Team:Wageningen UR/HumanBody

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= Human Body Model =
= Human Body Model =
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To be able to determain what the vlps and the medicine do in the human body we've constructed a human body model that is inspired by the model of the Slovenia 2012 team. With this model we are able to compare the traditional use of medicine with the use of our VLPs. If succesful it will open up a whole new era for the use of medicine.
+
To be able to determine what the VLPs and the medicine do in the human body we have constructed a human body model that is inspired by the model of the Slovenia 2012 team. With this model we are able to compare the traditional use of medicine with the use of our VLPs. If successful it will open up a whole new era for the use of medicine.
-
 
+
-
== PICTURE TESTING ==
+
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[[File:VLP1.png]]
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[[File:VLP2.PNG]]
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[[File:VLP3.png]]
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[[File:VLP4.png]]
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[[File:VLP5.png]]
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[[File:VLP6.png]]
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[[File:VLP7.png]]
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[[File:VLP8.png]]
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[[File:VLP9.png]]
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[[File:VLP9.png]]
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[[File:VLP10.png]]
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[[File:VLP11.png]]
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[[File:VLP12.png]]
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[[File:VLP13.png]]
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[[File:VLP14.png]]
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[[File:VLP15.png]]
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[[File:VLP16.png]]
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[[File:VLP17.png]]
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[[File:VLP18.png]]
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[[File:VLP19.png]]
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[[File:VLP20.png]]
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[[File:VLP21.png]]
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[[File:VLP22.png]]
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[[File:VLP23.png]]
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[[File:VLP24.png]]
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[[File:VLP25.png]]
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[[File:VLP26.png]]
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[[File:VLP27.png]]
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= Explanation of the model =
= Explanation of the model =
-
Our model is constructed in such a way that each compartment of the model represent an organ or multiple organs with the same physical properties. We decided to have separate compartments for the kidneys, liver, lungs and the intestine. All other organs are grouped in the rapid or slowly perfused tissue. In the case study we made a new compartment between the intestine and the liver to represents the intestine tumor. (figure: flow scheme human body)
+
Our model is constructed in such a way that each compartment of the model represents an organ or multiple organs with the same physical properties. We decided to have separate compartments for the kidneys, liver, lungs and the intestine. All other organs are grouped in the rapid or slowly perfused tissue. In the case study we made a new compartment between the intestine and the liver to represent the intestine tumor (figure 1).
-
[[File:VLPflow.png500px]]
+
[[File:VLPflow.png|500px|center|thumb|Figure 1: The flowscheme used for our model]]
-
In our model we’ve used three different mass balance equations for an organ. The first mass balance describes the concentration of all the VLPs in the organ, this is to see the overall change in the VLP concentration. The second mass balance equation describes the concentration of the unbound VLPs. This is because the unbound particles can move freely into the body while the bound particles stays into the organ. (figure: flow scheme organ) The final mass balance equation is for the concentration of the medicine in the organ. With these three mass balance equation we’ve developed our model
+
In our model we have used three different mass balance equations for an organ. The first mass balance describes the concentration of all the VLPs in the organ, this is to see the overall change in the VLP concentration. The second mass balance equation describes the concentration of the unbound VLPs. This is because the unbound particles can move freely into the body while the bound particles stays into the organ. The final mass balance equation is for the concentration of the medicine in the organ. With these three mass balance equations we’ve developed our model. At the botom of the page the model can be studied intensivly.
-
(figure: flow scheme organ)
 
-
[[File:VLP1.png]]
+
= Case study: colorectal cancer =
 +
 
 +
As our case study to use the human body model, we used colorectal cancer. Cancer as a disease is very destructive and is responsible for the deaths of millions. In 2007, 13% of all the deaths were cancer related [1]. We chose colorectal cancer because in Europe the 5 year survival the disease is less than 60% [2]. If our treatment shows a better treatment we can help the people to fight off the cancer.
 +
 
 +
== Treatment of Colorectal cancer ==
 +
The conventional way to treat colorectal cancer includes surgery and chemotherapy if the cancer is detected in an early stage, when it detected in a later stage treatment is often directed more at extending life and keeping people comfortable [2]. The agents used for chemotherapy are fluorouracil, capecitabine, UFT, leucovorin, irinotecan, or oxaliplatin. Side effects [3] of the agents are:
 +
<ul>
 +
<li>Acute central nervous system damage</li>
 +
<li>Bone marrow suppression</li>
 +
<li>Mucositis, inflammation of the mucus membranes of the GI track</li>
 +
<li>Dermatitis, inflammation of the skin</li>
 +
<li>Diarrhoea</li>
 +
<li>Nausea</li>
 +
<li>and many more</li>
 +
</ul>
 +
 
 +
We believe, if we can focus the agents around the tumor we’ll able to reduce the side effect and create a better chemotherapy treatment for cancer patients.
 +
 
 +
== Parameters ==
 +
For the distribution of VLPs throughout the human body, used parameters were obtained from the documentation Slovenia 2012 or from literature sources [4]. The estimated parameters for the organs in table 1 are explained as followed: Blood-flow, the amount of blood in liters flushing throughout the organs, Volumes, the size of the organ, Receptor, the concentration of receptors in &micro;M and the partition coefficient of the medicine that is packaged within the VLP.
 +
 
 +
 
 +
{| align="center" class="wikitable" style="text-align: center; color: black;"
 +
|+ Table 1: organ specific parameters
 +
|-
 +
|Organ||Blood-flow [L/min]||Volume [L]||Receptor 1 [uM]||Partition coefficient medicine
 +
|-
 +
|Rapidly perfused tissue||1||3.61||0.237||100
 +
|-
 +
|Slowly perfused tissue||2.12||53.2||0.237||100
 +
|-
 +
|Kidney||1.06||0.31||0.237||100
 +
|-
 +
|Liver||1.4||1.82||0.237||100
 +
|-
 +
|Lung||5.58||0.56||0.237||100
 +
|-
 +
|Intestine Healthy||0.94||4.41||0.237||100
 +
|-
 +
|Tumor||0.1||0.49||10.716||100
 +
|-
 +
|Arterial||5.58||1.7||0.237||100
 +
|-
 +
|Venous||5.58||3.9||237||100
 +
|}
 +
 
 +
 
 +
Parameters that were estimated for non organ variables are found in table 2 and are explained as followed. Affinity constant for receptor, is the binding affinity of the VLPs to the receptor on the cell surface. VLP elimination rate is the half-life of the VLPs. VLP Renal removal rate is the removal rate of the VLPs within the kidneys [5]. Medicine elimination rate is the removal/degradation of the medicine within the human body [6]. The last parameter is the packaging constant which encapsulate the amount of medicine in &micro;mol within a single VLP.
 +
 
 +
{| Align="center" class="wikitable" style="text-align: center; color: black;"
 +
|+  Table 2: non-organ specific parameters
 +
|-
 +
|Affinity constant for receptor||0.001
 +
|-
 +
|VLP elimination rate||0.000143
 +
|-
 +
|VLP Renal removal rate||0.000403
 +
|-
 +
|Medicine elimination rate||0.05
 +
|-
 +
|Packaging constant||300
 +
|}
 +
 
 +
== Results ==
 +
 
 +
 
 +
{|style="text-align: top; color: black; valign="top" align="left""
 +
|
 +
|'''Graph'''
 +
|'''Animation'''
 +
|'''Scale'''
 +
|-
 +
|style="width: 200px;" valign="top"|''Conventional treatment''
 +
|[[File:MEDconc.png|400px|left|thumb|Figure 2: x-axis: time in minutes, y-axis: concentration in &micro;mol.Initial dose is 1500 &micro;mol. Concentration over time of the medicine when not packaged within a VLP.]]
 +
|<html><iframe width="220" height="392" src="http://www.youtube.com/embed/AuuAYgv2Y6c?rel=0&loop=1&showinfo=0&autostart=1" frameborder="0" allowfullscreen></iframe></html>
 +
|[[File:MEDbar.png|400px|left|thumb]]
 +
|-
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|style="width: 200px;" valign="top"|''Our treatment: VLP concentration''
 +
|[[File:VLPconcWITHMED.png|400px|left|thumb|Figure 3: x-axis: time in minutes, y-axis: concentration in &micro;mol. Concentration over time of VLP within the human body according to the model.]]
 +
|<html><iframe width="220" height="392" src="http://www.youtube.com/embed/xXndmroipRk?rel=0&loop=1&showinfo=0&autostart=1" frameborder="0" allowfullscreen></iframe></html>
 +
|[[File:VLPbar.png|400px|left|thumb]]
 +
|-
 +
|style="width: 200px;" valign="top"|''Our treatment: Medicine concentration''
 +
|[[File:VLPWITHMEDconc.png|400px|left|thumb|Figure 4: x-axis: time in minutes, y-axis: concentration in &micro;mol. Concentration over time of medicine within the human body according to the model.]]
 +
|<html><iframe width="220" height="392" src="http://www.youtube.com/embed/BScdAOtgd_k?rel=0&loop=1&showinfo=0&autostart=1" frameborder="0" allowfullscreen></iframe></html>
 +
|[[File:MEDVLPbar.png|400px|left|thumb]]
 +
|}
 +
 
 +
In the human animations you see the difference in concentration for each organ. The tumor is represented as a small piece of the small intestine. The skin represents the slowly perfused tissue and the heart the rapidly perfused tissue. for the veins the left larger veins represents the venous blood, while the right smaller veins represents the arterial blood. On the right you'll see the colour bar with corresponding values in &micro;mol.
 +
 
 +
== Conclusion ==
 +
 
 +
The treatment with the medicine packaged VLPs shows promising results. As seen in the figures / movies above, there is an increase in VLP concentration in the tumor. When the VLPs are breaking apart, medicine is released, resulting in a 3-4 times higher concentration compared to the healthy tissues as seen in figure 4.
 +
 
 +
 
 +
If we compare the results of our treatment with the conventional treatment figure 2 we see a few things:
 +
<ul>
 +
<li>The organs get an initial shock of medicine through the body with the conventional treatment, while with our treatment the medicine is released slowly</li>
 +
<li>With our treatment the concentration of the medicine is higher in the tumor according to our model than conventional treatment</li>
 +
<li>The medicine remains longer within the tumor when using our treatment in comparison to the conventional treatment which is due to the slow release of medicine.</li>
 +
<li>Medicine concentration remains low in healthy tissue with our treatment, possibly reducing side effects</li>
 +
</ul>
 +
 
 +
 
 +
We find the comparison promising, this shows that our treatment is superior compared to the conventional method according to this method in multiple areas:
 +
<ul>
 +
<li>A low concentration of medicine in healthy tissue</li>
 +
<li>Longer exposure of the medicine in the tumor</li>
 +
<li>No initial dosage shock</li>
 +
</ul>
 +
 
 +
== Explanation of the parameters ==
 +
 
 +
 
 +
<ul>
 +
<li>C[F]: Concentration of the unbound VLPs in a organ</li>
 +
<li>C[T]: Concentration of all the VLPs in a organ</li>
 +
<li>C[Med]: Concentration of the medicine in a organ</li>
 +
<li>V: Volume of the organ</li>
 +
<li>Q: Flowrate of the organ</li>
 +
<li>Kel: Rate of decay of the VLPs, releasing the medicine</li>
 +
<li>K: Rate of elimination of the VLPs, removal of the blood via the urinal track</li>
 +
<li>RF: Concentration of unbound receptors</li>
 +
<li>Pb: Partition coefficient in a organ</li>
 +
<li>ymedvlp: Packeging capacity of the VLP</li>
 +
</ul>
 +
 
== General mass balance equations for all the VLPs ==
== General mass balance equations for all the VLPs ==
-
The equations below describe the change in concentration of all the VLPs in the different organs. The mass balances for the different organs consists out of multiple parts. Each organ as at least an flow that describes the concentration of VLPs that come into the organs and a flow that describes the VLP concentration that goes out of the organ. Also each organ has a rate of decay incorporated into the mass balance to describe the falling apart of the VLPs in the different organs. The mass balance of the kidney has also an equation for the removal of the VLPs via the urinal track.
+
The equations below describe the change in concentration of all the VLPs in the different organs. The mass balances for the different organs consist out of multiple parts. Each organ as at least an flow that describes the concentration of VLPs that come into the organs and a flow that describes the VLP concentration that goes out of the organ. Also each organ has a rate of decay incorporated into the mass balance to describe the falling apart of the VLPs in the different organs. The mass balance of the kidney has also an equation for the removal of the VLPs via the urinal track.
''Slowly perfused tissue''
''Slowly perfused tissue''
-
----
+
[[File:VLP1-1.png|center]]
-
[[File:VLP1-1.png]]
+
''Rapid perfused tissue''
''Rapid perfused tissue''
-
----
+
[[File:VLP2.PNG|center]]
-
[[File:VLP2.PNG]]
+
''Liver''
''Liver''
-
----
+
[[File:VLP3.png|center]]
-
[[File:VLP3.png]]
+
''Kidney''
''Kidney''
-
----
+
[[File:VLP4.png|center]]
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[[File:VLP4.png]]
+
''Venous''
''Venous''
-
----
+
[[File:VLP5.png|center]]
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[[File:VLP5.png]]
+
''Lung''
''Lung''
-
----
+
[[File:VLP6.png|center]]
-
[[File:VLP6.png]]
+
''Arterial''
''Arterial''
-
----
+
[[File:VLP7.png|center]]
-
[[File:VLP7.png]]
+
''Intestine Healthy''
''Intestine Healthy''
-
----
+
[[File:VLP8.png|center]]
-
[[File:VLP8.png]]
+
''Intestine Sick (Tumor)''
''Intestine Sick (Tumor)''
-
----
+
[[File:VLP9.png|center]]
-
[[File:VLP9.png]]
+
-
 
+
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''Slowly perfused tissue''
+
== General mass balance equations for the unbound VLPs ==
== General mass balance equations for the unbound VLPs ==
-
Besides needing an equation to describe the change in concentration of all the VLPs, we also need an equation to describe the change in concentration of the unbound VLPs for each organ. The mass balances for the different organs consists out of multiple parts. The mass balances are similar to the mass balance for all the VLPs, with a slight difference, it’s has a rate of VLP attachment. This rate describes the attachment of the VLPs onto the surface of the cell.
+
Besides needing an equation to describe the change in concentration of all the VLPs, we also need an equation to describe the change in concentration of the unbound VLPs for each organ. The mass balances for the different organs consists out of multiple parts. The mass balances are similar to the mass balance for all the VLPs, with a slight difference, it has a rate of VLP attachment. This rate describes the attachment of the VLPs onto the surface of the cells.
''Rapid perfused tissue''
''Rapid perfused tissue''
-
----
+
[[File:VLP10.png|center]]
-
[[File:VLP10.png]]
+
''Slowly perfused tissue''
''Slowly perfused tissue''
-
----
+
[[File:VLP11.png|center]]
-
[[File:VLP11.png]]
+
''Liver''
''Liver''
-
----
+
[[File:VLP12.png|center]]
-
[[File:VLP12.png]]
+
''Kidney''
''Kidney''
-
----
+
[[File:VLP13.png|center]]
-
[[File:VLP13.png]]
+
''Venous''
''Venous''
-
----
+
[[File:VLP14.png|center]]
-
[[File:VLP14.png]]
+
''Lung''
''Lung''
-
----
+
[[File:VLP15.png|center]]
-
[[File:VLP15.png]]
+
''Arterial''
''Arterial''
-
----
+
[[File:VLP16.png|center]]
-
[[File:VLP16.png]]
+
''Intestine Healthy''
''Intestine Healthy''
-
----
+
[[File:VLP17.png|center]]
-
[[File:VLP17.png]]
+
''Intestine Sick (Tumor)''
''Intestine Sick (Tumor)''
-
----
+
[[File:VLP18.png|center]]
-
[[File:VLP18.png]]
+
== General mass balance equations for the medicine ==
== General mass balance equations for the medicine ==
Line 139: Line 214:
''Rapid perfused tissue''
''Rapid perfused tissue''
-
----
+
[[File:VLP19.png|center]]
-
[[File:VLP19.png]]
+
''Slowly perfused tissue''
''Slowly perfused tissue''
-
----
+
[[File:VLP20.png|center]]
-
[[File:VLP20.png]]
+
''Intestine Healthy''
''Intestine Healthy''
-
----
+
[[File:VLP21.png|center]]
-
[[File:VLP21.png]]
+
''Intestine Sick (Tumor)''
''Intestine Sick (Tumor)''
-
----
+
[[File:VLP22.png|center]]
-
[[File:VLP22.png]]
+
''Liver''
''Liver''
-
----
+
[[File:VLP23.png|center]]
-
[[File:VLP23.png]]
+
''Kidney''
''Kidney''
-
----
+
[[File:VLP24.png|center]]
-
[[File:VLP24.png]]
+
''Venous''
''Venous''
-
----
+
[[File:VLP25.png|center]]
-
[[File:VLP25.png]]
+
''Lung''
''Lung''
-
----
+
[[File:VLP26.png|center]]
-
[[File:VLP26.png]]
+
''Arterial''
''Arterial''
-
----
+
[[File:VLP27.png|center]]
-
[[File:VLP27.png]]
+
-
= Case study: colorectal cancer =
 
-
 
-
As our case study to use the human body model, we used colorectal cancer. Cancer as a disease is very destructive and is responsible for the deaths of millions. In 2007, 13% of all the deaths were cancer related (1). We chose colorectal cancer because in Europe the 5 year survival the disease is less than 60% (2). If our treatment shows a better treatment we can help the people to fight off the cancer.
 
-
 
-
== Treatment of Colorectal cancer ==
 
-
The conventional way to treat colorectal cancer includes surgery and chemotherapy if the cancer is detected in an early stage, when it detected in a later stage treatment is often directed more at extending life and keeping people comfortable (2). The agents used for chemotherapy are fluorouracil, capecitabine, UFT, leucovorin, irinotecan, or oxaliplatin. Side effects of the agents are:
 
-
<ul>
 
-
<li>Acute central nervous system damage</li>
 
-
<li>Bone marrow suppression</li>
 
-
<li>Mucositis, inflammation of the mucus membranes of the GI track</li>
 
-
<li>Dermatitis, inflammation of the skin</li>
 
-
<li>Diarrhoea</li>
 
-
<li>Nausea</li>
 
-
<li>and many more</li>
 
-
</ul>
 
-
 
-
We believe, if we can focus the agent around the tumor we’ll able to reduce the side effect and create a better chemotherapy treatment for cancer patients.
 
-
 
-
== Parameters ==
 
-
For the distribution of VLPs throughout the human body, used parameters were obtained from the documentation Slovenia 2012 or from literature sources [1]. The estimated parameters for the organs in table XXX are explained as followed: Blood-flow, the amount of blood in liters flushing throughout the organs, Volumes, the size of the organ, Receptor, the concentration of receptors in &micro;M and the partition coefficient of the medicine that is packaged within the VLP.
 
-
 
-
{| class="wikitable" style="text-align: center; color: black;"
 
-
|+ Here is the awesome caption
 
-
|-
 
-
|Organ||Blood-flow [L/min]||Volume [L]||Receptor 1 [uM]||Partition coefficient medicine
 
-
|-
 
-
|Slowly perfused tissue||2.12||53.2||0.237||100
 
-
|-
 
-
|Rapidly perfused tissue||1||3.61||0.237||100
 
-
|-
 
-
|Kidney||1.06||0.31||0.237||100
 
-
|-
 
-
|Liver||1.4||1.82||0.237||100
 
-
|-
 
-
|Lung||5.58||0.56||0.237||100
 
-
|-
 
-
|Intestine Healthy||0.94||4.41||0.237||100
 
-
|-
 
-
|Tumor||0.1||0.49||10.716||100
 
-
|-
 
-
|Arterial||5.58||1.7||0.237||100
 
-
|-
 
-
|Venous||5.58||3.9||237||100
 
-
|}
 
-
 
-
 
-
Parameters that were estimated for non organ variables are found in table 2 and are explained as followed. Affinity constant for receptor, is the binding affinity of the VLPs to the receptor on the cell surface. VLP elimination rate is the half-life of the VLPs. VLP Renal removal rate is the removal rate of the VLPs within the kidneys. Medicine elimination rate is the removal/degradation of the medicine within the human body. The last parameter is the packaging constant which encapsulate the amount of medicine in &micro;mol? within a single VLP.
 
-
{| class="wikitable" style="text-align: center; color: black;"
 
-
|+ Here is the awesome caption
 
-
|-
 
-
|Affinity constant for receptor||0.001
 
-
|-
 
-
|VLP elimination rate||0.000143
 
-
|-
 
-
|VLP Renal removal rate||0.000403
 
-
|-
 
-
|Medicine elimination rate||0.05
 
-
|-
 
-
|Packaging constant||300
 
-
|}
 
-
 
-
== Results ==
 
-
Mark/Jasper
 
-
 
-
Concentration over time of VLP within the human body according to the model
 
-
----
 
-
[[File:VLPconcWITHMED.png]]
 
-
 
-
Concentration over time of medicine within the human body according to the model
 
-
----
 
-
[[File:VLPWITHMEDconc.png]]
 
-
 
-
Concentration over time of the medicine when not packaged within a VLP
 
-
----
 
-
[[File:MEDconc.png]]
 
-
 
-
== Discussion/Conclusion ==
 
-
Mark/Jasper
 
= Remarks =
= Remarks =
-
With this model it becomes possible to simulate the VLP and medicine distribution in the human body. However this model, like every model, has it's limitations. In this paragraph we'll discus the limitations and it's possibilities of this model and how we can improve this model.
+
With this model it becomes possible to simulate the VLP and medicine distribution in the human body. However this model, like every model, has it's limitations. Though there are several limitations in the model, it can be used for different scenarios involving the use of VLPs. In this paragraph we'll discus the limitations and it's possibilities of this model and how we can improve this model.
 +
 
== Important parameters ==
== Important parameters ==
-
Like in every model, there are certain parameters that are important to get a simulation that represends the reality. However finding these parameters can be difficult a data can be missing. This is a real limitation in every model, we have to assume parameters that are important, resulting in a biased result. Here below is a list of the parameters that is crucial to our model.
+
One of the major limitations of every model is the lack of information to determine the parameters. This is the same in this model, shown below is a list of the parameters we've estimated by the little information we've had. If better information becomes available we'll be able to predict a more precise simulation on how the medicine distribute around the body.
<ol>
<ol>
<li>Ratio of receptor concentration between tumor and healthy tissue</li>
<li>Ratio of receptor concentration between tumor and healthy tissue</li>
 +
<li>Distribution of receptors on cell surface</li>
 +
<li>Medicine absorption of tumor / healthy cells</li>
<li>Stability of the VLP</li>
<li>Stability of the VLP</li>
<li>Packaging quantity of the VLP</li>
<li>Packaging quantity of the VLP</li>
<li>Binding affinity of the VLP to the receptor</li>
<li>Binding affinity of the VLP to the receptor</li>
-
<li>Medicine absorption of tumor / healthy cells</li>
 
-
<li>Distribution of receptors on cell surface</li>
 
</ol>
</ol>
-
== Possibilities of the model ==
 
-
Even with it's limitations, the model has it's potential. With this model it becomes possible to.....
+
To determine the parameter of the receptor ratio ,receptor distribution and medicine absorption, clinical studies must be done to calculate the parameters. To determine the stability of the VLPs can be done by [[Team:Wageningen_UR/MethodsDetection|DLS]]. The packaging constant can be determined by loading the VLPs and let the particles decay so that you can calculate the medicine-particle ratio. To determine the binding affinity for the receptors, several experiments needs to be done to discover the affinity for the binding. It is also information available on the [http://www.bindingdb.org/bind/index.jsp binding database], however this information is not complete.
 +
 
 +
 
 +
== Future work ==
 +
 
 +
To improve this model several things can be done. First of all, research should be done on several parameters of the model. Specially parameters involving the number of receptors and the breaking down of VLPs. Second looking into other models to further improve the mass balance equations to get a more accurate and faster result. Besides looking for things to build upon, we also want to look at the limitations the model has and how to remove those limitations, creating a more solid model.
 +
 
 +
 
 +
= Source Code =
 +
The model was created within MatLab and the main file can be found here: [[File:HumanBodyMainB.txt]]
 +
 
 +
The function file is located here: [[File:HumanBodyFB.txt]]
-
== Future work / MoSCoW ==
 
= References =
= References =
-
Benjamin L. Shneider; Sherman, Philip M. (2008). Pediatric Gastrointestinal Disease. Connecticut: PMPH-USA. pp. 751.
+
<ol>
 +
<li>Jemal A, Bray, F, Center, MM, Ferlay, J, Ward, E, Forman, D; "Global cancer statistics", 2011, CA: a cancer journal for clinicians 61 (2): 69–90 </li>
 +
<li>Cunningham D, Atkin W, Lenz HJ, Lynch HT, Minsky B, Nordlinger B, Starling N; "Colorectal cancer.", 2010, Lancet 375 (9719): 1030–47  </li>
 +
<li>Dr. Mark D. Noble, Chemotherapy-induced Damage to the CNS as a Precursor Cell Disease, University of Rochester</li>
 +
<li>Benjamin L. Shneider; Sherman, Philip M, Pediatric Gastrointestinal Disease, 2008,Connecticut: PMPH-USA. pp. 751.</li>
 +
<li>Kaiser CR, et al., Biodistribution studies of protein cage nanoparticles demonstrate broad tissue distribution and rapid clearance in vivo, 2007, Int J Nanomedicine, 2(4):715-33.</li>
 +
<li>Longley DB, Harkin DP, Johnston PG, 5-fluorouracil: mechanisms of action and clinical strategies", 2007, Nat. Rev. Cancer 3 (5): 330–8</li>
 +
</ol>

Latest revision as of 21:30, 26 October 2012

Contents

Human Body Model

To be able to determine what the VLPs and the medicine do in the human body we have constructed a human body model that is inspired by the model of the Slovenia 2012 team. With this model we are able to compare the traditional use of medicine with the use of our VLPs. If successful it will open up a whole new era for the use of medicine.

Explanation of the model

Our model is constructed in such a way that each compartment of the model represents an organ or multiple organs with the same physical properties. We decided to have separate compartments for the kidneys, liver, lungs and the intestine. All other organs are grouped in the rapid or slowly perfused tissue. In the case study we made a new compartment between the intestine and the liver to represent the intestine tumor (figure 1).

Figure 1: The flowscheme used for our model


In our model we have used three different mass balance equations for an organ. The first mass balance describes the concentration of all the VLPs in the organ, this is to see the overall change in the VLP concentration. The second mass balance equation describes the concentration of the unbound VLPs. This is because the unbound particles can move freely into the body while the bound particles stays into the organ. The final mass balance equation is for the concentration of the medicine in the organ. With these three mass balance equations we’ve developed our model. At the botom of the page the model can be studied intensivly.


Case study: colorectal cancer

As our case study to use the human body model, we used colorectal cancer. Cancer as a disease is very destructive and is responsible for the deaths of millions. In 2007, 13% of all the deaths were cancer related [1]. We chose colorectal cancer because in Europe the 5 year survival the disease is less than 60% [2]. If our treatment shows a better treatment we can help the people to fight off the cancer.

Treatment of Colorectal cancer

The conventional way to treat colorectal cancer includes surgery and chemotherapy if the cancer is detected in an early stage, when it detected in a later stage treatment is often directed more at extending life and keeping people comfortable [2]. The agents used for chemotherapy are fluorouracil, capecitabine, UFT, leucovorin, irinotecan, or oxaliplatin. Side effects [3] of the agents are:

  • Acute central nervous system damage
  • Bone marrow suppression
  • Mucositis, inflammation of the mucus membranes of the GI track
  • Dermatitis, inflammation of the skin
  • Diarrhoea
  • Nausea
  • and many more

We believe, if we can focus the agents around the tumor we’ll able to reduce the side effect and create a better chemotherapy treatment for cancer patients.

Parameters

For the distribution of VLPs throughout the human body, used parameters were obtained from the documentation Slovenia 2012 or from literature sources [4]. The estimated parameters for the organs in table 1 are explained as followed: Blood-flow, the amount of blood in liters flushing throughout the organs, Volumes, the size of the organ, Receptor, the concentration of receptors in µM and the partition coefficient of the medicine that is packaged within the VLP.


Table 1: organ specific parameters
OrganBlood-flow [L/min]Volume [L]Receptor 1 [uM]Partition coefficient medicine
Rapidly perfused tissue13.610.237100
Slowly perfused tissue2.1253.20.237100
Kidney1.060.310.237100
Liver1.41.820.237100
Lung5.580.560.237100
Intestine Healthy0.944.410.237100
Tumor0.10.4910.716100
Arterial5.581.70.237100
Venous5.583.9237100


Parameters that were estimated for non organ variables are found in table 2 and are explained as followed. Affinity constant for receptor, is the binding affinity of the VLPs to the receptor on the cell surface. VLP elimination rate is the half-life of the VLPs. VLP Renal removal rate is the removal rate of the VLPs within the kidneys [5]. Medicine elimination rate is the removal/degradation of the medicine within the human body [6]. The last parameter is the packaging constant which encapsulate the amount of medicine in µmol within a single VLP.

Table 2: non-organ specific parameters
Affinity constant for receptor0.001
VLP elimination rate0.000143
VLP Renal removal rate0.000403
Medicine elimination rate0.05
Packaging constant300

Results

Graph Animation Scale
Conventional treatment
Figure 2: x-axis: time in minutes, y-axis: concentration in µmol.Initial dose is 1500 µmol. Concentration over time of the medicine when not packaged within a VLP.
MEDbar.png
Our treatment: VLP concentration
Figure 3: x-axis: time in minutes, y-axis: concentration in µmol. Concentration over time of VLP within the human body according to the model.
VLPbar.png
Our treatment: Medicine concentration
Figure 4: x-axis: time in minutes, y-axis: concentration in µmol. Concentration over time of medicine within the human body according to the model.
MEDVLPbar.png

In the human animations you see the difference in concentration for each organ. The tumor is represented as a small piece of the small intestine. The skin represents the slowly perfused tissue and the heart the rapidly perfused tissue. for the veins the left larger veins represents the venous blood, while the right smaller veins represents the arterial blood. On the right you'll see the colour bar with corresponding values in µmol.

Conclusion

The treatment with the medicine packaged VLPs shows promising results. As seen in the figures / movies above, there is an increase in VLP concentration in the tumor. When the VLPs are breaking apart, medicine is released, resulting in a 3-4 times higher concentration compared to the healthy tissues as seen in figure 4.


If we compare the results of our treatment with the conventional treatment figure 2 we see a few things:

  • The organs get an initial shock of medicine through the body with the conventional treatment, while with our treatment the medicine is released slowly
  • With our treatment the concentration of the medicine is higher in the tumor according to our model than conventional treatment
  • The medicine remains longer within the tumor when using our treatment in comparison to the conventional treatment which is due to the slow release of medicine.
  • Medicine concentration remains low in healthy tissue with our treatment, possibly reducing side effects


We find the comparison promising, this shows that our treatment is superior compared to the conventional method according to this method in multiple areas:

  • A low concentration of medicine in healthy tissue
  • Longer exposure of the medicine in the tumor
  • No initial dosage shock

Explanation of the parameters

  • C[F]: Concentration of the unbound VLPs in a organ
  • C[T]: Concentration of all the VLPs in a organ
  • C[Med]: Concentration of the medicine in a organ
  • V: Volume of the organ
  • Q: Flowrate of the organ
  • Kel: Rate of decay of the VLPs, releasing the medicine
  • K: Rate of elimination of the VLPs, removal of the blood via the urinal track
  • RF: Concentration of unbound receptors
  • Pb: Partition coefficient in a organ
  • ymedvlp: Packeging capacity of the VLP


General mass balance equations for all the VLPs

The equations below describe the change in concentration of all the VLPs in the different organs. The mass balances for the different organs consist out of multiple parts. Each organ as at least an flow that describes the concentration of VLPs that come into the organs and a flow that describes the VLP concentration that goes out of the organ. Also each organ has a rate of decay incorporated into the mass balance to describe the falling apart of the VLPs in the different organs. The mass balance of the kidney has also an equation for the removal of the VLPs via the urinal track.

Slowly perfused tissue

VLP1-1.png

Rapid perfused tissue

VLP2.PNG

Liver

VLP3.png

Kidney

VLP4.png

Venous

VLP5.png

Lung

VLP6.png

Arterial

VLP7.png

Intestine Healthy

VLP8.png

Intestine Sick (Tumor)

VLP9.png

General mass balance equations for the unbound VLPs

Besides needing an equation to describe the change in concentration of all the VLPs, we also need an equation to describe the change in concentration of the unbound VLPs for each organ. The mass balances for the different organs consists out of multiple parts. The mass balances are similar to the mass balance for all the VLPs, with a slight difference, it has a rate of VLP attachment. This rate describes the attachment of the VLPs onto the surface of the cells.

Rapid perfused tissue

VLP10.png

Slowly perfused tissue

VLP11.png

Liver

VLP12.png

Kidney

VLP13.png

Venous

VLP14.png

Lung

VLP15.png

Arterial

VLP16.png

Intestine Healthy

VLP17.png

Intestine Sick (Tumor)

VLP18.png

General mass balance equations for the medicine

The last set of mass balances are for the change of concentration of the medicine in the different organs. These equations consists out of multiple parts, similar to the previous set of mass balances. Each organ as at least an flow that describes the concentration of medicine that come into the organs and a flow that describes the medicine concentration that goes out of the organ. Also each organ has a rate of decay incorporated into the mass balance to describe the decay of medicine in the different organs. The mass balance of the kidney has also an equation for the removal of the medicine via the urinal track.

Rapid perfused tissue

VLP19.png

Slowly perfused tissue

VLP20.png

Intestine Healthy

VLP21.png

Intestine Sick (Tumor)

VLP22.png

Liver

VLP23.png

Kidney

VLP24.png

Venous

VLP25.png

Lung

VLP26.png

Arterial

VLP27.png


Remarks

With this model it becomes possible to simulate the VLP and medicine distribution in the human body. However this model, like every model, has it's limitations. Though there are several limitations in the model, it can be used for different scenarios involving the use of VLPs. In this paragraph we'll discus the limitations and it's possibilities of this model and how we can improve this model.


Important parameters

One of the major limitations of every model is the lack of information to determine the parameters. This is the same in this model, shown below is a list of the parameters we've estimated by the little information we've had. If better information becomes available we'll be able to predict a more precise simulation on how the medicine distribute around the body.

  1. Ratio of receptor concentration between tumor and healthy tissue
  2. Distribution of receptors on cell surface
  3. Medicine absorption of tumor / healthy cells
  4. Stability of the VLP
  5. Packaging quantity of the VLP
  6. Binding affinity of the VLP to the receptor


To determine the parameter of the receptor ratio ,receptor distribution and medicine absorption, clinical studies must be done to calculate the parameters. To determine the stability of the VLPs can be done by DLS. The packaging constant can be determined by loading the VLPs and let the particles decay so that you can calculate the medicine-particle ratio. To determine the binding affinity for the receptors, several experiments needs to be done to discover the affinity for the binding. It is also information available on the [http://www.bindingdb.org/bind/index.jsp binding database], however this information is not complete.


Future work

To improve this model several things can be done. First of all, research should be done on several parameters of the model. Specially parameters involving the number of receptors and the breaking down of VLPs. Second looking into other models to further improve the mass balance equations to get a more accurate and faster result. Besides looking for things to build upon, we also want to look at the limitations the model has and how to remove those limitations, creating a more solid model.


Source Code

The model was created within MatLab and the main file can be found here: File:HumanBodyMainB.txt

The function file is located here: File:HumanBodyFB.txt


References

  1. Jemal A, Bray, F, Center, MM, Ferlay, J, Ward, E, Forman, D; "Global cancer statistics", 2011, CA: a cancer journal for clinicians 61 (2): 69–90
  2. Cunningham D, Atkin W, Lenz HJ, Lynch HT, Minsky B, Nordlinger B, Starling N; "Colorectal cancer.", 2010, Lancet 375 (9719): 1030–47
  3. Dr. Mark D. Noble, Chemotherapy-induced Damage to the CNS as a Precursor Cell Disease, University of Rochester
  4. Benjamin L. Shneider; Sherman, Philip M, Pediatric Gastrointestinal Disease, 2008,Connecticut: PMPH-USA. pp. 751.
  5. Kaiser CR, et al., Biodistribution studies of protein cage nanoparticles demonstrate broad tissue distribution and rapid clearance in vivo, 2007, Int J Nanomedicine, 2(4):715-33.
  6. Longley DB, Harkin DP, Johnston PG, 5-fluorouracil: mechanisms of action and clinical strategies", 2007, Nat. Rev. Cancer 3 (5): 330–8
Retrieved from "http://2012.igem.org/Team:Wageningen_UR/HumanBody"