Appendix 1. The models of tumour growth, cell killing and resistance
The equations of the model of tumour growth shown in Figure
1 were thoroughly described by Bertuzzi, Gandolfi
et al [
21], thereafter referred as BG theory, assuming balanced exponential growth. From BG theory, neglecting for simplicity the distinction between G
1, S and G
2M phases and assuming "natural" cell loss only from quiescent cells, the density of proliferating cells of age "a" at time "t" is given by the formula
np (a, t) = C e
bt
e-ba
(1)
where C is a suitable constant and b is the growth rate constant (b = ln(2)/Td).
By integration on age over the cell cycle time Tc, we obtain the number of proliferating cells:
Np (t) = C e
bt
(1-e-bTc
)/b (2)
At a given time t, cells of age Tc end their cycle by division. Considering eq 1, their density is:
g(t) = C e-bTc
e
bt
(3)
It is useful to define the quantity u = g(t)/Np(t). In this way, using eq. 2 and eq. 3 we have:
u = g(t)/Np(t) = b/(e
bTc
-1) (4)
Notice that in the BG theory the following more general version of eq. 4 holds:
u = g(t)/Np(t) = β/(e
βTC
-1) (4bis)
where
β =
b +
μ (
β =
α +
μ in the original notation used in [
21]) and
μ is the cell loss rate of proliferating cells (assuming
μ
G1 =
μ
S =
μ
G2M =
μ and thus
β
G1 =
β
S =
β
G2M =
β). Eq. 4 bis can be readily demonstrated by combining the BG equation giving g(t) (eq. 13 in [
21]) with BG equations giving Np(t) (eqs. 20 and 21 in [
21], remembering that Np(t) = N
G1(t) + N
S(t) + N
G2M(t)).
Eq. 4 bis reduces to eq. 4 when neglecting "natural" cell loss in proliferating cells (μ = 0).
Summarizing the theory, we can say that in a small time and age interval (dt = da):
i)
u Np(t) dt cells divide originating 2·u Np(t) dt newborn cells, where u is given by eq. 4;
ii) θ·2·u Np(t) dt newborn cell enter the proliferating status with zero age and
iii) (1-θ)·2·u Np(t) dt newborn cell enter the quiescent compartment.
Noticeably, the age-dependence of the theory is no more explicit in these relationships, being conveyed by the quantity "u", which depends only on Tc and Td.
Considering non-infinitesimal time intervals, Δ, the number of dividing cells in the interval (t-Δ, t) is given by:
= u·Np(t-Δ)·
= u Np(t-Δ)·z where:
z = (e
bΔ-1)/b (5)
Similarly, the number of quiescent cells becoming proliferating or dying in the interval (t-Δ, t) is γ·Nq(t-Δ)·z and μ·Nq(t-Δ)·z respectively.
The above definitions and equations allowed to simulate tumour growth by finite differences with time step Δ (Δ = 1 day in the simulations presented in this paper), calculating the numbers of cycling (Np(t)) and quiescent (Nq(t)) cells at time t from those at time t-Δ, in the absence of treatment. In this way it was possible to save a huge amount of computational time and to implement the model in a flexible and interactive spreadsheet program. The resulting balance equations were the following:
Np(t) = (number of proliferating cells at time t-Δ) + (newborn proliferating cells)
- (cells which had divided) + (quiescent cells entered in the proliferative status)
= Np(t-Δ) + 2·θ·u·Np(t-Δ)·z - u·Np(t-Δ)·z + γ·Nq(t-Δ)·z
Nq(t) = (number of quiescent cells at time t-Δ) + (newborn quiescent cells)
- (dead quiescent cells) - (quiescent cells entered in the proliferative status)
= Nq(t-Δ) + 2·(1 - θ)·u·Np(t-Δ)·z - μ
q·Nq(t-Δ)·z - γ·Nq(t-Δ)·z
where u is given by eq. 4 and z by eq. 5.
z is close to Δ = 1 day, as bΔ = ln(2)·Δ/Td << 1, and allows to match exactly Td of the simulation with the theoretical Td during unperturbed balanced growth. After a treatment with differential efficacy (Sp ≠ Sq) the age distribution of proliferating cells will be unbalanced by quiescent cell entering the cycle (if γ ≠ 0). In this case both u and z were approximated values, and some discrepancy of the simulation respect to a full age-dependent model is expected, for a short time after treatment. Because the interval between subsequent data points was seven days or more, this approximation can give only a small contribute to the errors of the estimate of the parameters.
The same growth equations were applied also to resistant cells (Nrp(t) and Nrq(t)).
Dying cells enter and exit three stages (d1, d2, d3 ) of death before being lost as follows:
Nd1(t) = Nd1(t-Δ) - k·Nd1(t-Δ)
Nd2(t) = Nd2(t-Δ) + k·Nd1(t-Δ) - k·Nd2(t-Δ)
Nd3(t) = Nd3(t-Δ) + k·Nd2(t-Δ) - k·Nd3(t-Δ)
The overall number of dying-not-yet-lost cells is given by the sum of the cells in the three stages:
Nd(t) = Nd1(t) + Nd2(t) + Nd3(t)
The overall number of tumour cell at a time "t" is the sum of sensitive cycling, sensitive quiescent, resistant cycling, resistant quiescent and dying cells, namely:
N(t) = Np(t) + Nq(t) + Nrp(t) + Nrq(t) + Nd(t)
N(t) is the quantity compared with measured tumour volumes, via a proportionality constant. At the beginning of the treatment we have:
Np(0) = N(0)·GF·(1 - IniR )
Nq(0) = N(0)·(1 - GF)·(1 - IniR )
Nrp(0) = N(0)·GF·IniR
Nrq(0) = N(0)·(1 - GF)·IniR
where GF is the growth fraction, estimated by %Ki67+, and IniR represents the fraction of cells initially resistant to the drugs.
At the times of treatment, the situation immediately before (t-) is considered separately from that immediately after (t+) the treatment and the number of -surviving-cycling and quiescent cells is reduced as follows:
Np(t+) = Np(t-)·Sp
Nq(t+) = Nq(t-)·Sq
where Sp and Sq are the fraction of cells surviving the treatment, while non-surviving cells enter the first stage of dying cells:
Nd1(t+) = Nd(t-) + Np(t-)·(1-Sp ) + Nq(t-)·(1-Sq)
When considering drug-induced resistance, the equations of surviving cells become:
Np(t+) = Np(t-)·Sp·(1-Rind) Nrp(t+) = Nrp(t-) + Np(t-)·Sp·Rind
Nq(t+) = Nq(t+)·Sq·(1-Rind) Nrq(t+) = Nrq(t-) + Rs·Nq(t+)·Sq·Rind
where Rind represents the fraction of – surviving – cells which become resistant as a consequence of the treatment.
The contribution of spontaneous mutations to a resistant phenotype during the 100 days of treatment was considered negligible [
8].
Because the drugs were given contemporaneously, the effect of each of them cannot be evaluated separately. Thus Sp and Sq measure the effect of the combined treatment. Similarly, cells resistant to single drugs could be identified, and a single subpopulation of cells "resistant to treatment" was considered.
Because the same dosage was given each time to the patients, the same Sp and Sq were repeatedly applied on days 0, 22, 43, 64, 85, reproducing the true schedule of this study. In few instances, a more complex model was needed, shifting of the values of Sp and Sq to new Sp2 and Sq2 values in the course of the treatment.
The model is about numbers of tumour cells (N), while the data are tumour mass (V, volume), including non cancerous cells and tissues. Nevertheless, in the absence of specific information about non tumour cells (at each time and for each patient) we assumed proportionality between N and V, through the equivalence 1 cm3 = 109 tumour cells. The specific value of the proportionality constant does not affect the results.
Appendix 2. Selection of tumour growth types
In order to simplify the optimisation procedure, we fixed Td, Tc, γ , to representative values. This choice was justified by a preliminary study on our dataset, indicating that wide changes of these parameters only slightly modified the fits (not shown).
Representative values of the growth parameters were chosen as follows:
Td. Reports of doubling time of breast cancers indicate an average between 100 and 200 days, increasing with the age of the patient [
34]. In the statistics of Spratt [
35] only 1% have
Td < 30 gg. Thus we considered the values
Td = 30, 150 and 10000 days, as representative of fast, average, slow tumour, respectively.
Tc. The parameter represents the average length of the non-G0 part of the cycle (not to be confused with estimates of other reports [
36] where quiescent cells were not considered a part). Thus Tc values usually found in cell lines
in vitro (1–2 days) are a reasonable lower boundary. However such short Tc are not consistent in tumours with moderately high
GF, unless accepting very high natural cell loss. We considered the values
Tc = 2, 5 and 8 days, as representative of short, average, long cell cycle.
γ. The value of γ is in part automatically constrained by the values of the other parameters of the model of tumour growth. It is also the reciprocal of the mean residence time in the quiescent status. We consider two extreme values: 0, as representative of a tumour with negligible recycling from quiescence into the cycling stage, and 0.01, i.e. 1% quiescent cells becoming cycling per day, corresponding to an average residence time in G0 of 100 days.
Combining the values of Td = 30, 150, 10000 days, Tc = 2, 5 , 8 days and γ = 0, 0.01 we obtained eighteen different types (type1: Td = 30, Tc = 2, γ = 0; type2: Td = 150, Tc = 2, γ = 0; etc.) representative of tumour breast cancer growth.
For each tumour growth type, given the value of GF provided by %Ki67+, the theory [
21], with cell loss only within quiescent cells, allowed to calculate additional kinetics characteristics of the tumour, namely the potential doubling time and the rate of natural cell loss, using the following formulae:
Tpot = (
Td/
GF)·(e
ln(2)Tc/Td
- 1) (derived from eq. 30 in [
21])
μ
q = ln(2)·(1/
Tpot - 1/
Td )/(1 -
GF ) (derived from eqs. 19 and 29 in [
21])
θ = 0.5·e
ln(2)Tc/Td
- 0.5·
γ ·(2 - e
ln(2)Tc/Td
)/(
μ
q + ln(2)/
Td) (derived from eq. 15 in [
21])
Some combinations of
Td,
Tc,
GF,
γ were not biologically consistent because mathematically they would require a negative cell loss. For what concerns
Tpot we referred to the
Tpot estimates obtained with BrdU
in vivo in breast cancer patients by Rew and Wilson [
37]. Because in that database the highest Tpot value was 50 days, we conservatively accepted a combination of parameters as biologically consistent if Tpot < 75 days.
Thus, for each patient, only a subset of the eighteen types was considered for fitting, those with Tpot > 75 days or μ
q < 0 (if any) being excluded as biologically not consistent.
The data were in general poorly sensitive to the values adopted for the tumour growth parameters. In 19/35 cases, we found (Table
5) a fit statistically equivalent to the best with
Td = 30, 150 and 10000 days. In six instances only fast growing models were compatible with the data, while in another nine fast growth was excluded.
Table 5
Doubling time compatible with data
ND | 30–150–10000 | 19 | 54.3 |
Slow tumour | 150–10000 | 9 | 25.7 |
Fast/intermediate | 30–150 | 1 | 2.9 |
Fast tumour | 30 | 6 | 17.1 |
As concerns
Tc (Table
6), only in a minority of cases do the data indicate that two days or eight days should be preferred. In all the other cases the value remained uncertain.
Table 6
Cell cycle time compatible with data
ND | 2-5-8 | 4 | 11.4 |
Long Tc | 8 | 9 | 25.7 |
Intermediate/Long Tc | 5–8 | 14 | 40.0 |
Short/Intermediate Tc | 2–5 | 2 | 5.7 |
Short Tc | 2 | 6 | 17.1 |
The recycling rate remained undetermined in 22/35 instances (not shown), while for the reminder the fit indicated γ = 0.