Nonlinear Dynamical Models of Immune Response: Modeling CD4+ helper T lymphocytes and stimulated large B lymphocytes in the presence

of HIV virus
Liz Christenbury and Amy Li April 29, 2011

Abstract

We will model the interaction between healthy and HIV-infected CD4+ helper T lymphocytes, and B lymphocytes (or simply T cells and B cells in this paper) in the immune response system. When stimulated by CD4+ T cells, large B cells can dierentiate into plasma or memory cells, either producing antibodies or retaining information about the antigen present. However, the HIV virus diminishes the T cells ability to stimulate B cells, decreasing the bodys ability to make plasma or memory cells and hindering the immune response to infections.

Introduction to the Problem

Human immunodeciency virus (HIV) is one of the most prominent diseases in the world due to the nature of its transmission and incurability. It is commonly known that HIV destroys the immune system, rendering infected individuals unable to fend o everyday infections such as the common cold. More rigorously, the HIV virus targets CD4+ helper T cells. There are two types of immune cells in the body: T lymphocytes and B lymphocytes. B cells produce antibodies, which can either destroy bacteria and virus cells or mark them for elimination. Large stimulated B cells can dierentiate into plasma and memory cells. Plasma cells produce large volumes of antibodies more eciently, while memory cells help the immune system more eectively ght future infections and have longer lifespans. There are many types of T cells that serve a wide variety of functions: some T cells kill infected cells directly, while others are responsible for immune regulation or memory. We are specically interested in the CD4+ helper T cells, 1

which are responsible for stimulating large B cells to dierentiate into either plasma or memory cells. In our model, when HIV infects T cells, they enter rst into a stage of latent infection, when they do not actively produce virus and are still able to stimulate B cells (at a lower rate). After a period of latent infection, infected T cells become actively infected, at which point they no longer stimulate B cells and actively produce more HIV virus cells. Because HIV infection decreases T cells ability to stimulate B cells into dierentiation, the infection can also prevent the bodys ability to produce plasma and memory cells. This has a deleterious eect on the immune system as a whole and the bodys ability to ght o common infections.

The Question

How are B and T cell populations aected in an HIV-infected immune system?

First Version of the Model

We built our nal model primarily by combining models from two papers authored by Alan Perelson and his collaborators. The T cell model in Perelsons paper was crucial for our model and we made minor simplications of parameters for ease of calculations. We also incorporated the B cell model, creating a variation of the large B cell equation in Perelsons paper to only consider stimulated B cells (Perelsons large B cell equation includes all B cells, both stimulated and unstimulated) and the plasma and memory cell equations. The models below, with the exception of the B equation (which we modied) are taken from Perelsons papers. Variables: T=uninfected CD4+ T cells T =latently infected CD4+ T cells (infected with virus but not producing virus) T = actively infected CD4+ T cells (producing virus) V= free virus B= unstimulated large B lymphocyte cells (not stimulated by CD4+ T cells) B= stimulated large B lymphocyte cells (stimulated by CD4+ T cells) P= plasma cells M= memory cells T cell parameters: sT = supply of CD4+ T cell growth r = rate of CD4+ T cell growth Tmax = maximum CD4+ cell population level k1 = rate constant for CD4+ cells becoming infected by free virus

k2 = rate latently infected cells convert to actively infected b = death rate of actively CD4+ cells T = death rate of uninfected and latently infected CD4+ cells V = death rate of free virus N = number of free virus produced by lysing a CD4+ cell B cell parameters: S = supply of small B cells b1 = rate of dierentiation from small to large B cells b2 = rate of dierentiation from unstimulated to stimulated B cells D1 = time for dierentiation from small to large B cells D2 = time for dierentiation from unstimulated to stimulated B cells w1 = rate of stimulation by healthy T cells w2 = rate of stimulation by latently infected T cells 1 = death rate of large unstimulated B cells 2 = death rate of large stimulated B cells 3 = death rate of plasma cells 4 = death rate of memory cells H1 =dierentiation rate from stimulated large B cell to plasma cell H2 =dierentiation rate from stimulated large B cell to memory cell T cell model:[1] T + T + T dT = sT T T + rT (1 ) k1 V T dt Tmax dT = k1 V T T T k2 T dt dT = k2 T b T dt dV = N b T k1 V T V V dt B cell model:[2] dB b1 b2 =S B 1 B dt D1 D2 dB = BT w1 + BT w2 2 B (H1 + H2 )B dt dP = B H1 3 P dt dM = B H2 4 M dt

Simplied Models

In order to more eectively analyze our models, we needed to simplify them rst and reduce the number of variables and equations as much as possible. Variables: Z = stimulated large B lymphocyte cells (stimulated by CD4+ T cells) W = uninfected CD4+ T cells X = latently infected CD4+ T cells (infected with virus but not producing virus) Y= actively infected CD4+ T cells (producing virus) Z = free virus B cell model: dZ = aW + bX cZ dt T cell model: dW = d (e f )W gV W dt dX = gV W eX hX dt dY = hX jY dt dV = lY gV W nV dt New parameters: a = kw1 b = kw2 c = 2 d=s e = T f = r(1-M*) g = k1 h = k2 j = b l = N b n = v *M is a constant that represents the total number of T cells (W+X+Y) divided by the maximum number of T cells in the body. N is the population of free virus produced when an actively infected cell lyses, or breaks open and releases free virus into the body. Parameter values used: 4

a = 0.7 b = 0.3 c = 0.2 d = 10 e = 0.02 f = 0.03*(1-M) g = 0.000024 h = 0.003 j = 0.24 l = N*0.24 n=5 M = 0.665 N = varied We followed the parameter values given in Perelson et al.s Dynamics of HIV Infection of CD4+ T cells for parameters d, e, f, g, h, j, l, and n, though we estimated M and N. We estimated a, b, and c based on what we felt made sense because we created the variation for the large stimulated B cell equation and did not have good estimates from the paper. The cell populations that we calculated in our ndings were in the units per mm3 .

Numerical Methodology

Due to the complexity of the model, we were unable to do most of our analysis using analytical techniques. Instead, we had to use numerical methods to calculate cell populations. We used the forward Euler method and calculated values on Microsoft Excel. We initially also attempted to use XPP and Matlab, but felt that Excel could better accommodate the nature of our numerical analysis. In our analysis, we oored all cell population calculations at 0, because negative values would have been unrealistic.

Linearization, V=0 (Steady State of Uninfected System)

To check the validity of our model, we rst found xed points assuming V=0, the state in which there is no virus. Linearized model: dZ = aW + bX cZ dt dW = d (e f )W dt 5

dX = eX hX dt dY = hX jY dt dV = lY dt Finding xed points: dZ a b =0:Z= W + X dt c c dW d =0:W = dt ef dX =0:X=0 dt dY h =0:Y = X dt j dV =0:Y =0 dt Because Y=0, then X=0 d W = ef Z= So, the xed point is at ( ad d , , 0, 0, 0) c(e f ) e f a d cef

Using the parameters, we nd that the xed point in an uninfected system (V=0) is at (Z, W, X, Y, V ) = (3500, 1000, 0, 0, 0)

Stability of the Fixed Point (3500,1000,0,0,0)

In order to determine the stability of this linear xed point, (3500, 1000, 0, 0, 0), we used linear analysis to identify whether or not the behavior of each variables derivative around the xed point implied stability.

8.1

Stability of Z

For Z to be stable at 3500, Z < 0 when Z > 3500 and Z > 0 when Z < 3500. We will show this below: dZ |(3510,1000,0,0,0) = 1000a 3510c = 700 702 < 0 dt dZ |(3450,1000,0,0,0) = 1000a 3450c = 700 690 > 0. dt This shows that Z is stable

8.2

Stability of W

We will use the same analysis for W: dW |(3500,1010,0,0,0) = d (e f )(1010) = 10 (.02 6(.335)) 1010 = .0495 < 0 dt dW |(3500,990,0,0,0) = d (e f )(990) = 10 9.8505 = 0.1495 > 0 dt This shows the W is stable.

8.3

Stability of X
dX |(3500,1000,1,0,0) = (e + h)(1) = (.02 + .003)(1) < 0 dt

Since X cannot be less than 0, we will only consider perturbing X above X = 0.

which shows X is also stable.

8.4

Stability of Y
dY |3500,1000,0,1,0,) = hX jY = j (1) < 0. dt

Again, we will only consider perturbing Y above 0.

Therefore, Y is stable.

8.5

Stability of V

In the linear model, there is no virus present, so we will show the stability of V around V = 0 with the nonlinear model. Through these calculations, we have shown that indeed the linear model with no virus present has a stable steady state at (3500, 1000, 0, 0, 0).

Estimating M

M is a simplied constant that represents the total number of T cells in the body (W+X+Y) divided by the maximum number of T cells in the body. We did not want to add additional nonlinearities to our model to further complicate the system, so we decided to not follow Perelsons T cell model exactly and instead simplify the terms into one constant, M. Initially, we let M = 0.5. However, this estimate resulted in unrealistic results for cell populations in our model. Using (Z, W, X, Y, V) = (3500, 1000, 0, 0, 0) as initial conditions, we would expect that the cell populations would remain xed because there is no virus present in the system and no reason for populations to change. But, when M = 0.5, the cell populations did change even using the uninfected system initial conditions. So, we let M = 0.665, which allowed the cell populations to remain xed at (Z, W, X, Y, V) = (3500, 1000, 0, 0, 0), the most realistic outcome.

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Endemically Infected Steady State

When solving for xed points of the system, we found a second xed point for which V was not equal to 0. This is the steady state in an infected immune system.
dW dX dY To nd the values at which dV dt = 0 but V = 0, let dt , dt , dt = 0. This is realistic because at a stable xed point, the rate of change for all variables should be 0.

dX gV W =0:X= dt e+h h gV W dY =0:Y = dt j e+h By plugging in expressions of X and Y into

dV dt

, we can nd that

dV lh = 0 : V [( 1)gW n] = 0 dt j (e + h) This equation shows that for dV dt = 0, either V = 0, the uninfected systems lh steady state, or ( j (e+h) 1)gW n = 0. Because V = 0, ( j (elh +h) 1)gW n = 0. Using this equation, we can solve for W. W = n g ( j (elh +h) 1)

Because the rate of change for variables at a stable xed point should be 0, we also know that dW dt = 0. This means that d (e f )W gV W = 0 W = d (e f ) + gV

d n = lh (e f ) + gV g ( j (e+h) 1) Because the two Ws must be equal, we can set them equal to each other to calculate V. d +f e lh g ( j (e 1) +h) V = g Thus, we can calculate the steady states for W and V, which can then be used b to calculate steady states for X and Y. We let Z = a c W + c X. Using the parameters given, we nd that the steady state depends heavily on the value of N and M. When N = 2000 and M = 0.665, the xed point is at (Z, W, X, Y, V ) = (2938, 802, 88, 1, 105) Using these initial conditions, the system remains stable and xed for approximately 11 steps using the forward Euler method on Excel. The system is still extremely close to the steady state until approxiately step 21, where it begins to change dramatically. Eventually, the system arrives at a steady state that is not equal or close to the initial condition. We felt that it was possible for the sudden changes in the system to occur as a result of numerical errors from using Eulers method.
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Figure: Endemically stable state for small time scale

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Figure: Endemically stable state for longer time scale Using our calculations, we can see that as time goes on, the infected state becomes stable (but not at the xed point we calculated). The rst graph shown above is for a much smaller time scale and shows the period in which the calculated steady state does remain xed and the emergence of oscillations for the virus population, and the second graph is after a longer period of time where each population levels out. However, the validity of these initial conditions is somewhat ambiguous, because they can uctuate depending on N and M. When N = 1000 and M = 0.665, X, Y, and V produce negative values, which is theoretically impossible because when N = 1000, free virus should be present (this will be explained further in the section discussing bifurcations). Because we simplied M from the original dynamic equation, it is also possible that this simplication had a negative impact on the accuracy and consistency of our results. We believe that, based on the xed point remaining xed in the rst 10-20 steps, that it is possible for our analytical analysis to be correct, and that the inaccuracies come primarily from 1) the simplication of M and 2) the various errors associated with numerical analysis. So, we felt it would be more appropriate to use the equations for calculating W, X, Y, and V from Perelsons paper on T cells. We were able to follow the derivations of these equations, excepting the derivation of the nal V equation. While the xed points calculated using using these equations were more realistic, they did not yield perfect steady states. The system would generally immediately shift from the initial conditions (which we used the xed point for) before settling on a new xed point. We felt that this error could also be attributed to inexactness in the Euler methodology or in the process of calculating the steady states, as well as our simplication into the term M. However, we believe that a stable xed point does exist in an endemically infected system because the cell populations eventually become xed at certain constants.

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Figure: N=1000, Endemically Infected Steady State

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Figure: N=1000, Endemically Infected Steady State The above two graphs are based o the endemically infected steady states calculated in Perelsons T cell paper using two dierent values of parameter N. As noted previously, the calculated steady states as initial conditions do not remain xed, so they are not the correct xed points. However, it is possible to see that the system does arrive at xed points in both graphs. The dierences in the two graphs also emphasizes the importance of the parameter N. When N=2000, the values of the healthy T and B cells are lower than when N=1000. Values of healthy T and B cells are both lower than when V=0, which is expected because immune cell count should be higher in an uninfected system.

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Model including Plasma and Memory Cells

To make the model more realistic, we added equations for plasma and memory cells to our system to account for outow of stimulated large B cells due to dierentiation. The B cell equation cannot be fully accurate without consider11

ing the outow of dierentiating cells from the B equation. The equations are simplied from the Perelson paper on B cells: dP = r1 B s1 P dt dM = r2 B s2 M dt We estimated the parameter values: r1 = 0.3 r2 = 0.05 s1 = 0.5 r1 = 0.1
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Figure: Endemically Infected state with Plasma and Memory cell populations, N=1200
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Figure: Endemically Infected state with Plasma and Memory cell populations, N=1200, longer timescale

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As expected, the value of B cells is lower when plasma and memory cells are accounted for.

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Bifurcation

Perelson et al. conclude in Dynamics of HIV Infection of CD4+ T cells that a transcritical bifurcation occurs when N = Ncrit = 774. To show this, the authors calculated the Jacobian of the system. We will show their Jacobian also including the derivatives of Z . c a b 0 0 0 f e gV 0 0 gW 0 gV e h 0 gW J = 0 0 h j 0 0 gV 0 l gW n Solving this ve-dimensional system poses much diculty analytically, so to look at the bifurcation, we used numerical analysis to observe the change of qualitative behavior of the populations. For N < 774, the system remains steady at the uninfected steady state. The gure below shows the populations of cells at N = 700 starting at an initial condition of (3535, 1010, 0, 0, 0).
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Figure: Uninfected steady state Between N = 774 and N = 775, we observed the transcritical bifurcation below using the forward Euler method in Microsoft Excel:

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4000

3500

3000

2500 V 2000 W X 1500 Y Z 1000

500

0 1 61 121 181 241 301 361 421 481 541 601 661 721 781 841 901 961 1021 1081 1141 1201 1261 1321 1381 1441 1501 1561 1621 1681 1741 1801 1861 1921 1981 2041 2101 2161 2221 2281 2341 2401 2461 2521 2581 2641 2701

Figure: Bifurcation behavior when N=775 In this gure, our initial conditions were (3498, 999, 0.01, 0.6, 0.58), which is just a little o from the linear steady state. As we can see, at around t = 721, the infected T cells and virus increase, and at t = 600, the B cell and healthy T cell populations begin to decline to the infected steady state. As N increases past 775, the steady state changes, and the levels of virus and infected T cells increase accordingly.
4000

3500

3000

2500 V 2000 W X 1500 Y Z 1000

500

0 1 66 131 196 261 326 391 456 521 586 651 716 781 846 911 976 1041 1106 1171 1236 1301 1366 1431 1496 1561 1626 1691 1756 1821 1886 1951 2016 2081 2146 2211 2276 2341 2406 2471 2536 2601 2666 2731 2796 2861 2926

Figure: Infected steady state This graph shows the populations over time when N = 900. We can see that as N increased, the level of B cells and healthy T cells decreased from the steady state at a lower N value. Here, the B cells settle around 2670 and T cells settle around 708, whereas in the previous graph, the B cells settled at 2000 and T cells at 800. As mentioned in Section 10 discussing the stability of the endemically infected state, the steady state that Perelson et al. calculate in their article does not t exactly with our model. When we calculate the steady state using their formulas

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and N < 774, the formulas produce negative values of X, Y, and V. However, the authors comment that for values of N < 774, the X, Y, and V values are zero. Therefore, we inferred that they have oored the values of these variables in some way. Biologically, this makes sense because there cannot be a negative population of cells in the body. However, when we calculate the respective steady states for certain N values and use these as our initial conditions there is a slight discrepancy in the results. When we plug in the steady states that we calculate into the forward Euler method we use to graph the populations, the intial conditions do not stay at the steady state. Instead, the actual stable state that the populations settle into are slightly dierent than those calculated. Although these problems arise, we believe that they are due to the structure of our model. As we said in Section 10, we modied M to be constant instead of Ttot Tmax , which may have a slight eect on the quantitative aspects of the model. However, in the long run, the value of this fraction would not drastically change the qualitative behavior of the system. Also, we believe that the use of the forward Euler method may have also aected the accuracy of the representation of our system. Although our step size for the forward Euler method was 1, if we had decreased this step size it could have made the representation more accurate. We feel that by ooring our function in the numerical analysis, the results of the forward Euler method would have been aected and less precise. If we develop a better way to reect the values of the dierent populations, then there would not be the discrepancy between our results and the results of Perelson and his co-authors.

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Conclusions

We can form several conclusions: There are two xed points, one in an uninfected system with V=0 and one in an endemically infected system where V = 0. The T cell and B cell populations depend heavily on N, the population of virus produced when an actively infected T cell lyses (dies and releases virus). There exists a transcritical bifurcation at N = 774, where the uninfected steady state becomes unstable, and the endemically infected steady state becomes stable. As expected, B and T cell populations are lower in the presence of HIV virus, showing the severity of its impact on the strength of the human immune response system.

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Future Research

For future research, we would like to look more into dierent parameters that may aect the qualitative behavior of our system. The parameter that we concentrated most on was N, since it was the paremeter that caused the transcritical

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bifurcation in the system. However, other factors such as the death rate of HIV virus cells, and conversion rates from W to X to Y would also be interesting to look into. We would also be interested in examining the eect that M has on the sysTtot , tem. One goal to make for future research is to include Ms actual value, T max which would vary along with the dierential equations we have set up. We believe that changing this factor would make our model more accurate, but not qualitatively dierent from the results we found. We could also investigate the relationship between the plasma, memory, and B cell populations more, and see how changing the dierentiation rates would aect the system. As seen in our research here, the increase in virus population did decrease the population of B cells. However, changing the rate at which B cells dierentiate into plasma and memory cells (or even linking these rates to the HIV virus population) would be very interesting, especially in comparison to what we have already modelled. If the virus somehow had an eect on how fast B cells dierentiate, then the severity of HIV infection would be even greater. It is still possible that there are relationships unknown to researchers even now, and the more combinations of relations between virus and lymphocytes would aid in nding the exact behavior of an infected immune system.

References
[1] Alan S. Perelson, Dense E. Kirschner, and Rob de Boer: Dynamics of HIV Infection of CD4+ T cells. Mathematical Biosciences. Elsevier Science Publishing Co., Inc., New York, NY (1993). [2] Alan S. Perelson and Gerard Weisbuch: Immunology for Physicists. Reviews of Modern Physics. Vol. 69, No. 4. The American Physical Society (1997).

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