time, ID, .keep_all=TRUE)

plots <- function(y_axis_value,y_axis_name,sims,ylow,yhigh){

(ggplot(data = sims)+

geom_line(aes(x=(sims[,"time"]/1440),y=sims[,y_axis_value],color=as.factor(sims[,"ID"])))+

facet_wrap(~ sims[,"ID"]) +

theme(text = element_text(size=12,face='bold'),legend.position = "none") +

xlab('Time (days)') +

ylab(y_axis_name) +

ylim(ylow,yhigh)+

ggtitle(paste("cohort: Baseline Untreated")) )}

print(dose_plot_cohort <- plots(sims=results,y_axis_value="Gluc_24hr",y_axis_name="Gluc_24hr",ylow=70,yhigh=150))

##### Acknowledgments

Thank you Shaifali Saroha and Tanvi Joshi for collaborating on the code.

Access the following files here (a) Model file: GlucoseInsulinRegulation.cpp, (b) Simulation file: RunModel.R and (c) Parameter file: ModelParams.csv.

https://drive.google.com/drive/folders/1SWLgCO6DuKT6-dzAc22RsX1j3s6jAdSf

##### References

1. Allerheiligen, S.R.B. (2010), Next-Generation Model-Based Drug Discovery and Development: Quantitative and Systems Pharmacology. Clinical Pharmacology & Therapeutics, 88: 135-137. https://doi.org/10.1038/clpt.2010.81

2. Contreras, Sebastián, et al. “A novel synthetic model of the glucose-insulin system for patient-wise inference of physiological parameters from small-size OGTT data.” Frontiers in bioengineering and biotechnology 8 (2020): 195. https://doi.org/10.3389/fbioe.2020.00195

3.Ajmera, I., Swat, M., Laibe, C., Le Novère, N., & Chelliah, V. (2013). The impact of mathematical modeling on the understanding of diabetes and related complications. CPT: pharmacometrics & systems pharmacology, 2(7), e54. https://doi.org/10.1038/psp.2013.30.

4. Baron K (2023). mrgsolve: Simulate from ODE-Based Models. R package version 1.0.9. https://github.com/metrumresearchgroup/mrgsolve.